diff --git a/models/finetuned/bace/checkpoint_epoch_025/config.json b/models/finetuned/bace/checkpoint_epoch_025/config.json deleted file mode 100644 index 3811e21539577b37e06313eab31ec11e53f0cbbc..0000000000000000000000000000000000000000 --- a/models/finetuned/bace/checkpoint_epoch_025/config.json +++ /dev/null @@ -1,27 +0,0 @@ -{ - "_name_or_path": "/home/erva/SELFormerMM/data/pretrained_multimodal_chembl36", - "architectures": [ - "RobertaForMaskedLM" - ], - "attention_probs_dropout_prob": 0.1, - "bos_token_id": 0, - "classifier_dropout": null, - "eos_token_id": 2, - "hidden_act": "gelu", - "hidden_dropout_prob": 0.1, - "hidden_size": 768, - "initializer_range": 0.02, - "intermediate_size": 3072, - "layer_norm_eps": 1e-12, - "max_position_embeddings": 514, - "model_type": "roberta", - "num_attention_heads": 4, - "num_hidden_layers": 12, - "pad_token_id": 1, - "position_embedding_type": "absolute", - "torch_dtype": "float32", - "transformers_version": "4.26.1", - "type_vocab_size": 1, - "use_cache": true, - "vocab_size": 800 -} diff --git a/models/finetuned/bace/checkpoint_epoch_025/merges.txt b/models/finetuned/bace/checkpoint_epoch_025/merges.txt deleted file mode 100644 index 7cd5ec62809503c23f18c80afc0ba3bdf9d253d0..0000000000000000000000000000000000000000 --- a/models/finetuned/bace/checkpoint_epoch_025/merges.txt +++ /dev/null @@ -1,378 +0,0 @@ -#version: 0.2 - Trained by `huggingface/tokenizers` -B r -a n -c h -Br an -Bran ch -Branch 1 -= C -R i -n g -Ri ng -Ring 1 -= Branch1 -Branch 2 -= O -Ring 2 -H 1 -C @ -= N -# Branch1 -C@ @ -= Branch2 -C@ H1 -C@@ H1 -# Branch2 -# C -C l -/ C -N H1 -= Ring1 -+ 1 -- 1 -O -1 -N +1 -\ C -# N -/ N -= Ring2 -= S -=N +1 -\ N -N a -Na +1 -/ O -\ O -Br -1 -Branch 3 -\ S -S +1 -Cl -1 -I -1 -/ C@@H1 -S i -/ C@H1 -/ S -=N -1 -S e -= P -N -1 -Ring 3 -2 H -P +1 -K +1 -\ C@@H1 -\ C@H1 -/ N+1 -@ @ -C -1 -# N+1 -B -1 -+ 3 -Cl +3 -\ NH1 -L i -Li +1 -P H1 -1 8 -18 F -@ +1 -3 H -P @@ -H 0 -O H0 -1 2 -P @ -+ 2 -@@ +1 -S -1 -/ Br -- / -\ Cl --/ Ring2 -\ O-1 -1 1 -5 I -12 5I -11 C -H 3 -\ N+1 -- \ -/ C@@ -S @+1 -A s -/ Cl -11C H3 -=S e -S @@+1 -N @+1 -1 4 --\ Ring2 -14 C -\ F -/ C@ -T e -H 2 -H1 -1 -=O +1 -N @@+1 -C +1 -=S +1 -Z n -/ P -a +2 -/ I -O H1-1 -C a+2 -\ Br -M g -Zn +2 -A l -/ F -Mg +2 -12 3 -123 I -1 3 -I +1 -/ O-1 --\ Ring1 -B H2 -BH2 -1 -\ I -/ NH1 -O +1 -13 1 -131 I -= 14C -/ S+1 -= Ring3 -\ C@@ -H2 +1 -\ C@ -A g -= As -=Se +1 -N H2+1 -Se H1 --/ Ring1 -= Te -Al +3 -Na H1 -=Te +1 -NH1 +1 -Ag +1 -H1 +1 -NH1 -1 -\ P -14C H2 -13 C -14C H1 -= 11C -S @@ -=P @@ -Si H2 -H3 -1 -14C H3 -B H3-1 -S @ -=14C H1 -=P H1 -=P @ -=N H1+1 -\S +1 -12 4 -C H1-1 -S r -=S i -124 I -Sr +2 -#C -1 -/C -1 -N @ -/N -1 -13C H1 -/ B -1 9 -B a+2 -H 4 -S H1+1 -Se +1 -19 F -/ 125I -P @+1 -R b -Cl +1 -Si H4 -Rb +1 -= Branch3 -N @@ -As +1 -/ Si -B H1-1 -S H1 -/ 123I -3 2 -= Mg -H +1 -\ B -Si H1 -P@@ +1 -- 2 -1 5 -1 7 -3 5 -= 13CH1 -C s -=N H2+1 -=S H1 -Mg H2 -32 P -17 F -35 S -Cs +1 -# 11C -/ 131I -B i -\ 125I -=S @@ -\S -1 -6 Br -7 I -7 6Br -= B -e H1 -\N -1 -18 O -12 7I -11C H2 -14 C@@H1 -Te H2 -15 NH1 -Bi +3 -/ P+1 -/ 13C -/ 13CH1 -0 B -1 0B -= Al -= 18O -B H0 -F -1 -N H3 -S -2 -Br +2 -Cl +2 -\S i -/S -1 -=P H2 -14 C@H1 -NH3 +1 -# 14C -# O+1 -- 3 -2 2 -4 H -5 Se -5 Sr+2 -7 5Se -8 5Sr+2 -= B-1 -= 13C -@ -1 -B e -B @@ -B @-1 -C a -C H1 -I +3 -K H1 -O H1+1 -R a+2 -S H1-1 -\ PH1 -\ 123I -=C a -\C H1-1 -=S @ -\S eH1 -/S eH1 -Se -1 -Li H1 -18F -1 -125I H1 -11C H1 -Te H1 -Zn +1 -Zn -2 -Al -3 -13C H3 -15 N -Be +2 -B@@ -1 -# P -# S -- 4 -/ PH1 -/ P@@ -/ As -/ 14C -/ 14CH1 -2 K+1 -2 Rb+1 -3 Se -3 Ra+2 -4 5 -4 7 -4 2K+1 -5 I-1 -7 3Se -8 9 -8 2Rb+1 -= 32 -= 32P -C H0 -C H2 -I +2 -N H0 -N H4 -O H1 -P H2+1 -S H0 -S H2 -\ 3H -\ 11CH3 -\C -1 -\S e -Si @ -Si -1 -Si H1-1 -Si H3-1 -/S e -Se -2 -\NH1 -1 -18F H1 -12 5I-1 -11 C@@H1 -11 C-1 -As H1 -As -1 -14 C@@ -Te -1 -Mg +1 -123 I-1 -123 Te -123I H1 -13 5I -131 I-1 -Ag -4 -124 I-1 -76Br H1 -18O H1 -22 Na+1 -22 3Ra+2 -Ca H2 -45 Ca+2 -47 Ca+2 -89 Sr+2 -=32 PH1 -NH4 +1 diff --git a/models/finetuned/bace/checkpoint_epoch_025/model.pt b/models/finetuned/bace/checkpoint_epoch_025/model.pt deleted file mode 100644 index 34d885fdb2c94581c290984e5158af8aa821f504..0000000000000000000000000000000000000000 --- a/models/finetuned/bace/checkpoint_epoch_025/model.pt +++ /dev/null @@ -1,3 +0,0 @@ -version https://git-lfs.github.com/spec/v1 -oid sha256:155ae50273d6ae3fb3badd7bd9021a5737165434ae9487d89face60faccb20f6 -size 1022855293 diff --git a/models/finetuned/bace/checkpoint_epoch_025/special_tokens_map.json b/models/finetuned/bace/checkpoint_epoch_025/special_tokens_map.json deleted file mode 100644 index 06a55849fa69a91e7179d909e373179ff7467d8c..0000000000000000000000000000000000000000 --- a/models/finetuned/bace/checkpoint_epoch_025/special_tokens_map.json +++ /dev/null @@ -1,51 +0,0 @@ -{ - "bos_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "cls_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "eos_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "mask_token": { - "content": "", - "lstrip": true, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "pad_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "sep_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "unk_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - } -} diff --git a/models/finetuned/bace/checkpoint_epoch_025/tokenizer.json b/models/finetuned/bace/checkpoint_epoch_025/tokenizer.json deleted file mode 100644 index 3b64b273e6fa9799e2d8375722b9e815de9ebb8f..0000000000000000000000000000000000000000 --- a/models/finetuned/bace/checkpoint_epoch_025/tokenizer.json +++ /dev/null @@ -1,909 +0,0 @@ -{ - "version": "1.0", - "truncation": { - "direction": "Right", - "max_length": 128, - "strategy": "LongestFirst", - "stride": 0 - }, - "padding": { - "strategy": { - "Fixed": 128 - }, - "direction": "Right", - "pad_to_multiple_of": null, - "pad_id": 3, - "pad_type_id": 0, - "pad_token": "" - }, - "added_tokens": [ - { - "id": 0, - "content": "", - "single_word": false, - "lstrip": false, - "rstrip": false, - "normalized": true, - "special": true - }, - { - "id": 1, - "content": "", - "single_word": false, - "lstrip": false, - "rstrip": false, - "normalized": true, - "special": true - }, - { - "id": 2, - "content": "", - "single_word": false, - "lstrip": false, - "rstrip": false, - "normalized": true, - "special": true - }, - { - "id": 3, - "content": "", - "single_word": false, - "lstrip": false, - "rstrip": false, - "normalized": true, - "special": true - }, - { - "id": 4, - "content": "", - "single_word": false, - "lstrip": true, - "rstrip": false, - "normalized": true, - "special": true - } - ], - "normalizer": null, - "pre_tokenizer": { - "type": "ByteLevel", - "add_prefix_space": false, - "trim_offsets": true, - "use_regex": true - }, - "post_processor": { - "type": "RobertaProcessing", - "sep": [ - "", - 2 - ], - "cls": [ - "", - 1 - ], - "trim_offsets": true, - "add_prefix_space": false - }, - "decoder": { - "type": "ByteLevel", - "add_prefix_space": true, - "trim_offsets": true, - "use_regex": true - }, - "model": { - "type": "BPE", - "dropout": null, - "unk_token": null, - "continuing_subword_prefix": "", - "end_of_word_suffix": "", - "fuse_unk": false, - "vocab": { - "": 0, - "": 1, - "": 2, - "": 3, - "": 4, - "\n": 5, - "#": 6, - "+": 7, - "-": 8, - ".": 9, - "/": 10, - "0": 11, - "1": 12, - "2": 13, - "3": 14, - "4": 15, - "5": 16, - "6": 17, - "7": 18, - "8": 19, - "9": 20, - "=": 21, - "@": 22, - "A": 23, - "B": 24, - "C": 25, - "F": 26, - "H": 27, - "I": 28, - "K": 29, - "L": 30, - "M": 31, - "N": 32, - "O": 33, - "P": 34, - "R": 35, - "S": 36, - "T": 37, - "Z": 38, - "\\": 39, - "a": 40, - "b": 41, - "c": 42, - "e": 43, - "g": 44, - "h": 45, - "i": 46, - "l": 47, - "n": 48, - "r": 49, - "s": 50, - "Br": 51, - "an": 52, - "ch": 53, - "Bran": 54, - "Branch": 55, - "Branch1": 56, - "=C": 57, - "Ri": 58, - "ng": 59, - "Ring": 60, - "Ring1": 61, - "=Branch1": 62, - "Branch2": 63, - "=O": 64, - "Ring2": 65, - "H1": 66, - "C@": 67, - "=N": 68, - "#Branch1": 69, - "C@@": 70, - "=Branch2": 71, - "C@H1": 72, - "C@@H1": 73, - "#Branch2": 74, - "#C": 75, - "Cl": 76, - "/C": 77, - "NH1": 78, - "=Ring1": 79, - "+1": 80, - "-1": 81, - "O-1": 82, - "N+1": 83, - "\\C": 84, - "#N": 85, - "/N": 86, - "=Ring2": 87, - "=S": 88, - "=N+1": 89, - "\\N": 90, - "Na": 91, - "Na+1": 92, - "/O": 93, - "\\O": 94, - "Br-1": 95, - "Branch3": 96, - "\\S": 97, - "S+1": 98, - "Cl-1": 99, - "I-1": 100, - "/C@@H1": 101, - "Si": 102, - "/C@H1": 103, - "/S": 104, - "=N-1": 105, - "Se": 106, - "=P": 107, - "N-1": 108, - "Ring3": 109, - "2H": 110, - "P+1": 111, - "K+1": 112, - "\\C@@H1": 113, - "\\C@H1": 114, - "/N+1": 115, - "@@": 116, - "C-1": 117, - "#N+1": 118, - "B-1": 119, - "+3": 120, - "Cl+3": 121, - "\\NH1": 122, - "Li": 123, - "Li+1": 124, - "PH1": 125, - "18": 126, - "18F": 127, - "@+1": 128, - "3H": 129, - "P@@": 130, - "H0": 131, - "OH0": 132, - "12": 133, - "P@": 134, - "+2": 135, - "@@+1": 136, - "S-1": 137, - "/Br": 138, - "-/": 139, - "\\Cl": 140, - "-/Ring2": 141, - "\\O-1": 142, - "11": 143, - "5I": 144, - "125I": 145, - "11C": 146, - "H3": 147, - "\\N+1": 148, - "-\\": 149, - "/C@@": 150, - "S@+1": 151, - "As": 152, - "/Cl": 153, - "11CH3": 154, - "=Se": 155, - "S@@+1": 156, - "N@+1": 157, - "14": 158, - "-\\Ring2": 159, - "14C": 160, - "\\F": 161, - "/C@": 162, - "Te": 163, - "H2": 164, - "H1-1": 165, - "=O+1": 166, - "N@@+1": 167, - "C+1": 168, - "=S+1": 169, - "Zn": 170, - "/P": 171, - "a+2": 172, - "/I": 173, - "OH1-1": 174, - "Ca+2": 175, - "\\Br": 176, - "Mg": 177, - "Zn+2": 178, - "Al": 179, - "/F": 180, - "Mg+2": 181, - "123": 182, - "123I": 183, - "13": 184, - "I+1": 185, - "/O-1": 186, - "-\\Ring1": 187, - "BH2": 188, - "BH2-1": 189, - "\\I": 190, - "/NH1": 191, - "O+1": 192, - "131": 193, - "131I": 194, - "=14C": 195, - "/S+1": 196, - "=Ring3": 197, - "\\C@@": 198, - "H2+1": 199, - "\\C@": 200, - "Ag": 201, - "=As": 202, - "=Se+1": 203, - "NH2+1": 204, - "SeH1": 205, - "-/Ring1": 206, - "=Te": 207, - "Al+3": 208, - "NaH1": 209, - "=Te+1": 210, - "NH1+1": 211, - "Ag+1": 212, - "H1+1": 213, - "NH1-1": 214, - "\\P": 215, - "14CH2": 216, - "13C": 217, - "14CH1": 218, - "=11C": 219, - "S@@": 220, - "=P@@": 221, - "SiH2": 222, - "H3-1": 223, - "14CH3": 224, - "BH3-1": 225, - "S@": 226, - "=14CH1": 227, - "=PH1": 228, - "=P@": 229, - "=NH1+1": 230, - "\\S+1": 231, - "124": 232, - "CH1-1": 233, - "Sr": 234, - "=Si": 235, - "124I": 236, - "Sr+2": 237, - "#C-1": 238, - "/C-1": 239, - "N@": 240, - "/N-1": 241, - "13CH1": 242, - "/B": 243, - "19": 244, - "Ba+2": 245, - "H4": 246, - "SH1+1": 247, - "Se+1": 248, - "19F": 249, - "/125I": 250, - "P@+1": 251, - "Rb": 252, - "Cl+1": 253, - "SiH4": 254, - "Rb+1": 255, - "=Branch3": 256, - "N@@": 257, - "As+1": 258, - "/Si": 259, - "BH1-1": 260, - "SH1": 261, - "/123I": 262, - "32": 263, - "=Mg": 264, - "H+1": 265, - "\\B": 266, - "SiH1": 267, - "P@@+1": 268, - "-2": 269, - "15": 270, - "17": 271, - "35": 272, - "=13CH1": 273, - "Cs": 274, - "=NH2+1": 275, - "=SH1": 276, - "MgH2": 277, - "32P": 278, - "17F": 279, - "35S": 280, - "Cs+1": 281, - "#11C": 282, - "/131I": 283, - "Bi": 284, - "\\125I": 285, - "=S@@": 286, - "\\S-1": 287, - "6Br": 288, - "7I": 289, - "76Br": 290, - "=B": 291, - "eH1": 292, - "\\N-1": 293, - "18O": 294, - "127I": 295, - "11CH2": 296, - "14C@@H1": 297, - "TeH2": 298, - "15NH1": 299, - "Bi+3": 300, - "/P+1": 301, - "/13C": 302, - "/13CH1": 303, - "0B": 304, - "10B": 305, - "=Al": 306, - "=18O": 307, - "BH0": 308, - "F-1": 309, - "NH3": 310, - "S-2": 311, - "Br+2": 312, - "Cl+2": 313, - "\\Si": 314, - "/S-1": 315, - "=PH2": 316, - "14C@H1": 317, - "NH3+1": 318, - "#14C": 319, - "#O+1": 320, - "-3": 321, - "22": 322, - "4H": 323, - "5Se": 324, - "5Sr+2": 325, - "75Se": 326, - "85Sr+2": 327, - "=B-1": 328, - "=13C": 329, - "@-1": 330, - "Be": 331, - "B@@": 332, - "B@-1": 333, - "Ca": 334, - "CH1": 335, - "I+3": 336, - "KH1": 337, - "OH1+1": 338, - "Ra+2": 339, - "SH1-1": 340, - "\\PH1": 341, - "\\123I": 342, - "=Ca": 343, - "\\CH1-1": 344, - "=S@": 345, - "\\SeH1": 346, - "/SeH1": 347, - "Se-1": 348, - "LiH1": 349, - "18F-1": 350, - "125IH1": 351, - "11CH1": 352, - "TeH1": 353, - "Zn+1": 354, - "Zn-2": 355, - "Al-3": 356, - "13CH3": 357, - "15N": 358, - "Be+2": 359, - "B@@-1": 360, - "#P": 361, - "#S": 362, - "-4": 363, - "/PH1": 364, - "/P@@": 365, - "/As": 366, - "/14C": 367, - "/14CH1": 368, - "2K+1": 369, - "2Rb+1": 370, - "3Se": 371, - "3Ra+2": 372, - "45": 373, - "47": 374, - "42K+1": 375, - "5I-1": 376, - "73Se": 377, - "89": 378, - "82Rb+1": 379, - "=32": 380, - "=32P": 381, - "CH0": 382, - "CH2": 383, - "I+2": 384, - "NH0": 385, - "NH4": 386, - "OH1": 387, - "PH2+1": 388, - "SH0": 389, - "SH2": 390, - "\\3H": 391, - "\\11CH3": 392, - "\\C-1": 393, - "\\Se": 394, - "Si@": 395, - "Si-1": 396, - "SiH1-1": 397, - "SiH3-1": 398, - "/Se": 399, - "Se-2": 400, - "\\NH1-1": 401, - "18FH1": 402, - "125I-1": 403, - "11C@@H1": 404, - "11C-1": 405, - "AsH1": 406, - "As-1": 407, - "14C@@": 408, - "Te-1": 409, - "Mg+1": 410, - "123I-1": 411, - "123Te": 412, - "123IH1": 413, - "135I": 414, - "131I-1": 415, - "Ag-4": 416, - "124I-1": 417, - "76BrH1": 418, - "18OH1": 419, - "22Na+1": 420, - "223Ra+2": 421, - "CaH2": 422, - "45Ca+2": 423, - "47Ca+2": 424, - "89Sr+2": 425, - "=32PH1": 426, - "NH4+1": 427 - }, - "merges": [ - "B r", - "a n", - "c h", - "Br an", - "Bran ch", - "Branch 1", - "= C", - "R i", - "n g", - "Ri ng", - "Ring 1", - "= Branch1", - "Branch 2", - "= O", - "Ring 2", - "H 1", - "C @", - "= N", - "# Branch1", - "C@ @", - "= Branch2", - "C@ H1", - "C@@ H1", - "# Branch2", - "# C", - "C l", - "/ C", - "N H1", - "= Ring1", - "+ 1", - "- 1", - "O -1", - "N +1", - "\\ C", - "# N", - "/ N", - "= Ring2", - "= S", - "=N +1", - "\\ N", - "N a", - "Na +1", - "/ O", - "\\ O", - "Br -1", - "Branch 3", - "\\ S", - "S +1", - "Cl -1", - "I -1", - "/ C@@H1", - "S i", - "/ C@H1", - "/ S", - "=N -1", - "S e", - "= P", - "N -1", - "Ring 3", - "2 H", - "P +1", - "K +1", - "\\ C@@H1", - "\\ C@H1", - "/ N+1", - "@ @", - "C -1", - "# N+1", - "B -1", - "+ 3", - "Cl +3", - "\\ NH1", - "L i", - "Li +1", - "P H1", - "1 8", - "18 F", - "@ +1", - "3 H", - "P @@", - "H 0", - "O H0", - "1 2", - "P @", - "+ 2", - "@@ +1", - "S -1", - "/ Br", - "- /", - "\\ Cl", - "-/ Ring2", - "\\ O-1", - "1 1", - "5 I", - "12 5I", - "11 C", - "H 3", - "\\ N+1", - "- \\", - "/ C@@", - "S @+1", - "A s", - "/ Cl", - "11C H3", - "=S e", - "S @@+1", - "N @+1", - "1 4", - "-\\ Ring2", - "14 C", - "\\ F", - "/ C@", - "T e", - "H 2", - "H1 -1", - "=O +1", - "N @@+1", - "C +1", - "=S +1", - "Z n", - "/ P", - "a +2", - "/ I", - "O H1-1", - "C a+2", - "\\ Br", - "M g", - "Zn +2", - "A l", - "/ F", - "Mg +2", - "12 3", - "123 I", - "1 3", - "I +1", - "/ O-1", - "-\\ Ring1", - "B H2", - "BH2 -1", - "\\ I", - "/ NH1", - "O +1", - "13 1", - "131 I", - "= 14C", - "/ S+1", - "= Ring3", - "\\ C@@", - "H2 +1", - "\\ C@", - "A g", - "= As", - "=Se +1", - "N H2+1", - "Se H1", - "-/ Ring1", - "= Te", - "Al +3", - "Na H1", - "=Te +1", - "NH1 +1", - "Ag +1", - "H1 +1", - "NH1 -1", - "\\ P", - "14C H2", - "13 C", - "14C H1", - "= 11C", - "S @@", - "=P @@", - "Si H2", - "H3 -1", - "14C H3", - "B H3-1", - "S @", - "=14C H1", - "=P H1", - "=P @", - "=N H1+1", - "\\S +1", - "12 4", - "C H1-1", - "S r", - "=S i", - "124 I", - "Sr +2", - "#C -1", - "/C -1", - "N @", - "/N -1", - "13C H1", - "/ B", - "1 9", - "B a+2", - "H 4", - "S H1+1", - "Se +1", - "19 F", - "/ 125I", - "P @+1", - "R b", - "Cl +1", - "Si H4", - "Rb +1", - "= Branch3", - "N @@", - "As +1", - "/ Si", - "B H1-1", - "S H1", - "/ 123I", - "3 2", - "= Mg", - "H +1", - "\\ B", - "Si H1", - "P@@ +1", - "- 2", - "1 5", - "1 7", - "3 5", - "= 13CH1", - "C s", - "=N H2+1", - "=S H1", - "Mg H2", - "32 P", - "17 F", - "35 S", - "Cs +1", - "# 11C", - "/ 131I", - "B i", - "\\ 125I", - "=S @@", - "\\S -1", - "6 Br", - "7 I", - "7 6Br", - "= B", - "e H1", - "\\N -1", - "18 O", - "12 7I", - "11C H2", - "14 C@@H1", - "Te H2", - "15 NH1", - "Bi +3", - "/ P+1", - "/ 13C", - "/ 13CH1", - "0 B", - "1 0B", - "= Al", - "= 18O", - "B H0", - "F -1", - "N H3", - "S -2", - "Br +2", - "Cl +2", - "\\S i", - "/S -1", - "=P H2", - "14 C@H1", - "NH3 +1", - "# 14C", - "# O+1", - "- 3", - "2 2", - "4 H", - "5 Se", - "5 Sr+2", - "7 5Se", - "8 5Sr+2", - "= B-1", - "= 13C", - "@ -1", - "B e", - "B @@", - "B @-1", - "C a", - "C H1", - "I +3", - "K H1", - "O H1+1", - "R a+2", - "S H1-1", - "\\ PH1", - "\\ 123I", - "=C a", - "\\C H1-1", - "=S @", - "\\S eH1", - "/S eH1", - "Se -1", - "Li H1", - "18F -1", - "125I H1", - "11C H1", - "Te H1", - "Zn +1", - "Zn -2", - "Al -3", - "13C H3", - "15 N", - "Be +2", - "B@@ -1", - "# P", - "# S", - "- 4", - "/ PH1", - "/ P@@", - "/ As", - "/ 14C", - "/ 14CH1", - "2 K+1", - "2 Rb+1", - "3 Se", - "3 Ra+2", - "4 5", - "4 7", - "4 2K+1", - "5 I-1", - "7 3Se", - "8 9", - "8 2Rb+1", - "= 32", - "= 32P", - "C H0", - "C H2", - "I +2", - "N H0", - "N H4", - "O H1", - "P H2+1", - "S H0", - "S H2", - "\\ 3H", - "\\ 11CH3", - "\\C -1", - "\\S e", - "Si @", - "Si -1", - "Si H1-1", - "Si H3-1", - "/S e", - "Se -2", - "\\NH1 -1", - "18F H1", - "12 5I-1", - "11 C@@H1", - "11 C-1", - "As H1", - "As -1", - "14 C@@", - "Te -1", - "Mg +1", - "123 I-1", - "123 Te", - "123I H1", - "13 5I", - "131 I-1", - "Ag -4", - "124 I-1", - "76Br H1", - "18O H1", - "22 Na+1", - "22 3Ra+2", - "Ca H2", - "45 Ca+2", - "47 Ca+2", - "89 Sr+2", - "=32 PH1", - "NH4 +1" - ] - } -} \ No newline at end of file diff --git a/models/finetuned/bace/checkpoint_epoch_025/tokenizer_config.json b/models/finetuned/bace/checkpoint_epoch_025/tokenizer_config.json deleted file mode 100644 index 08860954acd34fad07fd77f7635298fa565f3149..0000000000000000000000000000000000000000 --- a/models/finetuned/bace/checkpoint_epoch_025/tokenizer_config.json +++ /dev/null @@ -1,65 +0,0 @@ -{ - "add_prefix_space": false, - "bos_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "cls_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "eos_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "errors": "replace", - "mask_token": { - "__type": "AddedToken", - "content": "", - "lstrip": true, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "model_max_length": 1000000000000000019884624838656, - "name_or_path": "/home/erva/SELFormerMM/data/pretrained_multimodal_chembl36", - "pad_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "sep_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "special_tokens_map_file": null, - "tokenizer_class": "RobertaTokenizer", - "trim_offsets": true, - "unk_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - } -} diff --git a/models/finetuned/bace/checkpoint_epoch_025/vocab.json b/models/finetuned/bace/checkpoint_epoch_025/vocab.json deleted file mode 100644 index f7e4cc22809f4e9035cc450ef189c8a7da8fd03e..0000000000000000000000000000000000000000 --- a/models/finetuned/bace/checkpoint_epoch_025/vocab.json +++ /dev/null @@ -1 +0,0 @@ -{"":0,"":1,"":2,"":3,"":4,"\n":5,"#":6,"+":7,"-":8,".":9,"/":10,"0":11,"1":12,"2":13,"3":14,"4":15,"5":16,"6":17,"7":18,"8":19,"9":20,"=":21,"@":22,"A":23,"B":24,"C":25,"F":26,"H":27,"I":28,"K":29,"L":30,"M":31,"N":32,"O":33,"P":34,"R":35,"S":36,"T":37,"Z":38,"\\":39,"a":40,"b":41,"c":42,"e":43,"g":44,"h":45,"i":46,"l":47,"n":48,"r":49,"s":50,"Br":51,"an":52,"ch":53,"Bran":54,"Branch":55,"Branch1":56,"=C":57,"Ri":58,"ng":59,"Ring":60,"Ring1":61,"=Branch1":62,"Branch2":63,"=O":64,"Ring2":65,"H1":66,"C@":67,"=N":68,"#Branch1":69,"C@@":70,"=Branch2":71,"C@H1":72,"C@@H1":73,"#Branch2":74,"#C":75,"Cl":76,"/C":77,"NH1":78,"=Ring1":79,"+1":80,"-1":81,"O-1":82,"N+1":83,"\\C":84,"#N":85,"/N":86,"=Ring2":87,"=S":88,"=N+1":89,"\\N":90,"Na":91,"Na+1":92,"/O":93,"\\O":94,"Br-1":95,"Branch3":96,"\\S":97,"S+1":98,"Cl-1":99,"I-1":100,"/C@@H1":101,"Si":102,"/C@H1":103,"/S":104,"=N-1":105,"Se":106,"=P":107,"N-1":108,"Ring3":109,"2H":110,"P+1":111,"K+1":112,"\\C@@H1":113,"\\C@H1":114,"/N+1":115,"@@":116,"C-1":117,"#N+1":118,"B-1":119,"+3":120,"Cl+3":121,"\\NH1":122,"Li":123,"Li+1":124,"PH1":125,"18":126,"18F":127,"@+1":128,"3H":129,"P@@":130,"H0":131,"OH0":132,"12":133,"P@":134,"+2":135,"@@+1":136,"S-1":137,"/Br":138,"-/":139,"\\Cl":140,"-/Ring2":141,"\\O-1":142,"11":143,"5I":144,"125I":145,"11C":146,"H3":147,"\\N+1":148,"-\\":149,"/C@@":150,"S@+1":151,"As":152,"/Cl":153,"11CH3":154,"=Se":155,"S@@+1":156,"N@+1":157,"14":158,"-\\Ring2":159,"14C":160,"\\F":161,"/C@":162,"Te":163,"H2":164,"H1-1":165,"=O+1":166,"N@@+1":167,"C+1":168,"=S+1":169,"Zn":170,"/P":171,"a+2":172,"/I":173,"OH1-1":174,"Ca+2":175,"\\Br":176,"Mg":177,"Zn+2":178,"Al":179,"/F":180,"Mg+2":181,"123":182,"123I":183,"13":184,"I+1":185,"/O-1":186,"-\\Ring1":187,"BH2":188,"BH2-1":189,"\\I":190,"/NH1":191,"O+1":192,"131":193,"131I":194,"=14C":195,"/S+1":196,"=Ring3":197,"\\C@@":198,"H2+1":199,"\\C@":200,"Ag":201,"=As":202,"=Se+1":203,"NH2+1":204,"SeH1":205,"-/Ring1":206,"=Te":207,"Al+3":208,"NaH1":209,"=Te+1":210,"NH1+1":211,"Ag+1":212,"H1+1":213,"NH1-1":214,"\\P":215,"14CH2":216,"13C":217,"14CH1":218,"=11C":219,"S@@":220,"=P@@":221,"SiH2":222,"H3-1":223,"14CH3":224,"BH3-1":225,"S@":226,"=14CH1":227,"=PH1":228,"=P@":229,"=NH1+1":230,"\\S+1":231,"124":232,"CH1-1":233,"Sr":234,"=Si":235,"124I":236,"Sr+2":237,"#C-1":238,"/C-1":239,"N@":240,"/N-1":241,"13CH1":242,"/B":243,"19":244,"Ba+2":245,"H4":246,"SH1+1":247,"Se+1":248,"19F":249,"/125I":250,"P@+1":251,"Rb":252,"Cl+1":253,"SiH4":254,"Rb+1":255,"=Branch3":256,"N@@":257,"As+1":258,"/Si":259,"BH1-1":260,"SH1":261,"/123I":262,"32":263,"=Mg":264,"H+1":265,"\\B":266,"SiH1":267,"P@@+1":268,"-2":269,"15":270,"17":271,"35":272,"=13CH1":273,"Cs":274,"=NH2+1":275,"=SH1":276,"MgH2":277,"32P":278,"17F":279,"35S":280,"Cs+1":281,"#11C":282,"/131I":283,"Bi":284,"\\125I":285,"=S@@":286,"\\S-1":287,"6Br":288,"7I":289,"76Br":290,"=B":291,"eH1":292,"\\N-1":293,"18O":294,"127I":295,"11CH2":296,"14C@@H1":297,"TeH2":298,"15NH1":299,"Bi+3":300,"/P+1":301,"/13C":302,"/13CH1":303,"0B":304,"10B":305,"=Al":306,"=18O":307,"BH0":308,"F-1":309,"NH3":310,"S-2":311,"Br+2":312,"Cl+2":313,"\\Si":314,"/S-1":315,"=PH2":316,"14C@H1":317,"NH3+1":318,"#14C":319,"#O+1":320,"-3":321,"22":322,"4H":323,"5Se":324,"5Sr+2":325,"75Se":326,"85Sr+2":327,"=B-1":328,"=13C":329,"@-1":330,"Be":331,"B@@":332,"B@-1":333,"Ca":334,"CH1":335,"I+3":336,"KH1":337,"OH1+1":338,"Ra+2":339,"SH1-1":340,"\\PH1":341,"\\123I":342,"=Ca":343,"\\CH1-1":344,"=S@":345,"\\SeH1":346,"/SeH1":347,"Se-1":348,"LiH1":349,"18F-1":350,"125IH1":351,"11CH1":352,"TeH1":353,"Zn+1":354,"Zn-2":355,"Al-3":356,"13CH3":357,"15N":358,"Be+2":359,"B@@-1":360,"#P":361,"#S":362,"-4":363,"/PH1":364,"/P@@":365,"/As":366,"/14C":367,"/14CH1":368,"2K+1":369,"2Rb+1":370,"3Se":371,"3Ra+2":372,"45":373,"47":374,"42K+1":375,"5I-1":376,"73Se":377,"89":378,"82Rb+1":379,"=32":380,"=32P":381,"CH0":382,"CH2":383,"I+2":384,"NH0":385,"NH4":386,"OH1":387,"PH2+1":388,"SH0":389,"SH2":390,"\\3H":391,"\\11CH3":392,"\\C-1":393,"\\Se":394,"Si@":395,"Si-1":396,"SiH1-1":397,"SiH3-1":398,"/Se":399,"Se-2":400,"\\NH1-1":401,"18FH1":402,"125I-1":403,"11C@@H1":404,"11C-1":405,"AsH1":406,"As-1":407,"14C@@":408,"Te-1":409,"Mg+1":410,"123I-1":411,"123Te":412,"123IH1":413,"135I":414,"131I-1":415,"Ag-4":416,"124I-1":417,"76BrH1":418,"18OH1":419,"22Na+1":420,"223Ra+2":421,"CaH2":422,"45Ca+2":423,"47Ca+2":424,"89Sr+2":425,"=32PH1":426,"NH4+1":427} \ No newline at end of file diff --git a/models/finetuned/bace/config.json b/models/finetuned/bace/config.json deleted file mode 100644 index 3811e21539577b37e06313eab31ec11e53f0cbbc..0000000000000000000000000000000000000000 --- a/models/finetuned/bace/config.json +++ /dev/null @@ -1,27 +0,0 @@ -{ - "_name_or_path": "/home/erva/SELFormerMM/data/pretrained_multimodal_chembl36", - "architectures": [ - "RobertaForMaskedLM" - ], - "attention_probs_dropout_prob": 0.1, - "bos_token_id": 0, - "classifier_dropout": null, - "eos_token_id": 2, - "hidden_act": "gelu", - "hidden_dropout_prob": 0.1, - "hidden_size": 768, - "initializer_range": 0.02, - "intermediate_size": 3072, - "layer_norm_eps": 1e-12, - "max_position_embeddings": 514, - "model_type": "roberta", - "num_attention_heads": 4, - "num_hidden_layers": 12, - "pad_token_id": 1, - "position_embedding_type": "absolute", - "torch_dtype": "float32", - "transformers_version": "4.26.1", - "type_vocab_size": 1, - "use_cache": true, - "vocab_size": 800 -} diff --git a/models/finetuned/bace/merges.txt b/models/finetuned/bace/merges.txt deleted file mode 100644 index 7cd5ec62809503c23f18c80afc0ba3bdf9d253d0..0000000000000000000000000000000000000000 --- a/models/finetuned/bace/merges.txt +++ /dev/null @@ -1,378 +0,0 @@ -#version: 0.2 - Trained by `huggingface/tokenizers` -B r -a n -c h -Br an -Bran ch -Branch 1 -= C -R i -n g -Ri ng -Ring 1 -= Branch1 -Branch 2 -= O -Ring 2 -H 1 -C @ -= N -# Branch1 -C@ @ -= Branch2 -C@ H1 -C@@ H1 -# Branch2 -# C -C l -/ C -N H1 -= Ring1 -+ 1 -- 1 -O -1 -N +1 -\ C -# N -/ N -= Ring2 -= S -=N +1 -\ N -N a -Na +1 -/ O -\ O -Br -1 -Branch 3 -\ S -S +1 -Cl -1 -I -1 -/ C@@H1 -S i -/ C@H1 -/ S -=N -1 -S e -= P -N -1 -Ring 3 -2 H -P +1 -K +1 -\ C@@H1 -\ C@H1 -/ N+1 -@ @ -C -1 -# N+1 -B -1 -+ 3 -Cl +3 -\ NH1 -L i -Li +1 -P H1 -1 8 -18 F -@ +1 -3 H -P @@ -H 0 -O H0 -1 2 -P @ -+ 2 -@@ +1 -S -1 -/ Br -- / -\ Cl --/ Ring2 -\ O-1 -1 1 -5 I -12 5I -11 C -H 3 -\ N+1 -- \ -/ C@@ -S @+1 -A s -/ Cl -11C H3 -=S e -S @@+1 -N @+1 -1 4 --\ Ring2 -14 C -\ F -/ C@ -T e -H 2 -H1 -1 -=O +1 -N @@+1 -C +1 -=S +1 -Z n -/ P -a +2 -/ I -O H1-1 -C a+2 -\ Br -M g -Zn +2 -A l -/ F -Mg +2 -12 3 -123 I -1 3 -I +1 -/ O-1 --\ Ring1 -B H2 -BH2 -1 -\ I -/ NH1 -O +1 -13 1 -131 I -= 14C -/ S+1 -= Ring3 -\ C@@ -H2 +1 -\ C@ -A g -= As -=Se +1 -N H2+1 -Se H1 --/ Ring1 -= Te -Al +3 -Na H1 -=Te +1 -NH1 +1 -Ag +1 -H1 +1 -NH1 -1 -\ P -14C H2 -13 C -14C H1 -= 11C -S @@ -=P @@ -Si H2 -H3 -1 -14C H3 -B H3-1 -S @ -=14C H1 -=P H1 -=P @ -=N H1+1 -\S +1 -12 4 -C H1-1 -S r -=S i -124 I -Sr +2 -#C -1 -/C -1 -N @ -/N -1 -13C H1 -/ B -1 9 -B a+2 -H 4 -S H1+1 -Se +1 -19 F -/ 125I -P @+1 -R b -Cl +1 -Si H4 -Rb +1 -= Branch3 -N @@ -As +1 -/ Si -B H1-1 -S H1 -/ 123I -3 2 -= Mg -H +1 -\ B -Si H1 -P@@ +1 -- 2 -1 5 -1 7 -3 5 -= 13CH1 -C s -=N H2+1 -=S H1 -Mg H2 -32 P -17 F -35 S -Cs +1 -# 11C -/ 131I -B i -\ 125I -=S @@ -\S -1 -6 Br -7 I -7 6Br -= B -e H1 -\N -1 -18 O -12 7I -11C H2 -14 C@@H1 -Te H2 -15 NH1 -Bi +3 -/ P+1 -/ 13C -/ 13CH1 -0 B -1 0B -= Al -= 18O -B H0 -F -1 -N H3 -S -2 -Br +2 -Cl +2 -\S i -/S -1 -=P H2 -14 C@H1 -NH3 +1 -# 14C -# O+1 -- 3 -2 2 -4 H -5 Se -5 Sr+2 -7 5Se -8 5Sr+2 -= B-1 -= 13C -@ -1 -B e -B @@ -B @-1 -C a -C H1 -I +3 -K H1 -O H1+1 -R a+2 -S H1-1 -\ PH1 -\ 123I -=C a -\C H1-1 -=S @ -\S eH1 -/S eH1 -Se -1 -Li H1 -18F -1 -125I H1 -11C H1 -Te H1 -Zn +1 -Zn -2 -Al -3 -13C H3 -15 N -Be +2 -B@@ -1 -# P -# S -- 4 -/ PH1 -/ P@@ -/ As -/ 14C -/ 14CH1 -2 K+1 -2 Rb+1 -3 Se -3 Ra+2 -4 5 -4 7 -4 2K+1 -5 I-1 -7 3Se -8 9 -8 2Rb+1 -= 32 -= 32P -C H0 -C H2 -I +2 -N H0 -N H4 -O H1 -P H2+1 -S H0 -S H2 -\ 3H -\ 11CH3 -\C -1 -\S e -Si @ -Si -1 -Si H1-1 -Si H3-1 -/S e -Se -2 -\NH1 -1 -18F H1 -12 5I-1 -11 C@@H1 -11 C-1 -As H1 -As -1 -14 C@@ -Te -1 -Mg +1 -123 I-1 -123 Te -123I H1 -13 5I -131 I-1 -Ag -4 -124 I-1 -76Br H1 -18O H1 -22 Na+1 -22 3Ra+2 -Ca H2 -45 Ca+2 -47 Ca+2 -89 Sr+2 -=32 PH1 -NH4 +1 diff --git a/models/finetuned/bace/model.pt b/models/finetuned/bace/model.pt deleted file mode 100644 index 5557f9c3c74f91a50aa359848815ba6469e3dce1..0000000000000000000000000000000000000000 --- a/models/finetuned/bace/model.pt +++ /dev/null @@ -1,3 +0,0 @@ -version https://git-lfs.github.com/spec/v1 -oid sha256:62289c1112babd62c4b045f6971b8dcdd42201fb5a17acf59a471db88f14a56e -size 1022855293 diff --git a/models/finetuned/bace/special_tokens_map.json b/models/finetuned/bace/special_tokens_map.json deleted file mode 100644 index 06a55849fa69a91e7179d909e373179ff7467d8c..0000000000000000000000000000000000000000 --- a/models/finetuned/bace/special_tokens_map.json +++ /dev/null @@ -1,51 +0,0 @@ -{ - "bos_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "cls_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "eos_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "mask_token": { - "content": "", - "lstrip": true, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "pad_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "sep_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "unk_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - } -} diff --git a/models/finetuned/bace/tokenizer.json b/models/finetuned/bace/tokenizer.json deleted file mode 100644 index 3b64b273e6fa9799e2d8375722b9e815de9ebb8f..0000000000000000000000000000000000000000 --- a/models/finetuned/bace/tokenizer.json +++ /dev/null @@ -1,909 +0,0 @@ -{ - "version": "1.0", - "truncation": { - "direction": "Right", - "max_length": 128, - "strategy": "LongestFirst", - "stride": 0 - }, - "padding": { - "strategy": { - "Fixed": 128 - }, - "direction": "Right", - "pad_to_multiple_of": null, - "pad_id": 3, - "pad_type_id": 0, - "pad_token": "" - }, - "added_tokens": [ - { - "id": 0, - "content": "", - "single_word": false, - "lstrip": false, - "rstrip": false, - "normalized": true, - "special": true - }, - { - "id": 1, - "content": "", - "single_word": false, - "lstrip": false, - "rstrip": false, - "normalized": true, - "special": true - }, - { - "id": 2, - "content": "", - "single_word": false, - "lstrip": false, - "rstrip": false, - "normalized": true, - "special": true - }, - { - "id": 3, - "content": "", - "single_word": false, - "lstrip": false, - "rstrip": false, - "normalized": true, - "special": true - }, - { - "id": 4, - "content": "", - "single_word": false, - "lstrip": true, - "rstrip": false, - "normalized": true, - "special": true - } - ], - "normalizer": null, - "pre_tokenizer": { - "type": "ByteLevel", - "add_prefix_space": false, - "trim_offsets": true, - "use_regex": true - }, - "post_processor": { - "type": "RobertaProcessing", - "sep": [ - "", - 2 - ], - "cls": [ - "", - 1 - ], - "trim_offsets": true, - "add_prefix_space": false - }, - "decoder": { - "type": "ByteLevel", - "add_prefix_space": true, - "trim_offsets": true, - "use_regex": true - }, - "model": { - "type": "BPE", - "dropout": null, - "unk_token": null, - "continuing_subword_prefix": "", - "end_of_word_suffix": "", - "fuse_unk": false, - "vocab": { - "": 0, - "": 1, - "": 2, - "": 3, - "": 4, - "\n": 5, - "#": 6, - "+": 7, - "-": 8, - ".": 9, - "/": 10, - "0": 11, - "1": 12, - "2": 13, - "3": 14, - "4": 15, - "5": 16, - "6": 17, - "7": 18, - "8": 19, - "9": 20, - "=": 21, - "@": 22, - "A": 23, - "B": 24, - "C": 25, - "F": 26, - "H": 27, - "I": 28, - "K": 29, - "L": 30, - "M": 31, - "N": 32, - "O": 33, - "P": 34, - "R": 35, - "S": 36, - "T": 37, - "Z": 38, - "\\": 39, - "a": 40, - "b": 41, - "c": 42, - "e": 43, - "g": 44, - "h": 45, - "i": 46, - "l": 47, - "n": 48, - "r": 49, - "s": 50, - "Br": 51, - "an": 52, - "ch": 53, - "Bran": 54, - "Branch": 55, - "Branch1": 56, - "=C": 57, - "Ri": 58, - "ng": 59, - "Ring": 60, - "Ring1": 61, - "=Branch1": 62, - "Branch2": 63, - "=O": 64, - "Ring2": 65, - "H1": 66, - "C@": 67, - "=N": 68, - "#Branch1": 69, - "C@@": 70, - "=Branch2": 71, - "C@H1": 72, - "C@@H1": 73, - "#Branch2": 74, - "#C": 75, - "Cl": 76, - "/C": 77, - "NH1": 78, - "=Ring1": 79, - "+1": 80, - "-1": 81, - "O-1": 82, - "N+1": 83, - "\\C": 84, - "#N": 85, - "/N": 86, - "=Ring2": 87, - "=S": 88, - "=N+1": 89, - "\\N": 90, - "Na": 91, - "Na+1": 92, - "/O": 93, - "\\O": 94, - "Br-1": 95, - "Branch3": 96, - "\\S": 97, - "S+1": 98, - "Cl-1": 99, - "I-1": 100, - "/C@@H1": 101, - "Si": 102, - "/C@H1": 103, - "/S": 104, - "=N-1": 105, - "Se": 106, - "=P": 107, - "N-1": 108, - "Ring3": 109, - "2H": 110, - "P+1": 111, - "K+1": 112, - "\\C@@H1": 113, - "\\C@H1": 114, - "/N+1": 115, - "@@": 116, - "C-1": 117, - "#N+1": 118, - "B-1": 119, - "+3": 120, - "Cl+3": 121, - "\\NH1": 122, - "Li": 123, - "Li+1": 124, - "PH1": 125, - "18": 126, - "18F": 127, - "@+1": 128, - "3H": 129, - "P@@": 130, - "H0": 131, - "OH0": 132, - "12": 133, - "P@": 134, - "+2": 135, - "@@+1": 136, - "S-1": 137, - "/Br": 138, - "-/": 139, - "\\Cl": 140, - "-/Ring2": 141, - "\\O-1": 142, - "11": 143, - "5I": 144, - "125I": 145, - "11C": 146, - "H3": 147, - "\\N+1": 148, - "-\\": 149, - "/C@@": 150, - "S@+1": 151, - "As": 152, - "/Cl": 153, - "11CH3": 154, - "=Se": 155, - "S@@+1": 156, - "N@+1": 157, - "14": 158, - "-\\Ring2": 159, - "14C": 160, - "\\F": 161, - "/C@": 162, - "Te": 163, - "H2": 164, - "H1-1": 165, - "=O+1": 166, - "N@@+1": 167, - "C+1": 168, - "=S+1": 169, - "Zn": 170, - "/P": 171, - "a+2": 172, - "/I": 173, - "OH1-1": 174, - "Ca+2": 175, - "\\Br": 176, - "Mg": 177, - "Zn+2": 178, - "Al": 179, - "/F": 180, - "Mg+2": 181, - "123": 182, - "123I": 183, - "13": 184, - "I+1": 185, - "/O-1": 186, - "-\\Ring1": 187, - "BH2": 188, - "BH2-1": 189, - "\\I": 190, - "/NH1": 191, - "O+1": 192, - "131": 193, - "131I": 194, - "=14C": 195, - "/S+1": 196, - "=Ring3": 197, - "\\C@@": 198, - "H2+1": 199, - "\\C@": 200, - "Ag": 201, - "=As": 202, - "=Se+1": 203, - "NH2+1": 204, - "SeH1": 205, - "-/Ring1": 206, - "=Te": 207, - "Al+3": 208, - "NaH1": 209, - "=Te+1": 210, - "NH1+1": 211, - "Ag+1": 212, - "H1+1": 213, - "NH1-1": 214, - "\\P": 215, - "14CH2": 216, - "13C": 217, - "14CH1": 218, - "=11C": 219, - "S@@": 220, - "=P@@": 221, - "SiH2": 222, - "H3-1": 223, - "14CH3": 224, - "BH3-1": 225, - "S@": 226, - "=14CH1": 227, - "=PH1": 228, - "=P@": 229, - "=NH1+1": 230, - "\\S+1": 231, - "124": 232, - "CH1-1": 233, - "Sr": 234, - "=Si": 235, - "124I": 236, - "Sr+2": 237, - "#C-1": 238, - "/C-1": 239, - "N@": 240, - "/N-1": 241, - "13CH1": 242, - "/B": 243, - "19": 244, - "Ba+2": 245, - "H4": 246, - "SH1+1": 247, - "Se+1": 248, - "19F": 249, - "/125I": 250, - "P@+1": 251, - "Rb": 252, - "Cl+1": 253, - "SiH4": 254, - "Rb+1": 255, - "=Branch3": 256, - "N@@": 257, - "As+1": 258, - "/Si": 259, - "BH1-1": 260, - "SH1": 261, - "/123I": 262, - "32": 263, - "=Mg": 264, - "H+1": 265, - "\\B": 266, - "SiH1": 267, - "P@@+1": 268, - "-2": 269, - "15": 270, - "17": 271, - "35": 272, - "=13CH1": 273, - "Cs": 274, - "=NH2+1": 275, - "=SH1": 276, - "MgH2": 277, - "32P": 278, - "17F": 279, - "35S": 280, - "Cs+1": 281, - "#11C": 282, - "/131I": 283, - "Bi": 284, - "\\125I": 285, - "=S@@": 286, - "\\S-1": 287, - "6Br": 288, - "7I": 289, - "76Br": 290, - "=B": 291, - "eH1": 292, - "\\N-1": 293, - "18O": 294, - "127I": 295, - "11CH2": 296, - "14C@@H1": 297, - "TeH2": 298, - "15NH1": 299, - "Bi+3": 300, - "/P+1": 301, - "/13C": 302, - "/13CH1": 303, - "0B": 304, - "10B": 305, - "=Al": 306, - "=18O": 307, - "BH0": 308, - "F-1": 309, - "NH3": 310, - "S-2": 311, - "Br+2": 312, - "Cl+2": 313, - "\\Si": 314, - "/S-1": 315, - "=PH2": 316, - "14C@H1": 317, - "NH3+1": 318, - "#14C": 319, - "#O+1": 320, - "-3": 321, - "22": 322, - "4H": 323, - "5Se": 324, - "5Sr+2": 325, - "75Se": 326, - "85Sr+2": 327, - "=B-1": 328, - "=13C": 329, - "@-1": 330, - "Be": 331, - "B@@": 332, - "B@-1": 333, - "Ca": 334, - "CH1": 335, - "I+3": 336, - "KH1": 337, - "OH1+1": 338, - "Ra+2": 339, - "SH1-1": 340, - "\\PH1": 341, - "\\123I": 342, - "=Ca": 343, - "\\CH1-1": 344, - "=S@": 345, - "\\SeH1": 346, - "/SeH1": 347, - "Se-1": 348, - "LiH1": 349, - "18F-1": 350, - "125IH1": 351, - "11CH1": 352, - "TeH1": 353, - "Zn+1": 354, - "Zn-2": 355, - "Al-3": 356, - "13CH3": 357, - "15N": 358, - "Be+2": 359, - "B@@-1": 360, - "#P": 361, - "#S": 362, - "-4": 363, - "/PH1": 364, - "/P@@": 365, - "/As": 366, - "/14C": 367, - "/14CH1": 368, - "2K+1": 369, - "2Rb+1": 370, - "3Se": 371, - "3Ra+2": 372, - "45": 373, - "47": 374, - "42K+1": 375, - "5I-1": 376, - "73Se": 377, - "89": 378, - "82Rb+1": 379, - "=32": 380, - "=32P": 381, - "CH0": 382, - "CH2": 383, - "I+2": 384, - "NH0": 385, - "NH4": 386, - "OH1": 387, - "PH2+1": 388, - "SH0": 389, - "SH2": 390, - "\\3H": 391, - "\\11CH3": 392, - "\\C-1": 393, - "\\Se": 394, - "Si@": 395, - "Si-1": 396, - "SiH1-1": 397, - "SiH3-1": 398, - "/Se": 399, - "Se-2": 400, - "\\NH1-1": 401, - "18FH1": 402, - "125I-1": 403, - "11C@@H1": 404, - "11C-1": 405, - "AsH1": 406, - "As-1": 407, - "14C@@": 408, - "Te-1": 409, - "Mg+1": 410, - "123I-1": 411, - "123Te": 412, - "123IH1": 413, - "135I": 414, - "131I-1": 415, - "Ag-4": 416, - "124I-1": 417, - "76BrH1": 418, - "18OH1": 419, - "22Na+1": 420, - "223Ra+2": 421, - "CaH2": 422, - "45Ca+2": 423, - "47Ca+2": 424, - "89Sr+2": 425, - "=32PH1": 426, - "NH4+1": 427 - }, - "merges": [ - "B r", - "a n", - "c h", - "Br an", - "Bran ch", - "Branch 1", - "= C", - "R i", - "n g", - "Ri ng", - "Ring 1", - "= Branch1", - "Branch 2", - "= O", - "Ring 2", - "H 1", - "C @", - "= N", - "# Branch1", - "C@ @", - "= Branch2", - "C@ H1", - "C@@ H1", - "# Branch2", - "# C", - "C l", - "/ C", - "N H1", - "= Ring1", - "+ 1", - "- 1", - "O -1", - "N +1", - "\\ C", - "# N", - "/ N", - "= Ring2", - "= S", - "=N +1", - "\\ N", - "N a", - "Na +1", - "/ O", - "\\ O", - "Br -1", - "Branch 3", - "\\ S", - "S +1", - "Cl -1", - "I -1", - "/ C@@H1", - "S i", - "/ C@H1", - "/ S", - "=N -1", - "S e", - "= P", - "N -1", - "Ring 3", - "2 H", - "P +1", - "K +1", - "\\ C@@H1", - "\\ C@H1", - "/ N+1", - "@ @", - "C -1", - "# N+1", - "B -1", - "+ 3", - "Cl +3", - "\\ NH1", - "L i", - "Li +1", - "P H1", - "1 8", - "18 F", - "@ +1", - "3 H", - "P @@", - "H 0", - "O H0", - "1 2", - "P @", - "+ 2", - "@@ +1", - "S -1", - "/ Br", - "- /", - "\\ Cl", - "-/ Ring2", - "\\ O-1", - "1 1", - "5 I", - "12 5I", - "11 C", - "H 3", - "\\ N+1", - "- \\", - "/ C@@", - "S @+1", - "A s", - "/ Cl", - "11C H3", - "=S e", - "S @@+1", - "N @+1", - "1 4", - "-\\ Ring2", - "14 C", - "\\ F", - "/ C@", - "T e", - "H 2", - "H1 -1", - "=O +1", - "N @@+1", - "C +1", - "=S +1", - "Z n", - "/ P", - "a +2", - "/ I", - "O H1-1", - "C a+2", - "\\ Br", - "M g", - "Zn +2", - "A l", - "/ F", - "Mg +2", - "12 3", - "123 I", - "1 3", - "I +1", - "/ O-1", - "-\\ Ring1", - "B H2", - "BH2 -1", - "\\ I", - "/ NH1", - "O +1", - "13 1", - "131 I", - "= 14C", - "/ S+1", - "= Ring3", - "\\ C@@", - "H2 +1", - "\\ C@", - "A g", - "= As", - "=Se +1", - "N H2+1", - "Se H1", - "-/ Ring1", - "= Te", - "Al +3", - "Na H1", - "=Te +1", - "NH1 +1", - "Ag +1", - "H1 +1", - "NH1 -1", - "\\ P", - "14C H2", - "13 C", - "14C H1", - "= 11C", - "S @@", - "=P @@", - "Si H2", - "H3 -1", - "14C H3", - "B H3-1", - "S @", - "=14C H1", - "=P H1", - "=P @", - "=N H1+1", - "\\S +1", - "12 4", - "C H1-1", - "S r", - "=S i", - "124 I", - "Sr +2", - "#C -1", - "/C -1", - "N @", - "/N -1", - "13C H1", - "/ B", - "1 9", - "B a+2", - "H 4", - "S H1+1", - "Se +1", - "19 F", - "/ 125I", - "P @+1", - "R b", - "Cl +1", - "Si H4", - "Rb +1", - "= Branch3", - "N @@", - "As +1", - "/ Si", - "B H1-1", - "S H1", - "/ 123I", - "3 2", - "= Mg", - "H +1", - "\\ B", - "Si H1", - "P@@ +1", - "- 2", - "1 5", - "1 7", - "3 5", - "= 13CH1", - "C s", - "=N H2+1", - "=S H1", - "Mg H2", - "32 P", - "17 F", - "35 S", - "Cs +1", - "# 11C", - "/ 131I", - "B i", - "\\ 125I", - "=S @@", - "\\S -1", - "6 Br", - "7 I", - "7 6Br", - "= B", - "e H1", - "\\N -1", - "18 O", - "12 7I", - "11C H2", - "14 C@@H1", - "Te H2", - "15 NH1", - "Bi +3", - "/ P+1", - "/ 13C", - "/ 13CH1", - "0 B", - "1 0B", - "= Al", - "= 18O", - "B H0", - "F -1", - "N H3", - "S -2", - "Br +2", - "Cl +2", - "\\S i", - "/S -1", - "=P H2", - "14 C@H1", - "NH3 +1", - "# 14C", - "# O+1", - "- 3", - "2 2", - "4 H", - "5 Se", - "5 Sr+2", - "7 5Se", - "8 5Sr+2", - "= B-1", - "= 13C", - "@ -1", - "B e", - "B @@", - "B @-1", - "C a", - "C H1", - "I +3", - "K H1", - "O H1+1", - "R a+2", - "S H1-1", - "\\ PH1", - "\\ 123I", - "=C a", - "\\C H1-1", - "=S @", - "\\S eH1", - "/S eH1", - "Se -1", - "Li H1", - "18F -1", - "125I H1", - "11C H1", - "Te H1", - "Zn +1", - "Zn -2", - "Al -3", - "13C H3", - "15 N", - "Be +2", - "B@@ -1", - "# P", - "# S", - "- 4", - "/ PH1", - "/ P@@", - "/ As", - "/ 14C", - "/ 14CH1", - "2 K+1", - "2 Rb+1", - "3 Se", - "3 Ra+2", - "4 5", - "4 7", - "4 2K+1", - "5 I-1", - "7 3Se", - "8 9", - "8 2Rb+1", - "= 32", - "= 32P", - "C H0", - "C H2", - "I +2", - "N H0", - "N H4", - "O H1", - "P H2+1", - "S H0", - "S H2", - "\\ 3H", - "\\ 11CH3", - "\\C -1", - "\\S e", - "Si @", - "Si -1", - "Si H1-1", - "Si H3-1", - "/S e", - "Se -2", - "\\NH1 -1", - "18F H1", - "12 5I-1", - "11 C@@H1", - "11 C-1", - "As H1", - "As -1", - "14 C@@", - "Te -1", - "Mg +1", - "123 I-1", - "123 Te", - "123I H1", - "13 5I", - "131 I-1", - "Ag -4", - "124 I-1", - "76Br H1", - "18O H1", - "22 Na+1", - "22 3Ra+2", - "Ca H2", - "45 Ca+2", - "47 Ca+2", - "89 Sr+2", - "=32 PH1", - "NH4 +1" - ] - } -} \ No newline at end of file diff --git a/models/finetuned/bace/tokenizer_config.json b/models/finetuned/bace/tokenizer_config.json deleted file mode 100644 index 08860954acd34fad07fd77f7635298fa565f3149..0000000000000000000000000000000000000000 --- a/models/finetuned/bace/tokenizer_config.json +++ /dev/null @@ -1,65 +0,0 @@ -{ - "add_prefix_space": false, - "bos_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "cls_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "eos_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "errors": "replace", - "mask_token": { - "__type": "AddedToken", - "content": "", - "lstrip": true, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "model_max_length": 1000000000000000019884624838656, - "name_or_path": "/home/erva/SELFormerMM/data/pretrained_multimodal_chembl36", - "pad_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "sep_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "special_tokens_map_file": null, - "tokenizer_class": "RobertaTokenizer", - "trim_offsets": true, - "unk_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - } -} diff --git a/models/finetuned/bace/train_stdout.log b/models/finetuned/bace/train_stdout.log deleted file mode 100644 index 03c26b0ae4120b70ae323542a7cffa79f8253ca4..0000000000000000000000000000000000000000 --- a/models/finetuned/bace/train_stdout.log +++ /dev/null @@ -1,91 +0,0 @@ -[finetune] starting -[finetune] device=cuda task_type=binary batch_size=16 max_len=128 backbone_lr=5e-05 head_lr=1e-05 weight_decay=0.1 epochs=50 -[finetune] dataset_meta_csv=/home/erva/SELFormerMM/data/new_finetuning_datasets/classification/bace/bace.csv -[finetune] dataset_embs_npz=/home/erva/SELFormerMM/data/new_finetuning_datasets/classification/bace/bace_embs.npz -[finetune] model_path=HUBioDataLab/SELFormer tokenizer_path=HUBioDataLab/SELFormer -[finetune] pretrained_multimodal_dir=/home/erva/SELFormerMM/data/pretrained_multimodal_chembl36 -[finetune] use_scaffold=True seed=42 fracs=(0.8,0.1,0.1) -[finetune] loading dataset bundle (meta csv + embs npz) ... -[finetune] splitting dataset... - - 0%| | 0/1513 [00:00":0,"":1,"":2,"":3,"":4,"\n":5,"#":6,"+":7,"-":8,".":9,"/":10,"0":11,"1":12,"2":13,"3":14,"4":15,"5":16,"6":17,"7":18,"8":19,"9":20,"=":21,"@":22,"A":23,"B":24,"C":25,"F":26,"H":27,"I":28,"K":29,"L":30,"M":31,"N":32,"O":33,"P":34,"R":35,"S":36,"T":37,"Z":38,"\\":39,"a":40,"b":41,"c":42,"e":43,"g":44,"h":45,"i":46,"l":47,"n":48,"r":49,"s":50,"Br":51,"an":52,"ch":53,"Bran":54,"Branch":55,"Branch1":56,"=C":57,"Ri":58,"ng":59,"Ring":60,"Ring1":61,"=Branch1":62,"Branch2":63,"=O":64,"Ring2":65,"H1":66,"C@":67,"=N":68,"#Branch1":69,"C@@":70,"=Branch2":71,"C@H1":72,"C@@H1":73,"#Branch2":74,"#C":75,"Cl":76,"/C":77,"NH1":78,"=Ring1":79,"+1":80,"-1":81,"O-1":82,"N+1":83,"\\C":84,"#N":85,"/N":86,"=Ring2":87,"=S":88,"=N+1":89,"\\N":90,"Na":91,"Na+1":92,"/O":93,"\\O":94,"Br-1":95,"Branch3":96,"\\S":97,"S+1":98,"Cl-1":99,"I-1":100,"/C@@H1":101,"Si":102,"/C@H1":103,"/S":104,"=N-1":105,"Se":106,"=P":107,"N-1":108,"Ring3":109,"2H":110,"P+1":111,"K+1":112,"\\C@@H1":113,"\\C@H1":114,"/N+1":115,"@@":116,"C-1":117,"#N+1":118,"B-1":119,"+3":120,"Cl+3":121,"\\NH1":122,"Li":123,"Li+1":124,"PH1":125,"18":126,"18F":127,"@+1":128,"3H":129,"P@@":130,"H0":131,"OH0":132,"12":133,"P@":134,"+2":135,"@@+1":136,"S-1":137,"/Br":138,"-/":139,"\\Cl":140,"-/Ring2":141,"\\O-1":142,"11":143,"5I":144,"125I":145,"11C":146,"H3":147,"\\N+1":148,"-\\":149,"/C@@":150,"S@+1":151,"As":152,"/Cl":153,"11CH3":154,"=Se":155,"S@@+1":156,"N@+1":157,"14":158,"-\\Ring2":159,"14C":160,"\\F":161,"/C@":162,"Te":163,"H2":164,"H1-1":165,"=O+1":166,"N@@+1":167,"C+1":168,"=S+1":169,"Zn":170,"/P":171,"a+2":172,"/I":173,"OH1-1":174,"Ca+2":175,"\\Br":176,"Mg":177,"Zn+2":178,"Al":179,"/F":180,"Mg+2":181,"123":182,"123I":183,"13":184,"I+1":185,"/O-1":186,"-\\Ring1":187,"BH2":188,"BH2-1":189,"\\I":190,"/NH1":191,"O+1":192,"131":193,"131I":194,"=14C":195,"/S+1":196,"=Ring3":197,"\\C@@":198,"H2+1":199,"\\C@":200,"Ag":201,"=As":202,"=Se+1":203,"NH2+1":204,"SeH1":205,"-/Ring1":206,"=Te":207,"Al+3":208,"NaH1":209,"=Te+1":210,"NH1+1":211,"Ag+1":212,"H1+1":213,"NH1-1":214,"\\P":215,"14CH2":216,"13C":217,"14CH1":218,"=11C":219,"S@@":220,"=P@@":221,"SiH2":222,"H3-1":223,"14CH3":224,"BH3-1":225,"S@":226,"=14CH1":227,"=PH1":228,"=P@":229,"=NH1+1":230,"\\S+1":231,"124":232,"CH1-1":233,"Sr":234,"=Si":235,"124I":236,"Sr+2":237,"#C-1":238,"/C-1":239,"N@":240,"/N-1":241,"13CH1":242,"/B":243,"19":244,"Ba+2":245,"H4":246,"SH1+1":247,"Se+1":248,"19F":249,"/125I":250,"P@+1":251,"Rb":252,"Cl+1":253,"SiH4":254,"Rb+1":255,"=Branch3":256,"N@@":257,"As+1":258,"/Si":259,"BH1-1":260,"SH1":261,"/123I":262,"32":263,"=Mg":264,"H+1":265,"\\B":266,"SiH1":267,"P@@+1":268,"-2":269,"15":270,"17":271,"35":272,"=13CH1":273,"Cs":274,"=NH2+1":275,"=SH1":276,"MgH2":277,"32P":278,"17F":279,"35S":280,"Cs+1":281,"#11C":282,"/131I":283,"Bi":284,"\\125I":285,"=S@@":286,"\\S-1":287,"6Br":288,"7I":289,"76Br":290,"=B":291,"eH1":292,"\\N-1":293,"18O":294,"127I":295,"11CH2":296,"14C@@H1":297,"TeH2":298,"15NH1":299,"Bi+3":300,"/P+1":301,"/13C":302,"/13CH1":303,"0B":304,"10B":305,"=Al":306,"=18O":307,"BH0":308,"F-1":309,"NH3":310,"S-2":311,"Br+2":312,"Cl+2":313,"\\Si":314,"/S-1":315,"=PH2":316,"14C@H1":317,"NH3+1":318,"#14C":319,"#O+1":320,"-3":321,"22":322,"4H":323,"5Se":324,"5Sr+2":325,"75Se":326,"85Sr+2":327,"=B-1":328,"=13C":329,"@-1":330,"Be":331,"B@@":332,"B@-1":333,"Ca":334,"CH1":335,"I+3":336,"KH1":337,"OH1+1":338,"Ra+2":339,"SH1-1":340,"\\PH1":341,"\\123I":342,"=Ca":343,"\\CH1-1":344,"=S@":345,"\\SeH1":346,"/SeH1":347,"Se-1":348,"LiH1":349,"18F-1":350,"125IH1":351,"11CH1":352,"TeH1":353,"Zn+1":354,"Zn-2":355,"Al-3":356,"13CH3":357,"15N":358,"Be+2":359,"B@@-1":360,"#P":361,"#S":362,"-4":363,"/PH1":364,"/P@@":365,"/As":366,"/14C":367,"/14CH1":368,"2K+1":369,"2Rb+1":370,"3Se":371,"3Ra+2":372,"45":373,"47":374,"42K+1":375,"5I-1":376,"73Se":377,"89":378,"82Rb+1":379,"=32":380,"=32P":381,"CH0":382,"CH2":383,"I+2":384,"NH0":385,"NH4":386,"OH1":387,"PH2+1":388,"SH0":389,"SH2":390,"\\3H":391,"\\11CH3":392,"\\C-1":393,"\\Se":394,"Si@":395,"Si-1":396,"SiH1-1":397,"SiH3-1":398,"/Se":399,"Se-2":400,"\\NH1-1":401,"18FH1":402,"125I-1":403,"11C@@H1":404,"11C-1":405,"AsH1":406,"As-1":407,"14C@@":408,"Te-1":409,"Mg+1":410,"123I-1":411,"123Te":412,"123IH1":413,"135I":414,"131I-1":415,"Ag-4":416,"124I-1":417,"76BrH1":418,"18OH1":419,"22Na+1":420,"223Ra+2":421,"CaH2":422,"45Ca+2":423,"47Ca+2":424,"89Sr+2":425,"=32PH1":426,"NH4+1":427} \ No newline at end of file diff --git a/models/finetuned/bbbp/checkpoint_epoch_025/config.json b/models/finetuned/bbbp/checkpoint_epoch_025/config.json deleted file mode 100644 index 3811e21539577b37e06313eab31ec11e53f0cbbc..0000000000000000000000000000000000000000 --- a/models/finetuned/bbbp/checkpoint_epoch_025/config.json +++ /dev/null @@ -1,27 +0,0 @@ -{ - "_name_or_path": "/home/erva/SELFormerMM/data/pretrained_multimodal_chembl36", - "architectures": [ - "RobertaForMaskedLM" - ], - "attention_probs_dropout_prob": 0.1, - "bos_token_id": 0, - "classifier_dropout": null, - "eos_token_id": 2, - "hidden_act": "gelu", - "hidden_dropout_prob": 0.1, - "hidden_size": 768, - "initializer_range": 0.02, - "intermediate_size": 3072, - "layer_norm_eps": 1e-12, - "max_position_embeddings": 514, - "model_type": "roberta", - "num_attention_heads": 4, - "num_hidden_layers": 12, - "pad_token_id": 1, - "position_embedding_type": "absolute", - "torch_dtype": "float32", - "transformers_version": "4.26.1", - "type_vocab_size": 1, - "use_cache": true, - "vocab_size": 800 -} diff --git a/models/finetuned/bbbp/checkpoint_epoch_025/merges.txt b/models/finetuned/bbbp/checkpoint_epoch_025/merges.txt deleted file mode 100644 index 7cd5ec62809503c23f18c80afc0ba3bdf9d253d0..0000000000000000000000000000000000000000 --- a/models/finetuned/bbbp/checkpoint_epoch_025/merges.txt +++ /dev/null @@ -1,378 +0,0 @@ -#version: 0.2 - Trained by `huggingface/tokenizers` -B r -a n -c h -Br an -Bran ch -Branch 1 -= C -R i -n g -Ri ng -Ring 1 -= Branch1 -Branch 2 -= O -Ring 2 -H 1 -C @ -= N -# Branch1 -C@ @ -= Branch2 -C@ H1 -C@@ H1 -# Branch2 -# C -C l -/ C -N H1 -= Ring1 -+ 1 -- 1 -O -1 -N +1 -\ C -# N -/ N -= Ring2 -= S -=N +1 -\ N -N a -Na +1 -/ O -\ O -Br -1 -Branch 3 -\ S -S +1 -Cl -1 -I -1 -/ C@@H1 -S i -/ C@H1 -/ S -=N -1 -S e -= P -N -1 -Ring 3 -2 H -P +1 -K +1 -\ C@@H1 -\ C@H1 -/ N+1 -@ @ -C -1 -# N+1 -B -1 -+ 3 -Cl +3 -\ NH1 -L i -Li +1 -P H1 -1 8 -18 F -@ +1 -3 H -P @@ -H 0 -O H0 -1 2 -P @ -+ 2 -@@ +1 -S -1 -/ Br -- / -\ Cl --/ Ring2 -\ O-1 -1 1 -5 I -12 5I -11 C -H 3 -\ N+1 -- \ -/ C@@ -S @+1 -A s -/ Cl -11C H3 -=S e -S @@+1 -N @+1 -1 4 --\ Ring2 -14 C -\ F -/ C@ -T e -H 2 -H1 -1 -=O +1 -N @@+1 -C +1 -=S +1 -Z n -/ P -a +2 -/ I -O H1-1 -C a+2 -\ Br -M g -Zn +2 -A l -/ F -Mg +2 -12 3 -123 I -1 3 -I +1 -/ O-1 --\ Ring1 -B H2 -BH2 -1 -\ I -/ NH1 -O +1 -13 1 -131 I -= 14C -/ S+1 -= Ring3 -\ C@@ -H2 +1 -\ C@ -A g -= As -=Se +1 -N H2+1 -Se H1 --/ Ring1 -= Te -Al +3 -Na H1 -=Te +1 -NH1 +1 -Ag +1 -H1 +1 -NH1 -1 -\ P -14C H2 -13 C -14C H1 -= 11C -S @@ -=P @@ -Si H2 -H3 -1 -14C H3 -B H3-1 -S @ -=14C H1 -=P H1 -=P @ -=N H1+1 -\S +1 -12 4 -C H1-1 -S r -=S i -124 I -Sr +2 -#C -1 -/C -1 -N @ -/N -1 -13C H1 -/ B -1 9 -B a+2 -H 4 -S H1+1 -Se +1 -19 F -/ 125I -P @+1 -R b -Cl +1 -Si H4 -Rb +1 -= Branch3 -N @@ -As +1 -/ Si -B H1-1 -S H1 -/ 123I -3 2 -= Mg -H +1 -\ B -Si H1 -P@@ +1 -- 2 -1 5 -1 7 -3 5 -= 13CH1 -C s -=N H2+1 -=S H1 -Mg H2 -32 P -17 F -35 S -Cs +1 -# 11C -/ 131I -B i -\ 125I -=S @@ -\S -1 -6 Br -7 I -7 6Br -= B -e H1 -\N -1 -18 O -12 7I -11C H2 -14 C@@H1 -Te H2 -15 NH1 -Bi +3 -/ P+1 -/ 13C -/ 13CH1 -0 B -1 0B -= Al -= 18O -B H0 -F -1 -N H3 -S -2 -Br +2 -Cl +2 -\S i -/S -1 -=P H2 -14 C@H1 -NH3 +1 -# 14C -# O+1 -- 3 -2 2 -4 H -5 Se -5 Sr+2 -7 5Se -8 5Sr+2 -= B-1 -= 13C -@ -1 -B e -B @@ -B @-1 -C a -C H1 -I +3 -K H1 -O H1+1 -R a+2 -S H1-1 -\ PH1 -\ 123I -=C a -\C H1-1 -=S @ -\S eH1 -/S eH1 -Se -1 -Li H1 -18F -1 -125I H1 -11C H1 -Te H1 -Zn +1 -Zn -2 -Al -3 -13C H3 -15 N -Be +2 -B@@ -1 -# P -# S -- 4 -/ PH1 -/ P@@ -/ As -/ 14C -/ 14CH1 -2 K+1 -2 Rb+1 -3 Se -3 Ra+2 -4 5 -4 7 -4 2K+1 -5 I-1 -7 3Se -8 9 -8 2Rb+1 -= 32 -= 32P -C H0 -C H2 -I +2 -N H0 -N H4 -O H1 -P H2+1 -S H0 -S H2 -\ 3H -\ 11CH3 -\C -1 -\S e -Si @ -Si -1 -Si H1-1 -Si H3-1 -/S e -Se -2 -\NH1 -1 -18F H1 -12 5I-1 -11 C@@H1 -11 C-1 -As H1 -As -1 -14 C@@ -Te -1 -Mg +1 -123 I-1 -123 Te -123I H1 -13 5I -131 I-1 -Ag -4 -124 I-1 -76Br H1 -18O H1 -22 Na+1 -22 3Ra+2 -Ca H2 -45 Ca+2 -47 Ca+2 -89 Sr+2 -=32 PH1 -NH4 +1 diff --git a/models/finetuned/bbbp/checkpoint_epoch_025/model.pt b/models/finetuned/bbbp/checkpoint_epoch_025/model.pt deleted file mode 100644 index 635d918ef72548978cdce205bcea6f42f7397b56..0000000000000000000000000000000000000000 --- a/models/finetuned/bbbp/checkpoint_epoch_025/model.pt +++ /dev/null @@ -1,3 +0,0 @@ -version https://git-lfs.github.com/spec/v1 -oid sha256:572adcc56b21fcab865200ba7d42bac8b619e8b42b29c2db7dd10e1e4e905a7a -size 1022855293 diff --git a/models/finetuned/bbbp/checkpoint_epoch_025/special_tokens_map.json b/models/finetuned/bbbp/checkpoint_epoch_025/special_tokens_map.json deleted file mode 100644 index 06a55849fa69a91e7179d909e373179ff7467d8c..0000000000000000000000000000000000000000 --- a/models/finetuned/bbbp/checkpoint_epoch_025/special_tokens_map.json +++ /dev/null @@ -1,51 +0,0 @@ -{ - "bos_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "cls_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "eos_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "mask_token": { - "content": "", - "lstrip": true, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "pad_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "sep_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "unk_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - } -} diff --git a/models/finetuned/bbbp/checkpoint_epoch_025/tokenizer.json b/models/finetuned/bbbp/checkpoint_epoch_025/tokenizer.json deleted file mode 100644 index 3b64b273e6fa9799e2d8375722b9e815de9ebb8f..0000000000000000000000000000000000000000 --- a/models/finetuned/bbbp/checkpoint_epoch_025/tokenizer.json +++ /dev/null @@ -1,909 +0,0 @@ -{ - "version": "1.0", - "truncation": { - "direction": "Right", - "max_length": 128, - "strategy": "LongestFirst", - "stride": 0 - }, - "padding": { - "strategy": { - "Fixed": 128 - }, - "direction": "Right", - "pad_to_multiple_of": null, - "pad_id": 3, - "pad_type_id": 0, - "pad_token": "" - }, - "added_tokens": [ - { - "id": 0, - "content": "", - "single_word": false, - "lstrip": false, - "rstrip": false, - "normalized": true, - "special": true - }, - { - "id": 1, - "content": "", - "single_word": false, - "lstrip": false, - "rstrip": false, - "normalized": true, - "special": true - }, - { - "id": 2, - "content": "", - "single_word": false, - "lstrip": false, - "rstrip": false, - "normalized": true, - "special": true - }, - { - "id": 3, - "content": "", - "single_word": false, - "lstrip": false, - "rstrip": false, - "normalized": true, - "special": true - }, - { - "id": 4, - "content": "", - "single_word": false, - "lstrip": true, - "rstrip": false, - "normalized": true, - "special": true - } - ], - "normalizer": null, - "pre_tokenizer": { - "type": "ByteLevel", - "add_prefix_space": false, - "trim_offsets": true, - "use_regex": true - }, - "post_processor": { - "type": "RobertaProcessing", - "sep": [ - "", - 2 - ], - "cls": [ - "", - 1 - ], - "trim_offsets": true, - "add_prefix_space": false - }, - "decoder": { - "type": "ByteLevel", - "add_prefix_space": true, - "trim_offsets": true, - "use_regex": true - }, - "model": { - "type": "BPE", - "dropout": null, - "unk_token": null, - "continuing_subword_prefix": "", - "end_of_word_suffix": "", - "fuse_unk": false, - "vocab": { - "": 0, - "": 1, - "": 2, - "": 3, - "": 4, - "\n": 5, - "#": 6, - "+": 7, - "-": 8, - ".": 9, - "/": 10, - "0": 11, - "1": 12, - "2": 13, - "3": 14, - "4": 15, - "5": 16, - "6": 17, - "7": 18, - "8": 19, - "9": 20, - "=": 21, - "@": 22, - "A": 23, - "B": 24, - "C": 25, - "F": 26, - "H": 27, - "I": 28, - "K": 29, - "L": 30, - "M": 31, - "N": 32, - "O": 33, - "P": 34, - "R": 35, - "S": 36, - "T": 37, - "Z": 38, - "\\": 39, - "a": 40, - "b": 41, - "c": 42, - "e": 43, - "g": 44, - "h": 45, - "i": 46, - "l": 47, - "n": 48, - "r": 49, - "s": 50, - "Br": 51, - "an": 52, - "ch": 53, - "Bran": 54, - "Branch": 55, - "Branch1": 56, - "=C": 57, - "Ri": 58, - "ng": 59, - "Ring": 60, - "Ring1": 61, - "=Branch1": 62, - "Branch2": 63, - "=O": 64, - "Ring2": 65, - "H1": 66, - "C@": 67, - "=N": 68, - "#Branch1": 69, - "C@@": 70, - "=Branch2": 71, - "C@H1": 72, - "C@@H1": 73, - "#Branch2": 74, - "#C": 75, - "Cl": 76, - "/C": 77, - "NH1": 78, - "=Ring1": 79, - "+1": 80, - "-1": 81, - "O-1": 82, - "N+1": 83, - "\\C": 84, - "#N": 85, - "/N": 86, - "=Ring2": 87, - "=S": 88, - "=N+1": 89, - "\\N": 90, - "Na": 91, - "Na+1": 92, - "/O": 93, - "\\O": 94, - "Br-1": 95, - "Branch3": 96, - "\\S": 97, - "S+1": 98, - "Cl-1": 99, - "I-1": 100, - "/C@@H1": 101, - "Si": 102, - "/C@H1": 103, - "/S": 104, - "=N-1": 105, - "Se": 106, - "=P": 107, - "N-1": 108, - "Ring3": 109, - "2H": 110, - "P+1": 111, - "K+1": 112, - "\\C@@H1": 113, - "\\C@H1": 114, - "/N+1": 115, - "@@": 116, - "C-1": 117, - "#N+1": 118, - "B-1": 119, - "+3": 120, - "Cl+3": 121, - "\\NH1": 122, - "Li": 123, - "Li+1": 124, - "PH1": 125, - "18": 126, - "18F": 127, - "@+1": 128, - "3H": 129, - "P@@": 130, - "H0": 131, - "OH0": 132, - "12": 133, - "P@": 134, - "+2": 135, - "@@+1": 136, - "S-1": 137, - "/Br": 138, - "-/": 139, - "\\Cl": 140, - "-/Ring2": 141, - "\\O-1": 142, - "11": 143, - "5I": 144, - "125I": 145, - "11C": 146, - "H3": 147, - "\\N+1": 148, - "-\\": 149, - "/C@@": 150, - "S@+1": 151, - "As": 152, - "/Cl": 153, - "11CH3": 154, - "=Se": 155, - "S@@+1": 156, - "N@+1": 157, - "14": 158, - "-\\Ring2": 159, - "14C": 160, - "\\F": 161, - "/C@": 162, - "Te": 163, - "H2": 164, - "H1-1": 165, - "=O+1": 166, - "N@@+1": 167, - "C+1": 168, - "=S+1": 169, - "Zn": 170, - "/P": 171, - "a+2": 172, - "/I": 173, - "OH1-1": 174, - "Ca+2": 175, - "\\Br": 176, - "Mg": 177, - "Zn+2": 178, - "Al": 179, - "/F": 180, - "Mg+2": 181, - "123": 182, - "123I": 183, - "13": 184, - "I+1": 185, - "/O-1": 186, - "-\\Ring1": 187, - "BH2": 188, - "BH2-1": 189, - "\\I": 190, - "/NH1": 191, - "O+1": 192, - "131": 193, - "131I": 194, - "=14C": 195, - "/S+1": 196, - "=Ring3": 197, - "\\C@@": 198, - "H2+1": 199, - "\\C@": 200, - "Ag": 201, - "=As": 202, - "=Se+1": 203, - "NH2+1": 204, - "SeH1": 205, - "-/Ring1": 206, - "=Te": 207, - "Al+3": 208, - "NaH1": 209, - "=Te+1": 210, - "NH1+1": 211, - "Ag+1": 212, - "H1+1": 213, - "NH1-1": 214, - "\\P": 215, - "14CH2": 216, - "13C": 217, - "14CH1": 218, - "=11C": 219, - "S@@": 220, - "=P@@": 221, - "SiH2": 222, - "H3-1": 223, - "14CH3": 224, - "BH3-1": 225, - "S@": 226, - "=14CH1": 227, - "=PH1": 228, - "=P@": 229, - "=NH1+1": 230, - "\\S+1": 231, - "124": 232, - "CH1-1": 233, - "Sr": 234, - "=Si": 235, - "124I": 236, - "Sr+2": 237, - "#C-1": 238, - "/C-1": 239, - "N@": 240, - "/N-1": 241, - "13CH1": 242, - "/B": 243, - "19": 244, - "Ba+2": 245, - "H4": 246, - "SH1+1": 247, - "Se+1": 248, - "19F": 249, - "/125I": 250, - "P@+1": 251, - "Rb": 252, - "Cl+1": 253, - "SiH4": 254, - "Rb+1": 255, - "=Branch3": 256, - "N@@": 257, - "As+1": 258, - "/Si": 259, - "BH1-1": 260, - "SH1": 261, - "/123I": 262, - "32": 263, - "=Mg": 264, - "H+1": 265, - "\\B": 266, - "SiH1": 267, - "P@@+1": 268, - "-2": 269, - "15": 270, - "17": 271, - "35": 272, - "=13CH1": 273, - "Cs": 274, - "=NH2+1": 275, - "=SH1": 276, - "MgH2": 277, - "32P": 278, - "17F": 279, - "35S": 280, - "Cs+1": 281, - "#11C": 282, - "/131I": 283, - "Bi": 284, - "\\125I": 285, - "=S@@": 286, - "\\S-1": 287, - "6Br": 288, - "7I": 289, - "76Br": 290, - "=B": 291, - "eH1": 292, - "\\N-1": 293, - "18O": 294, - "127I": 295, - "11CH2": 296, - "14C@@H1": 297, - "TeH2": 298, - "15NH1": 299, - "Bi+3": 300, - "/P+1": 301, - "/13C": 302, - "/13CH1": 303, - "0B": 304, - "10B": 305, - "=Al": 306, - "=18O": 307, - "BH0": 308, - "F-1": 309, - "NH3": 310, - "S-2": 311, - "Br+2": 312, - "Cl+2": 313, - "\\Si": 314, - "/S-1": 315, - "=PH2": 316, - "14C@H1": 317, - "NH3+1": 318, - "#14C": 319, - "#O+1": 320, - "-3": 321, - "22": 322, - "4H": 323, - "5Se": 324, - "5Sr+2": 325, - "75Se": 326, - "85Sr+2": 327, - "=B-1": 328, - "=13C": 329, - "@-1": 330, - "Be": 331, - "B@@": 332, - "B@-1": 333, - "Ca": 334, - "CH1": 335, - "I+3": 336, - "KH1": 337, - "OH1+1": 338, - "Ra+2": 339, - "SH1-1": 340, - "\\PH1": 341, - "\\123I": 342, - "=Ca": 343, - "\\CH1-1": 344, - "=S@": 345, - "\\SeH1": 346, - "/SeH1": 347, - "Se-1": 348, - "LiH1": 349, - "18F-1": 350, - "125IH1": 351, - "11CH1": 352, - "TeH1": 353, - "Zn+1": 354, - "Zn-2": 355, - "Al-3": 356, - "13CH3": 357, - "15N": 358, - "Be+2": 359, - "B@@-1": 360, - "#P": 361, - "#S": 362, - "-4": 363, - "/PH1": 364, - "/P@@": 365, - "/As": 366, - "/14C": 367, - "/14CH1": 368, - "2K+1": 369, - "2Rb+1": 370, - "3Se": 371, - "3Ra+2": 372, - "45": 373, - "47": 374, - "42K+1": 375, - "5I-1": 376, - "73Se": 377, - "89": 378, - "82Rb+1": 379, - "=32": 380, - "=32P": 381, - "CH0": 382, - "CH2": 383, - "I+2": 384, - "NH0": 385, - "NH4": 386, - "OH1": 387, - "PH2+1": 388, - "SH0": 389, - "SH2": 390, - "\\3H": 391, - "\\11CH3": 392, - "\\C-1": 393, - "\\Se": 394, - "Si@": 395, - "Si-1": 396, - "SiH1-1": 397, - "SiH3-1": 398, - "/Se": 399, - "Se-2": 400, - "\\NH1-1": 401, - "18FH1": 402, - "125I-1": 403, - "11C@@H1": 404, - "11C-1": 405, - "AsH1": 406, - "As-1": 407, - "14C@@": 408, - "Te-1": 409, - "Mg+1": 410, - "123I-1": 411, - "123Te": 412, - "123IH1": 413, - "135I": 414, - "131I-1": 415, - "Ag-4": 416, - "124I-1": 417, - "76BrH1": 418, - "18OH1": 419, - "22Na+1": 420, - "223Ra+2": 421, - "CaH2": 422, - "45Ca+2": 423, - "47Ca+2": 424, - "89Sr+2": 425, - "=32PH1": 426, - "NH4+1": 427 - }, - "merges": [ - "B r", - "a n", - "c h", - "Br an", - "Bran ch", - "Branch 1", - "= C", - "R i", - "n g", - "Ri ng", - "Ring 1", - "= Branch1", - "Branch 2", - "= O", - "Ring 2", - "H 1", - "C @", - "= N", - "# Branch1", - "C@ @", - "= Branch2", - "C@ H1", - "C@@ H1", - "# Branch2", - "# C", - "C l", - "/ C", - "N H1", - "= Ring1", - "+ 1", - "- 1", - "O -1", - "N +1", - "\\ C", - "# N", - "/ N", - "= Ring2", - "= S", - "=N +1", - "\\ N", - "N a", - "Na +1", - "/ O", - "\\ O", - "Br -1", - "Branch 3", - "\\ S", - "S +1", - "Cl -1", - "I -1", - "/ C@@H1", - "S i", - "/ C@H1", - "/ S", - "=N -1", - "S e", - "= P", - "N -1", - "Ring 3", - "2 H", - "P +1", - "K +1", - "\\ C@@H1", - "\\ C@H1", - "/ N+1", - "@ @", - "C -1", - "# N+1", - "B -1", - "+ 3", - "Cl +3", - "\\ NH1", - "L i", - "Li +1", - "P H1", - "1 8", - "18 F", - "@ +1", - "3 H", - "P @@", - "H 0", - "O H0", - "1 2", - "P @", - "+ 2", - "@@ +1", - "S -1", - "/ Br", - "- /", - "\\ Cl", - "-/ Ring2", - "\\ O-1", - "1 1", - "5 I", - "12 5I", - "11 C", - "H 3", - "\\ N+1", - "- \\", - "/ C@@", - "S @+1", - "A s", - "/ Cl", - "11C H3", - "=S e", - "S @@+1", - "N @+1", - "1 4", - "-\\ Ring2", - "14 C", - "\\ F", - "/ C@", - "T e", - "H 2", - "H1 -1", - "=O +1", - "N @@+1", - "C +1", - "=S +1", - "Z n", - "/ P", - "a +2", - "/ I", - "O H1-1", - "C a+2", - "\\ Br", - "M g", - "Zn +2", - "A l", - "/ F", - "Mg +2", - "12 3", - "123 I", - "1 3", - "I +1", - "/ O-1", - "-\\ Ring1", - "B H2", - "BH2 -1", - "\\ I", - "/ NH1", - "O +1", - "13 1", - "131 I", - "= 14C", - "/ S+1", - "= Ring3", - "\\ C@@", - "H2 +1", - "\\ C@", - "A g", - "= As", - "=Se +1", - "N H2+1", - "Se H1", - "-/ Ring1", - "= Te", - "Al +3", - "Na H1", - "=Te +1", - "NH1 +1", - "Ag +1", - "H1 +1", - "NH1 -1", - "\\ P", - "14C H2", - "13 C", - "14C H1", - "= 11C", - "S @@", - "=P @@", - "Si H2", - "H3 -1", - "14C H3", - "B H3-1", - "S @", - "=14C H1", - "=P H1", - "=P @", - "=N H1+1", - "\\S +1", - "12 4", - "C H1-1", - "S r", - "=S i", - "124 I", - "Sr +2", - "#C -1", - "/C -1", - "N @", - "/N -1", - "13C H1", - "/ B", - "1 9", - "B a+2", - "H 4", - "S H1+1", - "Se +1", - "19 F", - "/ 125I", - "P @+1", - "R b", - "Cl +1", - "Si H4", - "Rb +1", - "= Branch3", - "N @@", - "As +1", - "/ Si", - "B H1-1", - "S H1", - "/ 123I", - "3 2", - "= Mg", - "H +1", - "\\ B", - "Si H1", - "P@@ +1", - "- 2", - "1 5", - "1 7", - "3 5", - "= 13CH1", - "C s", - "=N H2+1", - "=S H1", - "Mg H2", - "32 P", - "17 F", - "35 S", - "Cs +1", - "# 11C", - "/ 131I", - "B i", - "\\ 125I", - "=S @@", - "\\S -1", - "6 Br", - "7 I", - "7 6Br", - "= B", - "e H1", - "\\N -1", - "18 O", - "12 7I", - "11C H2", - "14 C@@H1", - "Te H2", - "15 NH1", - "Bi +3", - "/ P+1", - "/ 13C", - "/ 13CH1", - "0 B", - "1 0B", - "= Al", - "= 18O", - "B H0", - "F -1", - "N H3", - "S -2", - "Br +2", - "Cl +2", - "\\S i", - "/S -1", - "=P H2", - "14 C@H1", - "NH3 +1", - "# 14C", - "# O+1", - "- 3", - "2 2", - "4 H", - "5 Se", - "5 Sr+2", - "7 5Se", - "8 5Sr+2", - "= B-1", - "= 13C", - "@ -1", - "B e", - "B @@", - "B @-1", - "C a", - "C H1", - "I +3", - "K H1", - "O H1+1", - "R a+2", - "S H1-1", - "\\ PH1", - "\\ 123I", - "=C a", - "\\C H1-1", - "=S @", - "\\S eH1", - "/S eH1", - "Se -1", - "Li H1", - "18F -1", - "125I H1", - "11C H1", - "Te H1", - "Zn +1", - "Zn -2", - "Al -3", - "13C H3", - "15 N", - "Be +2", - "B@@ -1", - "# P", - "# S", - "- 4", - "/ PH1", - "/ P@@", - "/ As", - "/ 14C", - "/ 14CH1", - "2 K+1", - "2 Rb+1", - "3 Se", - "3 Ra+2", - "4 5", - "4 7", - "4 2K+1", - "5 I-1", - "7 3Se", - "8 9", - "8 2Rb+1", - "= 32", - "= 32P", - "C H0", - "C H2", - "I +2", - "N H0", - "N H4", - "O H1", - "P H2+1", - "S H0", - "S H2", - "\\ 3H", - "\\ 11CH3", - "\\C -1", - "\\S e", - "Si @", - "Si -1", - "Si H1-1", - "Si H3-1", - "/S e", - "Se -2", - "\\NH1 -1", - "18F H1", - "12 5I-1", - "11 C@@H1", - "11 C-1", - "As H1", - "As -1", - "14 C@@", - "Te -1", - "Mg +1", - "123 I-1", - "123 Te", - "123I H1", - "13 5I", - "131 I-1", - "Ag -4", - "124 I-1", - "76Br H1", - "18O H1", - "22 Na+1", - "22 3Ra+2", - "Ca H2", - "45 Ca+2", - "47 Ca+2", - "89 Sr+2", - "=32 PH1", - "NH4 +1" - ] - } -} \ No newline at end of file diff --git a/models/finetuned/bbbp/checkpoint_epoch_025/tokenizer_config.json b/models/finetuned/bbbp/checkpoint_epoch_025/tokenizer_config.json deleted file mode 100644 index 08860954acd34fad07fd77f7635298fa565f3149..0000000000000000000000000000000000000000 --- a/models/finetuned/bbbp/checkpoint_epoch_025/tokenizer_config.json +++ /dev/null @@ -1,65 +0,0 @@ -{ - "add_prefix_space": false, - "bos_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "cls_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "eos_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "errors": "replace", - "mask_token": { - "__type": "AddedToken", - "content": "", - "lstrip": true, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "model_max_length": 1000000000000000019884624838656, - "name_or_path": "/home/erva/SELFormerMM/data/pretrained_multimodal_chembl36", - "pad_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "sep_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "special_tokens_map_file": null, - "tokenizer_class": "RobertaTokenizer", - "trim_offsets": true, - "unk_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - } -} diff --git a/models/finetuned/bbbp/checkpoint_epoch_025/vocab.json b/models/finetuned/bbbp/checkpoint_epoch_025/vocab.json deleted file mode 100644 index f7e4cc22809f4e9035cc450ef189c8a7da8fd03e..0000000000000000000000000000000000000000 --- a/models/finetuned/bbbp/checkpoint_epoch_025/vocab.json +++ /dev/null @@ -1 +0,0 @@ -{"":0,"":1,"":2,"":3,"":4,"\n":5,"#":6,"+":7,"-":8,".":9,"/":10,"0":11,"1":12,"2":13,"3":14,"4":15,"5":16,"6":17,"7":18,"8":19,"9":20,"=":21,"@":22,"A":23,"B":24,"C":25,"F":26,"H":27,"I":28,"K":29,"L":30,"M":31,"N":32,"O":33,"P":34,"R":35,"S":36,"T":37,"Z":38,"\\":39,"a":40,"b":41,"c":42,"e":43,"g":44,"h":45,"i":46,"l":47,"n":48,"r":49,"s":50,"Br":51,"an":52,"ch":53,"Bran":54,"Branch":55,"Branch1":56,"=C":57,"Ri":58,"ng":59,"Ring":60,"Ring1":61,"=Branch1":62,"Branch2":63,"=O":64,"Ring2":65,"H1":66,"C@":67,"=N":68,"#Branch1":69,"C@@":70,"=Branch2":71,"C@H1":72,"C@@H1":73,"#Branch2":74,"#C":75,"Cl":76,"/C":77,"NH1":78,"=Ring1":79,"+1":80,"-1":81,"O-1":82,"N+1":83,"\\C":84,"#N":85,"/N":86,"=Ring2":87,"=S":88,"=N+1":89,"\\N":90,"Na":91,"Na+1":92,"/O":93,"\\O":94,"Br-1":95,"Branch3":96,"\\S":97,"S+1":98,"Cl-1":99,"I-1":100,"/C@@H1":101,"Si":102,"/C@H1":103,"/S":104,"=N-1":105,"Se":106,"=P":107,"N-1":108,"Ring3":109,"2H":110,"P+1":111,"K+1":112,"\\C@@H1":113,"\\C@H1":114,"/N+1":115,"@@":116,"C-1":117,"#N+1":118,"B-1":119,"+3":120,"Cl+3":121,"\\NH1":122,"Li":123,"Li+1":124,"PH1":125,"18":126,"18F":127,"@+1":128,"3H":129,"P@@":130,"H0":131,"OH0":132,"12":133,"P@":134,"+2":135,"@@+1":136,"S-1":137,"/Br":138,"-/":139,"\\Cl":140,"-/Ring2":141,"\\O-1":142,"11":143,"5I":144,"125I":145,"11C":146,"H3":147,"\\N+1":148,"-\\":149,"/C@@":150,"S@+1":151,"As":152,"/Cl":153,"11CH3":154,"=Se":155,"S@@+1":156,"N@+1":157,"14":158,"-\\Ring2":159,"14C":160,"\\F":161,"/C@":162,"Te":163,"H2":164,"H1-1":165,"=O+1":166,"N@@+1":167,"C+1":168,"=S+1":169,"Zn":170,"/P":171,"a+2":172,"/I":173,"OH1-1":174,"Ca+2":175,"\\Br":176,"Mg":177,"Zn+2":178,"Al":179,"/F":180,"Mg+2":181,"123":182,"123I":183,"13":184,"I+1":185,"/O-1":186,"-\\Ring1":187,"BH2":188,"BH2-1":189,"\\I":190,"/NH1":191,"O+1":192,"131":193,"131I":194,"=14C":195,"/S+1":196,"=Ring3":197,"\\C@@":198,"H2+1":199,"\\C@":200,"Ag":201,"=As":202,"=Se+1":203,"NH2+1":204,"SeH1":205,"-/Ring1":206,"=Te":207,"Al+3":208,"NaH1":209,"=Te+1":210,"NH1+1":211,"Ag+1":212,"H1+1":213,"NH1-1":214,"\\P":215,"14CH2":216,"13C":217,"14CH1":218,"=11C":219,"S@@":220,"=P@@":221,"SiH2":222,"H3-1":223,"14CH3":224,"BH3-1":225,"S@":226,"=14CH1":227,"=PH1":228,"=P@":229,"=NH1+1":230,"\\S+1":231,"124":232,"CH1-1":233,"Sr":234,"=Si":235,"124I":236,"Sr+2":237,"#C-1":238,"/C-1":239,"N@":240,"/N-1":241,"13CH1":242,"/B":243,"19":244,"Ba+2":245,"H4":246,"SH1+1":247,"Se+1":248,"19F":249,"/125I":250,"P@+1":251,"Rb":252,"Cl+1":253,"SiH4":254,"Rb+1":255,"=Branch3":256,"N@@":257,"As+1":258,"/Si":259,"BH1-1":260,"SH1":261,"/123I":262,"32":263,"=Mg":264,"H+1":265,"\\B":266,"SiH1":267,"P@@+1":268,"-2":269,"15":270,"17":271,"35":272,"=13CH1":273,"Cs":274,"=NH2+1":275,"=SH1":276,"MgH2":277,"32P":278,"17F":279,"35S":280,"Cs+1":281,"#11C":282,"/131I":283,"Bi":284,"\\125I":285,"=S@@":286,"\\S-1":287,"6Br":288,"7I":289,"76Br":290,"=B":291,"eH1":292,"\\N-1":293,"18O":294,"127I":295,"11CH2":296,"14C@@H1":297,"TeH2":298,"15NH1":299,"Bi+3":300,"/P+1":301,"/13C":302,"/13CH1":303,"0B":304,"10B":305,"=Al":306,"=18O":307,"BH0":308,"F-1":309,"NH3":310,"S-2":311,"Br+2":312,"Cl+2":313,"\\Si":314,"/S-1":315,"=PH2":316,"14C@H1":317,"NH3+1":318,"#14C":319,"#O+1":320,"-3":321,"22":322,"4H":323,"5Se":324,"5Sr+2":325,"75Se":326,"85Sr+2":327,"=B-1":328,"=13C":329,"@-1":330,"Be":331,"B@@":332,"B@-1":333,"Ca":334,"CH1":335,"I+3":336,"KH1":337,"OH1+1":338,"Ra+2":339,"SH1-1":340,"\\PH1":341,"\\123I":342,"=Ca":343,"\\CH1-1":344,"=S@":345,"\\SeH1":346,"/SeH1":347,"Se-1":348,"LiH1":349,"18F-1":350,"125IH1":351,"11CH1":352,"TeH1":353,"Zn+1":354,"Zn-2":355,"Al-3":356,"13CH3":357,"15N":358,"Be+2":359,"B@@-1":360,"#P":361,"#S":362,"-4":363,"/PH1":364,"/P@@":365,"/As":366,"/14C":367,"/14CH1":368,"2K+1":369,"2Rb+1":370,"3Se":371,"3Ra+2":372,"45":373,"47":374,"42K+1":375,"5I-1":376,"73Se":377,"89":378,"82Rb+1":379,"=32":380,"=32P":381,"CH0":382,"CH2":383,"I+2":384,"NH0":385,"NH4":386,"OH1":387,"PH2+1":388,"SH0":389,"SH2":390,"\\3H":391,"\\11CH3":392,"\\C-1":393,"\\Se":394,"Si@":395,"Si-1":396,"SiH1-1":397,"SiH3-1":398,"/Se":399,"Se-2":400,"\\NH1-1":401,"18FH1":402,"125I-1":403,"11C@@H1":404,"11C-1":405,"AsH1":406,"As-1":407,"14C@@":408,"Te-1":409,"Mg+1":410,"123I-1":411,"123Te":412,"123IH1":413,"135I":414,"131I-1":415,"Ag-4":416,"124I-1":417,"76BrH1":418,"18OH1":419,"22Na+1":420,"223Ra+2":421,"CaH2":422,"45Ca+2":423,"47Ca+2":424,"89Sr+2":425,"=32PH1":426,"NH4+1":427} \ No newline at end of file diff --git a/models/finetuned/bbbp/checkpoint_epoch_050/config.json b/models/finetuned/bbbp/checkpoint_epoch_050/config.json deleted file mode 100644 index 3811e21539577b37e06313eab31ec11e53f0cbbc..0000000000000000000000000000000000000000 --- a/models/finetuned/bbbp/checkpoint_epoch_050/config.json +++ /dev/null @@ -1,27 +0,0 @@ -{ - "_name_or_path": "/home/erva/SELFormerMM/data/pretrained_multimodal_chembl36", - "architectures": [ - "RobertaForMaskedLM" - ], - "attention_probs_dropout_prob": 0.1, - "bos_token_id": 0, - "classifier_dropout": null, - "eos_token_id": 2, - "hidden_act": "gelu", - "hidden_dropout_prob": 0.1, - "hidden_size": 768, - "initializer_range": 0.02, - "intermediate_size": 3072, - "layer_norm_eps": 1e-12, - "max_position_embeddings": 514, - "model_type": "roberta", - "num_attention_heads": 4, - "num_hidden_layers": 12, - "pad_token_id": 1, - "position_embedding_type": "absolute", - "torch_dtype": "float32", - "transformers_version": "4.26.1", - "type_vocab_size": 1, - "use_cache": true, - "vocab_size": 800 -} diff --git a/models/finetuned/bbbp/checkpoint_epoch_050/merges.txt b/models/finetuned/bbbp/checkpoint_epoch_050/merges.txt deleted file mode 100644 index 7cd5ec62809503c23f18c80afc0ba3bdf9d253d0..0000000000000000000000000000000000000000 --- a/models/finetuned/bbbp/checkpoint_epoch_050/merges.txt +++ /dev/null @@ -1,378 +0,0 @@ -#version: 0.2 - Trained by `huggingface/tokenizers` -B r -a n -c h -Br an -Bran ch -Branch 1 -= C -R i -n g -Ri ng -Ring 1 -= Branch1 -Branch 2 -= O -Ring 2 -H 1 -C @ -= N -# Branch1 -C@ @ -= Branch2 -C@ H1 -C@@ H1 -# Branch2 -# C -C l -/ C -N H1 -= Ring1 -+ 1 -- 1 -O -1 -N +1 -\ C -# N -/ N -= Ring2 -= S -=N +1 -\ N -N a -Na +1 -/ O -\ O -Br -1 -Branch 3 -\ S -S +1 -Cl -1 -I -1 -/ C@@H1 -S i -/ C@H1 -/ S -=N -1 -S e -= P -N -1 -Ring 3 -2 H -P +1 -K +1 -\ C@@H1 -\ C@H1 -/ N+1 -@ @ -C -1 -# N+1 -B -1 -+ 3 -Cl +3 -\ NH1 -L i -Li +1 -P H1 -1 8 -18 F -@ +1 -3 H -P @@ -H 0 -O H0 -1 2 -P @ -+ 2 -@@ +1 -S -1 -/ Br -- / -\ Cl --/ Ring2 -\ O-1 -1 1 -5 I -12 5I -11 C -H 3 -\ N+1 -- \ -/ C@@ -S @+1 -A s -/ Cl -11C H3 -=S e -S @@+1 -N @+1 -1 4 --\ Ring2 -14 C -\ F -/ C@ -T e -H 2 -H1 -1 -=O +1 -N @@+1 -C +1 -=S +1 -Z n -/ P -a +2 -/ I -O H1-1 -C a+2 -\ Br -M g -Zn +2 -A l -/ F -Mg +2 -12 3 -123 I -1 3 -I +1 -/ O-1 --\ Ring1 -B H2 -BH2 -1 -\ I -/ NH1 -O +1 -13 1 -131 I -= 14C -/ S+1 -= Ring3 -\ C@@ -H2 +1 -\ C@ -A g -= As -=Se +1 -N H2+1 -Se H1 --/ Ring1 -= Te -Al +3 -Na H1 -=Te +1 -NH1 +1 -Ag +1 -H1 +1 -NH1 -1 -\ P -14C H2 -13 C -14C H1 -= 11C -S @@ -=P @@ -Si H2 -H3 -1 -14C H3 -B H3-1 -S @ -=14C H1 -=P H1 -=P @ -=N H1+1 -\S +1 -12 4 -C H1-1 -S r -=S i -124 I -Sr +2 -#C -1 -/C -1 -N @ -/N -1 -13C H1 -/ B -1 9 -B a+2 -H 4 -S H1+1 -Se +1 -19 F -/ 125I -P @+1 -R b -Cl +1 -Si H4 -Rb +1 -= Branch3 -N @@ -As +1 -/ Si -B H1-1 -S H1 -/ 123I -3 2 -= Mg -H +1 -\ B -Si H1 -P@@ +1 -- 2 -1 5 -1 7 -3 5 -= 13CH1 -C s -=N H2+1 -=S H1 -Mg H2 -32 P -17 F -35 S -Cs +1 -# 11C -/ 131I -B i -\ 125I -=S @@ -\S -1 -6 Br -7 I -7 6Br -= B -e H1 -\N -1 -18 O -12 7I -11C H2 -14 C@@H1 -Te H2 -15 NH1 -Bi +3 -/ P+1 -/ 13C -/ 13CH1 -0 B -1 0B -= Al -= 18O -B H0 -F -1 -N H3 -S -2 -Br +2 -Cl +2 -\S i -/S -1 -=P H2 -14 C@H1 -NH3 +1 -# 14C -# O+1 -- 3 -2 2 -4 H -5 Se -5 Sr+2 -7 5Se -8 5Sr+2 -= B-1 -= 13C -@ -1 -B e -B @@ -B @-1 -C a -C H1 -I +3 -K H1 -O H1+1 -R a+2 -S H1-1 -\ PH1 -\ 123I -=C a -\C H1-1 -=S @ -\S eH1 -/S eH1 -Se -1 -Li H1 -18F -1 -125I H1 -11C H1 -Te H1 -Zn +1 -Zn -2 -Al -3 -13C H3 -15 N -Be +2 -B@@ -1 -# P -# S -- 4 -/ PH1 -/ P@@ -/ As -/ 14C -/ 14CH1 -2 K+1 -2 Rb+1 -3 Se -3 Ra+2 -4 5 -4 7 -4 2K+1 -5 I-1 -7 3Se -8 9 -8 2Rb+1 -= 32 -= 32P -C H0 -C H2 -I +2 -N H0 -N H4 -O H1 -P H2+1 -S H0 -S H2 -\ 3H -\ 11CH3 -\C -1 -\S e -Si @ -Si -1 -Si H1-1 -Si H3-1 -/S e -Se -2 -\NH1 -1 -18F H1 -12 5I-1 -11 C@@H1 -11 C-1 -As H1 -As -1 -14 C@@ -Te -1 -Mg +1 -123 I-1 -123 Te -123I H1 -13 5I -131 I-1 -Ag -4 -124 I-1 -76Br H1 -18O H1 -22 Na+1 -22 3Ra+2 -Ca H2 -45 Ca+2 -47 Ca+2 -89 Sr+2 -=32 PH1 -NH4 +1 diff --git a/models/finetuned/bbbp/checkpoint_epoch_050/model.pt b/models/finetuned/bbbp/checkpoint_epoch_050/model.pt deleted file mode 100644 index a27b52e128ed17cabe4cf7875c06eb290f65abe8..0000000000000000000000000000000000000000 --- a/models/finetuned/bbbp/checkpoint_epoch_050/model.pt +++ /dev/null @@ -1,3 +0,0 @@ -version https://git-lfs.github.com/spec/v1 -oid sha256:56553557c9abbd004f18d16f7862060afa43a9b8a7b4f3a95956b77cc7e7ea27 -size 1022855293 diff --git a/models/finetuned/bbbp/checkpoint_epoch_050/special_tokens_map.json b/models/finetuned/bbbp/checkpoint_epoch_050/special_tokens_map.json deleted file mode 100644 index 06a55849fa69a91e7179d909e373179ff7467d8c..0000000000000000000000000000000000000000 --- a/models/finetuned/bbbp/checkpoint_epoch_050/special_tokens_map.json +++ /dev/null @@ -1,51 +0,0 @@ -{ - "bos_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "cls_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "eos_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "mask_token": { - "content": "", - "lstrip": true, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "pad_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "sep_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "unk_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - } -} diff --git a/models/finetuned/bbbp/checkpoint_epoch_050/tokenizer.json b/models/finetuned/bbbp/checkpoint_epoch_050/tokenizer.json deleted file mode 100644 index 3b64b273e6fa9799e2d8375722b9e815de9ebb8f..0000000000000000000000000000000000000000 --- a/models/finetuned/bbbp/checkpoint_epoch_050/tokenizer.json +++ /dev/null @@ -1,909 +0,0 @@ -{ - "version": "1.0", - "truncation": { - "direction": "Right", - "max_length": 128, - "strategy": "LongestFirst", - "stride": 0 - }, - "padding": { - "strategy": { - "Fixed": 128 - }, - "direction": "Right", - "pad_to_multiple_of": null, - "pad_id": 3, - "pad_type_id": 0, - "pad_token": "" - }, - "added_tokens": [ - { - "id": 0, - "content": "", - "single_word": false, - "lstrip": false, - "rstrip": false, - "normalized": true, - "special": true - }, - { - "id": 1, - "content": "", - "single_word": false, - "lstrip": false, - "rstrip": false, - "normalized": true, - "special": true - }, - { - "id": 2, - "content": "", - "single_word": false, - "lstrip": false, - "rstrip": false, - "normalized": true, - "special": true - }, - { - "id": 3, - "content": "", - "single_word": false, - "lstrip": false, - "rstrip": false, - "normalized": true, - "special": true - }, - { - "id": 4, - "content": "", - "single_word": false, - "lstrip": true, - "rstrip": false, - "normalized": true, - "special": true - } - ], - "normalizer": null, - "pre_tokenizer": { - "type": "ByteLevel", - "add_prefix_space": false, - "trim_offsets": true, - "use_regex": true - }, - "post_processor": { - "type": "RobertaProcessing", - "sep": [ - "", - 2 - ], - "cls": [ - "", - 1 - ], - "trim_offsets": true, - "add_prefix_space": false - }, - "decoder": { - "type": "ByteLevel", - "add_prefix_space": true, - "trim_offsets": true, - "use_regex": true - }, - "model": { - "type": "BPE", - "dropout": null, - "unk_token": null, - "continuing_subword_prefix": "", - "end_of_word_suffix": "", - "fuse_unk": false, - "vocab": { - "": 0, - "": 1, - "": 2, - "": 3, - "": 4, - "\n": 5, - "#": 6, - "+": 7, - "-": 8, - ".": 9, - "/": 10, - "0": 11, - "1": 12, - "2": 13, - "3": 14, - "4": 15, - "5": 16, - "6": 17, - "7": 18, - "8": 19, - "9": 20, - "=": 21, - "@": 22, - "A": 23, - "B": 24, - "C": 25, - "F": 26, - "H": 27, - "I": 28, - "K": 29, - "L": 30, - "M": 31, - "N": 32, - "O": 33, - "P": 34, - "R": 35, - "S": 36, - "T": 37, - "Z": 38, - "\\": 39, - "a": 40, - "b": 41, - "c": 42, - "e": 43, - "g": 44, - "h": 45, - "i": 46, - "l": 47, - "n": 48, - "r": 49, - "s": 50, - "Br": 51, - "an": 52, - "ch": 53, - "Bran": 54, - "Branch": 55, - "Branch1": 56, - "=C": 57, - "Ri": 58, - "ng": 59, - "Ring": 60, - "Ring1": 61, - "=Branch1": 62, - "Branch2": 63, - "=O": 64, - "Ring2": 65, - "H1": 66, - "C@": 67, - "=N": 68, - "#Branch1": 69, - "C@@": 70, - "=Branch2": 71, - "C@H1": 72, - "C@@H1": 73, - "#Branch2": 74, - "#C": 75, - "Cl": 76, - "/C": 77, - "NH1": 78, - "=Ring1": 79, - "+1": 80, - "-1": 81, - "O-1": 82, - "N+1": 83, - "\\C": 84, - "#N": 85, - "/N": 86, - "=Ring2": 87, - "=S": 88, - "=N+1": 89, - "\\N": 90, - "Na": 91, - "Na+1": 92, - "/O": 93, - "\\O": 94, - "Br-1": 95, - "Branch3": 96, - "\\S": 97, - "S+1": 98, - "Cl-1": 99, - "I-1": 100, - "/C@@H1": 101, - "Si": 102, - "/C@H1": 103, - "/S": 104, - "=N-1": 105, - "Se": 106, - "=P": 107, - "N-1": 108, - "Ring3": 109, - "2H": 110, - "P+1": 111, - "K+1": 112, - "\\C@@H1": 113, - "\\C@H1": 114, - "/N+1": 115, - "@@": 116, - "C-1": 117, - "#N+1": 118, - "B-1": 119, - "+3": 120, - "Cl+3": 121, - "\\NH1": 122, - "Li": 123, - "Li+1": 124, - "PH1": 125, - "18": 126, - "18F": 127, - "@+1": 128, - "3H": 129, - "P@@": 130, - "H0": 131, - "OH0": 132, - "12": 133, - "P@": 134, - "+2": 135, - "@@+1": 136, - "S-1": 137, - "/Br": 138, - "-/": 139, - "\\Cl": 140, - "-/Ring2": 141, - "\\O-1": 142, - "11": 143, - "5I": 144, - "125I": 145, - "11C": 146, - "H3": 147, - "\\N+1": 148, - "-\\": 149, - "/C@@": 150, - "S@+1": 151, - "As": 152, - "/Cl": 153, - "11CH3": 154, - "=Se": 155, - "S@@+1": 156, - "N@+1": 157, - "14": 158, - "-\\Ring2": 159, - "14C": 160, - "\\F": 161, - "/C@": 162, - "Te": 163, - "H2": 164, - "H1-1": 165, - "=O+1": 166, - "N@@+1": 167, - "C+1": 168, - "=S+1": 169, - "Zn": 170, - "/P": 171, - "a+2": 172, - "/I": 173, - "OH1-1": 174, - "Ca+2": 175, - "\\Br": 176, - "Mg": 177, - "Zn+2": 178, - "Al": 179, - "/F": 180, - "Mg+2": 181, - "123": 182, - "123I": 183, - "13": 184, - "I+1": 185, - "/O-1": 186, - "-\\Ring1": 187, - "BH2": 188, - "BH2-1": 189, - "\\I": 190, - "/NH1": 191, - "O+1": 192, - "131": 193, - "131I": 194, - "=14C": 195, - "/S+1": 196, - "=Ring3": 197, - "\\C@@": 198, - "H2+1": 199, - "\\C@": 200, - "Ag": 201, - "=As": 202, - "=Se+1": 203, - "NH2+1": 204, - "SeH1": 205, - "-/Ring1": 206, - "=Te": 207, - "Al+3": 208, - "NaH1": 209, - "=Te+1": 210, - "NH1+1": 211, - "Ag+1": 212, - "H1+1": 213, - "NH1-1": 214, - "\\P": 215, - "14CH2": 216, - "13C": 217, - "14CH1": 218, - "=11C": 219, - "S@@": 220, - "=P@@": 221, - "SiH2": 222, - "H3-1": 223, - "14CH3": 224, - "BH3-1": 225, - "S@": 226, - "=14CH1": 227, - "=PH1": 228, - "=P@": 229, - "=NH1+1": 230, - "\\S+1": 231, - "124": 232, - "CH1-1": 233, - "Sr": 234, - "=Si": 235, - "124I": 236, - "Sr+2": 237, - "#C-1": 238, - "/C-1": 239, - "N@": 240, - "/N-1": 241, - "13CH1": 242, - "/B": 243, - "19": 244, - "Ba+2": 245, - "H4": 246, - "SH1+1": 247, - "Se+1": 248, - "19F": 249, - "/125I": 250, - "P@+1": 251, - "Rb": 252, - "Cl+1": 253, - "SiH4": 254, - "Rb+1": 255, - "=Branch3": 256, - "N@@": 257, - "As+1": 258, - "/Si": 259, - "BH1-1": 260, - "SH1": 261, - "/123I": 262, - "32": 263, - "=Mg": 264, - "H+1": 265, - "\\B": 266, - "SiH1": 267, - "P@@+1": 268, - "-2": 269, - "15": 270, - "17": 271, - "35": 272, - "=13CH1": 273, - "Cs": 274, - "=NH2+1": 275, - "=SH1": 276, - "MgH2": 277, - "32P": 278, - "17F": 279, - "35S": 280, - "Cs+1": 281, - "#11C": 282, - "/131I": 283, - "Bi": 284, - "\\125I": 285, - "=S@@": 286, - "\\S-1": 287, - "6Br": 288, - "7I": 289, - "76Br": 290, - "=B": 291, - "eH1": 292, - "\\N-1": 293, - "18O": 294, - "127I": 295, - "11CH2": 296, - "14C@@H1": 297, - "TeH2": 298, - "15NH1": 299, - "Bi+3": 300, - "/P+1": 301, - "/13C": 302, - "/13CH1": 303, - "0B": 304, - "10B": 305, - "=Al": 306, - "=18O": 307, - "BH0": 308, - "F-1": 309, - "NH3": 310, - "S-2": 311, - "Br+2": 312, - "Cl+2": 313, - "\\Si": 314, - "/S-1": 315, - "=PH2": 316, - "14C@H1": 317, - "NH3+1": 318, - "#14C": 319, - "#O+1": 320, - "-3": 321, - "22": 322, - "4H": 323, - "5Se": 324, - "5Sr+2": 325, - "75Se": 326, - "85Sr+2": 327, - "=B-1": 328, - "=13C": 329, - "@-1": 330, - "Be": 331, - "B@@": 332, - "B@-1": 333, - "Ca": 334, - "CH1": 335, - "I+3": 336, - "KH1": 337, - "OH1+1": 338, - "Ra+2": 339, - "SH1-1": 340, - "\\PH1": 341, - "\\123I": 342, - "=Ca": 343, - "\\CH1-1": 344, - "=S@": 345, - "\\SeH1": 346, - "/SeH1": 347, - "Se-1": 348, - "LiH1": 349, - "18F-1": 350, - "125IH1": 351, - "11CH1": 352, - "TeH1": 353, - "Zn+1": 354, - "Zn-2": 355, - "Al-3": 356, - "13CH3": 357, - "15N": 358, - "Be+2": 359, - "B@@-1": 360, - "#P": 361, - "#S": 362, - "-4": 363, - "/PH1": 364, - "/P@@": 365, - "/As": 366, - "/14C": 367, - "/14CH1": 368, - "2K+1": 369, - "2Rb+1": 370, - "3Se": 371, - "3Ra+2": 372, - "45": 373, - "47": 374, - "42K+1": 375, - "5I-1": 376, - "73Se": 377, - "89": 378, - "82Rb+1": 379, - "=32": 380, - "=32P": 381, - "CH0": 382, - "CH2": 383, - "I+2": 384, - "NH0": 385, - "NH4": 386, - "OH1": 387, - "PH2+1": 388, - "SH0": 389, - "SH2": 390, - "\\3H": 391, - "\\11CH3": 392, - "\\C-1": 393, - "\\Se": 394, - "Si@": 395, - "Si-1": 396, - "SiH1-1": 397, - "SiH3-1": 398, - "/Se": 399, - "Se-2": 400, - "\\NH1-1": 401, - "18FH1": 402, - "125I-1": 403, - "11C@@H1": 404, - "11C-1": 405, - "AsH1": 406, - "As-1": 407, - "14C@@": 408, - "Te-1": 409, - "Mg+1": 410, - "123I-1": 411, - "123Te": 412, - "123IH1": 413, - "135I": 414, - "131I-1": 415, - "Ag-4": 416, - "124I-1": 417, - "76BrH1": 418, - "18OH1": 419, - "22Na+1": 420, - "223Ra+2": 421, - "CaH2": 422, - "45Ca+2": 423, - "47Ca+2": 424, - "89Sr+2": 425, - "=32PH1": 426, - "NH4+1": 427 - }, - "merges": [ - "B r", - "a n", - "c h", - "Br an", - "Bran ch", - "Branch 1", - "= C", - "R i", - "n g", - "Ri ng", - "Ring 1", - "= Branch1", - "Branch 2", - "= O", - "Ring 2", - "H 1", - "C @", - "= N", - "# Branch1", - "C@ @", - "= Branch2", - "C@ H1", - "C@@ H1", - "# Branch2", - "# C", - "C l", - "/ C", - "N H1", - "= Ring1", - "+ 1", - "- 1", - "O -1", - "N +1", - "\\ C", - "# N", - "/ N", - "= Ring2", - "= S", - "=N +1", - "\\ N", - "N a", - "Na +1", - "/ O", - "\\ O", - "Br -1", - "Branch 3", - "\\ S", - "S +1", - "Cl -1", - "I -1", - "/ C@@H1", - "S i", - "/ C@H1", - "/ S", - "=N -1", - "S e", - "= P", - "N -1", - "Ring 3", - "2 H", - "P +1", - "K +1", - "\\ C@@H1", - "\\ C@H1", - "/ N+1", - "@ @", - "C -1", - "# N+1", - "B -1", - "+ 3", - "Cl +3", - "\\ NH1", - "L i", - "Li +1", - "P H1", - "1 8", - "18 F", - "@ +1", - "3 H", - "P @@", - "H 0", - "O H0", - "1 2", - "P @", - "+ 2", - "@@ +1", - "S -1", - "/ Br", - "- /", - "\\ Cl", - "-/ Ring2", - "\\ O-1", - "1 1", - "5 I", - "12 5I", - "11 C", - "H 3", - "\\ N+1", - "- \\", - "/ C@@", - "S @+1", - "A s", - "/ Cl", - "11C H3", - "=S e", - "S @@+1", - "N @+1", - "1 4", - "-\\ Ring2", - "14 C", - "\\ F", - "/ C@", - "T e", - "H 2", - "H1 -1", - "=O +1", - "N @@+1", - "C +1", - "=S +1", - "Z n", - "/ P", - "a +2", - "/ I", - "O H1-1", - "C a+2", - "\\ Br", - "M g", - "Zn +2", - "A l", - "/ F", - "Mg +2", - "12 3", - "123 I", - "1 3", - "I +1", - "/ O-1", - "-\\ Ring1", - "B H2", - "BH2 -1", - "\\ I", - "/ NH1", - "O +1", - "13 1", - "131 I", - "= 14C", - "/ S+1", - "= Ring3", - "\\ C@@", - "H2 +1", - "\\ C@", - "A g", - "= As", - "=Se +1", - "N H2+1", - "Se H1", - "-/ Ring1", - "= Te", - "Al +3", - "Na H1", - "=Te +1", - "NH1 +1", - "Ag +1", - "H1 +1", - "NH1 -1", - "\\ P", - "14C H2", - "13 C", - "14C H1", - "= 11C", - "S @@", - "=P @@", - "Si H2", - "H3 -1", - "14C H3", - "B H3-1", - "S @", - "=14C H1", - "=P H1", - "=P @", - "=N H1+1", - "\\S +1", - "12 4", - "C H1-1", - "S r", - "=S i", - "124 I", - "Sr +2", - "#C -1", - "/C -1", - "N @", - "/N -1", - "13C H1", - "/ B", - "1 9", - "B a+2", - "H 4", - "S H1+1", - "Se +1", - "19 F", - "/ 125I", - "P @+1", - "R b", - "Cl +1", - "Si H4", - "Rb +1", - "= Branch3", - "N @@", - "As +1", - "/ Si", - "B H1-1", - "S H1", - "/ 123I", - "3 2", - "= Mg", - "H +1", - "\\ B", - "Si H1", - "P@@ +1", - "- 2", - "1 5", - "1 7", - "3 5", - "= 13CH1", - "C s", - "=N H2+1", - "=S H1", - "Mg H2", - "32 P", - "17 F", - "35 S", - "Cs +1", - "# 11C", - "/ 131I", - "B i", - "\\ 125I", - "=S @@", - "\\S -1", - "6 Br", - "7 I", - "7 6Br", - "= B", - "e H1", - "\\N -1", - "18 O", - "12 7I", - "11C H2", - "14 C@@H1", - "Te H2", - "15 NH1", - "Bi +3", - "/ P+1", - "/ 13C", - "/ 13CH1", - "0 B", - "1 0B", - "= Al", - "= 18O", - "B H0", - "F -1", - "N H3", - "S -2", - "Br +2", - "Cl +2", - "\\S i", - "/S -1", - "=P H2", - "14 C@H1", - "NH3 +1", - "# 14C", - "# O+1", - "- 3", - "2 2", - "4 H", - "5 Se", - "5 Sr+2", - "7 5Se", - "8 5Sr+2", - "= B-1", - "= 13C", - "@ -1", - "B e", - "B @@", - "B @-1", - "C a", - "C H1", - "I +3", - "K H1", - "O H1+1", - "R a+2", - "S H1-1", - "\\ PH1", - "\\ 123I", - "=C a", - "\\C H1-1", - "=S @", - "\\S eH1", - "/S eH1", - "Se -1", - "Li H1", - "18F -1", - "125I H1", - "11C H1", - "Te H1", - "Zn +1", - "Zn -2", - "Al -3", - "13C H3", - "15 N", - "Be +2", - "B@@ -1", - "# P", - "# S", - "- 4", - "/ PH1", - "/ P@@", - "/ As", - "/ 14C", - "/ 14CH1", - "2 K+1", - "2 Rb+1", - "3 Se", - "3 Ra+2", - "4 5", - "4 7", - "4 2K+1", - "5 I-1", - "7 3Se", - "8 9", - "8 2Rb+1", - "= 32", - "= 32P", - "C H0", - "C H2", - "I +2", - "N H0", - "N H4", - "O H1", - "P H2+1", - "S H0", - "S H2", - "\\ 3H", - "\\ 11CH3", - "\\C -1", - "\\S e", - "Si @", - "Si -1", - "Si H1-1", - "Si H3-1", - "/S e", - "Se -2", - "\\NH1 -1", - "18F H1", - "12 5I-1", - "11 C@@H1", - "11 C-1", - "As H1", - "As -1", - "14 C@@", - "Te -1", - "Mg +1", - "123 I-1", - "123 Te", - "123I H1", - "13 5I", - "131 I-1", - "Ag -4", - "124 I-1", - "76Br H1", - "18O H1", - "22 Na+1", - "22 3Ra+2", - "Ca H2", - "45 Ca+2", - "47 Ca+2", - "89 Sr+2", - "=32 PH1", - "NH4 +1" - ] - } -} \ No newline at end of file diff --git a/models/finetuned/bbbp/checkpoint_epoch_050/tokenizer_config.json b/models/finetuned/bbbp/checkpoint_epoch_050/tokenizer_config.json deleted file mode 100644 index 08860954acd34fad07fd77f7635298fa565f3149..0000000000000000000000000000000000000000 --- a/models/finetuned/bbbp/checkpoint_epoch_050/tokenizer_config.json +++ /dev/null @@ -1,65 +0,0 @@ -{ - "add_prefix_space": false, - "bos_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "cls_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "eos_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "errors": "replace", - "mask_token": { - "__type": "AddedToken", - "content": "", - "lstrip": true, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "model_max_length": 1000000000000000019884624838656, - "name_or_path": "/home/erva/SELFormerMM/data/pretrained_multimodal_chembl36", - "pad_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "sep_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "special_tokens_map_file": null, - "tokenizer_class": "RobertaTokenizer", - "trim_offsets": true, - "unk_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - } -} diff --git a/models/finetuned/bbbp/checkpoint_epoch_050/vocab.json b/models/finetuned/bbbp/checkpoint_epoch_050/vocab.json deleted file mode 100644 index f7e4cc22809f4e9035cc450ef189c8a7da8fd03e..0000000000000000000000000000000000000000 --- a/models/finetuned/bbbp/checkpoint_epoch_050/vocab.json +++ /dev/null @@ -1 +0,0 @@ -{"":0,"":1,"":2,"":3,"":4,"\n":5,"#":6,"+":7,"-":8,".":9,"/":10,"0":11,"1":12,"2":13,"3":14,"4":15,"5":16,"6":17,"7":18,"8":19,"9":20,"=":21,"@":22,"A":23,"B":24,"C":25,"F":26,"H":27,"I":28,"K":29,"L":30,"M":31,"N":32,"O":33,"P":34,"R":35,"S":36,"T":37,"Z":38,"\\":39,"a":40,"b":41,"c":42,"e":43,"g":44,"h":45,"i":46,"l":47,"n":48,"r":49,"s":50,"Br":51,"an":52,"ch":53,"Bran":54,"Branch":55,"Branch1":56,"=C":57,"Ri":58,"ng":59,"Ring":60,"Ring1":61,"=Branch1":62,"Branch2":63,"=O":64,"Ring2":65,"H1":66,"C@":67,"=N":68,"#Branch1":69,"C@@":70,"=Branch2":71,"C@H1":72,"C@@H1":73,"#Branch2":74,"#C":75,"Cl":76,"/C":77,"NH1":78,"=Ring1":79,"+1":80,"-1":81,"O-1":82,"N+1":83,"\\C":84,"#N":85,"/N":86,"=Ring2":87,"=S":88,"=N+1":89,"\\N":90,"Na":91,"Na+1":92,"/O":93,"\\O":94,"Br-1":95,"Branch3":96,"\\S":97,"S+1":98,"Cl-1":99,"I-1":100,"/C@@H1":101,"Si":102,"/C@H1":103,"/S":104,"=N-1":105,"Se":106,"=P":107,"N-1":108,"Ring3":109,"2H":110,"P+1":111,"K+1":112,"\\C@@H1":113,"\\C@H1":114,"/N+1":115,"@@":116,"C-1":117,"#N+1":118,"B-1":119,"+3":120,"Cl+3":121,"\\NH1":122,"Li":123,"Li+1":124,"PH1":125,"18":126,"18F":127,"@+1":128,"3H":129,"P@@":130,"H0":131,"OH0":132,"12":133,"P@":134,"+2":135,"@@+1":136,"S-1":137,"/Br":138,"-/":139,"\\Cl":140,"-/Ring2":141,"\\O-1":142,"11":143,"5I":144,"125I":145,"11C":146,"H3":147,"\\N+1":148,"-\\":149,"/C@@":150,"S@+1":151,"As":152,"/Cl":153,"11CH3":154,"=Se":155,"S@@+1":156,"N@+1":157,"14":158,"-\\Ring2":159,"14C":160,"\\F":161,"/C@":162,"Te":163,"H2":164,"H1-1":165,"=O+1":166,"N@@+1":167,"C+1":168,"=S+1":169,"Zn":170,"/P":171,"a+2":172,"/I":173,"OH1-1":174,"Ca+2":175,"\\Br":176,"Mg":177,"Zn+2":178,"Al":179,"/F":180,"Mg+2":181,"123":182,"123I":183,"13":184,"I+1":185,"/O-1":186,"-\\Ring1":187,"BH2":188,"BH2-1":189,"\\I":190,"/NH1":191,"O+1":192,"131":193,"131I":194,"=14C":195,"/S+1":196,"=Ring3":197,"\\C@@":198,"H2+1":199,"\\C@":200,"Ag":201,"=As":202,"=Se+1":203,"NH2+1":204,"SeH1":205,"-/Ring1":206,"=Te":207,"Al+3":208,"NaH1":209,"=Te+1":210,"NH1+1":211,"Ag+1":212,"H1+1":213,"NH1-1":214,"\\P":215,"14CH2":216,"13C":217,"14CH1":218,"=11C":219,"S@@":220,"=P@@":221,"SiH2":222,"H3-1":223,"14CH3":224,"BH3-1":225,"S@":226,"=14CH1":227,"=PH1":228,"=P@":229,"=NH1+1":230,"\\S+1":231,"124":232,"CH1-1":233,"Sr":234,"=Si":235,"124I":236,"Sr+2":237,"#C-1":238,"/C-1":239,"N@":240,"/N-1":241,"13CH1":242,"/B":243,"19":244,"Ba+2":245,"H4":246,"SH1+1":247,"Se+1":248,"19F":249,"/125I":250,"P@+1":251,"Rb":252,"Cl+1":253,"SiH4":254,"Rb+1":255,"=Branch3":256,"N@@":257,"As+1":258,"/Si":259,"BH1-1":260,"SH1":261,"/123I":262,"32":263,"=Mg":264,"H+1":265,"\\B":266,"SiH1":267,"P@@+1":268,"-2":269,"15":270,"17":271,"35":272,"=13CH1":273,"Cs":274,"=NH2+1":275,"=SH1":276,"MgH2":277,"32P":278,"17F":279,"35S":280,"Cs+1":281,"#11C":282,"/131I":283,"Bi":284,"\\125I":285,"=S@@":286,"\\S-1":287,"6Br":288,"7I":289,"76Br":290,"=B":291,"eH1":292,"\\N-1":293,"18O":294,"127I":295,"11CH2":296,"14C@@H1":297,"TeH2":298,"15NH1":299,"Bi+3":300,"/P+1":301,"/13C":302,"/13CH1":303,"0B":304,"10B":305,"=Al":306,"=18O":307,"BH0":308,"F-1":309,"NH3":310,"S-2":311,"Br+2":312,"Cl+2":313,"\\Si":314,"/S-1":315,"=PH2":316,"14C@H1":317,"NH3+1":318,"#14C":319,"#O+1":320,"-3":321,"22":322,"4H":323,"5Se":324,"5Sr+2":325,"75Se":326,"85Sr+2":327,"=B-1":328,"=13C":329,"@-1":330,"Be":331,"B@@":332,"B@-1":333,"Ca":334,"CH1":335,"I+3":336,"KH1":337,"OH1+1":338,"Ra+2":339,"SH1-1":340,"\\PH1":341,"\\123I":342,"=Ca":343,"\\CH1-1":344,"=S@":345,"\\SeH1":346,"/SeH1":347,"Se-1":348,"LiH1":349,"18F-1":350,"125IH1":351,"11CH1":352,"TeH1":353,"Zn+1":354,"Zn-2":355,"Al-3":356,"13CH3":357,"15N":358,"Be+2":359,"B@@-1":360,"#P":361,"#S":362,"-4":363,"/PH1":364,"/P@@":365,"/As":366,"/14C":367,"/14CH1":368,"2K+1":369,"2Rb+1":370,"3Se":371,"3Ra+2":372,"45":373,"47":374,"42K+1":375,"5I-1":376,"73Se":377,"89":378,"82Rb+1":379,"=32":380,"=32P":381,"CH0":382,"CH2":383,"I+2":384,"NH0":385,"NH4":386,"OH1":387,"PH2+1":388,"SH0":389,"SH2":390,"\\3H":391,"\\11CH3":392,"\\C-1":393,"\\Se":394,"Si@":395,"Si-1":396,"SiH1-1":397,"SiH3-1":398,"/Se":399,"Se-2":400,"\\NH1-1":401,"18FH1":402,"125I-1":403,"11C@@H1":404,"11C-1":405,"AsH1":406,"As-1":407,"14C@@":408,"Te-1":409,"Mg+1":410,"123I-1":411,"123Te":412,"123IH1":413,"135I":414,"131I-1":415,"Ag-4":416,"124I-1":417,"76BrH1":418,"18OH1":419,"22Na+1":420,"223Ra+2":421,"CaH2":422,"45Ca+2":423,"47Ca+2":424,"89Sr+2":425,"=32PH1":426,"NH4+1":427} \ No newline at end of file diff --git a/models/finetuned/bbbp/config.json b/models/finetuned/bbbp/config.json deleted file mode 100644 index 3811e21539577b37e06313eab31ec11e53f0cbbc..0000000000000000000000000000000000000000 --- a/models/finetuned/bbbp/config.json +++ /dev/null @@ -1,27 +0,0 @@ -{ - "_name_or_path": "/home/erva/SELFormerMM/data/pretrained_multimodal_chembl36", - "architectures": [ - "RobertaForMaskedLM" - ], - "attention_probs_dropout_prob": 0.1, - "bos_token_id": 0, - "classifier_dropout": null, - "eos_token_id": 2, - "hidden_act": "gelu", - "hidden_dropout_prob": 0.1, - "hidden_size": 768, - "initializer_range": 0.02, - "intermediate_size": 3072, - "layer_norm_eps": 1e-12, - "max_position_embeddings": 514, - "model_type": "roberta", - "num_attention_heads": 4, - "num_hidden_layers": 12, - "pad_token_id": 1, - "position_embedding_type": "absolute", - "torch_dtype": "float32", - "transformers_version": "4.26.1", - "type_vocab_size": 1, - "use_cache": true, - "vocab_size": 800 -} diff --git a/models/finetuned/bbbp/merges.txt b/models/finetuned/bbbp/merges.txt deleted file mode 100644 index 7cd5ec62809503c23f18c80afc0ba3bdf9d253d0..0000000000000000000000000000000000000000 --- a/models/finetuned/bbbp/merges.txt +++ /dev/null @@ -1,378 +0,0 @@ -#version: 0.2 - Trained by `huggingface/tokenizers` -B r -a n -c h -Br an -Bran ch -Branch 1 -= C -R i -n g -Ri ng -Ring 1 -= Branch1 -Branch 2 -= O -Ring 2 -H 1 -C @ -= N -# Branch1 -C@ @ -= Branch2 -C@ H1 -C@@ H1 -# Branch2 -# C -C l -/ C -N H1 -= Ring1 -+ 1 -- 1 -O -1 -N +1 -\ C -# N -/ N -= Ring2 -= S -=N +1 -\ N -N a -Na +1 -/ O -\ O -Br -1 -Branch 3 -\ S -S +1 -Cl -1 -I -1 -/ C@@H1 -S i -/ C@H1 -/ S -=N -1 -S e -= P -N -1 -Ring 3 -2 H -P +1 -K +1 -\ C@@H1 -\ C@H1 -/ N+1 -@ @ -C -1 -# N+1 -B -1 -+ 3 -Cl +3 -\ NH1 -L i -Li +1 -P H1 -1 8 -18 F -@ +1 -3 H -P @@ -H 0 -O H0 -1 2 -P @ -+ 2 -@@ +1 -S -1 -/ Br -- / -\ Cl --/ Ring2 -\ O-1 -1 1 -5 I -12 5I -11 C -H 3 -\ N+1 -- \ -/ C@@ -S @+1 -A s -/ Cl -11C H3 -=S e -S @@+1 -N @+1 -1 4 --\ Ring2 -14 C -\ F -/ C@ -T e -H 2 -H1 -1 -=O +1 -N @@+1 -C +1 -=S +1 -Z n -/ P -a +2 -/ I -O H1-1 -C a+2 -\ Br -M g -Zn +2 -A l -/ F -Mg +2 -12 3 -123 I -1 3 -I +1 -/ O-1 --\ Ring1 -B H2 -BH2 -1 -\ I -/ NH1 -O +1 -13 1 -131 I -= 14C -/ S+1 -= Ring3 -\ C@@ -H2 +1 -\ C@ -A g -= As -=Se +1 -N H2+1 -Se H1 --/ Ring1 -= Te -Al +3 -Na H1 -=Te +1 -NH1 +1 -Ag +1 -H1 +1 -NH1 -1 -\ P -14C H2 -13 C -14C H1 -= 11C -S @@ -=P @@ -Si H2 -H3 -1 -14C H3 -B H3-1 -S @ -=14C H1 -=P H1 -=P @ -=N H1+1 -\S +1 -12 4 -C H1-1 -S r -=S i -124 I -Sr +2 -#C -1 -/C -1 -N @ -/N -1 -13C H1 -/ B -1 9 -B a+2 -H 4 -S H1+1 -Se +1 -19 F -/ 125I -P @+1 -R b -Cl +1 -Si H4 -Rb +1 -= Branch3 -N @@ -As +1 -/ Si -B H1-1 -S H1 -/ 123I -3 2 -= Mg -H +1 -\ B -Si H1 -P@@ +1 -- 2 -1 5 -1 7 -3 5 -= 13CH1 -C s -=N H2+1 -=S H1 -Mg H2 -32 P -17 F -35 S -Cs +1 -# 11C -/ 131I -B i -\ 125I -=S @@ -\S -1 -6 Br -7 I -7 6Br -= B -e H1 -\N -1 -18 O -12 7I -11C H2 -14 C@@H1 -Te H2 -15 NH1 -Bi +3 -/ P+1 -/ 13C -/ 13CH1 -0 B -1 0B -= Al -= 18O -B H0 -F -1 -N H3 -S -2 -Br +2 -Cl +2 -\S i -/S -1 -=P H2 -14 C@H1 -NH3 +1 -# 14C -# O+1 -- 3 -2 2 -4 H -5 Se -5 Sr+2 -7 5Se -8 5Sr+2 -= B-1 -= 13C -@ -1 -B e -B @@ -B @-1 -C a -C H1 -I +3 -K H1 -O H1+1 -R a+2 -S H1-1 -\ PH1 -\ 123I -=C a -\C H1-1 -=S @ -\S eH1 -/S eH1 -Se -1 -Li H1 -18F -1 -125I H1 -11C H1 -Te H1 -Zn +1 -Zn -2 -Al -3 -13C H3 -15 N -Be +2 -B@@ -1 -# P -# S -- 4 -/ PH1 -/ P@@ -/ As -/ 14C -/ 14CH1 -2 K+1 -2 Rb+1 -3 Se -3 Ra+2 -4 5 -4 7 -4 2K+1 -5 I-1 -7 3Se -8 9 -8 2Rb+1 -= 32 -= 32P -C H0 -C H2 -I +2 -N H0 -N H4 -O H1 -P H2+1 -S H0 -S H2 -\ 3H -\ 11CH3 -\C -1 -\S e -Si @ -Si -1 -Si H1-1 -Si H3-1 -/S e -Se -2 -\NH1 -1 -18F H1 -12 5I-1 -11 C@@H1 -11 C-1 -As H1 -As -1 -14 C@@ -Te -1 -Mg +1 -123 I-1 -123 Te -123I H1 -13 5I -131 I-1 -Ag -4 -124 I-1 -76Br H1 -18O H1 -22 Na+1 -22 3Ra+2 -Ca H2 -45 Ca+2 -47 Ca+2 -89 Sr+2 -=32 PH1 -NH4 +1 diff --git a/models/finetuned/bbbp/model.pt b/models/finetuned/bbbp/model.pt deleted file mode 100644 index a27b52e128ed17cabe4cf7875c06eb290f65abe8..0000000000000000000000000000000000000000 --- a/models/finetuned/bbbp/model.pt +++ /dev/null @@ -1,3 +0,0 @@ -version https://git-lfs.github.com/spec/v1 -oid sha256:56553557c9abbd004f18d16f7862060afa43a9b8a7b4f3a95956b77cc7e7ea27 -size 1022855293 diff --git a/models/finetuned/bbbp/special_tokens_map.json b/models/finetuned/bbbp/special_tokens_map.json deleted file mode 100644 index 06a55849fa69a91e7179d909e373179ff7467d8c..0000000000000000000000000000000000000000 --- a/models/finetuned/bbbp/special_tokens_map.json +++ /dev/null @@ -1,51 +0,0 @@ -{ - "bos_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "cls_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "eos_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "mask_token": { - "content": "", - "lstrip": true, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "pad_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "sep_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "unk_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - } -} diff --git a/models/finetuned/bbbp/tokenizer.json b/models/finetuned/bbbp/tokenizer.json deleted file mode 100644 index 3b64b273e6fa9799e2d8375722b9e815de9ebb8f..0000000000000000000000000000000000000000 --- a/models/finetuned/bbbp/tokenizer.json +++ /dev/null @@ -1,909 +0,0 @@ -{ - "version": "1.0", - "truncation": { - "direction": "Right", - "max_length": 128, - "strategy": "LongestFirst", - "stride": 0 - }, - "padding": { - "strategy": { - "Fixed": 128 - }, - "direction": "Right", - "pad_to_multiple_of": null, - "pad_id": 3, - "pad_type_id": 0, - "pad_token": "" - }, - "added_tokens": [ - { - "id": 0, - "content": "", - "single_word": false, - "lstrip": false, - "rstrip": false, - "normalized": true, - "special": true - }, - { - "id": 1, - "content": "", - "single_word": false, - "lstrip": false, - "rstrip": false, - "normalized": true, - "special": true - }, - { - "id": 2, - "content": "", - "single_word": false, - "lstrip": false, - "rstrip": false, - "normalized": true, - "special": true - }, - { - "id": 3, - "content": "", - "single_word": false, - "lstrip": false, - "rstrip": false, - "normalized": true, - "special": true - }, - { - "id": 4, - "content": "", - "single_word": false, - "lstrip": true, - "rstrip": false, - "normalized": true, - "special": true - } - ], - "normalizer": null, - "pre_tokenizer": { - "type": "ByteLevel", - "add_prefix_space": false, - "trim_offsets": true, - "use_regex": true - }, - "post_processor": { - "type": "RobertaProcessing", - "sep": [ - "", - 2 - ], - "cls": [ - "", - 1 - ], - "trim_offsets": true, - "add_prefix_space": false - }, - "decoder": { - "type": "ByteLevel", - "add_prefix_space": true, - "trim_offsets": true, - "use_regex": true - }, - "model": { - "type": "BPE", - "dropout": null, - "unk_token": null, - "continuing_subword_prefix": "", - "end_of_word_suffix": "", - "fuse_unk": false, - "vocab": { - "": 0, - "": 1, - "": 2, - "": 3, - "": 4, - "\n": 5, - "#": 6, - "+": 7, - "-": 8, - ".": 9, - "/": 10, - "0": 11, - "1": 12, - "2": 13, - "3": 14, - "4": 15, - "5": 16, - "6": 17, - "7": 18, - "8": 19, - "9": 20, - "=": 21, - "@": 22, - "A": 23, - "B": 24, - "C": 25, - "F": 26, - "H": 27, - "I": 28, - "K": 29, - "L": 30, - "M": 31, - "N": 32, - "O": 33, - "P": 34, - "R": 35, - "S": 36, - "T": 37, - "Z": 38, - "\\": 39, - "a": 40, - "b": 41, - "c": 42, - "e": 43, - "g": 44, - "h": 45, - "i": 46, - "l": 47, - "n": 48, - "r": 49, - "s": 50, - "Br": 51, - "an": 52, - "ch": 53, - "Bran": 54, - "Branch": 55, - "Branch1": 56, - "=C": 57, - "Ri": 58, - "ng": 59, - "Ring": 60, - "Ring1": 61, - "=Branch1": 62, - "Branch2": 63, - "=O": 64, - "Ring2": 65, - "H1": 66, - "C@": 67, - "=N": 68, - "#Branch1": 69, - "C@@": 70, - "=Branch2": 71, - "C@H1": 72, - "C@@H1": 73, - "#Branch2": 74, - "#C": 75, - "Cl": 76, - "/C": 77, - "NH1": 78, - "=Ring1": 79, - "+1": 80, - "-1": 81, - "O-1": 82, - "N+1": 83, - "\\C": 84, - "#N": 85, - "/N": 86, - "=Ring2": 87, - "=S": 88, - "=N+1": 89, - "\\N": 90, - "Na": 91, - "Na+1": 92, - "/O": 93, - "\\O": 94, - "Br-1": 95, - "Branch3": 96, - "\\S": 97, - "S+1": 98, - "Cl-1": 99, - "I-1": 100, - "/C@@H1": 101, - "Si": 102, - "/C@H1": 103, - "/S": 104, - "=N-1": 105, - "Se": 106, - "=P": 107, - "N-1": 108, - "Ring3": 109, - "2H": 110, - "P+1": 111, - "K+1": 112, - "\\C@@H1": 113, - "\\C@H1": 114, - "/N+1": 115, - "@@": 116, - "C-1": 117, - "#N+1": 118, - "B-1": 119, - "+3": 120, - "Cl+3": 121, - "\\NH1": 122, - "Li": 123, - "Li+1": 124, - "PH1": 125, - "18": 126, - "18F": 127, - "@+1": 128, - "3H": 129, - "P@@": 130, - "H0": 131, - "OH0": 132, - "12": 133, - "P@": 134, - "+2": 135, - "@@+1": 136, - "S-1": 137, - "/Br": 138, - "-/": 139, - "\\Cl": 140, - "-/Ring2": 141, - "\\O-1": 142, - "11": 143, - "5I": 144, - "125I": 145, - "11C": 146, - "H3": 147, - "\\N+1": 148, - "-\\": 149, - "/C@@": 150, - "S@+1": 151, - "As": 152, - "/Cl": 153, - "11CH3": 154, - "=Se": 155, - "S@@+1": 156, - "N@+1": 157, - "14": 158, - "-\\Ring2": 159, - "14C": 160, - "\\F": 161, - "/C@": 162, - "Te": 163, - "H2": 164, - "H1-1": 165, - "=O+1": 166, - "N@@+1": 167, - "C+1": 168, - "=S+1": 169, - "Zn": 170, - "/P": 171, - "a+2": 172, - "/I": 173, - "OH1-1": 174, - "Ca+2": 175, - "\\Br": 176, - "Mg": 177, - "Zn+2": 178, - "Al": 179, - "/F": 180, - "Mg+2": 181, - "123": 182, - "123I": 183, - "13": 184, - "I+1": 185, - "/O-1": 186, - "-\\Ring1": 187, - "BH2": 188, - "BH2-1": 189, - "\\I": 190, - "/NH1": 191, - "O+1": 192, - "131": 193, - "131I": 194, - "=14C": 195, - "/S+1": 196, - "=Ring3": 197, - "\\C@@": 198, - "H2+1": 199, - "\\C@": 200, - "Ag": 201, - "=As": 202, - "=Se+1": 203, - "NH2+1": 204, - "SeH1": 205, - "-/Ring1": 206, - "=Te": 207, - "Al+3": 208, - "NaH1": 209, - "=Te+1": 210, - "NH1+1": 211, - "Ag+1": 212, - "H1+1": 213, - "NH1-1": 214, - "\\P": 215, - "14CH2": 216, - "13C": 217, - "14CH1": 218, - "=11C": 219, - "S@@": 220, - "=P@@": 221, - "SiH2": 222, - "H3-1": 223, - "14CH3": 224, - "BH3-1": 225, - "S@": 226, - "=14CH1": 227, - "=PH1": 228, - "=P@": 229, - "=NH1+1": 230, - "\\S+1": 231, - "124": 232, - "CH1-1": 233, - "Sr": 234, - "=Si": 235, - "124I": 236, - "Sr+2": 237, - "#C-1": 238, - "/C-1": 239, - "N@": 240, - "/N-1": 241, - "13CH1": 242, - "/B": 243, - "19": 244, - "Ba+2": 245, - "H4": 246, - "SH1+1": 247, - "Se+1": 248, - "19F": 249, - "/125I": 250, - "P@+1": 251, - "Rb": 252, - "Cl+1": 253, - "SiH4": 254, - "Rb+1": 255, - "=Branch3": 256, - "N@@": 257, - "As+1": 258, - "/Si": 259, - "BH1-1": 260, - "SH1": 261, - "/123I": 262, - "32": 263, - "=Mg": 264, - "H+1": 265, - "\\B": 266, - "SiH1": 267, - "P@@+1": 268, - "-2": 269, - "15": 270, - "17": 271, - "35": 272, - "=13CH1": 273, - "Cs": 274, - "=NH2+1": 275, - "=SH1": 276, - "MgH2": 277, - "32P": 278, - "17F": 279, - "35S": 280, - "Cs+1": 281, - "#11C": 282, - "/131I": 283, - "Bi": 284, - "\\125I": 285, - "=S@@": 286, - "\\S-1": 287, - "6Br": 288, - "7I": 289, - "76Br": 290, - "=B": 291, - "eH1": 292, - "\\N-1": 293, - "18O": 294, - "127I": 295, - "11CH2": 296, - "14C@@H1": 297, - "TeH2": 298, - "15NH1": 299, - "Bi+3": 300, - "/P+1": 301, - "/13C": 302, - "/13CH1": 303, - "0B": 304, - "10B": 305, - "=Al": 306, - "=18O": 307, - "BH0": 308, - "F-1": 309, - "NH3": 310, - "S-2": 311, - "Br+2": 312, - "Cl+2": 313, - "\\Si": 314, - "/S-1": 315, - "=PH2": 316, - "14C@H1": 317, - "NH3+1": 318, - "#14C": 319, - "#O+1": 320, - "-3": 321, - "22": 322, - "4H": 323, - "5Se": 324, - "5Sr+2": 325, - "75Se": 326, - "85Sr+2": 327, - "=B-1": 328, - "=13C": 329, - "@-1": 330, - "Be": 331, - "B@@": 332, - "B@-1": 333, - "Ca": 334, - "CH1": 335, - "I+3": 336, - "KH1": 337, - "OH1+1": 338, - "Ra+2": 339, - "SH1-1": 340, - "\\PH1": 341, - "\\123I": 342, - "=Ca": 343, - "\\CH1-1": 344, - "=S@": 345, - "\\SeH1": 346, - "/SeH1": 347, - "Se-1": 348, - "LiH1": 349, - "18F-1": 350, - "125IH1": 351, - "11CH1": 352, - "TeH1": 353, - "Zn+1": 354, - "Zn-2": 355, - "Al-3": 356, - "13CH3": 357, - "15N": 358, - "Be+2": 359, - "B@@-1": 360, - "#P": 361, - "#S": 362, - "-4": 363, - "/PH1": 364, - "/P@@": 365, - "/As": 366, - "/14C": 367, - "/14CH1": 368, - "2K+1": 369, - "2Rb+1": 370, - "3Se": 371, - "3Ra+2": 372, - "45": 373, - "47": 374, - "42K+1": 375, - "5I-1": 376, - "73Se": 377, - "89": 378, - "82Rb+1": 379, - "=32": 380, - "=32P": 381, - "CH0": 382, - "CH2": 383, - "I+2": 384, - "NH0": 385, - "NH4": 386, - "OH1": 387, - "PH2+1": 388, - "SH0": 389, - "SH2": 390, - "\\3H": 391, - "\\11CH3": 392, - "\\C-1": 393, - "\\Se": 394, - "Si@": 395, - "Si-1": 396, - "SiH1-1": 397, - "SiH3-1": 398, - "/Se": 399, - "Se-2": 400, - "\\NH1-1": 401, - "18FH1": 402, - "125I-1": 403, - "11C@@H1": 404, - "11C-1": 405, - "AsH1": 406, - "As-1": 407, - "14C@@": 408, - "Te-1": 409, - "Mg+1": 410, - "123I-1": 411, - "123Te": 412, - "123IH1": 413, - "135I": 414, - "131I-1": 415, - "Ag-4": 416, - "124I-1": 417, - "76BrH1": 418, - "18OH1": 419, - "22Na+1": 420, - "223Ra+2": 421, - "CaH2": 422, - "45Ca+2": 423, - "47Ca+2": 424, - "89Sr+2": 425, - "=32PH1": 426, - "NH4+1": 427 - }, - "merges": [ - "B r", - "a n", - "c h", - "Br an", - "Bran ch", - "Branch 1", - "= C", - "R i", - "n g", - "Ri ng", - "Ring 1", - "= Branch1", - "Branch 2", - "= O", - "Ring 2", - "H 1", - "C @", - "= N", - "# Branch1", - "C@ @", - "= Branch2", - "C@ H1", - "C@@ H1", - "# Branch2", - "# C", - "C l", - "/ C", - "N H1", - "= Ring1", - "+ 1", - "- 1", - "O -1", - "N +1", - "\\ C", - "# N", - "/ N", - "= Ring2", - "= S", - "=N +1", - "\\ N", - "N a", - "Na +1", - "/ O", - "\\ O", - "Br -1", - "Branch 3", - "\\ S", - "S +1", - "Cl -1", - "I -1", - "/ C@@H1", - "S i", - "/ C@H1", - "/ S", - "=N -1", - "S e", - "= P", - "N -1", - "Ring 3", - "2 H", - "P +1", - "K +1", - "\\ C@@H1", - "\\ C@H1", - "/ N+1", - "@ @", - "C -1", - "# N+1", - "B -1", - "+ 3", - "Cl +3", - "\\ NH1", - "L i", - "Li +1", - "P H1", - "1 8", - "18 F", - "@ +1", - "3 H", - "P @@", - "H 0", - "O H0", - "1 2", - "P @", - "+ 2", - "@@ +1", - "S -1", - "/ Br", - "- /", - "\\ Cl", - "-/ Ring2", - "\\ O-1", - "1 1", - "5 I", - "12 5I", - "11 C", - "H 3", - "\\ N+1", - "- \\", - "/ C@@", - "S @+1", - "A s", - "/ Cl", - "11C H3", - "=S e", - "S @@+1", - "N @+1", - "1 4", - "-\\ Ring2", - "14 C", - "\\ F", - "/ C@", - "T e", - "H 2", - "H1 -1", - "=O +1", - "N @@+1", - "C +1", - "=S +1", - "Z n", - "/ P", - "a +2", - "/ I", - "O H1-1", - "C a+2", - "\\ Br", - "M g", - "Zn +2", - "A l", - "/ F", - "Mg +2", - "12 3", - "123 I", - "1 3", - "I +1", - "/ O-1", - "-\\ Ring1", - "B H2", - "BH2 -1", - "\\ I", - "/ NH1", - "O +1", - "13 1", - "131 I", - "= 14C", - "/ S+1", - "= Ring3", - "\\ C@@", - "H2 +1", - "\\ C@", - "A g", - "= As", - "=Se +1", - "N H2+1", - "Se H1", - "-/ Ring1", - "= Te", - "Al +3", - "Na H1", - "=Te +1", - "NH1 +1", - "Ag +1", - "H1 +1", - "NH1 -1", - "\\ P", - "14C H2", - "13 C", - "14C H1", - "= 11C", - "S @@", - "=P @@", - "Si H2", - "H3 -1", - "14C H3", - "B H3-1", - "S @", - "=14C H1", - "=P H1", - "=P @", - "=N H1+1", - "\\S +1", - "12 4", - "C H1-1", - "S r", - "=S i", - "124 I", - "Sr +2", - "#C -1", - "/C -1", - "N @", - "/N -1", - "13C H1", - "/ B", - "1 9", - "B a+2", - "H 4", - "S H1+1", - "Se +1", - "19 F", - "/ 125I", - "P @+1", - "R b", - "Cl +1", - "Si H4", - "Rb +1", - "= Branch3", - "N @@", - "As +1", - "/ Si", - "B H1-1", - "S H1", - "/ 123I", - "3 2", - "= Mg", - "H +1", - "\\ B", - "Si H1", - "P@@ +1", - "- 2", - "1 5", - "1 7", - "3 5", - "= 13CH1", - "C s", - "=N H2+1", - "=S H1", - "Mg H2", - "32 P", - "17 F", - "35 S", - "Cs +1", - "# 11C", - "/ 131I", - "B i", - "\\ 125I", - "=S @@", - "\\S -1", - "6 Br", - "7 I", - "7 6Br", - "= B", - "e H1", - "\\N -1", - "18 O", - "12 7I", - "11C H2", - "14 C@@H1", - "Te H2", - "15 NH1", - "Bi +3", - "/ P+1", - "/ 13C", - "/ 13CH1", - "0 B", - "1 0B", - "= Al", - "= 18O", - "B H0", - "F -1", - "N H3", - "S -2", - "Br +2", - "Cl +2", - "\\S i", - "/S -1", - "=P H2", - "14 C@H1", - "NH3 +1", - "# 14C", - "# O+1", - "- 3", - "2 2", - "4 H", - "5 Se", - "5 Sr+2", - "7 5Se", - "8 5Sr+2", - "= B-1", - "= 13C", - "@ -1", - "B e", - "B @@", - "B @-1", - "C a", - "C H1", - "I +3", - "K H1", - "O H1+1", - "R a+2", - "S H1-1", - "\\ PH1", - "\\ 123I", - "=C a", - "\\C H1-1", - "=S @", - "\\S eH1", - "/S eH1", - "Se -1", - "Li H1", - "18F -1", - "125I H1", - "11C H1", - "Te H1", - "Zn +1", - "Zn -2", - "Al -3", - "13C H3", - "15 N", - "Be +2", - "B@@ -1", - "# P", - "# S", - "- 4", - "/ PH1", - "/ P@@", - "/ As", - "/ 14C", - "/ 14CH1", - "2 K+1", - "2 Rb+1", - "3 Se", - "3 Ra+2", - "4 5", - "4 7", - "4 2K+1", - "5 I-1", - "7 3Se", - "8 9", - "8 2Rb+1", - "= 32", - "= 32P", - "C H0", - "C H2", - "I +2", - "N H0", - "N H4", - "O H1", - "P H2+1", - "S H0", - "S H2", - "\\ 3H", - "\\ 11CH3", - "\\C -1", - "\\S e", - "Si @", - "Si -1", - "Si H1-1", - "Si H3-1", - "/S e", - "Se -2", - "\\NH1 -1", - "18F H1", - "12 5I-1", - "11 C@@H1", - "11 C-1", - "As H1", - "As -1", - "14 C@@", - "Te -1", - "Mg +1", - "123 I-1", - "123 Te", - "123I H1", - "13 5I", - "131 I-1", - "Ag -4", - "124 I-1", - "76Br H1", - "18O H1", - "22 Na+1", - "22 3Ra+2", - "Ca H2", - "45 Ca+2", - "47 Ca+2", - "89 Sr+2", - "=32 PH1", - "NH4 +1" - ] - } -} \ No newline at end of file diff --git a/models/finetuned/bbbp/tokenizer_config.json b/models/finetuned/bbbp/tokenizer_config.json deleted file mode 100644 index 08860954acd34fad07fd77f7635298fa565f3149..0000000000000000000000000000000000000000 --- a/models/finetuned/bbbp/tokenizer_config.json +++ /dev/null @@ -1,65 +0,0 @@ -{ - "add_prefix_space": false, - "bos_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "cls_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "eos_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "errors": "replace", - "mask_token": { - "__type": "AddedToken", - "content": "", - "lstrip": true, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "model_max_length": 1000000000000000019884624838656, - "name_or_path": "/home/erva/SELFormerMM/data/pretrained_multimodal_chembl36", - "pad_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "sep_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "special_tokens_map_file": null, - "tokenizer_class": "RobertaTokenizer", - "trim_offsets": true, - "unk_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - } -} diff --git a/models/finetuned/bbbp/train_stdout.log b/models/finetuned/bbbp/train_stdout.log deleted file mode 100644 index e6f1c4bb9d809523a6881395f093c8192e483169..0000000000000000000000000000000000000000 --- a/models/finetuned/bbbp/train_stdout.log +++ /dev/null @@ -1,91 +0,0 @@ -[finetune] starting -[finetune] device=cuda task_type=binary batch_size=32 max_len=128 backbone_lr=5e-05 head_lr=5e-05 weight_decay=0.01 epochs=50 -[finetune] dataset_meta_csv=/home/erva/SELFormerMM/data/new_finetuning_datasets/classification/bbbp/bbbp.csv -[finetune] dataset_embs_npz=/home/erva/SELFormerMM/data/new_finetuning_datasets/classification/bbbp/bbbp_embs.npz -[finetune] model_path=HUBioDataLab/SELFormer tokenizer_path=HUBioDataLab/SELFormer -[finetune] pretrained_multimodal_dir=/home/erva/SELFormerMM/data/pretrained_multimodal_chembl36 -[finetune] use_scaffold=True seed=42 fracs=(0.8,0.1,0.1) -[finetune] loading dataset bundle (meta csv + embs npz) ... -[finetune] splitting dataset... - - 0%| | 0/2039 [00:00":0,"":1,"":2,"":3,"":4,"\n":5,"#":6,"+":7,"-":8,".":9,"/":10,"0":11,"1":12,"2":13,"3":14,"4":15,"5":16,"6":17,"7":18,"8":19,"9":20,"=":21,"@":22,"A":23,"B":24,"C":25,"F":26,"H":27,"I":28,"K":29,"L":30,"M":31,"N":32,"O":33,"P":34,"R":35,"S":36,"T":37,"Z":38,"\\":39,"a":40,"b":41,"c":42,"e":43,"g":44,"h":45,"i":46,"l":47,"n":48,"r":49,"s":50,"Br":51,"an":52,"ch":53,"Bran":54,"Branch":55,"Branch1":56,"=C":57,"Ri":58,"ng":59,"Ring":60,"Ring1":61,"=Branch1":62,"Branch2":63,"=O":64,"Ring2":65,"H1":66,"C@":67,"=N":68,"#Branch1":69,"C@@":70,"=Branch2":71,"C@H1":72,"C@@H1":73,"#Branch2":74,"#C":75,"Cl":76,"/C":77,"NH1":78,"=Ring1":79,"+1":80,"-1":81,"O-1":82,"N+1":83,"\\C":84,"#N":85,"/N":86,"=Ring2":87,"=S":88,"=N+1":89,"\\N":90,"Na":91,"Na+1":92,"/O":93,"\\O":94,"Br-1":95,"Branch3":96,"\\S":97,"S+1":98,"Cl-1":99,"I-1":100,"/C@@H1":101,"Si":102,"/C@H1":103,"/S":104,"=N-1":105,"Se":106,"=P":107,"N-1":108,"Ring3":109,"2H":110,"P+1":111,"K+1":112,"\\C@@H1":113,"\\C@H1":114,"/N+1":115,"@@":116,"C-1":117,"#N+1":118,"B-1":119,"+3":120,"Cl+3":121,"\\NH1":122,"Li":123,"Li+1":124,"PH1":125,"18":126,"18F":127,"@+1":128,"3H":129,"P@@":130,"H0":131,"OH0":132,"12":133,"P@":134,"+2":135,"@@+1":136,"S-1":137,"/Br":138,"-/":139,"\\Cl":140,"-/Ring2":141,"\\O-1":142,"11":143,"5I":144,"125I":145,"11C":146,"H3":147,"\\N+1":148,"-\\":149,"/C@@":150,"S@+1":151,"As":152,"/Cl":153,"11CH3":154,"=Se":155,"S@@+1":156,"N@+1":157,"14":158,"-\\Ring2":159,"14C":160,"\\F":161,"/C@":162,"Te":163,"H2":164,"H1-1":165,"=O+1":166,"N@@+1":167,"C+1":168,"=S+1":169,"Zn":170,"/P":171,"a+2":172,"/I":173,"OH1-1":174,"Ca+2":175,"\\Br":176,"Mg":177,"Zn+2":178,"Al":179,"/F":180,"Mg+2":181,"123":182,"123I":183,"13":184,"I+1":185,"/O-1":186,"-\\Ring1":187,"BH2":188,"BH2-1":189,"\\I":190,"/NH1":191,"O+1":192,"131":193,"131I":194,"=14C":195,"/S+1":196,"=Ring3":197,"\\C@@":198,"H2+1":199,"\\C@":200,"Ag":201,"=As":202,"=Se+1":203,"NH2+1":204,"SeH1":205,"-/Ring1":206,"=Te":207,"Al+3":208,"NaH1":209,"=Te+1":210,"NH1+1":211,"Ag+1":212,"H1+1":213,"NH1-1":214,"\\P":215,"14CH2":216,"13C":217,"14CH1":218,"=11C":219,"S@@":220,"=P@@":221,"SiH2":222,"H3-1":223,"14CH3":224,"BH3-1":225,"S@":226,"=14CH1":227,"=PH1":228,"=P@":229,"=NH1+1":230,"\\S+1":231,"124":232,"CH1-1":233,"Sr":234,"=Si":235,"124I":236,"Sr+2":237,"#C-1":238,"/C-1":239,"N@":240,"/N-1":241,"13CH1":242,"/B":243,"19":244,"Ba+2":245,"H4":246,"SH1+1":247,"Se+1":248,"19F":249,"/125I":250,"P@+1":251,"Rb":252,"Cl+1":253,"SiH4":254,"Rb+1":255,"=Branch3":256,"N@@":257,"As+1":258,"/Si":259,"BH1-1":260,"SH1":261,"/123I":262,"32":263,"=Mg":264,"H+1":265,"\\B":266,"SiH1":267,"P@@+1":268,"-2":269,"15":270,"17":271,"35":272,"=13CH1":273,"Cs":274,"=NH2+1":275,"=SH1":276,"MgH2":277,"32P":278,"17F":279,"35S":280,"Cs+1":281,"#11C":282,"/131I":283,"Bi":284,"\\125I":285,"=S@@":286,"\\S-1":287,"6Br":288,"7I":289,"76Br":290,"=B":291,"eH1":292,"\\N-1":293,"18O":294,"127I":295,"11CH2":296,"14C@@H1":297,"TeH2":298,"15NH1":299,"Bi+3":300,"/P+1":301,"/13C":302,"/13CH1":303,"0B":304,"10B":305,"=Al":306,"=18O":307,"BH0":308,"F-1":309,"NH3":310,"S-2":311,"Br+2":312,"Cl+2":313,"\\Si":314,"/S-1":315,"=PH2":316,"14C@H1":317,"NH3+1":318,"#14C":319,"#O+1":320,"-3":321,"22":322,"4H":323,"5Se":324,"5Sr+2":325,"75Se":326,"85Sr+2":327,"=B-1":328,"=13C":329,"@-1":330,"Be":331,"B@@":332,"B@-1":333,"Ca":334,"CH1":335,"I+3":336,"KH1":337,"OH1+1":338,"Ra+2":339,"SH1-1":340,"\\PH1":341,"\\123I":342,"=Ca":343,"\\CH1-1":344,"=S@":345,"\\SeH1":346,"/SeH1":347,"Se-1":348,"LiH1":349,"18F-1":350,"125IH1":351,"11CH1":352,"TeH1":353,"Zn+1":354,"Zn-2":355,"Al-3":356,"13CH3":357,"15N":358,"Be+2":359,"B@@-1":360,"#P":361,"#S":362,"-4":363,"/PH1":364,"/P@@":365,"/As":366,"/14C":367,"/14CH1":368,"2K+1":369,"2Rb+1":370,"3Se":371,"3Ra+2":372,"45":373,"47":374,"42K+1":375,"5I-1":376,"73Se":377,"89":378,"82Rb+1":379,"=32":380,"=32P":381,"CH0":382,"CH2":383,"I+2":384,"NH0":385,"NH4":386,"OH1":387,"PH2+1":388,"SH0":389,"SH2":390,"\\3H":391,"\\11CH3":392,"\\C-1":393,"\\Se":394,"Si@":395,"Si-1":396,"SiH1-1":397,"SiH3-1":398,"/Se":399,"Se-2":400,"\\NH1-1":401,"18FH1":402,"125I-1":403,"11C@@H1":404,"11C-1":405,"AsH1":406,"As-1":407,"14C@@":408,"Te-1":409,"Mg+1":410,"123I-1":411,"123Te":412,"123IH1":413,"135I":414,"131I-1":415,"Ag-4":416,"124I-1":417,"76BrH1":418,"18OH1":419,"22Na+1":420,"223Ra+2":421,"CaH2":422,"45Ca+2":423,"47Ca+2":424,"89Sr+2":425,"=32PH1":426,"NH4+1":427} \ No newline at end of file diff --git a/models/finetuned/esol/checkpoint_epoch_025/config.json b/models/finetuned/esol/checkpoint_epoch_025/config.json deleted file mode 100644 index 3811e21539577b37e06313eab31ec11e53f0cbbc..0000000000000000000000000000000000000000 --- a/models/finetuned/esol/checkpoint_epoch_025/config.json +++ /dev/null @@ -1,27 +0,0 @@ -{ - "_name_or_path": "/home/erva/SELFormerMM/data/pretrained_multimodal_chembl36", - "architectures": [ - "RobertaForMaskedLM" - ], - "attention_probs_dropout_prob": 0.1, - "bos_token_id": 0, - "classifier_dropout": null, - "eos_token_id": 2, - "hidden_act": "gelu", - "hidden_dropout_prob": 0.1, - "hidden_size": 768, - "initializer_range": 0.02, - "intermediate_size": 3072, - "layer_norm_eps": 1e-12, - "max_position_embeddings": 514, - "model_type": "roberta", - "num_attention_heads": 4, - "num_hidden_layers": 12, - "pad_token_id": 1, - "position_embedding_type": "absolute", - "torch_dtype": "float32", - "transformers_version": "4.26.1", - "type_vocab_size": 1, - "use_cache": true, - "vocab_size": 800 -} diff --git a/models/finetuned/esol/checkpoint_epoch_025/merges.txt b/models/finetuned/esol/checkpoint_epoch_025/merges.txt deleted file mode 100644 index 7cd5ec62809503c23f18c80afc0ba3bdf9d253d0..0000000000000000000000000000000000000000 --- a/models/finetuned/esol/checkpoint_epoch_025/merges.txt +++ /dev/null @@ -1,378 +0,0 @@ -#version: 0.2 - Trained by `huggingface/tokenizers` -B r -a n -c h -Br an -Bran ch -Branch 1 -= C -R i -n g -Ri ng -Ring 1 -= Branch1 -Branch 2 -= O -Ring 2 -H 1 -C @ -= N -# Branch1 -C@ @ -= Branch2 -C@ H1 -C@@ H1 -# Branch2 -# C -C l -/ C -N H1 -= Ring1 -+ 1 -- 1 -O -1 -N +1 -\ C -# N -/ N -= Ring2 -= S -=N +1 -\ N -N a -Na +1 -/ O -\ O -Br -1 -Branch 3 -\ S -S +1 -Cl -1 -I -1 -/ C@@H1 -S i -/ C@H1 -/ S -=N -1 -S e -= P -N -1 -Ring 3 -2 H -P +1 -K +1 -\ C@@H1 -\ C@H1 -/ N+1 -@ @ -C -1 -# N+1 -B -1 -+ 3 -Cl +3 -\ NH1 -L i -Li +1 -P H1 -1 8 -18 F -@ +1 -3 H -P @@ -H 0 -O H0 -1 2 -P @ -+ 2 -@@ +1 -S -1 -/ Br -- / -\ Cl --/ Ring2 -\ O-1 -1 1 -5 I -12 5I -11 C -H 3 -\ N+1 -- \ -/ C@@ -S @+1 -A s -/ Cl -11C H3 -=S e -S @@+1 -N @+1 -1 4 --\ Ring2 -14 C -\ F -/ C@ -T e -H 2 -H1 -1 -=O +1 -N @@+1 -C +1 -=S +1 -Z n -/ P -a +2 -/ I -O H1-1 -C a+2 -\ Br -M g -Zn +2 -A l -/ F -Mg +2 -12 3 -123 I -1 3 -I +1 -/ O-1 --\ Ring1 -B H2 -BH2 -1 -\ I -/ NH1 -O +1 -13 1 -131 I -= 14C -/ S+1 -= Ring3 -\ C@@ -H2 +1 -\ C@ -A g -= As -=Se +1 -N H2+1 -Se H1 --/ Ring1 -= Te -Al +3 -Na H1 -=Te +1 -NH1 +1 -Ag +1 -H1 +1 -NH1 -1 -\ P -14C H2 -13 C -14C H1 -= 11C -S @@ -=P @@ -Si H2 -H3 -1 -14C H3 -B H3-1 -S @ -=14C H1 -=P H1 -=P @ -=N H1+1 -\S +1 -12 4 -C H1-1 -S r -=S i -124 I -Sr +2 -#C -1 -/C -1 -N @ -/N -1 -13C H1 -/ B -1 9 -B a+2 -H 4 -S H1+1 -Se +1 -19 F -/ 125I -P @+1 -R b -Cl +1 -Si H4 -Rb +1 -= Branch3 -N @@ -As +1 -/ Si -B H1-1 -S H1 -/ 123I -3 2 -= Mg -H +1 -\ B -Si H1 -P@@ +1 -- 2 -1 5 -1 7 -3 5 -= 13CH1 -C s -=N H2+1 -=S H1 -Mg H2 -32 P -17 F -35 S -Cs +1 -# 11C -/ 131I -B i -\ 125I -=S @@ -\S -1 -6 Br -7 I -7 6Br -= B -e H1 -\N -1 -18 O -12 7I -11C H2 -14 C@@H1 -Te H2 -15 NH1 -Bi +3 -/ P+1 -/ 13C -/ 13CH1 -0 B -1 0B -= Al -= 18O -B H0 -F -1 -N H3 -S -2 -Br +2 -Cl +2 -\S i -/S -1 -=P H2 -14 C@H1 -NH3 +1 -# 14C -# O+1 -- 3 -2 2 -4 H -5 Se -5 Sr+2 -7 5Se -8 5Sr+2 -= B-1 -= 13C -@ -1 -B e -B @@ -B @-1 -C a -C H1 -I +3 -K H1 -O H1+1 -R a+2 -S H1-1 -\ PH1 -\ 123I -=C a -\C H1-1 -=S @ -\S eH1 -/S eH1 -Se -1 -Li H1 -18F -1 -125I H1 -11C H1 -Te H1 -Zn +1 -Zn -2 -Al -3 -13C H3 -15 N -Be +2 -B@@ -1 -# P -# S -- 4 -/ PH1 -/ P@@ -/ As -/ 14C -/ 14CH1 -2 K+1 -2 Rb+1 -3 Se -3 Ra+2 -4 5 -4 7 -4 2K+1 -5 I-1 -7 3Se -8 9 -8 2Rb+1 -= 32 -= 32P -C H0 -C H2 -I +2 -N H0 -N H4 -O H1 -P H2+1 -S H0 -S H2 -\ 3H -\ 11CH3 -\C -1 -\S e -Si @ -Si -1 -Si H1-1 -Si H3-1 -/S e -Se -2 -\NH1 -1 -18F H1 -12 5I-1 -11 C@@H1 -11 C-1 -As H1 -As -1 -14 C@@ -Te -1 -Mg +1 -123 I-1 -123 Te -123I H1 -13 5I -131 I-1 -Ag -4 -124 I-1 -76Br H1 -18O H1 -22 Na+1 -22 3Ra+2 -Ca H2 -45 Ca+2 -47 Ca+2 -89 Sr+2 -=32 PH1 -NH4 +1 diff --git a/models/finetuned/esol/checkpoint_epoch_025/model.pt b/models/finetuned/esol/checkpoint_epoch_025/model.pt deleted file mode 100644 index 172bde9641a7e805bf4de474b175f77a7e38d5a5..0000000000000000000000000000000000000000 --- a/models/finetuned/esol/checkpoint_epoch_025/model.pt +++ /dev/null @@ -1,3 +0,0 @@ -version https://git-lfs.github.com/spec/v1 -oid sha256:1b864cf061c5ebe3019c8d724e63bbea3553c915546e126cced40c03803cacf6 -size 1022843005 diff --git a/models/finetuned/esol/checkpoint_epoch_025/special_tokens_map.json b/models/finetuned/esol/checkpoint_epoch_025/special_tokens_map.json deleted file mode 100644 index 06a55849fa69a91e7179d909e373179ff7467d8c..0000000000000000000000000000000000000000 --- a/models/finetuned/esol/checkpoint_epoch_025/special_tokens_map.json +++ /dev/null @@ -1,51 +0,0 @@ -{ - "bos_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "cls_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "eos_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "mask_token": { - "content": "", - "lstrip": true, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "pad_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "sep_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "unk_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - } -} diff --git a/models/finetuned/esol/checkpoint_epoch_025/tokenizer.json b/models/finetuned/esol/checkpoint_epoch_025/tokenizer.json deleted file mode 100644 index 3b64b273e6fa9799e2d8375722b9e815de9ebb8f..0000000000000000000000000000000000000000 --- a/models/finetuned/esol/checkpoint_epoch_025/tokenizer.json +++ /dev/null @@ -1,909 +0,0 @@ -{ - "version": "1.0", - "truncation": { - "direction": "Right", - "max_length": 128, - "strategy": "LongestFirst", - "stride": 0 - }, - "padding": { - "strategy": { - "Fixed": 128 - }, - "direction": "Right", - "pad_to_multiple_of": null, - "pad_id": 3, - "pad_type_id": 0, - "pad_token": "" - }, - "added_tokens": [ - { - "id": 0, - "content": "", - "single_word": false, - "lstrip": false, - "rstrip": false, - "normalized": true, - "special": true - }, - { - "id": 1, - "content": "", - "single_word": false, - "lstrip": false, - "rstrip": false, - "normalized": true, - "special": true - }, - { - "id": 2, - "content": "", - "single_word": false, - "lstrip": false, - "rstrip": false, - "normalized": true, - "special": true - }, - { - "id": 3, - "content": "", - "single_word": false, - "lstrip": false, - "rstrip": false, - "normalized": true, - "special": true - }, - { - "id": 4, - "content": "", - "single_word": false, - "lstrip": true, - "rstrip": false, - "normalized": true, - "special": true - } - ], - "normalizer": null, - "pre_tokenizer": { - "type": "ByteLevel", - "add_prefix_space": false, - "trim_offsets": true, - "use_regex": true - }, - "post_processor": { - "type": "RobertaProcessing", - "sep": [ - "", - 2 - ], - "cls": [ - "", - 1 - ], - "trim_offsets": true, - "add_prefix_space": false - }, - "decoder": { - "type": "ByteLevel", - "add_prefix_space": true, - "trim_offsets": true, - "use_regex": true - }, - "model": { - "type": "BPE", - "dropout": null, - "unk_token": null, - "continuing_subword_prefix": "", - "end_of_word_suffix": "", - "fuse_unk": false, - "vocab": { - "": 0, - "": 1, - "": 2, - "": 3, - "": 4, - "\n": 5, - "#": 6, - "+": 7, - "-": 8, - ".": 9, - "/": 10, - "0": 11, - "1": 12, - "2": 13, - "3": 14, - "4": 15, - "5": 16, - "6": 17, - "7": 18, - "8": 19, - "9": 20, - "=": 21, - "@": 22, - "A": 23, - "B": 24, - "C": 25, - "F": 26, - "H": 27, - "I": 28, - "K": 29, - "L": 30, - "M": 31, - "N": 32, - "O": 33, - "P": 34, - "R": 35, - "S": 36, - "T": 37, - "Z": 38, - "\\": 39, - "a": 40, - "b": 41, - "c": 42, - "e": 43, - "g": 44, - "h": 45, - "i": 46, - "l": 47, - "n": 48, - "r": 49, - "s": 50, - "Br": 51, - "an": 52, - "ch": 53, - "Bran": 54, - "Branch": 55, - "Branch1": 56, - "=C": 57, - "Ri": 58, - "ng": 59, - "Ring": 60, - "Ring1": 61, - "=Branch1": 62, - "Branch2": 63, - "=O": 64, - "Ring2": 65, - "H1": 66, - "C@": 67, - "=N": 68, - "#Branch1": 69, - "C@@": 70, - "=Branch2": 71, - "C@H1": 72, - "C@@H1": 73, - "#Branch2": 74, - "#C": 75, - "Cl": 76, - "/C": 77, - "NH1": 78, - "=Ring1": 79, - "+1": 80, - "-1": 81, - "O-1": 82, - "N+1": 83, - "\\C": 84, - "#N": 85, - "/N": 86, - "=Ring2": 87, - "=S": 88, - "=N+1": 89, - "\\N": 90, - "Na": 91, - "Na+1": 92, - "/O": 93, - "\\O": 94, - "Br-1": 95, - "Branch3": 96, - "\\S": 97, - "S+1": 98, - "Cl-1": 99, - "I-1": 100, - "/C@@H1": 101, - "Si": 102, - "/C@H1": 103, - "/S": 104, - "=N-1": 105, - "Se": 106, - "=P": 107, - "N-1": 108, - "Ring3": 109, - "2H": 110, - "P+1": 111, - "K+1": 112, - "\\C@@H1": 113, - "\\C@H1": 114, - "/N+1": 115, - "@@": 116, - "C-1": 117, - "#N+1": 118, - "B-1": 119, - "+3": 120, - "Cl+3": 121, - "\\NH1": 122, - "Li": 123, - "Li+1": 124, - "PH1": 125, - "18": 126, - "18F": 127, - "@+1": 128, - "3H": 129, - "P@@": 130, - "H0": 131, - "OH0": 132, - "12": 133, - "P@": 134, - "+2": 135, - "@@+1": 136, - "S-1": 137, - "/Br": 138, - "-/": 139, - "\\Cl": 140, - "-/Ring2": 141, - "\\O-1": 142, - "11": 143, - "5I": 144, - "125I": 145, - "11C": 146, - "H3": 147, - "\\N+1": 148, - "-\\": 149, - "/C@@": 150, - "S@+1": 151, - "As": 152, - "/Cl": 153, - "11CH3": 154, - "=Se": 155, - "S@@+1": 156, - "N@+1": 157, - "14": 158, - "-\\Ring2": 159, - "14C": 160, - "\\F": 161, - "/C@": 162, - "Te": 163, - "H2": 164, - "H1-1": 165, - "=O+1": 166, - "N@@+1": 167, - "C+1": 168, - "=S+1": 169, - "Zn": 170, - "/P": 171, - "a+2": 172, - "/I": 173, - "OH1-1": 174, - "Ca+2": 175, - "\\Br": 176, - "Mg": 177, - "Zn+2": 178, - "Al": 179, - "/F": 180, - "Mg+2": 181, - "123": 182, - "123I": 183, - "13": 184, - "I+1": 185, - "/O-1": 186, - "-\\Ring1": 187, - "BH2": 188, - "BH2-1": 189, - "\\I": 190, - "/NH1": 191, - "O+1": 192, - "131": 193, - "131I": 194, - "=14C": 195, - "/S+1": 196, - "=Ring3": 197, - "\\C@@": 198, - "H2+1": 199, - "\\C@": 200, - "Ag": 201, - "=As": 202, - "=Se+1": 203, - "NH2+1": 204, - "SeH1": 205, - "-/Ring1": 206, - "=Te": 207, - "Al+3": 208, - "NaH1": 209, - "=Te+1": 210, - "NH1+1": 211, - "Ag+1": 212, - "H1+1": 213, - "NH1-1": 214, - "\\P": 215, - "14CH2": 216, - "13C": 217, - "14CH1": 218, - "=11C": 219, - "S@@": 220, - "=P@@": 221, - "SiH2": 222, - "H3-1": 223, - "14CH3": 224, - "BH3-1": 225, - "S@": 226, - "=14CH1": 227, - "=PH1": 228, - "=P@": 229, - "=NH1+1": 230, - "\\S+1": 231, - "124": 232, - "CH1-1": 233, - "Sr": 234, - "=Si": 235, - "124I": 236, - "Sr+2": 237, - "#C-1": 238, - "/C-1": 239, - "N@": 240, - "/N-1": 241, - "13CH1": 242, - "/B": 243, - "19": 244, - "Ba+2": 245, - "H4": 246, - "SH1+1": 247, - "Se+1": 248, - "19F": 249, - "/125I": 250, - "P@+1": 251, - "Rb": 252, - "Cl+1": 253, - "SiH4": 254, - "Rb+1": 255, - "=Branch3": 256, - "N@@": 257, - "As+1": 258, - "/Si": 259, - "BH1-1": 260, - "SH1": 261, - "/123I": 262, - "32": 263, - "=Mg": 264, - "H+1": 265, - "\\B": 266, - "SiH1": 267, - "P@@+1": 268, - "-2": 269, - "15": 270, - "17": 271, - "35": 272, - "=13CH1": 273, - "Cs": 274, - "=NH2+1": 275, - "=SH1": 276, - "MgH2": 277, - "32P": 278, - "17F": 279, - "35S": 280, - "Cs+1": 281, - "#11C": 282, - "/131I": 283, - "Bi": 284, - "\\125I": 285, - "=S@@": 286, - "\\S-1": 287, - "6Br": 288, - "7I": 289, - "76Br": 290, - "=B": 291, - "eH1": 292, - "\\N-1": 293, - "18O": 294, - "127I": 295, - "11CH2": 296, - "14C@@H1": 297, - "TeH2": 298, - "15NH1": 299, - "Bi+3": 300, - "/P+1": 301, - "/13C": 302, - "/13CH1": 303, - "0B": 304, - "10B": 305, - "=Al": 306, - "=18O": 307, - "BH0": 308, - "F-1": 309, - "NH3": 310, - "S-2": 311, - "Br+2": 312, - "Cl+2": 313, - "\\Si": 314, - "/S-1": 315, - "=PH2": 316, - "14C@H1": 317, - "NH3+1": 318, - "#14C": 319, - "#O+1": 320, - "-3": 321, - "22": 322, - "4H": 323, - "5Se": 324, - "5Sr+2": 325, - "75Se": 326, - "85Sr+2": 327, - "=B-1": 328, - "=13C": 329, - "@-1": 330, - "Be": 331, - "B@@": 332, - "B@-1": 333, - "Ca": 334, - "CH1": 335, - "I+3": 336, - "KH1": 337, - "OH1+1": 338, - "Ra+2": 339, - "SH1-1": 340, - "\\PH1": 341, - "\\123I": 342, - "=Ca": 343, - "\\CH1-1": 344, - "=S@": 345, - "\\SeH1": 346, - "/SeH1": 347, - "Se-1": 348, - "LiH1": 349, - "18F-1": 350, - "125IH1": 351, - "11CH1": 352, - "TeH1": 353, - "Zn+1": 354, - "Zn-2": 355, - "Al-3": 356, - "13CH3": 357, - "15N": 358, - "Be+2": 359, - "B@@-1": 360, - "#P": 361, - "#S": 362, - "-4": 363, - "/PH1": 364, - "/P@@": 365, - "/As": 366, - "/14C": 367, - "/14CH1": 368, - "2K+1": 369, - "2Rb+1": 370, - "3Se": 371, - "3Ra+2": 372, - "45": 373, - "47": 374, - "42K+1": 375, - "5I-1": 376, - "73Se": 377, - "89": 378, - "82Rb+1": 379, - "=32": 380, - "=32P": 381, - "CH0": 382, - "CH2": 383, - "I+2": 384, - "NH0": 385, - "NH4": 386, - "OH1": 387, - "PH2+1": 388, - "SH0": 389, - "SH2": 390, - "\\3H": 391, - "\\11CH3": 392, - "\\C-1": 393, - "\\Se": 394, - "Si@": 395, - "Si-1": 396, - "SiH1-1": 397, - "SiH3-1": 398, - "/Se": 399, - "Se-2": 400, - "\\NH1-1": 401, - "18FH1": 402, - "125I-1": 403, - "11C@@H1": 404, - "11C-1": 405, - "AsH1": 406, - "As-1": 407, - "14C@@": 408, - "Te-1": 409, - "Mg+1": 410, - "123I-1": 411, - "123Te": 412, - "123IH1": 413, - "135I": 414, - "131I-1": 415, - "Ag-4": 416, - "124I-1": 417, - "76BrH1": 418, - "18OH1": 419, - "22Na+1": 420, - "223Ra+2": 421, - "CaH2": 422, - "45Ca+2": 423, - "47Ca+2": 424, - "89Sr+2": 425, - "=32PH1": 426, - "NH4+1": 427 - }, - "merges": [ - "B r", - "a n", - "c h", - "Br an", - "Bran ch", - "Branch 1", - "= C", - "R i", - "n g", - "Ri ng", - "Ring 1", - "= Branch1", - "Branch 2", - "= O", - "Ring 2", - "H 1", - "C @", - "= N", - "# Branch1", - "C@ @", - "= Branch2", - "C@ H1", - "C@@ H1", - "# Branch2", - "# C", - "C l", - "/ C", - "N H1", - "= Ring1", - "+ 1", - "- 1", - "O -1", - "N +1", - "\\ C", - "# N", - "/ N", - "= Ring2", - "= S", - "=N +1", - "\\ N", - "N a", - "Na +1", - "/ O", - "\\ O", - "Br -1", - "Branch 3", - "\\ S", - "S +1", - "Cl -1", - "I -1", - "/ C@@H1", - "S i", - "/ C@H1", - "/ S", - "=N -1", - "S e", - "= P", - "N -1", - "Ring 3", - "2 H", - "P +1", - "K +1", - "\\ C@@H1", - "\\ C@H1", - "/ N+1", - "@ @", - "C -1", - "# N+1", - "B -1", - "+ 3", - "Cl +3", - "\\ NH1", - "L i", - "Li +1", - "P H1", - "1 8", - "18 F", - "@ +1", - "3 H", - "P @@", - "H 0", - "O H0", - "1 2", - "P @", - "+ 2", - "@@ +1", - "S -1", - "/ Br", - "- /", - "\\ Cl", - "-/ Ring2", - "\\ O-1", - "1 1", - "5 I", - "12 5I", - "11 C", - "H 3", - "\\ N+1", - "- \\", - "/ C@@", - "S @+1", - "A s", - "/ Cl", - "11C H3", - "=S e", - "S @@+1", - "N @+1", - "1 4", - "-\\ Ring2", - "14 C", - "\\ F", - "/ C@", - "T e", - "H 2", - "H1 -1", - "=O +1", - "N @@+1", - "C +1", - "=S +1", - "Z n", - "/ P", - "a +2", - "/ I", - "O H1-1", - "C a+2", - "\\ Br", - "M g", - "Zn +2", - "A l", - "/ F", - "Mg +2", - "12 3", - "123 I", - "1 3", - "I +1", - "/ O-1", - "-\\ Ring1", - "B H2", - "BH2 -1", - "\\ I", - "/ NH1", - "O +1", - "13 1", - "131 I", - "= 14C", - "/ S+1", - "= Ring3", - "\\ C@@", - "H2 +1", - "\\ C@", - "A g", - "= As", - "=Se +1", - "N H2+1", - "Se H1", - "-/ Ring1", - "= Te", - "Al +3", - "Na H1", - "=Te +1", - "NH1 +1", - "Ag +1", - "H1 +1", - "NH1 -1", - "\\ P", - "14C H2", - "13 C", - "14C H1", - "= 11C", - "S @@", - "=P @@", - "Si H2", - "H3 -1", - "14C H3", - "B H3-1", - "S @", - "=14C H1", - "=P H1", - "=P @", - "=N H1+1", - "\\S +1", - "12 4", - "C H1-1", - "S r", - "=S i", - "124 I", - "Sr +2", - "#C -1", - "/C -1", - "N @", - "/N -1", - "13C H1", - "/ B", - "1 9", - "B a+2", - "H 4", - "S H1+1", - "Se +1", - "19 F", - "/ 125I", - "P @+1", - "R b", - "Cl +1", - "Si H4", - "Rb +1", - "= Branch3", - "N @@", - "As +1", - "/ Si", - "B H1-1", - "S H1", - "/ 123I", - "3 2", - "= Mg", - "H +1", - "\\ B", - "Si H1", - "P@@ +1", - "- 2", - "1 5", - "1 7", - "3 5", - "= 13CH1", - "C s", - "=N H2+1", - "=S H1", - "Mg H2", - "32 P", - "17 F", - "35 S", - "Cs +1", - "# 11C", - "/ 131I", - "B i", - "\\ 125I", - "=S @@", - "\\S -1", - "6 Br", - "7 I", - "7 6Br", - "= B", - "e H1", - "\\N -1", - "18 O", - "12 7I", - "11C H2", - "14 C@@H1", - "Te H2", - "15 NH1", - "Bi +3", - "/ P+1", - "/ 13C", - "/ 13CH1", - "0 B", - "1 0B", - "= Al", - "= 18O", - "B H0", - "F -1", - "N H3", - "S -2", - "Br +2", - "Cl +2", - "\\S i", - "/S -1", - "=P H2", - "14 C@H1", - "NH3 +1", - "# 14C", - "# O+1", - "- 3", - "2 2", - "4 H", - "5 Se", - "5 Sr+2", - "7 5Se", - "8 5Sr+2", - "= B-1", - "= 13C", - "@ -1", - "B e", - "B @@", - "B @-1", - "C a", - "C H1", - "I +3", - "K H1", - "O H1+1", - "R a+2", - "S H1-1", - "\\ PH1", - "\\ 123I", - "=C a", - "\\C H1-1", - "=S @", - "\\S eH1", - "/S eH1", - "Se -1", - "Li H1", - "18F -1", - "125I H1", - "11C H1", - "Te H1", - "Zn +1", - "Zn -2", - "Al -3", - "13C H3", - "15 N", - "Be +2", - "B@@ -1", - "# P", - "# S", - "- 4", - "/ PH1", - "/ P@@", - "/ As", - "/ 14C", - "/ 14CH1", - "2 K+1", - "2 Rb+1", - "3 Se", - "3 Ra+2", - "4 5", - "4 7", - "4 2K+1", - "5 I-1", - "7 3Se", - "8 9", - "8 2Rb+1", - "= 32", - "= 32P", - "C H0", - "C H2", - "I +2", - "N H0", - "N H4", - "O H1", - "P H2+1", - "S H0", - "S H2", - "\\ 3H", - "\\ 11CH3", - "\\C -1", - "\\S e", - "Si @", - "Si -1", - "Si H1-1", - "Si H3-1", - "/S e", - "Se -2", - "\\NH1 -1", - "18F H1", - "12 5I-1", - "11 C@@H1", - "11 C-1", - "As H1", - "As -1", - "14 C@@", - "Te -1", - "Mg +1", - "123 I-1", - "123 Te", - "123I H1", - "13 5I", - "131 I-1", - "Ag -4", - "124 I-1", - "76Br H1", - "18O H1", - "22 Na+1", - "22 3Ra+2", - "Ca H2", - "45 Ca+2", - "47 Ca+2", - "89 Sr+2", - "=32 PH1", - "NH4 +1" - ] - } -} \ No newline at end of file diff --git a/models/finetuned/esol/checkpoint_epoch_025/tokenizer_config.json b/models/finetuned/esol/checkpoint_epoch_025/tokenizer_config.json deleted file mode 100644 index 08860954acd34fad07fd77f7635298fa565f3149..0000000000000000000000000000000000000000 --- a/models/finetuned/esol/checkpoint_epoch_025/tokenizer_config.json +++ /dev/null @@ -1,65 +0,0 @@ -{ - "add_prefix_space": false, - "bos_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "cls_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "eos_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "errors": "replace", - "mask_token": { - "__type": "AddedToken", - "content": "", - "lstrip": true, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "model_max_length": 1000000000000000019884624838656, - "name_or_path": "/home/erva/SELFormerMM/data/pretrained_multimodal_chembl36", - "pad_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "sep_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "special_tokens_map_file": null, - "tokenizer_class": "RobertaTokenizer", - "trim_offsets": true, - "unk_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - } -} diff --git a/models/finetuned/esol/checkpoint_epoch_025/vocab.json b/models/finetuned/esol/checkpoint_epoch_025/vocab.json deleted file mode 100644 index f7e4cc22809f4e9035cc450ef189c8a7da8fd03e..0000000000000000000000000000000000000000 --- a/models/finetuned/esol/checkpoint_epoch_025/vocab.json +++ /dev/null @@ -1 +0,0 @@ -{"":0,"":1,"":2,"":3,"":4,"\n":5,"#":6,"+":7,"-":8,".":9,"/":10,"0":11,"1":12,"2":13,"3":14,"4":15,"5":16,"6":17,"7":18,"8":19,"9":20,"=":21,"@":22,"A":23,"B":24,"C":25,"F":26,"H":27,"I":28,"K":29,"L":30,"M":31,"N":32,"O":33,"P":34,"R":35,"S":36,"T":37,"Z":38,"\\":39,"a":40,"b":41,"c":42,"e":43,"g":44,"h":45,"i":46,"l":47,"n":48,"r":49,"s":50,"Br":51,"an":52,"ch":53,"Bran":54,"Branch":55,"Branch1":56,"=C":57,"Ri":58,"ng":59,"Ring":60,"Ring1":61,"=Branch1":62,"Branch2":63,"=O":64,"Ring2":65,"H1":66,"C@":67,"=N":68,"#Branch1":69,"C@@":70,"=Branch2":71,"C@H1":72,"C@@H1":73,"#Branch2":74,"#C":75,"Cl":76,"/C":77,"NH1":78,"=Ring1":79,"+1":80,"-1":81,"O-1":82,"N+1":83,"\\C":84,"#N":85,"/N":86,"=Ring2":87,"=S":88,"=N+1":89,"\\N":90,"Na":91,"Na+1":92,"/O":93,"\\O":94,"Br-1":95,"Branch3":96,"\\S":97,"S+1":98,"Cl-1":99,"I-1":100,"/C@@H1":101,"Si":102,"/C@H1":103,"/S":104,"=N-1":105,"Se":106,"=P":107,"N-1":108,"Ring3":109,"2H":110,"P+1":111,"K+1":112,"\\C@@H1":113,"\\C@H1":114,"/N+1":115,"@@":116,"C-1":117,"#N+1":118,"B-1":119,"+3":120,"Cl+3":121,"\\NH1":122,"Li":123,"Li+1":124,"PH1":125,"18":126,"18F":127,"@+1":128,"3H":129,"P@@":130,"H0":131,"OH0":132,"12":133,"P@":134,"+2":135,"@@+1":136,"S-1":137,"/Br":138,"-/":139,"\\Cl":140,"-/Ring2":141,"\\O-1":142,"11":143,"5I":144,"125I":145,"11C":146,"H3":147,"\\N+1":148,"-\\":149,"/C@@":150,"S@+1":151,"As":152,"/Cl":153,"11CH3":154,"=Se":155,"S@@+1":156,"N@+1":157,"14":158,"-\\Ring2":159,"14C":160,"\\F":161,"/C@":162,"Te":163,"H2":164,"H1-1":165,"=O+1":166,"N@@+1":167,"C+1":168,"=S+1":169,"Zn":170,"/P":171,"a+2":172,"/I":173,"OH1-1":174,"Ca+2":175,"\\Br":176,"Mg":177,"Zn+2":178,"Al":179,"/F":180,"Mg+2":181,"123":182,"123I":183,"13":184,"I+1":185,"/O-1":186,"-\\Ring1":187,"BH2":188,"BH2-1":189,"\\I":190,"/NH1":191,"O+1":192,"131":193,"131I":194,"=14C":195,"/S+1":196,"=Ring3":197,"\\C@@":198,"H2+1":199,"\\C@":200,"Ag":201,"=As":202,"=Se+1":203,"NH2+1":204,"SeH1":205,"-/Ring1":206,"=Te":207,"Al+3":208,"NaH1":209,"=Te+1":210,"NH1+1":211,"Ag+1":212,"H1+1":213,"NH1-1":214,"\\P":215,"14CH2":216,"13C":217,"14CH1":218,"=11C":219,"S@@":220,"=P@@":221,"SiH2":222,"H3-1":223,"14CH3":224,"BH3-1":225,"S@":226,"=14CH1":227,"=PH1":228,"=P@":229,"=NH1+1":230,"\\S+1":231,"124":232,"CH1-1":233,"Sr":234,"=Si":235,"124I":236,"Sr+2":237,"#C-1":238,"/C-1":239,"N@":240,"/N-1":241,"13CH1":242,"/B":243,"19":244,"Ba+2":245,"H4":246,"SH1+1":247,"Se+1":248,"19F":249,"/125I":250,"P@+1":251,"Rb":252,"Cl+1":253,"SiH4":254,"Rb+1":255,"=Branch3":256,"N@@":257,"As+1":258,"/Si":259,"BH1-1":260,"SH1":261,"/123I":262,"32":263,"=Mg":264,"H+1":265,"\\B":266,"SiH1":267,"P@@+1":268,"-2":269,"15":270,"17":271,"35":272,"=13CH1":273,"Cs":274,"=NH2+1":275,"=SH1":276,"MgH2":277,"32P":278,"17F":279,"35S":280,"Cs+1":281,"#11C":282,"/131I":283,"Bi":284,"\\125I":285,"=S@@":286,"\\S-1":287,"6Br":288,"7I":289,"76Br":290,"=B":291,"eH1":292,"\\N-1":293,"18O":294,"127I":295,"11CH2":296,"14C@@H1":297,"TeH2":298,"15NH1":299,"Bi+3":300,"/P+1":301,"/13C":302,"/13CH1":303,"0B":304,"10B":305,"=Al":306,"=18O":307,"BH0":308,"F-1":309,"NH3":310,"S-2":311,"Br+2":312,"Cl+2":313,"\\Si":314,"/S-1":315,"=PH2":316,"14C@H1":317,"NH3+1":318,"#14C":319,"#O+1":320,"-3":321,"22":322,"4H":323,"5Se":324,"5Sr+2":325,"75Se":326,"85Sr+2":327,"=B-1":328,"=13C":329,"@-1":330,"Be":331,"B@@":332,"B@-1":333,"Ca":334,"CH1":335,"I+3":336,"KH1":337,"OH1+1":338,"Ra+2":339,"SH1-1":340,"\\PH1":341,"\\123I":342,"=Ca":343,"\\CH1-1":344,"=S@":345,"\\SeH1":346,"/SeH1":347,"Se-1":348,"LiH1":349,"18F-1":350,"125IH1":351,"11CH1":352,"TeH1":353,"Zn+1":354,"Zn-2":355,"Al-3":356,"13CH3":357,"15N":358,"Be+2":359,"B@@-1":360,"#P":361,"#S":362,"-4":363,"/PH1":364,"/P@@":365,"/As":366,"/14C":367,"/14CH1":368,"2K+1":369,"2Rb+1":370,"3Se":371,"3Ra+2":372,"45":373,"47":374,"42K+1":375,"5I-1":376,"73Se":377,"89":378,"82Rb+1":379,"=32":380,"=32P":381,"CH0":382,"CH2":383,"I+2":384,"NH0":385,"NH4":386,"OH1":387,"PH2+1":388,"SH0":389,"SH2":390,"\\3H":391,"\\11CH3":392,"\\C-1":393,"\\Se":394,"Si@":395,"Si-1":396,"SiH1-1":397,"SiH3-1":398,"/Se":399,"Se-2":400,"\\NH1-1":401,"18FH1":402,"125I-1":403,"11C@@H1":404,"11C-1":405,"AsH1":406,"As-1":407,"14C@@":408,"Te-1":409,"Mg+1":410,"123I-1":411,"123Te":412,"123IH1":413,"135I":414,"131I-1":415,"Ag-4":416,"124I-1":417,"76BrH1":418,"18OH1":419,"22Na+1":420,"223Ra+2":421,"CaH2":422,"45Ca+2":423,"47Ca+2":424,"89Sr+2":425,"=32PH1":426,"NH4+1":427} \ No newline at end of file diff --git a/models/finetuned/esol/checkpoint_epoch_050/config.json b/models/finetuned/esol/checkpoint_epoch_050/config.json deleted file mode 100644 index 3811e21539577b37e06313eab31ec11e53f0cbbc..0000000000000000000000000000000000000000 --- a/models/finetuned/esol/checkpoint_epoch_050/config.json +++ /dev/null @@ -1,27 +0,0 @@ -{ - "_name_or_path": "/home/erva/SELFormerMM/data/pretrained_multimodal_chembl36", - "architectures": [ - "RobertaForMaskedLM" - ], - "attention_probs_dropout_prob": 0.1, - "bos_token_id": 0, - "classifier_dropout": null, - "eos_token_id": 2, - "hidden_act": "gelu", - "hidden_dropout_prob": 0.1, - "hidden_size": 768, - "initializer_range": 0.02, - "intermediate_size": 3072, - "layer_norm_eps": 1e-12, - "max_position_embeddings": 514, - "model_type": "roberta", - "num_attention_heads": 4, - "num_hidden_layers": 12, - "pad_token_id": 1, - "position_embedding_type": "absolute", - "torch_dtype": "float32", - "transformers_version": "4.26.1", - "type_vocab_size": 1, - "use_cache": true, - "vocab_size": 800 -} diff --git a/models/finetuned/esol/checkpoint_epoch_050/merges.txt b/models/finetuned/esol/checkpoint_epoch_050/merges.txt deleted file mode 100644 index 7cd5ec62809503c23f18c80afc0ba3bdf9d253d0..0000000000000000000000000000000000000000 --- a/models/finetuned/esol/checkpoint_epoch_050/merges.txt +++ /dev/null @@ -1,378 +0,0 @@ -#version: 0.2 - Trained by `huggingface/tokenizers` -B r -a n -c h -Br an -Bran ch -Branch 1 -= C -R i -n g -Ri ng -Ring 1 -= Branch1 -Branch 2 -= O -Ring 2 -H 1 -C @ -= N -# Branch1 -C@ @ -= Branch2 -C@ H1 -C@@ H1 -# Branch2 -# C -C l -/ C -N H1 -= Ring1 -+ 1 -- 1 -O -1 -N +1 -\ C -# N -/ N -= Ring2 -= S -=N +1 -\ N -N a -Na +1 -/ O -\ O -Br -1 -Branch 3 -\ S -S +1 -Cl -1 -I -1 -/ C@@H1 -S i -/ C@H1 -/ S -=N -1 -S e -= P -N -1 -Ring 3 -2 H -P +1 -K +1 -\ C@@H1 -\ C@H1 -/ N+1 -@ @ -C -1 -# N+1 -B -1 -+ 3 -Cl +3 -\ NH1 -L i -Li +1 -P H1 -1 8 -18 F -@ +1 -3 H -P @@ -H 0 -O H0 -1 2 -P @ -+ 2 -@@ +1 -S -1 -/ Br -- / -\ Cl --/ Ring2 -\ O-1 -1 1 -5 I -12 5I -11 C -H 3 -\ N+1 -- \ -/ C@@ -S @+1 -A s -/ Cl -11C H3 -=S e -S @@+1 -N @+1 -1 4 --\ Ring2 -14 C -\ F -/ C@ -T e -H 2 -H1 -1 -=O +1 -N @@+1 -C +1 -=S +1 -Z n -/ P -a +2 -/ I -O H1-1 -C a+2 -\ Br -M g -Zn +2 -A l -/ F -Mg +2 -12 3 -123 I -1 3 -I +1 -/ O-1 --\ Ring1 -B H2 -BH2 -1 -\ I -/ NH1 -O +1 -13 1 -131 I -= 14C -/ S+1 -= Ring3 -\ C@@ -H2 +1 -\ C@ -A g -= As -=Se +1 -N H2+1 -Se H1 --/ Ring1 -= Te -Al +3 -Na H1 -=Te +1 -NH1 +1 -Ag +1 -H1 +1 -NH1 -1 -\ P -14C H2 -13 C -14C H1 -= 11C -S @@ -=P @@ -Si H2 -H3 -1 -14C H3 -B H3-1 -S @ -=14C H1 -=P H1 -=P @ -=N H1+1 -\S +1 -12 4 -C H1-1 -S r -=S i -124 I -Sr +2 -#C -1 -/C -1 -N @ -/N -1 -13C H1 -/ B -1 9 -B a+2 -H 4 -S H1+1 -Se +1 -19 F -/ 125I -P @+1 -R b -Cl +1 -Si H4 -Rb +1 -= Branch3 -N @@ -As +1 -/ Si -B H1-1 -S H1 -/ 123I -3 2 -= Mg -H +1 -\ B -Si H1 -P@@ +1 -- 2 -1 5 -1 7 -3 5 -= 13CH1 -C s -=N H2+1 -=S H1 -Mg H2 -32 P -17 F -35 S -Cs +1 -# 11C -/ 131I -B i -\ 125I -=S @@ -\S -1 -6 Br -7 I -7 6Br -= B -e H1 -\N -1 -18 O -12 7I -11C H2 -14 C@@H1 -Te H2 -15 NH1 -Bi +3 -/ P+1 -/ 13C -/ 13CH1 -0 B -1 0B -= Al -= 18O -B H0 -F -1 -N H3 -S -2 -Br +2 -Cl +2 -\S i -/S -1 -=P H2 -14 C@H1 -NH3 +1 -# 14C -# O+1 -- 3 -2 2 -4 H -5 Se -5 Sr+2 -7 5Se -8 5Sr+2 -= B-1 -= 13C -@ -1 -B e -B @@ -B @-1 -C a -C H1 -I +3 -K H1 -O H1+1 -R a+2 -S H1-1 -\ PH1 -\ 123I -=C a -\C H1-1 -=S @ -\S eH1 -/S eH1 -Se -1 -Li H1 -18F -1 -125I H1 -11C H1 -Te H1 -Zn +1 -Zn -2 -Al -3 -13C H3 -15 N -Be +2 -B@@ -1 -# P -# S -- 4 -/ PH1 -/ P@@ -/ As -/ 14C -/ 14CH1 -2 K+1 -2 Rb+1 -3 Se -3 Ra+2 -4 5 -4 7 -4 2K+1 -5 I-1 -7 3Se -8 9 -8 2Rb+1 -= 32 -= 32P -C H0 -C H2 -I +2 -N H0 -N H4 -O H1 -P H2+1 -S H0 -S H2 -\ 3H -\ 11CH3 -\C -1 -\S e -Si @ -Si -1 -Si H1-1 -Si H3-1 -/S e -Se -2 -\NH1 -1 -18F H1 -12 5I-1 -11 C@@H1 -11 C-1 -As H1 -As -1 -14 C@@ -Te -1 -Mg +1 -123 I-1 -123 Te -123I H1 -13 5I -131 I-1 -Ag -4 -124 I-1 -76Br H1 -18O H1 -22 Na+1 -22 3Ra+2 -Ca H2 -45 Ca+2 -47 Ca+2 -89 Sr+2 -=32 PH1 -NH4 +1 diff --git a/models/finetuned/esol/checkpoint_epoch_050/model.pt b/models/finetuned/esol/checkpoint_epoch_050/model.pt deleted file mode 100644 index c7053f6e4ecac583450341274eaa264133d4cdf2..0000000000000000000000000000000000000000 --- a/models/finetuned/esol/checkpoint_epoch_050/model.pt +++ /dev/null @@ -1,3 +0,0 @@ -version https://git-lfs.github.com/spec/v1 -oid sha256:1cea5584251eff6c83eecaee68088f28a1b3cc0048d8380c6ed78beafcb5d031 -size 1022843005 diff --git a/models/finetuned/esol/checkpoint_epoch_050/special_tokens_map.json b/models/finetuned/esol/checkpoint_epoch_050/special_tokens_map.json deleted file mode 100644 index 06a55849fa69a91e7179d909e373179ff7467d8c..0000000000000000000000000000000000000000 --- a/models/finetuned/esol/checkpoint_epoch_050/special_tokens_map.json +++ /dev/null @@ -1,51 +0,0 @@ -{ - "bos_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "cls_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "eos_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "mask_token": { - "content": "", - "lstrip": true, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "pad_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "sep_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "unk_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - } -} diff --git a/models/finetuned/esol/checkpoint_epoch_050/tokenizer.json b/models/finetuned/esol/checkpoint_epoch_050/tokenizer.json deleted file mode 100644 index 3b64b273e6fa9799e2d8375722b9e815de9ebb8f..0000000000000000000000000000000000000000 --- a/models/finetuned/esol/checkpoint_epoch_050/tokenizer.json +++ /dev/null @@ -1,909 +0,0 @@ -{ - "version": "1.0", - "truncation": { - "direction": "Right", - "max_length": 128, - "strategy": "LongestFirst", - "stride": 0 - }, - "padding": { - "strategy": { - "Fixed": 128 - }, - "direction": "Right", - "pad_to_multiple_of": null, - "pad_id": 3, - "pad_type_id": 0, - "pad_token": "" - }, - "added_tokens": [ - { - "id": 0, - "content": "", - "single_word": false, - "lstrip": false, - "rstrip": false, - "normalized": true, - "special": true - }, - { - "id": 1, - "content": "", - "single_word": false, - "lstrip": false, - "rstrip": false, - "normalized": true, - "special": true - }, - { - "id": 2, - "content": "", - "single_word": false, - "lstrip": false, - "rstrip": false, - "normalized": true, - "special": true - }, - { - "id": 3, - "content": "", - "single_word": false, - "lstrip": false, - "rstrip": false, - "normalized": true, - "special": true - }, - { - "id": 4, - "content": "", - "single_word": false, - "lstrip": true, - "rstrip": false, - "normalized": true, - "special": true - } - ], - "normalizer": null, - "pre_tokenizer": { - "type": "ByteLevel", - "add_prefix_space": false, - "trim_offsets": true, - "use_regex": true - }, - "post_processor": { - "type": "RobertaProcessing", - "sep": [ - "", - 2 - ], - "cls": [ - "", - 1 - ], - "trim_offsets": true, - "add_prefix_space": false - }, - "decoder": { - "type": "ByteLevel", - "add_prefix_space": true, - "trim_offsets": true, - "use_regex": true - }, - "model": { - "type": "BPE", - "dropout": null, - "unk_token": null, - "continuing_subword_prefix": "", - "end_of_word_suffix": "", - "fuse_unk": false, - "vocab": { - "": 0, - "": 1, - "": 2, - "": 3, - "": 4, - "\n": 5, - "#": 6, - "+": 7, - "-": 8, - ".": 9, - "/": 10, - "0": 11, - "1": 12, - "2": 13, - "3": 14, - "4": 15, - "5": 16, - "6": 17, - "7": 18, - "8": 19, - "9": 20, - "=": 21, - "@": 22, - "A": 23, - "B": 24, - "C": 25, - "F": 26, - "H": 27, - "I": 28, - "K": 29, - "L": 30, - "M": 31, - "N": 32, - "O": 33, - "P": 34, - "R": 35, - "S": 36, - "T": 37, - "Z": 38, - "\\": 39, - "a": 40, - "b": 41, - "c": 42, - "e": 43, - "g": 44, - "h": 45, - "i": 46, - "l": 47, - "n": 48, - "r": 49, - "s": 50, - "Br": 51, - "an": 52, - "ch": 53, - "Bran": 54, - "Branch": 55, - "Branch1": 56, - "=C": 57, - "Ri": 58, - "ng": 59, - "Ring": 60, - "Ring1": 61, - "=Branch1": 62, - "Branch2": 63, - "=O": 64, - "Ring2": 65, - "H1": 66, - "C@": 67, - "=N": 68, - "#Branch1": 69, - "C@@": 70, - "=Branch2": 71, - "C@H1": 72, - "C@@H1": 73, - "#Branch2": 74, - "#C": 75, - "Cl": 76, - "/C": 77, - "NH1": 78, - "=Ring1": 79, - "+1": 80, - "-1": 81, - "O-1": 82, - "N+1": 83, - "\\C": 84, - "#N": 85, - "/N": 86, - "=Ring2": 87, - "=S": 88, - "=N+1": 89, - "\\N": 90, - "Na": 91, - "Na+1": 92, - "/O": 93, - "\\O": 94, - "Br-1": 95, - "Branch3": 96, - "\\S": 97, - "S+1": 98, - "Cl-1": 99, - "I-1": 100, - "/C@@H1": 101, - "Si": 102, - "/C@H1": 103, - "/S": 104, - "=N-1": 105, - "Se": 106, - "=P": 107, - "N-1": 108, - "Ring3": 109, - "2H": 110, - "P+1": 111, - "K+1": 112, - "\\C@@H1": 113, - "\\C@H1": 114, - "/N+1": 115, - "@@": 116, - "C-1": 117, - "#N+1": 118, - "B-1": 119, - "+3": 120, - "Cl+3": 121, - "\\NH1": 122, - "Li": 123, - "Li+1": 124, - "PH1": 125, - "18": 126, - "18F": 127, - "@+1": 128, - "3H": 129, - "P@@": 130, - "H0": 131, - "OH0": 132, - "12": 133, - "P@": 134, - "+2": 135, - "@@+1": 136, - "S-1": 137, - "/Br": 138, - "-/": 139, - "\\Cl": 140, - "-/Ring2": 141, - "\\O-1": 142, - "11": 143, - "5I": 144, - "125I": 145, - "11C": 146, - "H3": 147, - "\\N+1": 148, - "-\\": 149, - "/C@@": 150, - "S@+1": 151, - "As": 152, - "/Cl": 153, - "11CH3": 154, - "=Se": 155, - "S@@+1": 156, - "N@+1": 157, - "14": 158, - "-\\Ring2": 159, - "14C": 160, - "\\F": 161, - "/C@": 162, - "Te": 163, - "H2": 164, - "H1-1": 165, - "=O+1": 166, - "N@@+1": 167, - "C+1": 168, - "=S+1": 169, - "Zn": 170, - "/P": 171, - "a+2": 172, - "/I": 173, - "OH1-1": 174, - "Ca+2": 175, - "\\Br": 176, - "Mg": 177, - "Zn+2": 178, - "Al": 179, - "/F": 180, - "Mg+2": 181, - "123": 182, - "123I": 183, - "13": 184, - "I+1": 185, - "/O-1": 186, - "-\\Ring1": 187, - "BH2": 188, - "BH2-1": 189, - "\\I": 190, - "/NH1": 191, - "O+1": 192, - "131": 193, - "131I": 194, - "=14C": 195, - "/S+1": 196, - "=Ring3": 197, - "\\C@@": 198, - "H2+1": 199, - "\\C@": 200, - "Ag": 201, - "=As": 202, - "=Se+1": 203, - "NH2+1": 204, - "SeH1": 205, - "-/Ring1": 206, - "=Te": 207, - "Al+3": 208, - "NaH1": 209, - "=Te+1": 210, - "NH1+1": 211, - "Ag+1": 212, - "H1+1": 213, - "NH1-1": 214, - "\\P": 215, - "14CH2": 216, - "13C": 217, - "14CH1": 218, - "=11C": 219, - "S@@": 220, - "=P@@": 221, - "SiH2": 222, - "H3-1": 223, - "14CH3": 224, - "BH3-1": 225, - "S@": 226, - "=14CH1": 227, - "=PH1": 228, - "=P@": 229, - "=NH1+1": 230, - "\\S+1": 231, - "124": 232, - "CH1-1": 233, - "Sr": 234, - "=Si": 235, - "124I": 236, - "Sr+2": 237, - "#C-1": 238, - "/C-1": 239, - "N@": 240, - "/N-1": 241, - "13CH1": 242, - "/B": 243, - "19": 244, - "Ba+2": 245, - "H4": 246, - "SH1+1": 247, - "Se+1": 248, - "19F": 249, - "/125I": 250, - "P@+1": 251, - "Rb": 252, - "Cl+1": 253, - "SiH4": 254, - "Rb+1": 255, - "=Branch3": 256, - "N@@": 257, - "As+1": 258, - "/Si": 259, - "BH1-1": 260, - "SH1": 261, - "/123I": 262, - "32": 263, - "=Mg": 264, - "H+1": 265, - "\\B": 266, - "SiH1": 267, - "P@@+1": 268, - "-2": 269, - "15": 270, - "17": 271, - "35": 272, - "=13CH1": 273, - "Cs": 274, - "=NH2+1": 275, - "=SH1": 276, - "MgH2": 277, - "32P": 278, - "17F": 279, - "35S": 280, - "Cs+1": 281, - "#11C": 282, - "/131I": 283, - "Bi": 284, - "\\125I": 285, - "=S@@": 286, - "\\S-1": 287, - "6Br": 288, - "7I": 289, - "76Br": 290, - "=B": 291, - "eH1": 292, - "\\N-1": 293, - "18O": 294, - "127I": 295, - "11CH2": 296, - "14C@@H1": 297, - "TeH2": 298, - "15NH1": 299, - "Bi+3": 300, - "/P+1": 301, - "/13C": 302, - "/13CH1": 303, - "0B": 304, - "10B": 305, - "=Al": 306, - "=18O": 307, - "BH0": 308, - "F-1": 309, - "NH3": 310, - "S-2": 311, - "Br+2": 312, - "Cl+2": 313, - "\\Si": 314, - "/S-1": 315, - "=PH2": 316, - "14C@H1": 317, - "NH3+1": 318, - "#14C": 319, - "#O+1": 320, - "-3": 321, - "22": 322, - "4H": 323, - "5Se": 324, - "5Sr+2": 325, - "75Se": 326, - "85Sr+2": 327, - "=B-1": 328, - "=13C": 329, - "@-1": 330, - "Be": 331, - "B@@": 332, - "B@-1": 333, - "Ca": 334, - "CH1": 335, - "I+3": 336, - "KH1": 337, - "OH1+1": 338, - "Ra+2": 339, - "SH1-1": 340, - "\\PH1": 341, - "\\123I": 342, - "=Ca": 343, - "\\CH1-1": 344, - "=S@": 345, - "\\SeH1": 346, - "/SeH1": 347, - "Se-1": 348, - "LiH1": 349, - "18F-1": 350, - "125IH1": 351, - "11CH1": 352, - "TeH1": 353, - "Zn+1": 354, - "Zn-2": 355, - "Al-3": 356, - "13CH3": 357, - "15N": 358, - "Be+2": 359, - "B@@-1": 360, - "#P": 361, - "#S": 362, - "-4": 363, - "/PH1": 364, - "/P@@": 365, - "/As": 366, - "/14C": 367, - "/14CH1": 368, - "2K+1": 369, - "2Rb+1": 370, - "3Se": 371, - "3Ra+2": 372, - "45": 373, - "47": 374, - "42K+1": 375, - "5I-1": 376, - "73Se": 377, - "89": 378, - "82Rb+1": 379, - "=32": 380, - "=32P": 381, - "CH0": 382, - "CH2": 383, - "I+2": 384, - "NH0": 385, - "NH4": 386, - "OH1": 387, - "PH2+1": 388, - "SH0": 389, - "SH2": 390, - "\\3H": 391, - "\\11CH3": 392, - "\\C-1": 393, - "\\Se": 394, - "Si@": 395, - "Si-1": 396, - "SiH1-1": 397, - "SiH3-1": 398, - "/Se": 399, - "Se-2": 400, - "\\NH1-1": 401, - "18FH1": 402, - "125I-1": 403, - "11C@@H1": 404, - "11C-1": 405, - "AsH1": 406, - "As-1": 407, - "14C@@": 408, - "Te-1": 409, - "Mg+1": 410, - "123I-1": 411, - "123Te": 412, - "123IH1": 413, - "135I": 414, - "131I-1": 415, - "Ag-4": 416, - "124I-1": 417, - "76BrH1": 418, - "18OH1": 419, - "22Na+1": 420, - "223Ra+2": 421, - "CaH2": 422, - "45Ca+2": 423, - "47Ca+2": 424, - "89Sr+2": 425, - "=32PH1": 426, - "NH4+1": 427 - }, - "merges": [ - "B r", - "a n", - "c h", - "Br an", - "Bran ch", - "Branch 1", - "= C", - "R i", - "n g", - "Ri ng", - "Ring 1", - "= Branch1", - "Branch 2", - "= O", - "Ring 2", - "H 1", - "C @", - "= N", - "# Branch1", - "C@ @", - "= Branch2", - "C@ H1", - "C@@ H1", - "# Branch2", - "# C", - "C l", - "/ C", - "N H1", - "= Ring1", - "+ 1", - "- 1", - "O -1", - "N +1", - "\\ C", - "# N", - "/ N", - "= Ring2", - "= S", - "=N +1", - "\\ N", - "N a", - "Na +1", - "/ O", - "\\ O", - "Br -1", - "Branch 3", - "\\ S", - "S +1", - "Cl -1", - "I -1", - "/ C@@H1", - "S i", - "/ C@H1", - "/ S", - "=N -1", - "S e", - "= P", - "N -1", - "Ring 3", - "2 H", - "P +1", - "K +1", - "\\ C@@H1", - "\\ C@H1", - "/ N+1", - "@ @", - "C -1", - "# N+1", - "B -1", - "+ 3", - "Cl +3", - "\\ NH1", - "L i", - "Li +1", - "P H1", - "1 8", - "18 F", - "@ +1", - "3 H", - "P @@", - "H 0", - "O H0", - "1 2", - "P @", - "+ 2", - "@@ +1", - "S -1", - "/ Br", - "- /", - "\\ Cl", - "-/ Ring2", - "\\ O-1", - "1 1", - "5 I", - "12 5I", - "11 C", - "H 3", - "\\ N+1", - "- \\", - "/ C@@", - "S @+1", - "A s", - "/ Cl", - "11C H3", - "=S e", - "S @@+1", - "N @+1", - "1 4", - "-\\ Ring2", - "14 C", - "\\ F", - "/ C@", - "T e", - "H 2", - "H1 -1", - "=O +1", - "N @@+1", - "C +1", - "=S +1", - "Z n", - "/ P", - "a +2", - "/ I", - "O H1-1", - "C a+2", - "\\ Br", - "M g", - "Zn +2", - "A l", - "/ F", - "Mg +2", - "12 3", - "123 I", - "1 3", - "I +1", - "/ O-1", - "-\\ Ring1", - "B H2", - "BH2 -1", - "\\ I", - "/ NH1", - "O +1", - "13 1", - "131 I", - "= 14C", - "/ S+1", - "= Ring3", - "\\ C@@", - "H2 +1", - "\\ C@", - "A g", - "= As", - "=Se +1", - "N H2+1", - "Se H1", - "-/ Ring1", - "= Te", - "Al +3", - "Na H1", - "=Te +1", - "NH1 +1", - "Ag +1", - "H1 +1", - "NH1 -1", - "\\ P", - "14C H2", - "13 C", - "14C H1", - "= 11C", - "S @@", - "=P @@", - "Si H2", - "H3 -1", - "14C H3", - "B H3-1", - "S @", - "=14C H1", - "=P H1", - "=P @", - "=N H1+1", - "\\S +1", - "12 4", - "C H1-1", - "S r", - "=S i", - "124 I", - "Sr +2", - "#C -1", - "/C -1", - "N @", - "/N -1", - "13C H1", - "/ B", - "1 9", - "B a+2", - "H 4", - "S H1+1", - "Se +1", - "19 F", - "/ 125I", - "P @+1", - "R b", - "Cl +1", - "Si H4", - "Rb +1", - "= Branch3", - "N @@", - "As +1", - "/ Si", - "B H1-1", - "S H1", - "/ 123I", - "3 2", - "= Mg", - "H +1", - "\\ B", - "Si H1", - "P@@ +1", - "- 2", - "1 5", - "1 7", - "3 5", - "= 13CH1", - "C s", - "=N H2+1", - "=S H1", - "Mg H2", - "32 P", - "17 F", - "35 S", - "Cs +1", - "# 11C", - "/ 131I", - "B i", - "\\ 125I", - "=S @@", - "\\S -1", - "6 Br", - "7 I", - "7 6Br", - "= B", - "e H1", - "\\N -1", - "18 O", - "12 7I", - "11C H2", - "14 C@@H1", - "Te H2", - "15 NH1", - "Bi +3", - "/ P+1", - "/ 13C", - "/ 13CH1", - "0 B", - "1 0B", - "= Al", - "= 18O", - "B H0", - "F -1", - "N H3", - "S -2", - "Br +2", - "Cl +2", - "\\S i", - "/S -1", - "=P H2", - "14 C@H1", - "NH3 +1", - "# 14C", - "# O+1", - "- 3", - "2 2", - "4 H", - "5 Se", - "5 Sr+2", - "7 5Se", - "8 5Sr+2", - "= B-1", - "= 13C", - "@ -1", - "B e", - "B @@", - "B @-1", - "C a", - "C H1", - "I +3", - "K H1", - "O H1+1", - "R a+2", - "S H1-1", - "\\ PH1", - "\\ 123I", - "=C a", - "\\C H1-1", - "=S @", - "\\S eH1", - "/S eH1", - "Se -1", - "Li H1", - "18F -1", - "125I H1", - "11C H1", - "Te H1", - "Zn +1", - "Zn -2", - "Al -3", - "13C H3", - "15 N", - "Be +2", - "B@@ -1", - "# P", - "# S", - "- 4", - "/ PH1", - "/ P@@", - "/ As", - "/ 14C", - "/ 14CH1", - "2 K+1", - "2 Rb+1", - "3 Se", - "3 Ra+2", - "4 5", - "4 7", - "4 2K+1", - "5 I-1", - "7 3Se", - "8 9", - "8 2Rb+1", - "= 32", - "= 32P", - "C H0", - "C H2", - "I +2", - "N H0", - "N H4", - "O H1", - "P H2+1", - "S H0", - "S H2", - "\\ 3H", - "\\ 11CH3", - "\\C -1", - "\\S e", - "Si @", - "Si -1", - "Si H1-1", - "Si H3-1", - "/S e", - "Se -2", - "\\NH1 -1", - "18F H1", - "12 5I-1", - "11 C@@H1", - "11 C-1", - "As H1", - "As -1", - "14 C@@", - "Te -1", - "Mg +1", - "123 I-1", - "123 Te", - "123I H1", - "13 5I", - "131 I-1", - "Ag -4", - "124 I-1", - "76Br H1", - "18O H1", - "22 Na+1", - "22 3Ra+2", - "Ca H2", - "45 Ca+2", - "47 Ca+2", - "89 Sr+2", - "=32 PH1", - "NH4 +1" - ] - } -} \ No newline at end of file diff --git a/models/finetuned/esol/checkpoint_epoch_050/tokenizer_config.json b/models/finetuned/esol/checkpoint_epoch_050/tokenizer_config.json deleted file mode 100644 index 08860954acd34fad07fd77f7635298fa565f3149..0000000000000000000000000000000000000000 --- a/models/finetuned/esol/checkpoint_epoch_050/tokenizer_config.json +++ /dev/null @@ -1,65 +0,0 @@ -{ - "add_prefix_space": false, - "bos_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "cls_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "eos_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "errors": "replace", - "mask_token": { - "__type": "AddedToken", - "content": "", - "lstrip": true, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "model_max_length": 1000000000000000019884624838656, - "name_or_path": "/home/erva/SELFormerMM/data/pretrained_multimodal_chembl36", - "pad_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "sep_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "special_tokens_map_file": null, - "tokenizer_class": "RobertaTokenizer", - "trim_offsets": true, - "unk_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - } -} diff --git a/models/finetuned/esol/checkpoint_epoch_050/vocab.json b/models/finetuned/esol/checkpoint_epoch_050/vocab.json deleted file mode 100644 index f7e4cc22809f4e9035cc450ef189c8a7da8fd03e..0000000000000000000000000000000000000000 --- a/models/finetuned/esol/checkpoint_epoch_050/vocab.json +++ /dev/null @@ -1 +0,0 @@ -{"":0,"":1,"":2,"":3,"":4,"\n":5,"#":6,"+":7,"-":8,".":9,"/":10,"0":11,"1":12,"2":13,"3":14,"4":15,"5":16,"6":17,"7":18,"8":19,"9":20,"=":21,"@":22,"A":23,"B":24,"C":25,"F":26,"H":27,"I":28,"K":29,"L":30,"M":31,"N":32,"O":33,"P":34,"R":35,"S":36,"T":37,"Z":38,"\\":39,"a":40,"b":41,"c":42,"e":43,"g":44,"h":45,"i":46,"l":47,"n":48,"r":49,"s":50,"Br":51,"an":52,"ch":53,"Bran":54,"Branch":55,"Branch1":56,"=C":57,"Ri":58,"ng":59,"Ring":60,"Ring1":61,"=Branch1":62,"Branch2":63,"=O":64,"Ring2":65,"H1":66,"C@":67,"=N":68,"#Branch1":69,"C@@":70,"=Branch2":71,"C@H1":72,"C@@H1":73,"#Branch2":74,"#C":75,"Cl":76,"/C":77,"NH1":78,"=Ring1":79,"+1":80,"-1":81,"O-1":82,"N+1":83,"\\C":84,"#N":85,"/N":86,"=Ring2":87,"=S":88,"=N+1":89,"\\N":90,"Na":91,"Na+1":92,"/O":93,"\\O":94,"Br-1":95,"Branch3":96,"\\S":97,"S+1":98,"Cl-1":99,"I-1":100,"/C@@H1":101,"Si":102,"/C@H1":103,"/S":104,"=N-1":105,"Se":106,"=P":107,"N-1":108,"Ring3":109,"2H":110,"P+1":111,"K+1":112,"\\C@@H1":113,"\\C@H1":114,"/N+1":115,"@@":116,"C-1":117,"#N+1":118,"B-1":119,"+3":120,"Cl+3":121,"\\NH1":122,"Li":123,"Li+1":124,"PH1":125,"18":126,"18F":127,"@+1":128,"3H":129,"P@@":130,"H0":131,"OH0":132,"12":133,"P@":134,"+2":135,"@@+1":136,"S-1":137,"/Br":138,"-/":139,"\\Cl":140,"-/Ring2":141,"\\O-1":142,"11":143,"5I":144,"125I":145,"11C":146,"H3":147,"\\N+1":148,"-\\":149,"/C@@":150,"S@+1":151,"As":152,"/Cl":153,"11CH3":154,"=Se":155,"S@@+1":156,"N@+1":157,"14":158,"-\\Ring2":159,"14C":160,"\\F":161,"/C@":162,"Te":163,"H2":164,"H1-1":165,"=O+1":166,"N@@+1":167,"C+1":168,"=S+1":169,"Zn":170,"/P":171,"a+2":172,"/I":173,"OH1-1":174,"Ca+2":175,"\\Br":176,"Mg":177,"Zn+2":178,"Al":179,"/F":180,"Mg+2":181,"123":182,"123I":183,"13":184,"I+1":185,"/O-1":186,"-\\Ring1":187,"BH2":188,"BH2-1":189,"\\I":190,"/NH1":191,"O+1":192,"131":193,"131I":194,"=14C":195,"/S+1":196,"=Ring3":197,"\\C@@":198,"H2+1":199,"\\C@":200,"Ag":201,"=As":202,"=Se+1":203,"NH2+1":204,"SeH1":205,"-/Ring1":206,"=Te":207,"Al+3":208,"NaH1":209,"=Te+1":210,"NH1+1":211,"Ag+1":212,"H1+1":213,"NH1-1":214,"\\P":215,"14CH2":216,"13C":217,"14CH1":218,"=11C":219,"S@@":220,"=P@@":221,"SiH2":222,"H3-1":223,"14CH3":224,"BH3-1":225,"S@":226,"=14CH1":227,"=PH1":228,"=P@":229,"=NH1+1":230,"\\S+1":231,"124":232,"CH1-1":233,"Sr":234,"=Si":235,"124I":236,"Sr+2":237,"#C-1":238,"/C-1":239,"N@":240,"/N-1":241,"13CH1":242,"/B":243,"19":244,"Ba+2":245,"H4":246,"SH1+1":247,"Se+1":248,"19F":249,"/125I":250,"P@+1":251,"Rb":252,"Cl+1":253,"SiH4":254,"Rb+1":255,"=Branch3":256,"N@@":257,"As+1":258,"/Si":259,"BH1-1":260,"SH1":261,"/123I":262,"32":263,"=Mg":264,"H+1":265,"\\B":266,"SiH1":267,"P@@+1":268,"-2":269,"15":270,"17":271,"35":272,"=13CH1":273,"Cs":274,"=NH2+1":275,"=SH1":276,"MgH2":277,"32P":278,"17F":279,"35S":280,"Cs+1":281,"#11C":282,"/131I":283,"Bi":284,"\\125I":285,"=S@@":286,"\\S-1":287,"6Br":288,"7I":289,"76Br":290,"=B":291,"eH1":292,"\\N-1":293,"18O":294,"127I":295,"11CH2":296,"14C@@H1":297,"TeH2":298,"15NH1":299,"Bi+3":300,"/P+1":301,"/13C":302,"/13CH1":303,"0B":304,"10B":305,"=Al":306,"=18O":307,"BH0":308,"F-1":309,"NH3":310,"S-2":311,"Br+2":312,"Cl+2":313,"\\Si":314,"/S-1":315,"=PH2":316,"14C@H1":317,"NH3+1":318,"#14C":319,"#O+1":320,"-3":321,"22":322,"4H":323,"5Se":324,"5Sr+2":325,"75Se":326,"85Sr+2":327,"=B-1":328,"=13C":329,"@-1":330,"Be":331,"B@@":332,"B@-1":333,"Ca":334,"CH1":335,"I+3":336,"KH1":337,"OH1+1":338,"Ra+2":339,"SH1-1":340,"\\PH1":341,"\\123I":342,"=Ca":343,"\\CH1-1":344,"=S@":345,"\\SeH1":346,"/SeH1":347,"Se-1":348,"LiH1":349,"18F-1":350,"125IH1":351,"11CH1":352,"TeH1":353,"Zn+1":354,"Zn-2":355,"Al-3":356,"13CH3":357,"15N":358,"Be+2":359,"B@@-1":360,"#P":361,"#S":362,"-4":363,"/PH1":364,"/P@@":365,"/As":366,"/14C":367,"/14CH1":368,"2K+1":369,"2Rb+1":370,"3Se":371,"3Ra+2":372,"45":373,"47":374,"42K+1":375,"5I-1":376,"73Se":377,"89":378,"82Rb+1":379,"=32":380,"=32P":381,"CH0":382,"CH2":383,"I+2":384,"NH0":385,"NH4":386,"OH1":387,"PH2+1":388,"SH0":389,"SH2":390,"\\3H":391,"\\11CH3":392,"\\C-1":393,"\\Se":394,"Si@":395,"Si-1":396,"SiH1-1":397,"SiH3-1":398,"/Se":399,"Se-2":400,"\\NH1-1":401,"18FH1":402,"125I-1":403,"11C@@H1":404,"11C-1":405,"AsH1":406,"As-1":407,"14C@@":408,"Te-1":409,"Mg+1":410,"123I-1":411,"123Te":412,"123IH1":413,"135I":414,"131I-1":415,"Ag-4":416,"124I-1":417,"76BrH1":418,"18OH1":419,"22Na+1":420,"223Ra+2":421,"CaH2":422,"45Ca+2":423,"47Ca+2":424,"89Sr+2":425,"=32PH1":426,"NH4+1":427} \ No newline at end of file diff --git a/models/finetuned/esol/config.json b/models/finetuned/esol/config.json deleted file mode 100644 index 3811e21539577b37e06313eab31ec11e53f0cbbc..0000000000000000000000000000000000000000 --- a/models/finetuned/esol/config.json +++ /dev/null @@ -1,27 +0,0 @@ -{ - "_name_or_path": "/home/erva/SELFormerMM/data/pretrained_multimodal_chembl36", - "architectures": [ - "RobertaForMaskedLM" - ], - "attention_probs_dropout_prob": 0.1, - "bos_token_id": 0, - "classifier_dropout": null, - "eos_token_id": 2, - "hidden_act": "gelu", - "hidden_dropout_prob": 0.1, - "hidden_size": 768, - "initializer_range": 0.02, - "intermediate_size": 3072, - "layer_norm_eps": 1e-12, - "max_position_embeddings": 514, - "model_type": "roberta", - "num_attention_heads": 4, - "num_hidden_layers": 12, - "pad_token_id": 1, - "position_embedding_type": "absolute", - "torch_dtype": "float32", - "transformers_version": "4.26.1", - "type_vocab_size": 1, - "use_cache": true, - "vocab_size": 800 -} diff --git a/models/finetuned/esol/merges.txt b/models/finetuned/esol/merges.txt deleted file mode 100644 index 7cd5ec62809503c23f18c80afc0ba3bdf9d253d0..0000000000000000000000000000000000000000 --- a/models/finetuned/esol/merges.txt +++ /dev/null @@ -1,378 +0,0 @@ -#version: 0.2 - Trained by `huggingface/tokenizers` -B r -a n -c h -Br an -Bran ch -Branch 1 -= C -R i -n g -Ri ng -Ring 1 -= Branch1 -Branch 2 -= O -Ring 2 -H 1 -C @ -= N -# Branch1 -C@ @ -= Branch2 -C@ H1 -C@@ H1 -# Branch2 -# C -C l -/ C -N H1 -= Ring1 -+ 1 -- 1 -O -1 -N +1 -\ C -# N -/ N -= Ring2 -= S -=N +1 -\ N -N a -Na +1 -/ O -\ O -Br -1 -Branch 3 -\ S -S +1 -Cl -1 -I -1 -/ C@@H1 -S i -/ C@H1 -/ S -=N -1 -S e -= P -N -1 -Ring 3 -2 H -P +1 -K +1 -\ C@@H1 -\ C@H1 -/ N+1 -@ @ -C -1 -# N+1 -B -1 -+ 3 -Cl +3 -\ NH1 -L i -Li +1 -P H1 -1 8 -18 F -@ +1 -3 H -P @@ -H 0 -O H0 -1 2 -P @ -+ 2 -@@ +1 -S -1 -/ Br -- / -\ Cl --/ Ring2 -\ O-1 -1 1 -5 I -12 5I -11 C -H 3 -\ N+1 -- \ -/ C@@ -S @+1 -A s -/ Cl -11C H3 -=S e -S @@+1 -N @+1 -1 4 --\ Ring2 -14 C -\ F -/ C@ -T e -H 2 -H1 -1 -=O +1 -N @@+1 -C +1 -=S +1 -Z n -/ P -a +2 -/ I -O H1-1 -C a+2 -\ Br -M g -Zn +2 -A l -/ F -Mg +2 -12 3 -123 I -1 3 -I +1 -/ O-1 --\ Ring1 -B H2 -BH2 -1 -\ I -/ NH1 -O +1 -13 1 -131 I -= 14C -/ S+1 -= Ring3 -\ C@@ -H2 +1 -\ C@ -A g -= As -=Se +1 -N H2+1 -Se H1 --/ Ring1 -= Te -Al +3 -Na H1 -=Te +1 -NH1 +1 -Ag +1 -H1 +1 -NH1 -1 -\ P -14C H2 -13 C -14C H1 -= 11C -S @@ -=P @@ -Si H2 -H3 -1 -14C H3 -B H3-1 -S @ -=14C H1 -=P H1 -=P @ -=N H1+1 -\S +1 -12 4 -C H1-1 -S r -=S i -124 I -Sr +2 -#C -1 -/C -1 -N @ -/N -1 -13C H1 -/ B -1 9 -B a+2 -H 4 -S H1+1 -Se +1 -19 F -/ 125I -P @+1 -R b -Cl +1 -Si H4 -Rb +1 -= Branch3 -N @@ -As +1 -/ Si -B H1-1 -S H1 -/ 123I -3 2 -= Mg -H +1 -\ B -Si H1 -P@@ +1 -- 2 -1 5 -1 7 -3 5 -= 13CH1 -C s -=N H2+1 -=S H1 -Mg H2 -32 P -17 F -35 S -Cs +1 -# 11C -/ 131I -B i -\ 125I -=S @@ -\S -1 -6 Br -7 I -7 6Br -= B -e H1 -\N -1 -18 O -12 7I -11C H2 -14 C@@H1 -Te H2 -15 NH1 -Bi +3 -/ P+1 -/ 13C -/ 13CH1 -0 B -1 0B -= Al -= 18O -B H0 -F -1 -N H3 -S -2 -Br +2 -Cl +2 -\S i -/S -1 -=P H2 -14 C@H1 -NH3 +1 -# 14C -# O+1 -- 3 -2 2 -4 H -5 Se -5 Sr+2 -7 5Se -8 5Sr+2 -= B-1 -= 13C -@ -1 -B e -B @@ -B @-1 -C a -C H1 -I +3 -K H1 -O H1+1 -R a+2 -S H1-1 -\ PH1 -\ 123I -=C a -\C H1-1 -=S @ -\S eH1 -/S eH1 -Se -1 -Li H1 -18F -1 -125I H1 -11C H1 -Te H1 -Zn +1 -Zn -2 -Al -3 -13C H3 -15 N -Be +2 -B@@ -1 -# P -# S -- 4 -/ PH1 -/ P@@ -/ As -/ 14C -/ 14CH1 -2 K+1 -2 Rb+1 -3 Se -3 Ra+2 -4 5 -4 7 -4 2K+1 -5 I-1 -7 3Se -8 9 -8 2Rb+1 -= 32 -= 32P -C H0 -C H2 -I +2 -N H0 -N H4 -O H1 -P H2+1 -S H0 -S H2 -\ 3H -\ 11CH3 -\C -1 -\S e -Si @ -Si -1 -Si H1-1 -Si H3-1 -/S e -Se -2 -\NH1 -1 -18F H1 -12 5I-1 -11 C@@H1 -11 C-1 -As H1 -As -1 -14 C@@ -Te -1 -Mg +1 -123 I-1 -123 Te -123I H1 -13 5I -131 I-1 -Ag -4 -124 I-1 -76Br H1 -18O H1 -22 Na+1 -22 3Ra+2 -Ca H2 -45 Ca+2 -47 Ca+2 -89 Sr+2 -=32 PH1 -NH4 +1 diff --git a/models/finetuned/esol/model.pt b/models/finetuned/esol/model.pt deleted file mode 100644 index c7053f6e4ecac583450341274eaa264133d4cdf2..0000000000000000000000000000000000000000 --- a/models/finetuned/esol/model.pt +++ /dev/null @@ -1,3 +0,0 @@ -version https://git-lfs.github.com/spec/v1 -oid sha256:1cea5584251eff6c83eecaee68088f28a1b3cc0048d8380c6ed78beafcb5d031 -size 1022843005 diff --git a/models/finetuned/esol/special_tokens_map.json b/models/finetuned/esol/special_tokens_map.json deleted file mode 100644 index 06a55849fa69a91e7179d909e373179ff7467d8c..0000000000000000000000000000000000000000 --- a/models/finetuned/esol/special_tokens_map.json +++ /dev/null @@ -1,51 +0,0 @@ -{ - "bos_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "cls_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "eos_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "mask_token": { - "content": "", - "lstrip": true, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "pad_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "sep_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "unk_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - } -} diff --git a/models/finetuned/esol/tokenizer.json b/models/finetuned/esol/tokenizer.json deleted file mode 100644 index 3b64b273e6fa9799e2d8375722b9e815de9ebb8f..0000000000000000000000000000000000000000 --- a/models/finetuned/esol/tokenizer.json +++ /dev/null @@ -1,909 +0,0 @@ -{ - "version": "1.0", - "truncation": { - "direction": "Right", - "max_length": 128, - "strategy": "LongestFirst", - "stride": 0 - }, - "padding": { - "strategy": { - "Fixed": 128 - }, - "direction": "Right", - "pad_to_multiple_of": null, - "pad_id": 3, - "pad_type_id": 0, - "pad_token": "" - }, - "added_tokens": [ - { - "id": 0, - "content": "", - "single_word": false, - "lstrip": false, - "rstrip": false, - "normalized": true, - "special": true - }, - { - "id": 1, - "content": "", - "single_word": false, - "lstrip": false, - "rstrip": false, - "normalized": true, - "special": true - }, - { - "id": 2, - "content": "", - "single_word": false, - "lstrip": false, - "rstrip": false, - "normalized": true, - "special": true - }, - { - "id": 3, - "content": "", - "single_word": false, - "lstrip": false, - "rstrip": false, - "normalized": true, - "special": true - }, - { - "id": 4, - "content": "", - "single_word": false, - "lstrip": true, - "rstrip": false, - "normalized": true, - "special": true - } - ], - "normalizer": null, - "pre_tokenizer": { - "type": "ByteLevel", - "add_prefix_space": false, - "trim_offsets": true, - "use_regex": true - }, - "post_processor": { - "type": "RobertaProcessing", - "sep": [ - "", - 2 - ], - "cls": [ - "", - 1 - ], - "trim_offsets": true, - "add_prefix_space": false - }, - "decoder": { - "type": "ByteLevel", - "add_prefix_space": true, - "trim_offsets": true, - "use_regex": true - }, - "model": { - "type": "BPE", - "dropout": null, - "unk_token": null, - "continuing_subword_prefix": "", - "end_of_word_suffix": "", - "fuse_unk": false, - "vocab": { - "": 0, - "": 1, - "": 2, - "": 3, - "": 4, - "\n": 5, - "#": 6, - "+": 7, - "-": 8, - ".": 9, - "/": 10, - "0": 11, - "1": 12, - "2": 13, - "3": 14, - "4": 15, - "5": 16, - "6": 17, - "7": 18, - "8": 19, - "9": 20, - "=": 21, - "@": 22, - "A": 23, - "B": 24, - "C": 25, - "F": 26, - "H": 27, - "I": 28, - "K": 29, - "L": 30, - "M": 31, - "N": 32, - "O": 33, - "P": 34, - "R": 35, - "S": 36, - "T": 37, - "Z": 38, - "\\": 39, - "a": 40, - "b": 41, - "c": 42, - "e": 43, - "g": 44, - "h": 45, - "i": 46, - "l": 47, - "n": 48, - "r": 49, - "s": 50, - "Br": 51, - "an": 52, - "ch": 53, - "Bran": 54, - "Branch": 55, - "Branch1": 56, - "=C": 57, - "Ri": 58, - "ng": 59, - "Ring": 60, - "Ring1": 61, - "=Branch1": 62, - "Branch2": 63, - "=O": 64, - "Ring2": 65, - "H1": 66, - "C@": 67, - "=N": 68, - "#Branch1": 69, - "C@@": 70, - "=Branch2": 71, - "C@H1": 72, - "C@@H1": 73, - "#Branch2": 74, - "#C": 75, - "Cl": 76, - "/C": 77, - "NH1": 78, - "=Ring1": 79, - "+1": 80, - "-1": 81, - "O-1": 82, - "N+1": 83, - "\\C": 84, - "#N": 85, - "/N": 86, - "=Ring2": 87, - "=S": 88, - "=N+1": 89, - "\\N": 90, - "Na": 91, - "Na+1": 92, - "/O": 93, - "\\O": 94, - "Br-1": 95, - "Branch3": 96, - "\\S": 97, - "S+1": 98, - "Cl-1": 99, - "I-1": 100, - "/C@@H1": 101, - "Si": 102, - "/C@H1": 103, - "/S": 104, - "=N-1": 105, - "Se": 106, - "=P": 107, - "N-1": 108, - "Ring3": 109, - "2H": 110, - "P+1": 111, - "K+1": 112, - "\\C@@H1": 113, - "\\C@H1": 114, - "/N+1": 115, - "@@": 116, - "C-1": 117, - "#N+1": 118, - "B-1": 119, - "+3": 120, - "Cl+3": 121, - "\\NH1": 122, - "Li": 123, - "Li+1": 124, - "PH1": 125, - "18": 126, - "18F": 127, - "@+1": 128, - "3H": 129, - "P@@": 130, - "H0": 131, - "OH0": 132, - "12": 133, - "P@": 134, - "+2": 135, - "@@+1": 136, - "S-1": 137, - "/Br": 138, - "-/": 139, - "\\Cl": 140, - "-/Ring2": 141, - "\\O-1": 142, - "11": 143, - "5I": 144, - "125I": 145, - "11C": 146, - "H3": 147, - "\\N+1": 148, - "-\\": 149, - "/C@@": 150, - "S@+1": 151, - "As": 152, - "/Cl": 153, - "11CH3": 154, - "=Se": 155, - "S@@+1": 156, - "N@+1": 157, - "14": 158, - "-\\Ring2": 159, - "14C": 160, - "\\F": 161, - "/C@": 162, - "Te": 163, - "H2": 164, - "H1-1": 165, - "=O+1": 166, - "N@@+1": 167, - "C+1": 168, - "=S+1": 169, - "Zn": 170, - "/P": 171, - "a+2": 172, - "/I": 173, - "OH1-1": 174, - "Ca+2": 175, - "\\Br": 176, - "Mg": 177, - "Zn+2": 178, - "Al": 179, - "/F": 180, - "Mg+2": 181, - "123": 182, - "123I": 183, - "13": 184, - "I+1": 185, - "/O-1": 186, - "-\\Ring1": 187, - "BH2": 188, - "BH2-1": 189, - "\\I": 190, - "/NH1": 191, - "O+1": 192, - "131": 193, - "131I": 194, - "=14C": 195, - "/S+1": 196, - "=Ring3": 197, - "\\C@@": 198, - "H2+1": 199, - "\\C@": 200, - "Ag": 201, - "=As": 202, - "=Se+1": 203, - "NH2+1": 204, - "SeH1": 205, - "-/Ring1": 206, - "=Te": 207, - "Al+3": 208, - "NaH1": 209, - "=Te+1": 210, - "NH1+1": 211, - "Ag+1": 212, - "H1+1": 213, - "NH1-1": 214, - "\\P": 215, - "14CH2": 216, - "13C": 217, - "14CH1": 218, - "=11C": 219, - "S@@": 220, - "=P@@": 221, - "SiH2": 222, - "H3-1": 223, - "14CH3": 224, - "BH3-1": 225, - "S@": 226, - "=14CH1": 227, - "=PH1": 228, - "=P@": 229, - "=NH1+1": 230, - "\\S+1": 231, - "124": 232, - "CH1-1": 233, - "Sr": 234, - "=Si": 235, - "124I": 236, - "Sr+2": 237, - "#C-1": 238, - "/C-1": 239, - "N@": 240, - "/N-1": 241, - "13CH1": 242, - "/B": 243, - "19": 244, - "Ba+2": 245, - "H4": 246, - "SH1+1": 247, - "Se+1": 248, - "19F": 249, - "/125I": 250, - "P@+1": 251, - "Rb": 252, - "Cl+1": 253, - "SiH4": 254, - "Rb+1": 255, - "=Branch3": 256, - "N@@": 257, - "As+1": 258, - "/Si": 259, - "BH1-1": 260, - "SH1": 261, - "/123I": 262, - "32": 263, - "=Mg": 264, - "H+1": 265, - "\\B": 266, - "SiH1": 267, - "P@@+1": 268, - "-2": 269, - "15": 270, - "17": 271, - "35": 272, - "=13CH1": 273, - "Cs": 274, - "=NH2+1": 275, - "=SH1": 276, - "MgH2": 277, - "32P": 278, - "17F": 279, - "35S": 280, - "Cs+1": 281, - "#11C": 282, - "/131I": 283, - "Bi": 284, - "\\125I": 285, - "=S@@": 286, - "\\S-1": 287, - "6Br": 288, - "7I": 289, - "76Br": 290, - "=B": 291, - "eH1": 292, - "\\N-1": 293, - "18O": 294, - "127I": 295, - "11CH2": 296, - "14C@@H1": 297, - "TeH2": 298, - "15NH1": 299, - "Bi+3": 300, - "/P+1": 301, - "/13C": 302, - "/13CH1": 303, - "0B": 304, - "10B": 305, - "=Al": 306, - "=18O": 307, - "BH0": 308, - "F-1": 309, - "NH3": 310, - "S-2": 311, - "Br+2": 312, - "Cl+2": 313, - "\\Si": 314, - "/S-1": 315, - "=PH2": 316, - "14C@H1": 317, - "NH3+1": 318, - "#14C": 319, - "#O+1": 320, - "-3": 321, - "22": 322, - "4H": 323, - "5Se": 324, - "5Sr+2": 325, - "75Se": 326, - "85Sr+2": 327, - "=B-1": 328, - "=13C": 329, - "@-1": 330, - "Be": 331, - "B@@": 332, - "B@-1": 333, - "Ca": 334, - "CH1": 335, - "I+3": 336, - "KH1": 337, - "OH1+1": 338, - "Ra+2": 339, - "SH1-1": 340, - "\\PH1": 341, - "\\123I": 342, - "=Ca": 343, - "\\CH1-1": 344, - "=S@": 345, - "\\SeH1": 346, - "/SeH1": 347, - "Se-1": 348, - "LiH1": 349, - "18F-1": 350, - "125IH1": 351, - "11CH1": 352, - "TeH1": 353, - "Zn+1": 354, - "Zn-2": 355, - "Al-3": 356, - "13CH3": 357, - "15N": 358, - "Be+2": 359, - "B@@-1": 360, - "#P": 361, - "#S": 362, - "-4": 363, - "/PH1": 364, - "/P@@": 365, - "/As": 366, - "/14C": 367, - "/14CH1": 368, - "2K+1": 369, - "2Rb+1": 370, - "3Se": 371, - "3Ra+2": 372, - "45": 373, - "47": 374, - "42K+1": 375, - "5I-1": 376, - "73Se": 377, - "89": 378, - "82Rb+1": 379, - "=32": 380, - "=32P": 381, - "CH0": 382, - "CH2": 383, - "I+2": 384, - "NH0": 385, - "NH4": 386, - "OH1": 387, - "PH2+1": 388, - "SH0": 389, - "SH2": 390, - "\\3H": 391, - "\\11CH3": 392, - "\\C-1": 393, - "\\Se": 394, - "Si@": 395, - "Si-1": 396, - "SiH1-1": 397, - "SiH3-1": 398, - "/Se": 399, - "Se-2": 400, - "\\NH1-1": 401, - "18FH1": 402, - "125I-1": 403, - "11C@@H1": 404, - "11C-1": 405, - "AsH1": 406, - "As-1": 407, - "14C@@": 408, - "Te-1": 409, - "Mg+1": 410, - "123I-1": 411, - "123Te": 412, - "123IH1": 413, - "135I": 414, - "131I-1": 415, - "Ag-4": 416, - "124I-1": 417, - "76BrH1": 418, - "18OH1": 419, - "22Na+1": 420, - "223Ra+2": 421, - "CaH2": 422, - "45Ca+2": 423, - "47Ca+2": 424, - "89Sr+2": 425, - "=32PH1": 426, - "NH4+1": 427 - }, - "merges": [ - "B r", - "a n", - "c h", - "Br an", - "Bran ch", - "Branch 1", - "= C", - "R i", - "n g", - "Ri ng", - "Ring 1", - "= Branch1", - "Branch 2", - "= O", - "Ring 2", - "H 1", - "C @", - "= N", - "# Branch1", - "C@ @", - "= Branch2", - "C@ H1", - "C@@ H1", - "# Branch2", - "# C", - "C l", - "/ C", - "N H1", - "= Ring1", - "+ 1", - "- 1", - "O -1", - "N +1", - "\\ C", - "# N", - "/ N", - "= Ring2", - "= S", - "=N +1", - "\\ N", - "N a", - "Na +1", - "/ O", - "\\ O", - "Br -1", - "Branch 3", - "\\ S", - "S +1", - "Cl -1", - "I -1", - "/ C@@H1", - "S i", - "/ C@H1", - "/ S", - "=N -1", - "S e", - "= P", - "N -1", - "Ring 3", - "2 H", - "P +1", - "K +1", - "\\ C@@H1", - "\\ C@H1", - "/ N+1", - "@ @", - "C -1", - "# N+1", - "B -1", - "+ 3", - "Cl +3", - "\\ NH1", - "L i", - "Li +1", - "P H1", - "1 8", - "18 F", - "@ +1", - "3 H", - "P @@", - "H 0", - "O H0", - "1 2", - "P @", - "+ 2", - "@@ +1", - "S -1", - "/ Br", - "- /", - "\\ Cl", - "-/ Ring2", - "\\ O-1", - "1 1", - "5 I", - "12 5I", - "11 C", - "H 3", - "\\ N+1", - "- \\", - "/ C@@", - "S @+1", - "A s", - "/ Cl", - "11C H3", - "=S e", - "S @@+1", - "N @+1", - "1 4", - "-\\ Ring2", - "14 C", - "\\ F", - "/ C@", - "T e", - "H 2", - "H1 -1", - "=O +1", - "N @@+1", - "C +1", - "=S +1", - "Z n", - "/ P", - "a +2", - "/ I", - "O H1-1", - "C a+2", - "\\ Br", - "M g", - "Zn +2", - "A l", - "/ F", - "Mg +2", - "12 3", - "123 I", - "1 3", - "I +1", - "/ O-1", - "-\\ Ring1", - "B H2", - "BH2 -1", - "\\ I", - "/ NH1", - "O +1", - "13 1", - "131 I", - "= 14C", - "/ S+1", - "= Ring3", - "\\ C@@", - "H2 +1", - "\\ C@", - "A g", - "= As", - "=Se +1", - "N H2+1", - "Se H1", - "-/ Ring1", - "= Te", - "Al +3", - "Na H1", - "=Te +1", - "NH1 +1", - "Ag +1", - "H1 +1", - "NH1 -1", - "\\ P", - "14C H2", - "13 C", - "14C H1", - "= 11C", - "S @@", - "=P @@", - "Si H2", - "H3 -1", - "14C H3", - "B H3-1", - "S @", - "=14C H1", - "=P H1", - "=P @", - "=N H1+1", - "\\S +1", - "12 4", - "C H1-1", - "S r", - "=S i", - "124 I", - "Sr +2", - "#C -1", - "/C -1", - "N @", - "/N -1", - "13C H1", - "/ B", - "1 9", - "B a+2", - "H 4", - "S H1+1", - "Se +1", - "19 F", - "/ 125I", - "P @+1", - "R b", - "Cl +1", - "Si H4", - "Rb +1", - "= Branch3", - "N @@", - "As +1", - "/ Si", - "B H1-1", - "S H1", - "/ 123I", - "3 2", - "= Mg", - "H +1", - "\\ B", - "Si H1", - "P@@ +1", - "- 2", - "1 5", - "1 7", - "3 5", - "= 13CH1", - "C s", - "=N H2+1", - "=S H1", - "Mg H2", - "32 P", - "17 F", - "35 S", - "Cs +1", - "# 11C", - "/ 131I", - "B i", - "\\ 125I", - "=S @@", - "\\S -1", - "6 Br", - "7 I", - "7 6Br", - "= B", - "e H1", - "\\N -1", - "18 O", - "12 7I", - "11C H2", - "14 C@@H1", - "Te H2", - "15 NH1", - "Bi +3", - "/ P+1", - "/ 13C", - "/ 13CH1", - "0 B", - "1 0B", - "= Al", - "= 18O", - "B H0", - "F -1", - "N H3", - "S -2", - "Br +2", - "Cl +2", - "\\S i", - "/S -1", - "=P H2", - "14 C@H1", - "NH3 +1", - "# 14C", - "# O+1", - "- 3", - "2 2", - "4 H", - "5 Se", - "5 Sr+2", - "7 5Se", - "8 5Sr+2", - "= B-1", - "= 13C", - "@ -1", - "B e", - "B @@", - "B @-1", - "C a", - "C H1", - "I +3", - "K H1", - "O H1+1", - "R a+2", - "S H1-1", - "\\ PH1", - "\\ 123I", - "=C a", - "\\C H1-1", - "=S @", - "\\S eH1", - "/S eH1", - "Se -1", - "Li H1", - "18F -1", - "125I H1", - "11C H1", - "Te H1", - "Zn +1", - "Zn -2", - "Al -3", - "13C H3", - "15 N", - "Be +2", - "B@@ -1", - "# P", - "# S", - "- 4", - "/ PH1", - "/ P@@", - "/ As", - "/ 14C", - "/ 14CH1", - "2 K+1", - "2 Rb+1", - "3 Se", - "3 Ra+2", - "4 5", - "4 7", - "4 2K+1", - "5 I-1", - "7 3Se", - "8 9", - "8 2Rb+1", - "= 32", - "= 32P", - "C H0", - "C H2", - "I +2", - "N H0", - "N H4", - "O H1", - "P H2+1", - "S H0", - "S H2", - "\\ 3H", - "\\ 11CH3", - "\\C -1", - "\\S e", - "Si @", - "Si -1", - "Si H1-1", - "Si H3-1", - "/S e", - "Se -2", - "\\NH1 -1", - "18F H1", - "12 5I-1", - "11 C@@H1", - "11 C-1", - "As H1", - "As -1", - "14 C@@", - "Te -1", - "Mg +1", - "123 I-1", - "123 Te", - "123I H1", - "13 5I", - "131 I-1", - "Ag -4", - "124 I-1", - "76Br H1", - "18O H1", - "22 Na+1", - "22 3Ra+2", - "Ca H2", - "45 Ca+2", - "47 Ca+2", - "89 Sr+2", - "=32 PH1", - "NH4 +1" - ] - } -} \ No newline at end of file diff --git a/models/finetuned/esol/tokenizer_config.json b/models/finetuned/esol/tokenizer_config.json deleted file mode 100644 index 08860954acd34fad07fd77f7635298fa565f3149..0000000000000000000000000000000000000000 --- a/models/finetuned/esol/tokenizer_config.json +++ /dev/null @@ -1,65 +0,0 @@ -{ - "add_prefix_space": false, - "bos_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "cls_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "eos_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "errors": "replace", - "mask_token": { - "__type": "AddedToken", - "content": "", - "lstrip": true, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "model_max_length": 1000000000000000019884624838656, - "name_or_path": "/home/erva/SELFormerMM/data/pretrained_multimodal_chembl36", - "pad_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "sep_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "special_tokens_map_file": null, - "tokenizer_class": "RobertaTokenizer", - "trim_offsets": true, - "unk_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - } -} diff --git a/models/finetuned/esol/train_stdout.log b/models/finetuned/esol/train_stdout.log deleted file mode 100644 index ad7f63f0bfb065ea4587adce57b9b88b02103e03..0000000000000000000000000000000000000000 --- a/models/finetuned/esol/train_stdout.log +++ /dev/null @@ -1,84 +0,0 @@ -[finetune] starting -[finetune] device=cuda task_type=regression batch_size=16 max_len=128 backbone_lr=1e-05 head_lr=0.0005 weight_decay=0.1 epochs=50 -[finetune] dataset_meta_csv=/home/erva/SELFormerMM/data/new_finetuning_datasets/regression/esol/esol.csv -[finetune] dataset_embs_npz=/home/erva/SELFormerMM/data/new_finetuning_datasets/regression/esol/esol_embs.npz -[finetune] model_path=HUBioDataLab/SELFormer tokenizer_path=HUBioDataLab/SELFormer -[finetune] pretrained_multimodal_dir=/home/erva/SELFormerMM/data/pretrained_multimodal_chembl36 -[finetune] use_scaffold=False seed=42 fracs=(0.8,0.1,0.1) -[finetune] loading dataset bundle (meta csv + embs npz) ... -[finetune] splitting dataset... -[finetune] split sizes: train=902 val=113 test=113 -[finetune] train modality_non_empty: graph=902/902 text=797/902 kg=31/902 -[finetune] val modality_non_empty: graph=113/113 text=101/113 kg=7/113 -[finetune] test modality_non_empty: graph=113/113 text=98/113 kg=2/113 -[finetune] extracting labels... -[finetune] loading config/tokenizer/backbone... -[finetune] initializing multimodal model... -[finetune] loading multimodal pretrained weights: /home/erva/SELFormerMM/data/pretrained_multimodal_chembl36/pytorch_model.bin -[finetune] freezing roberta layers (trainable: encoder.layer.9-11)... -[finetune] backbone trainable params: 181,443,072/246,245,376 -[finetune] building datasets/dataloaders... -[finetune] train_steps_per_epoch=57 val_steps=8 test_steps=8 -[finetune] initialized head: in_dim=3072 out=1 -[finetune] initializing optimizer/scheduler/finetuner... -[finetune] optimizer groups: backbone_decay=45 backbone_nodecay=57 head_decay=2 head_nodecay=2 -[finetune] training loop... -[finetune] epoch 1/50: train_loss=2.1456 val_loss=0.7541 time=10.5s tod=23:34 -[finetune] epoch 2/50: train_loss=0.5921 val_loss=0.8212 time=10.6s tod=23:34 -[finetune] epoch 3/50: train_loss=0.4620 val_loss=1.0872 time=10.4s tod=23:34 -[finetune] epoch 4/50: train_loss=0.3742 val_loss=0.6175 time=10.6s tod=23:34 -[finetune] epoch 5/50: train_loss=0.3656 val_loss=0.5443 time=10.4s tod=23:34 -[finetune] epoch 6/50: train_loss=0.2373 val_loss=0.8940 time=10.4s tod=23:34 -[finetune] epoch 7/50: train_loss=0.2876 val_loss=0.7784 time=10.6s tod=23:35 -[finetune] epoch 8/50: train_loss=0.2574 val_loss=0.7644 time=10.4s tod=23:35 -[finetune] epoch 9/50: train_loss=0.1703 val_loss=0.5304 time=10.4s tod=23:35 -[finetune] epoch 10/50: train_loss=0.1926 val_loss=0.8380 time=10.4s tod=23:35 -[finetune] epoch 11/50: train_loss=0.1611 val_loss=0.5210 time=10.6s tod=23:35 -[finetune] epoch 12/50: train_loss=0.1468 val_loss=0.4703 time=10.3s tod=23:36 -[finetune] epoch 13/50: train_loss=0.1523 val_loss=0.5576 time=10.4s tod=23:36 -[finetune] epoch 14/50: train_loss=0.1304 val_loss=0.4909 time=10.6s tod=23:36 -[finetune] epoch 15/50: train_loss=0.1077 val_loss=0.5125 time=10.6s tod=23:36 -[finetune] epoch 16/50: train_loss=0.1145 val_loss=0.4894 time=10.3s tod=23:36 -[finetune] epoch 17/50: train_loss=0.1228 val_loss=0.4724 time=10.4s tod=23:36 -[finetune] epoch 18/50: train_loss=0.0919 val_loss=0.5175 time=10.6s tod=23:37 -[finetune] epoch 19/50: train_loss=0.0883 val_loss=0.4762 time=10.4s tod=23:37 -[finetune] epoch 20/50: train_loss=0.0836 val_loss=0.5046 time=8.3s tod=23:37 -[finetune] epoch 21/50: train_loss=0.0758 val_loss=0.5696 time=5.3s tod=23:37 -[finetune] epoch 22/50: train_loss=0.0667 val_loss=0.4784 time=5.3s tod=23:37 -[finetune] epoch 23/50: train_loss=0.0678 val_loss=0.4916 time=5.2s tod=23:37 -[finetune] epoch 24/50: train_loss=0.0691 val_loss=0.5081 time=5.3s tod=23:37 -[finetune] epoch 25/50: train_loss=0.0691 val_loss=0.5231 time=5.3s tod=23:37 -[finetune] test_metrics: epoch=25 loss=0.3905 mse=0.4388 rmse=0.6624 mae=0.4929 -[finetune] saved checkpoint (best rmse=0.6624): /media/ubuntu/8TB/erva/selformer-mm/output/new_finetune_sweeps/esol/a0w73dq7/checkpoint_epoch_025 -[finetune] epoch 26/50: train_loss=0.0674 val_loss=0.4815 time=8.0s tod=23:37 -[finetune] epoch 27/50: train_loss=0.0489 val_loss=0.5125 time=10.4s tod=23:38 -[finetune] epoch 28/50: train_loss=0.0520 val_loss=0.4919 time=10.4s tod=23:38 -[finetune] epoch 29/50: train_loss=0.0428 val_loss=0.5000 time=10.6s tod=23:38 -[finetune] epoch 30/50: train_loss=0.0476 val_loss=0.5481 time=10.4s tod=23:38 -[finetune] epoch 31/50: train_loss=0.0437 val_loss=0.5889 time=10.4s tod=23:38 -[finetune] epoch 32/50: train_loss=0.0469 val_loss=0.5447 time=10.6s tod=23:39 -[finetune] epoch 33/50: train_loss=0.0351 val_loss=0.4789 time=10.3s tod=23:39 -[finetune] epoch 34/50: train_loss=0.0427 val_loss=0.4710 time=10.4s tod=23:39 -[finetune] epoch 35/50: train_loss=0.0325 val_loss=0.4598 time=10.6s tod=23:39 -[finetune] epoch 36/50: train_loss=0.0285 val_loss=0.5224 time=10.4s tod=23:39 -[finetune] epoch 37/50: train_loss=0.0315 val_loss=0.4766 time=10.3s tod=23:39 -[finetune] epoch 38/50: train_loss=0.0259 val_loss=0.4907 time=10.4s tod=23:40 -[finetune] epoch 39/50: train_loss=0.0274 val_loss=0.4913 time=10.4s tod=23:40 -[finetune] epoch 40/50: train_loss=0.0245 val_loss=0.4672 time=10.6s tod=23:40 -[finetune] epoch 41/50: train_loss=0.0238 val_loss=0.4869 time=10.4s tod=23:40 -[finetune] epoch 42/50: train_loss=0.0229 val_loss=0.4674 time=10.4s tod=23:40 -[finetune] epoch 43/50: train_loss=0.0204 val_loss=0.5000 time=10.6s tod=23:40 -[finetune] epoch 44/50: train_loss=0.0198 val_loss=0.4839 time=10.2s tod=23:41 -[finetune] epoch 45/50: train_loss=0.0180 val_loss=0.4792 time=10.5s tod=23:41 -[finetune] epoch 46/50: train_loss=0.0175 val_loss=0.4750 time=10.6s tod=23:41 -[finetune] epoch 47/50: train_loss=0.0169 val_loss=0.4856 time=10.4s tod=23:41 -[finetune] epoch 48/50: train_loss=0.0140 val_loss=0.4864 time=10.4s tod=23:41 -[finetune] epoch 49/50: train_loss=0.0142 val_loss=0.4835 time=10.6s tod=23:42 -[finetune] epoch 50/50: train_loss=0.0130 val_loss=0.4823 time=10.4s tod=23:42 -[finetune] test_metrics: epoch=50 loss=0.3251 mse=0.3635 rmse=0.6029 mae=0.4456 -[finetune] saved checkpoint (best rmse=0.6029): /media/ubuntu/8TB/erva/selformer-mm/output/new_finetune_sweeps/esol/a0w73dq7/checkpoint_epoch_050 -[finetune] final evaluation on test split... -[finetune] test_metrics: loss=0.3251 mse=0.3635 rmse=0.6029 mae=0.4456 -[finetune] saving model... -[finetune] saved finetuned model to: /media/ubuntu/8TB/erva/selformer-mm/output/new_finetune_sweeps/esol/a0w73dq7 -[finetune] done in 503.2s diff --git a/models/finetuned/esol/vocab.json b/models/finetuned/esol/vocab.json deleted file mode 100644 index f7e4cc22809f4e9035cc450ef189c8a7da8fd03e..0000000000000000000000000000000000000000 --- a/models/finetuned/esol/vocab.json +++ /dev/null @@ -1 +0,0 @@ -{"":0,"":1,"":2,"":3,"":4,"\n":5,"#":6,"+":7,"-":8,".":9,"/":10,"0":11,"1":12,"2":13,"3":14,"4":15,"5":16,"6":17,"7":18,"8":19,"9":20,"=":21,"@":22,"A":23,"B":24,"C":25,"F":26,"H":27,"I":28,"K":29,"L":30,"M":31,"N":32,"O":33,"P":34,"R":35,"S":36,"T":37,"Z":38,"\\":39,"a":40,"b":41,"c":42,"e":43,"g":44,"h":45,"i":46,"l":47,"n":48,"r":49,"s":50,"Br":51,"an":52,"ch":53,"Bran":54,"Branch":55,"Branch1":56,"=C":57,"Ri":58,"ng":59,"Ring":60,"Ring1":61,"=Branch1":62,"Branch2":63,"=O":64,"Ring2":65,"H1":66,"C@":67,"=N":68,"#Branch1":69,"C@@":70,"=Branch2":71,"C@H1":72,"C@@H1":73,"#Branch2":74,"#C":75,"Cl":76,"/C":77,"NH1":78,"=Ring1":79,"+1":80,"-1":81,"O-1":82,"N+1":83,"\\C":84,"#N":85,"/N":86,"=Ring2":87,"=S":88,"=N+1":89,"\\N":90,"Na":91,"Na+1":92,"/O":93,"\\O":94,"Br-1":95,"Branch3":96,"\\S":97,"S+1":98,"Cl-1":99,"I-1":100,"/C@@H1":101,"Si":102,"/C@H1":103,"/S":104,"=N-1":105,"Se":106,"=P":107,"N-1":108,"Ring3":109,"2H":110,"P+1":111,"K+1":112,"\\C@@H1":113,"\\C@H1":114,"/N+1":115,"@@":116,"C-1":117,"#N+1":118,"B-1":119,"+3":120,"Cl+3":121,"\\NH1":122,"Li":123,"Li+1":124,"PH1":125,"18":126,"18F":127,"@+1":128,"3H":129,"P@@":130,"H0":131,"OH0":132,"12":133,"P@":134,"+2":135,"@@+1":136,"S-1":137,"/Br":138,"-/":139,"\\Cl":140,"-/Ring2":141,"\\O-1":142,"11":143,"5I":144,"125I":145,"11C":146,"H3":147,"\\N+1":148,"-\\":149,"/C@@":150,"S@+1":151,"As":152,"/Cl":153,"11CH3":154,"=Se":155,"S@@+1":156,"N@+1":157,"14":158,"-\\Ring2":159,"14C":160,"\\F":161,"/C@":162,"Te":163,"H2":164,"H1-1":165,"=O+1":166,"N@@+1":167,"C+1":168,"=S+1":169,"Zn":170,"/P":171,"a+2":172,"/I":173,"OH1-1":174,"Ca+2":175,"\\Br":176,"Mg":177,"Zn+2":178,"Al":179,"/F":180,"Mg+2":181,"123":182,"123I":183,"13":184,"I+1":185,"/O-1":186,"-\\Ring1":187,"BH2":188,"BH2-1":189,"\\I":190,"/NH1":191,"O+1":192,"131":193,"131I":194,"=14C":195,"/S+1":196,"=Ring3":197,"\\C@@":198,"H2+1":199,"\\C@":200,"Ag":201,"=As":202,"=Se+1":203,"NH2+1":204,"SeH1":205,"-/Ring1":206,"=Te":207,"Al+3":208,"NaH1":209,"=Te+1":210,"NH1+1":211,"Ag+1":212,"H1+1":213,"NH1-1":214,"\\P":215,"14CH2":216,"13C":217,"14CH1":218,"=11C":219,"S@@":220,"=P@@":221,"SiH2":222,"H3-1":223,"14CH3":224,"BH3-1":225,"S@":226,"=14CH1":227,"=PH1":228,"=P@":229,"=NH1+1":230,"\\S+1":231,"124":232,"CH1-1":233,"Sr":234,"=Si":235,"124I":236,"Sr+2":237,"#C-1":238,"/C-1":239,"N@":240,"/N-1":241,"13CH1":242,"/B":243,"19":244,"Ba+2":245,"H4":246,"SH1+1":247,"Se+1":248,"19F":249,"/125I":250,"P@+1":251,"Rb":252,"Cl+1":253,"SiH4":254,"Rb+1":255,"=Branch3":256,"N@@":257,"As+1":258,"/Si":259,"BH1-1":260,"SH1":261,"/123I":262,"32":263,"=Mg":264,"H+1":265,"\\B":266,"SiH1":267,"P@@+1":268,"-2":269,"15":270,"17":271,"35":272,"=13CH1":273,"Cs":274,"=NH2+1":275,"=SH1":276,"MgH2":277,"32P":278,"17F":279,"35S":280,"Cs+1":281,"#11C":282,"/131I":283,"Bi":284,"\\125I":285,"=S@@":286,"\\S-1":287,"6Br":288,"7I":289,"76Br":290,"=B":291,"eH1":292,"\\N-1":293,"18O":294,"127I":295,"11CH2":296,"14C@@H1":297,"TeH2":298,"15NH1":299,"Bi+3":300,"/P+1":301,"/13C":302,"/13CH1":303,"0B":304,"10B":305,"=Al":306,"=18O":307,"BH0":308,"F-1":309,"NH3":310,"S-2":311,"Br+2":312,"Cl+2":313,"\\Si":314,"/S-1":315,"=PH2":316,"14C@H1":317,"NH3+1":318,"#14C":319,"#O+1":320,"-3":321,"22":322,"4H":323,"5Se":324,"5Sr+2":325,"75Se":326,"85Sr+2":327,"=B-1":328,"=13C":329,"@-1":330,"Be":331,"B@@":332,"B@-1":333,"Ca":334,"CH1":335,"I+3":336,"KH1":337,"OH1+1":338,"Ra+2":339,"SH1-1":340,"\\PH1":341,"\\123I":342,"=Ca":343,"\\CH1-1":344,"=S@":345,"\\SeH1":346,"/SeH1":347,"Se-1":348,"LiH1":349,"18F-1":350,"125IH1":351,"11CH1":352,"TeH1":353,"Zn+1":354,"Zn-2":355,"Al-3":356,"13CH3":357,"15N":358,"Be+2":359,"B@@-1":360,"#P":361,"#S":362,"-4":363,"/PH1":364,"/P@@":365,"/As":366,"/14C":367,"/14CH1":368,"2K+1":369,"2Rb+1":370,"3Se":371,"3Ra+2":372,"45":373,"47":374,"42K+1":375,"5I-1":376,"73Se":377,"89":378,"82Rb+1":379,"=32":380,"=32P":381,"CH0":382,"CH2":383,"I+2":384,"NH0":385,"NH4":386,"OH1":387,"PH2+1":388,"SH0":389,"SH2":390,"\\3H":391,"\\11CH3":392,"\\C-1":393,"\\Se":394,"Si@":395,"Si-1":396,"SiH1-1":397,"SiH3-1":398,"/Se":399,"Se-2":400,"\\NH1-1":401,"18FH1":402,"125I-1":403,"11C@@H1":404,"11C-1":405,"AsH1":406,"As-1":407,"14C@@":408,"Te-1":409,"Mg+1":410,"123I-1":411,"123Te":412,"123IH1":413,"135I":414,"131I-1":415,"Ag-4":416,"124I-1":417,"76BrH1":418,"18OH1":419,"22Na+1":420,"223Ra+2":421,"CaH2":422,"45Ca+2":423,"47Ca+2":424,"89Sr+2":425,"=32PH1":426,"NH4+1":427} \ No newline at end of file diff --git a/models/finetuned/freesolv/checkpoint_epoch_025/config.json b/models/finetuned/freesolv/checkpoint_epoch_025/config.json deleted file mode 100644 index 3811e21539577b37e06313eab31ec11e53f0cbbc..0000000000000000000000000000000000000000 --- a/models/finetuned/freesolv/checkpoint_epoch_025/config.json +++ /dev/null @@ -1,27 +0,0 @@ -{ - "_name_or_path": "/home/erva/SELFormerMM/data/pretrained_multimodal_chembl36", - "architectures": [ - "RobertaForMaskedLM" - ], - "attention_probs_dropout_prob": 0.1, - "bos_token_id": 0, - "classifier_dropout": null, - "eos_token_id": 2, - "hidden_act": "gelu", - "hidden_dropout_prob": 0.1, - "hidden_size": 768, - "initializer_range": 0.02, - "intermediate_size": 3072, - "layer_norm_eps": 1e-12, - "max_position_embeddings": 514, - "model_type": "roberta", - "num_attention_heads": 4, - "num_hidden_layers": 12, - "pad_token_id": 1, - "position_embedding_type": "absolute", - "torch_dtype": "float32", - "transformers_version": "4.26.1", - "type_vocab_size": 1, - "use_cache": true, - "vocab_size": 800 -} diff --git a/models/finetuned/freesolv/checkpoint_epoch_025/merges.txt b/models/finetuned/freesolv/checkpoint_epoch_025/merges.txt deleted file mode 100644 index 7cd5ec62809503c23f18c80afc0ba3bdf9d253d0..0000000000000000000000000000000000000000 --- a/models/finetuned/freesolv/checkpoint_epoch_025/merges.txt +++ /dev/null @@ -1,378 +0,0 @@ -#version: 0.2 - Trained by `huggingface/tokenizers` -B r -a n -c h -Br an -Bran ch -Branch 1 -= C -R i -n g -Ri ng -Ring 1 -= Branch1 -Branch 2 -= O -Ring 2 -H 1 -C @ -= N -# Branch1 -C@ @ -= Branch2 -C@ H1 -C@@ H1 -# Branch2 -# C -C l -/ C -N H1 -= Ring1 -+ 1 -- 1 -O -1 -N +1 -\ C -# N -/ N -= Ring2 -= S -=N +1 -\ N -N a -Na +1 -/ O -\ O -Br -1 -Branch 3 -\ S -S +1 -Cl -1 -I -1 -/ C@@H1 -S i -/ C@H1 -/ S -=N -1 -S e -= P -N -1 -Ring 3 -2 H -P +1 -K +1 -\ C@@H1 -\ C@H1 -/ N+1 -@ @ -C -1 -# N+1 -B -1 -+ 3 -Cl +3 -\ NH1 -L i -Li +1 -P H1 -1 8 -18 F -@ +1 -3 H -P @@ -H 0 -O H0 -1 2 -P @ -+ 2 -@@ +1 -S -1 -/ Br -- / -\ Cl --/ Ring2 -\ O-1 -1 1 -5 I -12 5I -11 C -H 3 -\ N+1 -- \ -/ C@@ -S @+1 -A s -/ Cl -11C H3 -=S e -S @@+1 -N @+1 -1 4 --\ Ring2 -14 C -\ F -/ C@ -T e -H 2 -H1 -1 -=O +1 -N @@+1 -C +1 -=S +1 -Z n -/ P -a +2 -/ I -O H1-1 -C a+2 -\ Br -M g -Zn +2 -A l -/ F -Mg +2 -12 3 -123 I -1 3 -I +1 -/ O-1 --\ Ring1 -B H2 -BH2 -1 -\ I -/ NH1 -O +1 -13 1 -131 I -= 14C -/ S+1 -= Ring3 -\ C@@ -H2 +1 -\ C@ -A g -= As -=Se +1 -N H2+1 -Se H1 --/ Ring1 -= Te -Al +3 -Na H1 -=Te +1 -NH1 +1 -Ag +1 -H1 +1 -NH1 -1 -\ P -14C H2 -13 C -14C H1 -= 11C -S @@ -=P @@ -Si H2 -H3 -1 -14C H3 -B H3-1 -S @ -=14C H1 -=P H1 -=P @ -=N H1+1 -\S +1 -12 4 -C H1-1 -S r -=S i -124 I -Sr +2 -#C -1 -/C -1 -N @ -/N -1 -13C H1 -/ B -1 9 -B a+2 -H 4 -S H1+1 -Se +1 -19 F -/ 125I -P @+1 -R b -Cl +1 -Si H4 -Rb +1 -= Branch3 -N @@ -As +1 -/ Si -B H1-1 -S H1 -/ 123I -3 2 -= Mg -H +1 -\ B -Si H1 -P@@ +1 -- 2 -1 5 -1 7 -3 5 -= 13CH1 -C s -=N H2+1 -=S H1 -Mg H2 -32 P -17 F -35 S -Cs +1 -# 11C -/ 131I -B i -\ 125I -=S @@ -\S -1 -6 Br -7 I -7 6Br -= B -e H1 -\N -1 -18 O -12 7I -11C H2 -14 C@@H1 -Te H2 -15 NH1 -Bi +3 -/ P+1 -/ 13C -/ 13CH1 -0 B -1 0B -= Al -= 18O -B H0 -F -1 -N H3 -S -2 -Br +2 -Cl +2 -\S i -/S -1 -=P H2 -14 C@H1 -NH3 +1 -# 14C -# O+1 -- 3 -2 2 -4 H -5 Se -5 Sr+2 -7 5Se -8 5Sr+2 -= B-1 -= 13C -@ -1 -B e -B @@ -B @-1 -C a -C H1 -I +3 -K H1 -O H1+1 -R a+2 -S H1-1 -\ PH1 -\ 123I -=C a -\C H1-1 -=S @ -\S eH1 -/S eH1 -Se -1 -Li H1 -18F -1 -125I H1 -11C H1 -Te H1 -Zn +1 -Zn -2 -Al -3 -13C H3 -15 N -Be +2 -B@@ -1 -# P -# S -- 4 -/ PH1 -/ P@@ -/ As -/ 14C -/ 14CH1 -2 K+1 -2 Rb+1 -3 Se -3 Ra+2 -4 5 -4 7 -4 2K+1 -5 I-1 -7 3Se -8 9 -8 2Rb+1 -= 32 -= 32P -C H0 -C H2 -I +2 -N H0 -N H4 -O H1 -P H2+1 -S H0 -S H2 -\ 3H -\ 11CH3 -\C -1 -\S e -Si @ -Si -1 -Si H1-1 -Si H3-1 -/S e -Se -2 -\NH1 -1 -18F H1 -12 5I-1 -11 C@@H1 -11 C-1 -As H1 -As -1 -14 C@@ -Te -1 -Mg +1 -123 I-1 -123 Te -123I H1 -13 5I -131 I-1 -Ag -4 -124 I-1 -76Br H1 -18O H1 -22 Na+1 -22 3Ra+2 -Ca H2 -45 Ca+2 -47 Ca+2 -89 Sr+2 -=32 PH1 -NH4 +1 diff --git a/models/finetuned/freesolv/checkpoint_epoch_025/model.pt b/models/finetuned/freesolv/checkpoint_epoch_025/model.pt deleted file mode 100644 index b4c39ddfaaef7a18c0375b2bd5a792d5f81f38e7..0000000000000000000000000000000000000000 --- a/models/finetuned/freesolv/checkpoint_epoch_025/model.pt +++ /dev/null @@ -1,3 +0,0 @@ -version https://git-lfs.github.com/spec/v1 -oid sha256:d13a18f4a09651ebd134329b612d3d6ecdc9f84e8c37f802f8940e6e7631acd5 -size 1022843005 diff --git a/models/finetuned/freesolv/checkpoint_epoch_025/special_tokens_map.json b/models/finetuned/freesolv/checkpoint_epoch_025/special_tokens_map.json deleted file mode 100644 index 06a55849fa69a91e7179d909e373179ff7467d8c..0000000000000000000000000000000000000000 --- a/models/finetuned/freesolv/checkpoint_epoch_025/special_tokens_map.json +++ /dev/null @@ -1,51 +0,0 @@ -{ - "bos_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "cls_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "eos_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "mask_token": { - "content": "", - "lstrip": true, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "pad_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "sep_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "unk_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - } -} diff --git a/models/finetuned/freesolv/checkpoint_epoch_025/tokenizer.json b/models/finetuned/freesolv/checkpoint_epoch_025/tokenizer.json deleted file mode 100644 index 3b64b273e6fa9799e2d8375722b9e815de9ebb8f..0000000000000000000000000000000000000000 --- a/models/finetuned/freesolv/checkpoint_epoch_025/tokenizer.json +++ /dev/null @@ -1,909 +0,0 @@ -{ - "version": "1.0", - "truncation": { - "direction": "Right", - "max_length": 128, - "strategy": "LongestFirst", - "stride": 0 - }, - "padding": { - "strategy": { - "Fixed": 128 - }, - "direction": "Right", - "pad_to_multiple_of": null, - "pad_id": 3, - "pad_type_id": 0, - "pad_token": "" - }, - "added_tokens": [ - { - "id": 0, - "content": "", - "single_word": false, - "lstrip": false, - "rstrip": false, - "normalized": true, - "special": true - }, - { - "id": 1, - "content": "", - "single_word": false, - "lstrip": false, - "rstrip": false, - "normalized": true, - "special": true - }, - { - "id": 2, - "content": "", - "single_word": false, - "lstrip": false, - "rstrip": false, - "normalized": true, - "special": true - }, - { - "id": 3, - "content": "", - "single_word": false, - "lstrip": false, - "rstrip": false, - "normalized": true, - "special": true - }, - { - "id": 4, - "content": "", - "single_word": false, - "lstrip": true, - "rstrip": false, - "normalized": true, - "special": true - } - ], - "normalizer": null, - "pre_tokenizer": { - "type": "ByteLevel", - "add_prefix_space": false, - "trim_offsets": true, - "use_regex": true - }, - "post_processor": { - "type": "RobertaProcessing", - "sep": [ - "", - 2 - ], - "cls": [ - "", - 1 - ], - "trim_offsets": true, - "add_prefix_space": false - }, - "decoder": { - "type": "ByteLevel", - "add_prefix_space": true, - "trim_offsets": true, - "use_regex": true - }, - "model": { - "type": "BPE", - "dropout": null, - "unk_token": null, - "continuing_subword_prefix": "", - "end_of_word_suffix": "", - "fuse_unk": false, - "vocab": { - "": 0, - "": 1, - "": 2, - "": 3, - "": 4, - "\n": 5, - "#": 6, - "+": 7, - "-": 8, - ".": 9, - "/": 10, - "0": 11, - "1": 12, - "2": 13, - "3": 14, - "4": 15, - "5": 16, - "6": 17, - "7": 18, - "8": 19, - "9": 20, - "=": 21, - "@": 22, - "A": 23, - "B": 24, - "C": 25, - "F": 26, - "H": 27, - "I": 28, - "K": 29, - "L": 30, - "M": 31, - "N": 32, - "O": 33, - "P": 34, - "R": 35, - "S": 36, - "T": 37, - "Z": 38, - "\\": 39, - "a": 40, - "b": 41, - "c": 42, - "e": 43, - "g": 44, - "h": 45, - "i": 46, - "l": 47, - "n": 48, - "r": 49, - "s": 50, - "Br": 51, - "an": 52, - "ch": 53, - "Bran": 54, - "Branch": 55, - "Branch1": 56, - "=C": 57, - "Ri": 58, - "ng": 59, - "Ring": 60, - "Ring1": 61, - "=Branch1": 62, - "Branch2": 63, - "=O": 64, - "Ring2": 65, - "H1": 66, - "C@": 67, - "=N": 68, - "#Branch1": 69, - "C@@": 70, - "=Branch2": 71, - "C@H1": 72, - "C@@H1": 73, - "#Branch2": 74, - "#C": 75, - "Cl": 76, - "/C": 77, - "NH1": 78, - "=Ring1": 79, - "+1": 80, - "-1": 81, - "O-1": 82, - "N+1": 83, - "\\C": 84, - "#N": 85, - "/N": 86, - "=Ring2": 87, - "=S": 88, - "=N+1": 89, - "\\N": 90, - "Na": 91, - "Na+1": 92, - "/O": 93, - "\\O": 94, - "Br-1": 95, - "Branch3": 96, - "\\S": 97, - "S+1": 98, - "Cl-1": 99, - "I-1": 100, - "/C@@H1": 101, - "Si": 102, - "/C@H1": 103, - "/S": 104, - "=N-1": 105, - "Se": 106, - "=P": 107, - "N-1": 108, - "Ring3": 109, - "2H": 110, - "P+1": 111, - "K+1": 112, - "\\C@@H1": 113, - "\\C@H1": 114, - "/N+1": 115, - "@@": 116, - "C-1": 117, - "#N+1": 118, - "B-1": 119, - "+3": 120, - "Cl+3": 121, - "\\NH1": 122, - "Li": 123, - "Li+1": 124, - "PH1": 125, - "18": 126, - "18F": 127, - "@+1": 128, - "3H": 129, - "P@@": 130, - "H0": 131, - "OH0": 132, - "12": 133, - "P@": 134, - "+2": 135, - "@@+1": 136, - "S-1": 137, - "/Br": 138, - "-/": 139, - "\\Cl": 140, - "-/Ring2": 141, - "\\O-1": 142, - "11": 143, - "5I": 144, - "125I": 145, - "11C": 146, - "H3": 147, - "\\N+1": 148, - "-\\": 149, - "/C@@": 150, - "S@+1": 151, - "As": 152, - "/Cl": 153, - "11CH3": 154, - "=Se": 155, - "S@@+1": 156, - "N@+1": 157, - "14": 158, - "-\\Ring2": 159, - "14C": 160, - "\\F": 161, - "/C@": 162, - "Te": 163, - "H2": 164, - "H1-1": 165, - "=O+1": 166, - "N@@+1": 167, - "C+1": 168, - "=S+1": 169, - "Zn": 170, - "/P": 171, - "a+2": 172, - "/I": 173, - "OH1-1": 174, - "Ca+2": 175, - "\\Br": 176, - "Mg": 177, - "Zn+2": 178, - "Al": 179, - "/F": 180, - "Mg+2": 181, - "123": 182, - "123I": 183, - "13": 184, - "I+1": 185, - "/O-1": 186, - "-\\Ring1": 187, - "BH2": 188, - "BH2-1": 189, - "\\I": 190, - "/NH1": 191, - "O+1": 192, - "131": 193, - "131I": 194, - "=14C": 195, - "/S+1": 196, - "=Ring3": 197, - "\\C@@": 198, - "H2+1": 199, - "\\C@": 200, - "Ag": 201, - "=As": 202, - "=Se+1": 203, - "NH2+1": 204, - "SeH1": 205, - "-/Ring1": 206, - "=Te": 207, - "Al+3": 208, - "NaH1": 209, - "=Te+1": 210, - "NH1+1": 211, - "Ag+1": 212, - "H1+1": 213, - "NH1-1": 214, - "\\P": 215, - "14CH2": 216, - "13C": 217, - "14CH1": 218, - "=11C": 219, - "S@@": 220, - "=P@@": 221, - "SiH2": 222, - "H3-1": 223, - "14CH3": 224, - "BH3-1": 225, - "S@": 226, - "=14CH1": 227, - "=PH1": 228, - "=P@": 229, - "=NH1+1": 230, - "\\S+1": 231, - "124": 232, - "CH1-1": 233, - "Sr": 234, - "=Si": 235, - "124I": 236, - "Sr+2": 237, - "#C-1": 238, - "/C-1": 239, - "N@": 240, - "/N-1": 241, - "13CH1": 242, - "/B": 243, - "19": 244, - "Ba+2": 245, - "H4": 246, - "SH1+1": 247, - "Se+1": 248, - "19F": 249, - "/125I": 250, - "P@+1": 251, - "Rb": 252, - "Cl+1": 253, - "SiH4": 254, - "Rb+1": 255, - "=Branch3": 256, - "N@@": 257, - "As+1": 258, - "/Si": 259, - "BH1-1": 260, - "SH1": 261, - "/123I": 262, - "32": 263, - "=Mg": 264, - "H+1": 265, - "\\B": 266, - "SiH1": 267, - "P@@+1": 268, - "-2": 269, - "15": 270, - "17": 271, - "35": 272, - "=13CH1": 273, - "Cs": 274, - "=NH2+1": 275, - "=SH1": 276, - "MgH2": 277, - "32P": 278, - "17F": 279, - "35S": 280, - "Cs+1": 281, - "#11C": 282, - "/131I": 283, - "Bi": 284, - "\\125I": 285, - "=S@@": 286, - "\\S-1": 287, - "6Br": 288, - "7I": 289, - "76Br": 290, - "=B": 291, - "eH1": 292, - "\\N-1": 293, - "18O": 294, - "127I": 295, - "11CH2": 296, - "14C@@H1": 297, - "TeH2": 298, - "15NH1": 299, - "Bi+3": 300, - "/P+1": 301, - "/13C": 302, - "/13CH1": 303, - "0B": 304, - "10B": 305, - "=Al": 306, - "=18O": 307, - "BH0": 308, - "F-1": 309, - "NH3": 310, - "S-2": 311, - "Br+2": 312, - "Cl+2": 313, - "\\Si": 314, - "/S-1": 315, - "=PH2": 316, - "14C@H1": 317, - "NH3+1": 318, - "#14C": 319, - "#O+1": 320, - "-3": 321, - "22": 322, - "4H": 323, - "5Se": 324, - "5Sr+2": 325, - "75Se": 326, - "85Sr+2": 327, - "=B-1": 328, - "=13C": 329, - "@-1": 330, - "Be": 331, - "B@@": 332, - "B@-1": 333, - "Ca": 334, - "CH1": 335, - "I+3": 336, - "KH1": 337, - "OH1+1": 338, - "Ra+2": 339, - "SH1-1": 340, - "\\PH1": 341, - "\\123I": 342, - "=Ca": 343, - "\\CH1-1": 344, - "=S@": 345, - "\\SeH1": 346, - "/SeH1": 347, - "Se-1": 348, - "LiH1": 349, - "18F-1": 350, - "125IH1": 351, - "11CH1": 352, - "TeH1": 353, - "Zn+1": 354, - "Zn-2": 355, - "Al-3": 356, - "13CH3": 357, - "15N": 358, - "Be+2": 359, - "B@@-1": 360, - "#P": 361, - "#S": 362, - "-4": 363, - "/PH1": 364, - "/P@@": 365, - "/As": 366, - "/14C": 367, - "/14CH1": 368, - "2K+1": 369, - "2Rb+1": 370, - "3Se": 371, - "3Ra+2": 372, - "45": 373, - "47": 374, - "42K+1": 375, - "5I-1": 376, - "73Se": 377, - "89": 378, - "82Rb+1": 379, - "=32": 380, - "=32P": 381, - "CH0": 382, - "CH2": 383, - "I+2": 384, - "NH0": 385, - "NH4": 386, - "OH1": 387, - "PH2+1": 388, - "SH0": 389, - "SH2": 390, - "\\3H": 391, - "\\11CH3": 392, - "\\C-1": 393, - "\\Se": 394, - "Si@": 395, - "Si-1": 396, - "SiH1-1": 397, - "SiH3-1": 398, - "/Se": 399, - "Se-2": 400, - "\\NH1-1": 401, - "18FH1": 402, - "125I-1": 403, - "11C@@H1": 404, - "11C-1": 405, - "AsH1": 406, - "As-1": 407, - "14C@@": 408, - "Te-1": 409, - "Mg+1": 410, - "123I-1": 411, - "123Te": 412, - "123IH1": 413, - "135I": 414, - "131I-1": 415, - "Ag-4": 416, - "124I-1": 417, - "76BrH1": 418, - "18OH1": 419, - "22Na+1": 420, - "223Ra+2": 421, - "CaH2": 422, - "45Ca+2": 423, - "47Ca+2": 424, - "89Sr+2": 425, - "=32PH1": 426, - "NH4+1": 427 - }, - "merges": [ - "B r", - "a n", - "c h", - "Br an", - "Bran ch", - "Branch 1", - "= C", - "R i", - "n g", - "Ri ng", - "Ring 1", - "= Branch1", - "Branch 2", - "= O", - "Ring 2", - "H 1", - "C @", - "= N", - "# Branch1", - "C@ @", - "= Branch2", - "C@ H1", - "C@@ H1", - "# Branch2", - "# C", - "C l", - "/ C", - "N H1", - "= Ring1", - "+ 1", - "- 1", - "O -1", - "N +1", - "\\ C", - "# N", - "/ N", - "= Ring2", - "= S", - "=N +1", - "\\ N", - "N a", - "Na +1", - "/ O", - "\\ O", - "Br -1", - "Branch 3", - "\\ S", - "S +1", - "Cl -1", - "I -1", - "/ C@@H1", - "S i", - "/ C@H1", - "/ S", - "=N -1", - "S e", - "= P", - "N -1", - "Ring 3", - "2 H", - "P +1", - "K +1", - "\\ C@@H1", - "\\ C@H1", - "/ N+1", - "@ @", - "C -1", - "# N+1", - "B -1", - "+ 3", - "Cl +3", - "\\ NH1", - "L i", - "Li +1", - "P H1", - "1 8", - "18 F", - "@ +1", - "3 H", - "P @@", - "H 0", - "O H0", - "1 2", - "P @", - "+ 2", - "@@ +1", - "S -1", - "/ Br", - "- /", - "\\ Cl", - "-/ Ring2", - "\\ O-1", - "1 1", - "5 I", - "12 5I", - "11 C", - "H 3", - "\\ N+1", - "- \\", - "/ C@@", - "S @+1", - "A s", - "/ Cl", - "11C H3", - "=S e", - "S @@+1", - "N @+1", - "1 4", - "-\\ Ring2", - "14 C", - "\\ F", - "/ C@", - "T e", - "H 2", - "H1 -1", - "=O +1", - "N @@+1", - "C +1", - "=S +1", - "Z n", - "/ P", - "a +2", - "/ I", - "O H1-1", - "C a+2", - "\\ Br", - "M g", - "Zn +2", - "A l", - "/ F", - "Mg +2", - "12 3", - "123 I", - "1 3", - "I +1", - "/ O-1", - "-\\ Ring1", - "B H2", - "BH2 -1", - "\\ I", - "/ NH1", - "O +1", - "13 1", - "131 I", - "= 14C", - "/ S+1", - "= Ring3", - "\\ C@@", - "H2 +1", - "\\ C@", - "A g", - "= As", - "=Se +1", - "N H2+1", - "Se H1", - "-/ Ring1", - "= Te", - "Al +3", - "Na H1", - "=Te +1", - "NH1 +1", - "Ag +1", - "H1 +1", - "NH1 -1", - "\\ P", - "14C H2", - "13 C", - "14C H1", - "= 11C", - "S @@", - "=P @@", - "Si H2", - "H3 -1", - "14C H3", - "B H3-1", - "S @", - "=14C H1", - "=P H1", - "=P @", - "=N H1+1", - "\\S +1", - "12 4", - "C H1-1", - "S r", - "=S i", - "124 I", - "Sr +2", - "#C -1", - "/C -1", - "N @", - "/N -1", - "13C H1", - "/ B", - "1 9", - "B a+2", - "H 4", - "S H1+1", - "Se +1", - "19 F", - "/ 125I", - "P @+1", - "R b", - "Cl +1", - "Si H4", - "Rb +1", - "= Branch3", - "N @@", - "As +1", - "/ Si", - "B H1-1", - "S H1", - "/ 123I", - "3 2", - "= Mg", - "H +1", - "\\ B", - "Si H1", - "P@@ +1", - "- 2", - "1 5", - "1 7", - "3 5", - "= 13CH1", - "C s", - "=N H2+1", - "=S H1", - "Mg H2", - "32 P", - "17 F", - "35 S", - "Cs +1", - "# 11C", - "/ 131I", - "B i", - "\\ 125I", - "=S @@", - "\\S -1", - "6 Br", - "7 I", - "7 6Br", - "= B", - "e H1", - "\\N -1", - "18 O", - "12 7I", - "11C H2", - "14 C@@H1", - "Te H2", - "15 NH1", - "Bi +3", - "/ P+1", - "/ 13C", - "/ 13CH1", - "0 B", - "1 0B", - "= Al", - "= 18O", - "B H0", - "F -1", - "N H3", - "S -2", - "Br +2", - "Cl +2", - "\\S i", - "/S -1", - "=P H2", - "14 C@H1", - "NH3 +1", - "# 14C", - "# O+1", - "- 3", - "2 2", - "4 H", - "5 Se", - "5 Sr+2", - "7 5Se", - "8 5Sr+2", - "= B-1", - "= 13C", - "@ -1", - "B e", - "B @@", - "B @-1", - "C a", - "C H1", - "I +3", - "K H1", - "O H1+1", - "R a+2", - "S H1-1", - "\\ PH1", - "\\ 123I", - "=C a", - "\\C H1-1", - "=S @", - "\\S eH1", - "/S eH1", - "Se -1", - "Li H1", - "18F -1", - "125I H1", - "11C H1", - "Te H1", - "Zn +1", - "Zn -2", - "Al -3", - "13C H3", - "15 N", - "Be +2", - "B@@ -1", - "# P", - "# S", - "- 4", - "/ PH1", - "/ P@@", - "/ As", - "/ 14C", - "/ 14CH1", - "2 K+1", - "2 Rb+1", - "3 Se", - "3 Ra+2", - "4 5", - "4 7", - "4 2K+1", - "5 I-1", - "7 3Se", - "8 9", - "8 2Rb+1", - "= 32", - "= 32P", - "C H0", - "C H2", - "I +2", - "N H0", - "N H4", - "O H1", - "P H2+1", - "S H0", - "S H2", - "\\ 3H", - "\\ 11CH3", - "\\C -1", - "\\S e", - "Si @", - "Si -1", - "Si H1-1", - "Si H3-1", - "/S e", - "Se -2", - "\\NH1 -1", - "18F H1", - "12 5I-1", - "11 C@@H1", - "11 C-1", - "As H1", - "As -1", - "14 C@@", - "Te -1", - "Mg +1", - "123 I-1", - "123 Te", - "123I H1", - "13 5I", - "131 I-1", - "Ag -4", - "124 I-1", - "76Br H1", - "18O H1", - "22 Na+1", - "22 3Ra+2", - "Ca H2", - "45 Ca+2", - "47 Ca+2", - "89 Sr+2", - "=32 PH1", - "NH4 +1" - ] - } -} \ No newline at end of file diff --git a/models/finetuned/freesolv/checkpoint_epoch_025/tokenizer_config.json b/models/finetuned/freesolv/checkpoint_epoch_025/tokenizer_config.json deleted file mode 100644 index 08860954acd34fad07fd77f7635298fa565f3149..0000000000000000000000000000000000000000 --- a/models/finetuned/freesolv/checkpoint_epoch_025/tokenizer_config.json +++ /dev/null @@ -1,65 +0,0 @@ -{ - "add_prefix_space": false, - "bos_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "cls_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "eos_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "errors": "replace", - "mask_token": { - "__type": "AddedToken", - "content": "", - "lstrip": true, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "model_max_length": 1000000000000000019884624838656, - "name_or_path": "/home/erva/SELFormerMM/data/pretrained_multimodal_chembl36", - "pad_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "sep_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "special_tokens_map_file": null, - "tokenizer_class": "RobertaTokenizer", - "trim_offsets": true, - "unk_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - } -} diff --git a/models/finetuned/freesolv/checkpoint_epoch_025/vocab.json b/models/finetuned/freesolv/checkpoint_epoch_025/vocab.json deleted file mode 100644 index f7e4cc22809f4e9035cc450ef189c8a7da8fd03e..0000000000000000000000000000000000000000 --- a/models/finetuned/freesolv/checkpoint_epoch_025/vocab.json +++ /dev/null @@ -1 +0,0 @@ -{"":0,"":1,"":2,"":3,"":4,"\n":5,"#":6,"+":7,"-":8,".":9,"/":10,"0":11,"1":12,"2":13,"3":14,"4":15,"5":16,"6":17,"7":18,"8":19,"9":20,"=":21,"@":22,"A":23,"B":24,"C":25,"F":26,"H":27,"I":28,"K":29,"L":30,"M":31,"N":32,"O":33,"P":34,"R":35,"S":36,"T":37,"Z":38,"\\":39,"a":40,"b":41,"c":42,"e":43,"g":44,"h":45,"i":46,"l":47,"n":48,"r":49,"s":50,"Br":51,"an":52,"ch":53,"Bran":54,"Branch":55,"Branch1":56,"=C":57,"Ri":58,"ng":59,"Ring":60,"Ring1":61,"=Branch1":62,"Branch2":63,"=O":64,"Ring2":65,"H1":66,"C@":67,"=N":68,"#Branch1":69,"C@@":70,"=Branch2":71,"C@H1":72,"C@@H1":73,"#Branch2":74,"#C":75,"Cl":76,"/C":77,"NH1":78,"=Ring1":79,"+1":80,"-1":81,"O-1":82,"N+1":83,"\\C":84,"#N":85,"/N":86,"=Ring2":87,"=S":88,"=N+1":89,"\\N":90,"Na":91,"Na+1":92,"/O":93,"\\O":94,"Br-1":95,"Branch3":96,"\\S":97,"S+1":98,"Cl-1":99,"I-1":100,"/C@@H1":101,"Si":102,"/C@H1":103,"/S":104,"=N-1":105,"Se":106,"=P":107,"N-1":108,"Ring3":109,"2H":110,"P+1":111,"K+1":112,"\\C@@H1":113,"\\C@H1":114,"/N+1":115,"@@":116,"C-1":117,"#N+1":118,"B-1":119,"+3":120,"Cl+3":121,"\\NH1":122,"Li":123,"Li+1":124,"PH1":125,"18":126,"18F":127,"@+1":128,"3H":129,"P@@":130,"H0":131,"OH0":132,"12":133,"P@":134,"+2":135,"@@+1":136,"S-1":137,"/Br":138,"-/":139,"\\Cl":140,"-/Ring2":141,"\\O-1":142,"11":143,"5I":144,"125I":145,"11C":146,"H3":147,"\\N+1":148,"-\\":149,"/C@@":150,"S@+1":151,"As":152,"/Cl":153,"11CH3":154,"=Se":155,"S@@+1":156,"N@+1":157,"14":158,"-\\Ring2":159,"14C":160,"\\F":161,"/C@":162,"Te":163,"H2":164,"H1-1":165,"=O+1":166,"N@@+1":167,"C+1":168,"=S+1":169,"Zn":170,"/P":171,"a+2":172,"/I":173,"OH1-1":174,"Ca+2":175,"\\Br":176,"Mg":177,"Zn+2":178,"Al":179,"/F":180,"Mg+2":181,"123":182,"123I":183,"13":184,"I+1":185,"/O-1":186,"-\\Ring1":187,"BH2":188,"BH2-1":189,"\\I":190,"/NH1":191,"O+1":192,"131":193,"131I":194,"=14C":195,"/S+1":196,"=Ring3":197,"\\C@@":198,"H2+1":199,"\\C@":200,"Ag":201,"=As":202,"=Se+1":203,"NH2+1":204,"SeH1":205,"-/Ring1":206,"=Te":207,"Al+3":208,"NaH1":209,"=Te+1":210,"NH1+1":211,"Ag+1":212,"H1+1":213,"NH1-1":214,"\\P":215,"14CH2":216,"13C":217,"14CH1":218,"=11C":219,"S@@":220,"=P@@":221,"SiH2":222,"H3-1":223,"14CH3":224,"BH3-1":225,"S@":226,"=14CH1":227,"=PH1":228,"=P@":229,"=NH1+1":230,"\\S+1":231,"124":232,"CH1-1":233,"Sr":234,"=Si":235,"124I":236,"Sr+2":237,"#C-1":238,"/C-1":239,"N@":240,"/N-1":241,"13CH1":242,"/B":243,"19":244,"Ba+2":245,"H4":246,"SH1+1":247,"Se+1":248,"19F":249,"/125I":250,"P@+1":251,"Rb":252,"Cl+1":253,"SiH4":254,"Rb+1":255,"=Branch3":256,"N@@":257,"As+1":258,"/Si":259,"BH1-1":260,"SH1":261,"/123I":262,"32":263,"=Mg":264,"H+1":265,"\\B":266,"SiH1":267,"P@@+1":268,"-2":269,"15":270,"17":271,"35":272,"=13CH1":273,"Cs":274,"=NH2+1":275,"=SH1":276,"MgH2":277,"32P":278,"17F":279,"35S":280,"Cs+1":281,"#11C":282,"/131I":283,"Bi":284,"\\125I":285,"=S@@":286,"\\S-1":287,"6Br":288,"7I":289,"76Br":290,"=B":291,"eH1":292,"\\N-1":293,"18O":294,"127I":295,"11CH2":296,"14C@@H1":297,"TeH2":298,"15NH1":299,"Bi+3":300,"/P+1":301,"/13C":302,"/13CH1":303,"0B":304,"10B":305,"=Al":306,"=18O":307,"BH0":308,"F-1":309,"NH3":310,"S-2":311,"Br+2":312,"Cl+2":313,"\\Si":314,"/S-1":315,"=PH2":316,"14C@H1":317,"NH3+1":318,"#14C":319,"#O+1":320,"-3":321,"22":322,"4H":323,"5Se":324,"5Sr+2":325,"75Se":326,"85Sr+2":327,"=B-1":328,"=13C":329,"@-1":330,"Be":331,"B@@":332,"B@-1":333,"Ca":334,"CH1":335,"I+3":336,"KH1":337,"OH1+1":338,"Ra+2":339,"SH1-1":340,"\\PH1":341,"\\123I":342,"=Ca":343,"\\CH1-1":344,"=S@":345,"\\SeH1":346,"/SeH1":347,"Se-1":348,"LiH1":349,"18F-1":350,"125IH1":351,"11CH1":352,"TeH1":353,"Zn+1":354,"Zn-2":355,"Al-3":356,"13CH3":357,"15N":358,"Be+2":359,"B@@-1":360,"#P":361,"#S":362,"-4":363,"/PH1":364,"/P@@":365,"/As":366,"/14C":367,"/14CH1":368,"2K+1":369,"2Rb+1":370,"3Se":371,"3Ra+2":372,"45":373,"47":374,"42K+1":375,"5I-1":376,"73Se":377,"89":378,"82Rb+1":379,"=32":380,"=32P":381,"CH0":382,"CH2":383,"I+2":384,"NH0":385,"NH4":386,"OH1":387,"PH2+1":388,"SH0":389,"SH2":390,"\\3H":391,"\\11CH3":392,"\\C-1":393,"\\Se":394,"Si@":395,"Si-1":396,"SiH1-1":397,"SiH3-1":398,"/Se":399,"Se-2":400,"\\NH1-1":401,"18FH1":402,"125I-1":403,"11C@@H1":404,"11C-1":405,"AsH1":406,"As-1":407,"14C@@":408,"Te-1":409,"Mg+1":410,"123I-1":411,"123Te":412,"123IH1":413,"135I":414,"131I-1":415,"Ag-4":416,"124I-1":417,"76BrH1":418,"18OH1":419,"22Na+1":420,"223Ra+2":421,"CaH2":422,"45Ca+2":423,"47Ca+2":424,"89Sr+2":425,"=32PH1":426,"NH4+1":427} \ No newline at end of file diff --git a/models/finetuned/freesolv/checkpoint_epoch_050/config.json b/models/finetuned/freesolv/checkpoint_epoch_050/config.json deleted file mode 100644 index 3811e21539577b37e06313eab31ec11e53f0cbbc..0000000000000000000000000000000000000000 --- a/models/finetuned/freesolv/checkpoint_epoch_050/config.json +++ /dev/null @@ -1,27 +0,0 @@ -{ - "_name_or_path": "/home/erva/SELFormerMM/data/pretrained_multimodal_chembl36", - "architectures": [ - "RobertaForMaskedLM" - ], - "attention_probs_dropout_prob": 0.1, - "bos_token_id": 0, - "classifier_dropout": null, - "eos_token_id": 2, - "hidden_act": "gelu", - "hidden_dropout_prob": 0.1, - "hidden_size": 768, - "initializer_range": 0.02, - "intermediate_size": 3072, - "layer_norm_eps": 1e-12, - "max_position_embeddings": 514, - "model_type": "roberta", - "num_attention_heads": 4, - "num_hidden_layers": 12, - "pad_token_id": 1, - "position_embedding_type": "absolute", - "torch_dtype": "float32", - "transformers_version": "4.26.1", - "type_vocab_size": 1, - "use_cache": true, - "vocab_size": 800 -} diff --git a/models/finetuned/freesolv/checkpoint_epoch_050/merges.txt b/models/finetuned/freesolv/checkpoint_epoch_050/merges.txt deleted file mode 100644 index 7cd5ec62809503c23f18c80afc0ba3bdf9d253d0..0000000000000000000000000000000000000000 --- a/models/finetuned/freesolv/checkpoint_epoch_050/merges.txt +++ /dev/null @@ -1,378 +0,0 @@ -#version: 0.2 - Trained by `huggingface/tokenizers` -B r -a n -c h -Br an -Bran ch -Branch 1 -= C -R i -n g -Ri ng -Ring 1 -= Branch1 -Branch 2 -= O -Ring 2 -H 1 -C @ -= N -# Branch1 -C@ @ -= Branch2 -C@ H1 -C@@ H1 -# Branch2 -# C -C l -/ C -N H1 -= Ring1 -+ 1 -- 1 -O -1 -N +1 -\ C -# N -/ N -= Ring2 -= S -=N +1 -\ N -N a -Na +1 -/ O -\ O -Br -1 -Branch 3 -\ S -S +1 -Cl -1 -I -1 -/ C@@H1 -S i -/ C@H1 -/ S -=N -1 -S e -= P -N -1 -Ring 3 -2 H -P +1 -K +1 -\ C@@H1 -\ C@H1 -/ N+1 -@ @ -C -1 -# N+1 -B -1 -+ 3 -Cl +3 -\ NH1 -L i -Li +1 -P H1 -1 8 -18 F -@ +1 -3 H -P @@ -H 0 -O H0 -1 2 -P @ -+ 2 -@@ +1 -S -1 -/ Br -- / -\ Cl --/ Ring2 -\ O-1 -1 1 -5 I -12 5I -11 C -H 3 -\ N+1 -- \ -/ C@@ -S @+1 -A s -/ Cl -11C H3 -=S e -S @@+1 -N @+1 -1 4 --\ Ring2 -14 C -\ F -/ C@ -T e -H 2 -H1 -1 -=O +1 -N @@+1 -C +1 -=S +1 -Z n -/ P -a +2 -/ I -O H1-1 -C a+2 -\ Br -M g -Zn +2 -A l -/ F -Mg +2 -12 3 -123 I -1 3 -I +1 -/ O-1 --\ Ring1 -B H2 -BH2 -1 -\ I -/ NH1 -O +1 -13 1 -131 I -= 14C -/ S+1 -= Ring3 -\ C@@ -H2 +1 -\ C@ -A g -= As -=Se +1 -N H2+1 -Se H1 --/ Ring1 -= Te -Al +3 -Na H1 -=Te +1 -NH1 +1 -Ag +1 -H1 +1 -NH1 -1 -\ P -14C H2 -13 C -14C H1 -= 11C -S @@ -=P @@ -Si H2 -H3 -1 -14C H3 -B H3-1 -S @ -=14C H1 -=P H1 -=P @ -=N H1+1 -\S +1 -12 4 -C H1-1 -S r -=S i -124 I -Sr +2 -#C -1 -/C -1 -N @ -/N -1 -13C H1 -/ B -1 9 -B a+2 -H 4 -S H1+1 -Se +1 -19 F -/ 125I -P @+1 -R b -Cl +1 -Si H4 -Rb +1 -= Branch3 -N @@ -As +1 -/ Si -B H1-1 -S H1 -/ 123I -3 2 -= Mg -H +1 -\ B -Si H1 -P@@ +1 -- 2 -1 5 -1 7 -3 5 -= 13CH1 -C s -=N H2+1 -=S H1 -Mg H2 -32 P -17 F -35 S -Cs +1 -# 11C -/ 131I -B i -\ 125I -=S @@ -\S -1 -6 Br -7 I -7 6Br -= B -e H1 -\N -1 -18 O -12 7I -11C H2 -14 C@@H1 -Te H2 -15 NH1 -Bi +3 -/ P+1 -/ 13C -/ 13CH1 -0 B -1 0B -= Al -= 18O -B H0 -F -1 -N H3 -S -2 -Br +2 -Cl +2 -\S i -/S -1 -=P H2 -14 C@H1 -NH3 +1 -# 14C -# O+1 -- 3 -2 2 -4 H -5 Se -5 Sr+2 -7 5Se -8 5Sr+2 -= B-1 -= 13C -@ -1 -B e -B @@ -B @-1 -C a -C H1 -I +3 -K H1 -O H1+1 -R a+2 -S H1-1 -\ PH1 -\ 123I -=C a -\C H1-1 -=S @ -\S eH1 -/S eH1 -Se -1 -Li H1 -18F -1 -125I H1 -11C H1 -Te H1 -Zn +1 -Zn -2 -Al -3 -13C H3 -15 N -Be +2 -B@@ -1 -# P -# S -- 4 -/ PH1 -/ P@@ -/ As -/ 14C -/ 14CH1 -2 K+1 -2 Rb+1 -3 Se -3 Ra+2 -4 5 -4 7 -4 2K+1 -5 I-1 -7 3Se -8 9 -8 2Rb+1 -= 32 -= 32P -C H0 -C H2 -I +2 -N H0 -N H4 -O H1 -P H2+1 -S H0 -S H2 -\ 3H -\ 11CH3 -\C -1 -\S e -Si @ -Si -1 -Si H1-1 -Si H3-1 -/S e -Se -2 -\NH1 -1 -18F H1 -12 5I-1 -11 C@@H1 -11 C-1 -As H1 -As -1 -14 C@@ -Te -1 -Mg +1 -123 I-1 -123 Te -123I H1 -13 5I -131 I-1 -Ag -4 -124 I-1 -76Br H1 -18O H1 -22 Na+1 -22 3Ra+2 -Ca H2 -45 Ca+2 -47 Ca+2 -89 Sr+2 -=32 PH1 -NH4 +1 diff --git a/models/finetuned/freesolv/checkpoint_epoch_050/model.pt b/models/finetuned/freesolv/checkpoint_epoch_050/model.pt deleted file mode 100644 index b4db7d8c07d36db777c87860a91fdcbce7b97039..0000000000000000000000000000000000000000 --- a/models/finetuned/freesolv/checkpoint_epoch_050/model.pt +++ /dev/null @@ -1,3 +0,0 @@ -version https://git-lfs.github.com/spec/v1 -oid sha256:18d826a9910632f53115fa941647098fcfed72830b225c3d73c45a123e154d64 -size 1022843005 diff --git a/models/finetuned/freesolv/checkpoint_epoch_050/special_tokens_map.json b/models/finetuned/freesolv/checkpoint_epoch_050/special_tokens_map.json deleted file mode 100644 index 06a55849fa69a91e7179d909e373179ff7467d8c..0000000000000000000000000000000000000000 --- a/models/finetuned/freesolv/checkpoint_epoch_050/special_tokens_map.json +++ /dev/null @@ -1,51 +0,0 @@ -{ - "bos_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "cls_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "eos_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "mask_token": { - "content": "", - "lstrip": true, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "pad_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "sep_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "unk_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - } -} diff --git a/models/finetuned/freesolv/checkpoint_epoch_050/tokenizer.json b/models/finetuned/freesolv/checkpoint_epoch_050/tokenizer.json deleted file mode 100644 index 3b64b273e6fa9799e2d8375722b9e815de9ebb8f..0000000000000000000000000000000000000000 --- a/models/finetuned/freesolv/checkpoint_epoch_050/tokenizer.json +++ /dev/null @@ -1,909 +0,0 @@ -{ - "version": "1.0", - "truncation": { - "direction": "Right", - "max_length": 128, - "strategy": "LongestFirst", - "stride": 0 - }, - "padding": { - "strategy": { - "Fixed": 128 - }, - "direction": "Right", - "pad_to_multiple_of": null, - "pad_id": 3, - "pad_type_id": 0, - "pad_token": "" - }, - "added_tokens": [ - { - "id": 0, - "content": "", - "single_word": false, - "lstrip": false, - "rstrip": false, - "normalized": true, - "special": true - }, - { - "id": 1, - "content": "", - "single_word": false, - "lstrip": false, - "rstrip": false, - "normalized": true, - "special": true - }, - { - "id": 2, - "content": "", - "single_word": false, - "lstrip": false, - "rstrip": false, - "normalized": true, - "special": true - }, - { - "id": 3, - "content": "", - "single_word": false, - "lstrip": false, - "rstrip": false, - "normalized": true, - "special": true - }, - { - "id": 4, - "content": "", - "single_word": false, - "lstrip": true, - "rstrip": false, - "normalized": true, - "special": true - } - ], - "normalizer": null, - "pre_tokenizer": { - "type": "ByteLevel", - "add_prefix_space": false, - "trim_offsets": true, - "use_regex": true - }, - "post_processor": { - "type": "RobertaProcessing", - "sep": [ - "", - 2 - ], - "cls": [ - "", - 1 - ], - "trim_offsets": true, - "add_prefix_space": false - }, - "decoder": { - "type": "ByteLevel", - "add_prefix_space": true, - "trim_offsets": true, - "use_regex": true - }, - "model": { - "type": "BPE", - "dropout": null, - "unk_token": null, - "continuing_subword_prefix": "", - "end_of_word_suffix": "", - "fuse_unk": false, - "vocab": { - "": 0, - "": 1, - "": 2, - "": 3, - "": 4, - "\n": 5, - "#": 6, - "+": 7, - "-": 8, - ".": 9, - "/": 10, - "0": 11, - "1": 12, - "2": 13, - "3": 14, - "4": 15, - "5": 16, - "6": 17, - "7": 18, - "8": 19, - "9": 20, - "=": 21, - "@": 22, - "A": 23, - "B": 24, - "C": 25, - "F": 26, - "H": 27, - "I": 28, - "K": 29, - "L": 30, - "M": 31, - "N": 32, - "O": 33, - "P": 34, - "R": 35, - "S": 36, - "T": 37, - "Z": 38, - "\\": 39, - "a": 40, - "b": 41, - "c": 42, - "e": 43, - "g": 44, - "h": 45, - "i": 46, - "l": 47, - "n": 48, - "r": 49, - "s": 50, - "Br": 51, - "an": 52, - "ch": 53, - "Bran": 54, - "Branch": 55, - "Branch1": 56, - "=C": 57, - "Ri": 58, - "ng": 59, - "Ring": 60, - "Ring1": 61, - "=Branch1": 62, - "Branch2": 63, - "=O": 64, - "Ring2": 65, - "H1": 66, - "C@": 67, - "=N": 68, - "#Branch1": 69, - "C@@": 70, - "=Branch2": 71, - "C@H1": 72, - "C@@H1": 73, - "#Branch2": 74, - "#C": 75, - "Cl": 76, - "/C": 77, - "NH1": 78, - "=Ring1": 79, - "+1": 80, - "-1": 81, - "O-1": 82, - "N+1": 83, - "\\C": 84, - "#N": 85, - "/N": 86, - "=Ring2": 87, - "=S": 88, - "=N+1": 89, - "\\N": 90, - "Na": 91, - "Na+1": 92, - "/O": 93, - "\\O": 94, - "Br-1": 95, - "Branch3": 96, - "\\S": 97, - "S+1": 98, - "Cl-1": 99, - "I-1": 100, - "/C@@H1": 101, - "Si": 102, - "/C@H1": 103, - "/S": 104, - "=N-1": 105, - "Se": 106, - "=P": 107, - "N-1": 108, - "Ring3": 109, - "2H": 110, - "P+1": 111, - "K+1": 112, - "\\C@@H1": 113, - "\\C@H1": 114, - "/N+1": 115, - "@@": 116, - "C-1": 117, - "#N+1": 118, - "B-1": 119, - "+3": 120, - "Cl+3": 121, - "\\NH1": 122, - "Li": 123, - "Li+1": 124, - "PH1": 125, - "18": 126, - "18F": 127, - "@+1": 128, - "3H": 129, - "P@@": 130, - "H0": 131, - "OH0": 132, - "12": 133, - "P@": 134, - "+2": 135, - "@@+1": 136, - "S-1": 137, - "/Br": 138, - "-/": 139, - "\\Cl": 140, - "-/Ring2": 141, - "\\O-1": 142, - "11": 143, - "5I": 144, - "125I": 145, - "11C": 146, - "H3": 147, - "\\N+1": 148, - "-\\": 149, - "/C@@": 150, - "S@+1": 151, - "As": 152, - "/Cl": 153, - "11CH3": 154, - "=Se": 155, - "S@@+1": 156, - "N@+1": 157, - "14": 158, - "-\\Ring2": 159, - "14C": 160, - "\\F": 161, - "/C@": 162, - "Te": 163, - "H2": 164, - "H1-1": 165, - "=O+1": 166, - "N@@+1": 167, - "C+1": 168, - "=S+1": 169, - "Zn": 170, - "/P": 171, - "a+2": 172, - "/I": 173, - "OH1-1": 174, - "Ca+2": 175, - "\\Br": 176, - "Mg": 177, - "Zn+2": 178, - "Al": 179, - "/F": 180, - "Mg+2": 181, - "123": 182, - "123I": 183, - "13": 184, - "I+1": 185, - "/O-1": 186, - "-\\Ring1": 187, - "BH2": 188, - "BH2-1": 189, - "\\I": 190, - "/NH1": 191, - "O+1": 192, - "131": 193, - "131I": 194, - "=14C": 195, - "/S+1": 196, - "=Ring3": 197, - "\\C@@": 198, - "H2+1": 199, - "\\C@": 200, - "Ag": 201, - "=As": 202, - "=Se+1": 203, - "NH2+1": 204, - "SeH1": 205, - "-/Ring1": 206, - "=Te": 207, - "Al+3": 208, - "NaH1": 209, - "=Te+1": 210, - "NH1+1": 211, - "Ag+1": 212, - "H1+1": 213, - "NH1-1": 214, - "\\P": 215, - "14CH2": 216, - "13C": 217, - "14CH1": 218, - "=11C": 219, - "S@@": 220, - "=P@@": 221, - "SiH2": 222, - "H3-1": 223, - "14CH3": 224, - "BH3-1": 225, - "S@": 226, - "=14CH1": 227, - "=PH1": 228, - "=P@": 229, - "=NH1+1": 230, - "\\S+1": 231, - "124": 232, - "CH1-1": 233, - "Sr": 234, - "=Si": 235, - "124I": 236, - "Sr+2": 237, - "#C-1": 238, - "/C-1": 239, - "N@": 240, - "/N-1": 241, - "13CH1": 242, - "/B": 243, - "19": 244, - "Ba+2": 245, - "H4": 246, - "SH1+1": 247, - "Se+1": 248, - "19F": 249, - "/125I": 250, - "P@+1": 251, - "Rb": 252, - "Cl+1": 253, - "SiH4": 254, - "Rb+1": 255, - "=Branch3": 256, - "N@@": 257, - "As+1": 258, - "/Si": 259, - "BH1-1": 260, - "SH1": 261, - "/123I": 262, - "32": 263, - "=Mg": 264, - "H+1": 265, - "\\B": 266, - "SiH1": 267, - "P@@+1": 268, - "-2": 269, - "15": 270, - "17": 271, - "35": 272, - "=13CH1": 273, - "Cs": 274, - "=NH2+1": 275, - "=SH1": 276, - "MgH2": 277, - "32P": 278, - "17F": 279, - "35S": 280, - "Cs+1": 281, - "#11C": 282, - "/131I": 283, - "Bi": 284, - "\\125I": 285, - "=S@@": 286, - "\\S-1": 287, - "6Br": 288, - "7I": 289, - "76Br": 290, - "=B": 291, - "eH1": 292, - "\\N-1": 293, - "18O": 294, - "127I": 295, - "11CH2": 296, - "14C@@H1": 297, - "TeH2": 298, - "15NH1": 299, - "Bi+3": 300, - "/P+1": 301, - "/13C": 302, - "/13CH1": 303, - "0B": 304, - "10B": 305, - "=Al": 306, - "=18O": 307, - "BH0": 308, - "F-1": 309, - "NH3": 310, - "S-2": 311, - "Br+2": 312, - "Cl+2": 313, - "\\Si": 314, - "/S-1": 315, - "=PH2": 316, - "14C@H1": 317, - "NH3+1": 318, - "#14C": 319, - "#O+1": 320, - "-3": 321, - "22": 322, - "4H": 323, - "5Se": 324, - "5Sr+2": 325, - "75Se": 326, - "85Sr+2": 327, - "=B-1": 328, - "=13C": 329, - "@-1": 330, - "Be": 331, - "B@@": 332, - "B@-1": 333, - "Ca": 334, - "CH1": 335, - "I+3": 336, - "KH1": 337, - "OH1+1": 338, - "Ra+2": 339, - "SH1-1": 340, - "\\PH1": 341, - "\\123I": 342, - "=Ca": 343, - "\\CH1-1": 344, - "=S@": 345, - "\\SeH1": 346, - "/SeH1": 347, - "Se-1": 348, - "LiH1": 349, - "18F-1": 350, - "125IH1": 351, - "11CH1": 352, - "TeH1": 353, - "Zn+1": 354, - "Zn-2": 355, - "Al-3": 356, - "13CH3": 357, - "15N": 358, - "Be+2": 359, - "B@@-1": 360, - "#P": 361, - "#S": 362, - "-4": 363, - "/PH1": 364, - "/P@@": 365, - "/As": 366, - "/14C": 367, - "/14CH1": 368, - "2K+1": 369, - "2Rb+1": 370, - "3Se": 371, - "3Ra+2": 372, - "45": 373, - "47": 374, - "42K+1": 375, - "5I-1": 376, - "73Se": 377, - "89": 378, - "82Rb+1": 379, - "=32": 380, - "=32P": 381, - "CH0": 382, - "CH2": 383, - "I+2": 384, - "NH0": 385, - "NH4": 386, - "OH1": 387, - "PH2+1": 388, - "SH0": 389, - "SH2": 390, - "\\3H": 391, - "\\11CH3": 392, - "\\C-1": 393, - "\\Se": 394, - "Si@": 395, - "Si-1": 396, - "SiH1-1": 397, - "SiH3-1": 398, - "/Se": 399, - "Se-2": 400, - "\\NH1-1": 401, - "18FH1": 402, - "125I-1": 403, - "11C@@H1": 404, - "11C-1": 405, - "AsH1": 406, - "As-1": 407, - "14C@@": 408, - "Te-1": 409, - "Mg+1": 410, - "123I-1": 411, - "123Te": 412, - "123IH1": 413, - "135I": 414, - "131I-1": 415, - "Ag-4": 416, - "124I-1": 417, - "76BrH1": 418, - "18OH1": 419, - "22Na+1": 420, - "223Ra+2": 421, - "CaH2": 422, - "45Ca+2": 423, - "47Ca+2": 424, - "89Sr+2": 425, - "=32PH1": 426, - "NH4+1": 427 - }, - "merges": [ - "B r", - "a n", - "c h", - "Br an", - "Bran ch", - "Branch 1", - "= C", - "R i", - "n g", - "Ri ng", - "Ring 1", - "= Branch1", - "Branch 2", - "= O", - "Ring 2", - "H 1", - "C @", - "= N", - "# Branch1", - "C@ @", - "= Branch2", - "C@ H1", - "C@@ H1", - "# Branch2", - "# C", - "C l", - "/ C", - "N H1", - "= Ring1", - "+ 1", - "- 1", - "O -1", - "N +1", - "\\ C", - "# N", - "/ N", - "= Ring2", - "= S", - "=N +1", - "\\ N", - "N a", - "Na +1", - "/ O", - "\\ O", - "Br -1", - "Branch 3", - "\\ S", - "S +1", - "Cl -1", - "I -1", - "/ C@@H1", - "S i", - "/ C@H1", - "/ S", - "=N -1", - "S e", - "= P", - "N -1", - "Ring 3", - "2 H", - "P +1", - "K +1", - "\\ C@@H1", - "\\ C@H1", - "/ N+1", - "@ @", - "C -1", - "# N+1", - "B -1", - "+ 3", - "Cl +3", - "\\ NH1", - "L i", - "Li +1", - "P H1", - "1 8", - "18 F", - "@ +1", - "3 H", - "P @@", - "H 0", - "O H0", - "1 2", - "P @", - "+ 2", - "@@ +1", - "S -1", - "/ Br", - "- /", - "\\ Cl", - "-/ Ring2", - "\\ O-1", - "1 1", - "5 I", - "12 5I", - "11 C", - "H 3", - "\\ N+1", - "- \\", - "/ C@@", - "S @+1", - "A s", - "/ Cl", - "11C H3", - "=S e", - "S @@+1", - "N @+1", - "1 4", - "-\\ Ring2", - "14 C", - "\\ F", - "/ C@", - "T e", - "H 2", - "H1 -1", - "=O +1", - "N @@+1", - "C +1", - "=S +1", - "Z n", - "/ P", - "a +2", - "/ I", - "O H1-1", - "C a+2", - "\\ Br", - "M g", - "Zn +2", - "A l", - "/ F", - "Mg +2", - "12 3", - "123 I", - "1 3", - "I +1", - "/ O-1", - "-\\ Ring1", - "B H2", - "BH2 -1", - "\\ I", - "/ NH1", - "O +1", - "13 1", - "131 I", - "= 14C", - "/ S+1", - "= Ring3", - "\\ C@@", - "H2 +1", - "\\ C@", - "A g", - "= As", - "=Se +1", - "N H2+1", - "Se H1", - "-/ Ring1", - "= Te", - "Al +3", - "Na H1", - "=Te +1", - "NH1 +1", - "Ag +1", - "H1 +1", - "NH1 -1", - "\\ P", - "14C H2", - "13 C", - "14C H1", - "= 11C", - "S @@", - "=P @@", - "Si H2", - "H3 -1", - "14C H3", - "B H3-1", - "S @", - "=14C H1", - "=P H1", - "=P @", - "=N H1+1", - "\\S +1", - "12 4", - "C H1-1", - "S r", - "=S i", - "124 I", - "Sr +2", - "#C -1", - "/C -1", - "N @", - "/N -1", - "13C H1", - "/ B", - "1 9", - "B a+2", - "H 4", - "S H1+1", - "Se +1", - "19 F", - "/ 125I", - "P @+1", - "R b", - "Cl +1", - "Si H4", - "Rb +1", - "= Branch3", - "N @@", - "As +1", - "/ Si", - "B H1-1", - "S H1", - "/ 123I", - "3 2", - "= Mg", - "H +1", - "\\ B", - "Si H1", - "P@@ +1", - "- 2", - "1 5", - "1 7", - "3 5", - "= 13CH1", - "C s", - "=N H2+1", - "=S H1", - "Mg H2", - "32 P", - "17 F", - "35 S", - "Cs +1", - "# 11C", - "/ 131I", - "B i", - "\\ 125I", - "=S @@", - "\\S -1", - "6 Br", - "7 I", - "7 6Br", - "= B", - "e H1", - "\\N -1", - "18 O", - "12 7I", - "11C H2", - "14 C@@H1", - "Te H2", - "15 NH1", - "Bi +3", - "/ P+1", - "/ 13C", - "/ 13CH1", - "0 B", - "1 0B", - "= Al", - "= 18O", - "B H0", - "F -1", - "N H3", - "S -2", - "Br +2", - "Cl +2", - "\\S i", - "/S -1", - "=P H2", - "14 C@H1", - "NH3 +1", - "# 14C", - "# O+1", - "- 3", - "2 2", - "4 H", - "5 Se", - "5 Sr+2", - "7 5Se", - "8 5Sr+2", - "= B-1", - "= 13C", - "@ -1", - "B e", - "B @@", - "B @-1", - "C a", - "C H1", - "I +3", - "K H1", - "O H1+1", - "R a+2", - "S H1-1", - "\\ PH1", - "\\ 123I", - "=C a", - "\\C H1-1", - "=S @", - "\\S eH1", - "/S eH1", - "Se -1", - "Li H1", - "18F -1", - "125I H1", - "11C H1", - "Te H1", - "Zn +1", - "Zn -2", - "Al -3", - "13C H3", - "15 N", - "Be +2", - "B@@ -1", - "# P", - "# S", - "- 4", - "/ PH1", - "/ P@@", - "/ As", - "/ 14C", - "/ 14CH1", - "2 K+1", - "2 Rb+1", - "3 Se", - "3 Ra+2", - "4 5", - "4 7", - "4 2K+1", - "5 I-1", - "7 3Se", - "8 9", - "8 2Rb+1", - "= 32", - "= 32P", - "C H0", - "C H2", - "I +2", - "N H0", - "N H4", - "O H1", - "P H2+1", - "S H0", - "S H2", - "\\ 3H", - "\\ 11CH3", - "\\C -1", - "\\S e", - "Si @", - "Si -1", - "Si H1-1", - "Si H3-1", - "/S e", - "Se -2", - "\\NH1 -1", - "18F H1", - "12 5I-1", - "11 C@@H1", - "11 C-1", - "As H1", - "As -1", - "14 C@@", - "Te -1", - "Mg +1", - "123 I-1", - "123 Te", - "123I H1", - "13 5I", - "131 I-1", - "Ag -4", - "124 I-1", - "76Br H1", - "18O H1", - "22 Na+1", - "22 3Ra+2", - "Ca H2", - "45 Ca+2", - "47 Ca+2", - "89 Sr+2", - "=32 PH1", - "NH4 +1" - ] - } -} \ No newline at end of file diff --git a/models/finetuned/freesolv/checkpoint_epoch_050/tokenizer_config.json b/models/finetuned/freesolv/checkpoint_epoch_050/tokenizer_config.json deleted file mode 100644 index 08860954acd34fad07fd77f7635298fa565f3149..0000000000000000000000000000000000000000 --- a/models/finetuned/freesolv/checkpoint_epoch_050/tokenizer_config.json +++ /dev/null @@ -1,65 +0,0 @@ -{ - "add_prefix_space": false, - "bos_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "cls_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "eos_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "errors": "replace", - "mask_token": { - "__type": "AddedToken", - "content": "", - "lstrip": true, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "model_max_length": 1000000000000000019884624838656, - "name_or_path": "/home/erva/SELFormerMM/data/pretrained_multimodal_chembl36", - "pad_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "sep_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "special_tokens_map_file": null, - "tokenizer_class": "RobertaTokenizer", - "trim_offsets": true, - "unk_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - } -} diff --git a/models/finetuned/freesolv/checkpoint_epoch_050/vocab.json b/models/finetuned/freesolv/checkpoint_epoch_050/vocab.json deleted file mode 100644 index f7e4cc22809f4e9035cc450ef189c8a7da8fd03e..0000000000000000000000000000000000000000 --- a/models/finetuned/freesolv/checkpoint_epoch_050/vocab.json +++ /dev/null @@ -1 +0,0 @@ -{"":0,"":1,"":2,"":3,"":4,"\n":5,"#":6,"+":7,"-":8,".":9,"/":10,"0":11,"1":12,"2":13,"3":14,"4":15,"5":16,"6":17,"7":18,"8":19,"9":20,"=":21,"@":22,"A":23,"B":24,"C":25,"F":26,"H":27,"I":28,"K":29,"L":30,"M":31,"N":32,"O":33,"P":34,"R":35,"S":36,"T":37,"Z":38,"\\":39,"a":40,"b":41,"c":42,"e":43,"g":44,"h":45,"i":46,"l":47,"n":48,"r":49,"s":50,"Br":51,"an":52,"ch":53,"Bran":54,"Branch":55,"Branch1":56,"=C":57,"Ri":58,"ng":59,"Ring":60,"Ring1":61,"=Branch1":62,"Branch2":63,"=O":64,"Ring2":65,"H1":66,"C@":67,"=N":68,"#Branch1":69,"C@@":70,"=Branch2":71,"C@H1":72,"C@@H1":73,"#Branch2":74,"#C":75,"Cl":76,"/C":77,"NH1":78,"=Ring1":79,"+1":80,"-1":81,"O-1":82,"N+1":83,"\\C":84,"#N":85,"/N":86,"=Ring2":87,"=S":88,"=N+1":89,"\\N":90,"Na":91,"Na+1":92,"/O":93,"\\O":94,"Br-1":95,"Branch3":96,"\\S":97,"S+1":98,"Cl-1":99,"I-1":100,"/C@@H1":101,"Si":102,"/C@H1":103,"/S":104,"=N-1":105,"Se":106,"=P":107,"N-1":108,"Ring3":109,"2H":110,"P+1":111,"K+1":112,"\\C@@H1":113,"\\C@H1":114,"/N+1":115,"@@":116,"C-1":117,"#N+1":118,"B-1":119,"+3":120,"Cl+3":121,"\\NH1":122,"Li":123,"Li+1":124,"PH1":125,"18":126,"18F":127,"@+1":128,"3H":129,"P@@":130,"H0":131,"OH0":132,"12":133,"P@":134,"+2":135,"@@+1":136,"S-1":137,"/Br":138,"-/":139,"\\Cl":140,"-/Ring2":141,"\\O-1":142,"11":143,"5I":144,"125I":145,"11C":146,"H3":147,"\\N+1":148,"-\\":149,"/C@@":150,"S@+1":151,"As":152,"/Cl":153,"11CH3":154,"=Se":155,"S@@+1":156,"N@+1":157,"14":158,"-\\Ring2":159,"14C":160,"\\F":161,"/C@":162,"Te":163,"H2":164,"H1-1":165,"=O+1":166,"N@@+1":167,"C+1":168,"=S+1":169,"Zn":170,"/P":171,"a+2":172,"/I":173,"OH1-1":174,"Ca+2":175,"\\Br":176,"Mg":177,"Zn+2":178,"Al":179,"/F":180,"Mg+2":181,"123":182,"123I":183,"13":184,"I+1":185,"/O-1":186,"-\\Ring1":187,"BH2":188,"BH2-1":189,"\\I":190,"/NH1":191,"O+1":192,"131":193,"131I":194,"=14C":195,"/S+1":196,"=Ring3":197,"\\C@@":198,"H2+1":199,"\\C@":200,"Ag":201,"=As":202,"=Se+1":203,"NH2+1":204,"SeH1":205,"-/Ring1":206,"=Te":207,"Al+3":208,"NaH1":209,"=Te+1":210,"NH1+1":211,"Ag+1":212,"H1+1":213,"NH1-1":214,"\\P":215,"14CH2":216,"13C":217,"14CH1":218,"=11C":219,"S@@":220,"=P@@":221,"SiH2":222,"H3-1":223,"14CH3":224,"BH3-1":225,"S@":226,"=14CH1":227,"=PH1":228,"=P@":229,"=NH1+1":230,"\\S+1":231,"124":232,"CH1-1":233,"Sr":234,"=Si":235,"124I":236,"Sr+2":237,"#C-1":238,"/C-1":239,"N@":240,"/N-1":241,"13CH1":242,"/B":243,"19":244,"Ba+2":245,"H4":246,"SH1+1":247,"Se+1":248,"19F":249,"/125I":250,"P@+1":251,"Rb":252,"Cl+1":253,"SiH4":254,"Rb+1":255,"=Branch3":256,"N@@":257,"As+1":258,"/Si":259,"BH1-1":260,"SH1":261,"/123I":262,"32":263,"=Mg":264,"H+1":265,"\\B":266,"SiH1":267,"P@@+1":268,"-2":269,"15":270,"17":271,"35":272,"=13CH1":273,"Cs":274,"=NH2+1":275,"=SH1":276,"MgH2":277,"32P":278,"17F":279,"35S":280,"Cs+1":281,"#11C":282,"/131I":283,"Bi":284,"\\125I":285,"=S@@":286,"\\S-1":287,"6Br":288,"7I":289,"76Br":290,"=B":291,"eH1":292,"\\N-1":293,"18O":294,"127I":295,"11CH2":296,"14C@@H1":297,"TeH2":298,"15NH1":299,"Bi+3":300,"/P+1":301,"/13C":302,"/13CH1":303,"0B":304,"10B":305,"=Al":306,"=18O":307,"BH0":308,"F-1":309,"NH3":310,"S-2":311,"Br+2":312,"Cl+2":313,"\\Si":314,"/S-1":315,"=PH2":316,"14C@H1":317,"NH3+1":318,"#14C":319,"#O+1":320,"-3":321,"22":322,"4H":323,"5Se":324,"5Sr+2":325,"75Se":326,"85Sr+2":327,"=B-1":328,"=13C":329,"@-1":330,"Be":331,"B@@":332,"B@-1":333,"Ca":334,"CH1":335,"I+3":336,"KH1":337,"OH1+1":338,"Ra+2":339,"SH1-1":340,"\\PH1":341,"\\123I":342,"=Ca":343,"\\CH1-1":344,"=S@":345,"\\SeH1":346,"/SeH1":347,"Se-1":348,"LiH1":349,"18F-1":350,"125IH1":351,"11CH1":352,"TeH1":353,"Zn+1":354,"Zn-2":355,"Al-3":356,"13CH3":357,"15N":358,"Be+2":359,"B@@-1":360,"#P":361,"#S":362,"-4":363,"/PH1":364,"/P@@":365,"/As":366,"/14C":367,"/14CH1":368,"2K+1":369,"2Rb+1":370,"3Se":371,"3Ra+2":372,"45":373,"47":374,"42K+1":375,"5I-1":376,"73Se":377,"89":378,"82Rb+1":379,"=32":380,"=32P":381,"CH0":382,"CH2":383,"I+2":384,"NH0":385,"NH4":386,"OH1":387,"PH2+1":388,"SH0":389,"SH2":390,"\\3H":391,"\\11CH3":392,"\\C-1":393,"\\Se":394,"Si@":395,"Si-1":396,"SiH1-1":397,"SiH3-1":398,"/Se":399,"Se-2":400,"\\NH1-1":401,"18FH1":402,"125I-1":403,"11C@@H1":404,"11C-1":405,"AsH1":406,"As-1":407,"14C@@":408,"Te-1":409,"Mg+1":410,"123I-1":411,"123Te":412,"123IH1":413,"135I":414,"131I-1":415,"Ag-4":416,"124I-1":417,"76BrH1":418,"18OH1":419,"22Na+1":420,"223Ra+2":421,"CaH2":422,"45Ca+2":423,"47Ca+2":424,"89Sr+2":425,"=32PH1":426,"NH4+1":427} \ No newline at end of file diff --git a/models/finetuned/freesolv/config.json b/models/finetuned/freesolv/config.json deleted file mode 100644 index 3811e21539577b37e06313eab31ec11e53f0cbbc..0000000000000000000000000000000000000000 --- a/models/finetuned/freesolv/config.json +++ /dev/null @@ -1,27 +0,0 @@ -{ - "_name_or_path": "/home/erva/SELFormerMM/data/pretrained_multimodal_chembl36", - "architectures": [ - "RobertaForMaskedLM" - ], - "attention_probs_dropout_prob": 0.1, - "bos_token_id": 0, - "classifier_dropout": null, - "eos_token_id": 2, - "hidden_act": "gelu", - "hidden_dropout_prob": 0.1, - "hidden_size": 768, - "initializer_range": 0.02, - "intermediate_size": 3072, - "layer_norm_eps": 1e-12, - "max_position_embeddings": 514, - "model_type": "roberta", - "num_attention_heads": 4, - "num_hidden_layers": 12, - "pad_token_id": 1, - "position_embedding_type": "absolute", - "torch_dtype": "float32", - "transformers_version": "4.26.1", - "type_vocab_size": 1, - "use_cache": true, - "vocab_size": 800 -} diff --git a/models/finetuned/freesolv/merges.txt b/models/finetuned/freesolv/merges.txt deleted file mode 100644 index 7cd5ec62809503c23f18c80afc0ba3bdf9d253d0..0000000000000000000000000000000000000000 --- a/models/finetuned/freesolv/merges.txt +++ /dev/null @@ -1,378 +0,0 @@ -#version: 0.2 - Trained by `huggingface/tokenizers` -B r -a n -c h -Br an -Bran ch -Branch 1 -= C -R i -n g -Ri ng -Ring 1 -= Branch1 -Branch 2 -= O -Ring 2 -H 1 -C @ -= N -# Branch1 -C@ @ -= Branch2 -C@ H1 -C@@ H1 -# Branch2 -# C -C l -/ C -N H1 -= Ring1 -+ 1 -- 1 -O -1 -N +1 -\ C -# N -/ N -= Ring2 -= S -=N +1 -\ N -N a -Na +1 -/ O -\ O -Br -1 -Branch 3 -\ S -S +1 -Cl -1 -I -1 -/ C@@H1 -S i -/ C@H1 -/ S -=N -1 -S e -= P -N -1 -Ring 3 -2 H -P +1 -K +1 -\ C@@H1 -\ C@H1 -/ N+1 -@ @ -C -1 -# N+1 -B -1 -+ 3 -Cl +3 -\ NH1 -L i -Li +1 -P H1 -1 8 -18 F -@ +1 -3 H -P @@ -H 0 -O H0 -1 2 -P @ -+ 2 -@@ +1 -S -1 -/ Br -- / -\ Cl --/ Ring2 -\ O-1 -1 1 -5 I -12 5I -11 C -H 3 -\ N+1 -- \ -/ C@@ -S @+1 -A s -/ Cl -11C H3 -=S e -S @@+1 -N @+1 -1 4 --\ Ring2 -14 C -\ F -/ C@ -T e -H 2 -H1 -1 -=O +1 -N @@+1 -C +1 -=S +1 -Z n -/ P -a +2 -/ I -O H1-1 -C a+2 -\ Br -M g -Zn +2 -A l -/ F -Mg +2 -12 3 -123 I -1 3 -I +1 -/ O-1 --\ Ring1 -B H2 -BH2 -1 -\ I -/ NH1 -O +1 -13 1 -131 I -= 14C -/ S+1 -= Ring3 -\ C@@ -H2 +1 -\ C@ -A g -= As -=Se +1 -N H2+1 -Se H1 --/ Ring1 -= Te -Al +3 -Na H1 -=Te +1 -NH1 +1 -Ag +1 -H1 +1 -NH1 -1 -\ P -14C H2 -13 C -14C H1 -= 11C -S @@ -=P @@ -Si H2 -H3 -1 -14C H3 -B H3-1 -S @ -=14C H1 -=P H1 -=P @ -=N H1+1 -\S +1 -12 4 -C H1-1 -S r -=S i -124 I -Sr +2 -#C -1 -/C -1 -N @ -/N -1 -13C H1 -/ B -1 9 -B a+2 -H 4 -S H1+1 -Se +1 -19 F -/ 125I -P @+1 -R b -Cl +1 -Si H4 -Rb +1 -= Branch3 -N @@ -As +1 -/ Si -B H1-1 -S H1 -/ 123I -3 2 -= Mg -H +1 -\ B -Si H1 -P@@ +1 -- 2 -1 5 -1 7 -3 5 -= 13CH1 -C s -=N H2+1 -=S H1 -Mg H2 -32 P -17 F -35 S -Cs +1 -# 11C -/ 131I -B i -\ 125I -=S @@ -\S -1 -6 Br -7 I -7 6Br -= B -e H1 -\N -1 -18 O -12 7I -11C H2 -14 C@@H1 -Te H2 -15 NH1 -Bi +3 -/ P+1 -/ 13C -/ 13CH1 -0 B -1 0B -= Al -= 18O -B H0 -F -1 -N H3 -S -2 -Br +2 -Cl +2 -\S i -/S -1 -=P H2 -14 C@H1 -NH3 +1 -# 14C -# O+1 -- 3 -2 2 -4 H -5 Se -5 Sr+2 -7 5Se -8 5Sr+2 -= B-1 -= 13C -@ -1 -B e -B @@ -B @-1 -C a -C H1 -I +3 -K H1 -O H1+1 -R a+2 -S H1-1 -\ PH1 -\ 123I -=C a -\C H1-1 -=S @ -\S eH1 -/S eH1 -Se -1 -Li H1 -18F -1 -125I H1 -11C H1 -Te H1 -Zn +1 -Zn -2 -Al -3 -13C H3 -15 N -Be +2 -B@@ -1 -# P -# S -- 4 -/ PH1 -/ P@@ -/ As -/ 14C -/ 14CH1 -2 K+1 -2 Rb+1 -3 Se -3 Ra+2 -4 5 -4 7 -4 2K+1 -5 I-1 -7 3Se -8 9 -8 2Rb+1 -= 32 -= 32P -C H0 -C H2 -I +2 -N H0 -N H4 -O H1 -P H2+1 -S H0 -S H2 -\ 3H -\ 11CH3 -\C -1 -\S e -Si @ -Si -1 -Si H1-1 -Si H3-1 -/S e -Se -2 -\NH1 -1 -18F H1 -12 5I-1 -11 C@@H1 -11 C-1 -As H1 -As -1 -14 C@@ -Te -1 -Mg +1 -123 I-1 -123 Te -123I H1 -13 5I -131 I-1 -Ag -4 -124 I-1 -76Br H1 -18O H1 -22 Na+1 -22 3Ra+2 -Ca H2 -45 Ca+2 -47 Ca+2 -89 Sr+2 -=32 PH1 -NH4 +1 diff --git a/models/finetuned/freesolv/model.pt b/models/finetuned/freesolv/model.pt deleted file mode 100644 index b4db7d8c07d36db777c87860a91fdcbce7b97039..0000000000000000000000000000000000000000 --- a/models/finetuned/freesolv/model.pt +++ /dev/null @@ -1,3 +0,0 @@ -version https://git-lfs.github.com/spec/v1 -oid sha256:18d826a9910632f53115fa941647098fcfed72830b225c3d73c45a123e154d64 -size 1022843005 diff --git a/models/finetuned/freesolv/special_tokens_map.json b/models/finetuned/freesolv/special_tokens_map.json deleted file mode 100644 index 06a55849fa69a91e7179d909e373179ff7467d8c..0000000000000000000000000000000000000000 --- a/models/finetuned/freesolv/special_tokens_map.json +++ /dev/null @@ -1,51 +0,0 @@ -{ - "bos_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "cls_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "eos_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "mask_token": { - "content": "", - "lstrip": true, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "pad_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "sep_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "unk_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - } -} diff --git a/models/finetuned/freesolv/tokenizer.json b/models/finetuned/freesolv/tokenizer.json deleted file mode 100644 index 3b64b273e6fa9799e2d8375722b9e815de9ebb8f..0000000000000000000000000000000000000000 --- a/models/finetuned/freesolv/tokenizer.json +++ /dev/null @@ -1,909 +0,0 @@ -{ - "version": "1.0", - "truncation": { - "direction": "Right", - "max_length": 128, - "strategy": "LongestFirst", - "stride": 0 - }, - "padding": { - "strategy": { - "Fixed": 128 - }, - "direction": "Right", - "pad_to_multiple_of": null, - "pad_id": 3, - "pad_type_id": 0, - "pad_token": "" - }, - "added_tokens": [ - { - "id": 0, - "content": "", - "single_word": false, - "lstrip": false, - "rstrip": false, - "normalized": true, - "special": true - }, - { - "id": 1, - "content": "", - "single_word": false, - "lstrip": false, - "rstrip": false, - "normalized": true, - "special": true - }, - { - "id": 2, - "content": "", - "single_word": false, - "lstrip": false, - "rstrip": false, - "normalized": true, - "special": true - }, - { - "id": 3, - "content": "", - "single_word": false, - "lstrip": false, - "rstrip": false, - "normalized": true, - "special": true - }, - { - "id": 4, - "content": "", - "single_word": false, - "lstrip": true, - "rstrip": false, - "normalized": true, - "special": true - } - ], - "normalizer": null, - "pre_tokenizer": { - "type": "ByteLevel", - "add_prefix_space": false, - "trim_offsets": true, - "use_regex": true - }, - "post_processor": { - "type": "RobertaProcessing", - "sep": [ - "", - 2 - ], - "cls": [ - "", - 1 - ], - "trim_offsets": true, - "add_prefix_space": false - }, - "decoder": { - "type": "ByteLevel", - "add_prefix_space": true, - "trim_offsets": true, - "use_regex": true - }, - "model": { - "type": "BPE", - "dropout": null, - "unk_token": null, - "continuing_subword_prefix": "", - "end_of_word_suffix": "", - "fuse_unk": false, - "vocab": { - "": 0, - "": 1, - "": 2, - "": 3, - "": 4, - "\n": 5, - "#": 6, - "+": 7, - "-": 8, - ".": 9, - "/": 10, - "0": 11, - "1": 12, - "2": 13, - "3": 14, - "4": 15, - "5": 16, - "6": 17, - "7": 18, - "8": 19, - "9": 20, - "=": 21, - "@": 22, - "A": 23, - "B": 24, - "C": 25, - "F": 26, - "H": 27, - "I": 28, - "K": 29, - "L": 30, - "M": 31, - "N": 32, - "O": 33, - "P": 34, - "R": 35, - "S": 36, - "T": 37, - "Z": 38, - "\\": 39, - "a": 40, - "b": 41, - "c": 42, - "e": 43, - "g": 44, - "h": 45, - "i": 46, - "l": 47, - "n": 48, - "r": 49, - "s": 50, - "Br": 51, - "an": 52, - "ch": 53, - "Bran": 54, - "Branch": 55, - "Branch1": 56, - "=C": 57, - "Ri": 58, - "ng": 59, - "Ring": 60, - "Ring1": 61, - "=Branch1": 62, - "Branch2": 63, - "=O": 64, - "Ring2": 65, - "H1": 66, - "C@": 67, - "=N": 68, - "#Branch1": 69, - "C@@": 70, - "=Branch2": 71, - "C@H1": 72, - "C@@H1": 73, - "#Branch2": 74, - "#C": 75, - "Cl": 76, - "/C": 77, - "NH1": 78, - "=Ring1": 79, - "+1": 80, - "-1": 81, - "O-1": 82, - "N+1": 83, - "\\C": 84, - "#N": 85, - "/N": 86, - "=Ring2": 87, - "=S": 88, - "=N+1": 89, - "\\N": 90, - "Na": 91, - "Na+1": 92, - "/O": 93, - "\\O": 94, - "Br-1": 95, - "Branch3": 96, - "\\S": 97, - "S+1": 98, - "Cl-1": 99, - "I-1": 100, - "/C@@H1": 101, - "Si": 102, - "/C@H1": 103, - "/S": 104, - "=N-1": 105, - "Se": 106, - "=P": 107, - "N-1": 108, - "Ring3": 109, - "2H": 110, - "P+1": 111, - "K+1": 112, - "\\C@@H1": 113, - "\\C@H1": 114, - "/N+1": 115, - "@@": 116, - "C-1": 117, - "#N+1": 118, - "B-1": 119, - "+3": 120, - "Cl+3": 121, - "\\NH1": 122, - "Li": 123, - "Li+1": 124, - "PH1": 125, - "18": 126, - "18F": 127, - "@+1": 128, - "3H": 129, - "P@@": 130, - "H0": 131, - "OH0": 132, - "12": 133, - "P@": 134, - "+2": 135, - "@@+1": 136, - "S-1": 137, - "/Br": 138, - "-/": 139, - "\\Cl": 140, - "-/Ring2": 141, - "\\O-1": 142, - "11": 143, - "5I": 144, - "125I": 145, - "11C": 146, - "H3": 147, - "\\N+1": 148, - "-\\": 149, - "/C@@": 150, - "S@+1": 151, - "As": 152, - "/Cl": 153, - "11CH3": 154, - "=Se": 155, - "S@@+1": 156, - "N@+1": 157, - "14": 158, - "-\\Ring2": 159, - "14C": 160, - "\\F": 161, - "/C@": 162, - "Te": 163, - "H2": 164, - "H1-1": 165, - "=O+1": 166, - "N@@+1": 167, - "C+1": 168, - "=S+1": 169, - "Zn": 170, - "/P": 171, - "a+2": 172, - "/I": 173, - "OH1-1": 174, - "Ca+2": 175, - "\\Br": 176, - "Mg": 177, - "Zn+2": 178, - "Al": 179, - "/F": 180, - "Mg+2": 181, - "123": 182, - "123I": 183, - "13": 184, - "I+1": 185, - "/O-1": 186, - "-\\Ring1": 187, - "BH2": 188, - "BH2-1": 189, - "\\I": 190, - "/NH1": 191, - "O+1": 192, - "131": 193, - "131I": 194, - "=14C": 195, - "/S+1": 196, - "=Ring3": 197, - "\\C@@": 198, - "H2+1": 199, - "\\C@": 200, - "Ag": 201, - "=As": 202, - "=Se+1": 203, - "NH2+1": 204, - "SeH1": 205, - "-/Ring1": 206, - "=Te": 207, - "Al+3": 208, - "NaH1": 209, - "=Te+1": 210, - "NH1+1": 211, - "Ag+1": 212, - "H1+1": 213, - "NH1-1": 214, - "\\P": 215, - "14CH2": 216, - "13C": 217, - "14CH1": 218, - "=11C": 219, - "S@@": 220, - "=P@@": 221, - "SiH2": 222, - "H3-1": 223, - "14CH3": 224, - "BH3-1": 225, - "S@": 226, - "=14CH1": 227, - "=PH1": 228, - "=P@": 229, - "=NH1+1": 230, - "\\S+1": 231, - "124": 232, - "CH1-1": 233, - "Sr": 234, - "=Si": 235, - "124I": 236, - "Sr+2": 237, - "#C-1": 238, - "/C-1": 239, - "N@": 240, - "/N-1": 241, - "13CH1": 242, - "/B": 243, - "19": 244, - "Ba+2": 245, - "H4": 246, - "SH1+1": 247, - "Se+1": 248, - "19F": 249, - "/125I": 250, - "P@+1": 251, - "Rb": 252, - "Cl+1": 253, - "SiH4": 254, - "Rb+1": 255, - "=Branch3": 256, - "N@@": 257, - "As+1": 258, - "/Si": 259, - "BH1-1": 260, - "SH1": 261, - "/123I": 262, - "32": 263, - "=Mg": 264, - "H+1": 265, - "\\B": 266, - "SiH1": 267, - "P@@+1": 268, - "-2": 269, - "15": 270, - "17": 271, - "35": 272, - "=13CH1": 273, - "Cs": 274, - "=NH2+1": 275, - "=SH1": 276, - "MgH2": 277, - "32P": 278, - "17F": 279, - "35S": 280, - "Cs+1": 281, - "#11C": 282, - "/131I": 283, - "Bi": 284, - "\\125I": 285, - "=S@@": 286, - "\\S-1": 287, - "6Br": 288, - "7I": 289, - "76Br": 290, - "=B": 291, - "eH1": 292, - "\\N-1": 293, - "18O": 294, - "127I": 295, - "11CH2": 296, - "14C@@H1": 297, - "TeH2": 298, - "15NH1": 299, - "Bi+3": 300, - "/P+1": 301, - "/13C": 302, - "/13CH1": 303, - "0B": 304, - "10B": 305, - "=Al": 306, - "=18O": 307, - "BH0": 308, - "F-1": 309, - "NH3": 310, - "S-2": 311, - "Br+2": 312, - "Cl+2": 313, - "\\Si": 314, - "/S-1": 315, - "=PH2": 316, - "14C@H1": 317, - "NH3+1": 318, - "#14C": 319, - "#O+1": 320, - "-3": 321, - "22": 322, - "4H": 323, - "5Se": 324, - "5Sr+2": 325, - "75Se": 326, - "85Sr+2": 327, - "=B-1": 328, - "=13C": 329, - "@-1": 330, - "Be": 331, - "B@@": 332, - "B@-1": 333, - "Ca": 334, - "CH1": 335, - "I+3": 336, - "KH1": 337, - "OH1+1": 338, - "Ra+2": 339, - "SH1-1": 340, - "\\PH1": 341, - "\\123I": 342, - "=Ca": 343, - "\\CH1-1": 344, - "=S@": 345, - "\\SeH1": 346, - "/SeH1": 347, - "Se-1": 348, - "LiH1": 349, - "18F-1": 350, - "125IH1": 351, - "11CH1": 352, - "TeH1": 353, - "Zn+1": 354, - "Zn-2": 355, - "Al-3": 356, - "13CH3": 357, - "15N": 358, - "Be+2": 359, - "B@@-1": 360, - "#P": 361, - "#S": 362, - "-4": 363, - "/PH1": 364, - "/P@@": 365, - "/As": 366, - "/14C": 367, - "/14CH1": 368, - "2K+1": 369, - "2Rb+1": 370, - "3Se": 371, - "3Ra+2": 372, - "45": 373, - "47": 374, - "42K+1": 375, - "5I-1": 376, - "73Se": 377, - "89": 378, - "82Rb+1": 379, - "=32": 380, - "=32P": 381, - "CH0": 382, - "CH2": 383, - "I+2": 384, - "NH0": 385, - "NH4": 386, - "OH1": 387, - "PH2+1": 388, - "SH0": 389, - "SH2": 390, - "\\3H": 391, - "\\11CH3": 392, - "\\C-1": 393, - "\\Se": 394, - "Si@": 395, - "Si-1": 396, - "SiH1-1": 397, - "SiH3-1": 398, - "/Se": 399, - "Se-2": 400, - "\\NH1-1": 401, - "18FH1": 402, - "125I-1": 403, - "11C@@H1": 404, - "11C-1": 405, - "AsH1": 406, - "As-1": 407, - "14C@@": 408, - "Te-1": 409, - "Mg+1": 410, - "123I-1": 411, - "123Te": 412, - "123IH1": 413, - "135I": 414, - "131I-1": 415, - "Ag-4": 416, - "124I-1": 417, - "76BrH1": 418, - "18OH1": 419, - "22Na+1": 420, - "223Ra+2": 421, - "CaH2": 422, - "45Ca+2": 423, - "47Ca+2": 424, - "89Sr+2": 425, - "=32PH1": 426, - "NH4+1": 427 - }, - "merges": [ - "B r", - "a n", - "c h", - "Br an", - "Bran ch", - "Branch 1", - "= C", - "R i", - "n g", - "Ri ng", - "Ring 1", - "= Branch1", - "Branch 2", - "= O", - "Ring 2", - "H 1", - "C @", - "= N", - "# Branch1", - "C@ @", - "= Branch2", - "C@ H1", - "C@@ H1", - "# Branch2", - "# C", - "C l", - "/ C", - "N H1", - "= Ring1", - "+ 1", - "- 1", - "O -1", - "N +1", - "\\ C", - "# N", - "/ N", - "= Ring2", - "= S", - "=N +1", - "\\ N", - "N a", - "Na +1", - "/ O", - "\\ O", - "Br -1", - "Branch 3", - "\\ S", - "S +1", - "Cl -1", - "I -1", - "/ C@@H1", - "S i", - "/ C@H1", - "/ S", - "=N -1", - "S e", - "= P", - "N -1", - "Ring 3", - "2 H", - "P +1", - "K +1", - "\\ C@@H1", - "\\ C@H1", - "/ N+1", - "@ @", - "C -1", - "# N+1", - "B -1", - "+ 3", - "Cl +3", - "\\ NH1", - "L i", - "Li +1", - "P H1", - "1 8", - "18 F", - "@ +1", - "3 H", - "P @@", - "H 0", - "O H0", - "1 2", - "P @", - "+ 2", - "@@ +1", - "S -1", - "/ Br", - "- /", - "\\ Cl", - "-/ Ring2", - "\\ O-1", - "1 1", - "5 I", - "12 5I", - "11 C", - "H 3", - "\\ N+1", - "- \\", - "/ C@@", - "S @+1", - "A s", - "/ Cl", - "11C H3", - "=S e", - "S @@+1", - "N @+1", - "1 4", - "-\\ Ring2", - "14 C", - "\\ F", - "/ C@", - "T e", - "H 2", - "H1 -1", - "=O +1", - "N @@+1", - "C +1", - "=S +1", - "Z n", - "/ P", - "a +2", - "/ I", - "O H1-1", - "C a+2", - "\\ Br", - "M g", - "Zn +2", - "A l", - "/ F", - "Mg +2", - "12 3", - "123 I", - "1 3", - "I +1", - "/ O-1", - "-\\ Ring1", - "B H2", - "BH2 -1", - "\\ I", - "/ NH1", - "O +1", - "13 1", - "131 I", - "= 14C", - "/ S+1", - "= Ring3", - "\\ C@@", - "H2 +1", - "\\ C@", - "A g", - "= As", - "=Se +1", - "N H2+1", - "Se H1", - "-/ Ring1", - "= Te", - "Al +3", - "Na H1", - "=Te +1", - "NH1 +1", - "Ag +1", - "H1 +1", - "NH1 -1", - "\\ P", - "14C H2", - "13 C", - "14C H1", - "= 11C", - "S @@", - "=P @@", - "Si H2", - "H3 -1", - "14C H3", - "B H3-1", - "S @", - "=14C H1", - "=P H1", - "=P @", - "=N H1+1", - "\\S +1", - "12 4", - "C H1-1", - "S r", - "=S i", - "124 I", - "Sr +2", - "#C -1", - "/C -1", - "N @", - "/N -1", - "13C H1", - "/ B", - "1 9", - "B a+2", - "H 4", - "S H1+1", - "Se +1", - "19 F", - "/ 125I", - "P @+1", - "R b", - "Cl +1", - "Si H4", - "Rb +1", - "= Branch3", - "N @@", - "As +1", - "/ Si", - "B H1-1", - "S H1", - "/ 123I", - "3 2", - "= Mg", - "H +1", - "\\ B", - "Si H1", - "P@@ +1", - "- 2", - "1 5", - "1 7", - "3 5", - "= 13CH1", - "C s", - "=N H2+1", - "=S H1", - "Mg H2", - "32 P", - "17 F", - "35 S", - "Cs +1", - "# 11C", - "/ 131I", - "B i", - "\\ 125I", - "=S @@", - "\\S -1", - "6 Br", - "7 I", - "7 6Br", - "= B", - "e H1", - "\\N -1", - "18 O", - "12 7I", - "11C H2", - "14 C@@H1", - "Te H2", - "15 NH1", - "Bi +3", - "/ P+1", - "/ 13C", - "/ 13CH1", - "0 B", - "1 0B", - "= Al", - "= 18O", - "B H0", - "F -1", - "N H3", - "S -2", - "Br +2", - "Cl +2", - "\\S i", - "/S -1", - "=P H2", - "14 C@H1", - "NH3 +1", - "# 14C", - "# O+1", - "- 3", - "2 2", - "4 H", - "5 Se", - "5 Sr+2", - "7 5Se", - "8 5Sr+2", - "= B-1", - "= 13C", - "@ -1", - "B e", - "B @@", - "B @-1", - "C a", - "C H1", - "I +3", - "K H1", - "O H1+1", - "R a+2", - "S H1-1", - "\\ PH1", - "\\ 123I", - "=C a", - "\\C H1-1", - "=S @", - "\\S eH1", - "/S eH1", - "Se -1", - "Li H1", - "18F -1", - "125I H1", - "11C H1", - "Te H1", - "Zn +1", - "Zn -2", - "Al -3", - "13C H3", - "15 N", - "Be +2", - "B@@ -1", - "# P", - "# S", - "- 4", - "/ PH1", - "/ P@@", - "/ As", - "/ 14C", - "/ 14CH1", - "2 K+1", - "2 Rb+1", - "3 Se", - "3 Ra+2", - "4 5", - "4 7", - "4 2K+1", - "5 I-1", - "7 3Se", - "8 9", - "8 2Rb+1", - "= 32", - "= 32P", - "C H0", - "C H2", - "I +2", - "N H0", - "N H4", - "O H1", - "P H2+1", - "S H0", - "S H2", - "\\ 3H", - "\\ 11CH3", - "\\C -1", - "\\S e", - "Si @", - "Si -1", - "Si H1-1", - "Si H3-1", - "/S e", - "Se -2", - "\\NH1 -1", - "18F H1", - "12 5I-1", - "11 C@@H1", - "11 C-1", - "As H1", - "As -1", - "14 C@@", - "Te -1", - "Mg +1", - "123 I-1", - "123 Te", - "123I H1", - "13 5I", - "131 I-1", - "Ag -4", - "124 I-1", - "76Br H1", - "18O H1", - "22 Na+1", - "22 3Ra+2", - "Ca H2", - "45 Ca+2", - "47 Ca+2", - "89 Sr+2", - "=32 PH1", - "NH4 +1" - ] - } -} \ No newline at end of file diff --git a/models/finetuned/freesolv/tokenizer_config.json b/models/finetuned/freesolv/tokenizer_config.json deleted file mode 100644 index 08860954acd34fad07fd77f7635298fa565f3149..0000000000000000000000000000000000000000 --- a/models/finetuned/freesolv/tokenizer_config.json +++ /dev/null @@ -1,65 +0,0 @@ -{ - "add_prefix_space": false, - "bos_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "cls_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "eos_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "errors": "replace", - "mask_token": { - "__type": "AddedToken", - "content": "", - "lstrip": true, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "model_max_length": 1000000000000000019884624838656, - "name_or_path": "/home/erva/SELFormerMM/data/pretrained_multimodal_chembl36", - "pad_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "sep_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "special_tokens_map_file": null, - "tokenizer_class": "RobertaTokenizer", - "trim_offsets": true, - "unk_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - } -} diff --git a/models/finetuned/freesolv/train_stdout.log b/models/finetuned/freesolv/train_stdout.log deleted file mode 100644 index 183a4d5663bbb05b5adfeb7778283af490685b3b..0000000000000000000000000000000000000000 --- a/models/finetuned/freesolv/train_stdout.log +++ /dev/null @@ -1,84 +0,0 @@ -[finetune] starting -[finetune] device=cuda task_type=regression batch_size=8 max_len=128 backbone_lr=5e-05 head_lr=0.0005 weight_decay=0.01 epochs=50 -[finetune] dataset_meta_csv=/home/erva/SELFormerMM/data/new_finetuning_datasets/regression/freesolv/freesolv.csv -[finetune] dataset_embs_npz=/home/erva/SELFormerMM/data/new_finetuning_datasets/regression/freesolv/freesolv_embs.npz -[finetune] model_path=HUBioDataLab/SELFormer tokenizer_path=HUBioDataLab/SELFormer -[finetune] pretrained_multimodal_dir=/home/erva/SELFormerMM/data/pretrained_multimodal_chembl36 -[finetune] use_scaffold=False seed=42 fracs=(0.8,0.1,0.1) -[finetune] loading dataset bundle (meta csv + embs npz) ... -[finetune] splitting dataset... -[finetune] split sizes: train=513 val=64 test=65 -[finetune] train modality_non_empty: graph=513/513 text=470/513 kg=25/513 -[finetune] val modality_non_empty: graph=64/64 text=57/64 kg=6/64 -[finetune] test modality_non_empty: graph=65/65 text=61/65 kg=0/65 -[finetune] extracting labels... -[finetune] loading config/tokenizer/backbone... -[finetune] initializing multimodal model... -[finetune] loading multimodal pretrained weights: /home/erva/SELFormerMM/data/pretrained_multimodal_chembl36/pytorch_model.bin -[finetune] freezing roberta layers (trainable: encoder.layer.9-11)... -[finetune] backbone trainable params: 181,443,072/246,245,376 -[finetune] building datasets/dataloaders... -[finetune] train_steps_per_epoch=65 val_steps=8 test_steps=9 -[finetune] initialized head: in_dim=3072 out=1 -[finetune] initializing optimizer/scheduler/finetuner... -[finetune] optimizer groups: backbone_decay=45 backbone_nodecay=57 head_decay=2 head_nodecay=2 -[finetune] training loop... -[finetune] epoch 1/50: train_loss=8.8327 val_loss=8.6622 time=13.2s tod=16:56 -[finetune] epoch 2/50: train_loss=4.4709 val_loss=8.2606 time=12.7s tod=16:56 -[finetune] epoch 3/50: train_loss=3.8963 val_loss=4.6549 time=12.9s tod=16:56 -[finetune] epoch 4/50: train_loss=2.0273 val_loss=3.4323 time=12.2s tod=16:56 -[finetune] epoch 5/50: train_loss=1.5289 val_loss=2.8464 time=12.8s tod=16:56 -[finetune] epoch 6/50: train_loss=1.3175 val_loss=2.9690 time=12.8s tod=16:57 -[finetune] epoch 7/50: train_loss=1.2857 val_loss=2.2687 time=12.7s tod=16:57 -[finetune] epoch 8/50: train_loss=1.2503 val_loss=3.5530 time=12.8s tod=16:57 -[finetune] epoch 9/50: train_loss=1.2438 val_loss=1.9285 time=12.8s tod=16:57 -[finetune] epoch 10/50: train_loss=0.9841 val_loss=1.9874 time=12.3s tod=16:57 -[finetune] epoch 11/50: train_loss=0.9595 val_loss=2.1377 time=12.7s tod=16:58 -[finetune] epoch 12/50: train_loss=0.7905 val_loss=1.8522 time=12.8s tod=16:58 -[finetune] epoch 13/50: train_loss=0.6547 val_loss=2.2271 time=12.8s tod=16:58 -[finetune] epoch 14/50: train_loss=0.6922 val_loss=1.9394 time=12.7s tod=16:58 -[finetune] epoch 15/50: train_loss=0.5703 val_loss=2.7039 time=12.9s tod=16:58 -[finetune] epoch 16/50: train_loss=0.6377 val_loss=1.4721 time=12.7s tod=16:59 -[finetune] epoch 17/50: train_loss=0.5650 val_loss=2.9902 time=12.3s tod=16:59 -[finetune] epoch 18/50: train_loss=0.4907 val_loss=2.0984 time=12.8s tod=16:59 -[finetune] epoch 19/50: train_loss=0.4697 val_loss=2.9616 time=12.8s tod=16:59 -[finetune] epoch 20/50: train_loss=0.4219 val_loss=1.2584 time=12.6s tod=17:00 -[finetune] epoch 21/50: train_loss=0.4772 val_loss=1.4099 time=12.8s tod=17:00 -[finetune] epoch 22/50: train_loss=0.3259 val_loss=1.9489 time=12.8s tod=17:00 -[finetune] epoch 23/50: train_loss=0.3399 val_loss=1.6618 time=11.3s tod=17:00 -[finetune] epoch 24/50: train_loss=0.3765 val_loss=1.7658 time=8.7s tod=17:00 -[finetune] epoch 25/50: train_loss=0.3145 val_loss=2.0268 time=8.6s tod=17:00 -[finetune] test_metrics: epoch=25 loss=1.4893 mse=1.6323 rmse=1.2776 mae=0.9874 -[finetune] saved checkpoint (best rmse=1.2776): /media/ubuntu/8TB/erva/selformer-mm/output/new_finetune_sweeps/freesolv/4zs7c1p0/checkpoint_epoch_025 -[finetune] epoch 26/50: train_loss=0.3076 val_loss=1.5888 time=8.5s tod=17:01 -[finetune] epoch 27/50: train_loss=0.2732 val_loss=1.6552 time=10.7s tod=17:01 -[finetune] epoch 28/50: train_loss=0.2281 val_loss=1.2463 time=12.9s tod=17:01 -[finetune] epoch 29/50: train_loss=0.3385 val_loss=1.6431 time=12.3s tod=17:01 -[finetune] epoch 30/50: train_loss=0.2315 val_loss=1.0546 time=12.6s tod=17:01 -[finetune] epoch 31/50: train_loss=0.2672 val_loss=1.4163 time=12.8s tod=17:02 -[finetune] epoch 32/50: train_loss=0.1979 val_loss=1.1115 time=12.8s tod=17:02 -[finetune] epoch 33/50: train_loss=0.2258 val_loss=1.6268 time=12.8s tod=17:02 -[finetune] epoch 34/50: train_loss=0.1904 val_loss=1.4480 time=12.7s tod=17:02 -[finetune] epoch 35/50: train_loss=0.1873 val_loss=1.2501 time=12.9s tod=17:02 -[finetune] epoch 36/50: train_loss=0.1512 val_loss=1.5128 time=12.2s tod=17:03 -[finetune] epoch 37/50: train_loss=0.1381 val_loss=1.2301 time=12.8s tod=17:03 -[finetune] epoch 38/50: train_loss=0.1482 val_loss=1.5650 time=12.9s tod=17:03 -[finetune] epoch 39/50: train_loss=0.1227 val_loss=1.4072 time=12.7s tod=17:03 -[finetune] epoch 40/50: train_loss=0.1140 val_loss=1.1888 time=12.9s tod=17:04 -[finetune] epoch 41/50: train_loss=0.1237 val_loss=1.2910 time=12.7s tod=17:04 -[finetune] epoch 42/50: train_loss=0.1119 val_loss=1.5262 time=12.5s tod=17:04 -[finetune] epoch 43/50: train_loss=0.1147 val_loss=1.2782 time=12.6s tod=17:04 -[finetune] epoch 44/50: train_loss=0.0989 val_loss=1.2923 time=12.7s tod=17:04 -[finetune] epoch 45/50: train_loss=0.0900 val_loss=1.3757 time=12.8s tod=17:05 -[finetune] epoch 46/50: train_loss=0.0889 val_loss=1.4483 time=12.8s tod=17:05 -[finetune] epoch 47/50: train_loss=0.0858 val_loss=1.3142 time=12.8s tod=17:05 -[finetune] epoch 48/50: train_loss=0.0912 val_loss=1.3258 time=12.7s tod=17:05 -[finetune] epoch 49/50: train_loss=0.0762 val_loss=1.3466 time=12.4s tod=17:05 -[finetune] epoch 50/50: train_loss=0.0681 val_loss=1.3496 time=12.7s tod=17:06 -[finetune] test_metrics: epoch=50 loss=0.7098 mse=0.7796 rmse=0.8829 mae=0.6312 -[finetune] saved checkpoint (best rmse=0.8829): /media/ubuntu/8TB/erva/selformer-mm/output/new_finetune_sweeps/freesolv/4zs7c1p0/checkpoint_epoch_050 -[finetune] final evaluation on test split... -[finetune] test_metrics: loss=0.7098 mse=0.7796 rmse=0.8829 mae=0.6312 -[finetune] saving model... -[finetune] saved finetuned model to: /media/ubuntu/8TB/erva/selformer-mm/output/new_finetune_sweeps/freesolv/4zs7c1p0 -[finetune] done in 630.4s diff --git a/models/finetuned/freesolv/vocab.json b/models/finetuned/freesolv/vocab.json deleted file mode 100644 index f7e4cc22809f4e9035cc450ef189c8a7da8fd03e..0000000000000000000000000000000000000000 --- a/models/finetuned/freesolv/vocab.json +++ /dev/null @@ -1 +0,0 @@ -{"":0,"":1,"":2,"":3,"":4,"\n":5,"#":6,"+":7,"-":8,".":9,"/":10,"0":11,"1":12,"2":13,"3":14,"4":15,"5":16,"6":17,"7":18,"8":19,"9":20,"=":21,"@":22,"A":23,"B":24,"C":25,"F":26,"H":27,"I":28,"K":29,"L":30,"M":31,"N":32,"O":33,"P":34,"R":35,"S":36,"T":37,"Z":38,"\\":39,"a":40,"b":41,"c":42,"e":43,"g":44,"h":45,"i":46,"l":47,"n":48,"r":49,"s":50,"Br":51,"an":52,"ch":53,"Bran":54,"Branch":55,"Branch1":56,"=C":57,"Ri":58,"ng":59,"Ring":60,"Ring1":61,"=Branch1":62,"Branch2":63,"=O":64,"Ring2":65,"H1":66,"C@":67,"=N":68,"#Branch1":69,"C@@":70,"=Branch2":71,"C@H1":72,"C@@H1":73,"#Branch2":74,"#C":75,"Cl":76,"/C":77,"NH1":78,"=Ring1":79,"+1":80,"-1":81,"O-1":82,"N+1":83,"\\C":84,"#N":85,"/N":86,"=Ring2":87,"=S":88,"=N+1":89,"\\N":90,"Na":91,"Na+1":92,"/O":93,"\\O":94,"Br-1":95,"Branch3":96,"\\S":97,"S+1":98,"Cl-1":99,"I-1":100,"/C@@H1":101,"Si":102,"/C@H1":103,"/S":104,"=N-1":105,"Se":106,"=P":107,"N-1":108,"Ring3":109,"2H":110,"P+1":111,"K+1":112,"\\C@@H1":113,"\\C@H1":114,"/N+1":115,"@@":116,"C-1":117,"#N+1":118,"B-1":119,"+3":120,"Cl+3":121,"\\NH1":122,"Li":123,"Li+1":124,"PH1":125,"18":126,"18F":127,"@+1":128,"3H":129,"P@@":130,"H0":131,"OH0":132,"12":133,"P@":134,"+2":135,"@@+1":136,"S-1":137,"/Br":138,"-/":139,"\\Cl":140,"-/Ring2":141,"\\O-1":142,"11":143,"5I":144,"125I":145,"11C":146,"H3":147,"\\N+1":148,"-\\":149,"/C@@":150,"S@+1":151,"As":152,"/Cl":153,"11CH3":154,"=Se":155,"S@@+1":156,"N@+1":157,"14":158,"-\\Ring2":159,"14C":160,"\\F":161,"/C@":162,"Te":163,"H2":164,"H1-1":165,"=O+1":166,"N@@+1":167,"C+1":168,"=S+1":169,"Zn":170,"/P":171,"a+2":172,"/I":173,"OH1-1":174,"Ca+2":175,"\\Br":176,"Mg":177,"Zn+2":178,"Al":179,"/F":180,"Mg+2":181,"123":182,"123I":183,"13":184,"I+1":185,"/O-1":186,"-\\Ring1":187,"BH2":188,"BH2-1":189,"\\I":190,"/NH1":191,"O+1":192,"131":193,"131I":194,"=14C":195,"/S+1":196,"=Ring3":197,"\\C@@":198,"H2+1":199,"\\C@":200,"Ag":201,"=As":202,"=Se+1":203,"NH2+1":204,"SeH1":205,"-/Ring1":206,"=Te":207,"Al+3":208,"NaH1":209,"=Te+1":210,"NH1+1":211,"Ag+1":212,"H1+1":213,"NH1-1":214,"\\P":215,"14CH2":216,"13C":217,"14CH1":218,"=11C":219,"S@@":220,"=P@@":221,"SiH2":222,"H3-1":223,"14CH3":224,"BH3-1":225,"S@":226,"=14CH1":227,"=PH1":228,"=P@":229,"=NH1+1":230,"\\S+1":231,"124":232,"CH1-1":233,"Sr":234,"=Si":235,"124I":236,"Sr+2":237,"#C-1":238,"/C-1":239,"N@":240,"/N-1":241,"13CH1":242,"/B":243,"19":244,"Ba+2":245,"H4":246,"SH1+1":247,"Se+1":248,"19F":249,"/125I":250,"P@+1":251,"Rb":252,"Cl+1":253,"SiH4":254,"Rb+1":255,"=Branch3":256,"N@@":257,"As+1":258,"/Si":259,"BH1-1":260,"SH1":261,"/123I":262,"32":263,"=Mg":264,"H+1":265,"\\B":266,"SiH1":267,"P@@+1":268,"-2":269,"15":270,"17":271,"35":272,"=13CH1":273,"Cs":274,"=NH2+1":275,"=SH1":276,"MgH2":277,"32P":278,"17F":279,"35S":280,"Cs+1":281,"#11C":282,"/131I":283,"Bi":284,"\\125I":285,"=S@@":286,"\\S-1":287,"6Br":288,"7I":289,"76Br":290,"=B":291,"eH1":292,"\\N-1":293,"18O":294,"127I":295,"11CH2":296,"14C@@H1":297,"TeH2":298,"15NH1":299,"Bi+3":300,"/P+1":301,"/13C":302,"/13CH1":303,"0B":304,"10B":305,"=Al":306,"=18O":307,"BH0":308,"F-1":309,"NH3":310,"S-2":311,"Br+2":312,"Cl+2":313,"\\Si":314,"/S-1":315,"=PH2":316,"14C@H1":317,"NH3+1":318,"#14C":319,"#O+1":320,"-3":321,"22":322,"4H":323,"5Se":324,"5Sr+2":325,"75Se":326,"85Sr+2":327,"=B-1":328,"=13C":329,"@-1":330,"Be":331,"B@@":332,"B@-1":333,"Ca":334,"CH1":335,"I+3":336,"KH1":337,"OH1+1":338,"Ra+2":339,"SH1-1":340,"\\PH1":341,"\\123I":342,"=Ca":343,"\\CH1-1":344,"=S@":345,"\\SeH1":346,"/SeH1":347,"Se-1":348,"LiH1":349,"18F-1":350,"125IH1":351,"11CH1":352,"TeH1":353,"Zn+1":354,"Zn-2":355,"Al-3":356,"13CH3":357,"15N":358,"Be+2":359,"B@@-1":360,"#P":361,"#S":362,"-4":363,"/PH1":364,"/P@@":365,"/As":366,"/14C":367,"/14CH1":368,"2K+1":369,"2Rb+1":370,"3Se":371,"3Ra+2":372,"45":373,"47":374,"42K+1":375,"5I-1":376,"73Se":377,"89":378,"82Rb+1":379,"=32":380,"=32P":381,"CH0":382,"CH2":383,"I+2":384,"NH0":385,"NH4":386,"OH1":387,"PH2+1":388,"SH0":389,"SH2":390,"\\3H":391,"\\11CH3":392,"\\C-1":393,"\\Se":394,"Si@":395,"Si-1":396,"SiH1-1":397,"SiH3-1":398,"/Se":399,"Se-2":400,"\\NH1-1":401,"18FH1":402,"125I-1":403,"11C@@H1":404,"11C-1":405,"AsH1":406,"As-1":407,"14C@@":408,"Te-1":409,"Mg+1":410,"123I-1":411,"123Te":412,"123IH1":413,"135I":414,"131I-1":415,"Ag-4":416,"124I-1":417,"76BrH1":418,"18OH1":419,"22Na+1":420,"223Ra+2":421,"CaH2":422,"45Ca+2":423,"47Ca+2":424,"89Sr+2":425,"=32PH1":426,"NH4+1":427} \ No newline at end of file diff --git a/models/finetuned/hiv/config.json b/models/finetuned/hiv/config.json deleted file mode 100644 index 3811e21539577b37e06313eab31ec11e53f0cbbc..0000000000000000000000000000000000000000 --- a/models/finetuned/hiv/config.json +++ /dev/null @@ -1,27 +0,0 @@ -{ - "_name_or_path": "/home/erva/SELFormerMM/data/pretrained_multimodal_chembl36", - "architectures": [ - "RobertaForMaskedLM" - ], - "attention_probs_dropout_prob": 0.1, - "bos_token_id": 0, - "classifier_dropout": null, - "eos_token_id": 2, - "hidden_act": "gelu", - "hidden_dropout_prob": 0.1, - "hidden_size": 768, - "initializer_range": 0.02, - "intermediate_size": 3072, - "layer_norm_eps": 1e-12, - "max_position_embeddings": 514, - "model_type": "roberta", - "num_attention_heads": 4, - "num_hidden_layers": 12, - "pad_token_id": 1, - "position_embedding_type": "absolute", - "torch_dtype": "float32", - "transformers_version": "4.26.1", - "type_vocab_size": 1, - "use_cache": true, - "vocab_size": 800 -} diff --git a/models/finetuned/hiv/merges.txt b/models/finetuned/hiv/merges.txt deleted file mode 100644 index 7cd5ec62809503c23f18c80afc0ba3bdf9d253d0..0000000000000000000000000000000000000000 --- a/models/finetuned/hiv/merges.txt +++ /dev/null @@ -1,378 +0,0 @@ -#version: 0.2 - Trained by `huggingface/tokenizers` -B r -a n -c h -Br an -Bran ch -Branch 1 -= C -R i -n g -Ri ng -Ring 1 -= Branch1 -Branch 2 -= O -Ring 2 -H 1 -C @ -= N -# Branch1 -C@ @ -= Branch2 -C@ H1 -C@@ H1 -# Branch2 -# C -C l -/ C -N H1 -= Ring1 -+ 1 -- 1 -O -1 -N +1 -\ C -# N -/ N -= Ring2 -= S -=N +1 -\ N -N a -Na +1 -/ O -\ O -Br -1 -Branch 3 -\ S -S +1 -Cl -1 -I -1 -/ C@@H1 -S i -/ C@H1 -/ S -=N -1 -S e -= P -N -1 -Ring 3 -2 H -P +1 -K +1 -\ C@@H1 -\ C@H1 -/ N+1 -@ @ -C -1 -# N+1 -B -1 -+ 3 -Cl +3 -\ NH1 -L i -Li +1 -P H1 -1 8 -18 F -@ +1 -3 H -P @@ -H 0 -O H0 -1 2 -P @ -+ 2 -@@ +1 -S -1 -/ Br -- / -\ Cl --/ Ring2 -\ O-1 -1 1 -5 I -12 5I -11 C -H 3 -\ N+1 -- \ -/ C@@ -S @+1 -A s -/ Cl -11C H3 -=S e -S @@+1 -N @+1 -1 4 --\ Ring2 -14 C -\ F -/ C@ -T e -H 2 -H1 -1 -=O +1 -N @@+1 -C +1 -=S +1 -Z n -/ P -a +2 -/ I -O H1-1 -C a+2 -\ Br -M g -Zn +2 -A l -/ F -Mg +2 -12 3 -123 I -1 3 -I +1 -/ O-1 --\ Ring1 -B H2 -BH2 -1 -\ I -/ NH1 -O +1 -13 1 -131 I -= 14C -/ S+1 -= Ring3 -\ C@@ -H2 +1 -\ C@ -A g -= As -=Se +1 -N H2+1 -Se H1 --/ Ring1 -= Te -Al +3 -Na H1 -=Te +1 -NH1 +1 -Ag +1 -H1 +1 -NH1 -1 -\ P -14C H2 -13 C -14C H1 -= 11C -S @@ -=P @@ -Si H2 -H3 -1 -14C H3 -B H3-1 -S @ -=14C H1 -=P H1 -=P @ -=N H1+1 -\S +1 -12 4 -C H1-1 -S r -=S i -124 I -Sr +2 -#C -1 -/C -1 -N @ -/N -1 -13C H1 -/ B -1 9 -B a+2 -H 4 -S H1+1 -Se +1 -19 F -/ 125I -P @+1 -R b -Cl +1 -Si H4 -Rb +1 -= Branch3 -N @@ -As +1 -/ Si -B H1-1 -S H1 -/ 123I -3 2 -= Mg -H +1 -\ B -Si H1 -P@@ +1 -- 2 -1 5 -1 7 -3 5 -= 13CH1 -C s -=N H2+1 -=S H1 -Mg H2 -32 P -17 F -35 S -Cs +1 -# 11C -/ 131I -B i -\ 125I -=S @@ -\S -1 -6 Br -7 I -7 6Br -= B -e H1 -\N -1 -18 O -12 7I -11C H2 -14 C@@H1 -Te H2 -15 NH1 -Bi +3 -/ P+1 -/ 13C -/ 13CH1 -0 B -1 0B -= Al -= 18O -B H0 -F -1 -N H3 -S -2 -Br +2 -Cl +2 -\S i -/S -1 -=P H2 -14 C@H1 -NH3 +1 -# 14C -# O+1 -- 3 -2 2 -4 H -5 Se -5 Sr+2 -7 5Se -8 5Sr+2 -= B-1 -= 13C -@ -1 -B e -B @@ -B @-1 -C a -C H1 -I +3 -K H1 -O H1+1 -R a+2 -S H1-1 -\ PH1 -\ 123I -=C a -\C H1-1 -=S @ -\S eH1 -/S eH1 -Se -1 -Li H1 -18F -1 -125I H1 -11C H1 -Te H1 -Zn +1 -Zn -2 -Al -3 -13C H3 -15 N -Be +2 -B@@ -1 -# P -# S -- 4 -/ PH1 -/ P@@ -/ As -/ 14C -/ 14CH1 -2 K+1 -2 Rb+1 -3 Se -3 Ra+2 -4 5 -4 7 -4 2K+1 -5 I-1 -7 3Se -8 9 -8 2Rb+1 -= 32 -= 32P -C H0 -C H2 -I +2 -N H0 -N H4 -O H1 -P H2+1 -S H0 -S H2 -\ 3H -\ 11CH3 -\C -1 -\S e -Si @ -Si -1 -Si H1-1 -Si H3-1 -/S e -Se -2 -\NH1 -1 -18F H1 -12 5I-1 -11 C@@H1 -11 C-1 -As H1 -As -1 -14 C@@ -Te -1 -Mg +1 -123 I-1 -123 Te -123I H1 -13 5I -131 I-1 -Ag -4 -124 I-1 -76Br H1 -18O H1 -22 Na+1 -22 3Ra+2 -Ca H2 -45 Ca+2 -47 Ca+2 -89 Sr+2 -=32 PH1 -NH4 +1 diff --git a/models/finetuned/hiv/model.pt b/models/finetuned/hiv/model.pt deleted file mode 100644 index 87b0c30b31733df3b61cb311842030ca0b163d51..0000000000000000000000000000000000000000 --- a/models/finetuned/hiv/model.pt +++ /dev/null @@ -1,3 +0,0 @@ -version https://git-lfs.github.com/spec/v1 -oid sha256:e256d9c1f34dc1d3521586b383cb58b01238a2d5229e4383cb7a0cae792fb7a8 -size 1022855293 diff --git a/models/finetuned/hiv/special_tokens_map.json b/models/finetuned/hiv/special_tokens_map.json deleted file mode 100644 index 06a55849fa69a91e7179d909e373179ff7467d8c..0000000000000000000000000000000000000000 --- a/models/finetuned/hiv/special_tokens_map.json +++ /dev/null @@ -1,51 +0,0 @@ -{ - "bos_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "cls_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "eos_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "mask_token": { - "content": "", - "lstrip": true, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "pad_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "sep_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "unk_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - } -} diff --git a/models/finetuned/hiv/tokenizer.json b/models/finetuned/hiv/tokenizer.json deleted file mode 100644 index 3b64b273e6fa9799e2d8375722b9e815de9ebb8f..0000000000000000000000000000000000000000 --- a/models/finetuned/hiv/tokenizer.json +++ /dev/null @@ -1,909 +0,0 @@ -{ - "version": "1.0", - "truncation": { - "direction": "Right", - "max_length": 128, - "strategy": "LongestFirst", - "stride": 0 - }, - "padding": { - "strategy": { - "Fixed": 128 - }, - "direction": "Right", - "pad_to_multiple_of": null, - "pad_id": 3, - "pad_type_id": 0, - "pad_token": "" - }, - "added_tokens": [ - { - "id": 0, - "content": "", - "single_word": false, - "lstrip": false, - "rstrip": false, - "normalized": true, - "special": true - }, - { - "id": 1, - "content": "", - "single_word": false, - "lstrip": false, - "rstrip": false, - "normalized": true, - "special": true - }, - { - "id": 2, - "content": "", - "single_word": false, - "lstrip": false, - "rstrip": false, - "normalized": true, - "special": true - }, - { - "id": 3, - "content": "", - "single_word": false, - "lstrip": false, - "rstrip": false, - "normalized": true, - "special": true - }, - { - "id": 4, - "content": "", - "single_word": false, - "lstrip": true, - "rstrip": false, - "normalized": true, - "special": true - } - ], - "normalizer": null, - "pre_tokenizer": { - "type": "ByteLevel", - "add_prefix_space": false, - "trim_offsets": true, - "use_regex": true - }, - "post_processor": { - "type": "RobertaProcessing", - "sep": [ - "", - 2 - ], - "cls": [ - "", - 1 - ], - "trim_offsets": true, - "add_prefix_space": false - }, - "decoder": { - "type": "ByteLevel", - "add_prefix_space": true, - "trim_offsets": true, - "use_regex": true - }, - "model": { - "type": "BPE", - "dropout": null, - "unk_token": null, - "continuing_subword_prefix": "", - "end_of_word_suffix": "", - "fuse_unk": false, - "vocab": { - "": 0, - "": 1, - "": 2, - "": 3, - "": 4, - "\n": 5, - "#": 6, - "+": 7, - "-": 8, - ".": 9, - "/": 10, - "0": 11, - "1": 12, - "2": 13, - "3": 14, - "4": 15, - "5": 16, - "6": 17, - "7": 18, - "8": 19, - "9": 20, - "=": 21, - "@": 22, - "A": 23, - "B": 24, - "C": 25, - "F": 26, - "H": 27, - "I": 28, - "K": 29, - "L": 30, - "M": 31, - "N": 32, - "O": 33, - "P": 34, - "R": 35, - "S": 36, - "T": 37, - "Z": 38, - "\\": 39, - "a": 40, - "b": 41, - "c": 42, - "e": 43, - "g": 44, - "h": 45, - "i": 46, - "l": 47, - "n": 48, - "r": 49, - "s": 50, - "Br": 51, - "an": 52, - "ch": 53, - "Bran": 54, - "Branch": 55, - "Branch1": 56, - "=C": 57, - "Ri": 58, - "ng": 59, - "Ring": 60, - "Ring1": 61, - "=Branch1": 62, - "Branch2": 63, - "=O": 64, - "Ring2": 65, - "H1": 66, - "C@": 67, - "=N": 68, - "#Branch1": 69, - "C@@": 70, - "=Branch2": 71, - "C@H1": 72, - "C@@H1": 73, - "#Branch2": 74, - "#C": 75, - "Cl": 76, - "/C": 77, - "NH1": 78, - "=Ring1": 79, - "+1": 80, - "-1": 81, - "O-1": 82, - "N+1": 83, - "\\C": 84, - "#N": 85, - "/N": 86, - "=Ring2": 87, - "=S": 88, - "=N+1": 89, - "\\N": 90, - "Na": 91, - "Na+1": 92, - "/O": 93, - "\\O": 94, - "Br-1": 95, - "Branch3": 96, - "\\S": 97, - "S+1": 98, - "Cl-1": 99, - "I-1": 100, - "/C@@H1": 101, - "Si": 102, - "/C@H1": 103, - "/S": 104, - "=N-1": 105, - "Se": 106, - "=P": 107, - "N-1": 108, - "Ring3": 109, - "2H": 110, - "P+1": 111, - "K+1": 112, - "\\C@@H1": 113, - "\\C@H1": 114, - "/N+1": 115, - "@@": 116, - "C-1": 117, - "#N+1": 118, - "B-1": 119, - "+3": 120, - "Cl+3": 121, - "\\NH1": 122, - "Li": 123, - "Li+1": 124, - "PH1": 125, - "18": 126, - "18F": 127, - "@+1": 128, - "3H": 129, - "P@@": 130, - "H0": 131, - "OH0": 132, - "12": 133, - "P@": 134, - "+2": 135, - "@@+1": 136, - "S-1": 137, - "/Br": 138, - "-/": 139, - "\\Cl": 140, - "-/Ring2": 141, - "\\O-1": 142, - "11": 143, - "5I": 144, - "125I": 145, - "11C": 146, - "H3": 147, - "\\N+1": 148, - "-\\": 149, - "/C@@": 150, - "S@+1": 151, - "As": 152, - "/Cl": 153, - "11CH3": 154, - "=Se": 155, - "S@@+1": 156, - "N@+1": 157, - "14": 158, - "-\\Ring2": 159, - "14C": 160, - "\\F": 161, - "/C@": 162, - "Te": 163, - "H2": 164, - "H1-1": 165, - "=O+1": 166, - "N@@+1": 167, - "C+1": 168, - "=S+1": 169, - "Zn": 170, - "/P": 171, - "a+2": 172, - "/I": 173, - "OH1-1": 174, - "Ca+2": 175, - "\\Br": 176, - "Mg": 177, - "Zn+2": 178, - "Al": 179, - "/F": 180, - "Mg+2": 181, - "123": 182, - "123I": 183, - "13": 184, - "I+1": 185, - "/O-1": 186, - "-\\Ring1": 187, - "BH2": 188, - "BH2-1": 189, - "\\I": 190, - "/NH1": 191, - "O+1": 192, - "131": 193, - "131I": 194, - "=14C": 195, - "/S+1": 196, - "=Ring3": 197, - "\\C@@": 198, - "H2+1": 199, - "\\C@": 200, - "Ag": 201, - "=As": 202, - "=Se+1": 203, - "NH2+1": 204, - "SeH1": 205, - "-/Ring1": 206, - "=Te": 207, - "Al+3": 208, - "NaH1": 209, - "=Te+1": 210, - "NH1+1": 211, - "Ag+1": 212, - "H1+1": 213, - "NH1-1": 214, - "\\P": 215, - "14CH2": 216, - "13C": 217, - "14CH1": 218, - "=11C": 219, - "S@@": 220, - "=P@@": 221, - "SiH2": 222, - "H3-1": 223, - "14CH3": 224, - "BH3-1": 225, - "S@": 226, - "=14CH1": 227, - "=PH1": 228, - "=P@": 229, - "=NH1+1": 230, - "\\S+1": 231, - "124": 232, - "CH1-1": 233, - "Sr": 234, - "=Si": 235, - "124I": 236, - "Sr+2": 237, - "#C-1": 238, - "/C-1": 239, - "N@": 240, - "/N-1": 241, - "13CH1": 242, - "/B": 243, - "19": 244, - "Ba+2": 245, - "H4": 246, - "SH1+1": 247, - "Se+1": 248, - "19F": 249, - "/125I": 250, - "P@+1": 251, - "Rb": 252, - "Cl+1": 253, - "SiH4": 254, - "Rb+1": 255, - "=Branch3": 256, - "N@@": 257, - "As+1": 258, - "/Si": 259, - "BH1-1": 260, - "SH1": 261, - "/123I": 262, - "32": 263, - "=Mg": 264, - "H+1": 265, - "\\B": 266, - "SiH1": 267, - "P@@+1": 268, - "-2": 269, - "15": 270, - "17": 271, - "35": 272, - "=13CH1": 273, - "Cs": 274, - "=NH2+1": 275, - "=SH1": 276, - "MgH2": 277, - "32P": 278, - "17F": 279, - "35S": 280, - "Cs+1": 281, - "#11C": 282, - "/131I": 283, - "Bi": 284, - "\\125I": 285, - "=S@@": 286, - "\\S-1": 287, - "6Br": 288, - "7I": 289, - "76Br": 290, - "=B": 291, - "eH1": 292, - "\\N-1": 293, - "18O": 294, - "127I": 295, - "11CH2": 296, - "14C@@H1": 297, - "TeH2": 298, - "15NH1": 299, - "Bi+3": 300, - "/P+1": 301, - "/13C": 302, - "/13CH1": 303, - "0B": 304, - "10B": 305, - "=Al": 306, - "=18O": 307, - "BH0": 308, - "F-1": 309, - "NH3": 310, - "S-2": 311, - "Br+2": 312, - "Cl+2": 313, - "\\Si": 314, - "/S-1": 315, - "=PH2": 316, - "14C@H1": 317, - "NH3+1": 318, - "#14C": 319, - "#O+1": 320, - "-3": 321, - "22": 322, - "4H": 323, - "5Se": 324, - "5Sr+2": 325, - "75Se": 326, - "85Sr+2": 327, - "=B-1": 328, - "=13C": 329, - "@-1": 330, - "Be": 331, - "B@@": 332, - "B@-1": 333, - "Ca": 334, - "CH1": 335, - "I+3": 336, - "KH1": 337, - "OH1+1": 338, - "Ra+2": 339, - "SH1-1": 340, - "\\PH1": 341, - "\\123I": 342, - "=Ca": 343, - "\\CH1-1": 344, - "=S@": 345, - "\\SeH1": 346, - "/SeH1": 347, - "Se-1": 348, - "LiH1": 349, - "18F-1": 350, - "125IH1": 351, - "11CH1": 352, - "TeH1": 353, - "Zn+1": 354, - "Zn-2": 355, - "Al-3": 356, - "13CH3": 357, - "15N": 358, - "Be+2": 359, - "B@@-1": 360, - "#P": 361, - "#S": 362, - "-4": 363, - "/PH1": 364, - "/P@@": 365, - "/As": 366, - "/14C": 367, - "/14CH1": 368, - "2K+1": 369, - "2Rb+1": 370, - "3Se": 371, - "3Ra+2": 372, - "45": 373, - "47": 374, - "42K+1": 375, - "5I-1": 376, - "73Se": 377, - "89": 378, - "82Rb+1": 379, - "=32": 380, - "=32P": 381, - "CH0": 382, - "CH2": 383, - "I+2": 384, - "NH0": 385, - "NH4": 386, - "OH1": 387, - "PH2+1": 388, - "SH0": 389, - "SH2": 390, - "\\3H": 391, - "\\11CH3": 392, - "\\C-1": 393, - "\\Se": 394, - "Si@": 395, - "Si-1": 396, - "SiH1-1": 397, - "SiH3-1": 398, - "/Se": 399, - "Se-2": 400, - "\\NH1-1": 401, - "18FH1": 402, - "125I-1": 403, - "11C@@H1": 404, - "11C-1": 405, - "AsH1": 406, - "As-1": 407, - "14C@@": 408, - "Te-1": 409, - "Mg+1": 410, - "123I-1": 411, - "123Te": 412, - "123IH1": 413, - "135I": 414, - "131I-1": 415, - "Ag-4": 416, - "124I-1": 417, - "76BrH1": 418, - "18OH1": 419, - "22Na+1": 420, - "223Ra+2": 421, - "CaH2": 422, - "45Ca+2": 423, - "47Ca+2": 424, - "89Sr+2": 425, - "=32PH1": 426, - "NH4+1": 427 - }, - "merges": [ - "B r", - "a n", - "c h", - "Br an", - "Bran ch", - "Branch 1", - "= C", - "R i", - "n g", - "Ri ng", - "Ring 1", - "= Branch1", - "Branch 2", - "= O", - "Ring 2", - "H 1", - "C @", - "= N", - "# Branch1", - "C@ @", - "= Branch2", - "C@ H1", - "C@@ H1", - "# Branch2", - "# C", - "C l", - "/ C", - "N H1", - "= Ring1", - "+ 1", - "- 1", - "O -1", - "N +1", - "\\ C", - "# N", - "/ N", - "= Ring2", - "= S", - "=N +1", - "\\ N", - "N a", - "Na +1", - "/ O", - "\\ O", - "Br -1", - "Branch 3", - "\\ S", - "S +1", - "Cl -1", - "I -1", - "/ C@@H1", - "S i", - "/ C@H1", - "/ S", - "=N -1", - "S e", - "= P", - "N -1", - "Ring 3", - "2 H", - "P +1", - "K +1", - "\\ C@@H1", - "\\ C@H1", - "/ N+1", - "@ @", - "C -1", - "# N+1", - "B -1", - "+ 3", - "Cl +3", - "\\ NH1", - "L i", - "Li +1", - "P H1", - "1 8", - "18 F", - "@ +1", - "3 H", - "P @@", - "H 0", - "O H0", - "1 2", - "P @", - "+ 2", - "@@ +1", - "S -1", - "/ Br", - "- /", - "\\ Cl", - "-/ Ring2", - "\\ O-1", - "1 1", - "5 I", - "12 5I", - "11 C", - "H 3", - "\\ N+1", - "- \\", - "/ C@@", - "S @+1", - "A s", - "/ Cl", - "11C H3", - "=S e", - "S @@+1", - "N @+1", - "1 4", - "-\\ Ring2", - "14 C", - "\\ F", - "/ C@", - "T e", - "H 2", - "H1 -1", - "=O +1", - "N @@+1", - "C +1", - "=S +1", - "Z n", - "/ P", - "a +2", - "/ I", - "O H1-1", - "C a+2", - "\\ Br", - "M g", - "Zn +2", - "A l", - "/ F", - "Mg +2", - "12 3", - "123 I", - "1 3", - "I +1", - "/ O-1", - "-\\ Ring1", - "B H2", - "BH2 -1", - "\\ I", - "/ NH1", - "O +1", - "13 1", - "131 I", - "= 14C", - "/ S+1", - "= Ring3", - "\\ C@@", - "H2 +1", - "\\ C@", - "A g", - "= As", - "=Se +1", - "N H2+1", - "Se H1", - "-/ Ring1", - "= Te", - "Al +3", - "Na H1", - "=Te +1", - "NH1 +1", - "Ag +1", - "H1 +1", - "NH1 -1", - "\\ P", - "14C H2", - "13 C", - "14C H1", - "= 11C", - "S @@", - "=P @@", - "Si H2", - "H3 -1", - "14C H3", - "B H3-1", - "S @", - "=14C H1", - "=P H1", - "=P @", - "=N H1+1", - "\\S +1", - "12 4", - "C H1-1", - "S r", - "=S i", - "124 I", - "Sr +2", - "#C -1", - "/C -1", - "N @", - "/N -1", - "13C H1", - "/ B", - "1 9", - "B a+2", - "H 4", - "S H1+1", - "Se +1", - "19 F", - "/ 125I", - "P @+1", - "R b", - "Cl +1", - "Si H4", - "Rb +1", - "= Branch3", - "N @@", - "As +1", - "/ Si", - "B H1-1", - "S H1", - "/ 123I", - "3 2", - "= Mg", - "H +1", - "\\ B", - "Si H1", - "P@@ +1", - "- 2", - "1 5", - "1 7", - "3 5", - "= 13CH1", - "C s", - "=N H2+1", - "=S H1", - "Mg H2", - "32 P", - "17 F", - "35 S", - "Cs +1", - "# 11C", - "/ 131I", - "B i", - "\\ 125I", - "=S @@", - "\\S -1", - "6 Br", - "7 I", - "7 6Br", - "= B", - "e H1", - "\\N -1", - "18 O", - "12 7I", - "11C H2", - "14 C@@H1", - "Te H2", - "15 NH1", - "Bi +3", - "/ P+1", - "/ 13C", - "/ 13CH1", - "0 B", - "1 0B", - "= Al", - "= 18O", - "B H0", - "F -1", - "N H3", - "S -2", - "Br +2", - "Cl +2", - "\\S i", - "/S -1", - "=P H2", - "14 C@H1", - "NH3 +1", - "# 14C", - "# O+1", - "- 3", - "2 2", - "4 H", - "5 Se", - "5 Sr+2", - "7 5Se", - "8 5Sr+2", - "= B-1", - "= 13C", - "@ -1", - "B e", - "B @@", - "B @-1", - "C a", - "C H1", - "I +3", - "K H1", - "O H1+1", - "R a+2", - "S H1-1", - "\\ PH1", - "\\ 123I", - "=C a", - "\\C H1-1", - "=S @", - "\\S eH1", - "/S eH1", - "Se -1", - "Li H1", - "18F -1", - "125I H1", - "11C H1", - "Te H1", - "Zn +1", - "Zn -2", - "Al -3", - "13C H3", - "15 N", - "Be +2", - "B@@ -1", - "# P", - "# S", - "- 4", - "/ PH1", - "/ P@@", - "/ As", - "/ 14C", - "/ 14CH1", - "2 K+1", - "2 Rb+1", - "3 Se", - "3 Ra+2", - "4 5", - "4 7", - "4 2K+1", - "5 I-1", - "7 3Se", - "8 9", - "8 2Rb+1", - "= 32", - "= 32P", - "C H0", - "C H2", - "I +2", - "N H0", - "N H4", - "O H1", - "P H2+1", - "S H0", - "S H2", - "\\ 3H", - "\\ 11CH3", - "\\C -1", - "\\S e", - "Si @", - "Si -1", - "Si H1-1", - "Si H3-1", - "/S e", - "Se -2", - "\\NH1 -1", - "18F H1", - "12 5I-1", - "11 C@@H1", - "11 C-1", - "As H1", - "As -1", - "14 C@@", - "Te -1", - "Mg +1", - "123 I-1", - "123 Te", - "123I H1", - "13 5I", - "131 I-1", - "Ag -4", - "124 I-1", - "76Br H1", - "18O H1", - "22 Na+1", - "22 3Ra+2", - "Ca H2", - "45 Ca+2", - "47 Ca+2", - "89 Sr+2", - "=32 PH1", - "NH4 +1" - ] - } -} \ No newline at end of file diff --git a/models/finetuned/hiv/tokenizer_config.json b/models/finetuned/hiv/tokenizer_config.json deleted file mode 100644 index 08860954acd34fad07fd77f7635298fa565f3149..0000000000000000000000000000000000000000 --- a/models/finetuned/hiv/tokenizer_config.json +++ /dev/null @@ -1,65 +0,0 @@ -{ - "add_prefix_space": false, - "bos_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "cls_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "eos_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "errors": "replace", - "mask_token": { - "__type": "AddedToken", - "content": "", - "lstrip": true, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "model_max_length": 1000000000000000019884624838656, - "name_or_path": "/home/erva/SELFormerMM/data/pretrained_multimodal_chembl36", - "pad_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "sep_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "special_tokens_map_file": null, - "tokenizer_class": "RobertaTokenizer", - "trim_offsets": true, - "unk_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - } -} diff --git a/models/finetuned/hiv/vocab.json b/models/finetuned/hiv/vocab.json deleted file mode 100644 index f7e4cc22809f4e9035cc450ef189c8a7da8fd03e..0000000000000000000000000000000000000000 --- a/models/finetuned/hiv/vocab.json +++ /dev/null @@ -1 +0,0 @@ -{"":0,"":1,"":2,"":3,"":4,"\n":5,"#":6,"+":7,"-":8,".":9,"/":10,"0":11,"1":12,"2":13,"3":14,"4":15,"5":16,"6":17,"7":18,"8":19,"9":20,"=":21,"@":22,"A":23,"B":24,"C":25,"F":26,"H":27,"I":28,"K":29,"L":30,"M":31,"N":32,"O":33,"P":34,"R":35,"S":36,"T":37,"Z":38,"\\":39,"a":40,"b":41,"c":42,"e":43,"g":44,"h":45,"i":46,"l":47,"n":48,"r":49,"s":50,"Br":51,"an":52,"ch":53,"Bran":54,"Branch":55,"Branch1":56,"=C":57,"Ri":58,"ng":59,"Ring":60,"Ring1":61,"=Branch1":62,"Branch2":63,"=O":64,"Ring2":65,"H1":66,"C@":67,"=N":68,"#Branch1":69,"C@@":70,"=Branch2":71,"C@H1":72,"C@@H1":73,"#Branch2":74,"#C":75,"Cl":76,"/C":77,"NH1":78,"=Ring1":79,"+1":80,"-1":81,"O-1":82,"N+1":83,"\\C":84,"#N":85,"/N":86,"=Ring2":87,"=S":88,"=N+1":89,"\\N":90,"Na":91,"Na+1":92,"/O":93,"\\O":94,"Br-1":95,"Branch3":96,"\\S":97,"S+1":98,"Cl-1":99,"I-1":100,"/C@@H1":101,"Si":102,"/C@H1":103,"/S":104,"=N-1":105,"Se":106,"=P":107,"N-1":108,"Ring3":109,"2H":110,"P+1":111,"K+1":112,"\\C@@H1":113,"\\C@H1":114,"/N+1":115,"@@":116,"C-1":117,"#N+1":118,"B-1":119,"+3":120,"Cl+3":121,"\\NH1":122,"Li":123,"Li+1":124,"PH1":125,"18":126,"18F":127,"@+1":128,"3H":129,"P@@":130,"H0":131,"OH0":132,"12":133,"P@":134,"+2":135,"@@+1":136,"S-1":137,"/Br":138,"-/":139,"\\Cl":140,"-/Ring2":141,"\\O-1":142,"11":143,"5I":144,"125I":145,"11C":146,"H3":147,"\\N+1":148,"-\\":149,"/C@@":150,"S@+1":151,"As":152,"/Cl":153,"11CH3":154,"=Se":155,"S@@+1":156,"N@+1":157,"14":158,"-\\Ring2":159,"14C":160,"\\F":161,"/C@":162,"Te":163,"H2":164,"H1-1":165,"=O+1":166,"N@@+1":167,"C+1":168,"=S+1":169,"Zn":170,"/P":171,"a+2":172,"/I":173,"OH1-1":174,"Ca+2":175,"\\Br":176,"Mg":177,"Zn+2":178,"Al":179,"/F":180,"Mg+2":181,"123":182,"123I":183,"13":184,"I+1":185,"/O-1":186,"-\\Ring1":187,"BH2":188,"BH2-1":189,"\\I":190,"/NH1":191,"O+1":192,"131":193,"131I":194,"=14C":195,"/S+1":196,"=Ring3":197,"\\C@@":198,"H2+1":199,"\\C@":200,"Ag":201,"=As":202,"=Se+1":203,"NH2+1":204,"SeH1":205,"-/Ring1":206,"=Te":207,"Al+3":208,"NaH1":209,"=Te+1":210,"NH1+1":211,"Ag+1":212,"H1+1":213,"NH1-1":214,"\\P":215,"14CH2":216,"13C":217,"14CH1":218,"=11C":219,"S@@":220,"=P@@":221,"SiH2":222,"H3-1":223,"14CH3":224,"BH3-1":225,"S@":226,"=14CH1":227,"=PH1":228,"=P@":229,"=NH1+1":230,"\\S+1":231,"124":232,"CH1-1":233,"Sr":234,"=Si":235,"124I":236,"Sr+2":237,"#C-1":238,"/C-1":239,"N@":240,"/N-1":241,"13CH1":242,"/B":243,"19":244,"Ba+2":245,"H4":246,"SH1+1":247,"Se+1":248,"19F":249,"/125I":250,"P@+1":251,"Rb":252,"Cl+1":253,"SiH4":254,"Rb+1":255,"=Branch3":256,"N@@":257,"As+1":258,"/Si":259,"BH1-1":260,"SH1":261,"/123I":262,"32":263,"=Mg":264,"H+1":265,"\\B":266,"SiH1":267,"P@@+1":268,"-2":269,"15":270,"17":271,"35":272,"=13CH1":273,"Cs":274,"=NH2+1":275,"=SH1":276,"MgH2":277,"32P":278,"17F":279,"35S":280,"Cs+1":281,"#11C":282,"/131I":283,"Bi":284,"\\125I":285,"=S@@":286,"\\S-1":287,"6Br":288,"7I":289,"76Br":290,"=B":291,"eH1":292,"\\N-1":293,"18O":294,"127I":295,"11CH2":296,"14C@@H1":297,"TeH2":298,"15NH1":299,"Bi+3":300,"/P+1":301,"/13C":302,"/13CH1":303,"0B":304,"10B":305,"=Al":306,"=18O":307,"BH0":308,"F-1":309,"NH3":310,"S-2":311,"Br+2":312,"Cl+2":313,"\\Si":314,"/S-1":315,"=PH2":316,"14C@H1":317,"NH3+1":318,"#14C":319,"#O+1":320,"-3":321,"22":322,"4H":323,"5Se":324,"5Sr+2":325,"75Se":326,"85Sr+2":327,"=B-1":328,"=13C":329,"@-1":330,"Be":331,"B@@":332,"B@-1":333,"Ca":334,"CH1":335,"I+3":336,"KH1":337,"OH1+1":338,"Ra+2":339,"SH1-1":340,"\\PH1":341,"\\123I":342,"=Ca":343,"\\CH1-1":344,"=S@":345,"\\SeH1":346,"/SeH1":347,"Se-1":348,"LiH1":349,"18F-1":350,"125IH1":351,"11CH1":352,"TeH1":353,"Zn+1":354,"Zn-2":355,"Al-3":356,"13CH3":357,"15N":358,"Be+2":359,"B@@-1":360,"#P":361,"#S":362,"-4":363,"/PH1":364,"/P@@":365,"/As":366,"/14C":367,"/14CH1":368,"2K+1":369,"2Rb+1":370,"3Se":371,"3Ra+2":372,"45":373,"47":374,"42K+1":375,"5I-1":376,"73Se":377,"89":378,"82Rb+1":379,"=32":380,"=32P":381,"CH0":382,"CH2":383,"I+2":384,"NH0":385,"NH4":386,"OH1":387,"PH2+1":388,"SH0":389,"SH2":390,"\\3H":391,"\\11CH3":392,"\\C-1":393,"\\Se":394,"Si@":395,"Si-1":396,"SiH1-1":397,"SiH3-1":398,"/Se":399,"Se-2":400,"\\NH1-1":401,"18FH1":402,"125I-1":403,"11C@@H1":404,"11C-1":405,"AsH1":406,"As-1":407,"14C@@":408,"Te-1":409,"Mg+1":410,"123I-1":411,"123Te":412,"123IH1":413,"135I":414,"131I-1":415,"Ag-4":416,"124I-1":417,"76BrH1":418,"18OH1":419,"22Na+1":420,"223Ra+2":421,"CaH2":422,"45Ca+2":423,"47Ca+2":424,"89Sr+2":425,"=32PH1":426,"NH4+1":427} \ No newline at end of file diff --git a/models/finetuned/lipo/checkpoint_epoch_025/config.json b/models/finetuned/lipo/checkpoint_epoch_025/config.json deleted file mode 100644 index 3811e21539577b37e06313eab31ec11e53f0cbbc..0000000000000000000000000000000000000000 --- a/models/finetuned/lipo/checkpoint_epoch_025/config.json +++ /dev/null @@ -1,27 +0,0 @@ -{ - "_name_or_path": "/home/erva/SELFormerMM/data/pretrained_multimodal_chembl36", - "architectures": [ - "RobertaForMaskedLM" - ], - "attention_probs_dropout_prob": 0.1, - "bos_token_id": 0, - "classifier_dropout": null, - "eos_token_id": 2, - "hidden_act": "gelu", - "hidden_dropout_prob": 0.1, - "hidden_size": 768, - "initializer_range": 0.02, - "intermediate_size": 3072, - "layer_norm_eps": 1e-12, - "max_position_embeddings": 514, - "model_type": "roberta", - "num_attention_heads": 4, - "num_hidden_layers": 12, - "pad_token_id": 1, - "position_embedding_type": "absolute", - "torch_dtype": "float32", - "transformers_version": "4.26.1", - "type_vocab_size": 1, - "use_cache": true, - "vocab_size": 800 -} diff --git a/models/finetuned/lipo/checkpoint_epoch_025/merges.txt b/models/finetuned/lipo/checkpoint_epoch_025/merges.txt deleted file mode 100644 index 7cd5ec62809503c23f18c80afc0ba3bdf9d253d0..0000000000000000000000000000000000000000 --- a/models/finetuned/lipo/checkpoint_epoch_025/merges.txt +++ /dev/null @@ -1,378 +0,0 @@ -#version: 0.2 - Trained by `huggingface/tokenizers` -B r -a n -c h -Br an -Bran ch -Branch 1 -= C -R i -n g -Ri ng -Ring 1 -= Branch1 -Branch 2 -= O -Ring 2 -H 1 -C @ -= N -# Branch1 -C@ @ -= Branch2 -C@ H1 -C@@ H1 -# Branch2 -# C -C l -/ C -N H1 -= Ring1 -+ 1 -- 1 -O -1 -N +1 -\ C -# N -/ N -= Ring2 -= S -=N +1 -\ N -N a -Na +1 -/ O -\ O -Br -1 -Branch 3 -\ S -S +1 -Cl -1 -I -1 -/ C@@H1 -S i -/ C@H1 -/ S -=N -1 -S e -= P -N -1 -Ring 3 -2 H -P +1 -K +1 -\ C@@H1 -\ C@H1 -/ N+1 -@ @ -C -1 -# N+1 -B -1 -+ 3 -Cl +3 -\ NH1 -L i -Li +1 -P H1 -1 8 -18 F -@ +1 -3 H -P @@ -H 0 -O H0 -1 2 -P @ -+ 2 -@@ +1 -S -1 -/ Br -- / -\ Cl --/ Ring2 -\ O-1 -1 1 -5 I -12 5I -11 C -H 3 -\ N+1 -- \ -/ C@@ -S @+1 -A s -/ Cl -11C H3 -=S e -S @@+1 -N @+1 -1 4 --\ Ring2 -14 C -\ F -/ C@ -T e -H 2 -H1 -1 -=O +1 -N @@+1 -C +1 -=S +1 -Z n -/ P -a +2 -/ I -O H1-1 -C a+2 -\ Br -M g -Zn +2 -A l -/ F -Mg +2 -12 3 -123 I -1 3 -I +1 -/ O-1 --\ Ring1 -B H2 -BH2 -1 -\ I -/ NH1 -O +1 -13 1 -131 I -= 14C -/ S+1 -= Ring3 -\ C@@ -H2 +1 -\ C@ -A g -= As -=Se +1 -N H2+1 -Se H1 --/ Ring1 -= Te -Al +3 -Na H1 -=Te +1 -NH1 +1 -Ag +1 -H1 +1 -NH1 -1 -\ P -14C H2 -13 C -14C H1 -= 11C -S @@ -=P @@ -Si H2 -H3 -1 -14C H3 -B H3-1 -S @ -=14C H1 -=P H1 -=P @ -=N H1+1 -\S +1 -12 4 -C H1-1 -S r -=S i -124 I -Sr +2 -#C -1 -/C -1 -N @ -/N -1 -13C H1 -/ B -1 9 -B a+2 -H 4 -S H1+1 -Se +1 -19 F -/ 125I -P @+1 -R b -Cl +1 -Si H4 -Rb +1 -= Branch3 -N @@ -As +1 -/ Si -B H1-1 -S H1 -/ 123I -3 2 -= Mg -H +1 -\ B -Si H1 -P@@ +1 -- 2 -1 5 -1 7 -3 5 -= 13CH1 -C s -=N H2+1 -=S H1 -Mg H2 -32 P -17 F -35 S -Cs +1 -# 11C -/ 131I -B i -\ 125I -=S @@ -\S -1 -6 Br -7 I -7 6Br -= B -e H1 -\N -1 -18 O -12 7I -11C H2 -14 C@@H1 -Te H2 -15 NH1 -Bi +3 -/ P+1 -/ 13C -/ 13CH1 -0 B -1 0B -= Al -= 18O -B H0 -F -1 -N H3 -S -2 -Br +2 -Cl +2 -\S i -/S -1 -=P H2 -14 C@H1 -NH3 +1 -# 14C -# O+1 -- 3 -2 2 -4 H -5 Se -5 Sr+2 -7 5Se -8 5Sr+2 -= B-1 -= 13C -@ -1 -B e -B @@ -B @-1 -C a -C H1 -I +3 -K H1 -O H1+1 -R a+2 -S H1-1 -\ PH1 -\ 123I -=C a -\C H1-1 -=S @ -\S eH1 -/S eH1 -Se -1 -Li H1 -18F -1 -125I H1 -11C H1 -Te H1 -Zn +1 -Zn -2 -Al -3 -13C H3 -15 N -Be +2 -B@@ -1 -# P -# S -- 4 -/ PH1 -/ P@@ -/ As -/ 14C -/ 14CH1 -2 K+1 -2 Rb+1 -3 Se -3 Ra+2 -4 5 -4 7 -4 2K+1 -5 I-1 -7 3Se -8 9 -8 2Rb+1 -= 32 -= 32P -C H0 -C H2 -I +2 -N H0 -N H4 -O H1 -P H2+1 -S H0 -S H2 -\ 3H -\ 11CH3 -\C -1 -\S e -Si @ -Si -1 -Si H1-1 -Si H3-1 -/S e -Se -2 -\NH1 -1 -18F H1 -12 5I-1 -11 C@@H1 -11 C-1 -As H1 -As -1 -14 C@@ -Te -1 -Mg +1 -123 I-1 -123 Te -123I H1 -13 5I -131 I-1 -Ag -4 -124 I-1 -76Br H1 -18O H1 -22 Na+1 -22 3Ra+2 -Ca H2 -45 Ca+2 -47 Ca+2 -89 Sr+2 -=32 PH1 -NH4 +1 diff --git a/models/finetuned/lipo/checkpoint_epoch_025/model.pt b/models/finetuned/lipo/checkpoint_epoch_025/model.pt deleted file mode 100644 index c85c57aae30f87c843bb1e23ab33d810869532ac..0000000000000000000000000000000000000000 --- a/models/finetuned/lipo/checkpoint_epoch_025/model.pt +++ /dev/null @@ -1,3 +0,0 @@ -version https://git-lfs.github.com/spec/v1 -oid sha256:33b8625d3f581bd33d28f8191db5208a9932ce7f7a11403cdd343b409fe36e2f -size 1022843005 diff --git a/models/finetuned/lipo/checkpoint_epoch_025/special_tokens_map.json b/models/finetuned/lipo/checkpoint_epoch_025/special_tokens_map.json deleted file mode 100644 index 06a55849fa69a91e7179d909e373179ff7467d8c..0000000000000000000000000000000000000000 --- a/models/finetuned/lipo/checkpoint_epoch_025/special_tokens_map.json +++ /dev/null @@ -1,51 +0,0 @@ -{ - "bos_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "cls_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "eos_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "mask_token": { - "content": "", - "lstrip": true, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "pad_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "sep_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "unk_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - } -} diff --git a/models/finetuned/lipo/checkpoint_epoch_025/tokenizer.json b/models/finetuned/lipo/checkpoint_epoch_025/tokenizer.json deleted file mode 100644 index 3b64b273e6fa9799e2d8375722b9e815de9ebb8f..0000000000000000000000000000000000000000 --- a/models/finetuned/lipo/checkpoint_epoch_025/tokenizer.json +++ /dev/null @@ -1,909 +0,0 @@ -{ - "version": "1.0", - "truncation": { - "direction": "Right", - "max_length": 128, - "strategy": "LongestFirst", - "stride": 0 - }, - "padding": { - "strategy": { - "Fixed": 128 - }, - "direction": "Right", - "pad_to_multiple_of": null, - "pad_id": 3, - "pad_type_id": 0, - "pad_token": "" - }, - "added_tokens": [ - { - "id": 0, - "content": "", - "single_word": false, - "lstrip": false, - "rstrip": false, - "normalized": true, - "special": true - }, - { - "id": 1, - "content": "", - "single_word": false, - "lstrip": false, - "rstrip": false, - "normalized": true, - "special": true - }, - { - "id": 2, - "content": "", - "single_word": false, - "lstrip": false, - "rstrip": false, - "normalized": true, - "special": true - }, - { - "id": 3, - "content": "", - "single_word": false, - "lstrip": false, - "rstrip": false, - "normalized": true, - "special": true - }, - { - "id": 4, - "content": "", - "single_word": false, - "lstrip": true, - "rstrip": false, - "normalized": true, - "special": true - } - ], - "normalizer": null, - "pre_tokenizer": { - "type": "ByteLevel", - "add_prefix_space": false, - "trim_offsets": true, - "use_regex": true - }, - "post_processor": { - "type": "RobertaProcessing", - "sep": [ - "", - 2 - ], - "cls": [ - "", - 1 - ], - "trim_offsets": true, - "add_prefix_space": false - }, - "decoder": { - "type": "ByteLevel", - "add_prefix_space": true, - "trim_offsets": true, - "use_regex": true - }, - "model": { - "type": "BPE", - "dropout": null, - "unk_token": null, - "continuing_subword_prefix": "", - "end_of_word_suffix": "", - "fuse_unk": false, - "vocab": { - "": 0, - "": 1, - "": 2, - "": 3, - "": 4, - "\n": 5, - "#": 6, - "+": 7, - "-": 8, - ".": 9, - "/": 10, - "0": 11, - "1": 12, - "2": 13, - "3": 14, - "4": 15, - "5": 16, - "6": 17, - "7": 18, - "8": 19, - "9": 20, - "=": 21, - "@": 22, - "A": 23, - "B": 24, - "C": 25, - "F": 26, - "H": 27, - "I": 28, - "K": 29, - "L": 30, - "M": 31, - "N": 32, - "O": 33, - "P": 34, - "R": 35, - "S": 36, - "T": 37, - "Z": 38, - "\\": 39, - "a": 40, - "b": 41, - "c": 42, - "e": 43, - "g": 44, - "h": 45, - "i": 46, - "l": 47, - "n": 48, - "r": 49, - "s": 50, - "Br": 51, - "an": 52, - "ch": 53, - "Bran": 54, - "Branch": 55, - "Branch1": 56, - "=C": 57, - "Ri": 58, - "ng": 59, - "Ring": 60, - "Ring1": 61, - "=Branch1": 62, - "Branch2": 63, - "=O": 64, - "Ring2": 65, - "H1": 66, - "C@": 67, - "=N": 68, - "#Branch1": 69, - "C@@": 70, - "=Branch2": 71, - "C@H1": 72, - "C@@H1": 73, - "#Branch2": 74, - "#C": 75, - "Cl": 76, - "/C": 77, - "NH1": 78, - "=Ring1": 79, - "+1": 80, - "-1": 81, - "O-1": 82, - "N+1": 83, - "\\C": 84, - "#N": 85, - "/N": 86, - "=Ring2": 87, - "=S": 88, - "=N+1": 89, - "\\N": 90, - "Na": 91, - "Na+1": 92, - "/O": 93, - "\\O": 94, - "Br-1": 95, - "Branch3": 96, - "\\S": 97, - "S+1": 98, - "Cl-1": 99, - "I-1": 100, - "/C@@H1": 101, - "Si": 102, - "/C@H1": 103, - "/S": 104, - "=N-1": 105, - "Se": 106, - "=P": 107, - "N-1": 108, - "Ring3": 109, - "2H": 110, - "P+1": 111, - "K+1": 112, - "\\C@@H1": 113, - "\\C@H1": 114, - "/N+1": 115, - "@@": 116, - "C-1": 117, - "#N+1": 118, - "B-1": 119, - "+3": 120, - "Cl+3": 121, - "\\NH1": 122, - "Li": 123, - "Li+1": 124, - "PH1": 125, - "18": 126, - "18F": 127, - "@+1": 128, - "3H": 129, - "P@@": 130, - "H0": 131, - "OH0": 132, - "12": 133, - "P@": 134, - "+2": 135, - "@@+1": 136, - "S-1": 137, - "/Br": 138, - "-/": 139, - "\\Cl": 140, - "-/Ring2": 141, - "\\O-1": 142, - "11": 143, - "5I": 144, - "125I": 145, - "11C": 146, - "H3": 147, - "\\N+1": 148, - "-\\": 149, - "/C@@": 150, - "S@+1": 151, - "As": 152, - "/Cl": 153, - "11CH3": 154, - "=Se": 155, - "S@@+1": 156, - "N@+1": 157, - "14": 158, - "-\\Ring2": 159, - "14C": 160, - "\\F": 161, - "/C@": 162, - "Te": 163, - "H2": 164, - "H1-1": 165, - "=O+1": 166, - "N@@+1": 167, - "C+1": 168, - "=S+1": 169, - "Zn": 170, - "/P": 171, - "a+2": 172, - "/I": 173, - "OH1-1": 174, - "Ca+2": 175, - "\\Br": 176, - "Mg": 177, - "Zn+2": 178, - "Al": 179, - "/F": 180, - "Mg+2": 181, - "123": 182, - "123I": 183, - "13": 184, - "I+1": 185, - "/O-1": 186, - "-\\Ring1": 187, - "BH2": 188, - "BH2-1": 189, - "\\I": 190, - "/NH1": 191, - "O+1": 192, - "131": 193, - "131I": 194, - "=14C": 195, - "/S+1": 196, - "=Ring3": 197, - "\\C@@": 198, - "H2+1": 199, - "\\C@": 200, - "Ag": 201, - "=As": 202, - "=Se+1": 203, - "NH2+1": 204, - "SeH1": 205, - "-/Ring1": 206, - "=Te": 207, - "Al+3": 208, - "NaH1": 209, - "=Te+1": 210, - "NH1+1": 211, - "Ag+1": 212, - "H1+1": 213, - "NH1-1": 214, - "\\P": 215, - "14CH2": 216, - "13C": 217, - "14CH1": 218, - "=11C": 219, - "S@@": 220, - "=P@@": 221, - "SiH2": 222, - "H3-1": 223, - "14CH3": 224, - "BH3-1": 225, - "S@": 226, - "=14CH1": 227, - "=PH1": 228, - "=P@": 229, - "=NH1+1": 230, - "\\S+1": 231, - "124": 232, - "CH1-1": 233, - "Sr": 234, - "=Si": 235, - "124I": 236, - "Sr+2": 237, - "#C-1": 238, - "/C-1": 239, - "N@": 240, - "/N-1": 241, - "13CH1": 242, - "/B": 243, - "19": 244, - "Ba+2": 245, - "H4": 246, - "SH1+1": 247, - "Se+1": 248, - "19F": 249, - "/125I": 250, - "P@+1": 251, - "Rb": 252, - "Cl+1": 253, - "SiH4": 254, - "Rb+1": 255, - "=Branch3": 256, - "N@@": 257, - "As+1": 258, - "/Si": 259, - "BH1-1": 260, - "SH1": 261, - "/123I": 262, - "32": 263, - "=Mg": 264, - "H+1": 265, - "\\B": 266, - "SiH1": 267, - "P@@+1": 268, - "-2": 269, - "15": 270, - "17": 271, - "35": 272, - "=13CH1": 273, - "Cs": 274, - "=NH2+1": 275, - "=SH1": 276, - "MgH2": 277, - "32P": 278, - "17F": 279, - "35S": 280, - "Cs+1": 281, - "#11C": 282, - "/131I": 283, - "Bi": 284, - "\\125I": 285, - "=S@@": 286, - "\\S-1": 287, - "6Br": 288, - "7I": 289, - "76Br": 290, - "=B": 291, - "eH1": 292, - "\\N-1": 293, - "18O": 294, - "127I": 295, - "11CH2": 296, - "14C@@H1": 297, - "TeH2": 298, - "15NH1": 299, - "Bi+3": 300, - "/P+1": 301, - "/13C": 302, - "/13CH1": 303, - "0B": 304, - "10B": 305, - "=Al": 306, - "=18O": 307, - "BH0": 308, - "F-1": 309, - "NH3": 310, - "S-2": 311, - "Br+2": 312, - "Cl+2": 313, - "\\Si": 314, - "/S-1": 315, - "=PH2": 316, - "14C@H1": 317, - "NH3+1": 318, - "#14C": 319, - "#O+1": 320, - "-3": 321, - "22": 322, - "4H": 323, - "5Se": 324, - "5Sr+2": 325, - "75Se": 326, - "85Sr+2": 327, - "=B-1": 328, - "=13C": 329, - "@-1": 330, - "Be": 331, - "B@@": 332, - "B@-1": 333, - "Ca": 334, - "CH1": 335, - "I+3": 336, - "KH1": 337, - "OH1+1": 338, - "Ra+2": 339, - "SH1-1": 340, - "\\PH1": 341, - "\\123I": 342, - "=Ca": 343, - "\\CH1-1": 344, - "=S@": 345, - "\\SeH1": 346, - "/SeH1": 347, - "Se-1": 348, - "LiH1": 349, - "18F-1": 350, - "125IH1": 351, - "11CH1": 352, - "TeH1": 353, - "Zn+1": 354, - "Zn-2": 355, - "Al-3": 356, - "13CH3": 357, - "15N": 358, - "Be+2": 359, - "B@@-1": 360, - "#P": 361, - "#S": 362, - "-4": 363, - "/PH1": 364, - "/P@@": 365, - "/As": 366, - "/14C": 367, - "/14CH1": 368, - "2K+1": 369, - "2Rb+1": 370, - "3Se": 371, - "3Ra+2": 372, - "45": 373, - "47": 374, - "42K+1": 375, - "5I-1": 376, - "73Se": 377, - "89": 378, - "82Rb+1": 379, - "=32": 380, - "=32P": 381, - "CH0": 382, - "CH2": 383, - "I+2": 384, - "NH0": 385, - "NH4": 386, - "OH1": 387, - "PH2+1": 388, - "SH0": 389, - "SH2": 390, - "\\3H": 391, - "\\11CH3": 392, - "\\C-1": 393, - "\\Se": 394, - "Si@": 395, - "Si-1": 396, - "SiH1-1": 397, - "SiH3-1": 398, - "/Se": 399, - "Se-2": 400, - "\\NH1-1": 401, - "18FH1": 402, - "125I-1": 403, - "11C@@H1": 404, - "11C-1": 405, - "AsH1": 406, - "As-1": 407, - "14C@@": 408, - "Te-1": 409, - "Mg+1": 410, - "123I-1": 411, - "123Te": 412, - "123IH1": 413, - "135I": 414, - "131I-1": 415, - "Ag-4": 416, - "124I-1": 417, - "76BrH1": 418, - "18OH1": 419, - "22Na+1": 420, - "223Ra+2": 421, - "CaH2": 422, - "45Ca+2": 423, - "47Ca+2": 424, - "89Sr+2": 425, - "=32PH1": 426, - "NH4+1": 427 - }, - "merges": [ - "B r", - "a n", - "c h", - "Br an", - "Bran ch", - "Branch 1", - "= C", - "R i", - "n g", - "Ri ng", - "Ring 1", - "= Branch1", - "Branch 2", - "= O", - "Ring 2", - "H 1", - "C @", - "= N", - "# Branch1", - "C@ @", - "= Branch2", - "C@ H1", - "C@@ H1", - "# Branch2", - "# C", - "C l", - "/ C", - "N H1", - "= Ring1", - "+ 1", - "- 1", - "O -1", - "N +1", - "\\ C", - "# N", - "/ N", - "= Ring2", - "= S", - "=N +1", - "\\ N", - "N a", - "Na +1", - "/ O", - "\\ O", - "Br -1", - "Branch 3", - "\\ S", - "S +1", - "Cl -1", - "I -1", - "/ C@@H1", - "S i", - "/ C@H1", - "/ S", - "=N -1", - "S e", - "= P", - "N -1", - "Ring 3", - "2 H", - "P +1", - "K +1", - "\\ C@@H1", - "\\ C@H1", - "/ N+1", - "@ @", - "C -1", - "# N+1", - "B -1", - "+ 3", - "Cl +3", - "\\ NH1", - "L i", - "Li +1", - "P H1", - "1 8", - "18 F", - "@ +1", - "3 H", - "P @@", - "H 0", - "O H0", - "1 2", - "P @", - "+ 2", - "@@ +1", - "S -1", - "/ Br", - "- /", - "\\ Cl", - "-/ Ring2", - "\\ O-1", - "1 1", - "5 I", - "12 5I", - "11 C", - "H 3", - "\\ N+1", - "- \\", - "/ C@@", - "S @+1", - "A s", - "/ Cl", - "11C H3", - "=S e", - "S @@+1", - "N @+1", - "1 4", - "-\\ Ring2", - "14 C", - "\\ F", - "/ C@", - "T e", - "H 2", - "H1 -1", - "=O +1", - "N @@+1", - "C +1", - "=S +1", - "Z n", - "/ P", - "a +2", - "/ I", - "O H1-1", - "C a+2", - "\\ Br", - "M g", - "Zn +2", - "A l", - "/ F", - "Mg +2", - "12 3", - "123 I", - "1 3", - "I +1", - "/ O-1", - "-\\ Ring1", - "B H2", - "BH2 -1", - "\\ I", - "/ NH1", - "O +1", - "13 1", - "131 I", - "= 14C", - "/ S+1", - "= Ring3", - "\\ C@@", - "H2 +1", - "\\ C@", - "A g", - "= As", - "=Se +1", - "N H2+1", - "Se H1", - "-/ Ring1", - "= Te", - "Al +3", - "Na H1", - "=Te +1", - "NH1 +1", - "Ag +1", - "H1 +1", - "NH1 -1", - "\\ P", - "14C H2", - "13 C", - "14C H1", - "= 11C", - "S @@", - "=P @@", - "Si H2", - "H3 -1", - "14C H3", - "B H3-1", - "S @", - "=14C H1", - "=P H1", - "=P @", - "=N H1+1", - "\\S +1", - "12 4", - "C H1-1", - "S r", - "=S i", - "124 I", - "Sr +2", - "#C -1", - "/C -1", - "N @", - "/N -1", - "13C H1", - "/ B", - "1 9", - "B a+2", - "H 4", - "S H1+1", - "Se +1", - "19 F", - "/ 125I", - "P @+1", - "R b", - "Cl +1", - "Si H4", - "Rb +1", - "= Branch3", - "N @@", - "As +1", - "/ Si", - "B H1-1", - "S H1", - "/ 123I", - "3 2", - "= Mg", - "H +1", - "\\ B", - "Si H1", - "P@@ +1", - "- 2", - "1 5", - "1 7", - "3 5", - "= 13CH1", - "C s", - "=N H2+1", - "=S H1", - "Mg H2", - "32 P", - "17 F", - "35 S", - "Cs +1", - "# 11C", - "/ 131I", - "B i", - "\\ 125I", - "=S @@", - "\\S -1", - "6 Br", - "7 I", - "7 6Br", - "= B", - "e H1", - "\\N -1", - "18 O", - "12 7I", - "11C H2", - "14 C@@H1", - "Te H2", - "15 NH1", - "Bi +3", - "/ P+1", - "/ 13C", - "/ 13CH1", - "0 B", - "1 0B", - "= Al", - "= 18O", - "B H0", - "F -1", - "N H3", - "S -2", - "Br +2", - "Cl +2", - "\\S i", - "/S -1", - "=P H2", - "14 C@H1", - "NH3 +1", - "# 14C", - "# O+1", - "- 3", - "2 2", - "4 H", - "5 Se", - "5 Sr+2", - "7 5Se", - "8 5Sr+2", - "= B-1", - "= 13C", - "@ -1", - "B e", - "B @@", - "B @-1", - "C a", - "C H1", - "I +3", - "K H1", - "O H1+1", - "R a+2", - "S H1-1", - "\\ PH1", - "\\ 123I", - "=C a", - "\\C H1-1", - "=S @", - "\\S eH1", - "/S eH1", - "Se -1", - "Li H1", - "18F -1", - "125I H1", - "11C H1", - "Te H1", - "Zn +1", - "Zn -2", - "Al -3", - "13C H3", - "15 N", - "Be +2", - "B@@ -1", - "# P", - "# S", - "- 4", - "/ PH1", - "/ P@@", - "/ As", - "/ 14C", - "/ 14CH1", - "2 K+1", - "2 Rb+1", - "3 Se", - "3 Ra+2", - "4 5", - "4 7", - "4 2K+1", - "5 I-1", - "7 3Se", - "8 9", - "8 2Rb+1", - "= 32", - "= 32P", - "C H0", - "C H2", - "I +2", - "N H0", - "N H4", - "O H1", - "P H2+1", - "S H0", - "S H2", - "\\ 3H", - "\\ 11CH3", - "\\C -1", - "\\S e", - "Si @", - "Si -1", - "Si H1-1", - "Si H3-1", - "/S e", - "Se -2", - "\\NH1 -1", - "18F H1", - "12 5I-1", - "11 C@@H1", - "11 C-1", - "As H1", - "As -1", - "14 C@@", - "Te -1", - "Mg +1", - "123 I-1", - "123 Te", - "123I H1", - "13 5I", - "131 I-1", - "Ag -4", - "124 I-1", - "76Br H1", - "18O H1", - "22 Na+1", - "22 3Ra+2", - "Ca H2", - "45 Ca+2", - "47 Ca+2", - "89 Sr+2", - "=32 PH1", - "NH4 +1" - ] - } -} \ No newline at end of file diff --git a/models/finetuned/lipo/checkpoint_epoch_025/tokenizer_config.json b/models/finetuned/lipo/checkpoint_epoch_025/tokenizer_config.json deleted file mode 100644 index 08860954acd34fad07fd77f7635298fa565f3149..0000000000000000000000000000000000000000 --- a/models/finetuned/lipo/checkpoint_epoch_025/tokenizer_config.json +++ /dev/null @@ -1,65 +0,0 @@ -{ - "add_prefix_space": false, - "bos_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "cls_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "eos_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "errors": "replace", - "mask_token": { - "__type": "AddedToken", - "content": "", - "lstrip": true, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "model_max_length": 1000000000000000019884624838656, - "name_or_path": "/home/erva/SELFormerMM/data/pretrained_multimodal_chembl36", - "pad_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "sep_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "special_tokens_map_file": null, - "tokenizer_class": "RobertaTokenizer", - "trim_offsets": true, - "unk_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - } -} diff --git a/models/finetuned/lipo/checkpoint_epoch_025/vocab.json b/models/finetuned/lipo/checkpoint_epoch_025/vocab.json deleted file mode 100644 index f7e4cc22809f4e9035cc450ef189c8a7da8fd03e..0000000000000000000000000000000000000000 --- a/models/finetuned/lipo/checkpoint_epoch_025/vocab.json +++ /dev/null @@ -1 +0,0 @@ -{"":0,"":1,"":2,"":3,"":4,"\n":5,"#":6,"+":7,"-":8,".":9,"/":10,"0":11,"1":12,"2":13,"3":14,"4":15,"5":16,"6":17,"7":18,"8":19,"9":20,"=":21,"@":22,"A":23,"B":24,"C":25,"F":26,"H":27,"I":28,"K":29,"L":30,"M":31,"N":32,"O":33,"P":34,"R":35,"S":36,"T":37,"Z":38,"\\":39,"a":40,"b":41,"c":42,"e":43,"g":44,"h":45,"i":46,"l":47,"n":48,"r":49,"s":50,"Br":51,"an":52,"ch":53,"Bran":54,"Branch":55,"Branch1":56,"=C":57,"Ri":58,"ng":59,"Ring":60,"Ring1":61,"=Branch1":62,"Branch2":63,"=O":64,"Ring2":65,"H1":66,"C@":67,"=N":68,"#Branch1":69,"C@@":70,"=Branch2":71,"C@H1":72,"C@@H1":73,"#Branch2":74,"#C":75,"Cl":76,"/C":77,"NH1":78,"=Ring1":79,"+1":80,"-1":81,"O-1":82,"N+1":83,"\\C":84,"#N":85,"/N":86,"=Ring2":87,"=S":88,"=N+1":89,"\\N":90,"Na":91,"Na+1":92,"/O":93,"\\O":94,"Br-1":95,"Branch3":96,"\\S":97,"S+1":98,"Cl-1":99,"I-1":100,"/C@@H1":101,"Si":102,"/C@H1":103,"/S":104,"=N-1":105,"Se":106,"=P":107,"N-1":108,"Ring3":109,"2H":110,"P+1":111,"K+1":112,"\\C@@H1":113,"\\C@H1":114,"/N+1":115,"@@":116,"C-1":117,"#N+1":118,"B-1":119,"+3":120,"Cl+3":121,"\\NH1":122,"Li":123,"Li+1":124,"PH1":125,"18":126,"18F":127,"@+1":128,"3H":129,"P@@":130,"H0":131,"OH0":132,"12":133,"P@":134,"+2":135,"@@+1":136,"S-1":137,"/Br":138,"-/":139,"\\Cl":140,"-/Ring2":141,"\\O-1":142,"11":143,"5I":144,"125I":145,"11C":146,"H3":147,"\\N+1":148,"-\\":149,"/C@@":150,"S@+1":151,"As":152,"/Cl":153,"11CH3":154,"=Se":155,"S@@+1":156,"N@+1":157,"14":158,"-\\Ring2":159,"14C":160,"\\F":161,"/C@":162,"Te":163,"H2":164,"H1-1":165,"=O+1":166,"N@@+1":167,"C+1":168,"=S+1":169,"Zn":170,"/P":171,"a+2":172,"/I":173,"OH1-1":174,"Ca+2":175,"\\Br":176,"Mg":177,"Zn+2":178,"Al":179,"/F":180,"Mg+2":181,"123":182,"123I":183,"13":184,"I+1":185,"/O-1":186,"-\\Ring1":187,"BH2":188,"BH2-1":189,"\\I":190,"/NH1":191,"O+1":192,"131":193,"131I":194,"=14C":195,"/S+1":196,"=Ring3":197,"\\C@@":198,"H2+1":199,"\\C@":200,"Ag":201,"=As":202,"=Se+1":203,"NH2+1":204,"SeH1":205,"-/Ring1":206,"=Te":207,"Al+3":208,"NaH1":209,"=Te+1":210,"NH1+1":211,"Ag+1":212,"H1+1":213,"NH1-1":214,"\\P":215,"14CH2":216,"13C":217,"14CH1":218,"=11C":219,"S@@":220,"=P@@":221,"SiH2":222,"H3-1":223,"14CH3":224,"BH3-1":225,"S@":226,"=14CH1":227,"=PH1":228,"=P@":229,"=NH1+1":230,"\\S+1":231,"124":232,"CH1-1":233,"Sr":234,"=Si":235,"124I":236,"Sr+2":237,"#C-1":238,"/C-1":239,"N@":240,"/N-1":241,"13CH1":242,"/B":243,"19":244,"Ba+2":245,"H4":246,"SH1+1":247,"Se+1":248,"19F":249,"/125I":250,"P@+1":251,"Rb":252,"Cl+1":253,"SiH4":254,"Rb+1":255,"=Branch3":256,"N@@":257,"As+1":258,"/Si":259,"BH1-1":260,"SH1":261,"/123I":262,"32":263,"=Mg":264,"H+1":265,"\\B":266,"SiH1":267,"P@@+1":268,"-2":269,"15":270,"17":271,"35":272,"=13CH1":273,"Cs":274,"=NH2+1":275,"=SH1":276,"MgH2":277,"32P":278,"17F":279,"35S":280,"Cs+1":281,"#11C":282,"/131I":283,"Bi":284,"\\125I":285,"=S@@":286,"\\S-1":287,"6Br":288,"7I":289,"76Br":290,"=B":291,"eH1":292,"\\N-1":293,"18O":294,"127I":295,"11CH2":296,"14C@@H1":297,"TeH2":298,"15NH1":299,"Bi+3":300,"/P+1":301,"/13C":302,"/13CH1":303,"0B":304,"10B":305,"=Al":306,"=18O":307,"BH0":308,"F-1":309,"NH3":310,"S-2":311,"Br+2":312,"Cl+2":313,"\\Si":314,"/S-1":315,"=PH2":316,"14C@H1":317,"NH3+1":318,"#14C":319,"#O+1":320,"-3":321,"22":322,"4H":323,"5Se":324,"5Sr+2":325,"75Se":326,"85Sr+2":327,"=B-1":328,"=13C":329,"@-1":330,"Be":331,"B@@":332,"B@-1":333,"Ca":334,"CH1":335,"I+3":336,"KH1":337,"OH1+1":338,"Ra+2":339,"SH1-1":340,"\\PH1":341,"\\123I":342,"=Ca":343,"\\CH1-1":344,"=S@":345,"\\SeH1":346,"/SeH1":347,"Se-1":348,"LiH1":349,"18F-1":350,"125IH1":351,"11CH1":352,"TeH1":353,"Zn+1":354,"Zn-2":355,"Al-3":356,"13CH3":357,"15N":358,"Be+2":359,"B@@-1":360,"#P":361,"#S":362,"-4":363,"/PH1":364,"/P@@":365,"/As":366,"/14C":367,"/14CH1":368,"2K+1":369,"2Rb+1":370,"3Se":371,"3Ra+2":372,"45":373,"47":374,"42K+1":375,"5I-1":376,"73Se":377,"89":378,"82Rb+1":379,"=32":380,"=32P":381,"CH0":382,"CH2":383,"I+2":384,"NH0":385,"NH4":386,"OH1":387,"PH2+1":388,"SH0":389,"SH2":390,"\\3H":391,"\\11CH3":392,"\\C-1":393,"\\Se":394,"Si@":395,"Si-1":396,"SiH1-1":397,"SiH3-1":398,"/Se":399,"Se-2":400,"\\NH1-1":401,"18FH1":402,"125I-1":403,"11C@@H1":404,"11C-1":405,"AsH1":406,"As-1":407,"14C@@":408,"Te-1":409,"Mg+1":410,"123I-1":411,"123Te":412,"123IH1":413,"135I":414,"131I-1":415,"Ag-4":416,"124I-1":417,"76BrH1":418,"18OH1":419,"22Na+1":420,"223Ra+2":421,"CaH2":422,"45Ca+2":423,"47Ca+2":424,"89Sr+2":425,"=32PH1":426,"NH4+1":427} \ No newline at end of file diff --git a/models/finetuned/lipo/checkpoint_epoch_050/config.json b/models/finetuned/lipo/checkpoint_epoch_050/config.json deleted file mode 100644 index 3811e21539577b37e06313eab31ec11e53f0cbbc..0000000000000000000000000000000000000000 --- a/models/finetuned/lipo/checkpoint_epoch_050/config.json +++ /dev/null @@ -1,27 +0,0 @@ -{ - "_name_or_path": "/home/erva/SELFormerMM/data/pretrained_multimodal_chembl36", - "architectures": [ - "RobertaForMaskedLM" - ], - "attention_probs_dropout_prob": 0.1, - "bos_token_id": 0, - "classifier_dropout": null, - "eos_token_id": 2, - "hidden_act": "gelu", - "hidden_dropout_prob": 0.1, - "hidden_size": 768, - "initializer_range": 0.02, - "intermediate_size": 3072, - "layer_norm_eps": 1e-12, - "max_position_embeddings": 514, - "model_type": "roberta", - "num_attention_heads": 4, - "num_hidden_layers": 12, - "pad_token_id": 1, - "position_embedding_type": "absolute", - "torch_dtype": "float32", - "transformers_version": "4.26.1", - "type_vocab_size": 1, - "use_cache": true, - "vocab_size": 800 -} diff --git a/models/finetuned/lipo/checkpoint_epoch_050/merges.txt b/models/finetuned/lipo/checkpoint_epoch_050/merges.txt deleted file mode 100644 index 7cd5ec62809503c23f18c80afc0ba3bdf9d253d0..0000000000000000000000000000000000000000 --- a/models/finetuned/lipo/checkpoint_epoch_050/merges.txt +++ /dev/null @@ -1,378 +0,0 @@ -#version: 0.2 - Trained by `huggingface/tokenizers` -B r -a n -c h -Br an -Bran ch -Branch 1 -= C -R i -n g -Ri ng -Ring 1 -= Branch1 -Branch 2 -= O -Ring 2 -H 1 -C @ -= N -# Branch1 -C@ @ -= Branch2 -C@ H1 -C@@ H1 -# Branch2 -# C -C l -/ C -N H1 -= Ring1 -+ 1 -- 1 -O -1 -N +1 -\ C -# N -/ N -= Ring2 -= S -=N +1 -\ N -N a -Na +1 -/ O -\ O -Br -1 -Branch 3 -\ S -S +1 -Cl -1 -I -1 -/ C@@H1 -S i -/ C@H1 -/ S -=N -1 -S e -= P -N -1 -Ring 3 -2 H -P +1 -K +1 -\ C@@H1 -\ C@H1 -/ N+1 -@ @ -C -1 -# N+1 -B -1 -+ 3 -Cl +3 -\ NH1 -L i -Li +1 -P H1 -1 8 -18 F -@ +1 -3 H -P @@ -H 0 -O H0 -1 2 -P @ -+ 2 -@@ +1 -S -1 -/ Br -- / -\ Cl --/ Ring2 -\ O-1 -1 1 -5 I -12 5I -11 C -H 3 -\ N+1 -- \ -/ C@@ -S @+1 -A s -/ Cl -11C H3 -=S e -S @@+1 -N @+1 -1 4 --\ Ring2 -14 C -\ F -/ C@ -T e -H 2 -H1 -1 -=O +1 -N @@+1 -C +1 -=S +1 -Z n -/ P -a +2 -/ I -O H1-1 -C a+2 -\ Br -M g -Zn +2 -A l -/ F -Mg +2 -12 3 -123 I -1 3 -I +1 -/ O-1 --\ Ring1 -B H2 -BH2 -1 -\ I -/ NH1 -O +1 -13 1 -131 I -= 14C -/ S+1 -= Ring3 -\ C@@ -H2 +1 -\ C@ -A g -= As -=Se +1 -N H2+1 -Se H1 --/ Ring1 -= Te -Al +3 -Na H1 -=Te +1 -NH1 +1 -Ag +1 -H1 +1 -NH1 -1 -\ P -14C H2 -13 C -14C H1 -= 11C -S @@ -=P @@ -Si H2 -H3 -1 -14C H3 -B H3-1 -S @ -=14C H1 -=P H1 -=P @ -=N H1+1 -\S +1 -12 4 -C H1-1 -S r -=S i -124 I -Sr +2 -#C -1 -/C -1 -N @ -/N -1 -13C H1 -/ B -1 9 -B a+2 -H 4 -S H1+1 -Se +1 -19 F -/ 125I -P @+1 -R b -Cl +1 -Si H4 -Rb +1 -= Branch3 -N @@ -As +1 -/ Si -B H1-1 -S H1 -/ 123I -3 2 -= Mg -H +1 -\ B -Si H1 -P@@ +1 -- 2 -1 5 -1 7 -3 5 -= 13CH1 -C s -=N H2+1 -=S H1 -Mg H2 -32 P -17 F -35 S -Cs +1 -# 11C -/ 131I -B i -\ 125I -=S @@ -\S -1 -6 Br -7 I -7 6Br -= B -e H1 -\N -1 -18 O -12 7I -11C H2 -14 C@@H1 -Te H2 -15 NH1 -Bi +3 -/ P+1 -/ 13C -/ 13CH1 -0 B -1 0B -= Al -= 18O -B H0 -F -1 -N H3 -S -2 -Br +2 -Cl +2 -\S i -/S -1 -=P H2 -14 C@H1 -NH3 +1 -# 14C -# O+1 -- 3 -2 2 -4 H -5 Se -5 Sr+2 -7 5Se -8 5Sr+2 -= B-1 -= 13C -@ -1 -B e -B @@ -B @-1 -C a -C H1 -I +3 -K H1 -O H1+1 -R a+2 -S H1-1 -\ PH1 -\ 123I -=C a -\C H1-1 -=S @ -\S eH1 -/S eH1 -Se -1 -Li H1 -18F -1 -125I H1 -11C H1 -Te H1 -Zn +1 -Zn -2 -Al -3 -13C H3 -15 N -Be +2 -B@@ -1 -# P -# S -- 4 -/ PH1 -/ P@@ -/ As -/ 14C -/ 14CH1 -2 K+1 -2 Rb+1 -3 Se -3 Ra+2 -4 5 -4 7 -4 2K+1 -5 I-1 -7 3Se -8 9 -8 2Rb+1 -= 32 -= 32P -C H0 -C H2 -I +2 -N H0 -N H4 -O H1 -P H2+1 -S H0 -S H2 -\ 3H -\ 11CH3 -\C -1 -\S e -Si @ -Si -1 -Si H1-1 -Si H3-1 -/S e -Se -2 -\NH1 -1 -18F H1 -12 5I-1 -11 C@@H1 -11 C-1 -As H1 -As -1 -14 C@@ -Te -1 -Mg +1 -123 I-1 -123 Te -123I H1 -13 5I -131 I-1 -Ag -4 -124 I-1 -76Br H1 -18O H1 -22 Na+1 -22 3Ra+2 -Ca H2 -45 Ca+2 -47 Ca+2 -89 Sr+2 -=32 PH1 -NH4 +1 diff --git a/models/finetuned/lipo/checkpoint_epoch_050/model.pt b/models/finetuned/lipo/checkpoint_epoch_050/model.pt deleted file mode 100644 index a9132c4814a1423d6bba1195c3634687d83d02cc..0000000000000000000000000000000000000000 --- a/models/finetuned/lipo/checkpoint_epoch_050/model.pt +++ /dev/null @@ -1,3 +0,0 @@ -version https://git-lfs.github.com/spec/v1 -oid sha256:33bbc6c2499b3aeafd1c0daf364fb68847ff9a7fed370354ca735a2bac4574ff -size 1022843005 diff --git a/models/finetuned/lipo/checkpoint_epoch_050/special_tokens_map.json b/models/finetuned/lipo/checkpoint_epoch_050/special_tokens_map.json deleted file mode 100644 index 06a55849fa69a91e7179d909e373179ff7467d8c..0000000000000000000000000000000000000000 --- a/models/finetuned/lipo/checkpoint_epoch_050/special_tokens_map.json +++ /dev/null @@ -1,51 +0,0 @@ -{ - "bos_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "cls_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "eos_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "mask_token": { - "content": "", - "lstrip": true, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "pad_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "sep_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "unk_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - } -} diff --git a/models/finetuned/lipo/checkpoint_epoch_050/tokenizer.json b/models/finetuned/lipo/checkpoint_epoch_050/tokenizer.json deleted file mode 100644 index 3b64b273e6fa9799e2d8375722b9e815de9ebb8f..0000000000000000000000000000000000000000 --- a/models/finetuned/lipo/checkpoint_epoch_050/tokenizer.json +++ /dev/null @@ -1,909 +0,0 @@ -{ - "version": "1.0", - "truncation": { - "direction": "Right", - "max_length": 128, - "strategy": "LongestFirst", - "stride": 0 - }, - "padding": { - "strategy": { - "Fixed": 128 - }, - "direction": "Right", - "pad_to_multiple_of": null, - "pad_id": 3, - "pad_type_id": 0, - "pad_token": "" - }, - "added_tokens": [ - { - "id": 0, - "content": "", - "single_word": false, - "lstrip": false, - "rstrip": false, - "normalized": true, - "special": true - }, - { - "id": 1, - "content": "", - "single_word": false, - "lstrip": false, - "rstrip": false, - "normalized": true, - "special": true - }, - { - "id": 2, - "content": "", - "single_word": false, - "lstrip": false, - "rstrip": false, - "normalized": true, - "special": true - }, - { - "id": 3, - "content": "", - "single_word": false, - "lstrip": false, - "rstrip": false, - "normalized": true, - "special": true - }, - { - "id": 4, - "content": "", - "single_word": false, - "lstrip": true, - "rstrip": false, - "normalized": true, - "special": true - } - ], - "normalizer": null, - "pre_tokenizer": { - "type": "ByteLevel", - "add_prefix_space": false, - "trim_offsets": true, - "use_regex": true - }, - "post_processor": { - "type": "RobertaProcessing", - "sep": [ - "", - 2 - ], - "cls": [ - "", - 1 - ], - "trim_offsets": true, - "add_prefix_space": false - }, - "decoder": { - "type": "ByteLevel", - "add_prefix_space": true, - "trim_offsets": true, - "use_regex": true - }, - "model": { - "type": "BPE", - "dropout": null, - "unk_token": null, - "continuing_subword_prefix": "", - "end_of_word_suffix": "", - "fuse_unk": false, - "vocab": { - "": 0, - "": 1, - "": 2, - "": 3, - "": 4, - "\n": 5, - "#": 6, - "+": 7, - "-": 8, - ".": 9, - "/": 10, - "0": 11, - "1": 12, - "2": 13, - "3": 14, - "4": 15, - "5": 16, - "6": 17, - "7": 18, - "8": 19, - "9": 20, - "=": 21, - "@": 22, - "A": 23, - "B": 24, - "C": 25, - "F": 26, - "H": 27, - "I": 28, - "K": 29, - "L": 30, - "M": 31, - "N": 32, - "O": 33, - "P": 34, - "R": 35, - "S": 36, - "T": 37, - "Z": 38, - "\\": 39, - "a": 40, - "b": 41, - "c": 42, - "e": 43, - "g": 44, - "h": 45, - "i": 46, - "l": 47, - "n": 48, - "r": 49, - "s": 50, - "Br": 51, - "an": 52, - "ch": 53, - "Bran": 54, - "Branch": 55, - "Branch1": 56, - "=C": 57, - "Ri": 58, - "ng": 59, - "Ring": 60, - "Ring1": 61, - "=Branch1": 62, - "Branch2": 63, - "=O": 64, - "Ring2": 65, - "H1": 66, - "C@": 67, - "=N": 68, - "#Branch1": 69, - "C@@": 70, - "=Branch2": 71, - "C@H1": 72, - "C@@H1": 73, - "#Branch2": 74, - "#C": 75, - "Cl": 76, - "/C": 77, - "NH1": 78, - "=Ring1": 79, - "+1": 80, - "-1": 81, - "O-1": 82, - "N+1": 83, - "\\C": 84, - "#N": 85, - "/N": 86, - "=Ring2": 87, - "=S": 88, - "=N+1": 89, - "\\N": 90, - "Na": 91, - "Na+1": 92, - "/O": 93, - "\\O": 94, - "Br-1": 95, - "Branch3": 96, - "\\S": 97, - "S+1": 98, - "Cl-1": 99, - "I-1": 100, - "/C@@H1": 101, - "Si": 102, - "/C@H1": 103, - "/S": 104, - "=N-1": 105, - "Se": 106, - "=P": 107, - "N-1": 108, - "Ring3": 109, - "2H": 110, - "P+1": 111, - "K+1": 112, - "\\C@@H1": 113, - "\\C@H1": 114, - "/N+1": 115, - "@@": 116, - "C-1": 117, - "#N+1": 118, - "B-1": 119, - "+3": 120, - "Cl+3": 121, - "\\NH1": 122, - "Li": 123, - "Li+1": 124, - "PH1": 125, - "18": 126, - "18F": 127, - "@+1": 128, - "3H": 129, - "P@@": 130, - "H0": 131, - "OH0": 132, - "12": 133, - "P@": 134, - "+2": 135, - "@@+1": 136, - "S-1": 137, - "/Br": 138, - "-/": 139, - "\\Cl": 140, - "-/Ring2": 141, - "\\O-1": 142, - "11": 143, - "5I": 144, - "125I": 145, - "11C": 146, - "H3": 147, - "\\N+1": 148, - "-\\": 149, - "/C@@": 150, - "S@+1": 151, - "As": 152, - "/Cl": 153, - "11CH3": 154, - "=Se": 155, - "S@@+1": 156, - "N@+1": 157, - "14": 158, - "-\\Ring2": 159, - "14C": 160, - "\\F": 161, - "/C@": 162, - "Te": 163, - "H2": 164, - "H1-1": 165, - "=O+1": 166, - "N@@+1": 167, - "C+1": 168, - "=S+1": 169, - "Zn": 170, - "/P": 171, - "a+2": 172, - "/I": 173, - "OH1-1": 174, - "Ca+2": 175, - "\\Br": 176, - "Mg": 177, - "Zn+2": 178, - "Al": 179, - "/F": 180, - "Mg+2": 181, - "123": 182, - "123I": 183, - "13": 184, - "I+1": 185, - "/O-1": 186, - "-\\Ring1": 187, - "BH2": 188, - "BH2-1": 189, - "\\I": 190, - "/NH1": 191, - "O+1": 192, - "131": 193, - "131I": 194, - "=14C": 195, - "/S+1": 196, - "=Ring3": 197, - "\\C@@": 198, - "H2+1": 199, - "\\C@": 200, - "Ag": 201, - "=As": 202, - "=Se+1": 203, - "NH2+1": 204, - "SeH1": 205, - "-/Ring1": 206, - "=Te": 207, - "Al+3": 208, - "NaH1": 209, - "=Te+1": 210, - "NH1+1": 211, - "Ag+1": 212, - "H1+1": 213, - "NH1-1": 214, - "\\P": 215, - "14CH2": 216, - "13C": 217, - "14CH1": 218, - "=11C": 219, - "S@@": 220, - "=P@@": 221, - "SiH2": 222, - "H3-1": 223, - "14CH3": 224, - "BH3-1": 225, - "S@": 226, - "=14CH1": 227, - "=PH1": 228, - "=P@": 229, - "=NH1+1": 230, - "\\S+1": 231, - "124": 232, - "CH1-1": 233, - "Sr": 234, - "=Si": 235, - "124I": 236, - "Sr+2": 237, - "#C-1": 238, - "/C-1": 239, - "N@": 240, - "/N-1": 241, - "13CH1": 242, - "/B": 243, - "19": 244, - "Ba+2": 245, - "H4": 246, - "SH1+1": 247, - "Se+1": 248, - "19F": 249, - "/125I": 250, - "P@+1": 251, - "Rb": 252, - "Cl+1": 253, - "SiH4": 254, - "Rb+1": 255, - "=Branch3": 256, - "N@@": 257, - "As+1": 258, - "/Si": 259, - "BH1-1": 260, - "SH1": 261, - "/123I": 262, - "32": 263, - "=Mg": 264, - "H+1": 265, - "\\B": 266, - "SiH1": 267, - "P@@+1": 268, - "-2": 269, - "15": 270, - "17": 271, - "35": 272, - "=13CH1": 273, - "Cs": 274, - "=NH2+1": 275, - "=SH1": 276, - "MgH2": 277, - "32P": 278, - "17F": 279, - "35S": 280, - "Cs+1": 281, - "#11C": 282, - "/131I": 283, - "Bi": 284, - "\\125I": 285, - "=S@@": 286, - "\\S-1": 287, - "6Br": 288, - "7I": 289, - "76Br": 290, - "=B": 291, - "eH1": 292, - "\\N-1": 293, - "18O": 294, - "127I": 295, - "11CH2": 296, - "14C@@H1": 297, - "TeH2": 298, - "15NH1": 299, - "Bi+3": 300, - "/P+1": 301, - "/13C": 302, - "/13CH1": 303, - "0B": 304, - "10B": 305, - "=Al": 306, - "=18O": 307, - "BH0": 308, - "F-1": 309, - "NH3": 310, - "S-2": 311, - "Br+2": 312, - "Cl+2": 313, - "\\Si": 314, - "/S-1": 315, - "=PH2": 316, - "14C@H1": 317, - "NH3+1": 318, - "#14C": 319, - "#O+1": 320, - "-3": 321, - "22": 322, - "4H": 323, - "5Se": 324, - "5Sr+2": 325, - "75Se": 326, - "85Sr+2": 327, - "=B-1": 328, - "=13C": 329, - "@-1": 330, - "Be": 331, - "B@@": 332, - "B@-1": 333, - "Ca": 334, - "CH1": 335, - "I+3": 336, - "KH1": 337, - "OH1+1": 338, - "Ra+2": 339, - "SH1-1": 340, - "\\PH1": 341, - "\\123I": 342, - "=Ca": 343, - "\\CH1-1": 344, - "=S@": 345, - "\\SeH1": 346, - "/SeH1": 347, - "Se-1": 348, - "LiH1": 349, - "18F-1": 350, - "125IH1": 351, - "11CH1": 352, - "TeH1": 353, - "Zn+1": 354, - "Zn-2": 355, - "Al-3": 356, - "13CH3": 357, - "15N": 358, - "Be+2": 359, - "B@@-1": 360, - "#P": 361, - "#S": 362, - "-4": 363, - "/PH1": 364, - "/P@@": 365, - "/As": 366, - "/14C": 367, - "/14CH1": 368, - "2K+1": 369, - "2Rb+1": 370, - "3Se": 371, - "3Ra+2": 372, - "45": 373, - "47": 374, - "42K+1": 375, - "5I-1": 376, - "73Se": 377, - "89": 378, - "82Rb+1": 379, - "=32": 380, - "=32P": 381, - "CH0": 382, - "CH2": 383, - "I+2": 384, - "NH0": 385, - "NH4": 386, - "OH1": 387, - "PH2+1": 388, - "SH0": 389, - "SH2": 390, - "\\3H": 391, - "\\11CH3": 392, - "\\C-1": 393, - "\\Se": 394, - "Si@": 395, - "Si-1": 396, - "SiH1-1": 397, - "SiH3-1": 398, - "/Se": 399, - "Se-2": 400, - "\\NH1-1": 401, - "18FH1": 402, - "125I-1": 403, - "11C@@H1": 404, - "11C-1": 405, - "AsH1": 406, - "As-1": 407, - "14C@@": 408, - "Te-1": 409, - "Mg+1": 410, - "123I-1": 411, - "123Te": 412, - "123IH1": 413, - "135I": 414, - "131I-1": 415, - "Ag-4": 416, - "124I-1": 417, - "76BrH1": 418, - "18OH1": 419, - "22Na+1": 420, - "223Ra+2": 421, - "CaH2": 422, - "45Ca+2": 423, - "47Ca+2": 424, - "89Sr+2": 425, - "=32PH1": 426, - "NH4+1": 427 - }, - "merges": [ - "B r", - "a n", - "c h", - "Br an", - "Bran ch", - "Branch 1", - "= C", - "R i", - "n g", - "Ri ng", - "Ring 1", - "= Branch1", - "Branch 2", - "= O", - "Ring 2", - "H 1", - "C @", - "= N", - "# Branch1", - "C@ @", - "= Branch2", - "C@ H1", - "C@@ H1", - "# Branch2", - "# C", - "C l", - "/ C", - "N H1", - "= Ring1", - "+ 1", - "- 1", - "O -1", - "N +1", - "\\ C", - "# N", - "/ N", - "= Ring2", - "= S", - "=N +1", - "\\ N", - "N a", - "Na +1", - "/ O", - "\\ O", - "Br -1", - "Branch 3", - "\\ S", - "S +1", - "Cl -1", - "I -1", - "/ C@@H1", - "S i", - "/ C@H1", - "/ S", - "=N -1", - "S e", - "= P", - "N -1", - "Ring 3", - "2 H", - "P +1", - "K +1", - "\\ C@@H1", - "\\ C@H1", - "/ N+1", - "@ @", - "C -1", - "# N+1", - "B -1", - "+ 3", - "Cl +3", - "\\ NH1", - "L i", - "Li +1", - "P H1", - "1 8", - "18 F", - "@ +1", - "3 H", - "P @@", - "H 0", - "O H0", - "1 2", - "P @", - "+ 2", - "@@ +1", - "S -1", - "/ Br", - "- /", - "\\ Cl", - "-/ Ring2", - "\\ O-1", - "1 1", - "5 I", - "12 5I", - "11 C", - "H 3", - "\\ N+1", - "- \\", - "/ C@@", - "S @+1", - "A s", - "/ Cl", - "11C H3", - "=S e", - "S @@+1", - "N @+1", - "1 4", - "-\\ Ring2", - "14 C", - "\\ F", - "/ C@", - "T e", - "H 2", - "H1 -1", - "=O +1", - "N @@+1", - "C +1", - "=S +1", - "Z n", - "/ P", - "a +2", - "/ I", - "O H1-1", - "C a+2", - "\\ Br", - "M g", - "Zn +2", - "A l", - "/ F", - "Mg +2", - "12 3", - "123 I", - "1 3", - "I +1", - "/ O-1", - "-\\ Ring1", - "B H2", - "BH2 -1", - "\\ I", - "/ NH1", - "O +1", - "13 1", - "131 I", - "= 14C", - "/ S+1", - "= Ring3", - "\\ C@@", - "H2 +1", - "\\ C@", - "A g", - "= As", - "=Se +1", - "N H2+1", - "Se H1", - "-/ Ring1", - "= Te", - "Al +3", - "Na H1", - "=Te +1", - "NH1 +1", - "Ag +1", - "H1 +1", - "NH1 -1", - "\\ P", - "14C H2", - "13 C", - "14C H1", - "= 11C", - "S @@", - "=P @@", - "Si H2", - "H3 -1", - "14C H3", - "B H3-1", - "S @", - "=14C H1", - "=P H1", - "=P @", - "=N H1+1", - "\\S +1", - "12 4", - "C H1-1", - "S r", - "=S i", - "124 I", - "Sr +2", - "#C -1", - "/C -1", - "N @", - "/N -1", - "13C H1", - "/ B", - "1 9", - "B a+2", - "H 4", - "S H1+1", - "Se +1", - "19 F", - "/ 125I", - "P @+1", - "R b", - "Cl +1", - "Si H4", - "Rb +1", - "= Branch3", - "N @@", - "As +1", - "/ Si", - "B H1-1", - "S H1", - "/ 123I", - "3 2", - "= Mg", - "H +1", - "\\ B", - "Si H1", - "P@@ +1", - "- 2", - "1 5", - "1 7", - "3 5", - "= 13CH1", - "C s", - "=N H2+1", - "=S H1", - "Mg H2", - "32 P", - "17 F", - "35 S", - "Cs +1", - "# 11C", - "/ 131I", - "B i", - "\\ 125I", - "=S @@", - "\\S -1", - "6 Br", - "7 I", - "7 6Br", - "= B", - "e H1", - "\\N -1", - "18 O", - "12 7I", - "11C H2", - "14 C@@H1", - "Te H2", - "15 NH1", - "Bi +3", - "/ P+1", - "/ 13C", - "/ 13CH1", - "0 B", - "1 0B", - "= Al", - "= 18O", - "B H0", - "F -1", - "N H3", - "S -2", - "Br +2", - "Cl +2", - "\\S i", - "/S -1", - "=P H2", - "14 C@H1", - "NH3 +1", - "# 14C", - "# O+1", - "- 3", - "2 2", - "4 H", - "5 Se", - "5 Sr+2", - "7 5Se", - "8 5Sr+2", - "= B-1", - "= 13C", - "@ -1", - "B e", - "B @@", - "B @-1", - "C a", - "C H1", - "I +3", - "K H1", - "O H1+1", - "R a+2", - "S H1-1", - "\\ PH1", - "\\ 123I", - "=C a", - "\\C H1-1", - "=S @", - "\\S eH1", - "/S eH1", - "Se -1", - "Li H1", - "18F -1", - "125I H1", - "11C H1", - "Te H1", - "Zn +1", - "Zn -2", - "Al -3", - "13C H3", - "15 N", - "Be +2", - "B@@ -1", - "# P", - "# S", - "- 4", - "/ PH1", - "/ P@@", - "/ As", - "/ 14C", - "/ 14CH1", - "2 K+1", - "2 Rb+1", - "3 Se", - "3 Ra+2", - "4 5", - "4 7", - "4 2K+1", - "5 I-1", - "7 3Se", - "8 9", - "8 2Rb+1", - "= 32", - "= 32P", - "C H0", - "C H2", - "I +2", - "N H0", - "N H4", - "O H1", - "P H2+1", - "S H0", - "S H2", - "\\ 3H", - "\\ 11CH3", - "\\C -1", - "\\S e", - "Si @", - "Si -1", - "Si H1-1", - "Si H3-1", - "/S e", - "Se -2", - "\\NH1 -1", - "18F H1", - "12 5I-1", - "11 C@@H1", - "11 C-1", - "As H1", - "As -1", - "14 C@@", - "Te -1", - "Mg +1", - "123 I-1", - "123 Te", - "123I H1", - "13 5I", - "131 I-1", - "Ag -4", - "124 I-1", - "76Br H1", - "18O H1", - "22 Na+1", - "22 3Ra+2", - "Ca H2", - "45 Ca+2", - "47 Ca+2", - "89 Sr+2", - "=32 PH1", - "NH4 +1" - ] - } -} \ No newline at end of file diff --git a/models/finetuned/lipo/checkpoint_epoch_050/tokenizer_config.json b/models/finetuned/lipo/checkpoint_epoch_050/tokenizer_config.json deleted file mode 100644 index 08860954acd34fad07fd77f7635298fa565f3149..0000000000000000000000000000000000000000 --- a/models/finetuned/lipo/checkpoint_epoch_050/tokenizer_config.json +++ /dev/null @@ -1,65 +0,0 @@ -{ - "add_prefix_space": false, - "bos_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "cls_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "eos_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "errors": "replace", - "mask_token": { - "__type": "AddedToken", - "content": "", - "lstrip": true, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "model_max_length": 1000000000000000019884624838656, - "name_or_path": "/home/erva/SELFormerMM/data/pretrained_multimodal_chembl36", - "pad_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "sep_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "special_tokens_map_file": null, - "tokenizer_class": "RobertaTokenizer", - "trim_offsets": true, - "unk_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - } -} diff --git a/models/finetuned/lipo/checkpoint_epoch_050/vocab.json b/models/finetuned/lipo/checkpoint_epoch_050/vocab.json deleted file mode 100644 index f7e4cc22809f4e9035cc450ef189c8a7da8fd03e..0000000000000000000000000000000000000000 --- a/models/finetuned/lipo/checkpoint_epoch_050/vocab.json +++ /dev/null @@ -1 +0,0 @@ -{"":0,"":1,"":2,"":3,"":4,"\n":5,"#":6,"+":7,"-":8,".":9,"/":10,"0":11,"1":12,"2":13,"3":14,"4":15,"5":16,"6":17,"7":18,"8":19,"9":20,"=":21,"@":22,"A":23,"B":24,"C":25,"F":26,"H":27,"I":28,"K":29,"L":30,"M":31,"N":32,"O":33,"P":34,"R":35,"S":36,"T":37,"Z":38,"\\":39,"a":40,"b":41,"c":42,"e":43,"g":44,"h":45,"i":46,"l":47,"n":48,"r":49,"s":50,"Br":51,"an":52,"ch":53,"Bran":54,"Branch":55,"Branch1":56,"=C":57,"Ri":58,"ng":59,"Ring":60,"Ring1":61,"=Branch1":62,"Branch2":63,"=O":64,"Ring2":65,"H1":66,"C@":67,"=N":68,"#Branch1":69,"C@@":70,"=Branch2":71,"C@H1":72,"C@@H1":73,"#Branch2":74,"#C":75,"Cl":76,"/C":77,"NH1":78,"=Ring1":79,"+1":80,"-1":81,"O-1":82,"N+1":83,"\\C":84,"#N":85,"/N":86,"=Ring2":87,"=S":88,"=N+1":89,"\\N":90,"Na":91,"Na+1":92,"/O":93,"\\O":94,"Br-1":95,"Branch3":96,"\\S":97,"S+1":98,"Cl-1":99,"I-1":100,"/C@@H1":101,"Si":102,"/C@H1":103,"/S":104,"=N-1":105,"Se":106,"=P":107,"N-1":108,"Ring3":109,"2H":110,"P+1":111,"K+1":112,"\\C@@H1":113,"\\C@H1":114,"/N+1":115,"@@":116,"C-1":117,"#N+1":118,"B-1":119,"+3":120,"Cl+3":121,"\\NH1":122,"Li":123,"Li+1":124,"PH1":125,"18":126,"18F":127,"@+1":128,"3H":129,"P@@":130,"H0":131,"OH0":132,"12":133,"P@":134,"+2":135,"@@+1":136,"S-1":137,"/Br":138,"-/":139,"\\Cl":140,"-/Ring2":141,"\\O-1":142,"11":143,"5I":144,"125I":145,"11C":146,"H3":147,"\\N+1":148,"-\\":149,"/C@@":150,"S@+1":151,"As":152,"/Cl":153,"11CH3":154,"=Se":155,"S@@+1":156,"N@+1":157,"14":158,"-\\Ring2":159,"14C":160,"\\F":161,"/C@":162,"Te":163,"H2":164,"H1-1":165,"=O+1":166,"N@@+1":167,"C+1":168,"=S+1":169,"Zn":170,"/P":171,"a+2":172,"/I":173,"OH1-1":174,"Ca+2":175,"\\Br":176,"Mg":177,"Zn+2":178,"Al":179,"/F":180,"Mg+2":181,"123":182,"123I":183,"13":184,"I+1":185,"/O-1":186,"-\\Ring1":187,"BH2":188,"BH2-1":189,"\\I":190,"/NH1":191,"O+1":192,"131":193,"131I":194,"=14C":195,"/S+1":196,"=Ring3":197,"\\C@@":198,"H2+1":199,"\\C@":200,"Ag":201,"=As":202,"=Se+1":203,"NH2+1":204,"SeH1":205,"-/Ring1":206,"=Te":207,"Al+3":208,"NaH1":209,"=Te+1":210,"NH1+1":211,"Ag+1":212,"H1+1":213,"NH1-1":214,"\\P":215,"14CH2":216,"13C":217,"14CH1":218,"=11C":219,"S@@":220,"=P@@":221,"SiH2":222,"H3-1":223,"14CH3":224,"BH3-1":225,"S@":226,"=14CH1":227,"=PH1":228,"=P@":229,"=NH1+1":230,"\\S+1":231,"124":232,"CH1-1":233,"Sr":234,"=Si":235,"124I":236,"Sr+2":237,"#C-1":238,"/C-1":239,"N@":240,"/N-1":241,"13CH1":242,"/B":243,"19":244,"Ba+2":245,"H4":246,"SH1+1":247,"Se+1":248,"19F":249,"/125I":250,"P@+1":251,"Rb":252,"Cl+1":253,"SiH4":254,"Rb+1":255,"=Branch3":256,"N@@":257,"As+1":258,"/Si":259,"BH1-1":260,"SH1":261,"/123I":262,"32":263,"=Mg":264,"H+1":265,"\\B":266,"SiH1":267,"P@@+1":268,"-2":269,"15":270,"17":271,"35":272,"=13CH1":273,"Cs":274,"=NH2+1":275,"=SH1":276,"MgH2":277,"32P":278,"17F":279,"35S":280,"Cs+1":281,"#11C":282,"/131I":283,"Bi":284,"\\125I":285,"=S@@":286,"\\S-1":287,"6Br":288,"7I":289,"76Br":290,"=B":291,"eH1":292,"\\N-1":293,"18O":294,"127I":295,"11CH2":296,"14C@@H1":297,"TeH2":298,"15NH1":299,"Bi+3":300,"/P+1":301,"/13C":302,"/13CH1":303,"0B":304,"10B":305,"=Al":306,"=18O":307,"BH0":308,"F-1":309,"NH3":310,"S-2":311,"Br+2":312,"Cl+2":313,"\\Si":314,"/S-1":315,"=PH2":316,"14C@H1":317,"NH3+1":318,"#14C":319,"#O+1":320,"-3":321,"22":322,"4H":323,"5Se":324,"5Sr+2":325,"75Se":326,"85Sr+2":327,"=B-1":328,"=13C":329,"@-1":330,"Be":331,"B@@":332,"B@-1":333,"Ca":334,"CH1":335,"I+3":336,"KH1":337,"OH1+1":338,"Ra+2":339,"SH1-1":340,"\\PH1":341,"\\123I":342,"=Ca":343,"\\CH1-1":344,"=S@":345,"\\SeH1":346,"/SeH1":347,"Se-1":348,"LiH1":349,"18F-1":350,"125IH1":351,"11CH1":352,"TeH1":353,"Zn+1":354,"Zn-2":355,"Al-3":356,"13CH3":357,"15N":358,"Be+2":359,"B@@-1":360,"#P":361,"#S":362,"-4":363,"/PH1":364,"/P@@":365,"/As":366,"/14C":367,"/14CH1":368,"2K+1":369,"2Rb+1":370,"3Se":371,"3Ra+2":372,"45":373,"47":374,"42K+1":375,"5I-1":376,"73Se":377,"89":378,"82Rb+1":379,"=32":380,"=32P":381,"CH0":382,"CH2":383,"I+2":384,"NH0":385,"NH4":386,"OH1":387,"PH2+1":388,"SH0":389,"SH2":390,"\\3H":391,"\\11CH3":392,"\\C-1":393,"\\Se":394,"Si@":395,"Si-1":396,"SiH1-1":397,"SiH3-1":398,"/Se":399,"Se-2":400,"\\NH1-1":401,"18FH1":402,"125I-1":403,"11C@@H1":404,"11C-1":405,"AsH1":406,"As-1":407,"14C@@":408,"Te-1":409,"Mg+1":410,"123I-1":411,"123Te":412,"123IH1":413,"135I":414,"131I-1":415,"Ag-4":416,"124I-1":417,"76BrH1":418,"18OH1":419,"22Na+1":420,"223Ra+2":421,"CaH2":422,"45Ca+2":423,"47Ca+2":424,"89Sr+2":425,"=32PH1":426,"NH4+1":427} \ No newline at end of file diff --git a/models/finetuned/lipo/config.json b/models/finetuned/lipo/config.json deleted file mode 100644 index 3811e21539577b37e06313eab31ec11e53f0cbbc..0000000000000000000000000000000000000000 --- a/models/finetuned/lipo/config.json +++ /dev/null @@ -1,27 +0,0 @@ -{ - "_name_or_path": "/home/erva/SELFormerMM/data/pretrained_multimodal_chembl36", - "architectures": [ - "RobertaForMaskedLM" - ], - "attention_probs_dropout_prob": 0.1, - "bos_token_id": 0, - "classifier_dropout": null, - "eos_token_id": 2, - "hidden_act": "gelu", - "hidden_dropout_prob": 0.1, - "hidden_size": 768, - "initializer_range": 0.02, - "intermediate_size": 3072, - "layer_norm_eps": 1e-12, - "max_position_embeddings": 514, - "model_type": "roberta", - "num_attention_heads": 4, - "num_hidden_layers": 12, - "pad_token_id": 1, - "position_embedding_type": "absolute", - "torch_dtype": "float32", - "transformers_version": "4.26.1", - "type_vocab_size": 1, - "use_cache": true, - "vocab_size": 800 -} diff --git a/models/finetuned/lipo/merges.txt b/models/finetuned/lipo/merges.txt deleted file mode 100644 index 7cd5ec62809503c23f18c80afc0ba3bdf9d253d0..0000000000000000000000000000000000000000 --- a/models/finetuned/lipo/merges.txt +++ /dev/null @@ -1,378 +0,0 @@ -#version: 0.2 - Trained by `huggingface/tokenizers` -B r -a n -c h -Br an -Bran ch -Branch 1 -= C -R i -n g -Ri ng -Ring 1 -= Branch1 -Branch 2 -= O -Ring 2 -H 1 -C @ -= N -# Branch1 -C@ @ -= Branch2 -C@ H1 -C@@ H1 -# Branch2 -# C -C l -/ C -N H1 -= Ring1 -+ 1 -- 1 -O -1 -N +1 -\ C -# N -/ N -= Ring2 -= S -=N +1 -\ N -N a -Na +1 -/ O -\ O -Br -1 -Branch 3 -\ S -S +1 -Cl -1 -I -1 -/ C@@H1 -S i -/ C@H1 -/ S -=N -1 -S e -= P -N -1 -Ring 3 -2 H -P +1 -K +1 -\ C@@H1 -\ C@H1 -/ N+1 -@ @ -C -1 -# N+1 -B -1 -+ 3 -Cl +3 -\ NH1 -L i -Li +1 -P H1 -1 8 -18 F -@ +1 -3 H -P @@ -H 0 -O H0 -1 2 -P @ -+ 2 -@@ +1 -S -1 -/ Br -- / -\ Cl --/ Ring2 -\ O-1 -1 1 -5 I -12 5I -11 C -H 3 -\ N+1 -- \ -/ C@@ -S @+1 -A s -/ Cl -11C H3 -=S e -S @@+1 -N @+1 -1 4 --\ Ring2 -14 C -\ F -/ C@ -T e -H 2 -H1 -1 -=O +1 -N @@+1 -C +1 -=S +1 -Z n -/ P -a +2 -/ I -O H1-1 -C a+2 -\ Br -M g -Zn +2 -A l -/ F -Mg +2 -12 3 -123 I -1 3 -I +1 -/ O-1 --\ Ring1 -B H2 -BH2 -1 -\ I -/ NH1 -O +1 -13 1 -131 I -= 14C -/ S+1 -= Ring3 -\ C@@ -H2 +1 -\ C@ -A g -= As -=Se +1 -N H2+1 -Se H1 --/ Ring1 -= Te -Al +3 -Na H1 -=Te +1 -NH1 +1 -Ag +1 -H1 +1 -NH1 -1 -\ P -14C H2 -13 C -14C H1 -= 11C -S @@ -=P @@ -Si H2 -H3 -1 -14C H3 -B H3-1 -S @ -=14C H1 -=P H1 -=P @ -=N H1+1 -\S +1 -12 4 -C H1-1 -S r -=S i -124 I -Sr +2 -#C -1 -/C -1 -N @ -/N -1 -13C H1 -/ B -1 9 -B a+2 -H 4 -S H1+1 -Se +1 -19 F -/ 125I -P @+1 -R b -Cl +1 -Si H4 -Rb +1 -= Branch3 -N @@ -As +1 -/ Si -B H1-1 -S H1 -/ 123I -3 2 -= Mg -H +1 -\ B -Si H1 -P@@ +1 -- 2 -1 5 -1 7 -3 5 -= 13CH1 -C s -=N H2+1 -=S H1 -Mg H2 -32 P -17 F -35 S -Cs +1 -# 11C -/ 131I -B i -\ 125I -=S @@ -\S -1 -6 Br -7 I -7 6Br -= B -e H1 -\N -1 -18 O -12 7I -11C H2 -14 C@@H1 -Te H2 -15 NH1 -Bi +3 -/ P+1 -/ 13C -/ 13CH1 -0 B -1 0B -= Al -= 18O -B H0 -F -1 -N H3 -S -2 -Br +2 -Cl +2 -\S i -/S -1 -=P H2 -14 C@H1 -NH3 +1 -# 14C -# O+1 -- 3 -2 2 -4 H -5 Se -5 Sr+2 -7 5Se -8 5Sr+2 -= B-1 -= 13C -@ -1 -B e -B @@ -B @-1 -C a -C H1 -I +3 -K H1 -O H1+1 -R a+2 -S H1-1 -\ PH1 -\ 123I -=C a -\C H1-1 -=S @ -\S eH1 -/S eH1 -Se -1 -Li H1 -18F -1 -125I H1 -11C H1 -Te H1 -Zn +1 -Zn -2 -Al -3 -13C H3 -15 N -Be +2 -B@@ -1 -# P -# S -- 4 -/ PH1 -/ P@@ -/ As -/ 14C -/ 14CH1 -2 K+1 -2 Rb+1 -3 Se -3 Ra+2 -4 5 -4 7 -4 2K+1 -5 I-1 -7 3Se -8 9 -8 2Rb+1 -= 32 -= 32P -C H0 -C H2 -I +2 -N H0 -N H4 -O H1 -P H2+1 -S H0 -S H2 -\ 3H -\ 11CH3 -\C -1 -\S e -Si @ -Si -1 -Si H1-1 -Si H3-1 -/S e -Se -2 -\NH1 -1 -18F H1 -12 5I-1 -11 C@@H1 -11 C-1 -As H1 -As -1 -14 C@@ -Te -1 -Mg +1 -123 I-1 -123 Te -123I H1 -13 5I -131 I-1 -Ag -4 -124 I-1 -76Br H1 -18O H1 -22 Na+1 -22 3Ra+2 -Ca H2 -45 Ca+2 -47 Ca+2 -89 Sr+2 -=32 PH1 -NH4 +1 diff --git a/models/finetuned/lipo/model.pt b/models/finetuned/lipo/model.pt deleted file mode 100644 index a9132c4814a1423d6bba1195c3634687d83d02cc..0000000000000000000000000000000000000000 --- a/models/finetuned/lipo/model.pt +++ /dev/null @@ -1,3 +0,0 @@ -version https://git-lfs.github.com/spec/v1 -oid sha256:33bbc6c2499b3aeafd1c0daf364fb68847ff9a7fed370354ca735a2bac4574ff -size 1022843005 diff --git a/models/finetuned/lipo/special_tokens_map.json b/models/finetuned/lipo/special_tokens_map.json deleted file mode 100644 index 06a55849fa69a91e7179d909e373179ff7467d8c..0000000000000000000000000000000000000000 --- a/models/finetuned/lipo/special_tokens_map.json +++ /dev/null @@ -1,51 +0,0 @@ -{ - "bos_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "cls_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "eos_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "mask_token": { - "content": "", - "lstrip": true, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "pad_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "sep_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "unk_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - } -} diff --git a/models/finetuned/lipo/tokenizer.json b/models/finetuned/lipo/tokenizer.json deleted file mode 100644 index 3b64b273e6fa9799e2d8375722b9e815de9ebb8f..0000000000000000000000000000000000000000 --- a/models/finetuned/lipo/tokenizer.json +++ /dev/null @@ -1,909 +0,0 @@ -{ - "version": "1.0", - "truncation": { - "direction": "Right", - "max_length": 128, - "strategy": "LongestFirst", - "stride": 0 - }, - "padding": { - "strategy": { - "Fixed": 128 - }, - "direction": "Right", - "pad_to_multiple_of": null, - "pad_id": 3, - "pad_type_id": 0, - "pad_token": "" - }, - "added_tokens": [ - { - "id": 0, - "content": "", - "single_word": false, - "lstrip": false, - "rstrip": false, - "normalized": true, - "special": true - }, - { - "id": 1, - "content": "", - "single_word": false, - "lstrip": false, - "rstrip": false, - "normalized": true, - "special": true - }, - { - "id": 2, - "content": "", - "single_word": false, - "lstrip": false, - "rstrip": false, - "normalized": true, - "special": true - }, - { - "id": 3, - "content": "", - "single_word": false, - "lstrip": false, - "rstrip": false, - "normalized": true, - "special": true - }, - { - "id": 4, - "content": "", - "single_word": false, - "lstrip": true, - "rstrip": false, - "normalized": true, - "special": true - } - ], - "normalizer": null, - "pre_tokenizer": { - "type": "ByteLevel", - "add_prefix_space": false, - "trim_offsets": true, - "use_regex": true - }, - "post_processor": { - "type": "RobertaProcessing", - "sep": [ - "", - 2 - ], - "cls": [ - "", - 1 - ], - "trim_offsets": true, - "add_prefix_space": false - }, - "decoder": { - "type": "ByteLevel", - "add_prefix_space": true, - "trim_offsets": true, - "use_regex": true - }, - "model": { - "type": "BPE", - "dropout": null, - "unk_token": null, - "continuing_subword_prefix": "", - "end_of_word_suffix": "", - "fuse_unk": false, - "vocab": { - "": 0, - "": 1, - "": 2, - "": 3, - "": 4, - "\n": 5, - "#": 6, - "+": 7, - "-": 8, - ".": 9, - "/": 10, - "0": 11, - "1": 12, - "2": 13, - "3": 14, - "4": 15, - "5": 16, - "6": 17, - "7": 18, - "8": 19, - "9": 20, - "=": 21, - "@": 22, - "A": 23, - "B": 24, - "C": 25, - "F": 26, - "H": 27, - "I": 28, - "K": 29, - "L": 30, - "M": 31, - "N": 32, - "O": 33, - "P": 34, - "R": 35, - "S": 36, - "T": 37, - "Z": 38, - "\\": 39, - "a": 40, - "b": 41, - "c": 42, - "e": 43, - "g": 44, - "h": 45, - "i": 46, - "l": 47, - "n": 48, - "r": 49, - "s": 50, - "Br": 51, - "an": 52, - "ch": 53, - "Bran": 54, - "Branch": 55, - "Branch1": 56, - "=C": 57, - "Ri": 58, - "ng": 59, - "Ring": 60, - "Ring1": 61, - "=Branch1": 62, - "Branch2": 63, - "=O": 64, - "Ring2": 65, - "H1": 66, - "C@": 67, - "=N": 68, - "#Branch1": 69, - "C@@": 70, - "=Branch2": 71, - "C@H1": 72, - "C@@H1": 73, - "#Branch2": 74, - "#C": 75, - "Cl": 76, - "/C": 77, - "NH1": 78, - "=Ring1": 79, - "+1": 80, - "-1": 81, - "O-1": 82, - "N+1": 83, - "\\C": 84, - "#N": 85, - "/N": 86, - "=Ring2": 87, - "=S": 88, - "=N+1": 89, - "\\N": 90, - "Na": 91, - "Na+1": 92, - "/O": 93, - "\\O": 94, - "Br-1": 95, - "Branch3": 96, - "\\S": 97, - "S+1": 98, - "Cl-1": 99, - "I-1": 100, - "/C@@H1": 101, - "Si": 102, - "/C@H1": 103, - "/S": 104, - "=N-1": 105, - "Se": 106, - "=P": 107, - "N-1": 108, - "Ring3": 109, - "2H": 110, - "P+1": 111, - "K+1": 112, - "\\C@@H1": 113, - "\\C@H1": 114, - "/N+1": 115, - "@@": 116, - "C-1": 117, - "#N+1": 118, - "B-1": 119, - "+3": 120, - "Cl+3": 121, - "\\NH1": 122, - "Li": 123, - "Li+1": 124, - "PH1": 125, - "18": 126, - "18F": 127, - "@+1": 128, - "3H": 129, - "P@@": 130, - "H0": 131, - "OH0": 132, - "12": 133, - "P@": 134, - "+2": 135, - "@@+1": 136, - "S-1": 137, - "/Br": 138, - "-/": 139, - "\\Cl": 140, - "-/Ring2": 141, - "\\O-1": 142, - "11": 143, - "5I": 144, - "125I": 145, - "11C": 146, - "H3": 147, - "\\N+1": 148, - "-\\": 149, - "/C@@": 150, - "S@+1": 151, - "As": 152, - "/Cl": 153, - "11CH3": 154, - "=Se": 155, - "S@@+1": 156, - "N@+1": 157, - "14": 158, - "-\\Ring2": 159, - "14C": 160, - "\\F": 161, - "/C@": 162, - "Te": 163, - "H2": 164, - "H1-1": 165, - "=O+1": 166, - "N@@+1": 167, - "C+1": 168, - "=S+1": 169, - "Zn": 170, - "/P": 171, - "a+2": 172, - "/I": 173, - "OH1-1": 174, - "Ca+2": 175, - "\\Br": 176, - "Mg": 177, - "Zn+2": 178, - "Al": 179, - "/F": 180, - "Mg+2": 181, - "123": 182, - "123I": 183, - "13": 184, - "I+1": 185, - "/O-1": 186, - "-\\Ring1": 187, - "BH2": 188, - "BH2-1": 189, - "\\I": 190, - "/NH1": 191, - "O+1": 192, - "131": 193, - "131I": 194, - "=14C": 195, - "/S+1": 196, - "=Ring3": 197, - "\\C@@": 198, - "H2+1": 199, - "\\C@": 200, - "Ag": 201, - "=As": 202, - "=Se+1": 203, - "NH2+1": 204, - "SeH1": 205, - "-/Ring1": 206, - "=Te": 207, - "Al+3": 208, - "NaH1": 209, - "=Te+1": 210, - "NH1+1": 211, - "Ag+1": 212, - "H1+1": 213, - "NH1-1": 214, - "\\P": 215, - "14CH2": 216, - "13C": 217, - "14CH1": 218, - "=11C": 219, - "S@@": 220, - "=P@@": 221, - "SiH2": 222, - "H3-1": 223, - "14CH3": 224, - "BH3-1": 225, - "S@": 226, - "=14CH1": 227, - "=PH1": 228, - "=P@": 229, - "=NH1+1": 230, - "\\S+1": 231, - "124": 232, - "CH1-1": 233, - "Sr": 234, - "=Si": 235, - "124I": 236, - "Sr+2": 237, - "#C-1": 238, - "/C-1": 239, - "N@": 240, - "/N-1": 241, - "13CH1": 242, - "/B": 243, - "19": 244, - "Ba+2": 245, - "H4": 246, - "SH1+1": 247, - "Se+1": 248, - "19F": 249, - "/125I": 250, - "P@+1": 251, - "Rb": 252, - "Cl+1": 253, - "SiH4": 254, - "Rb+1": 255, - "=Branch3": 256, - "N@@": 257, - "As+1": 258, - "/Si": 259, - "BH1-1": 260, - "SH1": 261, - "/123I": 262, - "32": 263, - "=Mg": 264, - "H+1": 265, - "\\B": 266, - "SiH1": 267, - "P@@+1": 268, - "-2": 269, - "15": 270, - "17": 271, - "35": 272, - "=13CH1": 273, - "Cs": 274, - "=NH2+1": 275, - "=SH1": 276, - "MgH2": 277, - "32P": 278, - "17F": 279, - "35S": 280, - "Cs+1": 281, - "#11C": 282, - "/131I": 283, - "Bi": 284, - "\\125I": 285, - "=S@@": 286, - "\\S-1": 287, - "6Br": 288, - "7I": 289, - "76Br": 290, - "=B": 291, - "eH1": 292, - "\\N-1": 293, - "18O": 294, - "127I": 295, - "11CH2": 296, - "14C@@H1": 297, - "TeH2": 298, - "15NH1": 299, - "Bi+3": 300, - "/P+1": 301, - "/13C": 302, - "/13CH1": 303, - "0B": 304, - "10B": 305, - "=Al": 306, - "=18O": 307, - "BH0": 308, - "F-1": 309, - "NH3": 310, - "S-2": 311, - "Br+2": 312, - "Cl+2": 313, - "\\Si": 314, - "/S-1": 315, - "=PH2": 316, - "14C@H1": 317, - "NH3+1": 318, - "#14C": 319, - "#O+1": 320, - "-3": 321, - "22": 322, - "4H": 323, - "5Se": 324, - "5Sr+2": 325, - "75Se": 326, - "85Sr+2": 327, - "=B-1": 328, - "=13C": 329, - "@-1": 330, - "Be": 331, - "B@@": 332, - "B@-1": 333, - "Ca": 334, - "CH1": 335, - "I+3": 336, - "KH1": 337, - "OH1+1": 338, - "Ra+2": 339, - "SH1-1": 340, - "\\PH1": 341, - "\\123I": 342, - "=Ca": 343, - "\\CH1-1": 344, - "=S@": 345, - "\\SeH1": 346, - "/SeH1": 347, - "Se-1": 348, - "LiH1": 349, - "18F-1": 350, - "125IH1": 351, - "11CH1": 352, - "TeH1": 353, - "Zn+1": 354, - "Zn-2": 355, - "Al-3": 356, - "13CH3": 357, - "15N": 358, - "Be+2": 359, - "B@@-1": 360, - "#P": 361, - "#S": 362, - "-4": 363, - "/PH1": 364, - "/P@@": 365, - "/As": 366, - "/14C": 367, - "/14CH1": 368, - "2K+1": 369, - "2Rb+1": 370, - "3Se": 371, - "3Ra+2": 372, - "45": 373, - "47": 374, - "42K+1": 375, - "5I-1": 376, - "73Se": 377, - "89": 378, - "82Rb+1": 379, - "=32": 380, - "=32P": 381, - "CH0": 382, - "CH2": 383, - "I+2": 384, - "NH0": 385, - "NH4": 386, - "OH1": 387, - "PH2+1": 388, - "SH0": 389, - "SH2": 390, - "\\3H": 391, - "\\11CH3": 392, - "\\C-1": 393, - "\\Se": 394, - "Si@": 395, - "Si-1": 396, - "SiH1-1": 397, - "SiH3-1": 398, - "/Se": 399, - "Se-2": 400, - "\\NH1-1": 401, - "18FH1": 402, - "125I-1": 403, - "11C@@H1": 404, - "11C-1": 405, - "AsH1": 406, - "As-1": 407, - "14C@@": 408, - "Te-1": 409, - "Mg+1": 410, - "123I-1": 411, - "123Te": 412, - "123IH1": 413, - "135I": 414, - "131I-1": 415, - "Ag-4": 416, - "124I-1": 417, - "76BrH1": 418, - "18OH1": 419, - "22Na+1": 420, - "223Ra+2": 421, - "CaH2": 422, - "45Ca+2": 423, - "47Ca+2": 424, - "89Sr+2": 425, - "=32PH1": 426, - "NH4+1": 427 - }, - "merges": [ - "B r", - "a n", - "c h", - "Br an", - "Bran ch", - "Branch 1", - "= C", - "R i", - "n g", - "Ri ng", - "Ring 1", - "= Branch1", - "Branch 2", - "= O", - "Ring 2", - "H 1", - "C @", - "= N", - "# Branch1", - "C@ @", - "= Branch2", - "C@ H1", - "C@@ H1", - "# Branch2", - "# C", - "C l", - "/ C", - "N H1", - "= Ring1", - "+ 1", - "- 1", - "O -1", - "N +1", - "\\ C", - "# N", - "/ N", - "= Ring2", - "= S", - "=N +1", - "\\ N", - "N a", - "Na +1", - "/ O", - "\\ O", - "Br -1", - "Branch 3", - "\\ S", - "S +1", - "Cl -1", - "I -1", - "/ C@@H1", - "S i", - "/ C@H1", - "/ S", - "=N -1", - "S e", - "= P", - "N -1", - "Ring 3", - "2 H", - "P +1", - "K +1", - "\\ C@@H1", - "\\ C@H1", - "/ N+1", - "@ @", - "C -1", - "# N+1", - "B -1", - "+ 3", - "Cl +3", - "\\ NH1", - "L i", - "Li +1", - "P H1", - "1 8", - "18 F", - "@ +1", - "3 H", - "P @@", - "H 0", - "O H0", - "1 2", - "P @", - "+ 2", - "@@ +1", - "S -1", - "/ Br", - "- /", - "\\ Cl", - "-/ Ring2", - "\\ O-1", - "1 1", - "5 I", - "12 5I", - "11 C", - "H 3", - "\\ N+1", - "- \\", - "/ C@@", - "S @+1", - "A s", - "/ Cl", - "11C H3", - "=S e", - "S @@+1", - "N @+1", - "1 4", - "-\\ Ring2", - "14 C", - "\\ F", - "/ C@", - "T e", - "H 2", - "H1 -1", - "=O +1", - "N @@+1", - "C +1", - "=S +1", - "Z n", - "/ P", - "a +2", - "/ I", - "O H1-1", - "C a+2", - "\\ Br", - "M g", - "Zn +2", - "A l", - "/ F", - "Mg +2", - "12 3", - "123 I", - "1 3", - "I +1", - "/ O-1", - "-\\ Ring1", - "B H2", - "BH2 -1", - "\\ I", - "/ NH1", - "O +1", - "13 1", - "131 I", - "= 14C", - "/ S+1", - "= Ring3", - "\\ C@@", - "H2 +1", - "\\ C@", - "A g", - "= As", - "=Se +1", - "N H2+1", - "Se H1", - "-/ Ring1", - "= Te", - "Al +3", - "Na H1", - "=Te +1", - "NH1 +1", - "Ag +1", - "H1 +1", - "NH1 -1", - "\\ P", - "14C H2", - "13 C", - "14C H1", - "= 11C", - "S @@", - "=P @@", - "Si H2", - "H3 -1", - "14C H3", - "B H3-1", - "S @", - "=14C H1", - "=P H1", - "=P @", - "=N H1+1", - "\\S +1", - "12 4", - "C H1-1", - "S r", - "=S i", - "124 I", - "Sr +2", - "#C -1", - "/C -1", - "N @", - "/N -1", - "13C H1", - "/ B", - "1 9", - "B a+2", - "H 4", - "S H1+1", - "Se +1", - "19 F", - "/ 125I", - "P @+1", - "R b", - "Cl +1", - "Si H4", - "Rb +1", - "= Branch3", - "N @@", - "As +1", - "/ Si", - "B H1-1", - "S H1", - "/ 123I", - "3 2", - "= Mg", - "H +1", - "\\ B", - "Si H1", - "P@@ +1", - "- 2", - "1 5", - "1 7", - "3 5", - "= 13CH1", - "C s", - "=N H2+1", - "=S H1", - "Mg H2", - "32 P", - "17 F", - "35 S", - "Cs +1", - "# 11C", - "/ 131I", - "B i", - "\\ 125I", - "=S @@", - "\\S -1", - "6 Br", - "7 I", - "7 6Br", - "= B", - "e H1", - "\\N -1", - "18 O", - "12 7I", - "11C H2", - "14 C@@H1", - "Te H2", - "15 NH1", - "Bi +3", - "/ P+1", - "/ 13C", - "/ 13CH1", - "0 B", - "1 0B", - "= Al", - "= 18O", - "B H0", - "F -1", - "N H3", - "S -2", - "Br +2", - "Cl +2", - "\\S i", - "/S -1", - "=P H2", - "14 C@H1", - "NH3 +1", - "# 14C", - "# O+1", - "- 3", - "2 2", - "4 H", - "5 Se", - "5 Sr+2", - "7 5Se", - "8 5Sr+2", - "= B-1", - "= 13C", - "@ -1", - "B e", - "B @@", - "B @-1", - "C a", - "C H1", - "I +3", - "K H1", - "O H1+1", - "R a+2", - "S H1-1", - "\\ PH1", - "\\ 123I", - "=C a", - "\\C H1-1", - "=S @", - "\\S eH1", - "/S eH1", - "Se -1", - "Li H1", - "18F -1", - "125I H1", - "11C H1", - "Te H1", - "Zn +1", - "Zn -2", - "Al -3", - "13C H3", - "15 N", - "Be +2", - "B@@ -1", - "# P", - "# S", - "- 4", - "/ PH1", - "/ P@@", - "/ As", - "/ 14C", - "/ 14CH1", - "2 K+1", - "2 Rb+1", - "3 Se", - "3 Ra+2", - "4 5", - "4 7", - "4 2K+1", - "5 I-1", - "7 3Se", - "8 9", - "8 2Rb+1", - "= 32", - "= 32P", - "C H0", - "C H2", - "I +2", - "N H0", - "N H4", - "O H1", - "P H2+1", - "S H0", - "S H2", - "\\ 3H", - "\\ 11CH3", - "\\C -1", - "\\S e", - "Si @", - "Si -1", - "Si H1-1", - "Si H3-1", - "/S e", - "Se -2", - "\\NH1 -1", - "18F H1", - "12 5I-1", - "11 C@@H1", - "11 C-1", - "As H1", - "As -1", - "14 C@@", - "Te -1", - "Mg +1", - "123 I-1", - "123 Te", - "123I H1", - "13 5I", - "131 I-1", - "Ag -4", - "124 I-1", - "76Br H1", - "18O H1", - "22 Na+1", - "22 3Ra+2", - "Ca H2", - "45 Ca+2", - "47 Ca+2", - "89 Sr+2", - "=32 PH1", - "NH4 +1" - ] - } -} \ No newline at end of file diff --git a/models/finetuned/lipo/tokenizer_config.json b/models/finetuned/lipo/tokenizer_config.json deleted file mode 100644 index 08860954acd34fad07fd77f7635298fa565f3149..0000000000000000000000000000000000000000 --- a/models/finetuned/lipo/tokenizer_config.json +++ /dev/null @@ -1,65 +0,0 @@ -{ - "add_prefix_space": false, - "bos_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "cls_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "eos_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "errors": "replace", - "mask_token": { - "__type": "AddedToken", - "content": "", - "lstrip": true, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "model_max_length": 1000000000000000019884624838656, - "name_or_path": "/home/erva/SELFormerMM/data/pretrained_multimodal_chembl36", - "pad_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "sep_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "special_tokens_map_file": null, - "tokenizer_class": "RobertaTokenizer", - "trim_offsets": true, - "unk_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - } -} diff --git a/models/finetuned/lipo/train_stdout.log b/models/finetuned/lipo/train_stdout.log deleted file mode 100644 index acd2e33136a7ff829af04264977e9249e5aaad87..0000000000000000000000000000000000000000 --- a/models/finetuned/lipo/train_stdout.log +++ /dev/null @@ -1,84 +0,0 @@ -[finetune] starting -[finetune] device=cuda task_type=regression batch_size=32 max_len=128 backbone_lr=5e-05 head_lr=0.0005 weight_decay=0.1 epochs=50 -[finetune] dataset_meta_csv=/home/erva/SELFormerMM/data/new_finetuning_datasets/regression/lipo/lipo.csv -[finetune] dataset_embs_npz=/home/erva/SELFormerMM/data/new_finetuning_datasets/regression/lipo/lipo_embs.npz -[finetune] model_path=HUBioDataLab/SELFormer tokenizer_path=HUBioDataLab/SELFormer -[finetune] pretrained_multimodal_dir=/home/erva/SELFormerMM/data/pretrained_multimodal_chembl36 -[finetune] use_scaffold=False seed=42 fracs=(0.8,0.1,0.1) -[finetune] loading dataset bundle (meta csv + embs npz) ... -[finetune] splitting dataset... -[finetune] split sizes: train=3,360 val=420 test=420 -[finetune] train modality_non_empty: graph=3,360/3,360 text=1,092/3,360 kg=815/3,360 -[finetune] val modality_non_empty: graph=420/420 text=126/420 kg=99/420 -[finetune] test modality_non_empty: graph=420/420 text=134/420 kg=96/420 -[finetune] extracting labels... -[finetune] loading config/tokenizer/backbone... -[finetune] initializing multimodal model... -[finetune] loading multimodal pretrained weights: /home/erva/SELFormerMM/data/pretrained_multimodal_chembl36/pytorch_model.bin -[finetune] freezing roberta layers (trainable: encoder.layer.9-11)... -[finetune] backbone trainable params: 181,443,072/246,245,376 -[finetune] building datasets/dataloaders... -[finetune] train_steps_per_epoch=105 val_steps=14 test_steps=14 -[finetune] initialized head: in_dim=3072 out=1 -[finetune] initializing optimizer/scheduler/finetuner... -[finetune] optimizer groups: backbone_decay=45 backbone_nodecay=57 head_decay=2 head_nodecay=2 -[finetune] training loop... -[finetune] epoch 1/50: train_loss=1.0260 val_loss=0.5933 time=37.0s tod=01:20 -[finetune] epoch 2/50: train_loss=0.4242 val_loss=0.5410 time=34.5s tod=01:20 -[finetune] epoch 3/50: train_loss=0.2867 val_loss=0.4757 time=42.7s tod=01:21 -[finetune] epoch 4/50: train_loss=0.2087 val_loss=0.4417 time=41.9s tod=01:22 -[finetune] epoch 5/50: train_loss=0.1613 val_loss=0.4787 time=43.0s tod=01:22 -[finetune] epoch 6/50: train_loss=0.1394 val_loss=0.3972 time=43.0s tod=01:23 -[finetune] epoch 7/50: train_loss=0.1148 val_loss=0.4614 time=42.9s tod=01:24 -[finetune] epoch 8/50: train_loss=0.1038 val_loss=0.4147 time=42.9s tod=01:24 -[finetune] epoch 9/50: train_loss=0.0841 val_loss=0.4036 time=43.1s tod=01:25 -[finetune] epoch 10/50: train_loss=0.0834 val_loss=0.4152 time=42.8s tod=01:26 -[finetune] epoch 11/50: train_loss=0.0781 val_loss=0.4173 time=43.1s tod=01:27 -[finetune] epoch 12/50: train_loss=0.0680 val_loss=0.4063 time=42.2s tod=01:27 -[finetune] epoch 13/50: train_loss=0.0608 val_loss=0.3898 time=42.9s tod=01:28 -[finetune] epoch 14/50: train_loss=0.0573 val_loss=0.3987 time=42.9s tod=01:29 -[finetune] epoch 15/50: train_loss=0.0568 val_loss=0.4186 time=43.0s tod=01:29 -[finetune] epoch 16/50: train_loss=0.0498 val_loss=0.4147 time=43.1s tod=01:30 -[finetune] epoch 17/50: train_loss=0.0471 val_loss=0.4005 time=43.0s tod=01:31 -[finetune] epoch 18/50: train_loss=0.0452 val_loss=0.4167 time=42.8s tod=01:32 -[finetune] epoch 19/50: train_loss=0.0440 val_loss=0.4071 time=42.9s tod=01:32 -[finetune] epoch 20/50: train_loss=0.0386 val_loss=0.4185 time=43.1s tod=01:33 -[finetune] epoch 21/50: train_loss=0.0373 val_loss=0.4106 time=36.2s tod=01:34 -[finetune] epoch 22/50: train_loss=0.0348 val_loss=0.4107 time=34.1s tod=01:34 -[finetune] epoch 23/50: train_loss=0.0337 val_loss=0.3840 time=42.9s tod=01:35 -[finetune] epoch 24/50: train_loss=0.0340 val_loss=0.3960 time=42.8s tod=01:36 -[finetune] epoch 25/50: train_loss=0.0304 val_loss=0.3962 time=42.8s tod=01:36 -[finetune] test_metrics: epoch=25 loss=0.3360 mse=0.3397 rmse=0.5828 mae=0.4434 -[finetune] saved checkpoint (best rmse=0.5828): /media/ubuntu/8TB/erva/selformer-mm/output/new_finetune_sweeps/lipo/ejiyn98r/checkpoint_epoch_025 -[finetune] epoch 26/50: train_loss=0.0285 val_loss=0.3949 time=42.7s tod=01:37 -[finetune] epoch 27/50: train_loss=0.0268 val_loss=0.4015 time=43.0s tod=01:38 -[finetune] epoch 28/50: train_loss=0.0247 val_loss=0.3962 time=42.7s tod=01:39 -[finetune] epoch 29/50: train_loss=0.0252 val_loss=0.4017 time=42.8s tod=01:39 -[finetune] epoch 30/50: train_loss=0.0270 val_loss=0.3894 time=42.9s tod=01:40 -[finetune] epoch 31/50: train_loss=0.0240 val_loss=0.3859 time=42.0s tod=01:41 -[finetune] epoch 32/50: train_loss=0.0222 val_loss=0.3969 time=42.8s tod=01:41 -[finetune] epoch 33/50: train_loss=0.0228 val_loss=0.3901 time=42.8s tod=01:42 -[finetune] epoch 34/50: train_loss=0.0218 val_loss=0.3887 time=42.8s tod=01:43 -[finetune] epoch 35/50: train_loss=0.0197 val_loss=0.3904 time=42.9s tod=01:44 -[finetune] epoch 36/50: train_loss=0.0197 val_loss=0.4033 time=42.8s tod=01:44 -[finetune] epoch 37/50: train_loss=0.0179 val_loss=0.4006 time=43.0s tod=01:45 -[finetune] epoch 38/50: train_loss=0.0180 val_loss=0.4014 time=42.8s tod=01:46 -[finetune] epoch 39/50: train_loss=0.0173 val_loss=0.3929 time=38.0s tod=01:46 -[finetune] epoch 40/50: train_loss=0.0156 val_loss=0.3943 time=32.6s tod=01:47 -[finetune] epoch 41/50: train_loss=0.0156 val_loss=0.3950 time=35.6s tod=01:47 -[finetune] epoch 42/50: train_loss=0.0150 val_loss=0.3858 time=37.5s tod=01:48 -[finetune] epoch 43/50: train_loss=0.0142 val_loss=0.3958 time=44.4s tod=01:49 -[finetune] epoch 44/50: train_loss=0.0142 val_loss=0.3989 time=44.4s tod=01:50 -[finetune] epoch 45/50: train_loss=0.0136 val_loss=0.3931 time=44.3s tod=01:50 -[finetune] epoch 46/50: train_loss=0.0129 val_loss=0.3934 time=44.4s tod=01:51 -[finetune] epoch 47/50: train_loss=0.0132 val_loss=0.3925 time=44.4s tod=01:52 -[finetune] epoch 48/50: train_loss=0.0127 val_loss=0.3911 time=44.2s tod=01:53 -[finetune] epoch 49/50: train_loss=0.0121 val_loss=0.3897 time=44.4s tod=01:53 -[finetune] epoch 50/50: train_loss=0.0120 val_loss=0.3900 time=44.5s tod=01:54 -[finetune] test_metrics: epoch=50 loss=0.3241 mse=0.3293 rmse=0.5739 mae=0.4349 -[finetune] saved checkpoint (best rmse=0.5739): /media/ubuntu/8TB/erva/selformer-mm/output/new_finetune_sweeps/lipo/ejiyn98r/checkpoint_epoch_050 -[finetune] final evaluation on test split... -[finetune] test_metrics: loss=0.3241 mse=0.3293 rmse=0.5739 mae=0.4349 -[finetune] saving model... -[finetune] saved finetuned model to: /media/ubuntu/8TB/erva/selformer-mm/output/new_finetune_sweeps/lipo/ejiyn98r -[finetune] done in 2114.9s diff --git a/models/finetuned/lipo/vocab.json b/models/finetuned/lipo/vocab.json deleted file mode 100644 index f7e4cc22809f4e9035cc450ef189c8a7da8fd03e..0000000000000000000000000000000000000000 --- a/models/finetuned/lipo/vocab.json +++ /dev/null @@ -1 +0,0 @@ -{"":0,"":1,"":2,"":3,"":4,"\n":5,"#":6,"+":7,"-":8,".":9,"/":10,"0":11,"1":12,"2":13,"3":14,"4":15,"5":16,"6":17,"7":18,"8":19,"9":20,"=":21,"@":22,"A":23,"B":24,"C":25,"F":26,"H":27,"I":28,"K":29,"L":30,"M":31,"N":32,"O":33,"P":34,"R":35,"S":36,"T":37,"Z":38,"\\":39,"a":40,"b":41,"c":42,"e":43,"g":44,"h":45,"i":46,"l":47,"n":48,"r":49,"s":50,"Br":51,"an":52,"ch":53,"Bran":54,"Branch":55,"Branch1":56,"=C":57,"Ri":58,"ng":59,"Ring":60,"Ring1":61,"=Branch1":62,"Branch2":63,"=O":64,"Ring2":65,"H1":66,"C@":67,"=N":68,"#Branch1":69,"C@@":70,"=Branch2":71,"C@H1":72,"C@@H1":73,"#Branch2":74,"#C":75,"Cl":76,"/C":77,"NH1":78,"=Ring1":79,"+1":80,"-1":81,"O-1":82,"N+1":83,"\\C":84,"#N":85,"/N":86,"=Ring2":87,"=S":88,"=N+1":89,"\\N":90,"Na":91,"Na+1":92,"/O":93,"\\O":94,"Br-1":95,"Branch3":96,"\\S":97,"S+1":98,"Cl-1":99,"I-1":100,"/C@@H1":101,"Si":102,"/C@H1":103,"/S":104,"=N-1":105,"Se":106,"=P":107,"N-1":108,"Ring3":109,"2H":110,"P+1":111,"K+1":112,"\\C@@H1":113,"\\C@H1":114,"/N+1":115,"@@":116,"C-1":117,"#N+1":118,"B-1":119,"+3":120,"Cl+3":121,"\\NH1":122,"Li":123,"Li+1":124,"PH1":125,"18":126,"18F":127,"@+1":128,"3H":129,"P@@":130,"H0":131,"OH0":132,"12":133,"P@":134,"+2":135,"@@+1":136,"S-1":137,"/Br":138,"-/":139,"\\Cl":140,"-/Ring2":141,"\\O-1":142,"11":143,"5I":144,"125I":145,"11C":146,"H3":147,"\\N+1":148,"-\\":149,"/C@@":150,"S@+1":151,"As":152,"/Cl":153,"11CH3":154,"=Se":155,"S@@+1":156,"N@+1":157,"14":158,"-\\Ring2":159,"14C":160,"\\F":161,"/C@":162,"Te":163,"H2":164,"H1-1":165,"=O+1":166,"N@@+1":167,"C+1":168,"=S+1":169,"Zn":170,"/P":171,"a+2":172,"/I":173,"OH1-1":174,"Ca+2":175,"\\Br":176,"Mg":177,"Zn+2":178,"Al":179,"/F":180,"Mg+2":181,"123":182,"123I":183,"13":184,"I+1":185,"/O-1":186,"-\\Ring1":187,"BH2":188,"BH2-1":189,"\\I":190,"/NH1":191,"O+1":192,"131":193,"131I":194,"=14C":195,"/S+1":196,"=Ring3":197,"\\C@@":198,"H2+1":199,"\\C@":200,"Ag":201,"=As":202,"=Se+1":203,"NH2+1":204,"SeH1":205,"-/Ring1":206,"=Te":207,"Al+3":208,"NaH1":209,"=Te+1":210,"NH1+1":211,"Ag+1":212,"H1+1":213,"NH1-1":214,"\\P":215,"14CH2":216,"13C":217,"14CH1":218,"=11C":219,"S@@":220,"=P@@":221,"SiH2":222,"H3-1":223,"14CH3":224,"BH3-1":225,"S@":226,"=14CH1":227,"=PH1":228,"=P@":229,"=NH1+1":230,"\\S+1":231,"124":232,"CH1-1":233,"Sr":234,"=Si":235,"124I":236,"Sr+2":237,"#C-1":238,"/C-1":239,"N@":240,"/N-1":241,"13CH1":242,"/B":243,"19":244,"Ba+2":245,"H4":246,"SH1+1":247,"Se+1":248,"19F":249,"/125I":250,"P@+1":251,"Rb":252,"Cl+1":253,"SiH4":254,"Rb+1":255,"=Branch3":256,"N@@":257,"As+1":258,"/Si":259,"BH1-1":260,"SH1":261,"/123I":262,"32":263,"=Mg":264,"H+1":265,"\\B":266,"SiH1":267,"P@@+1":268,"-2":269,"15":270,"17":271,"35":272,"=13CH1":273,"Cs":274,"=NH2+1":275,"=SH1":276,"MgH2":277,"32P":278,"17F":279,"35S":280,"Cs+1":281,"#11C":282,"/131I":283,"Bi":284,"\\125I":285,"=S@@":286,"\\S-1":287,"6Br":288,"7I":289,"76Br":290,"=B":291,"eH1":292,"\\N-1":293,"18O":294,"127I":295,"11CH2":296,"14C@@H1":297,"TeH2":298,"15NH1":299,"Bi+3":300,"/P+1":301,"/13C":302,"/13CH1":303,"0B":304,"10B":305,"=Al":306,"=18O":307,"BH0":308,"F-1":309,"NH3":310,"S-2":311,"Br+2":312,"Cl+2":313,"\\Si":314,"/S-1":315,"=PH2":316,"14C@H1":317,"NH3+1":318,"#14C":319,"#O+1":320,"-3":321,"22":322,"4H":323,"5Se":324,"5Sr+2":325,"75Se":326,"85Sr+2":327,"=B-1":328,"=13C":329,"@-1":330,"Be":331,"B@@":332,"B@-1":333,"Ca":334,"CH1":335,"I+3":336,"KH1":337,"OH1+1":338,"Ra+2":339,"SH1-1":340,"\\PH1":341,"\\123I":342,"=Ca":343,"\\CH1-1":344,"=S@":345,"\\SeH1":346,"/SeH1":347,"Se-1":348,"LiH1":349,"18F-1":350,"125IH1":351,"11CH1":352,"TeH1":353,"Zn+1":354,"Zn-2":355,"Al-3":356,"13CH3":357,"15N":358,"Be+2":359,"B@@-1":360,"#P":361,"#S":362,"-4":363,"/PH1":364,"/P@@":365,"/As":366,"/14C":367,"/14CH1":368,"2K+1":369,"2Rb+1":370,"3Se":371,"3Ra+2":372,"45":373,"47":374,"42K+1":375,"5I-1":376,"73Se":377,"89":378,"82Rb+1":379,"=32":380,"=32P":381,"CH0":382,"CH2":383,"I+2":384,"NH0":385,"NH4":386,"OH1":387,"PH2+1":388,"SH0":389,"SH2":390,"\\3H":391,"\\11CH3":392,"\\C-1":393,"\\Se":394,"Si@":395,"Si-1":396,"SiH1-1":397,"SiH3-1":398,"/Se":399,"Se-2":400,"\\NH1-1":401,"18FH1":402,"125I-1":403,"11C@@H1":404,"11C-1":405,"AsH1":406,"As-1":407,"14C@@":408,"Te-1":409,"Mg+1":410,"123I-1":411,"123Te":412,"123IH1":413,"135I":414,"131I-1":415,"Ag-4":416,"124I-1":417,"76BrH1":418,"18OH1":419,"22Na+1":420,"223Ra+2":421,"CaH2":422,"45Ca+2":423,"47Ca+2":424,"89Sr+2":425,"=32PH1":426,"NH4+1":427} \ No newline at end of file diff --git a/models/finetuned/pdbbind_full/checkpoint_epoch_025/config.json b/models/finetuned/pdbbind_full/checkpoint_epoch_025/config.json deleted file mode 100644 index 3811e21539577b37e06313eab31ec11e53f0cbbc..0000000000000000000000000000000000000000 --- a/models/finetuned/pdbbind_full/checkpoint_epoch_025/config.json +++ /dev/null @@ -1,27 +0,0 @@ -{ - "_name_or_path": "/home/erva/SELFormerMM/data/pretrained_multimodal_chembl36", - "architectures": [ - "RobertaForMaskedLM" - ], - "attention_probs_dropout_prob": 0.1, - "bos_token_id": 0, - "classifier_dropout": null, - "eos_token_id": 2, - "hidden_act": "gelu", - "hidden_dropout_prob": 0.1, - "hidden_size": 768, - "initializer_range": 0.02, - "intermediate_size": 3072, - "layer_norm_eps": 1e-12, - "max_position_embeddings": 514, - "model_type": "roberta", - "num_attention_heads": 4, - "num_hidden_layers": 12, - "pad_token_id": 1, - "position_embedding_type": "absolute", - "torch_dtype": "float32", - "transformers_version": "4.26.1", - "type_vocab_size": 1, - "use_cache": true, - "vocab_size": 800 -} diff --git a/models/finetuned/pdbbind_full/checkpoint_epoch_025/merges.txt b/models/finetuned/pdbbind_full/checkpoint_epoch_025/merges.txt deleted file mode 100644 index 7cd5ec62809503c23f18c80afc0ba3bdf9d253d0..0000000000000000000000000000000000000000 --- a/models/finetuned/pdbbind_full/checkpoint_epoch_025/merges.txt +++ /dev/null @@ -1,378 +0,0 @@ -#version: 0.2 - Trained by `huggingface/tokenizers` -B r -a n -c h -Br an -Bran ch -Branch 1 -= C -R i -n g -Ri ng -Ring 1 -= Branch1 -Branch 2 -= O -Ring 2 -H 1 -C @ -= N -# Branch1 -C@ @ -= Branch2 -C@ H1 -C@@ H1 -# Branch2 -# C -C l -/ C -N H1 -= Ring1 -+ 1 -- 1 -O -1 -N +1 -\ C -# N -/ N -= Ring2 -= S -=N +1 -\ N -N a -Na +1 -/ O -\ O -Br -1 -Branch 3 -\ S -S +1 -Cl -1 -I -1 -/ C@@H1 -S i -/ C@H1 -/ S -=N -1 -S e -= P -N -1 -Ring 3 -2 H -P +1 -K +1 -\ C@@H1 -\ C@H1 -/ N+1 -@ @ -C -1 -# N+1 -B -1 -+ 3 -Cl +3 -\ NH1 -L i -Li +1 -P H1 -1 8 -18 F -@ +1 -3 H -P @@ -H 0 -O H0 -1 2 -P @ -+ 2 -@@ +1 -S -1 -/ Br -- / -\ Cl --/ Ring2 -\ O-1 -1 1 -5 I -12 5I -11 C -H 3 -\ N+1 -- \ -/ C@@ -S @+1 -A s -/ Cl -11C H3 -=S e -S @@+1 -N @+1 -1 4 --\ Ring2 -14 C -\ F -/ C@ -T e -H 2 -H1 -1 -=O +1 -N @@+1 -C +1 -=S +1 -Z n -/ P -a +2 -/ I -O H1-1 -C a+2 -\ Br -M g -Zn +2 -A l -/ F -Mg +2 -12 3 -123 I -1 3 -I +1 -/ O-1 --\ Ring1 -B H2 -BH2 -1 -\ I -/ NH1 -O +1 -13 1 -131 I -= 14C -/ S+1 -= Ring3 -\ C@@ -H2 +1 -\ C@ -A g -= As -=Se +1 -N H2+1 -Se H1 --/ Ring1 -= Te -Al +3 -Na H1 -=Te +1 -NH1 +1 -Ag +1 -H1 +1 -NH1 -1 -\ P -14C H2 -13 C -14C H1 -= 11C -S @@ -=P @@ -Si H2 -H3 -1 -14C H3 -B H3-1 -S @ -=14C H1 -=P H1 -=P @ -=N H1+1 -\S +1 -12 4 -C H1-1 -S r -=S i -124 I -Sr +2 -#C -1 -/C -1 -N @ -/N -1 -13C H1 -/ B -1 9 -B a+2 -H 4 -S H1+1 -Se +1 -19 F -/ 125I -P @+1 -R b -Cl +1 -Si H4 -Rb +1 -= Branch3 -N @@ -As +1 -/ Si -B H1-1 -S H1 -/ 123I -3 2 -= Mg -H +1 -\ B -Si H1 -P@@ +1 -- 2 -1 5 -1 7 -3 5 -= 13CH1 -C s -=N H2+1 -=S H1 -Mg H2 -32 P -17 F -35 S -Cs +1 -# 11C -/ 131I -B i -\ 125I -=S @@ -\S -1 -6 Br -7 I -7 6Br -= B -e H1 -\N -1 -18 O -12 7I -11C H2 -14 C@@H1 -Te H2 -15 NH1 -Bi +3 -/ P+1 -/ 13C -/ 13CH1 -0 B -1 0B -= Al -= 18O -B H0 -F -1 -N H3 -S -2 -Br +2 -Cl +2 -\S i -/S -1 -=P H2 -14 C@H1 -NH3 +1 -# 14C -# O+1 -- 3 -2 2 -4 H -5 Se -5 Sr+2 -7 5Se -8 5Sr+2 -= B-1 -= 13C -@ -1 -B e -B @@ -B @-1 -C a -C H1 -I +3 -K H1 -O H1+1 -R a+2 -S H1-1 -\ PH1 -\ 123I -=C a -\C H1-1 -=S @ -\S eH1 -/S eH1 -Se -1 -Li H1 -18F -1 -125I H1 -11C H1 -Te H1 -Zn +1 -Zn -2 -Al -3 -13C H3 -15 N -Be +2 -B@@ -1 -# P -# S -- 4 -/ PH1 -/ P@@ -/ As -/ 14C -/ 14CH1 -2 K+1 -2 Rb+1 -3 Se -3 Ra+2 -4 5 -4 7 -4 2K+1 -5 I-1 -7 3Se -8 9 -8 2Rb+1 -= 32 -= 32P -C H0 -C H2 -I +2 -N H0 -N H4 -O H1 -P H2+1 -S H0 -S H2 -\ 3H -\ 11CH3 -\C -1 -\S e -Si @ -Si -1 -Si H1-1 -Si H3-1 -/S e -Se -2 -\NH1 -1 -18F H1 -12 5I-1 -11 C@@H1 -11 C-1 -As H1 -As -1 -14 C@@ -Te -1 -Mg +1 -123 I-1 -123 Te -123I H1 -13 5I -131 I-1 -Ag -4 -124 I-1 -76Br H1 -18O H1 -22 Na+1 -22 3Ra+2 -Ca H2 -45 Ca+2 -47 Ca+2 -89 Sr+2 -=32 PH1 -NH4 +1 diff --git a/models/finetuned/pdbbind_full/checkpoint_epoch_025/model.pt b/models/finetuned/pdbbind_full/checkpoint_epoch_025/model.pt deleted file mode 100644 index 00970a4febd336802d0db95d26f86cfeb77f132d..0000000000000000000000000000000000000000 --- a/models/finetuned/pdbbind_full/checkpoint_epoch_025/model.pt +++ /dev/null @@ -1,3 +0,0 @@ -version https://git-lfs.github.com/spec/v1 -oid sha256:b390d86637786c1060a0963c402b0a74ee166e2a13fb442fd27770f9d91fbe52 -size 1022843005 diff --git a/models/finetuned/pdbbind_full/checkpoint_epoch_025/special_tokens_map.json b/models/finetuned/pdbbind_full/checkpoint_epoch_025/special_tokens_map.json deleted file mode 100644 index 06a55849fa69a91e7179d909e373179ff7467d8c..0000000000000000000000000000000000000000 --- a/models/finetuned/pdbbind_full/checkpoint_epoch_025/special_tokens_map.json +++ /dev/null @@ -1,51 +0,0 @@ -{ - "bos_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "cls_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "eos_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "mask_token": { - "content": "", - "lstrip": true, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "pad_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "sep_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "unk_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - } -} diff --git a/models/finetuned/pdbbind_full/checkpoint_epoch_025/tokenizer.json b/models/finetuned/pdbbind_full/checkpoint_epoch_025/tokenizer.json deleted file mode 100644 index 3b64b273e6fa9799e2d8375722b9e815de9ebb8f..0000000000000000000000000000000000000000 --- a/models/finetuned/pdbbind_full/checkpoint_epoch_025/tokenizer.json +++ /dev/null @@ -1,909 +0,0 @@ -{ - "version": "1.0", - "truncation": { - "direction": "Right", - "max_length": 128, - "strategy": "LongestFirst", - "stride": 0 - }, - "padding": { - "strategy": { - "Fixed": 128 - }, - "direction": "Right", - "pad_to_multiple_of": null, - "pad_id": 3, - "pad_type_id": 0, - "pad_token": "" - }, - "added_tokens": [ - { - "id": 0, - "content": "", - "single_word": false, - "lstrip": false, - "rstrip": false, - "normalized": true, - "special": true - }, - { - "id": 1, - "content": "", - "single_word": false, - "lstrip": false, - "rstrip": false, - "normalized": true, - "special": true - }, - { - "id": 2, - "content": "", - "single_word": false, - "lstrip": false, - "rstrip": false, - "normalized": true, - "special": true - }, - { - "id": 3, - "content": "", - "single_word": false, - "lstrip": false, - "rstrip": false, - "normalized": true, - "special": true - }, - { - "id": 4, - "content": "", - "single_word": false, - "lstrip": true, - "rstrip": false, - "normalized": true, - "special": true - } - ], - "normalizer": null, - "pre_tokenizer": { - "type": "ByteLevel", - "add_prefix_space": false, - "trim_offsets": true, - "use_regex": true - }, - "post_processor": { - "type": "RobertaProcessing", - "sep": [ - "", - 2 - ], - "cls": [ - "", - 1 - ], - "trim_offsets": true, - "add_prefix_space": false - }, - "decoder": { - "type": "ByteLevel", - "add_prefix_space": true, - "trim_offsets": true, - "use_regex": true - }, - "model": { - "type": "BPE", - "dropout": null, - "unk_token": null, - "continuing_subword_prefix": "", - "end_of_word_suffix": "", - "fuse_unk": false, - "vocab": { - "": 0, - "": 1, - "": 2, - "": 3, - "": 4, - "\n": 5, - "#": 6, - "+": 7, - "-": 8, - ".": 9, - "/": 10, - "0": 11, - "1": 12, - "2": 13, - "3": 14, - "4": 15, - "5": 16, - "6": 17, - "7": 18, - "8": 19, - "9": 20, - "=": 21, - "@": 22, - "A": 23, - "B": 24, - "C": 25, - "F": 26, - "H": 27, - "I": 28, - "K": 29, - "L": 30, - "M": 31, - "N": 32, - "O": 33, - "P": 34, - "R": 35, - "S": 36, - "T": 37, - "Z": 38, - "\\": 39, - "a": 40, - "b": 41, - "c": 42, - "e": 43, - "g": 44, - "h": 45, - "i": 46, - "l": 47, - "n": 48, - "r": 49, - "s": 50, - "Br": 51, - "an": 52, - "ch": 53, - "Bran": 54, - "Branch": 55, - "Branch1": 56, - "=C": 57, - "Ri": 58, - "ng": 59, - "Ring": 60, - "Ring1": 61, - "=Branch1": 62, - "Branch2": 63, - "=O": 64, - "Ring2": 65, - "H1": 66, - "C@": 67, - "=N": 68, - "#Branch1": 69, - "C@@": 70, - "=Branch2": 71, - "C@H1": 72, - "C@@H1": 73, - "#Branch2": 74, - "#C": 75, - "Cl": 76, - "/C": 77, - "NH1": 78, - "=Ring1": 79, - "+1": 80, - "-1": 81, - "O-1": 82, - "N+1": 83, - "\\C": 84, - "#N": 85, - "/N": 86, - "=Ring2": 87, - "=S": 88, - "=N+1": 89, - "\\N": 90, - "Na": 91, - "Na+1": 92, - "/O": 93, - "\\O": 94, - "Br-1": 95, - "Branch3": 96, - "\\S": 97, - "S+1": 98, - "Cl-1": 99, - "I-1": 100, - "/C@@H1": 101, - "Si": 102, - "/C@H1": 103, - "/S": 104, - "=N-1": 105, - "Se": 106, - "=P": 107, - "N-1": 108, - "Ring3": 109, - "2H": 110, - "P+1": 111, - "K+1": 112, - "\\C@@H1": 113, - "\\C@H1": 114, - "/N+1": 115, - "@@": 116, - "C-1": 117, - "#N+1": 118, - "B-1": 119, - "+3": 120, - "Cl+3": 121, - "\\NH1": 122, - "Li": 123, - "Li+1": 124, - "PH1": 125, - "18": 126, - "18F": 127, - "@+1": 128, - "3H": 129, - "P@@": 130, - "H0": 131, - "OH0": 132, - "12": 133, - "P@": 134, - "+2": 135, - "@@+1": 136, - "S-1": 137, - "/Br": 138, - "-/": 139, - "\\Cl": 140, - "-/Ring2": 141, - "\\O-1": 142, - "11": 143, - "5I": 144, - "125I": 145, - "11C": 146, - "H3": 147, - "\\N+1": 148, - "-\\": 149, - "/C@@": 150, - "S@+1": 151, - "As": 152, - "/Cl": 153, - "11CH3": 154, - "=Se": 155, - "S@@+1": 156, - "N@+1": 157, - "14": 158, - "-\\Ring2": 159, - "14C": 160, - "\\F": 161, - "/C@": 162, - "Te": 163, - "H2": 164, - "H1-1": 165, - "=O+1": 166, - "N@@+1": 167, - "C+1": 168, - "=S+1": 169, - "Zn": 170, - "/P": 171, - "a+2": 172, - "/I": 173, - "OH1-1": 174, - "Ca+2": 175, - "\\Br": 176, - "Mg": 177, - "Zn+2": 178, - "Al": 179, - "/F": 180, - "Mg+2": 181, - "123": 182, - "123I": 183, - "13": 184, - "I+1": 185, - "/O-1": 186, - "-\\Ring1": 187, - "BH2": 188, - "BH2-1": 189, - "\\I": 190, - "/NH1": 191, - "O+1": 192, - "131": 193, - "131I": 194, - "=14C": 195, - "/S+1": 196, - "=Ring3": 197, - "\\C@@": 198, - "H2+1": 199, - "\\C@": 200, - "Ag": 201, - "=As": 202, - "=Se+1": 203, - "NH2+1": 204, - "SeH1": 205, - "-/Ring1": 206, - "=Te": 207, - "Al+3": 208, - "NaH1": 209, - "=Te+1": 210, - "NH1+1": 211, - "Ag+1": 212, - "H1+1": 213, - "NH1-1": 214, - "\\P": 215, - "14CH2": 216, - "13C": 217, - "14CH1": 218, - "=11C": 219, - "S@@": 220, - "=P@@": 221, - "SiH2": 222, - "H3-1": 223, - "14CH3": 224, - "BH3-1": 225, - "S@": 226, - "=14CH1": 227, - "=PH1": 228, - "=P@": 229, - "=NH1+1": 230, - "\\S+1": 231, - "124": 232, - "CH1-1": 233, - "Sr": 234, - "=Si": 235, - "124I": 236, - "Sr+2": 237, - "#C-1": 238, - "/C-1": 239, - "N@": 240, - "/N-1": 241, - "13CH1": 242, - "/B": 243, - "19": 244, - "Ba+2": 245, - "H4": 246, - "SH1+1": 247, - "Se+1": 248, - "19F": 249, - "/125I": 250, - "P@+1": 251, - "Rb": 252, - "Cl+1": 253, - "SiH4": 254, - "Rb+1": 255, - "=Branch3": 256, - "N@@": 257, - "As+1": 258, - "/Si": 259, - "BH1-1": 260, - "SH1": 261, - "/123I": 262, - "32": 263, - "=Mg": 264, - "H+1": 265, - "\\B": 266, - "SiH1": 267, - "P@@+1": 268, - "-2": 269, - "15": 270, - "17": 271, - "35": 272, - "=13CH1": 273, - "Cs": 274, - "=NH2+1": 275, - "=SH1": 276, - "MgH2": 277, - "32P": 278, - "17F": 279, - "35S": 280, - "Cs+1": 281, - "#11C": 282, - "/131I": 283, - "Bi": 284, - "\\125I": 285, - "=S@@": 286, - "\\S-1": 287, - "6Br": 288, - "7I": 289, - "76Br": 290, - "=B": 291, - "eH1": 292, - "\\N-1": 293, - "18O": 294, - "127I": 295, - "11CH2": 296, - "14C@@H1": 297, - "TeH2": 298, - "15NH1": 299, - "Bi+3": 300, - "/P+1": 301, - "/13C": 302, - "/13CH1": 303, - "0B": 304, - "10B": 305, - "=Al": 306, - "=18O": 307, - "BH0": 308, - "F-1": 309, - "NH3": 310, - "S-2": 311, - "Br+2": 312, - "Cl+2": 313, - "\\Si": 314, - "/S-1": 315, - "=PH2": 316, - "14C@H1": 317, - "NH3+1": 318, - "#14C": 319, - "#O+1": 320, - "-3": 321, - "22": 322, - "4H": 323, - "5Se": 324, - "5Sr+2": 325, - "75Se": 326, - "85Sr+2": 327, - "=B-1": 328, - "=13C": 329, - "@-1": 330, - "Be": 331, - "B@@": 332, - "B@-1": 333, - "Ca": 334, - "CH1": 335, - "I+3": 336, - "KH1": 337, - "OH1+1": 338, - "Ra+2": 339, - "SH1-1": 340, - "\\PH1": 341, - "\\123I": 342, - "=Ca": 343, - "\\CH1-1": 344, - "=S@": 345, - "\\SeH1": 346, - "/SeH1": 347, - "Se-1": 348, - "LiH1": 349, - "18F-1": 350, - "125IH1": 351, - "11CH1": 352, - "TeH1": 353, - "Zn+1": 354, - "Zn-2": 355, - "Al-3": 356, - "13CH3": 357, - "15N": 358, - "Be+2": 359, - "B@@-1": 360, - "#P": 361, - "#S": 362, - "-4": 363, - "/PH1": 364, - "/P@@": 365, - "/As": 366, - "/14C": 367, - "/14CH1": 368, - "2K+1": 369, - "2Rb+1": 370, - "3Se": 371, - "3Ra+2": 372, - "45": 373, - "47": 374, - "42K+1": 375, - "5I-1": 376, - "73Se": 377, - "89": 378, - "82Rb+1": 379, - "=32": 380, - "=32P": 381, - "CH0": 382, - "CH2": 383, - "I+2": 384, - "NH0": 385, - "NH4": 386, - "OH1": 387, - "PH2+1": 388, - "SH0": 389, - "SH2": 390, - "\\3H": 391, - "\\11CH3": 392, - "\\C-1": 393, - "\\Se": 394, - "Si@": 395, - "Si-1": 396, - "SiH1-1": 397, - "SiH3-1": 398, - "/Se": 399, - "Se-2": 400, - "\\NH1-1": 401, - "18FH1": 402, - "125I-1": 403, - "11C@@H1": 404, - "11C-1": 405, - "AsH1": 406, - "As-1": 407, - "14C@@": 408, - "Te-1": 409, - "Mg+1": 410, - "123I-1": 411, - "123Te": 412, - "123IH1": 413, - "135I": 414, - "131I-1": 415, - "Ag-4": 416, - "124I-1": 417, - "76BrH1": 418, - "18OH1": 419, - "22Na+1": 420, - "223Ra+2": 421, - "CaH2": 422, - "45Ca+2": 423, - "47Ca+2": 424, - "89Sr+2": 425, - "=32PH1": 426, - "NH4+1": 427 - }, - "merges": [ - "B r", - "a n", - "c h", - "Br an", - "Bran ch", - "Branch 1", - "= C", - "R i", - "n g", - "Ri ng", - "Ring 1", - "= Branch1", - "Branch 2", - "= O", - "Ring 2", - "H 1", - "C @", - "= N", - "# Branch1", - "C@ @", - "= Branch2", - "C@ H1", - "C@@ H1", - "# Branch2", - "# C", - "C l", - "/ C", - "N H1", - "= Ring1", - "+ 1", - "- 1", - "O -1", - "N +1", - "\\ C", - "# N", - "/ N", - "= Ring2", - "= S", - "=N +1", - "\\ N", - "N a", - "Na +1", - "/ O", - "\\ O", - "Br -1", - "Branch 3", - "\\ S", - "S +1", - "Cl -1", - "I -1", - "/ C@@H1", - "S i", - "/ C@H1", - "/ S", - "=N -1", - "S e", - "= P", - "N -1", - "Ring 3", - "2 H", - "P +1", - "K +1", - "\\ C@@H1", - "\\ C@H1", - "/ N+1", - "@ @", - "C -1", - "# N+1", - "B -1", - "+ 3", - "Cl +3", - "\\ NH1", - "L i", - "Li +1", - "P H1", - "1 8", - "18 F", - "@ +1", - "3 H", - "P @@", - "H 0", - "O H0", - "1 2", - "P @", - "+ 2", - "@@ +1", - "S -1", - "/ Br", - "- /", - "\\ Cl", - "-/ Ring2", - "\\ O-1", - "1 1", - "5 I", - "12 5I", - "11 C", - "H 3", - "\\ N+1", - "- \\", - "/ C@@", - "S @+1", - "A s", - "/ Cl", - "11C H3", - "=S e", - "S @@+1", - "N @+1", - "1 4", - "-\\ Ring2", - "14 C", - "\\ F", - "/ C@", - "T e", - "H 2", - "H1 -1", - "=O +1", - "N @@+1", - "C +1", - "=S +1", - "Z n", - "/ P", - "a +2", - "/ I", - "O H1-1", - "C a+2", - "\\ Br", - "M g", - "Zn +2", - "A l", - "/ F", - "Mg +2", - "12 3", - "123 I", - "1 3", - "I +1", - "/ O-1", - "-\\ Ring1", - "B H2", - "BH2 -1", - "\\ I", - "/ NH1", - "O +1", - "13 1", - "131 I", - "= 14C", - "/ S+1", - "= Ring3", - "\\ C@@", - "H2 +1", - "\\ C@", - "A g", - "= As", - "=Se +1", - "N H2+1", - "Se H1", - "-/ Ring1", - "= Te", - "Al +3", - "Na H1", - "=Te +1", - "NH1 +1", - "Ag +1", - "H1 +1", - "NH1 -1", - "\\ P", - "14C H2", - "13 C", - "14C H1", - "= 11C", - "S @@", - "=P @@", - "Si H2", - "H3 -1", - "14C H3", - "B H3-1", - "S @", - "=14C H1", - "=P H1", - "=P @", - "=N H1+1", - "\\S +1", - "12 4", - "C H1-1", - "S r", - "=S i", - "124 I", - "Sr +2", - "#C -1", - "/C -1", - "N @", - "/N -1", - "13C H1", - "/ B", - "1 9", - "B a+2", - "H 4", - "S H1+1", - "Se +1", - "19 F", - "/ 125I", - "P @+1", - "R b", - "Cl +1", - "Si H4", - "Rb +1", - "= Branch3", - "N @@", - "As +1", - "/ Si", - "B H1-1", - "S H1", - "/ 123I", - "3 2", - "= Mg", - "H +1", - "\\ B", - "Si H1", - "P@@ +1", - "- 2", - "1 5", - "1 7", - "3 5", - "= 13CH1", - "C s", - "=N H2+1", - "=S H1", - "Mg H2", - "32 P", - "17 F", - "35 S", - "Cs +1", - "# 11C", - "/ 131I", - "B i", - "\\ 125I", - "=S @@", - "\\S -1", - "6 Br", - "7 I", - "7 6Br", - "= B", - "e H1", - "\\N -1", - "18 O", - "12 7I", - "11C H2", - "14 C@@H1", - "Te H2", - "15 NH1", - "Bi +3", - "/ P+1", - "/ 13C", - "/ 13CH1", - "0 B", - "1 0B", - "= Al", - "= 18O", - "B H0", - "F -1", - "N H3", - "S -2", - "Br +2", - "Cl +2", - "\\S i", - "/S -1", - "=P H2", - "14 C@H1", - "NH3 +1", - "# 14C", - "# O+1", - "- 3", - "2 2", - "4 H", - "5 Se", - "5 Sr+2", - "7 5Se", - "8 5Sr+2", - "= B-1", - "= 13C", - "@ -1", - "B e", - "B @@", - "B @-1", - "C a", - "C H1", - "I +3", - "K H1", - "O H1+1", - "R a+2", - "S H1-1", - "\\ PH1", - "\\ 123I", - "=C a", - "\\C H1-1", - "=S @", - "\\S eH1", - "/S eH1", - "Se -1", - "Li H1", - "18F -1", - "125I H1", - "11C H1", - "Te H1", - "Zn +1", - "Zn -2", - "Al -3", - "13C H3", - "15 N", - "Be +2", - "B@@ -1", - "# P", - "# S", - "- 4", - "/ PH1", - "/ P@@", - "/ As", - "/ 14C", - "/ 14CH1", - "2 K+1", - "2 Rb+1", - "3 Se", - "3 Ra+2", - "4 5", - "4 7", - "4 2K+1", - "5 I-1", - "7 3Se", - "8 9", - "8 2Rb+1", - "= 32", - "= 32P", - "C H0", - "C H2", - "I +2", - "N H0", - "N H4", - "O H1", - "P H2+1", - "S H0", - "S H2", - "\\ 3H", - "\\ 11CH3", - "\\C -1", - "\\S e", - "Si @", - "Si -1", - "Si H1-1", - "Si H3-1", - "/S e", - "Se -2", - "\\NH1 -1", - "18F H1", - "12 5I-1", - "11 C@@H1", - "11 C-1", - "As H1", - "As -1", - "14 C@@", - "Te -1", - "Mg +1", - "123 I-1", - "123 Te", - "123I H1", - "13 5I", - "131 I-1", - "Ag -4", - "124 I-1", - "76Br H1", - "18O H1", - "22 Na+1", - "22 3Ra+2", - "Ca H2", - "45 Ca+2", - "47 Ca+2", - "89 Sr+2", - "=32 PH1", - "NH4 +1" - ] - } -} \ No newline at end of file diff --git a/models/finetuned/pdbbind_full/checkpoint_epoch_025/tokenizer_config.json b/models/finetuned/pdbbind_full/checkpoint_epoch_025/tokenizer_config.json deleted file mode 100644 index 08860954acd34fad07fd77f7635298fa565f3149..0000000000000000000000000000000000000000 --- a/models/finetuned/pdbbind_full/checkpoint_epoch_025/tokenizer_config.json +++ /dev/null @@ -1,65 +0,0 @@ -{ - "add_prefix_space": false, - "bos_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "cls_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "eos_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "errors": "replace", - "mask_token": { - "__type": "AddedToken", - "content": "", - "lstrip": true, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "model_max_length": 1000000000000000019884624838656, - "name_or_path": "/home/erva/SELFormerMM/data/pretrained_multimodal_chembl36", - "pad_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "sep_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "special_tokens_map_file": null, - "tokenizer_class": "RobertaTokenizer", - "trim_offsets": true, - "unk_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - } -} diff --git a/models/finetuned/pdbbind_full/checkpoint_epoch_025/vocab.json b/models/finetuned/pdbbind_full/checkpoint_epoch_025/vocab.json deleted file mode 100644 index f7e4cc22809f4e9035cc450ef189c8a7da8fd03e..0000000000000000000000000000000000000000 --- a/models/finetuned/pdbbind_full/checkpoint_epoch_025/vocab.json +++ /dev/null @@ -1 +0,0 @@ -{"":0,"":1,"":2,"":3,"":4,"\n":5,"#":6,"+":7,"-":8,".":9,"/":10,"0":11,"1":12,"2":13,"3":14,"4":15,"5":16,"6":17,"7":18,"8":19,"9":20,"=":21,"@":22,"A":23,"B":24,"C":25,"F":26,"H":27,"I":28,"K":29,"L":30,"M":31,"N":32,"O":33,"P":34,"R":35,"S":36,"T":37,"Z":38,"\\":39,"a":40,"b":41,"c":42,"e":43,"g":44,"h":45,"i":46,"l":47,"n":48,"r":49,"s":50,"Br":51,"an":52,"ch":53,"Bran":54,"Branch":55,"Branch1":56,"=C":57,"Ri":58,"ng":59,"Ring":60,"Ring1":61,"=Branch1":62,"Branch2":63,"=O":64,"Ring2":65,"H1":66,"C@":67,"=N":68,"#Branch1":69,"C@@":70,"=Branch2":71,"C@H1":72,"C@@H1":73,"#Branch2":74,"#C":75,"Cl":76,"/C":77,"NH1":78,"=Ring1":79,"+1":80,"-1":81,"O-1":82,"N+1":83,"\\C":84,"#N":85,"/N":86,"=Ring2":87,"=S":88,"=N+1":89,"\\N":90,"Na":91,"Na+1":92,"/O":93,"\\O":94,"Br-1":95,"Branch3":96,"\\S":97,"S+1":98,"Cl-1":99,"I-1":100,"/C@@H1":101,"Si":102,"/C@H1":103,"/S":104,"=N-1":105,"Se":106,"=P":107,"N-1":108,"Ring3":109,"2H":110,"P+1":111,"K+1":112,"\\C@@H1":113,"\\C@H1":114,"/N+1":115,"@@":116,"C-1":117,"#N+1":118,"B-1":119,"+3":120,"Cl+3":121,"\\NH1":122,"Li":123,"Li+1":124,"PH1":125,"18":126,"18F":127,"@+1":128,"3H":129,"P@@":130,"H0":131,"OH0":132,"12":133,"P@":134,"+2":135,"@@+1":136,"S-1":137,"/Br":138,"-/":139,"\\Cl":140,"-/Ring2":141,"\\O-1":142,"11":143,"5I":144,"125I":145,"11C":146,"H3":147,"\\N+1":148,"-\\":149,"/C@@":150,"S@+1":151,"As":152,"/Cl":153,"11CH3":154,"=Se":155,"S@@+1":156,"N@+1":157,"14":158,"-\\Ring2":159,"14C":160,"\\F":161,"/C@":162,"Te":163,"H2":164,"H1-1":165,"=O+1":166,"N@@+1":167,"C+1":168,"=S+1":169,"Zn":170,"/P":171,"a+2":172,"/I":173,"OH1-1":174,"Ca+2":175,"\\Br":176,"Mg":177,"Zn+2":178,"Al":179,"/F":180,"Mg+2":181,"123":182,"123I":183,"13":184,"I+1":185,"/O-1":186,"-\\Ring1":187,"BH2":188,"BH2-1":189,"\\I":190,"/NH1":191,"O+1":192,"131":193,"131I":194,"=14C":195,"/S+1":196,"=Ring3":197,"\\C@@":198,"H2+1":199,"\\C@":200,"Ag":201,"=As":202,"=Se+1":203,"NH2+1":204,"SeH1":205,"-/Ring1":206,"=Te":207,"Al+3":208,"NaH1":209,"=Te+1":210,"NH1+1":211,"Ag+1":212,"H1+1":213,"NH1-1":214,"\\P":215,"14CH2":216,"13C":217,"14CH1":218,"=11C":219,"S@@":220,"=P@@":221,"SiH2":222,"H3-1":223,"14CH3":224,"BH3-1":225,"S@":226,"=14CH1":227,"=PH1":228,"=P@":229,"=NH1+1":230,"\\S+1":231,"124":232,"CH1-1":233,"Sr":234,"=Si":235,"124I":236,"Sr+2":237,"#C-1":238,"/C-1":239,"N@":240,"/N-1":241,"13CH1":242,"/B":243,"19":244,"Ba+2":245,"H4":246,"SH1+1":247,"Se+1":248,"19F":249,"/125I":250,"P@+1":251,"Rb":252,"Cl+1":253,"SiH4":254,"Rb+1":255,"=Branch3":256,"N@@":257,"As+1":258,"/Si":259,"BH1-1":260,"SH1":261,"/123I":262,"32":263,"=Mg":264,"H+1":265,"\\B":266,"SiH1":267,"P@@+1":268,"-2":269,"15":270,"17":271,"35":272,"=13CH1":273,"Cs":274,"=NH2+1":275,"=SH1":276,"MgH2":277,"32P":278,"17F":279,"35S":280,"Cs+1":281,"#11C":282,"/131I":283,"Bi":284,"\\125I":285,"=S@@":286,"\\S-1":287,"6Br":288,"7I":289,"76Br":290,"=B":291,"eH1":292,"\\N-1":293,"18O":294,"127I":295,"11CH2":296,"14C@@H1":297,"TeH2":298,"15NH1":299,"Bi+3":300,"/P+1":301,"/13C":302,"/13CH1":303,"0B":304,"10B":305,"=Al":306,"=18O":307,"BH0":308,"F-1":309,"NH3":310,"S-2":311,"Br+2":312,"Cl+2":313,"\\Si":314,"/S-1":315,"=PH2":316,"14C@H1":317,"NH3+1":318,"#14C":319,"#O+1":320,"-3":321,"22":322,"4H":323,"5Se":324,"5Sr+2":325,"75Se":326,"85Sr+2":327,"=B-1":328,"=13C":329,"@-1":330,"Be":331,"B@@":332,"B@-1":333,"Ca":334,"CH1":335,"I+3":336,"KH1":337,"OH1+1":338,"Ra+2":339,"SH1-1":340,"\\PH1":341,"\\123I":342,"=Ca":343,"\\CH1-1":344,"=S@":345,"\\SeH1":346,"/SeH1":347,"Se-1":348,"LiH1":349,"18F-1":350,"125IH1":351,"11CH1":352,"TeH1":353,"Zn+1":354,"Zn-2":355,"Al-3":356,"13CH3":357,"15N":358,"Be+2":359,"B@@-1":360,"#P":361,"#S":362,"-4":363,"/PH1":364,"/P@@":365,"/As":366,"/14C":367,"/14CH1":368,"2K+1":369,"2Rb+1":370,"3Se":371,"3Ra+2":372,"45":373,"47":374,"42K+1":375,"5I-1":376,"73Se":377,"89":378,"82Rb+1":379,"=32":380,"=32P":381,"CH0":382,"CH2":383,"I+2":384,"NH0":385,"NH4":386,"OH1":387,"PH2+1":388,"SH0":389,"SH2":390,"\\3H":391,"\\11CH3":392,"\\C-1":393,"\\Se":394,"Si@":395,"Si-1":396,"SiH1-1":397,"SiH3-1":398,"/Se":399,"Se-2":400,"\\NH1-1":401,"18FH1":402,"125I-1":403,"11C@@H1":404,"11C-1":405,"AsH1":406,"As-1":407,"14C@@":408,"Te-1":409,"Mg+1":410,"123I-1":411,"123Te":412,"123IH1":413,"135I":414,"131I-1":415,"Ag-4":416,"124I-1":417,"76BrH1":418,"18OH1":419,"22Na+1":420,"223Ra+2":421,"CaH2":422,"45Ca+2":423,"47Ca+2":424,"89Sr+2":425,"=32PH1":426,"NH4+1":427} \ No newline at end of file diff --git a/models/finetuned/pdbbind_full/config.json b/models/finetuned/pdbbind_full/config.json deleted file mode 100644 index 3811e21539577b37e06313eab31ec11e53f0cbbc..0000000000000000000000000000000000000000 --- a/models/finetuned/pdbbind_full/config.json +++ /dev/null @@ -1,27 +0,0 @@ -{ - "_name_or_path": "/home/erva/SELFormerMM/data/pretrained_multimodal_chembl36", - "architectures": [ - "RobertaForMaskedLM" - ], - "attention_probs_dropout_prob": 0.1, - "bos_token_id": 0, - "classifier_dropout": null, - "eos_token_id": 2, - "hidden_act": "gelu", - "hidden_dropout_prob": 0.1, - "hidden_size": 768, - "initializer_range": 0.02, - "intermediate_size": 3072, - "layer_norm_eps": 1e-12, - "max_position_embeddings": 514, - "model_type": "roberta", - "num_attention_heads": 4, - "num_hidden_layers": 12, - "pad_token_id": 1, - "position_embedding_type": "absolute", - "torch_dtype": "float32", - "transformers_version": "4.26.1", - "type_vocab_size": 1, - "use_cache": true, - "vocab_size": 800 -} diff --git a/models/finetuned/pdbbind_full/merges.txt b/models/finetuned/pdbbind_full/merges.txt deleted file mode 100644 index 7cd5ec62809503c23f18c80afc0ba3bdf9d253d0..0000000000000000000000000000000000000000 --- a/models/finetuned/pdbbind_full/merges.txt +++ /dev/null @@ -1,378 +0,0 @@ -#version: 0.2 - Trained by `huggingface/tokenizers` -B r -a n -c h -Br an -Bran ch -Branch 1 -= C -R i -n g -Ri ng -Ring 1 -= Branch1 -Branch 2 -= O -Ring 2 -H 1 -C @ -= N -# Branch1 -C@ @ -= Branch2 -C@ H1 -C@@ H1 -# Branch2 -# C -C l -/ C -N H1 -= Ring1 -+ 1 -- 1 -O -1 -N +1 -\ C -# N -/ N -= Ring2 -= S -=N +1 -\ N -N a -Na +1 -/ O -\ O -Br -1 -Branch 3 -\ S -S +1 -Cl -1 -I -1 -/ C@@H1 -S i -/ C@H1 -/ S -=N -1 -S e -= P -N -1 -Ring 3 -2 H -P +1 -K +1 -\ C@@H1 -\ C@H1 -/ N+1 -@ @ -C -1 -# N+1 -B -1 -+ 3 -Cl +3 -\ NH1 -L i -Li +1 -P H1 -1 8 -18 F -@ +1 -3 H -P @@ -H 0 -O H0 -1 2 -P @ -+ 2 -@@ +1 -S -1 -/ Br -- / -\ Cl --/ Ring2 -\ O-1 -1 1 -5 I -12 5I -11 C -H 3 -\ N+1 -- \ -/ C@@ -S @+1 -A s -/ Cl -11C H3 -=S e -S @@+1 -N @+1 -1 4 --\ Ring2 -14 C -\ F -/ C@ -T e -H 2 -H1 -1 -=O +1 -N @@+1 -C +1 -=S +1 -Z n -/ P -a +2 -/ I -O H1-1 -C a+2 -\ Br -M g -Zn +2 -A l -/ F -Mg +2 -12 3 -123 I -1 3 -I +1 -/ O-1 --\ Ring1 -B H2 -BH2 -1 -\ I -/ NH1 -O +1 -13 1 -131 I -= 14C -/ S+1 -= Ring3 -\ C@@ -H2 +1 -\ C@ -A g -= As -=Se +1 -N H2+1 -Se H1 --/ Ring1 -= Te -Al +3 -Na H1 -=Te +1 -NH1 +1 -Ag +1 -H1 +1 -NH1 -1 -\ P -14C H2 -13 C -14C H1 -= 11C -S @@ -=P @@ -Si H2 -H3 -1 -14C H3 -B H3-1 -S @ -=14C H1 -=P H1 -=P @ -=N H1+1 -\S +1 -12 4 -C H1-1 -S r -=S i -124 I -Sr +2 -#C -1 -/C -1 -N @ -/N -1 -13C H1 -/ B -1 9 -B a+2 -H 4 -S H1+1 -Se +1 -19 F -/ 125I -P @+1 -R b -Cl +1 -Si H4 -Rb +1 -= Branch3 -N @@ -As +1 -/ Si -B H1-1 -S H1 -/ 123I -3 2 -= Mg -H +1 -\ B -Si H1 -P@@ +1 -- 2 -1 5 -1 7 -3 5 -= 13CH1 -C s -=N H2+1 -=S H1 -Mg H2 -32 P -17 F -35 S -Cs +1 -# 11C -/ 131I -B i -\ 125I -=S @@ -\S -1 -6 Br -7 I -7 6Br -= B -e H1 -\N -1 -18 O -12 7I -11C H2 -14 C@@H1 -Te H2 -15 NH1 -Bi +3 -/ P+1 -/ 13C -/ 13CH1 -0 B -1 0B -= Al -= 18O -B H0 -F -1 -N H3 -S -2 -Br +2 -Cl +2 -\S i -/S -1 -=P H2 -14 C@H1 -NH3 +1 -# 14C -# O+1 -- 3 -2 2 -4 H -5 Se -5 Sr+2 -7 5Se -8 5Sr+2 -= B-1 -= 13C -@ -1 -B e -B @@ -B @-1 -C a -C H1 -I +3 -K H1 -O H1+1 -R a+2 -S H1-1 -\ PH1 -\ 123I -=C a -\C H1-1 -=S @ -\S eH1 -/S eH1 -Se -1 -Li H1 -18F -1 -125I H1 -11C H1 -Te H1 -Zn +1 -Zn -2 -Al -3 -13C H3 -15 N -Be +2 -B@@ -1 -# P -# S -- 4 -/ PH1 -/ P@@ -/ As -/ 14C -/ 14CH1 -2 K+1 -2 Rb+1 -3 Se -3 Ra+2 -4 5 -4 7 -4 2K+1 -5 I-1 -7 3Se -8 9 -8 2Rb+1 -= 32 -= 32P -C H0 -C H2 -I +2 -N H0 -N H4 -O H1 -P H2+1 -S H0 -S H2 -\ 3H -\ 11CH3 -\C -1 -\S e -Si @ -Si -1 -Si H1-1 -Si H3-1 -/S e -Se -2 -\NH1 -1 -18F H1 -12 5I-1 -11 C@@H1 -11 C-1 -As H1 -As -1 -14 C@@ -Te -1 -Mg +1 -123 I-1 -123 Te -123I H1 -13 5I -131 I-1 -Ag -4 -124 I-1 -76Br H1 -18O H1 -22 Na+1 -22 3Ra+2 -Ca H2 -45 Ca+2 -47 Ca+2 -89 Sr+2 -=32 PH1 -NH4 +1 diff --git a/models/finetuned/pdbbind_full/model.pt b/models/finetuned/pdbbind_full/model.pt deleted file mode 100644 index 102758e7a8d32d3985000cd9969676e9d113b026..0000000000000000000000000000000000000000 --- a/models/finetuned/pdbbind_full/model.pt +++ /dev/null @@ -1,3 +0,0 @@ -version https://git-lfs.github.com/spec/v1 -oid sha256:8b8dedbde23c4e767ffd787e61ccb7516e88bdd94c2071c2bb06be3f09a83125 -size 1022843005 diff --git a/models/finetuned/pdbbind_full/special_tokens_map.json b/models/finetuned/pdbbind_full/special_tokens_map.json deleted file mode 100644 index 06a55849fa69a91e7179d909e373179ff7467d8c..0000000000000000000000000000000000000000 --- a/models/finetuned/pdbbind_full/special_tokens_map.json +++ /dev/null @@ -1,51 +0,0 @@ -{ - "bos_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "cls_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "eos_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "mask_token": { - "content": "", - "lstrip": true, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "pad_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "sep_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "unk_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - } -} diff --git a/models/finetuned/pdbbind_full/tokenizer.json b/models/finetuned/pdbbind_full/tokenizer.json deleted file mode 100644 index 3b64b273e6fa9799e2d8375722b9e815de9ebb8f..0000000000000000000000000000000000000000 --- a/models/finetuned/pdbbind_full/tokenizer.json +++ /dev/null @@ -1,909 +0,0 @@ -{ - "version": "1.0", - "truncation": { - "direction": "Right", - "max_length": 128, - "strategy": "LongestFirst", - "stride": 0 - }, - "padding": { - "strategy": { - "Fixed": 128 - }, - "direction": "Right", - "pad_to_multiple_of": null, - "pad_id": 3, - "pad_type_id": 0, - "pad_token": "" - }, - "added_tokens": [ - { - "id": 0, - "content": "", - "single_word": false, - "lstrip": false, - "rstrip": false, - "normalized": true, - "special": true - }, - { - "id": 1, - "content": "", - "single_word": false, - "lstrip": false, - "rstrip": false, - "normalized": true, - "special": true - }, - { - "id": 2, - "content": "", - "single_word": false, - "lstrip": false, - "rstrip": false, - "normalized": true, - "special": true - }, - { - "id": 3, - "content": "", - "single_word": false, - "lstrip": false, - "rstrip": false, - "normalized": true, - "special": true - }, - { - "id": 4, - "content": "", - "single_word": false, - "lstrip": true, - "rstrip": false, - "normalized": true, - "special": true - } - ], - "normalizer": null, - "pre_tokenizer": { - "type": "ByteLevel", - "add_prefix_space": false, - "trim_offsets": true, - "use_regex": true - }, - "post_processor": { - "type": "RobertaProcessing", - "sep": [ - "", - 2 - ], - "cls": [ - "", - 1 - ], - "trim_offsets": true, - "add_prefix_space": false - }, - "decoder": { - "type": "ByteLevel", - "add_prefix_space": true, - "trim_offsets": true, - "use_regex": true - }, - "model": { - "type": "BPE", - "dropout": null, - "unk_token": null, - "continuing_subword_prefix": "", - "end_of_word_suffix": "", - "fuse_unk": false, - "vocab": { - "": 0, - "": 1, - "": 2, - "": 3, - "": 4, - "\n": 5, - "#": 6, - "+": 7, - "-": 8, - ".": 9, - "/": 10, - "0": 11, - "1": 12, - "2": 13, - "3": 14, - "4": 15, - "5": 16, - "6": 17, - "7": 18, - "8": 19, - "9": 20, - "=": 21, - "@": 22, - "A": 23, - "B": 24, - "C": 25, - "F": 26, - "H": 27, - "I": 28, - "K": 29, - "L": 30, - "M": 31, - "N": 32, - "O": 33, - "P": 34, - "R": 35, - "S": 36, - "T": 37, - "Z": 38, - "\\": 39, - "a": 40, - "b": 41, - "c": 42, - "e": 43, - "g": 44, - "h": 45, - "i": 46, - "l": 47, - "n": 48, - "r": 49, - "s": 50, - "Br": 51, - "an": 52, - "ch": 53, - "Bran": 54, - "Branch": 55, - "Branch1": 56, - "=C": 57, - "Ri": 58, - "ng": 59, - "Ring": 60, - "Ring1": 61, - "=Branch1": 62, - "Branch2": 63, - "=O": 64, - "Ring2": 65, - "H1": 66, - "C@": 67, - "=N": 68, - "#Branch1": 69, - "C@@": 70, - "=Branch2": 71, - "C@H1": 72, - "C@@H1": 73, - "#Branch2": 74, - "#C": 75, - "Cl": 76, - "/C": 77, - "NH1": 78, - "=Ring1": 79, - "+1": 80, - "-1": 81, - "O-1": 82, - "N+1": 83, - "\\C": 84, - "#N": 85, - "/N": 86, - "=Ring2": 87, - "=S": 88, - "=N+1": 89, - "\\N": 90, - "Na": 91, - "Na+1": 92, - "/O": 93, - "\\O": 94, - "Br-1": 95, - "Branch3": 96, - "\\S": 97, - "S+1": 98, - "Cl-1": 99, - "I-1": 100, - "/C@@H1": 101, - "Si": 102, - "/C@H1": 103, - "/S": 104, - "=N-1": 105, - "Se": 106, - "=P": 107, - "N-1": 108, - "Ring3": 109, - "2H": 110, - "P+1": 111, - "K+1": 112, - "\\C@@H1": 113, - "\\C@H1": 114, - "/N+1": 115, - "@@": 116, - "C-1": 117, - "#N+1": 118, - "B-1": 119, - "+3": 120, - "Cl+3": 121, - "\\NH1": 122, - "Li": 123, - "Li+1": 124, - "PH1": 125, - "18": 126, - "18F": 127, - "@+1": 128, - "3H": 129, - "P@@": 130, - "H0": 131, - "OH0": 132, - "12": 133, - "P@": 134, - "+2": 135, - "@@+1": 136, - "S-1": 137, - "/Br": 138, - "-/": 139, - "\\Cl": 140, - "-/Ring2": 141, - "\\O-1": 142, - "11": 143, - "5I": 144, - "125I": 145, - "11C": 146, - "H3": 147, - "\\N+1": 148, - "-\\": 149, - "/C@@": 150, - "S@+1": 151, - "As": 152, - "/Cl": 153, - "11CH3": 154, - "=Se": 155, - "S@@+1": 156, - "N@+1": 157, - "14": 158, - "-\\Ring2": 159, - "14C": 160, - "\\F": 161, - "/C@": 162, - "Te": 163, - "H2": 164, - "H1-1": 165, - "=O+1": 166, - "N@@+1": 167, - "C+1": 168, - "=S+1": 169, - "Zn": 170, - "/P": 171, - "a+2": 172, - "/I": 173, - "OH1-1": 174, - "Ca+2": 175, - "\\Br": 176, - "Mg": 177, - "Zn+2": 178, - "Al": 179, - "/F": 180, - "Mg+2": 181, - "123": 182, - "123I": 183, - "13": 184, - "I+1": 185, - "/O-1": 186, - "-\\Ring1": 187, - "BH2": 188, - "BH2-1": 189, - "\\I": 190, - "/NH1": 191, - "O+1": 192, - "131": 193, - "131I": 194, - "=14C": 195, - "/S+1": 196, - "=Ring3": 197, - "\\C@@": 198, - "H2+1": 199, - "\\C@": 200, - "Ag": 201, - "=As": 202, - "=Se+1": 203, - "NH2+1": 204, - "SeH1": 205, - "-/Ring1": 206, - "=Te": 207, - "Al+3": 208, - "NaH1": 209, - "=Te+1": 210, - "NH1+1": 211, - "Ag+1": 212, - "H1+1": 213, - "NH1-1": 214, - "\\P": 215, - "14CH2": 216, - "13C": 217, - "14CH1": 218, - "=11C": 219, - "S@@": 220, - "=P@@": 221, - "SiH2": 222, - "H3-1": 223, - "14CH3": 224, - "BH3-1": 225, - "S@": 226, - "=14CH1": 227, - "=PH1": 228, - "=P@": 229, - "=NH1+1": 230, - "\\S+1": 231, - "124": 232, - "CH1-1": 233, - "Sr": 234, - "=Si": 235, - "124I": 236, - "Sr+2": 237, - "#C-1": 238, - "/C-1": 239, - "N@": 240, - "/N-1": 241, - "13CH1": 242, - "/B": 243, - "19": 244, - "Ba+2": 245, - "H4": 246, - "SH1+1": 247, - "Se+1": 248, - "19F": 249, - "/125I": 250, - "P@+1": 251, - "Rb": 252, - "Cl+1": 253, - "SiH4": 254, - "Rb+1": 255, - "=Branch3": 256, - "N@@": 257, - "As+1": 258, - "/Si": 259, - "BH1-1": 260, - "SH1": 261, - "/123I": 262, - "32": 263, - "=Mg": 264, - "H+1": 265, - "\\B": 266, - "SiH1": 267, - "P@@+1": 268, - "-2": 269, - "15": 270, - "17": 271, - "35": 272, - "=13CH1": 273, - "Cs": 274, - "=NH2+1": 275, - "=SH1": 276, - "MgH2": 277, - "32P": 278, - "17F": 279, - "35S": 280, - "Cs+1": 281, - "#11C": 282, - "/131I": 283, - "Bi": 284, - "\\125I": 285, - "=S@@": 286, - "\\S-1": 287, - "6Br": 288, - "7I": 289, - "76Br": 290, - "=B": 291, - "eH1": 292, - "\\N-1": 293, - "18O": 294, - "127I": 295, - "11CH2": 296, - "14C@@H1": 297, - "TeH2": 298, - "15NH1": 299, - "Bi+3": 300, - "/P+1": 301, - "/13C": 302, - "/13CH1": 303, - "0B": 304, - "10B": 305, - "=Al": 306, - "=18O": 307, - "BH0": 308, - "F-1": 309, - "NH3": 310, - "S-2": 311, - "Br+2": 312, - "Cl+2": 313, - "\\Si": 314, - "/S-1": 315, - "=PH2": 316, - "14C@H1": 317, - "NH3+1": 318, - "#14C": 319, - "#O+1": 320, - "-3": 321, - "22": 322, - "4H": 323, - "5Se": 324, - "5Sr+2": 325, - "75Se": 326, - "85Sr+2": 327, - "=B-1": 328, - "=13C": 329, - "@-1": 330, - "Be": 331, - "B@@": 332, - "B@-1": 333, - "Ca": 334, - "CH1": 335, - "I+3": 336, - "KH1": 337, - "OH1+1": 338, - "Ra+2": 339, - "SH1-1": 340, - "\\PH1": 341, - "\\123I": 342, - "=Ca": 343, - "\\CH1-1": 344, - "=S@": 345, - "\\SeH1": 346, - "/SeH1": 347, - "Se-1": 348, - "LiH1": 349, - "18F-1": 350, - "125IH1": 351, - "11CH1": 352, - "TeH1": 353, - "Zn+1": 354, - "Zn-2": 355, - "Al-3": 356, - "13CH3": 357, - "15N": 358, - "Be+2": 359, - "B@@-1": 360, - "#P": 361, - "#S": 362, - "-4": 363, - "/PH1": 364, - "/P@@": 365, - "/As": 366, - "/14C": 367, - "/14CH1": 368, - "2K+1": 369, - "2Rb+1": 370, - "3Se": 371, - "3Ra+2": 372, - "45": 373, - "47": 374, - "42K+1": 375, - "5I-1": 376, - "73Se": 377, - "89": 378, - "82Rb+1": 379, - "=32": 380, - "=32P": 381, - "CH0": 382, - "CH2": 383, - "I+2": 384, - "NH0": 385, - "NH4": 386, - "OH1": 387, - "PH2+1": 388, - "SH0": 389, - "SH2": 390, - "\\3H": 391, - "\\11CH3": 392, - "\\C-1": 393, - "\\Se": 394, - "Si@": 395, - "Si-1": 396, - "SiH1-1": 397, - "SiH3-1": 398, - "/Se": 399, - "Se-2": 400, - "\\NH1-1": 401, - "18FH1": 402, - "125I-1": 403, - "11C@@H1": 404, - "11C-1": 405, - "AsH1": 406, - "As-1": 407, - "14C@@": 408, - "Te-1": 409, - "Mg+1": 410, - "123I-1": 411, - "123Te": 412, - "123IH1": 413, - "135I": 414, - "131I-1": 415, - "Ag-4": 416, - "124I-1": 417, - "76BrH1": 418, - "18OH1": 419, - "22Na+1": 420, - "223Ra+2": 421, - "CaH2": 422, - "45Ca+2": 423, - "47Ca+2": 424, - "89Sr+2": 425, - "=32PH1": 426, - "NH4+1": 427 - }, - "merges": [ - "B r", - "a n", - "c h", - "Br an", - "Bran ch", - "Branch 1", - "= C", - "R i", - "n g", - "Ri ng", - "Ring 1", - "= Branch1", - "Branch 2", - "= O", - "Ring 2", - "H 1", - "C @", - "= N", - "# Branch1", - "C@ @", - "= Branch2", - "C@ H1", - "C@@ H1", - "# Branch2", - "# C", - "C l", - "/ C", - "N H1", - "= Ring1", - "+ 1", - "- 1", - "O -1", - "N +1", - "\\ C", - "# N", - "/ N", - "= Ring2", - "= S", - "=N +1", - "\\ N", - "N a", - "Na +1", - "/ O", - "\\ O", - "Br -1", - "Branch 3", - "\\ S", - "S +1", - "Cl -1", - "I -1", - "/ C@@H1", - "S i", - "/ C@H1", - "/ S", - "=N -1", - "S e", - "= P", - "N -1", - "Ring 3", - "2 H", - "P +1", - "K +1", - "\\ C@@H1", - "\\ C@H1", - "/ N+1", - "@ @", - "C -1", - "# N+1", - "B -1", - "+ 3", - "Cl +3", - "\\ NH1", - "L i", - "Li +1", - "P H1", - "1 8", - "18 F", - "@ +1", - "3 H", - "P @@", - "H 0", - "O H0", - "1 2", - "P @", - "+ 2", - "@@ +1", - "S -1", - "/ Br", - "- /", - "\\ Cl", - "-/ Ring2", - "\\ O-1", - "1 1", - "5 I", - "12 5I", - "11 C", - "H 3", - "\\ N+1", - "- \\", - "/ C@@", - "S @+1", - "A s", - "/ Cl", - "11C H3", - "=S e", - "S @@+1", - "N @+1", - "1 4", - "-\\ Ring2", - "14 C", - "\\ F", - "/ C@", - "T e", - "H 2", - "H1 -1", - "=O +1", - "N @@+1", - "C +1", - "=S +1", - "Z n", - "/ P", - "a +2", - "/ I", - "O H1-1", - "C a+2", - "\\ Br", - "M g", - "Zn +2", - "A l", - "/ F", - "Mg +2", - "12 3", - "123 I", - "1 3", - "I +1", - "/ O-1", - "-\\ Ring1", - "B H2", - "BH2 -1", - "\\ I", - "/ NH1", - "O +1", - "13 1", - "131 I", - "= 14C", - "/ S+1", - "= Ring3", - "\\ C@@", - "H2 +1", - "\\ C@", - "A g", - "= As", - "=Se +1", - "N H2+1", - "Se H1", - "-/ Ring1", - "= Te", - "Al +3", - "Na H1", - "=Te +1", - "NH1 +1", - "Ag +1", - "H1 +1", - "NH1 -1", - "\\ P", - "14C H2", - "13 C", - "14C H1", - "= 11C", - "S @@", - "=P @@", - "Si H2", - "H3 -1", - "14C H3", - "B H3-1", - "S @", - "=14C H1", - "=P H1", - "=P @", - "=N H1+1", - "\\S +1", - "12 4", - "C H1-1", - "S r", - "=S i", - "124 I", - "Sr +2", - "#C -1", - "/C -1", - "N @", - "/N -1", - "13C H1", - "/ B", - "1 9", - "B a+2", - "H 4", - "S H1+1", - "Se +1", - "19 F", - "/ 125I", - "P @+1", - "R b", - "Cl +1", - "Si H4", - "Rb +1", - "= Branch3", - "N @@", - "As +1", - "/ Si", - "B H1-1", - "S H1", - "/ 123I", - "3 2", - "= Mg", - "H +1", - "\\ B", - "Si H1", - "P@@ +1", - "- 2", - "1 5", - "1 7", - "3 5", - "= 13CH1", - "C s", - "=N H2+1", - "=S H1", - "Mg H2", - "32 P", - "17 F", - "35 S", - "Cs +1", - "# 11C", - "/ 131I", - "B i", - "\\ 125I", - "=S @@", - "\\S -1", - "6 Br", - "7 I", - "7 6Br", - "= B", - "e H1", - "\\N -1", - "18 O", - "12 7I", - "11C H2", - "14 C@@H1", - "Te H2", - "15 NH1", - "Bi +3", - "/ P+1", - "/ 13C", - "/ 13CH1", - "0 B", - "1 0B", - "= Al", - "= 18O", - "B H0", - "F -1", - "N H3", - "S -2", - "Br +2", - "Cl +2", - "\\S i", - "/S -1", - "=P H2", - "14 C@H1", - "NH3 +1", - "# 14C", - "# O+1", - "- 3", - "2 2", - "4 H", - "5 Se", - "5 Sr+2", - "7 5Se", - "8 5Sr+2", - "= B-1", - "= 13C", - "@ -1", - "B e", - "B @@", - "B @-1", - "C a", - "C H1", - "I +3", - "K H1", - "O H1+1", - "R a+2", - "S H1-1", - "\\ PH1", - "\\ 123I", - "=C a", - "\\C H1-1", - "=S @", - "\\S eH1", - "/S eH1", - "Se -1", - "Li H1", - "18F -1", - "125I H1", - "11C H1", - "Te H1", - "Zn +1", - "Zn -2", - "Al -3", - "13C H3", - "15 N", - "Be +2", - "B@@ -1", - "# P", - "# S", - "- 4", - "/ PH1", - "/ P@@", - "/ As", - "/ 14C", - "/ 14CH1", - "2 K+1", - "2 Rb+1", - "3 Se", - "3 Ra+2", - "4 5", - "4 7", - "4 2K+1", - "5 I-1", - "7 3Se", - "8 9", - "8 2Rb+1", - "= 32", - "= 32P", - "C H0", - "C H2", - "I +2", - "N H0", - "N H4", - "O H1", - "P H2+1", - "S H0", - "S H2", - "\\ 3H", - "\\ 11CH3", - "\\C -1", - "\\S e", - "Si @", - "Si -1", - "Si H1-1", - "Si H3-1", - "/S e", - "Se -2", - "\\NH1 -1", - "18F H1", - "12 5I-1", - "11 C@@H1", - "11 C-1", - "As H1", - "As -1", - "14 C@@", - "Te -1", - "Mg +1", - "123 I-1", - "123 Te", - "123I H1", - "13 5I", - "131 I-1", - "Ag -4", - "124 I-1", - "76Br H1", - "18O H1", - "22 Na+1", - "22 3Ra+2", - "Ca H2", - "45 Ca+2", - "47 Ca+2", - "89 Sr+2", - "=32 PH1", - "NH4 +1" - ] - } -} \ No newline at end of file diff --git a/models/finetuned/pdbbind_full/tokenizer_config.json b/models/finetuned/pdbbind_full/tokenizer_config.json deleted file mode 100644 index 08860954acd34fad07fd77f7635298fa565f3149..0000000000000000000000000000000000000000 --- a/models/finetuned/pdbbind_full/tokenizer_config.json +++ /dev/null @@ -1,65 +0,0 @@ -{ - "add_prefix_space": false, - "bos_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "cls_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "eos_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "errors": "replace", - "mask_token": { - "__type": "AddedToken", - "content": "", - "lstrip": true, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "model_max_length": 1000000000000000019884624838656, - "name_or_path": "/home/erva/SELFormerMM/data/pretrained_multimodal_chembl36", - "pad_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "sep_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "special_tokens_map_file": null, - "tokenizer_class": "RobertaTokenizer", - "trim_offsets": true, - "unk_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - } -} diff --git a/models/finetuned/pdbbind_full/train_stdout.log b/models/finetuned/pdbbind_full/train_stdout.log deleted file mode 100644 index 311f4ebdcdfc122bcb5a7fd77c685c4193f4a7b6..0000000000000000000000000000000000000000 --- a/models/finetuned/pdbbind_full/train_stdout.log +++ /dev/null @@ -1,84 +0,0 @@ -[finetune] starting -[finetune] device=cuda task_type=regression batch_size=32 max_len=128 backbone_lr=1e-05 head_lr=1e-06 weight_decay=0.001 epochs=50 -[finetune] dataset_meta_csv=/home/erva/SELFormerMM/data/new_finetuning_datasets/regression/pdbbind_full/pdbbind_full.csv -[finetune] dataset_embs_npz=/home/erva/SELFormerMM/data/new_finetuning_datasets/regression/pdbbind_full/pdbbind_full_embs.npz -[finetune] model_path=HUBioDataLab/SELFormer tokenizer_path=HUBioDataLab/SELFormer -[finetune] pretrained_multimodal_dir=/home/erva/SELFormerMM/data/pretrained_multimodal_chembl36 -[finetune] use_scaffold=False seed=42 fracs=(0.8,0.1,0.1) -[finetune] loading dataset bundle (meta csv + embs npz) ... -[finetune] splitting dataset... -[finetune] split sizes: train=7,904 val=988 test=988 -[finetune] train modality_non_empty: graph=7,897/7,904 text=1,871/7,904 kg=388/7,904 -[finetune] val modality_non_empty: graph=988/988 text=231/988 kg=57/988 -[finetune] test modality_non_empty: graph=986/988 text=236/988 kg=45/988 -[finetune] extracting labels... -[finetune] loading config/tokenizer/backbone... -[finetune] initializing multimodal model... -[finetune] loading multimodal pretrained weights: /home/erva/SELFormerMM/data/pretrained_multimodal_chembl36/pytorch_model.bin -[finetune] freezing roberta layers (trainable: encoder.layer.9-11)... -[finetune] backbone trainable params: 181,443,072/246,245,376 -[finetune] building datasets/dataloaders... -[finetune] train_steps_per_epoch=247 val_steps=31 test_steps=31 -[finetune] initialized head: in_dim=3072 out=1 -[finetune] initializing optimizer/scheduler/finetuner... -[finetune] optimizer groups: backbone_decay=45 backbone_nodecay=57 head_decay=2 head_nodecay=2 -[finetune] training loop... -[finetune] epoch 1/50: train_loss=5.5868 val_loss=2.2110 time=37.0s tod=10:21 -[finetune] epoch 2/50: train_loss=1.9830 val_loss=2.1185 time=36.5s tod=10:21 -[finetune] epoch 3/50: train_loss=1.8369 val_loss=1.9493 time=36.5s tod=10:22 -[finetune] epoch 4/50: train_loss=1.6677 val_loss=1.8721 time=36.5s tod=10:22 -[finetune] epoch 5/50: train_loss=1.5533 val_loss=1.9191 time=36.4s tod=10:23 -[finetune] epoch 6/50: train_loss=1.4599 val_loss=1.8973 time=36.5s tod=10:24 -[finetune] epoch 7/50: train_loss=1.3654 val_loss=1.8004 time=36.2s tod=10:24 -[finetune] epoch 8/50: train_loss=1.2898 val_loss=1.7818 time=36.5s tod=10:25 -[finetune] epoch 9/50: train_loss=1.2106 val_loss=1.9329 time=36.5s tod=10:25 -[finetune] epoch 10/50: train_loss=1.1396 val_loss=1.8307 time=36.5s tod=10:26 -[finetune] epoch 11/50: train_loss=1.0760 val_loss=1.8189 time=36.7s tod=10:27 -[finetune] epoch 12/50: train_loss=1.0274 val_loss=1.9702 time=36.3s tod=10:27 -[finetune] epoch 13/50: train_loss=0.9712 val_loss=1.7947 time=36.6s tod=10:28 -[finetune] epoch 14/50: train_loss=0.9133 val_loss=1.7824 time=36.5s tod=10:29 -[finetune] epoch 15/50: train_loss=0.8634 val_loss=1.8319 time=36.2s tod=10:29 -[finetune] epoch 16/50: train_loss=0.8148 val_loss=1.9180 time=36.5s tod=10:30 -[finetune] epoch 17/50: train_loss=0.7857 val_loss=1.9476 time=36.5s tod=10:30 -[finetune] epoch 18/50: train_loss=0.7387 val_loss=1.8473 time=36.6s tod=10:31 -[finetune] epoch 19/50: train_loss=0.6946 val_loss=1.8302 time=36.6s tod=10:32 -[finetune] epoch 20/50: train_loss=0.6552 val_loss=1.8975 time=36.6s tod=10:32 -[finetune] epoch 21/50: train_loss=0.6345 val_loss=1.8368 time=36.4s tod=10:33 -[finetune] epoch 22/50: train_loss=0.6189 val_loss=1.9089 time=36.4s tod=10:33 -[finetune] epoch 23/50: train_loss=0.5669 val_loss=1.9858 time=36.5s tod=10:34 -[finetune] epoch 24/50: train_loss=0.5540 val_loss=1.9184 time=36.4s tod=10:35 -[finetune] epoch 25/50: train_loss=0.5332 val_loss=1.8838 time=36.6s tod=10:35 -[finetune] test_metrics: epoch=25 loss=1.7602 mse=1.7634 rmse=1.3279 mae=1.0330 -[finetune] saved checkpoint (best rmse=1.3279): /media/ubuntu/8TB/erva/selformer-mm/output/new_finetune_sweeps/pdbbind_full/ntqfan0j/checkpoint_epoch_025 -[finetune] epoch 26/50: train_loss=0.5093 val_loss=1.8506 time=36.6s tod=10:36 -[finetune] epoch 27/50: train_loss=0.4882 val_loss=1.8703 time=36.6s tod=10:37 -[finetune] epoch 28/50: train_loss=0.4750 val_loss=1.9481 time=36.7s tod=10:37 -[finetune] epoch 29/50: train_loss=0.4604 val_loss=1.9254 time=36.3s tod=10:38 -[finetune] epoch 30/50: train_loss=0.4280 val_loss=1.9441 time=36.4s tod=10:38 -[finetune] epoch 31/50: train_loss=0.4231 val_loss=1.9181 time=36.6s tod=10:39 -[finetune] epoch 32/50: train_loss=0.4140 val_loss=1.9401 time=36.6s tod=10:40 -[finetune] epoch 33/50: train_loss=0.3994 val_loss=1.8978 time=36.4s tod=10:40 -[finetune] epoch 34/50: train_loss=0.3918 val_loss=2.0566 time=36.4s tod=10:41 -[finetune] epoch 35/50: train_loss=0.3855 val_loss=1.9523 time=36.4s tod=10:41 -[finetune] epoch 36/50: train_loss=0.3770 val_loss=1.9759 time=36.6s tod=10:42 -[finetune] epoch 37/50: train_loss=0.3655 val_loss=1.9533 time=36.5s tod=10:43 -[finetune] epoch 38/50: train_loss=0.3534 val_loss=1.9834 time=36.6s tod=10:43 -[finetune] epoch 39/50: train_loss=0.3458 val_loss=2.0582 time=36.7s tod=10:44 -[finetune] epoch 40/50: train_loss=0.3442 val_loss=1.9665 time=36.6s tod=10:44 -[finetune] epoch 41/50: train_loss=0.3312 val_loss=1.9377 time=36.5s tod=10:45 -[finetune] epoch 42/50: train_loss=0.3235 val_loss=1.9249 time=36.7s tod=10:46 -[finetune] epoch 43/50: train_loss=0.3167 val_loss=1.9429 time=36.5s tod=10:46 -[finetune] epoch 44/50: train_loss=0.3108 val_loss=1.9271 time=36.5s tod=10:47 -[finetune] epoch 45/50: train_loss=0.3076 val_loss=1.9263 time=36.5s tod=10:47 -[finetune] epoch 46/50: train_loss=0.2961 val_loss=1.9143 time=36.6s tod=10:48 -[finetune] epoch 47/50: train_loss=0.2949 val_loss=1.9215 time=36.5s tod=10:49 -[finetune] epoch 48/50: train_loss=0.2856 val_loss=1.9664 time=36.5s tod=10:49 -[finetune] epoch 49/50: train_loss=0.2852 val_loss=1.9501 time=36.3s tod=10:50 -[finetune] epoch 50/50: train_loss=0.2774 val_loss=1.9502 time=36.4s tod=10:51 -[finetune] test_metrics: epoch=50 loss=1.8280 mse=1.8309 rmse=1.3531 mae=1.0394 -[finetune] checkpoint skipped (current rmse=1.3531 vs best=1.3279 at epoch 25) -[finetune] final evaluation on test split... -[finetune] test_metrics: loss=1.8280 mse=1.8309 rmse=1.3531 mae=1.0394 -[finetune] saving model... -[finetune] saved finetuned model to: /media/ubuntu/8TB/erva/selformer-mm/output/new_finetune_sweeps/pdbbind_full/ntqfan0j -[finetune] done in 1839.9s diff --git a/models/finetuned/pdbbind_full/vocab.json b/models/finetuned/pdbbind_full/vocab.json deleted file mode 100644 index f7e4cc22809f4e9035cc450ef189c8a7da8fd03e..0000000000000000000000000000000000000000 --- a/models/finetuned/pdbbind_full/vocab.json +++ /dev/null @@ -1 +0,0 @@ -{"":0,"":1,"":2,"":3,"":4,"\n":5,"#":6,"+":7,"-":8,".":9,"/":10,"0":11,"1":12,"2":13,"3":14,"4":15,"5":16,"6":17,"7":18,"8":19,"9":20,"=":21,"@":22,"A":23,"B":24,"C":25,"F":26,"H":27,"I":28,"K":29,"L":30,"M":31,"N":32,"O":33,"P":34,"R":35,"S":36,"T":37,"Z":38,"\\":39,"a":40,"b":41,"c":42,"e":43,"g":44,"h":45,"i":46,"l":47,"n":48,"r":49,"s":50,"Br":51,"an":52,"ch":53,"Bran":54,"Branch":55,"Branch1":56,"=C":57,"Ri":58,"ng":59,"Ring":60,"Ring1":61,"=Branch1":62,"Branch2":63,"=O":64,"Ring2":65,"H1":66,"C@":67,"=N":68,"#Branch1":69,"C@@":70,"=Branch2":71,"C@H1":72,"C@@H1":73,"#Branch2":74,"#C":75,"Cl":76,"/C":77,"NH1":78,"=Ring1":79,"+1":80,"-1":81,"O-1":82,"N+1":83,"\\C":84,"#N":85,"/N":86,"=Ring2":87,"=S":88,"=N+1":89,"\\N":90,"Na":91,"Na+1":92,"/O":93,"\\O":94,"Br-1":95,"Branch3":96,"\\S":97,"S+1":98,"Cl-1":99,"I-1":100,"/C@@H1":101,"Si":102,"/C@H1":103,"/S":104,"=N-1":105,"Se":106,"=P":107,"N-1":108,"Ring3":109,"2H":110,"P+1":111,"K+1":112,"\\C@@H1":113,"\\C@H1":114,"/N+1":115,"@@":116,"C-1":117,"#N+1":118,"B-1":119,"+3":120,"Cl+3":121,"\\NH1":122,"Li":123,"Li+1":124,"PH1":125,"18":126,"18F":127,"@+1":128,"3H":129,"P@@":130,"H0":131,"OH0":132,"12":133,"P@":134,"+2":135,"@@+1":136,"S-1":137,"/Br":138,"-/":139,"\\Cl":140,"-/Ring2":141,"\\O-1":142,"11":143,"5I":144,"125I":145,"11C":146,"H3":147,"\\N+1":148,"-\\":149,"/C@@":150,"S@+1":151,"As":152,"/Cl":153,"11CH3":154,"=Se":155,"S@@+1":156,"N@+1":157,"14":158,"-\\Ring2":159,"14C":160,"\\F":161,"/C@":162,"Te":163,"H2":164,"H1-1":165,"=O+1":166,"N@@+1":167,"C+1":168,"=S+1":169,"Zn":170,"/P":171,"a+2":172,"/I":173,"OH1-1":174,"Ca+2":175,"\\Br":176,"Mg":177,"Zn+2":178,"Al":179,"/F":180,"Mg+2":181,"123":182,"123I":183,"13":184,"I+1":185,"/O-1":186,"-\\Ring1":187,"BH2":188,"BH2-1":189,"\\I":190,"/NH1":191,"O+1":192,"131":193,"131I":194,"=14C":195,"/S+1":196,"=Ring3":197,"\\C@@":198,"H2+1":199,"\\C@":200,"Ag":201,"=As":202,"=Se+1":203,"NH2+1":204,"SeH1":205,"-/Ring1":206,"=Te":207,"Al+3":208,"NaH1":209,"=Te+1":210,"NH1+1":211,"Ag+1":212,"H1+1":213,"NH1-1":214,"\\P":215,"14CH2":216,"13C":217,"14CH1":218,"=11C":219,"S@@":220,"=P@@":221,"SiH2":222,"H3-1":223,"14CH3":224,"BH3-1":225,"S@":226,"=14CH1":227,"=PH1":228,"=P@":229,"=NH1+1":230,"\\S+1":231,"124":232,"CH1-1":233,"Sr":234,"=Si":235,"124I":236,"Sr+2":237,"#C-1":238,"/C-1":239,"N@":240,"/N-1":241,"13CH1":242,"/B":243,"19":244,"Ba+2":245,"H4":246,"SH1+1":247,"Se+1":248,"19F":249,"/125I":250,"P@+1":251,"Rb":252,"Cl+1":253,"SiH4":254,"Rb+1":255,"=Branch3":256,"N@@":257,"As+1":258,"/Si":259,"BH1-1":260,"SH1":261,"/123I":262,"32":263,"=Mg":264,"H+1":265,"\\B":266,"SiH1":267,"P@@+1":268,"-2":269,"15":270,"17":271,"35":272,"=13CH1":273,"Cs":274,"=NH2+1":275,"=SH1":276,"MgH2":277,"32P":278,"17F":279,"35S":280,"Cs+1":281,"#11C":282,"/131I":283,"Bi":284,"\\125I":285,"=S@@":286,"\\S-1":287,"6Br":288,"7I":289,"76Br":290,"=B":291,"eH1":292,"\\N-1":293,"18O":294,"127I":295,"11CH2":296,"14C@@H1":297,"TeH2":298,"15NH1":299,"Bi+3":300,"/P+1":301,"/13C":302,"/13CH1":303,"0B":304,"10B":305,"=Al":306,"=18O":307,"BH0":308,"F-1":309,"NH3":310,"S-2":311,"Br+2":312,"Cl+2":313,"\\Si":314,"/S-1":315,"=PH2":316,"14C@H1":317,"NH3+1":318,"#14C":319,"#O+1":320,"-3":321,"22":322,"4H":323,"5Se":324,"5Sr+2":325,"75Se":326,"85Sr+2":327,"=B-1":328,"=13C":329,"@-1":330,"Be":331,"B@@":332,"B@-1":333,"Ca":334,"CH1":335,"I+3":336,"KH1":337,"OH1+1":338,"Ra+2":339,"SH1-1":340,"\\PH1":341,"\\123I":342,"=Ca":343,"\\CH1-1":344,"=S@":345,"\\SeH1":346,"/SeH1":347,"Se-1":348,"LiH1":349,"18F-1":350,"125IH1":351,"11CH1":352,"TeH1":353,"Zn+1":354,"Zn-2":355,"Al-3":356,"13CH3":357,"15N":358,"Be+2":359,"B@@-1":360,"#P":361,"#S":362,"-4":363,"/PH1":364,"/P@@":365,"/As":366,"/14C":367,"/14CH1":368,"2K+1":369,"2Rb+1":370,"3Se":371,"3Ra+2":372,"45":373,"47":374,"42K+1":375,"5I-1":376,"73Se":377,"89":378,"82Rb+1":379,"=32":380,"=32P":381,"CH0":382,"CH2":383,"I+2":384,"NH0":385,"NH4":386,"OH1":387,"PH2+1":388,"SH0":389,"SH2":390,"\\3H":391,"\\11CH3":392,"\\C-1":393,"\\Se":394,"Si@":395,"Si-1":396,"SiH1-1":397,"SiH3-1":398,"/Se":399,"Se-2":400,"\\NH1-1":401,"18FH1":402,"125I-1":403,"11C@@H1":404,"11C-1":405,"AsH1":406,"As-1":407,"14C@@":408,"Te-1":409,"Mg+1":410,"123I-1":411,"123Te":412,"123IH1":413,"135I":414,"131I-1":415,"Ag-4":416,"124I-1":417,"76BrH1":418,"18OH1":419,"22Na+1":420,"223Ra+2":421,"CaH2":422,"45Ca+2":423,"47Ca+2":424,"89Sr+2":425,"=32PH1":426,"NH4+1":427} \ No newline at end of file diff --git a/models/finetuned/sider/checkpoint_epoch_025/config.json b/models/finetuned/sider/checkpoint_epoch_025/config.json deleted file mode 100644 index 3811e21539577b37e06313eab31ec11e53f0cbbc..0000000000000000000000000000000000000000 --- a/models/finetuned/sider/checkpoint_epoch_025/config.json +++ /dev/null @@ -1,27 +0,0 @@ -{ - "_name_or_path": "/home/erva/SELFormerMM/data/pretrained_multimodal_chembl36", - "architectures": [ - "RobertaForMaskedLM" - ], - "attention_probs_dropout_prob": 0.1, - "bos_token_id": 0, - "classifier_dropout": null, - "eos_token_id": 2, - "hidden_act": "gelu", - "hidden_dropout_prob": 0.1, - "hidden_size": 768, - "initializer_range": 0.02, - "intermediate_size": 3072, - "layer_norm_eps": 1e-12, - "max_position_embeddings": 514, - "model_type": "roberta", - "num_attention_heads": 4, - "num_hidden_layers": 12, - "pad_token_id": 1, - "position_embedding_type": "absolute", - "torch_dtype": "float32", - "transformers_version": "4.26.1", - "type_vocab_size": 1, - "use_cache": true, - "vocab_size": 800 -} diff --git a/models/finetuned/sider/checkpoint_epoch_025/merges.txt b/models/finetuned/sider/checkpoint_epoch_025/merges.txt deleted file mode 100644 index 7cd5ec62809503c23f18c80afc0ba3bdf9d253d0..0000000000000000000000000000000000000000 --- a/models/finetuned/sider/checkpoint_epoch_025/merges.txt +++ /dev/null @@ -1,378 +0,0 @@ -#version: 0.2 - Trained by `huggingface/tokenizers` -B r -a n -c h -Br an -Bran ch -Branch 1 -= C -R i -n g -Ri ng -Ring 1 -= Branch1 -Branch 2 -= O -Ring 2 -H 1 -C @ -= N -# Branch1 -C@ @ -= Branch2 -C@ H1 -C@@ H1 -# Branch2 -# C -C l -/ C -N H1 -= Ring1 -+ 1 -- 1 -O -1 -N +1 -\ C -# N -/ N -= Ring2 -= S -=N +1 -\ N -N a -Na +1 -/ O -\ O -Br -1 -Branch 3 -\ S -S +1 -Cl -1 -I -1 -/ C@@H1 -S i -/ C@H1 -/ S -=N -1 -S e -= P -N -1 -Ring 3 -2 H -P +1 -K +1 -\ C@@H1 -\ C@H1 -/ N+1 -@ @ -C -1 -# N+1 -B -1 -+ 3 -Cl +3 -\ NH1 -L i -Li +1 -P H1 -1 8 -18 F -@ +1 -3 H -P @@ -H 0 -O H0 -1 2 -P @ -+ 2 -@@ +1 -S -1 -/ Br -- / -\ Cl --/ Ring2 -\ O-1 -1 1 -5 I -12 5I -11 C -H 3 -\ N+1 -- \ -/ C@@ -S @+1 -A s -/ Cl -11C H3 -=S e -S @@+1 -N @+1 -1 4 --\ Ring2 -14 C -\ F -/ C@ -T e -H 2 -H1 -1 -=O +1 -N @@+1 -C +1 -=S +1 -Z n -/ P -a +2 -/ I -O H1-1 -C a+2 -\ Br -M g -Zn +2 -A l -/ F -Mg +2 -12 3 -123 I -1 3 -I +1 -/ O-1 --\ Ring1 -B H2 -BH2 -1 -\ I -/ NH1 -O +1 -13 1 -131 I -= 14C -/ S+1 -= Ring3 -\ C@@ -H2 +1 -\ C@ -A g -= As -=Se +1 -N H2+1 -Se H1 --/ Ring1 -= Te -Al +3 -Na H1 -=Te +1 -NH1 +1 -Ag +1 -H1 +1 -NH1 -1 -\ P -14C H2 -13 C -14C H1 -= 11C -S @@ -=P @@ -Si H2 -H3 -1 -14C H3 -B H3-1 -S @ -=14C H1 -=P H1 -=P @ -=N H1+1 -\S +1 -12 4 -C H1-1 -S r -=S i -124 I -Sr +2 -#C -1 -/C -1 -N @ -/N -1 -13C H1 -/ B -1 9 -B a+2 -H 4 -S H1+1 -Se +1 -19 F -/ 125I -P @+1 -R b -Cl +1 -Si H4 -Rb +1 -= Branch3 -N @@ -As +1 -/ Si -B H1-1 -S H1 -/ 123I -3 2 -= Mg -H +1 -\ B -Si H1 -P@@ +1 -- 2 -1 5 -1 7 -3 5 -= 13CH1 -C s -=N H2+1 -=S H1 -Mg H2 -32 P -17 F -35 S -Cs +1 -# 11C -/ 131I -B i -\ 125I -=S @@ -\S -1 -6 Br -7 I -7 6Br -= B -e H1 -\N -1 -18 O -12 7I -11C H2 -14 C@@H1 -Te H2 -15 NH1 -Bi +3 -/ P+1 -/ 13C -/ 13CH1 -0 B -1 0B -= Al -= 18O -B H0 -F -1 -N H3 -S -2 -Br +2 -Cl +2 -\S i -/S -1 -=P H2 -14 C@H1 -NH3 +1 -# 14C -# O+1 -- 3 -2 2 -4 H -5 Se -5 Sr+2 -7 5Se -8 5Sr+2 -= B-1 -= 13C -@ -1 -B e -B @@ -B @-1 -C a -C H1 -I +3 -K H1 -O H1+1 -R a+2 -S H1-1 -\ PH1 -\ 123I -=C a -\C H1-1 -=S @ -\S eH1 -/S eH1 -Se -1 -Li H1 -18F -1 -125I H1 -11C H1 -Te H1 -Zn +1 -Zn -2 -Al -3 -13C H3 -15 N -Be +2 -B@@ -1 -# P -# S -- 4 -/ PH1 -/ P@@ -/ As -/ 14C -/ 14CH1 -2 K+1 -2 Rb+1 -3 Se -3 Ra+2 -4 5 -4 7 -4 2K+1 -5 I-1 -7 3Se -8 9 -8 2Rb+1 -= 32 -= 32P -C H0 -C H2 -I +2 -N H0 -N H4 -O H1 -P H2+1 -S H0 -S H2 -\ 3H -\ 11CH3 -\C -1 -\S e -Si @ -Si -1 -Si H1-1 -Si H3-1 -/S e -Se -2 -\NH1 -1 -18F H1 -12 5I-1 -11 C@@H1 -11 C-1 -As H1 -As -1 -14 C@@ -Te -1 -Mg +1 -123 I-1 -123 Te -123I H1 -13 5I -131 I-1 -Ag -4 -124 I-1 -76Br H1 -18O H1 -22 Na+1 -22 3Ra+2 -Ca H2 -45 Ca+2 -47 Ca+2 -89 Sr+2 -=32 PH1 -NH4 +1 diff --git a/models/finetuned/sider/checkpoint_epoch_025/model.pt b/models/finetuned/sider/checkpoint_epoch_025/model.pt deleted file mode 100644 index 313881dbf9033030494b20f9d155e81d369caf12..0000000000000000000000000000000000000000 --- a/models/finetuned/sider/checkpoint_epoch_025/model.pt +++ /dev/null @@ -1,3 +0,0 @@ -version https://git-lfs.github.com/spec/v1 -oid sha256:498223ce5998e46369288fb8d43fa745e771265e4d285cd6975b3cd6263f4371 -size 1023174845 diff --git a/models/finetuned/sider/checkpoint_epoch_025/special_tokens_map.json b/models/finetuned/sider/checkpoint_epoch_025/special_tokens_map.json deleted file mode 100644 index 06a55849fa69a91e7179d909e373179ff7467d8c..0000000000000000000000000000000000000000 --- a/models/finetuned/sider/checkpoint_epoch_025/special_tokens_map.json +++ /dev/null @@ -1,51 +0,0 @@ -{ - "bos_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "cls_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "eos_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "mask_token": { - "content": "", - "lstrip": true, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "pad_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "sep_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "unk_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - } -} diff --git a/models/finetuned/sider/checkpoint_epoch_025/tokenizer.json b/models/finetuned/sider/checkpoint_epoch_025/tokenizer.json deleted file mode 100644 index 3b64b273e6fa9799e2d8375722b9e815de9ebb8f..0000000000000000000000000000000000000000 --- a/models/finetuned/sider/checkpoint_epoch_025/tokenizer.json +++ /dev/null @@ -1,909 +0,0 @@ -{ - "version": "1.0", - "truncation": { - "direction": "Right", - "max_length": 128, - "strategy": "LongestFirst", - "stride": 0 - }, - "padding": { - "strategy": { - "Fixed": 128 - }, - "direction": "Right", - "pad_to_multiple_of": null, - "pad_id": 3, - "pad_type_id": 0, - "pad_token": "" - }, - "added_tokens": [ - { - "id": 0, - "content": "", - "single_word": false, - "lstrip": false, - "rstrip": false, - "normalized": true, - "special": true - }, - { - "id": 1, - "content": "", - "single_word": false, - "lstrip": false, - "rstrip": false, - "normalized": true, - "special": true - }, - { - "id": 2, - "content": "", - "single_word": false, - "lstrip": false, - "rstrip": false, - "normalized": true, - "special": true - }, - { - "id": 3, - "content": "", - "single_word": false, - "lstrip": false, - "rstrip": false, - "normalized": true, - "special": true - }, - { - "id": 4, - "content": "", - "single_word": false, - "lstrip": true, - "rstrip": false, - "normalized": true, - "special": true - } - ], - "normalizer": null, - "pre_tokenizer": { - "type": "ByteLevel", - "add_prefix_space": false, - "trim_offsets": true, - "use_regex": true - }, - "post_processor": { - "type": "RobertaProcessing", - "sep": [ - "", - 2 - ], - "cls": [ - "", - 1 - ], - "trim_offsets": true, - "add_prefix_space": false - }, - "decoder": { - "type": "ByteLevel", - "add_prefix_space": true, - "trim_offsets": true, - "use_regex": true - }, - "model": { - "type": "BPE", - "dropout": null, - "unk_token": null, - "continuing_subword_prefix": "", - "end_of_word_suffix": "", - "fuse_unk": false, - "vocab": { - "": 0, - "": 1, - "": 2, - "": 3, - "": 4, - "\n": 5, - "#": 6, - "+": 7, - "-": 8, - ".": 9, - "/": 10, - "0": 11, - "1": 12, - "2": 13, - "3": 14, - "4": 15, - "5": 16, - "6": 17, - "7": 18, - "8": 19, - "9": 20, - "=": 21, - "@": 22, - "A": 23, - "B": 24, - "C": 25, - "F": 26, - "H": 27, - "I": 28, - "K": 29, - "L": 30, - "M": 31, - "N": 32, - "O": 33, - "P": 34, - "R": 35, - "S": 36, - "T": 37, - "Z": 38, - "\\": 39, - "a": 40, - "b": 41, - "c": 42, - "e": 43, - "g": 44, - "h": 45, - "i": 46, - "l": 47, - "n": 48, - "r": 49, - "s": 50, - "Br": 51, - "an": 52, - "ch": 53, - "Bran": 54, - "Branch": 55, - "Branch1": 56, - "=C": 57, - "Ri": 58, - "ng": 59, - "Ring": 60, - "Ring1": 61, - "=Branch1": 62, - "Branch2": 63, - "=O": 64, - "Ring2": 65, - "H1": 66, - "C@": 67, - "=N": 68, - "#Branch1": 69, - "C@@": 70, - "=Branch2": 71, - "C@H1": 72, - "C@@H1": 73, - "#Branch2": 74, - "#C": 75, - "Cl": 76, - "/C": 77, - "NH1": 78, - "=Ring1": 79, - "+1": 80, - "-1": 81, - "O-1": 82, - "N+1": 83, - "\\C": 84, - "#N": 85, - "/N": 86, - "=Ring2": 87, - "=S": 88, - "=N+1": 89, - "\\N": 90, - "Na": 91, - "Na+1": 92, - "/O": 93, - "\\O": 94, - "Br-1": 95, - "Branch3": 96, - "\\S": 97, - "S+1": 98, - "Cl-1": 99, - "I-1": 100, - "/C@@H1": 101, - "Si": 102, - "/C@H1": 103, - "/S": 104, - "=N-1": 105, - "Se": 106, - "=P": 107, - "N-1": 108, - "Ring3": 109, - "2H": 110, - "P+1": 111, - "K+1": 112, - "\\C@@H1": 113, - "\\C@H1": 114, - "/N+1": 115, - "@@": 116, - "C-1": 117, - "#N+1": 118, - "B-1": 119, - "+3": 120, - "Cl+3": 121, - "\\NH1": 122, - "Li": 123, - "Li+1": 124, - "PH1": 125, - "18": 126, - "18F": 127, - "@+1": 128, - "3H": 129, - "P@@": 130, - "H0": 131, - "OH0": 132, - "12": 133, - "P@": 134, - "+2": 135, - "@@+1": 136, - "S-1": 137, - "/Br": 138, - "-/": 139, - "\\Cl": 140, - "-/Ring2": 141, - "\\O-1": 142, - "11": 143, - "5I": 144, - "125I": 145, - "11C": 146, - "H3": 147, - "\\N+1": 148, - "-\\": 149, - "/C@@": 150, - "S@+1": 151, - "As": 152, - "/Cl": 153, - "11CH3": 154, - "=Se": 155, - "S@@+1": 156, - "N@+1": 157, - "14": 158, - "-\\Ring2": 159, - "14C": 160, - "\\F": 161, - "/C@": 162, - "Te": 163, - "H2": 164, - "H1-1": 165, - "=O+1": 166, - "N@@+1": 167, - "C+1": 168, - "=S+1": 169, - "Zn": 170, - "/P": 171, - "a+2": 172, - "/I": 173, - "OH1-1": 174, - "Ca+2": 175, - "\\Br": 176, - "Mg": 177, - "Zn+2": 178, - "Al": 179, - "/F": 180, - "Mg+2": 181, - "123": 182, - "123I": 183, - "13": 184, - "I+1": 185, - "/O-1": 186, - "-\\Ring1": 187, - "BH2": 188, - "BH2-1": 189, - "\\I": 190, - "/NH1": 191, - "O+1": 192, - "131": 193, - "131I": 194, - "=14C": 195, - "/S+1": 196, - "=Ring3": 197, - "\\C@@": 198, - "H2+1": 199, - "\\C@": 200, - "Ag": 201, - "=As": 202, - "=Se+1": 203, - "NH2+1": 204, - "SeH1": 205, - "-/Ring1": 206, - "=Te": 207, - "Al+3": 208, - "NaH1": 209, - "=Te+1": 210, - "NH1+1": 211, - "Ag+1": 212, - "H1+1": 213, - "NH1-1": 214, - "\\P": 215, - "14CH2": 216, - "13C": 217, - "14CH1": 218, - "=11C": 219, - "S@@": 220, - "=P@@": 221, - "SiH2": 222, - "H3-1": 223, - "14CH3": 224, - "BH3-1": 225, - "S@": 226, - "=14CH1": 227, - "=PH1": 228, - "=P@": 229, - "=NH1+1": 230, - "\\S+1": 231, - "124": 232, - "CH1-1": 233, - "Sr": 234, - "=Si": 235, - "124I": 236, - "Sr+2": 237, - "#C-1": 238, - "/C-1": 239, - "N@": 240, - "/N-1": 241, - "13CH1": 242, - "/B": 243, - "19": 244, - "Ba+2": 245, - "H4": 246, - "SH1+1": 247, - "Se+1": 248, - "19F": 249, - "/125I": 250, - "P@+1": 251, - "Rb": 252, - "Cl+1": 253, - "SiH4": 254, - "Rb+1": 255, - "=Branch3": 256, - "N@@": 257, - "As+1": 258, - "/Si": 259, - "BH1-1": 260, - "SH1": 261, - "/123I": 262, - "32": 263, - "=Mg": 264, - "H+1": 265, - "\\B": 266, - "SiH1": 267, - "P@@+1": 268, - "-2": 269, - "15": 270, - "17": 271, - "35": 272, - "=13CH1": 273, - "Cs": 274, - "=NH2+1": 275, - "=SH1": 276, - "MgH2": 277, - "32P": 278, - "17F": 279, - "35S": 280, - "Cs+1": 281, - "#11C": 282, - "/131I": 283, - "Bi": 284, - "\\125I": 285, - "=S@@": 286, - "\\S-1": 287, - "6Br": 288, - "7I": 289, - "76Br": 290, - "=B": 291, - "eH1": 292, - "\\N-1": 293, - "18O": 294, - "127I": 295, - "11CH2": 296, - "14C@@H1": 297, - "TeH2": 298, - "15NH1": 299, - "Bi+3": 300, - "/P+1": 301, - "/13C": 302, - "/13CH1": 303, - "0B": 304, - "10B": 305, - "=Al": 306, - "=18O": 307, - "BH0": 308, - "F-1": 309, - "NH3": 310, - "S-2": 311, - "Br+2": 312, - "Cl+2": 313, - "\\Si": 314, - "/S-1": 315, - "=PH2": 316, - "14C@H1": 317, - "NH3+1": 318, - "#14C": 319, - "#O+1": 320, - "-3": 321, - "22": 322, - "4H": 323, - "5Se": 324, - "5Sr+2": 325, - "75Se": 326, - "85Sr+2": 327, - "=B-1": 328, - "=13C": 329, - "@-1": 330, - "Be": 331, - "B@@": 332, - "B@-1": 333, - "Ca": 334, - "CH1": 335, - "I+3": 336, - "KH1": 337, - "OH1+1": 338, - "Ra+2": 339, - "SH1-1": 340, - "\\PH1": 341, - "\\123I": 342, - "=Ca": 343, - "\\CH1-1": 344, - "=S@": 345, - "\\SeH1": 346, - "/SeH1": 347, - "Se-1": 348, - "LiH1": 349, - "18F-1": 350, - "125IH1": 351, - "11CH1": 352, - "TeH1": 353, - "Zn+1": 354, - "Zn-2": 355, - "Al-3": 356, - "13CH3": 357, - "15N": 358, - "Be+2": 359, - "B@@-1": 360, - "#P": 361, - "#S": 362, - "-4": 363, - "/PH1": 364, - "/P@@": 365, - "/As": 366, - "/14C": 367, - "/14CH1": 368, - "2K+1": 369, - "2Rb+1": 370, - "3Se": 371, - "3Ra+2": 372, - "45": 373, - "47": 374, - "42K+1": 375, - "5I-1": 376, - "73Se": 377, - "89": 378, - "82Rb+1": 379, - "=32": 380, - "=32P": 381, - "CH0": 382, - "CH2": 383, - "I+2": 384, - "NH0": 385, - "NH4": 386, - "OH1": 387, - "PH2+1": 388, - "SH0": 389, - "SH2": 390, - "\\3H": 391, - "\\11CH3": 392, - "\\C-1": 393, - "\\Se": 394, - "Si@": 395, - "Si-1": 396, - "SiH1-1": 397, - "SiH3-1": 398, - "/Se": 399, - "Se-2": 400, - "\\NH1-1": 401, - "18FH1": 402, - "125I-1": 403, - "11C@@H1": 404, - "11C-1": 405, - "AsH1": 406, - "As-1": 407, - "14C@@": 408, - "Te-1": 409, - "Mg+1": 410, - "123I-1": 411, - "123Te": 412, - "123IH1": 413, - "135I": 414, - "131I-1": 415, - "Ag-4": 416, - "124I-1": 417, - "76BrH1": 418, - "18OH1": 419, - "22Na+1": 420, - "223Ra+2": 421, - "CaH2": 422, - "45Ca+2": 423, - "47Ca+2": 424, - "89Sr+2": 425, - "=32PH1": 426, - "NH4+1": 427 - }, - "merges": [ - "B r", - "a n", - "c h", - "Br an", - "Bran ch", - "Branch 1", - "= C", - "R i", - "n g", - "Ri ng", - "Ring 1", - "= Branch1", - "Branch 2", - "= O", - "Ring 2", - "H 1", - "C @", - "= N", - "# Branch1", - "C@ @", - "= Branch2", - "C@ H1", - "C@@ H1", - "# Branch2", - "# C", - "C l", - "/ C", - "N H1", - "= Ring1", - "+ 1", - "- 1", - "O -1", - "N +1", - "\\ C", - "# N", - "/ N", - "= Ring2", - "= S", - "=N +1", - "\\ N", - "N a", - "Na +1", - "/ O", - "\\ O", - "Br -1", - "Branch 3", - "\\ S", - "S +1", - "Cl -1", - "I -1", - "/ C@@H1", - "S i", - "/ C@H1", - "/ S", - "=N -1", - "S e", - "= P", - "N -1", - "Ring 3", - "2 H", - "P +1", - "K +1", - "\\ C@@H1", - "\\ C@H1", - "/ N+1", - "@ @", - "C -1", - "# N+1", - "B -1", - "+ 3", - "Cl +3", - "\\ NH1", - "L i", - "Li +1", - "P H1", - "1 8", - "18 F", - "@ +1", - "3 H", - "P @@", - "H 0", - "O H0", - "1 2", - "P @", - "+ 2", - "@@ +1", - "S -1", - "/ Br", - "- /", - "\\ Cl", - "-/ Ring2", - "\\ O-1", - "1 1", - "5 I", - "12 5I", - "11 C", - "H 3", - "\\ N+1", - "- \\", - "/ C@@", - "S @+1", - "A s", - "/ Cl", - "11C H3", - "=S e", - "S @@+1", - "N @+1", - "1 4", - "-\\ Ring2", - "14 C", - "\\ F", - "/ C@", - "T e", - "H 2", - "H1 -1", - "=O +1", - "N @@+1", - "C +1", - "=S +1", - "Z n", - "/ P", - "a +2", - "/ I", - "O H1-1", - "C a+2", - "\\ Br", - "M g", - "Zn +2", - "A l", - "/ F", - "Mg +2", - "12 3", - "123 I", - "1 3", - "I +1", - "/ O-1", - "-\\ Ring1", - "B H2", - "BH2 -1", - "\\ I", - "/ NH1", - "O +1", - "13 1", - "131 I", - "= 14C", - "/ S+1", - "= Ring3", - "\\ C@@", - "H2 +1", - "\\ C@", - "A g", - "= As", - "=Se +1", - "N H2+1", - "Se H1", - "-/ Ring1", - "= Te", - "Al +3", - "Na H1", - "=Te +1", - "NH1 +1", - "Ag +1", - "H1 +1", - "NH1 -1", - "\\ P", - "14C H2", - "13 C", - "14C H1", - "= 11C", - "S @@", - "=P @@", - "Si H2", - "H3 -1", - "14C H3", - "B H3-1", - "S @", - "=14C H1", - "=P H1", - "=P @", - "=N H1+1", - "\\S +1", - "12 4", - "C H1-1", - "S r", - "=S i", - "124 I", - "Sr +2", - "#C -1", - "/C -1", - "N @", - "/N -1", - "13C H1", - "/ B", - "1 9", - "B a+2", - "H 4", - "S H1+1", - "Se +1", - "19 F", - "/ 125I", - "P @+1", - "R b", - "Cl +1", - "Si H4", - "Rb +1", - "= Branch3", - "N @@", - "As +1", - "/ Si", - "B H1-1", - "S H1", - "/ 123I", - "3 2", - "= Mg", - "H +1", - "\\ B", - "Si H1", - "P@@ +1", - "- 2", - "1 5", - "1 7", - "3 5", - "= 13CH1", - "C s", - "=N H2+1", - "=S H1", - "Mg H2", - "32 P", - "17 F", - "35 S", - "Cs +1", - "# 11C", - "/ 131I", - "B i", - "\\ 125I", - "=S @@", - "\\S -1", - "6 Br", - "7 I", - "7 6Br", - "= B", - "e H1", - "\\N -1", - "18 O", - "12 7I", - "11C H2", - "14 C@@H1", - "Te H2", - "15 NH1", - "Bi +3", - "/ P+1", - "/ 13C", - "/ 13CH1", - "0 B", - "1 0B", - "= Al", - "= 18O", - "B H0", - "F -1", - "N H3", - "S -2", - "Br +2", - "Cl +2", - "\\S i", - "/S -1", - "=P H2", - "14 C@H1", - "NH3 +1", - "# 14C", - "# O+1", - "- 3", - "2 2", - "4 H", - "5 Se", - "5 Sr+2", - "7 5Se", - "8 5Sr+2", - "= B-1", - "= 13C", - "@ -1", - "B e", - "B @@", - "B @-1", - "C a", - "C H1", - "I +3", - "K H1", - "O H1+1", - "R a+2", - "S H1-1", - "\\ PH1", - "\\ 123I", - "=C a", - "\\C H1-1", - "=S @", - "\\S eH1", - "/S eH1", - "Se -1", - "Li H1", - "18F -1", - "125I H1", - "11C H1", - "Te H1", - "Zn +1", - "Zn -2", - "Al -3", - "13C H3", - "15 N", - "Be +2", - "B@@ -1", - "# P", - "# S", - "- 4", - "/ PH1", - "/ P@@", - "/ As", - "/ 14C", - "/ 14CH1", - "2 K+1", - "2 Rb+1", - "3 Se", - "3 Ra+2", - "4 5", - "4 7", - "4 2K+1", - "5 I-1", - "7 3Se", - "8 9", - "8 2Rb+1", - "= 32", - "= 32P", - "C H0", - "C H2", - "I +2", - "N H0", - "N H4", - "O H1", - "P H2+1", - "S H0", - "S H2", - "\\ 3H", - "\\ 11CH3", - "\\C -1", - "\\S e", - "Si @", - "Si -1", - "Si H1-1", - "Si H3-1", - "/S e", - "Se -2", - "\\NH1 -1", - "18F H1", - "12 5I-1", - "11 C@@H1", - "11 C-1", - "As H1", - "As -1", - "14 C@@", - "Te -1", - "Mg +1", - "123 I-1", - "123 Te", - "123I H1", - "13 5I", - "131 I-1", - "Ag -4", - "124 I-1", - "76Br H1", - "18O H1", - "22 Na+1", - "22 3Ra+2", - "Ca H2", - "45 Ca+2", - "47 Ca+2", - "89 Sr+2", - "=32 PH1", - "NH4 +1" - ] - } -} \ No newline at end of file diff --git a/models/finetuned/sider/checkpoint_epoch_025/tokenizer_config.json b/models/finetuned/sider/checkpoint_epoch_025/tokenizer_config.json deleted file mode 100644 index 08860954acd34fad07fd77f7635298fa565f3149..0000000000000000000000000000000000000000 --- a/models/finetuned/sider/checkpoint_epoch_025/tokenizer_config.json +++ /dev/null @@ -1,65 +0,0 @@ -{ - "add_prefix_space": false, - "bos_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "cls_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "eos_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "errors": "replace", - "mask_token": { - "__type": "AddedToken", - "content": "", - "lstrip": true, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "model_max_length": 1000000000000000019884624838656, - "name_or_path": "/home/erva/SELFormerMM/data/pretrained_multimodal_chembl36", - "pad_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "sep_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "special_tokens_map_file": null, - "tokenizer_class": "RobertaTokenizer", - "trim_offsets": true, - "unk_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - } -} diff --git a/models/finetuned/sider/checkpoint_epoch_025/vocab.json b/models/finetuned/sider/checkpoint_epoch_025/vocab.json deleted file mode 100644 index f7e4cc22809f4e9035cc450ef189c8a7da8fd03e..0000000000000000000000000000000000000000 --- a/models/finetuned/sider/checkpoint_epoch_025/vocab.json +++ /dev/null @@ -1 +0,0 @@ -{"":0,"":1,"":2,"":3,"":4,"\n":5,"#":6,"+":7,"-":8,".":9,"/":10,"0":11,"1":12,"2":13,"3":14,"4":15,"5":16,"6":17,"7":18,"8":19,"9":20,"=":21,"@":22,"A":23,"B":24,"C":25,"F":26,"H":27,"I":28,"K":29,"L":30,"M":31,"N":32,"O":33,"P":34,"R":35,"S":36,"T":37,"Z":38,"\\":39,"a":40,"b":41,"c":42,"e":43,"g":44,"h":45,"i":46,"l":47,"n":48,"r":49,"s":50,"Br":51,"an":52,"ch":53,"Bran":54,"Branch":55,"Branch1":56,"=C":57,"Ri":58,"ng":59,"Ring":60,"Ring1":61,"=Branch1":62,"Branch2":63,"=O":64,"Ring2":65,"H1":66,"C@":67,"=N":68,"#Branch1":69,"C@@":70,"=Branch2":71,"C@H1":72,"C@@H1":73,"#Branch2":74,"#C":75,"Cl":76,"/C":77,"NH1":78,"=Ring1":79,"+1":80,"-1":81,"O-1":82,"N+1":83,"\\C":84,"#N":85,"/N":86,"=Ring2":87,"=S":88,"=N+1":89,"\\N":90,"Na":91,"Na+1":92,"/O":93,"\\O":94,"Br-1":95,"Branch3":96,"\\S":97,"S+1":98,"Cl-1":99,"I-1":100,"/C@@H1":101,"Si":102,"/C@H1":103,"/S":104,"=N-1":105,"Se":106,"=P":107,"N-1":108,"Ring3":109,"2H":110,"P+1":111,"K+1":112,"\\C@@H1":113,"\\C@H1":114,"/N+1":115,"@@":116,"C-1":117,"#N+1":118,"B-1":119,"+3":120,"Cl+3":121,"\\NH1":122,"Li":123,"Li+1":124,"PH1":125,"18":126,"18F":127,"@+1":128,"3H":129,"P@@":130,"H0":131,"OH0":132,"12":133,"P@":134,"+2":135,"@@+1":136,"S-1":137,"/Br":138,"-/":139,"\\Cl":140,"-/Ring2":141,"\\O-1":142,"11":143,"5I":144,"125I":145,"11C":146,"H3":147,"\\N+1":148,"-\\":149,"/C@@":150,"S@+1":151,"As":152,"/Cl":153,"11CH3":154,"=Se":155,"S@@+1":156,"N@+1":157,"14":158,"-\\Ring2":159,"14C":160,"\\F":161,"/C@":162,"Te":163,"H2":164,"H1-1":165,"=O+1":166,"N@@+1":167,"C+1":168,"=S+1":169,"Zn":170,"/P":171,"a+2":172,"/I":173,"OH1-1":174,"Ca+2":175,"\\Br":176,"Mg":177,"Zn+2":178,"Al":179,"/F":180,"Mg+2":181,"123":182,"123I":183,"13":184,"I+1":185,"/O-1":186,"-\\Ring1":187,"BH2":188,"BH2-1":189,"\\I":190,"/NH1":191,"O+1":192,"131":193,"131I":194,"=14C":195,"/S+1":196,"=Ring3":197,"\\C@@":198,"H2+1":199,"\\C@":200,"Ag":201,"=As":202,"=Se+1":203,"NH2+1":204,"SeH1":205,"-/Ring1":206,"=Te":207,"Al+3":208,"NaH1":209,"=Te+1":210,"NH1+1":211,"Ag+1":212,"H1+1":213,"NH1-1":214,"\\P":215,"14CH2":216,"13C":217,"14CH1":218,"=11C":219,"S@@":220,"=P@@":221,"SiH2":222,"H3-1":223,"14CH3":224,"BH3-1":225,"S@":226,"=14CH1":227,"=PH1":228,"=P@":229,"=NH1+1":230,"\\S+1":231,"124":232,"CH1-1":233,"Sr":234,"=Si":235,"124I":236,"Sr+2":237,"#C-1":238,"/C-1":239,"N@":240,"/N-1":241,"13CH1":242,"/B":243,"19":244,"Ba+2":245,"H4":246,"SH1+1":247,"Se+1":248,"19F":249,"/125I":250,"P@+1":251,"Rb":252,"Cl+1":253,"SiH4":254,"Rb+1":255,"=Branch3":256,"N@@":257,"As+1":258,"/Si":259,"BH1-1":260,"SH1":261,"/123I":262,"32":263,"=Mg":264,"H+1":265,"\\B":266,"SiH1":267,"P@@+1":268,"-2":269,"15":270,"17":271,"35":272,"=13CH1":273,"Cs":274,"=NH2+1":275,"=SH1":276,"MgH2":277,"32P":278,"17F":279,"35S":280,"Cs+1":281,"#11C":282,"/131I":283,"Bi":284,"\\125I":285,"=S@@":286,"\\S-1":287,"6Br":288,"7I":289,"76Br":290,"=B":291,"eH1":292,"\\N-1":293,"18O":294,"127I":295,"11CH2":296,"14C@@H1":297,"TeH2":298,"15NH1":299,"Bi+3":300,"/P+1":301,"/13C":302,"/13CH1":303,"0B":304,"10B":305,"=Al":306,"=18O":307,"BH0":308,"F-1":309,"NH3":310,"S-2":311,"Br+2":312,"Cl+2":313,"\\Si":314,"/S-1":315,"=PH2":316,"14C@H1":317,"NH3+1":318,"#14C":319,"#O+1":320,"-3":321,"22":322,"4H":323,"5Se":324,"5Sr+2":325,"75Se":326,"85Sr+2":327,"=B-1":328,"=13C":329,"@-1":330,"Be":331,"B@@":332,"B@-1":333,"Ca":334,"CH1":335,"I+3":336,"KH1":337,"OH1+1":338,"Ra+2":339,"SH1-1":340,"\\PH1":341,"\\123I":342,"=Ca":343,"\\CH1-1":344,"=S@":345,"\\SeH1":346,"/SeH1":347,"Se-1":348,"LiH1":349,"18F-1":350,"125IH1":351,"11CH1":352,"TeH1":353,"Zn+1":354,"Zn-2":355,"Al-3":356,"13CH3":357,"15N":358,"Be+2":359,"B@@-1":360,"#P":361,"#S":362,"-4":363,"/PH1":364,"/P@@":365,"/As":366,"/14C":367,"/14CH1":368,"2K+1":369,"2Rb+1":370,"3Se":371,"3Ra+2":372,"45":373,"47":374,"42K+1":375,"5I-1":376,"73Se":377,"89":378,"82Rb+1":379,"=32":380,"=32P":381,"CH0":382,"CH2":383,"I+2":384,"NH0":385,"NH4":386,"OH1":387,"PH2+1":388,"SH0":389,"SH2":390,"\\3H":391,"\\11CH3":392,"\\C-1":393,"\\Se":394,"Si@":395,"Si-1":396,"SiH1-1":397,"SiH3-1":398,"/Se":399,"Se-2":400,"\\NH1-1":401,"18FH1":402,"125I-1":403,"11C@@H1":404,"11C-1":405,"AsH1":406,"As-1":407,"14C@@":408,"Te-1":409,"Mg+1":410,"123I-1":411,"123Te":412,"123IH1":413,"135I":414,"131I-1":415,"Ag-4":416,"124I-1":417,"76BrH1":418,"18OH1":419,"22Na+1":420,"223Ra+2":421,"CaH2":422,"45Ca+2":423,"47Ca+2":424,"89Sr+2":425,"=32PH1":426,"NH4+1":427} \ No newline at end of file diff --git a/models/finetuned/sider/checkpoint_epoch_050/config.json b/models/finetuned/sider/checkpoint_epoch_050/config.json deleted file mode 100644 index 3811e21539577b37e06313eab31ec11e53f0cbbc..0000000000000000000000000000000000000000 --- a/models/finetuned/sider/checkpoint_epoch_050/config.json +++ /dev/null @@ -1,27 +0,0 @@ -{ - "_name_or_path": "/home/erva/SELFormerMM/data/pretrained_multimodal_chembl36", - "architectures": [ - "RobertaForMaskedLM" - ], - "attention_probs_dropout_prob": 0.1, - "bos_token_id": 0, - "classifier_dropout": null, - "eos_token_id": 2, - "hidden_act": "gelu", - "hidden_dropout_prob": 0.1, - "hidden_size": 768, - "initializer_range": 0.02, - "intermediate_size": 3072, - "layer_norm_eps": 1e-12, - "max_position_embeddings": 514, - "model_type": "roberta", - "num_attention_heads": 4, - "num_hidden_layers": 12, - "pad_token_id": 1, - "position_embedding_type": "absolute", - "torch_dtype": "float32", - "transformers_version": "4.26.1", - "type_vocab_size": 1, - "use_cache": true, - "vocab_size": 800 -} diff --git a/models/finetuned/sider/checkpoint_epoch_050/merges.txt b/models/finetuned/sider/checkpoint_epoch_050/merges.txt deleted file mode 100644 index 7cd5ec62809503c23f18c80afc0ba3bdf9d253d0..0000000000000000000000000000000000000000 --- a/models/finetuned/sider/checkpoint_epoch_050/merges.txt +++ /dev/null @@ -1,378 +0,0 @@ -#version: 0.2 - Trained by `huggingface/tokenizers` -B r -a n -c h -Br an -Bran ch -Branch 1 -= C -R i -n g -Ri ng -Ring 1 -= Branch1 -Branch 2 -= O -Ring 2 -H 1 -C @ -= N -# Branch1 -C@ @ -= Branch2 -C@ H1 -C@@ H1 -# Branch2 -# C -C l -/ C -N H1 -= Ring1 -+ 1 -- 1 -O -1 -N +1 -\ C -# N -/ N -= Ring2 -= S -=N +1 -\ N -N a -Na +1 -/ O -\ O -Br -1 -Branch 3 -\ S -S +1 -Cl -1 -I -1 -/ C@@H1 -S i -/ C@H1 -/ S -=N -1 -S e -= P -N -1 -Ring 3 -2 H -P +1 -K +1 -\ C@@H1 -\ C@H1 -/ N+1 -@ @ -C -1 -# N+1 -B -1 -+ 3 -Cl +3 -\ NH1 -L i -Li +1 -P H1 -1 8 -18 F -@ +1 -3 H -P @@ -H 0 -O H0 -1 2 -P @ -+ 2 -@@ +1 -S -1 -/ Br -- / -\ Cl --/ Ring2 -\ O-1 -1 1 -5 I -12 5I -11 C -H 3 -\ N+1 -- \ -/ C@@ -S @+1 -A s -/ Cl -11C H3 -=S e -S @@+1 -N @+1 -1 4 --\ Ring2 -14 C -\ F -/ C@ -T e -H 2 -H1 -1 -=O +1 -N @@+1 -C +1 -=S +1 -Z n -/ P -a +2 -/ I -O H1-1 -C a+2 -\ Br -M g -Zn +2 -A l -/ F -Mg +2 -12 3 -123 I -1 3 -I +1 -/ O-1 --\ Ring1 -B H2 -BH2 -1 -\ I -/ NH1 -O +1 -13 1 -131 I -= 14C -/ S+1 -= Ring3 -\ C@@ -H2 +1 -\ C@ -A g -= As -=Se +1 -N H2+1 -Se H1 --/ Ring1 -= Te -Al +3 -Na H1 -=Te +1 -NH1 +1 -Ag +1 -H1 +1 -NH1 -1 -\ P -14C H2 -13 C -14C H1 -= 11C -S @@ -=P @@ -Si H2 -H3 -1 -14C H3 -B H3-1 -S @ -=14C H1 -=P H1 -=P @ -=N H1+1 -\S +1 -12 4 -C H1-1 -S r -=S i -124 I -Sr +2 -#C -1 -/C -1 -N @ -/N -1 -13C H1 -/ B -1 9 -B a+2 -H 4 -S H1+1 -Se +1 -19 F -/ 125I -P @+1 -R b -Cl +1 -Si H4 -Rb +1 -= Branch3 -N @@ -As +1 -/ Si -B H1-1 -S H1 -/ 123I -3 2 -= Mg -H +1 -\ B -Si H1 -P@@ +1 -- 2 -1 5 -1 7 -3 5 -= 13CH1 -C s -=N H2+1 -=S H1 -Mg H2 -32 P -17 F -35 S -Cs +1 -# 11C -/ 131I -B i -\ 125I -=S @@ -\S -1 -6 Br -7 I -7 6Br -= B -e H1 -\N -1 -18 O -12 7I -11C H2 -14 C@@H1 -Te H2 -15 NH1 -Bi +3 -/ P+1 -/ 13C -/ 13CH1 -0 B -1 0B -= Al -= 18O -B H0 -F -1 -N H3 -S -2 -Br +2 -Cl +2 -\S i -/S -1 -=P H2 -14 C@H1 -NH3 +1 -# 14C -# O+1 -- 3 -2 2 -4 H -5 Se -5 Sr+2 -7 5Se -8 5Sr+2 -= B-1 -= 13C -@ -1 -B e -B @@ -B @-1 -C a -C H1 -I +3 -K H1 -O H1+1 -R a+2 -S H1-1 -\ PH1 -\ 123I -=C a -\C H1-1 -=S @ -\S eH1 -/S eH1 -Se -1 -Li H1 -18F -1 -125I H1 -11C H1 -Te H1 -Zn +1 -Zn -2 -Al -3 -13C H3 -15 N -Be +2 -B@@ -1 -# P -# S -- 4 -/ PH1 -/ P@@ -/ As -/ 14C -/ 14CH1 -2 K+1 -2 Rb+1 -3 Se -3 Ra+2 -4 5 -4 7 -4 2K+1 -5 I-1 -7 3Se -8 9 -8 2Rb+1 -= 32 -= 32P -C H0 -C H2 -I +2 -N H0 -N H4 -O H1 -P H2+1 -S H0 -S H2 -\ 3H -\ 11CH3 -\C -1 -\S e -Si @ -Si -1 -Si H1-1 -Si H3-1 -/S e -Se -2 -\NH1 -1 -18F H1 -12 5I-1 -11 C@@H1 -11 C-1 -As H1 -As -1 -14 C@@ -Te -1 -Mg +1 -123 I-1 -123 Te -123I H1 -13 5I -131 I-1 -Ag -4 -124 I-1 -76Br H1 -18O H1 -22 Na+1 -22 3Ra+2 -Ca H2 -45 Ca+2 -47 Ca+2 -89 Sr+2 -=32 PH1 -NH4 +1 diff --git a/models/finetuned/sider/checkpoint_epoch_050/model.pt b/models/finetuned/sider/checkpoint_epoch_050/model.pt deleted file mode 100644 index d5262ada0a1773d2f5142c00c258de47e32fbb41..0000000000000000000000000000000000000000 --- a/models/finetuned/sider/checkpoint_epoch_050/model.pt +++ /dev/null @@ -1,3 +0,0 @@ -version https://git-lfs.github.com/spec/v1 -oid sha256:da1c7d30cd890211ba9b7db75d9c59a4b465aa3ca4e8de458cad8b54e2af215d -size 1023174845 diff --git a/models/finetuned/sider/checkpoint_epoch_050/special_tokens_map.json b/models/finetuned/sider/checkpoint_epoch_050/special_tokens_map.json deleted file mode 100644 index 06a55849fa69a91e7179d909e373179ff7467d8c..0000000000000000000000000000000000000000 --- a/models/finetuned/sider/checkpoint_epoch_050/special_tokens_map.json +++ /dev/null @@ -1,51 +0,0 @@ -{ - "bos_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "cls_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "eos_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "mask_token": { - "content": "", - "lstrip": true, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "pad_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "sep_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "unk_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - } -} diff --git a/models/finetuned/sider/checkpoint_epoch_050/tokenizer.json b/models/finetuned/sider/checkpoint_epoch_050/tokenizer.json deleted file mode 100644 index 3b64b273e6fa9799e2d8375722b9e815de9ebb8f..0000000000000000000000000000000000000000 --- a/models/finetuned/sider/checkpoint_epoch_050/tokenizer.json +++ /dev/null @@ -1,909 +0,0 @@ -{ - "version": "1.0", - "truncation": { - "direction": "Right", - "max_length": 128, - "strategy": "LongestFirst", - "stride": 0 - }, - "padding": { - "strategy": { - "Fixed": 128 - }, - "direction": "Right", - "pad_to_multiple_of": null, - "pad_id": 3, - "pad_type_id": 0, - "pad_token": "" - }, - "added_tokens": [ - { - "id": 0, - "content": "", - "single_word": false, - "lstrip": false, - "rstrip": false, - "normalized": true, - "special": true - }, - { - "id": 1, - "content": "", - "single_word": false, - "lstrip": false, - "rstrip": false, - "normalized": true, - "special": true - }, - { - "id": 2, - "content": "", - "single_word": false, - "lstrip": false, - "rstrip": false, - "normalized": true, - "special": true - }, - { - "id": 3, - "content": "", - "single_word": false, - "lstrip": false, - "rstrip": false, - "normalized": true, - "special": true - }, - { - "id": 4, - "content": "", - "single_word": false, - "lstrip": true, - "rstrip": false, - "normalized": true, - "special": true - } - ], - "normalizer": null, - "pre_tokenizer": { - "type": "ByteLevel", - "add_prefix_space": false, - "trim_offsets": true, - "use_regex": true - }, - "post_processor": { - "type": "RobertaProcessing", - "sep": [ - "", - 2 - ], - "cls": [ - "", - 1 - ], - "trim_offsets": true, - "add_prefix_space": false - }, - "decoder": { - "type": "ByteLevel", - "add_prefix_space": true, - "trim_offsets": true, - "use_regex": true - }, - "model": { - "type": "BPE", - "dropout": null, - "unk_token": null, - "continuing_subword_prefix": "", - "end_of_word_suffix": "", - "fuse_unk": false, - "vocab": { - "": 0, - "": 1, - "": 2, - "": 3, - "": 4, - "\n": 5, - "#": 6, - "+": 7, - "-": 8, - ".": 9, - "/": 10, - "0": 11, - "1": 12, - "2": 13, - "3": 14, - "4": 15, - "5": 16, - "6": 17, - "7": 18, - "8": 19, - "9": 20, - "=": 21, - "@": 22, - "A": 23, - "B": 24, - "C": 25, - "F": 26, - "H": 27, - "I": 28, - "K": 29, - "L": 30, - "M": 31, - "N": 32, - "O": 33, - "P": 34, - "R": 35, - "S": 36, - "T": 37, - "Z": 38, - "\\": 39, - "a": 40, - "b": 41, - "c": 42, - "e": 43, - "g": 44, - "h": 45, - "i": 46, - "l": 47, - "n": 48, - "r": 49, - "s": 50, - "Br": 51, - "an": 52, - "ch": 53, - "Bran": 54, - "Branch": 55, - "Branch1": 56, - "=C": 57, - "Ri": 58, - "ng": 59, - "Ring": 60, - "Ring1": 61, - "=Branch1": 62, - "Branch2": 63, - "=O": 64, - "Ring2": 65, - "H1": 66, - "C@": 67, - "=N": 68, - "#Branch1": 69, - "C@@": 70, - "=Branch2": 71, - "C@H1": 72, - "C@@H1": 73, - "#Branch2": 74, - "#C": 75, - "Cl": 76, - "/C": 77, - "NH1": 78, - "=Ring1": 79, - "+1": 80, - "-1": 81, - "O-1": 82, - "N+1": 83, - "\\C": 84, - "#N": 85, - "/N": 86, - "=Ring2": 87, - "=S": 88, - "=N+1": 89, - "\\N": 90, - "Na": 91, - "Na+1": 92, - "/O": 93, - "\\O": 94, - "Br-1": 95, - "Branch3": 96, - "\\S": 97, - "S+1": 98, - "Cl-1": 99, - "I-1": 100, - "/C@@H1": 101, - "Si": 102, - "/C@H1": 103, - "/S": 104, - "=N-1": 105, - "Se": 106, - "=P": 107, - "N-1": 108, - "Ring3": 109, - "2H": 110, - "P+1": 111, - "K+1": 112, - "\\C@@H1": 113, - "\\C@H1": 114, - "/N+1": 115, - "@@": 116, - "C-1": 117, - "#N+1": 118, - "B-1": 119, - "+3": 120, - "Cl+3": 121, - "\\NH1": 122, - "Li": 123, - "Li+1": 124, - "PH1": 125, - "18": 126, - "18F": 127, - "@+1": 128, - "3H": 129, - "P@@": 130, - "H0": 131, - "OH0": 132, - "12": 133, - "P@": 134, - "+2": 135, - "@@+1": 136, - "S-1": 137, - "/Br": 138, - "-/": 139, - "\\Cl": 140, - "-/Ring2": 141, - "\\O-1": 142, - "11": 143, - "5I": 144, - "125I": 145, - "11C": 146, - "H3": 147, - "\\N+1": 148, - "-\\": 149, - "/C@@": 150, - "S@+1": 151, - "As": 152, - "/Cl": 153, - "11CH3": 154, - "=Se": 155, - "S@@+1": 156, - "N@+1": 157, - "14": 158, - "-\\Ring2": 159, - "14C": 160, - "\\F": 161, - "/C@": 162, - "Te": 163, - "H2": 164, - "H1-1": 165, - "=O+1": 166, - "N@@+1": 167, - "C+1": 168, - "=S+1": 169, - "Zn": 170, - "/P": 171, - "a+2": 172, - "/I": 173, - "OH1-1": 174, - "Ca+2": 175, - "\\Br": 176, - "Mg": 177, - "Zn+2": 178, - "Al": 179, - "/F": 180, - "Mg+2": 181, - "123": 182, - "123I": 183, - "13": 184, - "I+1": 185, - "/O-1": 186, - "-\\Ring1": 187, - "BH2": 188, - "BH2-1": 189, - "\\I": 190, - "/NH1": 191, - "O+1": 192, - "131": 193, - "131I": 194, - "=14C": 195, - "/S+1": 196, - "=Ring3": 197, - "\\C@@": 198, - "H2+1": 199, - "\\C@": 200, - "Ag": 201, - "=As": 202, - "=Se+1": 203, - "NH2+1": 204, - "SeH1": 205, - "-/Ring1": 206, - "=Te": 207, - "Al+3": 208, - "NaH1": 209, - "=Te+1": 210, - "NH1+1": 211, - "Ag+1": 212, - "H1+1": 213, - "NH1-1": 214, - "\\P": 215, - "14CH2": 216, - "13C": 217, - "14CH1": 218, - "=11C": 219, - "S@@": 220, - "=P@@": 221, - "SiH2": 222, - "H3-1": 223, - "14CH3": 224, - "BH3-1": 225, - "S@": 226, - "=14CH1": 227, - "=PH1": 228, - "=P@": 229, - "=NH1+1": 230, - "\\S+1": 231, - "124": 232, - "CH1-1": 233, - "Sr": 234, - "=Si": 235, - "124I": 236, - "Sr+2": 237, - "#C-1": 238, - "/C-1": 239, - "N@": 240, - "/N-1": 241, - "13CH1": 242, - "/B": 243, - "19": 244, - "Ba+2": 245, - "H4": 246, - "SH1+1": 247, - "Se+1": 248, - "19F": 249, - "/125I": 250, - "P@+1": 251, - "Rb": 252, - "Cl+1": 253, - "SiH4": 254, - "Rb+1": 255, - "=Branch3": 256, - "N@@": 257, - "As+1": 258, - "/Si": 259, - "BH1-1": 260, - "SH1": 261, - "/123I": 262, - "32": 263, - "=Mg": 264, - "H+1": 265, - "\\B": 266, - "SiH1": 267, - "P@@+1": 268, - "-2": 269, - "15": 270, - "17": 271, - "35": 272, - "=13CH1": 273, - "Cs": 274, - "=NH2+1": 275, - "=SH1": 276, - "MgH2": 277, - "32P": 278, - "17F": 279, - "35S": 280, - "Cs+1": 281, - "#11C": 282, - "/131I": 283, - "Bi": 284, - "\\125I": 285, - "=S@@": 286, - "\\S-1": 287, - "6Br": 288, - "7I": 289, - "76Br": 290, - "=B": 291, - "eH1": 292, - "\\N-1": 293, - "18O": 294, - "127I": 295, - "11CH2": 296, - "14C@@H1": 297, - "TeH2": 298, - "15NH1": 299, - "Bi+3": 300, - "/P+1": 301, - "/13C": 302, - "/13CH1": 303, - "0B": 304, - "10B": 305, - "=Al": 306, - "=18O": 307, - "BH0": 308, - "F-1": 309, - "NH3": 310, - "S-2": 311, - "Br+2": 312, - "Cl+2": 313, - "\\Si": 314, - "/S-1": 315, - "=PH2": 316, - "14C@H1": 317, - "NH3+1": 318, - "#14C": 319, - "#O+1": 320, - "-3": 321, - "22": 322, - "4H": 323, - "5Se": 324, - "5Sr+2": 325, - "75Se": 326, - "85Sr+2": 327, - "=B-1": 328, - "=13C": 329, - "@-1": 330, - "Be": 331, - "B@@": 332, - "B@-1": 333, - "Ca": 334, - "CH1": 335, - "I+3": 336, - "KH1": 337, - "OH1+1": 338, - "Ra+2": 339, - "SH1-1": 340, - "\\PH1": 341, - "\\123I": 342, - "=Ca": 343, - "\\CH1-1": 344, - "=S@": 345, - "\\SeH1": 346, - "/SeH1": 347, - "Se-1": 348, - "LiH1": 349, - "18F-1": 350, - "125IH1": 351, - "11CH1": 352, - "TeH1": 353, - "Zn+1": 354, - "Zn-2": 355, - "Al-3": 356, - "13CH3": 357, - "15N": 358, - "Be+2": 359, - "B@@-1": 360, - "#P": 361, - "#S": 362, - "-4": 363, - "/PH1": 364, - "/P@@": 365, - "/As": 366, - "/14C": 367, - "/14CH1": 368, - "2K+1": 369, - "2Rb+1": 370, - "3Se": 371, - "3Ra+2": 372, - "45": 373, - "47": 374, - "42K+1": 375, - "5I-1": 376, - "73Se": 377, - "89": 378, - "82Rb+1": 379, - "=32": 380, - "=32P": 381, - "CH0": 382, - "CH2": 383, - "I+2": 384, - "NH0": 385, - "NH4": 386, - "OH1": 387, - "PH2+1": 388, - "SH0": 389, - "SH2": 390, - "\\3H": 391, - "\\11CH3": 392, - "\\C-1": 393, - "\\Se": 394, - "Si@": 395, - "Si-1": 396, - "SiH1-1": 397, - "SiH3-1": 398, - "/Se": 399, - "Se-2": 400, - "\\NH1-1": 401, - "18FH1": 402, - "125I-1": 403, - "11C@@H1": 404, - "11C-1": 405, - "AsH1": 406, - "As-1": 407, - "14C@@": 408, - "Te-1": 409, - "Mg+1": 410, - "123I-1": 411, - "123Te": 412, - "123IH1": 413, - "135I": 414, - "131I-1": 415, - "Ag-4": 416, - "124I-1": 417, - "76BrH1": 418, - "18OH1": 419, - "22Na+1": 420, - "223Ra+2": 421, - "CaH2": 422, - "45Ca+2": 423, - "47Ca+2": 424, - "89Sr+2": 425, - "=32PH1": 426, - "NH4+1": 427 - }, - "merges": [ - "B r", - "a n", - "c h", - "Br an", - "Bran ch", - "Branch 1", - "= C", - "R i", - "n g", - "Ri ng", - "Ring 1", - "= Branch1", - "Branch 2", - "= O", - "Ring 2", - "H 1", - "C @", - "= N", - "# Branch1", - "C@ @", - "= Branch2", - "C@ H1", - "C@@ H1", - "# Branch2", - "# C", - "C l", - "/ C", - "N H1", - "= Ring1", - "+ 1", - "- 1", - "O -1", - "N +1", - "\\ C", - "# N", - "/ N", - "= Ring2", - "= S", - "=N +1", - "\\ N", - "N a", - "Na +1", - "/ O", - "\\ O", - "Br -1", - "Branch 3", - "\\ S", - "S +1", - "Cl -1", - "I -1", - "/ C@@H1", - "S i", - "/ C@H1", - "/ S", - "=N -1", - "S e", - "= P", - "N -1", - "Ring 3", - "2 H", - "P +1", - "K +1", - "\\ C@@H1", - "\\ C@H1", - "/ N+1", - "@ @", - "C -1", - "# N+1", - "B -1", - "+ 3", - "Cl +3", - "\\ NH1", - "L i", - "Li +1", - "P H1", - "1 8", - "18 F", - "@ +1", - "3 H", - "P @@", - "H 0", - "O H0", - "1 2", - "P @", - "+ 2", - "@@ +1", - "S -1", - "/ Br", - "- /", - "\\ Cl", - "-/ Ring2", - "\\ O-1", - "1 1", - "5 I", - "12 5I", - "11 C", - "H 3", - "\\ N+1", - "- \\", - "/ C@@", - "S @+1", - "A s", - "/ Cl", - "11C H3", - "=S e", - "S @@+1", - "N @+1", - "1 4", - "-\\ Ring2", - "14 C", - "\\ F", - "/ C@", - "T e", - "H 2", - "H1 -1", - "=O +1", - "N @@+1", - "C +1", - "=S +1", - "Z n", - "/ P", - "a +2", - "/ I", - "O H1-1", - "C a+2", - "\\ Br", - "M g", - "Zn +2", - "A l", - "/ F", - "Mg +2", - "12 3", - "123 I", - "1 3", - "I +1", - "/ O-1", - "-\\ Ring1", - "B H2", - "BH2 -1", - "\\ I", - "/ NH1", - "O +1", - "13 1", - "131 I", - "= 14C", - "/ S+1", - "= Ring3", - "\\ C@@", - "H2 +1", - "\\ C@", - "A g", - "= As", - "=Se +1", - "N H2+1", - "Se H1", - "-/ Ring1", - "= Te", - "Al +3", - "Na H1", - "=Te +1", - "NH1 +1", - "Ag +1", - "H1 +1", - "NH1 -1", - "\\ P", - "14C H2", - "13 C", - "14C H1", - "= 11C", - "S @@", - "=P @@", - "Si H2", - "H3 -1", - "14C H3", - "B H3-1", - "S @", - "=14C H1", - "=P H1", - "=P @", - "=N H1+1", - "\\S +1", - "12 4", - "C H1-1", - "S r", - "=S i", - "124 I", - "Sr +2", - "#C -1", - "/C -1", - "N @", - "/N -1", - "13C H1", - "/ B", - "1 9", - "B a+2", - "H 4", - "S H1+1", - "Se +1", - "19 F", - "/ 125I", - "P @+1", - "R b", - "Cl +1", - "Si H4", - "Rb +1", - "= Branch3", - "N @@", - "As +1", - "/ Si", - "B H1-1", - "S H1", - "/ 123I", - "3 2", - "= Mg", - "H +1", - "\\ B", - "Si H1", - "P@@ +1", - "- 2", - "1 5", - "1 7", - "3 5", - "= 13CH1", - "C s", - "=N H2+1", - "=S H1", - "Mg H2", - "32 P", - "17 F", - "35 S", - "Cs +1", - "# 11C", - "/ 131I", - "B i", - "\\ 125I", - "=S @@", - "\\S -1", - "6 Br", - "7 I", - "7 6Br", - "= B", - "e H1", - "\\N -1", - "18 O", - "12 7I", - "11C H2", - "14 C@@H1", - "Te H2", - "15 NH1", - "Bi +3", - "/ P+1", - "/ 13C", - "/ 13CH1", - "0 B", - "1 0B", - "= Al", - "= 18O", - "B H0", - "F -1", - "N H3", - "S -2", - "Br +2", - "Cl +2", - "\\S i", - "/S -1", - "=P H2", - "14 C@H1", - "NH3 +1", - "# 14C", - "# O+1", - "- 3", - "2 2", - "4 H", - "5 Se", - "5 Sr+2", - "7 5Se", - "8 5Sr+2", - "= B-1", - "= 13C", - "@ -1", - "B e", - "B @@", - "B @-1", - "C a", - "C H1", - "I +3", - "K H1", - "O H1+1", - "R a+2", - "S H1-1", - "\\ PH1", - "\\ 123I", - "=C a", - "\\C H1-1", - "=S @", - "\\S eH1", - "/S eH1", - "Se -1", - "Li H1", - "18F -1", - "125I H1", - "11C H1", - "Te H1", - "Zn +1", - "Zn -2", - "Al -3", - "13C H3", - "15 N", - "Be +2", - "B@@ -1", - "# P", - "# S", - "- 4", - "/ PH1", - "/ P@@", - "/ As", - "/ 14C", - "/ 14CH1", - "2 K+1", - "2 Rb+1", - "3 Se", - "3 Ra+2", - "4 5", - "4 7", - "4 2K+1", - "5 I-1", - "7 3Se", - "8 9", - "8 2Rb+1", - "= 32", - "= 32P", - "C H0", - "C H2", - "I +2", - "N H0", - "N H4", - "O H1", - "P H2+1", - "S H0", - "S H2", - "\\ 3H", - "\\ 11CH3", - "\\C -1", - "\\S e", - "Si @", - "Si -1", - "Si H1-1", - "Si H3-1", - "/S e", - "Se -2", - "\\NH1 -1", - "18F H1", - "12 5I-1", - "11 C@@H1", - "11 C-1", - "As H1", - "As -1", - "14 C@@", - "Te -1", - "Mg +1", - "123 I-1", - "123 Te", - "123I H1", - "13 5I", - "131 I-1", - "Ag -4", - "124 I-1", - "76Br H1", - "18O H1", - "22 Na+1", - "22 3Ra+2", - "Ca H2", - "45 Ca+2", - "47 Ca+2", - "89 Sr+2", - "=32 PH1", - "NH4 +1" - ] - } -} \ No newline at end of file diff --git a/models/finetuned/sider/checkpoint_epoch_050/tokenizer_config.json b/models/finetuned/sider/checkpoint_epoch_050/tokenizer_config.json deleted file mode 100644 index 08860954acd34fad07fd77f7635298fa565f3149..0000000000000000000000000000000000000000 --- a/models/finetuned/sider/checkpoint_epoch_050/tokenizer_config.json +++ /dev/null @@ -1,65 +0,0 @@ -{ - "add_prefix_space": false, - "bos_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "cls_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "eos_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "errors": "replace", - "mask_token": { - "__type": "AddedToken", - "content": "", - "lstrip": true, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "model_max_length": 1000000000000000019884624838656, - "name_or_path": "/home/erva/SELFormerMM/data/pretrained_multimodal_chembl36", - "pad_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "sep_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "special_tokens_map_file": null, - "tokenizer_class": "RobertaTokenizer", - "trim_offsets": true, - "unk_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - } -} diff --git a/models/finetuned/sider/checkpoint_epoch_050/vocab.json b/models/finetuned/sider/checkpoint_epoch_050/vocab.json deleted file mode 100644 index f7e4cc22809f4e9035cc450ef189c8a7da8fd03e..0000000000000000000000000000000000000000 --- a/models/finetuned/sider/checkpoint_epoch_050/vocab.json +++ /dev/null @@ -1 +0,0 @@ -{"":0,"":1,"":2,"":3,"":4,"\n":5,"#":6,"+":7,"-":8,".":9,"/":10,"0":11,"1":12,"2":13,"3":14,"4":15,"5":16,"6":17,"7":18,"8":19,"9":20,"=":21,"@":22,"A":23,"B":24,"C":25,"F":26,"H":27,"I":28,"K":29,"L":30,"M":31,"N":32,"O":33,"P":34,"R":35,"S":36,"T":37,"Z":38,"\\":39,"a":40,"b":41,"c":42,"e":43,"g":44,"h":45,"i":46,"l":47,"n":48,"r":49,"s":50,"Br":51,"an":52,"ch":53,"Bran":54,"Branch":55,"Branch1":56,"=C":57,"Ri":58,"ng":59,"Ring":60,"Ring1":61,"=Branch1":62,"Branch2":63,"=O":64,"Ring2":65,"H1":66,"C@":67,"=N":68,"#Branch1":69,"C@@":70,"=Branch2":71,"C@H1":72,"C@@H1":73,"#Branch2":74,"#C":75,"Cl":76,"/C":77,"NH1":78,"=Ring1":79,"+1":80,"-1":81,"O-1":82,"N+1":83,"\\C":84,"#N":85,"/N":86,"=Ring2":87,"=S":88,"=N+1":89,"\\N":90,"Na":91,"Na+1":92,"/O":93,"\\O":94,"Br-1":95,"Branch3":96,"\\S":97,"S+1":98,"Cl-1":99,"I-1":100,"/C@@H1":101,"Si":102,"/C@H1":103,"/S":104,"=N-1":105,"Se":106,"=P":107,"N-1":108,"Ring3":109,"2H":110,"P+1":111,"K+1":112,"\\C@@H1":113,"\\C@H1":114,"/N+1":115,"@@":116,"C-1":117,"#N+1":118,"B-1":119,"+3":120,"Cl+3":121,"\\NH1":122,"Li":123,"Li+1":124,"PH1":125,"18":126,"18F":127,"@+1":128,"3H":129,"P@@":130,"H0":131,"OH0":132,"12":133,"P@":134,"+2":135,"@@+1":136,"S-1":137,"/Br":138,"-/":139,"\\Cl":140,"-/Ring2":141,"\\O-1":142,"11":143,"5I":144,"125I":145,"11C":146,"H3":147,"\\N+1":148,"-\\":149,"/C@@":150,"S@+1":151,"As":152,"/Cl":153,"11CH3":154,"=Se":155,"S@@+1":156,"N@+1":157,"14":158,"-\\Ring2":159,"14C":160,"\\F":161,"/C@":162,"Te":163,"H2":164,"H1-1":165,"=O+1":166,"N@@+1":167,"C+1":168,"=S+1":169,"Zn":170,"/P":171,"a+2":172,"/I":173,"OH1-1":174,"Ca+2":175,"\\Br":176,"Mg":177,"Zn+2":178,"Al":179,"/F":180,"Mg+2":181,"123":182,"123I":183,"13":184,"I+1":185,"/O-1":186,"-\\Ring1":187,"BH2":188,"BH2-1":189,"\\I":190,"/NH1":191,"O+1":192,"131":193,"131I":194,"=14C":195,"/S+1":196,"=Ring3":197,"\\C@@":198,"H2+1":199,"\\C@":200,"Ag":201,"=As":202,"=Se+1":203,"NH2+1":204,"SeH1":205,"-/Ring1":206,"=Te":207,"Al+3":208,"NaH1":209,"=Te+1":210,"NH1+1":211,"Ag+1":212,"H1+1":213,"NH1-1":214,"\\P":215,"14CH2":216,"13C":217,"14CH1":218,"=11C":219,"S@@":220,"=P@@":221,"SiH2":222,"H3-1":223,"14CH3":224,"BH3-1":225,"S@":226,"=14CH1":227,"=PH1":228,"=P@":229,"=NH1+1":230,"\\S+1":231,"124":232,"CH1-1":233,"Sr":234,"=Si":235,"124I":236,"Sr+2":237,"#C-1":238,"/C-1":239,"N@":240,"/N-1":241,"13CH1":242,"/B":243,"19":244,"Ba+2":245,"H4":246,"SH1+1":247,"Se+1":248,"19F":249,"/125I":250,"P@+1":251,"Rb":252,"Cl+1":253,"SiH4":254,"Rb+1":255,"=Branch3":256,"N@@":257,"As+1":258,"/Si":259,"BH1-1":260,"SH1":261,"/123I":262,"32":263,"=Mg":264,"H+1":265,"\\B":266,"SiH1":267,"P@@+1":268,"-2":269,"15":270,"17":271,"35":272,"=13CH1":273,"Cs":274,"=NH2+1":275,"=SH1":276,"MgH2":277,"32P":278,"17F":279,"35S":280,"Cs+1":281,"#11C":282,"/131I":283,"Bi":284,"\\125I":285,"=S@@":286,"\\S-1":287,"6Br":288,"7I":289,"76Br":290,"=B":291,"eH1":292,"\\N-1":293,"18O":294,"127I":295,"11CH2":296,"14C@@H1":297,"TeH2":298,"15NH1":299,"Bi+3":300,"/P+1":301,"/13C":302,"/13CH1":303,"0B":304,"10B":305,"=Al":306,"=18O":307,"BH0":308,"F-1":309,"NH3":310,"S-2":311,"Br+2":312,"Cl+2":313,"\\Si":314,"/S-1":315,"=PH2":316,"14C@H1":317,"NH3+1":318,"#14C":319,"#O+1":320,"-3":321,"22":322,"4H":323,"5Se":324,"5Sr+2":325,"75Se":326,"85Sr+2":327,"=B-1":328,"=13C":329,"@-1":330,"Be":331,"B@@":332,"B@-1":333,"Ca":334,"CH1":335,"I+3":336,"KH1":337,"OH1+1":338,"Ra+2":339,"SH1-1":340,"\\PH1":341,"\\123I":342,"=Ca":343,"\\CH1-1":344,"=S@":345,"\\SeH1":346,"/SeH1":347,"Se-1":348,"LiH1":349,"18F-1":350,"125IH1":351,"11CH1":352,"TeH1":353,"Zn+1":354,"Zn-2":355,"Al-3":356,"13CH3":357,"15N":358,"Be+2":359,"B@@-1":360,"#P":361,"#S":362,"-4":363,"/PH1":364,"/P@@":365,"/As":366,"/14C":367,"/14CH1":368,"2K+1":369,"2Rb+1":370,"3Se":371,"3Ra+2":372,"45":373,"47":374,"42K+1":375,"5I-1":376,"73Se":377,"89":378,"82Rb+1":379,"=32":380,"=32P":381,"CH0":382,"CH2":383,"I+2":384,"NH0":385,"NH4":386,"OH1":387,"PH2+1":388,"SH0":389,"SH2":390,"\\3H":391,"\\11CH3":392,"\\C-1":393,"\\Se":394,"Si@":395,"Si-1":396,"SiH1-1":397,"SiH3-1":398,"/Se":399,"Se-2":400,"\\NH1-1":401,"18FH1":402,"125I-1":403,"11C@@H1":404,"11C-1":405,"AsH1":406,"As-1":407,"14C@@":408,"Te-1":409,"Mg+1":410,"123I-1":411,"123Te":412,"123IH1":413,"135I":414,"131I-1":415,"Ag-4":416,"124I-1":417,"76BrH1":418,"18OH1":419,"22Na+1":420,"223Ra+2":421,"CaH2":422,"45Ca+2":423,"47Ca+2":424,"89Sr+2":425,"=32PH1":426,"NH4+1":427} \ No newline at end of file diff --git a/models/finetuned/sider/config.json b/models/finetuned/sider/config.json deleted file mode 100644 index 3811e21539577b37e06313eab31ec11e53f0cbbc..0000000000000000000000000000000000000000 --- a/models/finetuned/sider/config.json +++ /dev/null @@ -1,27 +0,0 @@ -{ - "_name_or_path": "/home/erva/SELFormerMM/data/pretrained_multimodal_chembl36", - "architectures": [ - "RobertaForMaskedLM" - ], - "attention_probs_dropout_prob": 0.1, - "bos_token_id": 0, - "classifier_dropout": null, - "eos_token_id": 2, - "hidden_act": "gelu", - "hidden_dropout_prob": 0.1, - "hidden_size": 768, - "initializer_range": 0.02, - "intermediate_size": 3072, - "layer_norm_eps": 1e-12, - "max_position_embeddings": 514, - "model_type": "roberta", - "num_attention_heads": 4, - "num_hidden_layers": 12, - "pad_token_id": 1, - "position_embedding_type": "absolute", - "torch_dtype": "float32", - "transformers_version": "4.26.1", - "type_vocab_size": 1, - "use_cache": true, - "vocab_size": 800 -} diff --git a/models/finetuned/sider/merges.txt b/models/finetuned/sider/merges.txt deleted file mode 100644 index 7cd5ec62809503c23f18c80afc0ba3bdf9d253d0..0000000000000000000000000000000000000000 --- a/models/finetuned/sider/merges.txt +++ /dev/null @@ -1,378 +0,0 @@ -#version: 0.2 - Trained by `huggingface/tokenizers` -B r -a n -c h -Br an -Bran ch -Branch 1 -= C -R i -n g -Ri ng -Ring 1 -= Branch1 -Branch 2 -= O -Ring 2 -H 1 -C @ -= N -# Branch1 -C@ @ -= Branch2 -C@ H1 -C@@ H1 -# Branch2 -# C -C l -/ C -N H1 -= Ring1 -+ 1 -- 1 -O -1 -N +1 -\ C -# N -/ N -= Ring2 -= S -=N +1 -\ N -N a -Na +1 -/ O -\ O -Br -1 -Branch 3 -\ S -S +1 -Cl -1 -I -1 -/ C@@H1 -S i -/ C@H1 -/ S -=N -1 -S e -= P -N -1 -Ring 3 -2 H -P +1 -K +1 -\ C@@H1 -\ C@H1 -/ N+1 -@ @ -C -1 -# N+1 -B -1 -+ 3 -Cl +3 -\ NH1 -L i -Li +1 -P H1 -1 8 -18 F -@ +1 -3 H -P @@ -H 0 -O H0 -1 2 -P @ -+ 2 -@@ +1 -S -1 -/ Br -- / -\ Cl --/ Ring2 -\ O-1 -1 1 -5 I -12 5I -11 C -H 3 -\ N+1 -- \ -/ C@@ -S @+1 -A s -/ Cl -11C H3 -=S e -S @@+1 -N @+1 -1 4 --\ Ring2 -14 C -\ F -/ C@ -T e -H 2 -H1 -1 -=O +1 -N @@+1 -C +1 -=S +1 -Z n -/ P -a +2 -/ I -O H1-1 -C a+2 -\ Br -M g -Zn +2 -A l -/ F -Mg +2 -12 3 -123 I -1 3 -I +1 -/ O-1 --\ Ring1 -B H2 -BH2 -1 -\ I -/ NH1 -O +1 -13 1 -131 I -= 14C -/ S+1 -= Ring3 -\ C@@ -H2 +1 -\ C@ -A g -= As -=Se +1 -N H2+1 -Se H1 --/ Ring1 -= Te -Al +3 -Na H1 -=Te +1 -NH1 +1 -Ag +1 -H1 +1 -NH1 -1 -\ P -14C H2 -13 C -14C H1 -= 11C -S @@ -=P @@ -Si H2 -H3 -1 -14C H3 -B H3-1 -S @ -=14C H1 -=P H1 -=P @ -=N H1+1 -\S +1 -12 4 -C H1-1 -S r -=S i -124 I -Sr +2 -#C -1 -/C -1 -N @ -/N -1 -13C H1 -/ B -1 9 -B a+2 -H 4 -S H1+1 -Se +1 -19 F -/ 125I -P @+1 -R b -Cl +1 -Si H4 -Rb +1 -= Branch3 -N @@ -As +1 -/ Si -B H1-1 -S H1 -/ 123I -3 2 -= Mg -H +1 -\ B -Si H1 -P@@ +1 -- 2 -1 5 -1 7 -3 5 -= 13CH1 -C s -=N H2+1 -=S H1 -Mg H2 -32 P -17 F -35 S -Cs +1 -# 11C -/ 131I -B i -\ 125I -=S @@ -\S -1 -6 Br -7 I -7 6Br -= B -e H1 -\N -1 -18 O -12 7I -11C H2 -14 C@@H1 -Te H2 -15 NH1 -Bi +3 -/ P+1 -/ 13C -/ 13CH1 -0 B -1 0B -= Al -= 18O -B H0 -F -1 -N H3 -S -2 -Br +2 -Cl +2 -\S i -/S -1 -=P H2 -14 C@H1 -NH3 +1 -# 14C -# O+1 -- 3 -2 2 -4 H -5 Se -5 Sr+2 -7 5Se -8 5Sr+2 -= B-1 -= 13C -@ -1 -B e -B @@ -B @-1 -C a -C H1 -I +3 -K H1 -O H1+1 -R a+2 -S H1-1 -\ PH1 -\ 123I -=C a -\C H1-1 -=S @ -\S eH1 -/S eH1 -Se -1 -Li H1 -18F -1 -125I H1 -11C H1 -Te H1 -Zn +1 -Zn -2 -Al -3 -13C H3 -15 N -Be +2 -B@@ -1 -# P -# S -- 4 -/ PH1 -/ P@@ -/ As -/ 14C -/ 14CH1 -2 K+1 -2 Rb+1 -3 Se -3 Ra+2 -4 5 -4 7 -4 2K+1 -5 I-1 -7 3Se -8 9 -8 2Rb+1 -= 32 -= 32P -C H0 -C H2 -I +2 -N H0 -N H4 -O H1 -P H2+1 -S H0 -S H2 -\ 3H -\ 11CH3 -\C -1 -\S e -Si @ -Si -1 -Si H1-1 -Si H3-1 -/S e -Se -2 -\NH1 -1 -18F H1 -12 5I-1 -11 C@@H1 -11 C-1 -As H1 -As -1 -14 C@@ -Te -1 -Mg +1 -123 I-1 -123 Te -123I H1 -13 5I -131 I-1 -Ag -4 -124 I-1 -76Br H1 -18O H1 -22 Na+1 -22 3Ra+2 -Ca H2 -45 Ca+2 -47 Ca+2 -89 Sr+2 -=32 PH1 -NH4 +1 diff --git a/models/finetuned/sider/model.pt b/models/finetuned/sider/model.pt deleted file mode 100644 index d5262ada0a1773d2f5142c00c258de47e32fbb41..0000000000000000000000000000000000000000 --- a/models/finetuned/sider/model.pt +++ /dev/null @@ -1,3 +0,0 @@ -version https://git-lfs.github.com/spec/v1 -oid sha256:da1c7d30cd890211ba9b7db75d9c59a4b465aa3ca4e8de458cad8b54e2af215d -size 1023174845 diff --git a/models/finetuned/sider/special_tokens_map.json b/models/finetuned/sider/special_tokens_map.json deleted file mode 100644 index 06a55849fa69a91e7179d909e373179ff7467d8c..0000000000000000000000000000000000000000 --- a/models/finetuned/sider/special_tokens_map.json +++ /dev/null @@ -1,51 +0,0 @@ -{ - "bos_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "cls_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "eos_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "mask_token": { - "content": "", - "lstrip": true, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "pad_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "sep_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "unk_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - } -} diff --git a/models/finetuned/sider/tokenizer.json b/models/finetuned/sider/tokenizer.json deleted file mode 100644 index 3b64b273e6fa9799e2d8375722b9e815de9ebb8f..0000000000000000000000000000000000000000 --- a/models/finetuned/sider/tokenizer.json +++ /dev/null @@ -1,909 +0,0 @@ -{ - "version": "1.0", - "truncation": { - "direction": "Right", - "max_length": 128, - "strategy": "LongestFirst", - "stride": 0 - }, - "padding": { - "strategy": { - "Fixed": 128 - }, - "direction": "Right", - "pad_to_multiple_of": null, - "pad_id": 3, - "pad_type_id": 0, - "pad_token": "" - }, - "added_tokens": [ - { - "id": 0, - "content": "", - "single_word": false, - "lstrip": false, - "rstrip": false, - "normalized": true, - "special": true - }, - { - "id": 1, - "content": "", - "single_word": false, - "lstrip": false, - "rstrip": false, - "normalized": true, - "special": true - }, - { - "id": 2, - "content": "", - "single_word": false, - "lstrip": false, - "rstrip": false, - "normalized": true, - "special": true - }, - { - "id": 3, - "content": "", - "single_word": false, - "lstrip": false, - "rstrip": false, - "normalized": true, - "special": true - }, - { - "id": 4, - "content": "", - "single_word": false, - "lstrip": true, - "rstrip": false, - "normalized": true, - "special": true - } - ], - "normalizer": null, - "pre_tokenizer": { - "type": "ByteLevel", - "add_prefix_space": false, - "trim_offsets": true, - "use_regex": true - }, - "post_processor": { - "type": "RobertaProcessing", - "sep": [ - "", - 2 - ], - "cls": [ - "", - 1 - ], - "trim_offsets": true, - "add_prefix_space": false - }, - "decoder": { - "type": "ByteLevel", - "add_prefix_space": true, - "trim_offsets": true, - "use_regex": true - }, - "model": { - "type": "BPE", - "dropout": null, - "unk_token": null, - "continuing_subword_prefix": "", - "end_of_word_suffix": "", - "fuse_unk": false, - "vocab": { - "": 0, - "": 1, - "": 2, - "": 3, - "": 4, - "\n": 5, - "#": 6, - "+": 7, - "-": 8, - ".": 9, - "/": 10, - "0": 11, - "1": 12, - "2": 13, - "3": 14, - "4": 15, - "5": 16, - "6": 17, - "7": 18, - "8": 19, - "9": 20, - "=": 21, - "@": 22, - "A": 23, - "B": 24, - "C": 25, - "F": 26, - "H": 27, - "I": 28, - "K": 29, - "L": 30, - "M": 31, - "N": 32, - "O": 33, - "P": 34, - "R": 35, - "S": 36, - "T": 37, - "Z": 38, - "\\": 39, - "a": 40, - "b": 41, - "c": 42, - "e": 43, - "g": 44, - "h": 45, - "i": 46, - "l": 47, - "n": 48, - "r": 49, - "s": 50, - "Br": 51, - "an": 52, - "ch": 53, - "Bran": 54, - "Branch": 55, - "Branch1": 56, - "=C": 57, - "Ri": 58, - "ng": 59, - "Ring": 60, - "Ring1": 61, - "=Branch1": 62, - "Branch2": 63, - "=O": 64, - "Ring2": 65, - "H1": 66, - "C@": 67, - "=N": 68, - "#Branch1": 69, - "C@@": 70, - "=Branch2": 71, - "C@H1": 72, - "C@@H1": 73, - "#Branch2": 74, - "#C": 75, - "Cl": 76, - "/C": 77, - "NH1": 78, - "=Ring1": 79, - "+1": 80, - "-1": 81, - "O-1": 82, - "N+1": 83, - "\\C": 84, - "#N": 85, - "/N": 86, - "=Ring2": 87, - "=S": 88, - "=N+1": 89, - "\\N": 90, - "Na": 91, - "Na+1": 92, - "/O": 93, - "\\O": 94, - "Br-1": 95, - "Branch3": 96, - "\\S": 97, - "S+1": 98, - "Cl-1": 99, - "I-1": 100, - "/C@@H1": 101, - "Si": 102, - "/C@H1": 103, - "/S": 104, - "=N-1": 105, - "Se": 106, - "=P": 107, - "N-1": 108, - "Ring3": 109, - "2H": 110, - "P+1": 111, - "K+1": 112, - "\\C@@H1": 113, - "\\C@H1": 114, - "/N+1": 115, - "@@": 116, - "C-1": 117, - "#N+1": 118, - "B-1": 119, - "+3": 120, - "Cl+3": 121, - "\\NH1": 122, - "Li": 123, - "Li+1": 124, - "PH1": 125, - "18": 126, - "18F": 127, - "@+1": 128, - "3H": 129, - "P@@": 130, - "H0": 131, - "OH0": 132, - "12": 133, - "P@": 134, - "+2": 135, - "@@+1": 136, - "S-1": 137, - "/Br": 138, - "-/": 139, - "\\Cl": 140, - "-/Ring2": 141, - "\\O-1": 142, - "11": 143, - "5I": 144, - "125I": 145, - "11C": 146, - "H3": 147, - "\\N+1": 148, - "-\\": 149, - "/C@@": 150, - "S@+1": 151, - "As": 152, - "/Cl": 153, - "11CH3": 154, - "=Se": 155, - "S@@+1": 156, - "N@+1": 157, - "14": 158, - "-\\Ring2": 159, - "14C": 160, - "\\F": 161, - "/C@": 162, - "Te": 163, - "H2": 164, - "H1-1": 165, - "=O+1": 166, - "N@@+1": 167, - "C+1": 168, - "=S+1": 169, - "Zn": 170, - "/P": 171, - "a+2": 172, - "/I": 173, - "OH1-1": 174, - "Ca+2": 175, - "\\Br": 176, - "Mg": 177, - "Zn+2": 178, - "Al": 179, - "/F": 180, - "Mg+2": 181, - "123": 182, - "123I": 183, - "13": 184, - "I+1": 185, - "/O-1": 186, - "-\\Ring1": 187, - "BH2": 188, - "BH2-1": 189, - "\\I": 190, - "/NH1": 191, - "O+1": 192, - "131": 193, - "131I": 194, - "=14C": 195, - "/S+1": 196, - "=Ring3": 197, - "\\C@@": 198, - "H2+1": 199, - "\\C@": 200, - "Ag": 201, - "=As": 202, - "=Se+1": 203, - "NH2+1": 204, - "SeH1": 205, - "-/Ring1": 206, - "=Te": 207, - "Al+3": 208, - "NaH1": 209, - "=Te+1": 210, - "NH1+1": 211, - "Ag+1": 212, - "H1+1": 213, - "NH1-1": 214, - "\\P": 215, - "14CH2": 216, - "13C": 217, - "14CH1": 218, - "=11C": 219, - "S@@": 220, - "=P@@": 221, - "SiH2": 222, - "H3-1": 223, - "14CH3": 224, - "BH3-1": 225, - "S@": 226, - "=14CH1": 227, - "=PH1": 228, - "=P@": 229, - "=NH1+1": 230, - "\\S+1": 231, - "124": 232, - "CH1-1": 233, - "Sr": 234, - "=Si": 235, - "124I": 236, - "Sr+2": 237, - "#C-1": 238, - "/C-1": 239, - "N@": 240, - "/N-1": 241, - "13CH1": 242, - "/B": 243, - "19": 244, - "Ba+2": 245, - "H4": 246, - "SH1+1": 247, - "Se+1": 248, - "19F": 249, - "/125I": 250, - "P@+1": 251, - "Rb": 252, - "Cl+1": 253, - "SiH4": 254, - "Rb+1": 255, - "=Branch3": 256, - "N@@": 257, - "As+1": 258, - "/Si": 259, - "BH1-1": 260, - "SH1": 261, - "/123I": 262, - "32": 263, - "=Mg": 264, - "H+1": 265, - "\\B": 266, - "SiH1": 267, - "P@@+1": 268, - "-2": 269, - "15": 270, - "17": 271, - "35": 272, - "=13CH1": 273, - "Cs": 274, - "=NH2+1": 275, - "=SH1": 276, - "MgH2": 277, - "32P": 278, - "17F": 279, - "35S": 280, - "Cs+1": 281, - "#11C": 282, - "/131I": 283, - "Bi": 284, - "\\125I": 285, - "=S@@": 286, - "\\S-1": 287, - "6Br": 288, - "7I": 289, - "76Br": 290, - "=B": 291, - "eH1": 292, - "\\N-1": 293, - "18O": 294, - "127I": 295, - "11CH2": 296, - "14C@@H1": 297, - "TeH2": 298, - "15NH1": 299, - "Bi+3": 300, - "/P+1": 301, - "/13C": 302, - "/13CH1": 303, - "0B": 304, - "10B": 305, - "=Al": 306, - "=18O": 307, - "BH0": 308, - "F-1": 309, - "NH3": 310, - "S-2": 311, - "Br+2": 312, - "Cl+2": 313, - "\\Si": 314, - "/S-1": 315, - "=PH2": 316, - "14C@H1": 317, - "NH3+1": 318, - "#14C": 319, - "#O+1": 320, - "-3": 321, - "22": 322, - "4H": 323, - "5Se": 324, - "5Sr+2": 325, - "75Se": 326, - "85Sr+2": 327, - "=B-1": 328, - "=13C": 329, - "@-1": 330, - "Be": 331, - "B@@": 332, - "B@-1": 333, - "Ca": 334, - "CH1": 335, - "I+3": 336, - "KH1": 337, - "OH1+1": 338, - "Ra+2": 339, - "SH1-1": 340, - "\\PH1": 341, - "\\123I": 342, - "=Ca": 343, - "\\CH1-1": 344, - "=S@": 345, - "\\SeH1": 346, - "/SeH1": 347, - "Se-1": 348, - "LiH1": 349, - "18F-1": 350, - "125IH1": 351, - "11CH1": 352, - "TeH1": 353, - "Zn+1": 354, - "Zn-2": 355, - "Al-3": 356, - "13CH3": 357, - "15N": 358, - "Be+2": 359, - "B@@-1": 360, - "#P": 361, - "#S": 362, - "-4": 363, - "/PH1": 364, - "/P@@": 365, - "/As": 366, - "/14C": 367, - "/14CH1": 368, - "2K+1": 369, - "2Rb+1": 370, - "3Se": 371, - "3Ra+2": 372, - "45": 373, - "47": 374, - "42K+1": 375, - "5I-1": 376, - "73Se": 377, - "89": 378, - "82Rb+1": 379, - "=32": 380, - "=32P": 381, - "CH0": 382, - "CH2": 383, - "I+2": 384, - "NH0": 385, - "NH4": 386, - "OH1": 387, - "PH2+1": 388, - "SH0": 389, - "SH2": 390, - "\\3H": 391, - "\\11CH3": 392, - "\\C-1": 393, - "\\Se": 394, - "Si@": 395, - "Si-1": 396, - "SiH1-1": 397, - "SiH3-1": 398, - "/Se": 399, - "Se-2": 400, - "\\NH1-1": 401, - "18FH1": 402, - "125I-1": 403, - "11C@@H1": 404, - "11C-1": 405, - "AsH1": 406, - "As-1": 407, - "14C@@": 408, - "Te-1": 409, - "Mg+1": 410, - "123I-1": 411, - "123Te": 412, - "123IH1": 413, - "135I": 414, - "131I-1": 415, - "Ag-4": 416, - "124I-1": 417, - "76BrH1": 418, - "18OH1": 419, - "22Na+1": 420, - "223Ra+2": 421, - "CaH2": 422, - "45Ca+2": 423, - "47Ca+2": 424, - "89Sr+2": 425, - "=32PH1": 426, - "NH4+1": 427 - }, - "merges": [ - "B r", - "a n", - "c h", - "Br an", - "Bran ch", - "Branch 1", - "= C", - "R i", - "n g", - "Ri ng", - "Ring 1", - "= Branch1", - "Branch 2", - "= O", - "Ring 2", - "H 1", - "C @", - "= N", - "# Branch1", - "C@ @", - "= Branch2", - "C@ H1", - "C@@ H1", - "# Branch2", - "# C", - "C l", - "/ C", - "N H1", - "= Ring1", - "+ 1", - "- 1", - "O -1", - "N +1", - "\\ C", - "# N", - "/ N", - "= Ring2", - "= S", - "=N +1", - "\\ N", - "N a", - "Na +1", - "/ O", - "\\ O", - "Br -1", - "Branch 3", - "\\ S", - "S +1", - "Cl -1", - "I -1", - "/ C@@H1", - "S i", - "/ C@H1", - "/ S", - "=N -1", - "S e", - "= P", - "N -1", - "Ring 3", - "2 H", - "P +1", - "K +1", - "\\ C@@H1", - "\\ C@H1", - "/ N+1", - "@ @", - "C -1", - "# N+1", - "B -1", - "+ 3", - "Cl +3", - "\\ NH1", - "L i", - "Li +1", - "P H1", - "1 8", - "18 F", - "@ +1", - "3 H", - "P @@", - "H 0", - "O H0", - "1 2", - "P @", - "+ 2", - "@@ +1", - "S -1", - "/ Br", - "- /", - "\\ Cl", - "-/ Ring2", - "\\ O-1", - "1 1", - "5 I", - "12 5I", - "11 C", - "H 3", - "\\ N+1", - "- \\", - "/ C@@", - "S @+1", - "A s", - "/ Cl", - "11C H3", - "=S e", - "S @@+1", - "N @+1", - "1 4", - "-\\ Ring2", - "14 C", - "\\ F", - "/ C@", - "T e", - "H 2", - "H1 -1", - "=O +1", - "N @@+1", - "C +1", - "=S +1", - "Z n", - "/ P", - "a +2", - "/ I", - "O H1-1", - "C a+2", - "\\ Br", - "M g", - "Zn +2", - "A l", - "/ F", - "Mg +2", - "12 3", - "123 I", - "1 3", - "I +1", - "/ O-1", - "-\\ Ring1", - "B H2", - "BH2 -1", - "\\ I", - "/ NH1", - "O +1", - "13 1", - "131 I", - "= 14C", - "/ S+1", - "= Ring3", - "\\ C@@", - "H2 +1", - "\\ C@", - "A g", - "= As", - "=Se +1", - "N H2+1", - "Se H1", - "-/ Ring1", - "= Te", - "Al +3", - "Na H1", - "=Te +1", - "NH1 +1", - "Ag +1", - "H1 +1", - "NH1 -1", - "\\ P", - "14C H2", - "13 C", - "14C H1", - "= 11C", - "S @@", - "=P @@", - "Si H2", - "H3 -1", - "14C H3", - "B H3-1", - "S @", - "=14C H1", - "=P H1", - "=P @", - "=N H1+1", - "\\S +1", - "12 4", - "C H1-1", - "S r", - "=S i", - "124 I", - "Sr +2", - "#C -1", - "/C -1", - "N @", - "/N -1", - "13C H1", - "/ B", - "1 9", - "B a+2", - "H 4", - "S H1+1", - "Se +1", - "19 F", - "/ 125I", - "P @+1", - "R b", - "Cl +1", - "Si H4", - "Rb +1", - "= Branch3", - "N @@", - "As +1", - "/ Si", - "B H1-1", - "S H1", - "/ 123I", - "3 2", - "= Mg", - "H +1", - "\\ B", - "Si H1", - "P@@ +1", - "- 2", - "1 5", - "1 7", - "3 5", - "= 13CH1", - "C s", - "=N H2+1", - "=S H1", - "Mg H2", - "32 P", - "17 F", - "35 S", - "Cs +1", - "# 11C", - "/ 131I", - "B i", - "\\ 125I", - "=S @@", - "\\S -1", - "6 Br", - "7 I", - "7 6Br", - "= B", - "e H1", - "\\N -1", - "18 O", - "12 7I", - "11C H2", - "14 C@@H1", - "Te H2", - "15 NH1", - "Bi +3", - "/ P+1", - "/ 13C", - "/ 13CH1", - "0 B", - "1 0B", - "= Al", - "= 18O", - "B H0", - "F -1", - "N H3", - "S -2", - "Br +2", - "Cl +2", - "\\S i", - "/S -1", - "=P H2", - "14 C@H1", - "NH3 +1", - "# 14C", - "# O+1", - "- 3", - "2 2", - "4 H", - "5 Se", - "5 Sr+2", - "7 5Se", - "8 5Sr+2", - "= B-1", - "= 13C", - "@ -1", - "B e", - "B @@", - "B @-1", - "C a", - "C H1", - "I +3", - "K H1", - "O H1+1", - "R a+2", - "S H1-1", - "\\ PH1", - "\\ 123I", - "=C a", - "\\C H1-1", - "=S @", - "\\S eH1", - "/S eH1", - "Se -1", - "Li H1", - "18F -1", - "125I H1", - "11C H1", - "Te H1", - "Zn +1", - "Zn -2", - "Al -3", - "13C H3", - "15 N", - "Be +2", - "B@@ -1", - "# P", - "# S", - "- 4", - "/ PH1", - "/ P@@", - "/ As", - "/ 14C", - "/ 14CH1", - "2 K+1", - "2 Rb+1", - "3 Se", - "3 Ra+2", - "4 5", - "4 7", - "4 2K+1", - "5 I-1", - "7 3Se", - "8 9", - "8 2Rb+1", - "= 32", - "= 32P", - "C H0", - "C H2", - "I +2", - "N H0", - "N H4", - "O H1", - "P H2+1", - "S H0", - "S H2", - "\\ 3H", - "\\ 11CH3", - "\\C -1", - "\\S e", - "Si @", - "Si -1", - "Si H1-1", - "Si H3-1", - "/S e", - "Se -2", - "\\NH1 -1", - "18F H1", - "12 5I-1", - "11 C@@H1", - "11 C-1", - "As H1", - "As -1", - "14 C@@", - "Te -1", - "Mg +1", - "123 I-1", - "123 Te", - "123I H1", - "13 5I", - "131 I-1", - "Ag -4", - "124 I-1", - "76Br H1", - "18O H1", - "22 Na+1", - "22 3Ra+2", - "Ca H2", - "45 Ca+2", - "47 Ca+2", - "89 Sr+2", - "=32 PH1", - "NH4 +1" - ] - } -} \ No newline at end of file diff --git a/models/finetuned/sider/tokenizer_config.json b/models/finetuned/sider/tokenizer_config.json deleted file mode 100644 index 08860954acd34fad07fd77f7635298fa565f3149..0000000000000000000000000000000000000000 --- a/models/finetuned/sider/tokenizer_config.json +++ /dev/null @@ -1,65 +0,0 @@ -{ - "add_prefix_space": false, - "bos_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "cls_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "eos_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "errors": "replace", - "mask_token": { - "__type": "AddedToken", - "content": "", - "lstrip": true, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "model_max_length": 1000000000000000019884624838656, - "name_or_path": "/home/erva/SELFormerMM/data/pretrained_multimodal_chembl36", - "pad_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "sep_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "special_tokens_map_file": null, - "tokenizer_class": "RobertaTokenizer", - "trim_offsets": true, - "unk_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - } -} diff --git a/models/finetuned/sider/train_stdout.log b/models/finetuned/sider/train_stdout.log deleted file mode 100644 index a523764f132bdef6e1ba601f9f150225da05096f..0000000000000000000000000000000000000000 --- a/models/finetuned/sider/train_stdout.log +++ /dev/null @@ -1,86 +0,0 @@ -[finetune] starting -[finetune] device=cuda task_type=multilabel batch_size=16 max_len=128 backbone_lr=1e-05 head_lr=0.0005 weight_decay=0.001 epochs=50 -[finetune] dataset_meta_csv=/home/erva/SELFormerMM/data/new_finetuning_datasets/classification/sider/sider.csv -[finetune] dataset_embs_npz=/home/erva/SELFormerMM/data/new_finetuning_datasets/classification/sider/sider_embs.npz -[finetune] model_path=HUBioDataLab/SELFormer tokenizer_path=HUBioDataLab/SELFormer -[finetune] pretrained_multimodal_dir=/home/erva/SELFormerMM/data/pretrained_multimodal_chembl36 -[finetune] use_scaffold=False seed=42 fracs=(0.8,0.1,0.1) -[finetune] loading dataset bundle (meta csv + embs npz) ... -[finetune] splitting dataset... -[finetune] split sizes: train=1,141 val=143 test=143 -[finetune] train modality_non_empty: graph=1,040/1,141 text=922/1,141 kg=24/1,141 -[finetune] val modality_non_empty: graph=132/143 text=115/143 kg=2/143 -[finetune] test modality_non_empty: graph=127/143 text=114/143 kg=1/143 -[finetune] extracting labels... -[finetune] multilabel: num_labels_in_csv=28 -[finetune] loading config/tokenizer/backbone... -[finetune] initializing multimodal model... -[finetune] loading multimodal pretrained weights: /home/erva/SELFormerMM/data/pretrained_multimodal_chembl36/pytorch_model.bin -[finetune] freezing roberta layers (trainable: encoder.layer.9-11)... -[finetune] backbone trainable params: 181,443,072/246,245,376 -[finetune] building datasets/dataloaders... -[finetune] train_steps_per_epoch=72 val_steps=9 test_steps=9 -[finetune] overriding --num_labels=1 with num_labels_in_csv=28 -[finetune] initialized head: in_dim=3072 out=28 -[finetune] initializing optimizer/scheduler/finetuner... -[finetune] optimizer groups: backbone_decay=45 backbone_nodecay=57 head_decay=2 head_nodecay=2 -[finetune] training loop... -[finetune] epoch 1/50: train_loss=-2463.0879 val_loss=-8632.9700 time=19.9s tod=04:59 -[finetune] epoch 2/50: train_loss=-29240.3907 val_loss=-28515.0196 time=19.6s tod=04:59 -[finetune] epoch 3/50: train_loss=-56493.8012 val_loss=-42786.8129 time=19.4s tod=05:00 -[finetune] epoch 4/50: train_loss=-78403.9442 val_loss=-54933.7142 time=17.1s tod=05:00 -[finetune] epoch 5/50: train_loss=-98390.0560 val_loss=-61163.0579 time=13.3s tod=05:00 -[finetune] epoch 6/50: train_loss=-73340.5962 val_loss=-70785.7020 time=13.2s tod=05:01 -[finetune] epoch 7/50: train_loss=-102700.5125 val_loss=-16367.9551 time=16.9s tod=05:01 -[finetune] epoch 8/50: train_loss=-75565.5855 val_loss=-87597.7900 time=19.6s tod=05:01 -[finetune] epoch 9/50: train_loss=-101224.8124 val_loss=-56896.3166 time=19.6s tod=05:01 -[finetune] epoch 10/50: train_loss=-100191.3469 val_loss=-102080.0145 time=19.4s tod=05:02 -[finetune] epoch 11/50: train_loss=-141172.0164 val_loss=-109301.1324 time=19.6s tod=05:02 -[finetune] epoch 12/50: train_loss=-169078.9591 val_loss=-37835.9162 time=19.6s tod=05:02 -[finetune] epoch 13/50: train_loss=-96474.2053 val_loss=-30286.5900 time=19.5s tod=05:03 -[finetune] epoch 14/50: train_loss=-105256.3000 val_loss=-35972.5983 time=19.6s tod=05:03 -[finetune] epoch 15/50: train_loss=-178900.2351 val_loss=-37852.0637 time=19.7s tod=05:03 -[finetune] epoch 16/50: train_loss=-186680.4031 val_loss=-37577.4352 time=19.5s tod=05:04 -[finetune] epoch 17/50: train_loss=-195649.4959 val_loss=-90268.9497 time=19.5s tod=05:04 -[finetune] epoch 18/50: train_loss=-220532.2620 val_loss=-46100.1349 time=19.6s tod=05:04 -[finetune] epoch 19/50: train_loss=-246434.8544 val_loss=-46121.6348 time=19.6s tod=05:05 -[finetune] epoch 20/50: train_loss=-250533.9357 val_loss=-44846.5984 time=19.6s tod=05:05 -[finetune] epoch 21/50: train_loss=-269410.9093 val_loss=-48019.9503 time=19.6s tod=05:05 -[finetune] epoch 22/50: train_loss=-313211.1312 val_loss=-75566.5165 time=19.5s tod=05:06 -[finetune] epoch 23/50: train_loss=-327284.1272 val_loss=-58031.5497 time=19.5s tod=05:06 -[finetune] epoch 24/50: train_loss=-352373.0084 val_loss=-57549.3987 time=19.6s tod=05:06 -[finetune] epoch 25/50: train_loss=-364050.6847 val_loss=-54414.9680 time=18.6s tod=05:07 -[finetune] test_metrics: epoch=25 loss=-88607.4092 accuracy=0.7391 precision=0.7331 recall=0.8057 f1=0.7677 roc-auc=0.7350 prc-auc=0.7070 -[finetune] saved checkpoint (best roc-auc=0.7350): /media/ubuntu/8TB/erva/selformer-mm/output/new_finetune_sweeps/sider/ew0k1kqo/checkpoint_epoch_025 -[finetune] epoch 26/50: train_loss=-385099.2705 val_loss=-54985.2346 time=19.4s tod=05:07 -[finetune] epoch 27/50: train_loss=-399822.8386 val_loss=-56467.5216 time=19.7s tod=05:07 -[finetune] epoch 28/50: train_loss=-415828.3384 val_loss=-52419.7444 time=19.5s tod=05:08 -[finetune] epoch 29/50: train_loss=-431865.9807 val_loss=-62103.1590 time=19.5s tod=05:08 -[finetune] epoch 30/50: train_loss=-447456.9427 val_loss=-56188.3156 time=19.6s tod=05:08 -[finetune] epoch 31/50: train_loss=-462273.6884 val_loss=-54661.3517 time=19.5s tod=05:09 -[finetune] epoch 32/50: train_loss=-508797.7937 val_loss=-60571.6111 time=18.8s tod=05:09 -[finetune] epoch 33/50: train_loss=-485794.6108 val_loss=-74456.0105 time=19.6s tod=05:09 -[finetune] epoch 34/50: train_loss=-497895.8270 val_loss=-72051.5103 time=19.5s tod=05:10 -[finetune] epoch 35/50: train_loss=-506471.9879 val_loss=-82966.3256 time=19.5s tod=05:10 -[finetune] epoch 36/50: train_loss=-516857.2304 val_loss=-65550.5172 time=19.6s tod=05:10 -[finetune] epoch 37/50: train_loss=-528256.5853 val_loss=-76332.1525 time=19.5s tod=05:11 -[finetune] epoch 38/50: train_loss=-536697.0948 val_loss=-67379.6054 time=19.6s tod=05:11 -[finetune] epoch 39/50: train_loss=-543221.3290 val_loss=-59524.8871 time=19.6s tod=05:11 -[finetune] epoch 40/50: train_loss=-560865.7400 val_loss=-71147.7508 time=19.5s tod=05:12 -[finetune] epoch 41/50: train_loss=-558859.0678 val_loss=-67798.4771 time=19.5s tod=05:12 -[finetune] epoch 42/50: train_loss=-564936.8555 val_loss=-82237.9927 time=19.5s tod=05:12 -[finetune] epoch 43/50: train_loss=-593958.3045 val_loss=-71737.9733 time=19.5s tod=05:13 -[finetune] epoch 44/50: train_loss=-649648.8877 val_loss=-73129.3121 time=19.6s tod=05:13 -[finetune] epoch 45/50: train_loss=-579354.1524 val_loss=-65233.4437 time=19.6s tod=05:13 -[finetune] epoch 46/50: train_loss=-583970.5857 val_loss=-69687.3034 time=19.5s tod=05:14 -[finetune] epoch 47/50: train_loss=-624626.7817 val_loss=-71989.2865 time=19.5s tod=05:14 -[finetune] epoch 48/50: train_loss=-586496.3253 val_loss=-69742.6843 time=19.6s tod=05:14 -[finetune] epoch 49/50: train_loss=-587622.2958 val_loss=-71131.1176 time=19.5s tod=05:15 -[finetune] epoch 50/50: train_loss=-616375.0225 val_loss=-70154.7495 time=19.5s tod=05:15 -[finetune] test_metrics: epoch=50 loss=-121892.1985 accuracy=0.7541 precision=0.7395 recall=0.8342 f1=0.7840 roc-auc=0.7490 prc-auc=0.7221 -[finetune] saved checkpoint (best roc-auc=0.7490): /media/ubuntu/8TB/erva/selformer-mm/output/new_finetune_sweeps/sider/ew0k1kqo/checkpoint_epoch_050 -[finetune] final evaluation on test split... -[finetune] test_metrics: loss=-121892.1985 accuracy=0.7541 precision=0.7395 recall=0.8342 f1=0.7840 roc-auc=0.7490 prc-auc=0.7221 -[finetune] saving model... -[finetune] saved finetuned model to: /media/ubuntu/8TB/erva/selformer-mm/output/new_finetune_sweeps/sider/ew0k1kqo -[finetune] done in 971.3s diff --git a/models/finetuned/sider/vocab.json b/models/finetuned/sider/vocab.json deleted file mode 100644 index f7e4cc22809f4e9035cc450ef189c8a7da8fd03e..0000000000000000000000000000000000000000 --- a/models/finetuned/sider/vocab.json +++ /dev/null @@ -1 +0,0 @@ -{"":0,"":1,"":2,"":3,"":4,"\n":5,"#":6,"+":7,"-":8,".":9,"/":10,"0":11,"1":12,"2":13,"3":14,"4":15,"5":16,"6":17,"7":18,"8":19,"9":20,"=":21,"@":22,"A":23,"B":24,"C":25,"F":26,"H":27,"I":28,"K":29,"L":30,"M":31,"N":32,"O":33,"P":34,"R":35,"S":36,"T":37,"Z":38,"\\":39,"a":40,"b":41,"c":42,"e":43,"g":44,"h":45,"i":46,"l":47,"n":48,"r":49,"s":50,"Br":51,"an":52,"ch":53,"Bran":54,"Branch":55,"Branch1":56,"=C":57,"Ri":58,"ng":59,"Ring":60,"Ring1":61,"=Branch1":62,"Branch2":63,"=O":64,"Ring2":65,"H1":66,"C@":67,"=N":68,"#Branch1":69,"C@@":70,"=Branch2":71,"C@H1":72,"C@@H1":73,"#Branch2":74,"#C":75,"Cl":76,"/C":77,"NH1":78,"=Ring1":79,"+1":80,"-1":81,"O-1":82,"N+1":83,"\\C":84,"#N":85,"/N":86,"=Ring2":87,"=S":88,"=N+1":89,"\\N":90,"Na":91,"Na+1":92,"/O":93,"\\O":94,"Br-1":95,"Branch3":96,"\\S":97,"S+1":98,"Cl-1":99,"I-1":100,"/C@@H1":101,"Si":102,"/C@H1":103,"/S":104,"=N-1":105,"Se":106,"=P":107,"N-1":108,"Ring3":109,"2H":110,"P+1":111,"K+1":112,"\\C@@H1":113,"\\C@H1":114,"/N+1":115,"@@":116,"C-1":117,"#N+1":118,"B-1":119,"+3":120,"Cl+3":121,"\\NH1":122,"Li":123,"Li+1":124,"PH1":125,"18":126,"18F":127,"@+1":128,"3H":129,"P@@":130,"H0":131,"OH0":132,"12":133,"P@":134,"+2":135,"@@+1":136,"S-1":137,"/Br":138,"-/":139,"\\Cl":140,"-/Ring2":141,"\\O-1":142,"11":143,"5I":144,"125I":145,"11C":146,"H3":147,"\\N+1":148,"-\\":149,"/C@@":150,"S@+1":151,"As":152,"/Cl":153,"11CH3":154,"=Se":155,"S@@+1":156,"N@+1":157,"14":158,"-\\Ring2":159,"14C":160,"\\F":161,"/C@":162,"Te":163,"H2":164,"H1-1":165,"=O+1":166,"N@@+1":167,"C+1":168,"=S+1":169,"Zn":170,"/P":171,"a+2":172,"/I":173,"OH1-1":174,"Ca+2":175,"\\Br":176,"Mg":177,"Zn+2":178,"Al":179,"/F":180,"Mg+2":181,"123":182,"123I":183,"13":184,"I+1":185,"/O-1":186,"-\\Ring1":187,"BH2":188,"BH2-1":189,"\\I":190,"/NH1":191,"O+1":192,"131":193,"131I":194,"=14C":195,"/S+1":196,"=Ring3":197,"\\C@@":198,"H2+1":199,"\\C@":200,"Ag":201,"=As":202,"=Se+1":203,"NH2+1":204,"SeH1":205,"-/Ring1":206,"=Te":207,"Al+3":208,"NaH1":209,"=Te+1":210,"NH1+1":211,"Ag+1":212,"H1+1":213,"NH1-1":214,"\\P":215,"14CH2":216,"13C":217,"14CH1":218,"=11C":219,"S@@":220,"=P@@":221,"SiH2":222,"H3-1":223,"14CH3":224,"BH3-1":225,"S@":226,"=14CH1":227,"=PH1":228,"=P@":229,"=NH1+1":230,"\\S+1":231,"124":232,"CH1-1":233,"Sr":234,"=Si":235,"124I":236,"Sr+2":237,"#C-1":238,"/C-1":239,"N@":240,"/N-1":241,"13CH1":242,"/B":243,"19":244,"Ba+2":245,"H4":246,"SH1+1":247,"Se+1":248,"19F":249,"/125I":250,"P@+1":251,"Rb":252,"Cl+1":253,"SiH4":254,"Rb+1":255,"=Branch3":256,"N@@":257,"As+1":258,"/Si":259,"BH1-1":260,"SH1":261,"/123I":262,"32":263,"=Mg":264,"H+1":265,"\\B":266,"SiH1":267,"P@@+1":268,"-2":269,"15":270,"17":271,"35":272,"=13CH1":273,"Cs":274,"=NH2+1":275,"=SH1":276,"MgH2":277,"32P":278,"17F":279,"35S":280,"Cs+1":281,"#11C":282,"/131I":283,"Bi":284,"\\125I":285,"=S@@":286,"\\S-1":287,"6Br":288,"7I":289,"76Br":290,"=B":291,"eH1":292,"\\N-1":293,"18O":294,"127I":295,"11CH2":296,"14C@@H1":297,"TeH2":298,"15NH1":299,"Bi+3":300,"/P+1":301,"/13C":302,"/13CH1":303,"0B":304,"10B":305,"=Al":306,"=18O":307,"BH0":308,"F-1":309,"NH3":310,"S-2":311,"Br+2":312,"Cl+2":313,"\\Si":314,"/S-1":315,"=PH2":316,"14C@H1":317,"NH3+1":318,"#14C":319,"#O+1":320,"-3":321,"22":322,"4H":323,"5Se":324,"5Sr+2":325,"75Se":326,"85Sr+2":327,"=B-1":328,"=13C":329,"@-1":330,"Be":331,"B@@":332,"B@-1":333,"Ca":334,"CH1":335,"I+3":336,"KH1":337,"OH1+1":338,"Ra+2":339,"SH1-1":340,"\\PH1":341,"\\123I":342,"=Ca":343,"\\CH1-1":344,"=S@":345,"\\SeH1":346,"/SeH1":347,"Se-1":348,"LiH1":349,"18F-1":350,"125IH1":351,"11CH1":352,"TeH1":353,"Zn+1":354,"Zn-2":355,"Al-3":356,"13CH3":357,"15N":358,"Be+2":359,"B@@-1":360,"#P":361,"#S":362,"-4":363,"/PH1":364,"/P@@":365,"/As":366,"/14C":367,"/14CH1":368,"2K+1":369,"2Rb+1":370,"3Se":371,"3Ra+2":372,"45":373,"47":374,"42K+1":375,"5I-1":376,"73Se":377,"89":378,"82Rb+1":379,"=32":380,"=32P":381,"CH0":382,"CH2":383,"I+2":384,"NH0":385,"NH4":386,"OH1":387,"PH2+1":388,"SH0":389,"SH2":390,"\\3H":391,"\\11CH3":392,"\\C-1":393,"\\Se":394,"Si@":395,"Si-1":396,"SiH1-1":397,"SiH3-1":398,"/Se":399,"Se-2":400,"\\NH1-1":401,"18FH1":402,"125I-1":403,"11C@@H1":404,"11C-1":405,"AsH1":406,"As-1":407,"14C@@":408,"Te-1":409,"Mg+1":410,"123I-1":411,"123Te":412,"123IH1":413,"135I":414,"131I-1":415,"Ag-4":416,"124I-1":417,"76BrH1":418,"18OH1":419,"22Na+1":420,"223Ra+2":421,"CaH2":422,"45Ca+2":423,"47Ca+2":424,"89Sr+2":425,"=32PH1":426,"NH4+1":427} \ No newline at end of file diff --git a/models/finetuned/tox21/checkpoint_epoch_025/config.json b/models/finetuned/tox21/checkpoint_epoch_025/config.json deleted file mode 100644 index 3811e21539577b37e06313eab31ec11e53f0cbbc..0000000000000000000000000000000000000000 --- a/models/finetuned/tox21/checkpoint_epoch_025/config.json +++ /dev/null @@ -1,27 +0,0 @@ -{ - "_name_or_path": "/home/erva/SELFormerMM/data/pretrained_multimodal_chembl36", - "architectures": [ - "RobertaForMaskedLM" - ], - "attention_probs_dropout_prob": 0.1, - "bos_token_id": 0, - "classifier_dropout": null, - "eos_token_id": 2, - "hidden_act": "gelu", - "hidden_dropout_prob": 0.1, - "hidden_size": 768, - "initializer_range": 0.02, - "intermediate_size": 3072, - "layer_norm_eps": 1e-12, - "max_position_embeddings": 514, - "model_type": "roberta", - "num_attention_heads": 4, - "num_hidden_layers": 12, - "pad_token_id": 1, - "position_embedding_type": "absolute", - "torch_dtype": "float32", - "transformers_version": "4.26.1", - "type_vocab_size": 1, - "use_cache": true, - "vocab_size": 800 -} diff --git a/models/finetuned/tox21/checkpoint_epoch_025/merges.txt b/models/finetuned/tox21/checkpoint_epoch_025/merges.txt deleted file mode 100644 index 7cd5ec62809503c23f18c80afc0ba3bdf9d253d0..0000000000000000000000000000000000000000 --- a/models/finetuned/tox21/checkpoint_epoch_025/merges.txt +++ /dev/null @@ -1,378 +0,0 @@ -#version: 0.2 - Trained by `huggingface/tokenizers` -B r -a n -c h -Br an -Bran ch -Branch 1 -= C -R i -n g -Ri ng -Ring 1 -= Branch1 -Branch 2 -= O -Ring 2 -H 1 -C @ -= N -# Branch1 -C@ @ -= Branch2 -C@ H1 -C@@ H1 -# Branch2 -# C -C l -/ C -N H1 -= Ring1 -+ 1 -- 1 -O -1 -N +1 -\ C -# N -/ N -= Ring2 -= S -=N +1 -\ N -N a -Na +1 -/ O -\ O -Br -1 -Branch 3 -\ S -S +1 -Cl -1 -I -1 -/ C@@H1 -S i -/ C@H1 -/ S -=N -1 -S e -= P -N -1 -Ring 3 -2 H -P +1 -K +1 -\ C@@H1 -\ C@H1 -/ N+1 -@ @ -C -1 -# N+1 -B -1 -+ 3 -Cl +3 -\ NH1 -L i -Li +1 -P H1 -1 8 -18 F -@ +1 -3 H -P @@ -H 0 -O H0 -1 2 -P @ -+ 2 -@@ +1 -S -1 -/ Br -- / -\ Cl --/ Ring2 -\ O-1 -1 1 -5 I -12 5I -11 C -H 3 -\ N+1 -- \ -/ C@@ -S @+1 -A s -/ Cl -11C H3 -=S e -S @@+1 -N @+1 -1 4 --\ Ring2 -14 C -\ F -/ C@ -T e -H 2 -H1 -1 -=O +1 -N @@+1 -C +1 -=S +1 -Z n -/ P -a +2 -/ I -O H1-1 -C a+2 -\ Br -M g -Zn +2 -A l -/ F -Mg +2 -12 3 -123 I -1 3 -I +1 -/ O-1 --\ Ring1 -B H2 -BH2 -1 -\ I -/ NH1 -O +1 -13 1 -131 I -= 14C -/ S+1 -= Ring3 -\ C@@ -H2 +1 -\ C@ -A g -= As -=Se +1 -N H2+1 -Se H1 --/ Ring1 -= Te -Al +3 -Na H1 -=Te +1 -NH1 +1 -Ag +1 -H1 +1 -NH1 -1 -\ P -14C H2 -13 C -14C H1 -= 11C -S @@ -=P @@ -Si H2 -H3 -1 -14C H3 -B H3-1 -S @ -=14C H1 -=P H1 -=P @ -=N H1+1 -\S +1 -12 4 -C H1-1 -S r -=S i -124 I -Sr +2 -#C -1 -/C -1 -N @ -/N -1 -13C H1 -/ B -1 9 -B a+2 -H 4 -S H1+1 -Se +1 -19 F -/ 125I -P @+1 -R b -Cl +1 -Si H4 -Rb +1 -= Branch3 -N @@ -As +1 -/ Si -B H1-1 -S H1 -/ 123I -3 2 -= Mg -H +1 -\ B -Si H1 -P@@ +1 -- 2 -1 5 -1 7 -3 5 -= 13CH1 -C s -=N H2+1 -=S H1 -Mg H2 -32 P -17 F -35 S -Cs +1 -# 11C -/ 131I -B i -\ 125I -=S @@ -\S -1 -6 Br -7 I -7 6Br -= B -e H1 -\N -1 -18 O -12 7I -11C H2 -14 C@@H1 -Te H2 -15 NH1 -Bi +3 -/ P+1 -/ 13C -/ 13CH1 -0 B -1 0B -= Al -= 18O -B H0 -F -1 -N H3 -S -2 -Br +2 -Cl +2 -\S i -/S -1 -=P H2 -14 C@H1 -NH3 +1 -# 14C -# O+1 -- 3 -2 2 -4 H -5 Se -5 Sr+2 -7 5Se -8 5Sr+2 -= B-1 -= 13C -@ -1 -B e -B @@ -B @-1 -C a -C H1 -I +3 -K H1 -O H1+1 -R a+2 -S H1-1 -\ PH1 -\ 123I -=C a -\C H1-1 -=S @ -\S eH1 -/S eH1 -Se -1 -Li H1 -18F -1 -125I H1 -11C H1 -Te H1 -Zn +1 -Zn -2 -Al -3 -13C H3 -15 N -Be +2 -B@@ -1 -# P -# S -- 4 -/ PH1 -/ P@@ -/ As -/ 14C -/ 14CH1 -2 K+1 -2 Rb+1 -3 Se -3 Ra+2 -4 5 -4 7 -4 2K+1 -5 I-1 -7 3Se -8 9 -8 2Rb+1 -= 32 -= 32P -C H0 -C H2 -I +2 -N H0 -N H4 -O H1 -P H2+1 -S H0 -S H2 -\ 3H -\ 11CH3 -\C -1 -\S e -Si @ -Si -1 -Si H1-1 -Si H3-1 -/S e -Se -2 -\NH1 -1 -18F H1 -12 5I-1 -11 C@@H1 -11 C-1 -As H1 -As -1 -14 C@@ -Te -1 -Mg +1 -123 I-1 -123 Te -123I H1 -13 5I -131 I-1 -Ag -4 -124 I-1 -76Br H1 -18O H1 -22 Na+1 -22 3Ra+2 -Ca H2 -45 Ca+2 -47 Ca+2 -89 Sr+2 -=32 PH1 -NH4 +1 diff --git a/models/finetuned/tox21/checkpoint_epoch_025/model.pt b/models/finetuned/tox21/checkpoint_epoch_025/model.pt deleted file mode 100644 index 9544fcb372d96d972f4eb8cf9ce4968d35835faf..0000000000000000000000000000000000000000 --- a/models/finetuned/tox21/checkpoint_epoch_025/model.pt +++ /dev/null @@ -1,3 +0,0 @@ -version https://git-lfs.github.com/spec/v1 -oid sha256:e25cbe3f5881ab600c4db1295a97d3e859cc4562fbcb45000ab3dab8af84186f -size 1022990461 diff --git a/models/finetuned/tox21/checkpoint_epoch_025/special_tokens_map.json b/models/finetuned/tox21/checkpoint_epoch_025/special_tokens_map.json deleted file mode 100644 index 06a55849fa69a91e7179d909e373179ff7467d8c..0000000000000000000000000000000000000000 --- a/models/finetuned/tox21/checkpoint_epoch_025/special_tokens_map.json +++ /dev/null @@ -1,51 +0,0 @@ -{ - "bos_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "cls_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "eos_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "mask_token": { - "content": "", - "lstrip": true, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "pad_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "sep_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "unk_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - } -} diff --git a/models/finetuned/tox21/checkpoint_epoch_025/tokenizer.json b/models/finetuned/tox21/checkpoint_epoch_025/tokenizer.json deleted file mode 100644 index 3b64b273e6fa9799e2d8375722b9e815de9ebb8f..0000000000000000000000000000000000000000 --- a/models/finetuned/tox21/checkpoint_epoch_025/tokenizer.json +++ /dev/null @@ -1,909 +0,0 @@ -{ - "version": "1.0", - "truncation": { - "direction": "Right", - "max_length": 128, - "strategy": "LongestFirst", - "stride": 0 - }, - "padding": { - "strategy": { - "Fixed": 128 - }, - "direction": "Right", - "pad_to_multiple_of": null, - "pad_id": 3, - "pad_type_id": 0, - "pad_token": "" - }, - "added_tokens": [ - { - "id": 0, - "content": "", - "single_word": false, - "lstrip": false, - "rstrip": false, - "normalized": true, - "special": true - }, - { - "id": 1, - "content": "", - "single_word": false, - "lstrip": false, - "rstrip": false, - "normalized": true, - "special": true - }, - { - "id": 2, - "content": "", - "single_word": false, - "lstrip": false, - "rstrip": false, - "normalized": true, - "special": true - }, - { - "id": 3, - "content": "", - "single_word": false, - "lstrip": false, - "rstrip": false, - "normalized": true, - "special": true - }, - { - "id": 4, - "content": "", - "single_word": false, - "lstrip": true, - "rstrip": false, - "normalized": true, - "special": true - } - ], - "normalizer": null, - "pre_tokenizer": { - "type": "ByteLevel", - "add_prefix_space": false, - "trim_offsets": true, - "use_regex": true - }, - "post_processor": { - "type": "RobertaProcessing", - "sep": [ - "", - 2 - ], - "cls": [ - "", - 1 - ], - "trim_offsets": true, - "add_prefix_space": false - }, - "decoder": { - "type": "ByteLevel", - "add_prefix_space": true, - "trim_offsets": true, - "use_regex": true - }, - "model": { - "type": "BPE", - "dropout": null, - "unk_token": null, - "continuing_subword_prefix": "", - "end_of_word_suffix": "", - "fuse_unk": false, - "vocab": { - "": 0, - "": 1, - "": 2, - "": 3, - "": 4, - "\n": 5, - "#": 6, - "+": 7, - "-": 8, - ".": 9, - "/": 10, - "0": 11, - "1": 12, - "2": 13, - "3": 14, - "4": 15, - "5": 16, - "6": 17, - "7": 18, - "8": 19, - "9": 20, - "=": 21, - "@": 22, - "A": 23, - "B": 24, - "C": 25, - "F": 26, - "H": 27, - "I": 28, - "K": 29, - "L": 30, - "M": 31, - "N": 32, - "O": 33, - "P": 34, - "R": 35, - "S": 36, - "T": 37, - "Z": 38, - "\\": 39, - "a": 40, - "b": 41, - "c": 42, - "e": 43, - "g": 44, - "h": 45, - "i": 46, - "l": 47, - "n": 48, - "r": 49, - "s": 50, - "Br": 51, - "an": 52, - "ch": 53, - "Bran": 54, - "Branch": 55, - "Branch1": 56, - "=C": 57, - "Ri": 58, - "ng": 59, - "Ring": 60, - "Ring1": 61, - "=Branch1": 62, - "Branch2": 63, - "=O": 64, - "Ring2": 65, - "H1": 66, - "C@": 67, - "=N": 68, - "#Branch1": 69, - "C@@": 70, - "=Branch2": 71, - "C@H1": 72, - "C@@H1": 73, - "#Branch2": 74, - "#C": 75, - "Cl": 76, - "/C": 77, - "NH1": 78, - "=Ring1": 79, - "+1": 80, - "-1": 81, - "O-1": 82, - "N+1": 83, - "\\C": 84, - "#N": 85, - "/N": 86, - "=Ring2": 87, - "=S": 88, - "=N+1": 89, - "\\N": 90, - "Na": 91, - "Na+1": 92, - "/O": 93, - "\\O": 94, - "Br-1": 95, - "Branch3": 96, - "\\S": 97, - "S+1": 98, - "Cl-1": 99, - "I-1": 100, - "/C@@H1": 101, - "Si": 102, - "/C@H1": 103, - "/S": 104, - "=N-1": 105, - "Se": 106, - "=P": 107, - "N-1": 108, - "Ring3": 109, - "2H": 110, - "P+1": 111, - "K+1": 112, - "\\C@@H1": 113, - "\\C@H1": 114, - "/N+1": 115, - "@@": 116, - "C-1": 117, - "#N+1": 118, - "B-1": 119, - "+3": 120, - "Cl+3": 121, - "\\NH1": 122, - "Li": 123, - "Li+1": 124, - "PH1": 125, - "18": 126, - "18F": 127, - "@+1": 128, - "3H": 129, - "P@@": 130, - "H0": 131, - "OH0": 132, - "12": 133, - "P@": 134, - "+2": 135, - "@@+1": 136, - "S-1": 137, - "/Br": 138, - "-/": 139, - "\\Cl": 140, - "-/Ring2": 141, - "\\O-1": 142, - "11": 143, - "5I": 144, - "125I": 145, - "11C": 146, - "H3": 147, - "\\N+1": 148, - "-\\": 149, - "/C@@": 150, - "S@+1": 151, - "As": 152, - "/Cl": 153, - "11CH3": 154, - "=Se": 155, - "S@@+1": 156, - "N@+1": 157, - "14": 158, - "-\\Ring2": 159, - "14C": 160, - "\\F": 161, - "/C@": 162, - "Te": 163, - "H2": 164, - "H1-1": 165, - "=O+1": 166, - "N@@+1": 167, - "C+1": 168, - "=S+1": 169, - "Zn": 170, - "/P": 171, - "a+2": 172, - "/I": 173, - "OH1-1": 174, - "Ca+2": 175, - "\\Br": 176, - "Mg": 177, - "Zn+2": 178, - "Al": 179, - "/F": 180, - "Mg+2": 181, - "123": 182, - "123I": 183, - "13": 184, - "I+1": 185, - "/O-1": 186, - "-\\Ring1": 187, - "BH2": 188, - "BH2-1": 189, - "\\I": 190, - "/NH1": 191, - "O+1": 192, - "131": 193, - "131I": 194, - "=14C": 195, - "/S+1": 196, - "=Ring3": 197, - "\\C@@": 198, - "H2+1": 199, - "\\C@": 200, - "Ag": 201, - "=As": 202, - "=Se+1": 203, - "NH2+1": 204, - "SeH1": 205, - "-/Ring1": 206, - "=Te": 207, - "Al+3": 208, - "NaH1": 209, - "=Te+1": 210, - "NH1+1": 211, - "Ag+1": 212, - "H1+1": 213, - "NH1-1": 214, - "\\P": 215, - "14CH2": 216, - "13C": 217, - "14CH1": 218, - "=11C": 219, - "S@@": 220, - "=P@@": 221, - "SiH2": 222, - "H3-1": 223, - "14CH3": 224, - "BH3-1": 225, - "S@": 226, - "=14CH1": 227, - "=PH1": 228, - "=P@": 229, - "=NH1+1": 230, - "\\S+1": 231, - "124": 232, - "CH1-1": 233, - "Sr": 234, - "=Si": 235, - "124I": 236, - "Sr+2": 237, - "#C-1": 238, - "/C-1": 239, - "N@": 240, - "/N-1": 241, - "13CH1": 242, - "/B": 243, - "19": 244, - "Ba+2": 245, - "H4": 246, - "SH1+1": 247, - "Se+1": 248, - "19F": 249, - "/125I": 250, - "P@+1": 251, - "Rb": 252, - "Cl+1": 253, - "SiH4": 254, - "Rb+1": 255, - "=Branch3": 256, - "N@@": 257, - "As+1": 258, - "/Si": 259, - "BH1-1": 260, - "SH1": 261, - "/123I": 262, - "32": 263, - "=Mg": 264, - "H+1": 265, - "\\B": 266, - "SiH1": 267, - "P@@+1": 268, - "-2": 269, - "15": 270, - "17": 271, - "35": 272, - "=13CH1": 273, - "Cs": 274, - "=NH2+1": 275, - "=SH1": 276, - "MgH2": 277, - "32P": 278, - "17F": 279, - "35S": 280, - "Cs+1": 281, - "#11C": 282, - "/131I": 283, - "Bi": 284, - "\\125I": 285, - "=S@@": 286, - "\\S-1": 287, - "6Br": 288, - "7I": 289, - "76Br": 290, - "=B": 291, - "eH1": 292, - "\\N-1": 293, - "18O": 294, - "127I": 295, - "11CH2": 296, - "14C@@H1": 297, - "TeH2": 298, - "15NH1": 299, - "Bi+3": 300, - "/P+1": 301, - "/13C": 302, - "/13CH1": 303, - "0B": 304, - "10B": 305, - "=Al": 306, - "=18O": 307, - "BH0": 308, - "F-1": 309, - "NH3": 310, - "S-2": 311, - "Br+2": 312, - "Cl+2": 313, - "\\Si": 314, - "/S-1": 315, - "=PH2": 316, - "14C@H1": 317, - "NH3+1": 318, - "#14C": 319, - "#O+1": 320, - "-3": 321, - "22": 322, - "4H": 323, - "5Se": 324, - "5Sr+2": 325, - "75Se": 326, - "85Sr+2": 327, - "=B-1": 328, - "=13C": 329, - "@-1": 330, - "Be": 331, - "B@@": 332, - "B@-1": 333, - "Ca": 334, - "CH1": 335, - "I+3": 336, - "KH1": 337, - "OH1+1": 338, - "Ra+2": 339, - "SH1-1": 340, - "\\PH1": 341, - "\\123I": 342, - "=Ca": 343, - "\\CH1-1": 344, - "=S@": 345, - "\\SeH1": 346, - "/SeH1": 347, - "Se-1": 348, - "LiH1": 349, - "18F-1": 350, - "125IH1": 351, - "11CH1": 352, - "TeH1": 353, - "Zn+1": 354, - "Zn-2": 355, - "Al-3": 356, - "13CH3": 357, - "15N": 358, - "Be+2": 359, - "B@@-1": 360, - "#P": 361, - "#S": 362, - "-4": 363, - "/PH1": 364, - "/P@@": 365, - "/As": 366, - "/14C": 367, - "/14CH1": 368, - "2K+1": 369, - "2Rb+1": 370, - "3Se": 371, - "3Ra+2": 372, - "45": 373, - "47": 374, - "42K+1": 375, - "5I-1": 376, - "73Se": 377, - "89": 378, - "82Rb+1": 379, - "=32": 380, - "=32P": 381, - "CH0": 382, - "CH2": 383, - "I+2": 384, - "NH0": 385, - "NH4": 386, - "OH1": 387, - "PH2+1": 388, - "SH0": 389, - "SH2": 390, - "\\3H": 391, - "\\11CH3": 392, - "\\C-1": 393, - "\\Se": 394, - "Si@": 395, - "Si-1": 396, - "SiH1-1": 397, - "SiH3-1": 398, - "/Se": 399, - "Se-2": 400, - "\\NH1-1": 401, - "18FH1": 402, - "125I-1": 403, - "11C@@H1": 404, - "11C-1": 405, - "AsH1": 406, - "As-1": 407, - "14C@@": 408, - "Te-1": 409, - "Mg+1": 410, - "123I-1": 411, - "123Te": 412, - "123IH1": 413, - "135I": 414, - "131I-1": 415, - "Ag-4": 416, - "124I-1": 417, - "76BrH1": 418, - "18OH1": 419, - "22Na+1": 420, - "223Ra+2": 421, - "CaH2": 422, - "45Ca+2": 423, - "47Ca+2": 424, - "89Sr+2": 425, - "=32PH1": 426, - "NH4+1": 427 - }, - "merges": [ - "B r", - "a n", - "c h", - "Br an", - "Bran ch", - "Branch 1", - "= C", - "R i", - "n g", - "Ri ng", - "Ring 1", - "= Branch1", - "Branch 2", - "= O", - "Ring 2", - "H 1", - "C @", - "= N", - "# Branch1", - "C@ @", - "= Branch2", - "C@ H1", - "C@@ H1", - "# Branch2", - "# C", - "C l", - "/ C", - "N H1", - "= Ring1", - "+ 1", - "- 1", - "O -1", - "N +1", - "\\ C", - "# N", - "/ N", - "= Ring2", - "= S", - "=N +1", - "\\ N", - "N a", - "Na +1", - "/ O", - "\\ O", - "Br -1", - "Branch 3", - "\\ S", - "S +1", - "Cl -1", - "I -1", - "/ C@@H1", - "S i", - "/ C@H1", - "/ S", - "=N -1", - "S e", - "= P", - "N -1", - "Ring 3", - "2 H", - "P +1", - "K +1", - "\\ C@@H1", - "\\ C@H1", - "/ N+1", - "@ @", - "C -1", - "# N+1", - "B -1", - "+ 3", - "Cl +3", - "\\ NH1", - "L i", - "Li +1", - "P H1", - "1 8", - "18 F", - "@ +1", - "3 H", - "P @@", - "H 0", - "O H0", - "1 2", - "P @", - "+ 2", - "@@ +1", - "S -1", - "/ Br", - "- /", - "\\ Cl", - "-/ Ring2", - "\\ O-1", - "1 1", - "5 I", - "12 5I", - "11 C", - "H 3", - "\\ N+1", - "- \\", - "/ C@@", - "S @+1", - "A s", - "/ Cl", - "11C H3", - "=S e", - "S @@+1", - "N @+1", - "1 4", - "-\\ Ring2", - "14 C", - "\\ F", - "/ C@", - "T e", - "H 2", - "H1 -1", - "=O +1", - "N @@+1", - "C +1", - "=S +1", - "Z n", - "/ P", - "a +2", - "/ I", - "O H1-1", - "C a+2", - "\\ Br", - "M g", - "Zn +2", - "A l", - "/ F", - "Mg +2", - "12 3", - "123 I", - "1 3", - "I +1", - "/ O-1", - "-\\ Ring1", - "B H2", - "BH2 -1", - "\\ I", - "/ NH1", - "O +1", - "13 1", - "131 I", - "= 14C", - "/ S+1", - "= Ring3", - "\\ C@@", - "H2 +1", - "\\ C@", - "A g", - "= As", - "=Se +1", - "N H2+1", - "Se H1", - "-/ Ring1", - "= Te", - "Al +3", - "Na H1", - "=Te +1", - "NH1 +1", - "Ag +1", - "H1 +1", - "NH1 -1", - "\\ P", - "14C H2", - "13 C", - "14C H1", - "= 11C", - "S @@", - "=P @@", - "Si H2", - "H3 -1", - "14C H3", - "B H3-1", - "S @", - "=14C H1", - "=P H1", - "=P @", - "=N H1+1", - "\\S +1", - "12 4", - "C H1-1", - "S r", - "=S i", - "124 I", - "Sr +2", - "#C -1", - "/C -1", - "N @", - "/N -1", - "13C H1", - "/ B", - "1 9", - "B a+2", - "H 4", - "S H1+1", - "Se +1", - "19 F", - "/ 125I", - "P @+1", - "R b", - "Cl +1", - "Si H4", - "Rb +1", - "= Branch3", - "N @@", - "As +1", - "/ Si", - "B H1-1", - "S H1", - "/ 123I", - "3 2", - "= Mg", - "H +1", - "\\ B", - "Si H1", - "P@@ +1", - "- 2", - "1 5", - "1 7", - "3 5", - "= 13CH1", - "C s", - "=N H2+1", - "=S H1", - "Mg H2", - "32 P", - "17 F", - "35 S", - "Cs +1", - "# 11C", - "/ 131I", - "B i", - "\\ 125I", - "=S @@", - "\\S -1", - "6 Br", - "7 I", - "7 6Br", - "= B", - "e H1", - "\\N -1", - "18 O", - "12 7I", - "11C H2", - "14 C@@H1", - "Te H2", - "15 NH1", - "Bi +3", - "/ P+1", - "/ 13C", - "/ 13CH1", - "0 B", - "1 0B", - "= Al", - "= 18O", - "B H0", - "F -1", - "N H3", - "S -2", - "Br +2", - "Cl +2", - "\\S i", - "/S -1", - "=P H2", - "14 C@H1", - "NH3 +1", - "# 14C", - "# O+1", - "- 3", - "2 2", - "4 H", - "5 Se", - "5 Sr+2", - "7 5Se", - "8 5Sr+2", - "= B-1", - "= 13C", - "@ -1", - "B e", - "B @@", - "B @-1", - "C a", - "C H1", - "I +3", - "K H1", - "O H1+1", - "R a+2", - "S H1-1", - "\\ PH1", - "\\ 123I", - "=C a", - "\\C H1-1", - "=S @", - "\\S eH1", - "/S eH1", - "Se -1", - "Li H1", - "18F -1", - "125I H1", - "11C H1", - "Te H1", - "Zn +1", - "Zn -2", - "Al -3", - "13C H3", - "15 N", - "Be +2", - "B@@ -1", - "# P", - "# S", - "- 4", - "/ PH1", - "/ P@@", - "/ As", - "/ 14C", - "/ 14CH1", - "2 K+1", - "2 Rb+1", - "3 Se", - "3 Ra+2", - "4 5", - "4 7", - "4 2K+1", - "5 I-1", - "7 3Se", - "8 9", - "8 2Rb+1", - "= 32", - "= 32P", - "C H0", - "C H2", - "I +2", - "N H0", - "N H4", - "O H1", - "P H2+1", - "S H0", - "S H2", - "\\ 3H", - "\\ 11CH3", - "\\C -1", - "\\S e", - "Si @", - "Si -1", - "Si H1-1", - "Si H3-1", - "/S e", - "Se -2", - "\\NH1 -1", - "18F H1", - "12 5I-1", - "11 C@@H1", - "11 C-1", - "As H1", - "As -1", - "14 C@@", - "Te -1", - "Mg +1", - "123 I-1", - "123 Te", - "123I H1", - "13 5I", - "131 I-1", - "Ag -4", - "124 I-1", - "76Br H1", - "18O H1", - "22 Na+1", - "22 3Ra+2", - "Ca H2", - "45 Ca+2", - "47 Ca+2", - "89 Sr+2", - "=32 PH1", - "NH4 +1" - ] - } -} \ No newline at end of file diff --git a/models/finetuned/tox21/checkpoint_epoch_025/tokenizer_config.json b/models/finetuned/tox21/checkpoint_epoch_025/tokenizer_config.json deleted file mode 100644 index 08860954acd34fad07fd77f7635298fa565f3149..0000000000000000000000000000000000000000 --- a/models/finetuned/tox21/checkpoint_epoch_025/tokenizer_config.json +++ /dev/null @@ -1,65 +0,0 @@ -{ - "add_prefix_space": false, - "bos_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "cls_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "eos_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "errors": "replace", - "mask_token": { - "__type": "AddedToken", - "content": "", - "lstrip": true, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "model_max_length": 1000000000000000019884624838656, - "name_or_path": "/home/erva/SELFormerMM/data/pretrained_multimodal_chembl36", - "pad_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "sep_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "special_tokens_map_file": null, - "tokenizer_class": "RobertaTokenizer", - "trim_offsets": true, - "unk_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - } -} diff --git a/models/finetuned/tox21/checkpoint_epoch_025/vocab.json b/models/finetuned/tox21/checkpoint_epoch_025/vocab.json deleted file mode 100644 index f7e4cc22809f4e9035cc450ef189c8a7da8fd03e..0000000000000000000000000000000000000000 --- a/models/finetuned/tox21/checkpoint_epoch_025/vocab.json +++ /dev/null @@ -1 +0,0 @@ -{"":0,"":1,"":2,"":3,"":4,"\n":5,"#":6,"+":7,"-":8,".":9,"/":10,"0":11,"1":12,"2":13,"3":14,"4":15,"5":16,"6":17,"7":18,"8":19,"9":20,"=":21,"@":22,"A":23,"B":24,"C":25,"F":26,"H":27,"I":28,"K":29,"L":30,"M":31,"N":32,"O":33,"P":34,"R":35,"S":36,"T":37,"Z":38,"\\":39,"a":40,"b":41,"c":42,"e":43,"g":44,"h":45,"i":46,"l":47,"n":48,"r":49,"s":50,"Br":51,"an":52,"ch":53,"Bran":54,"Branch":55,"Branch1":56,"=C":57,"Ri":58,"ng":59,"Ring":60,"Ring1":61,"=Branch1":62,"Branch2":63,"=O":64,"Ring2":65,"H1":66,"C@":67,"=N":68,"#Branch1":69,"C@@":70,"=Branch2":71,"C@H1":72,"C@@H1":73,"#Branch2":74,"#C":75,"Cl":76,"/C":77,"NH1":78,"=Ring1":79,"+1":80,"-1":81,"O-1":82,"N+1":83,"\\C":84,"#N":85,"/N":86,"=Ring2":87,"=S":88,"=N+1":89,"\\N":90,"Na":91,"Na+1":92,"/O":93,"\\O":94,"Br-1":95,"Branch3":96,"\\S":97,"S+1":98,"Cl-1":99,"I-1":100,"/C@@H1":101,"Si":102,"/C@H1":103,"/S":104,"=N-1":105,"Se":106,"=P":107,"N-1":108,"Ring3":109,"2H":110,"P+1":111,"K+1":112,"\\C@@H1":113,"\\C@H1":114,"/N+1":115,"@@":116,"C-1":117,"#N+1":118,"B-1":119,"+3":120,"Cl+3":121,"\\NH1":122,"Li":123,"Li+1":124,"PH1":125,"18":126,"18F":127,"@+1":128,"3H":129,"P@@":130,"H0":131,"OH0":132,"12":133,"P@":134,"+2":135,"@@+1":136,"S-1":137,"/Br":138,"-/":139,"\\Cl":140,"-/Ring2":141,"\\O-1":142,"11":143,"5I":144,"125I":145,"11C":146,"H3":147,"\\N+1":148,"-\\":149,"/C@@":150,"S@+1":151,"As":152,"/Cl":153,"11CH3":154,"=Se":155,"S@@+1":156,"N@+1":157,"14":158,"-\\Ring2":159,"14C":160,"\\F":161,"/C@":162,"Te":163,"H2":164,"H1-1":165,"=O+1":166,"N@@+1":167,"C+1":168,"=S+1":169,"Zn":170,"/P":171,"a+2":172,"/I":173,"OH1-1":174,"Ca+2":175,"\\Br":176,"Mg":177,"Zn+2":178,"Al":179,"/F":180,"Mg+2":181,"123":182,"123I":183,"13":184,"I+1":185,"/O-1":186,"-\\Ring1":187,"BH2":188,"BH2-1":189,"\\I":190,"/NH1":191,"O+1":192,"131":193,"131I":194,"=14C":195,"/S+1":196,"=Ring3":197,"\\C@@":198,"H2+1":199,"\\C@":200,"Ag":201,"=As":202,"=Se+1":203,"NH2+1":204,"SeH1":205,"-/Ring1":206,"=Te":207,"Al+3":208,"NaH1":209,"=Te+1":210,"NH1+1":211,"Ag+1":212,"H1+1":213,"NH1-1":214,"\\P":215,"14CH2":216,"13C":217,"14CH1":218,"=11C":219,"S@@":220,"=P@@":221,"SiH2":222,"H3-1":223,"14CH3":224,"BH3-1":225,"S@":226,"=14CH1":227,"=PH1":228,"=P@":229,"=NH1+1":230,"\\S+1":231,"124":232,"CH1-1":233,"Sr":234,"=Si":235,"124I":236,"Sr+2":237,"#C-1":238,"/C-1":239,"N@":240,"/N-1":241,"13CH1":242,"/B":243,"19":244,"Ba+2":245,"H4":246,"SH1+1":247,"Se+1":248,"19F":249,"/125I":250,"P@+1":251,"Rb":252,"Cl+1":253,"SiH4":254,"Rb+1":255,"=Branch3":256,"N@@":257,"As+1":258,"/Si":259,"BH1-1":260,"SH1":261,"/123I":262,"32":263,"=Mg":264,"H+1":265,"\\B":266,"SiH1":267,"P@@+1":268,"-2":269,"15":270,"17":271,"35":272,"=13CH1":273,"Cs":274,"=NH2+1":275,"=SH1":276,"MgH2":277,"32P":278,"17F":279,"35S":280,"Cs+1":281,"#11C":282,"/131I":283,"Bi":284,"\\125I":285,"=S@@":286,"\\S-1":287,"6Br":288,"7I":289,"76Br":290,"=B":291,"eH1":292,"\\N-1":293,"18O":294,"127I":295,"11CH2":296,"14C@@H1":297,"TeH2":298,"15NH1":299,"Bi+3":300,"/P+1":301,"/13C":302,"/13CH1":303,"0B":304,"10B":305,"=Al":306,"=18O":307,"BH0":308,"F-1":309,"NH3":310,"S-2":311,"Br+2":312,"Cl+2":313,"\\Si":314,"/S-1":315,"=PH2":316,"14C@H1":317,"NH3+1":318,"#14C":319,"#O+1":320,"-3":321,"22":322,"4H":323,"5Se":324,"5Sr+2":325,"75Se":326,"85Sr+2":327,"=B-1":328,"=13C":329,"@-1":330,"Be":331,"B@@":332,"B@-1":333,"Ca":334,"CH1":335,"I+3":336,"KH1":337,"OH1+1":338,"Ra+2":339,"SH1-1":340,"\\PH1":341,"\\123I":342,"=Ca":343,"\\CH1-1":344,"=S@":345,"\\SeH1":346,"/SeH1":347,"Se-1":348,"LiH1":349,"18F-1":350,"125IH1":351,"11CH1":352,"TeH1":353,"Zn+1":354,"Zn-2":355,"Al-3":356,"13CH3":357,"15N":358,"Be+2":359,"B@@-1":360,"#P":361,"#S":362,"-4":363,"/PH1":364,"/P@@":365,"/As":366,"/14C":367,"/14CH1":368,"2K+1":369,"2Rb+1":370,"3Se":371,"3Ra+2":372,"45":373,"47":374,"42K+1":375,"5I-1":376,"73Se":377,"89":378,"82Rb+1":379,"=32":380,"=32P":381,"CH0":382,"CH2":383,"I+2":384,"NH0":385,"NH4":386,"OH1":387,"PH2+1":388,"SH0":389,"SH2":390,"\\3H":391,"\\11CH3":392,"\\C-1":393,"\\Se":394,"Si@":395,"Si-1":396,"SiH1-1":397,"SiH3-1":398,"/Se":399,"Se-2":400,"\\NH1-1":401,"18FH1":402,"125I-1":403,"11C@@H1":404,"11C-1":405,"AsH1":406,"As-1":407,"14C@@":408,"Te-1":409,"Mg+1":410,"123I-1":411,"123Te":412,"123IH1":413,"135I":414,"131I-1":415,"Ag-4":416,"124I-1":417,"76BrH1":418,"18OH1":419,"22Na+1":420,"223Ra+2":421,"CaH2":422,"45Ca+2":423,"47Ca+2":424,"89Sr+2":425,"=32PH1":426,"NH4+1":427} \ No newline at end of file diff --git a/models/finetuned/tox21/config.json b/models/finetuned/tox21/config.json deleted file mode 100644 index 3811e21539577b37e06313eab31ec11e53f0cbbc..0000000000000000000000000000000000000000 --- a/models/finetuned/tox21/config.json +++ /dev/null @@ -1,27 +0,0 @@ -{ - "_name_or_path": "/home/erva/SELFormerMM/data/pretrained_multimodal_chembl36", - "architectures": [ - "RobertaForMaskedLM" - ], - "attention_probs_dropout_prob": 0.1, - "bos_token_id": 0, - "classifier_dropout": null, - "eos_token_id": 2, - "hidden_act": "gelu", - "hidden_dropout_prob": 0.1, - "hidden_size": 768, - "initializer_range": 0.02, - "intermediate_size": 3072, - "layer_norm_eps": 1e-12, - "max_position_embeddings": 514, - "model_type": "roberta", - "num_attention_heads": 4, - "num_hidden_layers": 12, - "pad_token_id": 1, - "position_embedding_type": "absolute", - "torch_dtype": "float32", - "transformers_version": "4.26.1", - "type_vocab_size": 1, - "use_cache": true, - "vocab_size": 800 -} diff --git a/models/finetuned/tox21/merges.txt b/models/finetuned/tox21/merges.txt deleted file mode 100644 index 7cd5ec62809503c23f18c80afc0ba3bdf9d253d0..0000000000000000000000000000000000000000 --- a/models/finetuned/tox21/merges.txt +++ /dev/null @@ -1,378 +0,0 @@ -#version: 0.2 - Trained by `huggingface/tokenizers` -B r -a n -c h -Br an -Bran ch -Branch 1 -= C -R i -n g -Ri ng -Ring 1 -= Branch1 -Branch 2 -= O -Ring 2 -H 1 -C @ -= N -# Branch1 -C@ @ -= Branch2 -C@ H1 -C@@ H1 -# Branch2 -# C -C l -/ C -N H1 -= Ring1 -+ 1 -- 1 -O -1 -N +1 -\ C -# N -/ N -= Ring2 -= S -=N +1 -\ N -N a -Na +1 -/ O -\ O -Br -1 -Branch 3 -\ S -S +1 -Cl -1 -I -1 -/ C@@H1 -S i -/ C@H1 -/ S -=N -1 -S e -= P -N -1 -Ring 3 -2 H -P +1 -K +1 -\ C@@H1 -\ C@H1 -/ N+1 -@ @ -C -1 -# N+1 -B -1 -+ 3 -Cl +3 -\ NH1 -L i -Li +1 -P H1 -1 8 -18 F -@ +1 -3 H -P @@ -H 0 -O H0 -1 2 -P @ -+ 2 -@@ +1 -S -1 -/ Br -- / -\ Cl --/ Ring2 -\ O-1 -1 1 -5 I -12 5I -11 C -H 3 -\ N+1 -- \ -/ C@@ -S @+1 -A s -/ Cl -11C H3 -=S e -S @@+1 -N @+1 -1 4 --\ Ring2 -14 C -\ F -/ C@ -T e -H 2 -H1 -1 -=O +1 -N @@+1 -C +1 -=S +1 -Z n -/ P -a +2 -/ I -O H1-1 -C a+2 -\ Br -M g -Zn +2 -A l -/ F -Mg +2 -12 3 -123 I -1 3 -I +1 -/ O-1 --\ Ring1 -B H2 -BH2 -1 -\ I -/ NH1 -O +1 -13 1 -131 I -= 14C -/ S+1 -= Ring3 -\ C@@ -H2 +1 -\ C@ -A g -= As -=Se +1 -N H2+1 -Se H1 --/ Ring1 -= Te -Al +3 -Na H1 -=Te +1 -NH1 +1 -Ag +1 -H1 +1 -NH1 -1 -\ P -14C H2 -13 C -14C H1 -= 11C -S @@ -=P @@ -Si H2 -H3 -1 -14C H3 -B H3-1 -S @ -=14C H1 -=P H1 -=P @ -=N H1+1 -\S +1 -12 4 -C H1-1 -S r -=S i -124 I -Sr +2 -#C -1 -/C -1 -N @ -/N -1 -13C H1 -/ B -1 9 -B a+2 -H 4 -S H1+1 -Se +1 -19 F -/ 125I -P @+1 -R b -Cl +1 -Si H4 -Rb +1 -= Branch3 -N @@ -As +1 -/ Si -B H1-1 -S H1 -/ 123I -3 2 -= Mg -H +1 -\ B -Si H1 -P@@ +1 -- 2 -1 5 -1 7 -3 5 -= 13CH1 -C s -=N H2+1 -=S H1 -Mg H2 -32 P -17 F -35 S -Cs +1 -# 11C -/ 131I -B i -\ 125I -=S @@ -\S -1 -6 Br -7 I -7 6Br -= B -e H1 -\N -1 -18 O -12 7I -11C H2 -14 C@@H1 -Te H2 -15 NH1 -Bi +3 -/ P+1 -/ 13C -/ 13CH1 -0 B -1 0B -= Al -= 18O -B H0 -F -1 -N H3 -S -2 -Br +2 -Cl +2 -\S i -/S -1 -=P H2 -14 C@H1 -NH3 +1 -# 14C -# O+1 -- 3 -2 2 -4 H -5 Se -5 Sr+2 -7 5Se -8 5Sr+2 -= B-1 -= 13C -@ -1 -B e -B @@ -B @-1 -C a -C H1 -I +3 -K H1 -O H1+1 -R a+2 -S H1-1 -\ PH1 -\ 123I -=C a -\C H1-1 -=S @ -\S eH1 -/S eH1 -Se -1 -Li H1 -18F -1 -125I H1 -11C H1 -Te H1 -Zn +1 -Zn -2 -Al -3 -13C H3 -15 N -Be +2 -B@@ -1 -# P -# S -- 4 -/ PH1 -/ P@@ -/ As -/ 14C -/ 14CH1 -2 K+1 -2 Rb+1 -3 Se -3 Ra+2 -4 5 -4 7 -4 2K+1 -5 I-1 -7 3Se -8 9 -8 2Rb+1 -= 32 -= 32P -C H0 -C H2 -I +2 -N H0 -N H4 -O H1 -P H2+1 -S H0 -S H2 -\ 3H -\ 11CH3 -\C -1 -\S e -Si @ -Si -1 -Si H1-1 -Si H3-1 -/S e -Se -2 -\NH1 -1 -18F H1 -12 5I-1 -11 C@@H1 -11 C-1 -As H1 -As -1 -14 C@@ -Te -1 -Mg +1 -123 I-1 -123 Te -123I H1 -13 5I -131 I-1 -Ag -4 -124 I-1 -76Br H1 -18O H1 -22 Na+1 -22 3Ra+2 -Ca H2 -45 Ca+2 -47 Ca+2 -89 Sr+2 -=32 PH1 -NH4 +1 diff --git a/models/finetuned/tox21/model.pt b/models/finetuned/tox21/model.pt deleted file mode 100644 index 325f6ea1b1d99bc89c07b9206975695cac0ce067..0000000000000000000000000000000000000000 --- a/models/finetuned/tox21/model.pt +++ /dev/null @@ -1,3 +0,0 @@ -version https://git-lfs.github.com/spec/v1 -oid sha256:c958fad0f8f2b485c9e2a8839f74fac88eb616d464b69d272613c564a27f2e8b -size 1022990461 diff --git a/models/finetuned/tox21/special_tokens_map.json b/models/finetuned/tox21/special_tokens_map.json deleted file mode 100644 index 06a55849fa69a91e7179d909e373179ff7467d8c..0000000000000000000000000000000000000000 --- a/models/finetuned/tox21/special_tokens_map.json +++ /dev/null @@ -1,51 +0,0 @@ -{ - "bos_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "cls_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "eos_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "mask_token": { - "content": "", - "lstrip": true, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "pad_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "sep_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "unk_token": { - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - } -} diff --git a/models/finetuned/tox21/tokenizer.json b/models/finetuned/tox21/tokenizer.json deleted file mode 100644 index 3b64b273e6fa9799e2d8375722b9e815de9ebb8f..0000000000000000000000000000000000000000 --- a/models/finetuned/tox21/tokenizer.json +++ /dev/null @@ -1,909 +0,0 @@ -{ - "version": "1.0", - "truncation": { - "direction": "Right", - "max_length": 128, - "strategy": "LongestFirst", - "stride": 0 - }, - "padding": { - "strategy": { - "Fixed": 128 - }, - "direction": "Right", - "pad_to_multiple_of": null, - "pad_id": 3, - "pad_type_id": 0, - "pad_token": "" - }, - "added_tokens": [ - { - "id": 0, - "content": "", - "single_word": false, - "lstrip": false, - "rstrip": false, - "normalized": true, - "special": true - }, - { - "id": 1, - "content": "", - "single_word": false, - "lstrip": false, - "rstrip": false, - "normalized": true, - "special": true - }, - { - "id": 2, - "content": "", - "single_word": false, - "lstrip": false, - "rstrip": false, - "normalized": true, - "special": true - }, - { - "id": 3, - "content": "", - "single_word": false, - "lstrip": false, - "rstrip": false, - "normalized": true, - "special": true - }, - { - "id": 4, - "content": "", - "single_word": false, - "lstrip": true, - "rstrip": false, - "normalized": true, - "special": true - } - ], - "normalizer": null, - "pre_tokenizer": { - "type": "ByteLevel", - "add_prefix_space": false, - "trim_offsets": true, - "use_regex": true - }, - "post_processor": { - "type": "RobertaProcessing", - "sep": [ - "", - 2 - ], - "cls": [ - "", - 1 - ], - "trim_offsets": true, - "add_prefix_space": false - }, - "decoder": { - "type": "ByteLevel", - "add_prefix_space": true, - "trim_offsets": true, - "use_regex": true - }, - "model": { - "type": "BPE", - "dropout": null, - "unk_token": null, - "continuing_subword_prefix": "", - "end_of_word_suffix": "", - "fuse_unk": false, - "vocab": { - "": 0, - "": 1, - "": 2, - "": 3, - "": 4, - "\n": 5, - "#": 6, - "+": 7, - "-": 8, - ".": 9, - "/": 10, - "0": 11, - "1": 12, - "2": 13, - "3": 14, - "4": 15, - "5": 16, - "6": 17, - "7": 18, - "8": 19, - "9": 20, - "=": 21, - "@": 22, - "A": 23, - "B": 24, - "C": 25, - "F": 26, - "H": 27, - "I": 28, - "K": 29, - "L": 30, - "M": 31, - "N": 32, - "O": 33, - "P": 34, - "R": 35, - "S": 36, - "T": 37, - "Z": 38, - "\\": 39, - "a": 40, - "b": 41, - "c": 42, - "e": 43, - "g": 44, - "h": 45, - "i": 46, - "l": 47, - "n": 48, - "r": 49, - "s": 50, - "Br": 51, - "an": 52, - "ch": 53, - "Bran": 54, - "Branch": 55, - "Branch1": 56, - "=C": 57, - "Ri": 58, - "ng": 59, - "Ring": 60, - "Ring1": 61, - "=Branch1": 62, - "Branch2": 63, - "=O": 64, - "Ring2": 65, - "H1": 66, - "C@": 67, - "=N": 68, - "#Branch1": 69, - "C@@": 70, - "=Branch2": 71, - "C@H1": 72, - "C@@H1": 73, - "#Branch2": 74, - "#C": 75, - "Cl": 76, - "/C": 77, - "NH1": 78, - "=Ring1": 79, - "+1": 80, - "-1": 81, - "O-1": 82, - "N+1": 83, - "\\C": 84, - "#N": 85, - "/N": 86, - "=Ring2": 87, - "=S": 88, - "=N+1": 89, - "\\N": 90, - "Na": 91, - "Na+1": 92, - "/O": 93, - "\\O": 94, - "Br-1": 95, - "Branch3": 96, - "\\S": 97, - "S+1": 98, - "Cl-1": 99, - "I-1": 100, - "/C@@H1": 101, - "Si": 102, - "/C@H1": 103, - "/S": 104, - "=N-1": 105, - "Se": 106, - "=P": 107, - "N-1": 108, - "Ring3": 109, - "2H": 110, - "P+1": 111, - "K+1": 112, - "\\C@@H1": 113, - "\\C@H1": 114, - "/N+1": 115, - "@@": 116, - "C-1": 117, - "#N+1": 118, - "B-1": 119, - "+3": 120, - "Cl+3": 121, - "\\NH1": 122, - "Li": 123, - "Li+1": 124, - "PH1": 125, - "18": 126, - "18F": 127, - "@+1": 128, - "3H": 129, - "P@@": 130, - "H0": 131, - "OH0": 132, - "12": 133, - "P@": 134, - "+2": 135, - "@@+1": 136, - "S-1": 137, - "/Br": 138, - "-/": 139, - "\\Cl": 140, - "-/Ring2": 141, - "\\O-1": 142, - "11": 143, - "5I": 144, - "125I": 145, - "11C": 146, - "H3": 147, - "\\N+1": 148, - "-\\": 149, - "/C@@": 150, - "S@+1": 151, - "As": 152, - "/Cl": 153, - "11CH3": 154, - "=Se": 155, - "S@@+1": 156, - "N@+1": 157, - "14": 158, - "-\\Ring2": 159, - "14C": 160, - "\\F": 161, - "/C@": 162, - "Te": 163, - "H2": 164, - "H1-1": 165, - "=O+1": 166, - "N@@+1": 167, - "C+1": 168, - "=S+1": 169, - "Zn": 170, - "/P": 171, - "a+2": 172, - "/I": 173, - "OH1-1": 174, - "Ca+2": 175, - "\\Br": 176, - "Mg": 177, - "Zn+2": 178, - "Al": 179, - "/F": 180, - "Mg+2": 181, - "123": 182, - "123I": 183, - "13": 184, - "I+1": 185, - "/O-1": 186, - "-\\Ring1": 187, - "BH2": 188, - "BH2-1": 189, - "\\I": 190, - "/NH1": 191, - "O+1": 192, - "131": 193, - "131I": 194, - "=14C": 195, - "/S+1": 196, - "=Ring3": 197, - "\\C@@": 198, - "H2+1": 199, - "\\C@": 200, - "Ag": 201, - "=As": 202, - "=Se+1": 203, - "NH2+1": 204, - "SeH1": 205, - "-/Ring1": 206, - "=Te": 207, - "Al+3": 208, - "NaH1": 209, - "=Te+1": 210, - "NH1+1": 211, - "Ag+1": 212, - "H1+1": 213, - "NH1-1": 214, - "\\P": 215, - "14CH2": 216, - "13C": 217, - "14CH1": 218, - "=11C": 219, - "S@@": 220, - "=P@@": 221, - "SiH2": 222, - "H3-1": 223, - "14CH3": 224, - "BH3-1": 225, - "S@": 226, - "=14CH1": 227, - "=PH1": 228, - "=P@": 229, - "=NH1+1": 230, - "\\S+1": 231, - "124": 232, - "CH1-1": 233, - "Sr": 234, - "=Si": 235, - "124I": 236, - "Sr+2": 237, - "#C-1": 238, - "/C-1": 239, - "N@": 240, - "/N-1": 241, - "13CH1": 242, - "/B": 243, - "19": 244, - "Ba+2": 245, - "H4": 246, - "SH1+1": 247, - "Se+1": 248, - "19F": 249, - "/125I": 250, - "P@+1": 251, - "Rb": 252, - "Cl+1": 253, - "SiH4": 254, - "Rb+1": 255, - "=Branch3": 256, - "N@@": 257, - "As+1": 258, - "/Si": 259, - "BH1-1": 260, - "SH1": 261, - "/123I": 262, - "32": 263, - "=Mg": 264, - "H+1": 265, - "\\B": 266, - "SiH1": 267, - "P@@+1": 268, - "-2": 269, - "15": 270, - "17": 271, - "35": 272, - "=13CH1": 273, - "Cs": 274, - "=NH2+1": 275, - "=SH1": 276, - "MgH2": 277, - "32P": 278, - "17F": 279, - "35S": 280, - "Cs+1": 281, - "#11C": 282, - "/131I": 283, - "Bi": 284, - "\\125I": 285, - "=S@@": 286, - "\\S-1": 287, - "6Br": 288, - "7I": 289, - "76Br": 290, - "=B": 291, - "eH1": 292, - "\\N-1": 293, - "18O": 294, - "127I": 295, - "11CH2": 296, - "14C@@H1": 297, - "TeH2": 298, - "15NH1": 299, - "Bi+3": 300, - "/P+1": 301, - "/13C": 302, - "/13CH1": 303, - "0B": 304, - "10B": 305, - "=Al": 306, - "=18O": 307, - "BH0": 308, - "F-1": 309, - "NH3": 310, - "S-2": 311, - "Br+2": 312, - "Cl+2": 313, - "\\Si": 314, - "/S-1": 315, - "=PH2": 316, - "14C@H1": 317, - "NH3+1": 318, - "#14C": 319, - "#O+1": 320, - "-3": 321, - "22": 322, - "4H": 323, - "5Se": 324, - "5Sr+2": 325, - "75Se": 326, - "85Sr+2": 327, - "=B-1": 328, - "=13C": 329, - "@-1": 330, - "Be": 331, - "B@@": 332, - "B@-1": 333, - "Ca": 334, - "CH1": 335, - "I+3": 336, - "KH1": 337, - "OH1+1": 338, - "Ra+2": 339, - "SH1-1": 340, - "\\PH1": 341, - "\\123I": 342, - "=Ca": 343, - "\\CH1-1": 344, - "=S@": 345, - "\\SeH1": 346, - "/SeH1": 347, - "Se-1": 348, - "LiH1": 349, - "18F-1": 350, - "125IH1": 351, - "11CH1": 352, - "TeH1": 353, - "Zn+1": 354, - "Zn-2": 355, - "Al-3": 356, - "13CH3": 357, - "15N": 358, - "Be+2": 359, - "B@@-1": 360, - "#P": 361, - "#S": 362, - "-4": 363, - "/PH1": 364, - "/P@@": 365, - "/As": 366, - "/14C": 367, - "/14CH1": 368, - "2K+1": 369, - "2Rb+1": 370, - "3Se": 371, - "3Ra+2": 372, - "45": 373, - "47": 374, - "42K+1": 375, - "5I-1": 376, - "73Se": 377, - "89": 378, - "82Rb+1": 379, - "=32": 380, - "=32P": 381, - "CH0": 382, - "CH2": 383, - "I+2": 384, - "NH0": 385, - "NH4": 386, - "OH1": 387, - "PH2+1": 388, - "SH0": 389, - "SH2": 390, - "\\3H": 391, - "\\11CH3": 392, - "\\C-1": 393, - "\\Se": 394, - "Si@": 395, - "Si-1": 396, - "SiH1-1": 397, - "SiH3-1": 398, - "/Se": 399, - "Se-2": 400, - "\\NH1-1": 401, - "18FH1": 402, - "125I-1": 403, - "11C@@H1": 404, - "11C-1": 405, - "AsH1": 406, - "As-1": 407, - "14C@@": 408, - "Te-1": 409, - "Mg+1": 410, - "123I-1": 411, - "123Te": 412, - "123IH1": 413, - "135I": 414, - "131I-1": 415, - "Ag-4": 416, - "124I-1": 417, - "76BrH1": 418, - "18OH1": 419, - "22Na+1": 420, - "223Ra+2": 421, - "CaH2": 422, - "45Ca+2": 423, - "47Ca+2": 424, - "89Sr+2": 425, - "=32PH1": 426, - "NH4+1": 427 - }, - "merges": [ - "B r", - "a n", - "c h", - "Br an", - "Bran ch", - "Branch 1", - "= C", - "R i", - "n g", - "Ri ng", - "Ring 1", - "= Branch1", - "Branch 2", - "= O", - "Ring 2", - "H 1", - "C @", - "= N", - "# Branch1", - "C@ @", - "= Branch2", - "C@ H1", - "C@@ H1", - "# Branch2", - "# C", - "C l", - "/ C", - "N H1", - "= Ring1", - "+ 1", - "- 1", - "O -1", - "N +1", - "\\ C", - "# N", - "/ N", - "= Ring2", - "= S", - "=N +1", - "\\ N", - "N a", - "Na +1", - "/ O", - "\\ O", - "Br -1", - "Branch 3", - "\\ S", - "S +1", - "Cl -1", - "I -1", - "/ C@@H1", - "S i", - "/ C@H1", - "/ S", - "=N -1", - "S e", - "= P", - "N -1", - "Ring 3", - "2 H", - "P +1", - "K +1", - "\\ C@@H1", - "\\ C@H1", - "/ N+1", - "@ @", - "C -1", - "# N+1", - "B -1", - "+ 3", - "Cl +3", - "\\ NH1", - "L i", - "Li +1", - "P H1", - "1 8", - "18 F", - "@ +1", - "3 H", - "P @@", - "H 0", - "O H0", - "1 2", - "P @", - "+ 2", - "@@ +1", - "S -1", - "/ Br", - "- /", - "\\ Cl", - "-/ Ring2", - "\\ O-1", - "1 1", - "5 I", - "12 5I", - "11 C", - "H 3", - "\\ N+1", - "- \\", - "/ C@@", - "S @+1", - "A s", - "/ Cl", - "11C H3", - "=S e", - "S @@+1", - "N @+1", - "1 4", - "-\\ Ring2", - "14 C", - "\\ F", - "/ C@", - "T e", - "H 2", - "H1 -1", - "=O +1", - "N @@+1", - "C +1", - "=S +1", - "Z n", - "/ P", - "a +2", - "/ I", - "O H1-1", - "C a+2", - "\\ Br", - "M g", - "Zn +2", - "A l", - "/ F", - "Mg +2", - "12 3", - "123 I", - "1 3", - "I +1", - "/ O-1", - "-\\ Ring1", - "B H2", - "BH2 -1", - "\\ I", - "/ NH1", - "O +1", - "13 1", - "131 I", - "= 14C", - "/ S+1", - "= Ring3", - "\\ C@@", - "H2 +1", - "\\ C@", - "A g", - "= As", - "=Se +1", - "N H2+1", - "Se H1", - "-/ Ring1", - "= Te", - "Al +3", - "Na H1", - "=Te +1", - "NH1 +1", - "Ag +1", - "H1 +1", - "NH1 -1", - "\\ P", - "14C H2", - "13 C", - "14C H1", - "= 11C", - "S @@", - "=P @@", - "Si H2", - "H3 -1", - "14C H3", - "B H3-1", - "S @", - "=14C H1", - "=P H1", - "=P @", - "=N H1+1", - "\\S +1", - "12 4", - "C H1-1", - "S r", - "=S i", - "124 I", - "Sr +2", - "#C -1", - "/C -1", - "N @", - "/N -1", - "13C H1", - "/ B", - "1 9", - "B a+2", - "H 4", - "S H1+1", - "Se +1", - "19 F", - "/ 125I", - "P @+1", - "R b", - "Cl +1", - "Si H4", - "Rb +1", - "= Branch3", - "N @@", - "As +1", - "/ Si", - "B H1-1", - "S H1", - "/ 123I", - "3 2", - "= Mg", - "H +1", - "\\ B", - "Si H1", - "P@@ +1", - "- 2", - "1 5", - "1 7", - "3 5", - "= 13CH1", - "C s", - "=N H2+1", - "=S H1", - "Mg H2", - "32 P", - "17 F", - "35 S", - "Cs +1", - "# 11C", - "/ 131I", - "B i", - "\\ 125I", - "=S @@", - "\\S -1", - "6 Br", - "7 I", - "7 6Br", - "= B", - "e H1", - "\\N -1", - "18 O", - "12 7I", - "11C H2", - "14 C@@H1", - "Te H2", - "15 NH1", - "Bi +3", - "/ P+1", - "/ 13C", - "/ 13CH1", - "0 B", - "1 0B", - "= Al", - "= 18O", - "B H0", - "F -1", - "N H3", - "S -2", - "Br +2", - "Cl +2", - "\\S i", - "/S -1", - "=P H2", - "14 C@H1", - "NH3 +1", - "# 14C", - "# O+1", - "- 3", - "2 2", - "4 H", - "5 Se", - "5 Sr+2", - "7 5Se", - "8 5Sr+2", - "= B-1", - "= 13C", - "@ -1", - "B e", - "B @@", - "B @-1", - "C a", - "C H1", - "I +3", - "K H1", - "O H1+1", - "R a+2", - "S H1-1", - "\\ PH1", - "\\ 123I", - "=C a", - "\\C H1-1", - "=S @", - "\\S eH1", - "/S eH1", - "Se -1", - "Li H1", - "18F -1", - "125I H1", - "11C H1", - "Te H1", - "Zn +1", - "Zn -2", - "Al -3", - "13C H3", - "15 N", - "Be +2", - "B@@ -1", - "# P", - "# S", - "- 4", - "/ PH1", - "/ P@@", - "/ As", - "/ 14C", - "/ 14CH1", - "2 K+1", - "2 Rb+1", - "3 Se", - "3 Ra+2", - "4 5", - "4 7", - "4 2K+1", - "5 I-1", - "7 3Se", - "8 9", - "8 2Rb+1", - "= 32", - "= 32P", - "C H0", - "C H2", - "I +2", - "N H0", - "N H4", - "O H1", - "P H2+1", - "S H0", - "S H2", - "\\ 3H", - "\\ 11CH3", - "\\C -1", - "\\S e", - "Si @", - "Si -1", - "Si H1-1", - "Si H3-1", - "/S e", - "Se -2", - "\\NH1 -1", - "18F H1", - "12 5I-1", - "11 C@@H1", - "11 C-1", - "As H1", - "As -1", - "14 C@@", - "Te -1", - "Mg +1", - "123 I-1", - "123 Te", - "123I H1", - "13 5I", - "131 I-1", - "Ag -4", - "124 I-1", - "76Br H1", - "18O H1", - "22 Na+1", - "22 3Ra+2", - "Ca H2", - "45 Ca+2", - "47 Ca+2", - "89 Sr+2", - "=32 PH1", - "NH4 +1" - ] - } -} \ No newline at end of file diff --git a/models/finetuned/tox21/tokenizer_config.json b/models/finetuned/tox21/tokenizer_config.json deleted file mode 100644 index 08860954acd34fad07fd77f7635298fa565f3149..0000000000000000000000000000000000000000 --- a/models/finetuned/tox21/tokenizer_config.json +++ /dev/null @@ -1,65 +0,0 @@ -{ - "add_prefix_space": false, - "bos_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "cls_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "eos_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "errors": "replace", - "mask_token": { - "__type": "AddedToken", - "content": "", - "lstrip": true, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "model_max_length": 1000000000000000019884624838656, - "name_or_path": "/home/erva/SELFormerMM/data/pretrained_multimodal_chembl36", - "pad_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "sep_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - }, - "special_tokens_map_file": null, - "tokenizer_class": "RobertaTokenizer", - "trim_offsets": true, - "unk_token": { - "__type": "AddedToken", - "content": "", - "lstrip": false, - "normalized": true, - "rstrip": false, - "single_word": false - } -} diff --git a/models/finetuned/tox21/train_stdout.log b/models/finetuned/tox21/train_stdout.log deleted file mode 100644 index 3360f20215181e93710f5f5cf87e7964fe267b0f..0000000000000000000000000000000000000000 --- a/models/finetuned/tox21/train_stdout.log +++ /dev/null @@ -1,92 +0,0 @@ -[finetune] starting -[finetune] device=cuda task_type=multilabel batch_size=8 max_len=128 backbone_lr=1e-05 head_lr=0.0005 weight_decay=0.001 epochs=50 -[finetune] dataset_meta_csv=/home/erva/SELFormerMM/data/new_finetuning_datasets/classification/tox21/tox21.csv -[finetune] dataset_embs_npz=/home/erva/SELFormerMM/data/new_finetuning_datasets/classification/tox21/tox21_embs.npz -[finetune] model_path=HUBioDataLab/SELFormer tokenizer_path=HUBioDataLab/SELFormer -[finetune] pretrained_multimodal_dir=/home/erva/SELFormerMM/data/pretrained_multimodal_chembl36 -[finetune] use_scaffold=False seed=42 fracs=(0.8,0.1,0.1) -[finetune] loading dataset bundle (meta csv + embs npz) ... -[finetune] splitting dataset... -[finetune] split sizes: train=6,264 val=783 test=784 -[finetune] train modality_non_empty: graph=6,258/6,264 text=4,796/6,264 kg=298/6,264 -[finetune] val modality_non_empty: graph=782/783 text=623/783 kg=25/783 -[finetune] test modality_non_empty: graph=783/784 text=592/784 kg=38/784 -[finetune] extracting labels... -[finetune] multilabel: num_labels_in_csv=13 -[finetune] loading config/tokenizer/backbone... -[finetune] initializing multimodal model... -[finetune] loading multimodal pretrained weights: /home/erva/SELFormerMM/data/pretrained_multimodal_chembl36/pytorch_model.bin -[finetune] freezing roberta layers (trainable: encoder.layer.9-11)... -[finetune] backbone trainable params: 181,443,072/246,245,376 -[finetune] building datasets/dataloaders... -[finetune] train_steps_per_epoch=783 val_steps=98 test_steps=98 -[finetune] overriding --num_labels=1 with num_labels_in_csv=13 -[finetune] initialized head: in_dim=3072 out=13 -[finetune] initializing optimizer/scheduler/finetuner... -[finetune] optimizer groups: backbone_decay=45 backbone_nodecay=57 head_decay=2 head_nodecay=2 -[finetune] training loop... -[finetune] epoch 1/50: train_loss=-216193.6333 val_loss=-113671.4013 time=54.7s tod=16:14 -[finetune] epoch 2/50: train_loss=-412453.9276 val_loss=-440000.0230 time=54.0s tod=16:15 -[finetune] epoch 3/50: train_loss=-887676.8236 val_loss=-952418.1257 time=54.5s tod=16:16 -[finetune] epoch 4/50: train_loss=-1524831.5284 val_loss=-1035367.8295 time=53.7s tod=16:17 -[finetune] epoch 5/50: train_loss=-2351748.6775 val_loss=-1452939.0927 time=54.0s tod=16:17 -[finetune] epoch 6/50: train_loss=-3184443.9216 val_loss=-1768902.9329 time=53.7s tod=16:18 -[finetune] epoch 7/50: train_loss=-4038405.9811 val_loss=-2172572.4858 time=53.4s tod=16:19 -[finetune] epoch 8/50: train_loss=-4937786.7989 val_loss=-2350164.7637 time=53.8s tod=16:20 -[finetune] epoch 9/50: train_loss=-5681205.7596 val_loss=-2605011.2469 time=54.0s tod=16:21 -[finetune] epoch 10/50: train_loss=-6567555.5207 val_loss=-2593369.0649 time=53.4s tod=16:22 -[finetune] epoch 11/50: train_loss=-7387322.5679 val_loss=-3612002.6768 time=54.1s tod=16:23 -[finetune] epoch 12/50: train_loss=-8185306.1467 val_loss=-2633102.3551 time=53.6s tod=16:24 -[finetune] epoch 13/50: train_loss=-8990810.3031 val_loss=-3891463.0388 time=53.9s tod=16:25 -[finetune] epoch 14/50: train_loss=-9759411.5767 val_loss=-4663161.3781 time=53.8s tod=16:25 -[finetune] epoch 15/50: train_loss=-10479519.1598 val_loss=-4013720.2909 time=53.3s tod=16:26 -[finetune] epoch 16/50: train_loss=-11349079.8151 val_loss=-3809875.2072 time=53.8s tod=16:27 -[finetune] epoch 17/50: train_loss=-12140997.0294 val_loss=-4012518.1141 time=53.9s tod=16:28 -[finetune] epoch 18/50: train_loss=-12888118.4571 val_loss=-4380830.4794 time=53.4s tod=16:29 -[finetune] epoch 19/50: train_loss=-13520204.9583 val_loss=-4382646.9831 time=54.1s tod=16:30 -[finetune] epoch 20/50: train_loss=-14241493.7080 val_loss=-5114424.9447 time=54.3s tod=16:31 -[finetune] epoch 21/50: train_loss=-14975536.1623 val_loss=-5732739.2004 time=53.6s tod=16:32 -[finetune] epoch 22/50: train_loss=-15634874.3266 val_loss=-5503666.0586 time=53.5s tod=16:33 -[finetune] epoch 23/50: train_loss=-16297291.1342 val_loss=-5298696.2058 time=54.2s tod=16:34 -[finetune] epoch 24/50: train_loss=-17026477.4266 val_loss=-4584186.9219 time=53.5s tod=16:34 -[finetune] epoch 25/50: train_loss=-17412736.1286 val_loss=-6193778.4885 time=54.4s tod=16:35 -/home/erva/SELFormerMM/train_finetuning.py:155: RuntimeWarning: overflow encountered in exp - return 1.0 / (1.0 + np.exp(-x)) -[finetune] test_metrics: epoch=25 loss=-10717827.3358 accuracy=0.9269 precision=0.3792 recall=0.2921 f1=0.3300 roc-auc=0.6336 prc-auc=0.1858 -[finetune] saved checkpoint (best roc-auc=0.6336): /media/ubuntu/8TB/erva/selformer-mm/output/new_finetune_sweeps/tox21/xyrw6rkc/checkpoint_epoch_025 -[finetune] epoch 26/50: train_loss=-18012359.0458 val_loss=-5623670.3106 time=54.0s tod=16:36 -[finetune] epoch 27/50: train_loss=-18672690.9479 val_loss=-6479933.9914 time=53.3s tod=16:37 -[finetune] epoch 28/50: train_loss=-19280746.8376 val_loss=-5831075.7259 time=54.2s tod=16:38 -[finetune] epoch 29/50: train_loss=-19729831.8720 val_loss=-7317136.4007 time=54.1s tod=16:39 -[finetune] epoch 30/50: train_loss=-20169510.6495 val_loss=-6095962.3972 time=53.9s tod=16:40 -[finetune] epoch 31/50: train_loss=-20712630.3428 val_loss=-6431097.9831 time=53.3s tod=16:41 -[finetune] epoch 32/50: train_loss=-21138979.2127 val_loss=-6581554.7533 time=53.1s tod=16:42 -[finetune] epoch 33/50: train_loss=-21585666.2917 val_loss=-6187379.4101 time=53.4s tod=16:43 -[finetune] epoch 34/50: train_loss=-21839427.5970 val_loss=-6638206.6535 time=53.3s tod=16:43 -[finetune] epoch 35/50: train_loss=-22323325.7181 val_loss=-7626298.3497 time=53.7s tod=16:44 -[finetune] epoch 36/50: train_loss=-22618891.8809 val_loss=-7537031.2214 time=52.6s tod=16:45 -[finetune] epoch 37/50: train_loss=-22912492.7341 val_loss=-6675574.5707 time=53.0s tod=16:46 -[finetune] epoch 38/50: train_loss=-23171182.0316 val_loss=-7554391.4859 time=53.0s tod=16:47 -[finetune] epoch 39/50: train_loss=-23530399.3391 val_loss=-7706676.0849 time=53.2s tod=16:48 -[finetune] epoch 40/50: train_loss=-23791565.5375 val_loss=-7679242.5749 time=54.1s tod=16:49 -[finetune] epoch 41/50: train_loss=-23953559.3519 val_loss=-7454979.6627 time=53.9s tod=16:50 -[finetune] epoch 42/50: train_loss=-24229901.7895 val_loss=-7261276.1295 time=53.6s tod=16:51 -[finetune] epoch 43/50: train_loss=-24433469.5779 val_loss=-7703355.7898 time=51.6s tod=16:51 -[finetune] epoch 44/50: train_loss=-24593268.4133 val_loss=-7843873.5753 time=54.6s tod=16:52 -[finetune] epoch 45/50: train_loss=-24648599.9635 val_loss=-8010940.1643 time=52.9s tod=16:53 -[finetune] epoch 46/50: train_loss=-24824771.2119 val_loss=-7650992.9769 time=54.5s tod=16:54 -[finetune] epoch 47/50: train_loss=-24919698.8539 val_loss=-7686188.3593 time=53.5s tod=16:55 -[finetune] epoch 48/50: train_loss=-24983982.4635 val_loss=-7849183.9679 time=53.2s tod=16:56 -[finetune] epoch 49/50: train_loss=-25026115.0519 val_loss=-8320514.8827 time=53.4s tod=16:57 -[finetune] epoch 50/50: train_loss=-25057941.0290 val_loss=-8258987.8504 time=52.9s tod=16:58 -/home/erva/SELFormerMM/train_finetuning.py:155: RuntimeWarning: overflow encountered in exp - return 1.0 / (1.0 + np.exp(-x)) -[finetune] test_metrics: epoch=50 loss=-13557626.8894 accuracy=0.9364 precision=0.4714 recall=0.2648 f1=0.3392 roc-auc=0.6260 prc-auc=0.2032 -[finetune] checkpoint skipped (current roc-auc=0.6260 vs best=0.6336 at epoch 25) -[finetune] final evaluation on test split... -/home/erva/SELFormerMM/train_finetuning.py:155: RuntimeWarning: overflow encountered in exp - return 1.0 / (1.0 + np.exp(-x)) -[finetune] test_metrics: loss=-13557626.8894 accuracy=0.9364 precision=0.4714 recall=0.2648 f1=0.3392 roc-auc=0.6260 prc-auc=0.2032 -[finetune] saving model... -[finetune] saved finetuned model to: /media/ubuntu/8TB/erva/selformer-mm/output/new_finetune_sweeps/tox21/xyrw6rkc -[finetune] done in 2697.0s diff --git a/models/finetuned/tox21/vocab.json b/models/finetuned/tox21/vocab.json deleted file mode 100644 index f7e4cc22809f4e9035cc450ef189c8a7da8fd03e..0000000000000000000000000000000000000000 --- a/models/finetuned/tox21/vocab.json +++ /dev/null @@ -1 +0,0 @@ -{"":0,"":1,"":2,"":3,"":4,"\n":5,"#":6,"+":7,"-":8,".":9,"/":10,"0":11,"1":12,"2":13,"3":14,"4":15,"5":16,"6":17,"7":18,"8":19,"9":20,"=":21,"@":22,"A":23,"B":24,"C":25,"F":26,"H":27,"I":28,"K":29,"L":30,"M":31,"N":32,"O":33,"P":34,"R":35,"S":36,"T":37,"Z":38,"\\":39,"a":40,"b":41,"c":42,"e":43,"g":44,"h":45,"i":46,"l":47,"n":48,"r":49,"s":50,"Br":51,"an":52,"ch":53,"Bran":54,"Branch":55,"Branch1":56,"=C":57,"Ri":58,"ng":59,"Ring":60,"Ring1":61,"=Branch1":62,"Branch2":63,"=O":64,"Ring2":65,"H1":66,"C@":67,"=N":68,"#Branch1":69,"C@@":70,"=Branch2":71,"C@H1":72,"C@@H1":73,"#Branch2":74,"#C":75,"Cl":76,"/C":77,"NH1":78,"=Ring1":79,"+1":80,"-1":81,"O-1":82,"N+1":83,"\\C":84,"#N":85,"/N":86,"=Ring2":87,"=S":88,"=N+1":89,"\\N":90,"Na":91,"Na+1":92,"/O":93,"\\O":94,"Br-1":95,"Branch3":96,"\\S":97,"S+1":98,"Cl-1":99,"I-1":100,"/C@@H1":101,"Si":102,"/C@H1":103,"/S":104,"=N-1":105,"Se":106,"=P":107,"N-1":108,"Ring3":109,"2H":110,"P+1":111,"K+1":112,"\\C@@H1":113,"\\C@H1":114,"/N+1":115,"@@":116,"C-1":117,"#N+1":118,"B-1":119,"+3":120,"Cl+3":121,"\\NH1":122,"Li":123,"Li+1":124,"PH1":125,"18":126,"18F":127,"@+1":128,"3H":129,"P@@":130,"H0":131,"OH0":132,"12":133,"P@":134,"+2":135,"@@+1":136,"S-1":137,"/Br":138,"-/":139,"\\Cl":140,"-/Ring2":141,"\\O-1":142,"11":143,"5I":144,"125I":145,"11C":146,"H3":147,"\\N+1":148,"-\\":149,"/C@@":150,"S@+1":151,"As":152,"/Cl":153,"11CH3":154,"=Se":155,"S@@+1":156,"N@+1":157,"14":158,"-\\Ring2":159,"14C":160,"\\F":161,"/C@":162,"Te":163,"H2":164,"H1-1":165,"=O+1":166,"N@@+1":167,"C+1":168,"=S+1":169,"Zn":170,"/P":171,"a+2":172,"/I":173,"OH1-1":174,"Ca+2":175,"\\Br":176,"Mg":177,"Zn+2":178,"Al":179,"/F":180,"Mg+2":181,"123":182,"123I":183,"13":184,"I+1":185,"/O-1":186,"-\\Ring1":187,"BH2":188,"BH2-1":189,"\\I":190,"/NH1":191,"O+1":192,"131":193,"131I":194,"=14C":195,"/S+1":196,"=Ring3":197,"\\C@@":198,"H2+1":199,"\\C@":200,"Ag":201,"=As":202,"=Se+1":203,"NH2+1":204,"SeH1":205,"-/Ring1":206,"=Te":207,"Al+3":208,"NaH1":209,"=Te+1":210,"NH1+1":211,"Ag+1":212,"H1+1":213,"NH1-1":214,"\\P":215,"14CH2":216,"13C":217,"14CH1":218,"=11C":219,"S@@":220,"=P@@":221,"SiH2":222,"H3-1":223,"14CH3":224,"BH3-1":225,"S@":226,"=14CH1":227,"=PH1":228,"=P@":229,"=NH1+1":230,"\\S+1":231,"124":232,"CH1-1":233,"Sr":234,"=Si":235,"124I":236,"Sr+2":237,"#C-1":238,"/C-1":239,"N@":240,"/N-1":241,"13CH1":242,"/B":243,"19":244,"Ba+2":245,"H4":246,"SH1+1":247,"Se+1":248,"19F":249,"/125I":250,"P@+1":251,"Rb":252,"Cl+1":253,"SiH4":254,"Rb+1":255,"=Branch3":256,"N@@":257,"As+1":258,"/Si":259,"BH1-1":260,"SH1":261,"/123I":262,"32":263,"=Mg":264,"H+1":265,"\\B":266,"SiH1":267,"P@@+1":268,"-2":269,"15":270,"17":271,"35":272,"=13CH1":273,"Cs":274,"=NH2+1":275,"=SH1":276,"MgH2":277,"32P":278,"17F":279,"35S":280,"Cs+1":281,"#11C":282,"/131I":283,"Bi":284,"\\125I":285,"=S@@":286,"\\S-1":287,"6Br":288,"7I":289,"76Br":290,"=B":291,"eH1":292,"\\N-1":293,"18O":294,"127I":295,"11CH2":296,"14C@@H1":297,"TeH2":298,"15NH1":299,"Bi+3":300,"/P+1":301,"/13C":302,"/13CH1":303,"0B":304,"10B":305,"=Al":306,"=18O":307,"BH0":308,"F-1":309,"NH3":310,"S-2":311,"Br+2":312,"Cl+2":313,"\\Si":314,"/S-1":315,"=PH2":316,"14C@H1":317,"NH3+1":318,"#14C":319,"#O+1":320,"-3":321,"22":322,"4H":323,"5Se":324,"5Sr+2":325,"75Se":326,"85Sr+2":327,"=B-1":328,"=13C":329,"@-1":330,"Be":331,"B@@":332,"B@-1":333,"Ca":334,"CH1":335,"I+3":336,"KH1":337,"OH1+1":338,"Ra+2":339,"SH1-1":340,"\\PH1":341,"\\123I":342,"=Ca":343,"\\CH1-1":344,"=S@":345,"\\SeH1":346,"/SeH1":347,"Se-1":348,"LiH1":349,"18F-1":350,"125IH1":351,"11CH1":352,"TeH1":353,"Zn+1":354,"Zn-2":355,"Al-3":356,"13CH3":357,"15N":358,"Be+2":359,"B@@-1":360,"#P":361,"#S":362,"-4":363,"/PH1":364,"/P@@":365,"/As":366,"/14C":367,"/14CH1":368,"2K+1":369,"2Rb+1":370,"3Se":371,"3Ra+2":372,"45":373,"47":374,"42K+1":375,"5I-1":376,"73Se":377,"89":378,"82Rb+1":379,"=32":380,"=32P":381,"CH0":382,"CH2":383,"I+2":384,"NH0":385,"NH4":386,"OH1":387,"PH2+1":388,"SH0":389,"SH2":390,"\\3H":391,"\\11CH3":392,"\\C-1":393,"\\Se":394,"Si@":395,"Si-1":396,"SiH1-1":397,"SiH3-1":398,"/Se":399,"Se-2":400,"\\NH1-1":401,"18FH1":402,"125I-1":403,"11C@@H1":404,"11C-1":405,"AsH1":406,"As-1":407,"14C@@":408,"Te-1":409,"Mg+1":410,"123I-1":411,"123Te":412,"123IH1":413,"135I":414,"131I-1":415,"Ag-4":416,"124I-1":417,"76BrH1":418,"18OH1":419,"22Na+1":420,"223Ra+2":421,"CaH2":422,"45Ca+2":423,"47Ca+2":424,"89Sr+2":425,"=32PH1":426,"NH4+1":427} \ No newline at end of file