diff --git a/models/finetuned/bace/config.json b/models/finetuned/bace/config.json new file mode 100644 index 0000000000000000000000000000000000000000..3811e21539577b37e06313eab31ec11e53f0cbbc --- /dev/null +++ b/models/finetuned/bace/config.json @@ -0,0 +1,27 @@ +{ + "_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/finetuning_optimized_config.json b/models/finetuned/bace/finetuning_optimized_config.json new file mode 100644 index 0000000000000000000000000000000000000000..c5dd0f9500858e7e83619273025ac7c3557c0485 --- /dev/null +++ b/models/finetuned/bace/finetuning_optimized_config.json @@ -0,0 +1,24 @@ +{ + "dataset_meta_csv": "data/finetuning_datasets/classification/bace/bace.csv", + "dataset_embs_npz": "data/finetuning_datasets/classification/bace/bace_embs.npz", + "use_scaffold": 1, + "seed": 42, + "train_frac": 0.8, + "val_frac": 0.1, + "test_frac": 0.1, + "model_path": "HUBioDataLab/SELFormer", + "tokenizer_path": "HUBioDataLab/SELFormer", + "pretrained_multimodal_dir": "data/models/SELFormerMM", + "task_type": "binary", + "label_column": "Class", + "num_labels": 2, + "batch_size": 16, + "max_len": 128, + "epochs": 25, + "backbone_lr": 5e-05, + "head_lr": 1e-05, + "weight_decay": 0.1, + "checkpoint_every": 25, + "test_eval_every": 0, + "save_dir": "data/models/finetuned/bace" +} diff --git a/models/finetuned/bace/merges.txt b/models/finetuned/bace/merges.txt new file mode 100644 index 0000000000000000000000000000000000000000..7cd5ec62809503c23f18c80afc0ba3bdf9d253d0 --- /dev/null +++ b/models/finetuned/bace/merges.txt @@ -0,0 +1,378 @@ +#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 new file mode 100644 index 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"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", + 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\ No newline at end of file diff --git a/models/finetuned/bbbp/config.json b/models/finetuned/bbbp/config.json new file mode 100644 index 0000000000000000000000000000000000000000..3811e21539577b37e06313eab31ec11e53f0cbbc --- /dev/null +++ b/models/finetuned/bbbp/config.json @@ -0,0 +1,27 @@ +{ + "_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/finetuning_optimized_config.json b/models/finetuned/bbbp/finetuning_optimized_config.json new file mode 100644 index 0000000000000000000000000000000000000000..7d3476aa13e564831a639fa900c9a920ec6c040a --- /dev/null +++ b/models/finetuned/bbbp/finetuning_optimized_config.json @@ -0,0 +1,24 @@ +{ + "dataset_meta_csv": "data/finetuning_datasets/classification/bbbp/bbbp.csv", + "dataset_embs_npz": "data/finetuning_datasets/classification/bbbp/bbbp_embs.npz", + "use_scaffold": 1, + "seed": 42, + "train_frac": 0.8, + "val_frac": 0.1, + "test_frac": 0.1, + "model_path": "HUBioDataLab/SELFormer", + "tokenizer_path": "HUBioDataLab/SELFormer", + "pretrained_multimodal_dir": "data/models/SELFormerMM", + "task_type": "binary", + "label_column": "p_np", + "num_labels": 2, + "batch_size": 32, + "max_len": 128, + "epochs": 50, + "backbone_lr": 5e-05, + "head_lr": 5e-05, + "weight_decay": 0.01, + "checkpoint_every": 25, + "test_eval_every": 0, + "save_dir": "data/models/finetuned/bbbp" +} diff --git a/models/finetuned/bbbp/merges.txt b/models/finetuned/bbbp/merges.txt new file mode 100644 index 0000000000000000000000000000000000000000..7cd5ec62809503c23f18c80afc0ba3bdf9d253d0 --- /dev/null +++ b/models/finetuned/bbbp/merges.txt @@ -0,0 +1,378 @@ +#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 new file mode 100644 index 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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", 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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 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"vocab_size": 800 +} diff --git a/models/finetuned/freesolv/finetuning_optimized_config.json b/models/finetuned/freesolv/finetuning_optimized_config.json new file mode 100644 index 0000000000000000000000000000000000000000..c523de489b509dd00510ba534875bceb7f34876f --- /dev/null +++ b/models/finetuned/freesolv/finetuning_optimized_config.json @@ -0,0 +1,24 @@ +{ + "dataset_meta_csv": "data/finetuning_datasets/regression/freesolv/freesolv.csv", + "dataset_embs_npz": "data/finetuning_datasets/regression/freesolv/freesolv_embs.npz", + "use_scaffold": 0, + "seed": 42, + "train_frac": 0.8, + "val_frac": 0.1, + "test_frac": 0.1, + "model_path": "HUBioDataLab/SELFormer", + "tokenizer_path": "HUBioDataLab/SELFormer", + "pretrained_multimodal_dir": "data/models/SELFormerMM", + "task_type": "regression", + "label_column": "freesolv", + "num_labels": 1, + "batch_size": 8, + "max_len": 128, + "epochs": 50, + "backbone_lr": 5e-05, + "head_lr": 0.0005, + "weight_decay": 0.01, + "checkpoint_every": 25, + "test_eval_every": 0, + "save_dir": "data/models/finetuned/freesolv" +} diff --git a/models/finetuned/freesolv/merges.txt b/models/finetuned/freesolv/merges.txt new file mode 100644 index 0000000000000000000000000000000000000000..7cd5ec62809503c23f18c80afc0ba3bdf9d253d0 --- /dev/null +++ b/models/finetuned/freesolv/merges.txt @@ -0,0 +1,378 @@ +#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 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+} diff --git a/models/finetuned/hiv/finetuning_optimized_config.json b/models/finetuned/hiv/finetuning_optimized_config.json new file mode 100644 index 0000000000000000000000000000000000000000..c83842257d4c1e98018376ba0924df5ca5daa6d8 --- /dev/null +++ b/models/finetuned/hiv/finetuning_optimized_config.json @@ -0,0 +1,24 @@ +{ + "dataset_meta_csv": "data/finetuning_datasets/classification/hiv/hiv.csv", + "dataset_embs_npz": "data/finetuning_datasets/classification/hiv/hiv_embs.npz", + "use_scaffold": 1, + "seed": 42, + "train_frac": 0.8, + "val_frac": 0.1, + "test_frac": 0.1, + "model_path": "HUBioDataLab/SELFormer", + "tokenizer_path": "HUBioDataLab/SELFormer", + "pretrained_multimodal_dir": "data/models/SELFormerMM", + "task_type": "binary", + "label_column": "HIV_active", + "num_labels": 2, + "batch_size": 16, + "max_len": 128, + "epochs": 50, + "backbone_lr": 5e-5, + "head_lr": 5e-5, + "weight_decay": 0.0, + "checkpoint_every": 25, + "test_eval_every": 0, + "save_dir": "data/models/finetuned/hiv" +} diff --git a/models/finetuned/hiv/merges.txt b/models/finetuned/hiv/merges.txt new file mode 100644 index 0000000000000000000000000000000000000000..7cd5ec62809503c23f18c80afc0ba3bdf9d253d0 --- /dev/null +++ b/models/finetuned/hiv/merges.txt @@ -0,0 +1,378 @@ +#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 new file mode 100644 index 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800 +} diff --git a/models/finetuned/lipo/finetuning_optimized_config.json b/models/finetuned/lipo/finetuning_optimized_config.json new file mode 100644 index 0000000000000000000000000000000000000000..464c6ce1d655c82c8acb741623fe23dfb8003310 --- /dev/null +++ b/models/finetuned/lipo/finetuning_optimized_config.json @@ -0,0 +1,24 @@ +{ + "dataset_meta_csv": "data/finetuning_datasets/regression/lipo/lipo.csv", + "dataset_embs_npz": "data/finetuning_datasets/regression/lipo/lipo_embs.npz", + "use_scaffold": 0, + "seed": 42, + "train_frac": 0.8, + "val_frac": 0.1, + "test_frac": 0.1, + "model_path": "HUBioDataLab/SELFormer", + "tokenizer_path": "HUBioDataLab/SELFormer", + "pretrained_multimodal_dir": "data/models/SELFormerMM", + "task_type": "regression", + "label_column": "lipo", + "num_labels": 1, + "batch_size": 32, + "max_len": 128, + "epochs": 50, + "backbone_lr": 5e-05, + "head_lr": 0.0005, + "weight_decay": 0.1, + "checkpoint_every": 25, + "test_eval_every": 0, + "save_dir": "data/models/finetuned/lipo" +} diff --git a/models/finetuned/lipo/merges.txt b/models/finetuned/lipo/merges.txt new file mode 100644 index 0000000000000000000000000000000000000000..7cd5ec62809503c23f18c80afc0ba3bdf9d253d0 --- /dev/null +++ b/models/finetuned/lipo/merges.txt @@ -0,0 +1,378 @@ +#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 new file mode 100644 index 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"use_cache": true, + "vocab_size": 800 +} diff --git a/models/finetuned/pdbbind_full/finetuning_optimized_config.json b/models/finetuned/pdbbind_full/finetuning_optimized_config.json new file mode 100644 index 0000000000000000000000000000000000000000..aec6ca9ccd27a9ccb955c071d7b46b49bf91973c --- /dev/null +++ b/models/finetuned/pdbbind_full/finetuning_optimized_config.json @@ -0,0 +1,24 @@ +{ + "dataset_meta_csv": "data/finetuning_datasets/regression/pdbbind_full/pdbbind_full.csv", + "dataset_embs_npz": "data/finetuning_datasets/regression/pdbbind_full/pdbbind_full_embs.npz", + "use_scaffold": 0, + "seed": 42, + "train_frac": 0.8, + "val_frac": 0.1, + "test_frac": 0.1, + "model_path": "HUBioDataLab/SELFormer", + "tokenizer_path": "HUBioDataLab/SELFormer", + "pretrained_multimodal_dir": "data/models/SELFormerMM", + "task_type": "regression", + "label_column": "-logKd/Ki", + "num_labels": 1, + "batch_size": 32, + "max_len": 128, + "epochs": 50, + "backbone_lr": 1e-05, + "head_lr": 1e-06, + "weight_decay": 0.001, + "checkpoint_every": 25, + "test_eval_every": 0, + "save_dir": "data/models/finetuned/pdbbind_full" +} diff --git a/models/finetuned/pdbbind_full/merges.txt b/models/finetuned/pdbbind_full/merges.txt new file mode 100644 index 0000000000000000000000000000000000000000..7cd5ec62809503c23f18c80afc0ba3bdf9d253d0 --- /dev/null +++ b/models/finetuned/pdbbind_full/merges.txt @@ -0,0 +1,378 @@ +#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 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"vocab_size": 800 +} diff --git a/models/finetuned/sider/finetuning_optimized_config.json b/models/finetuned/sider/finetuning_optimized_config.json new file mode 100644 index 0000000000000000000000000000000000000000..5527ad4b1966158d9ab685f3a51874d655d2222f --- /dev/null +++ b/models/finetuned/sider/finetuning_optimized_config.json @@ -0,0 +1,23 @@ +{ + "dataset_meta_csv": "data/finetuning_datasets/classification/sider/sider.csv", + "dataset_embs_npz": "data/finetuning_datasets/classification/sider/sider_embs.npz", + "use_scaffold": 0, + "seed": 42, + "train_frac": 0.8, + "val_frac": 0.1, + "test_frac": 0.1, + "model_path": "HUBioDataLab/SELFormer", + "tokenizer_path": "HUBioDataLab/SELFormer", + "pretrained_multimodal_dir": "data/models/SELFormerMM", + "task_type": "multilabel", + "num_labels": 0, + "batch_size": 16, + "max_len": 128, + "epochs": 50, + "backbone_lr": 1e-05, + "head_lr": 0.0005, + "weight_decay": 0.001, + "checkpoint_every": 25, + "test_eval_every": 0, + "save_dir": "data/models/finetuned/sider" +} diff --git a/models/finetuned/sider/merges.txt b/models/finetuned/sider/merges.txt new file mode 100644 index 0000000000000000000000000000000000000000..7cd5ec62809503c23f18c80afc0ba3bdf9d253d0 --- /dev/null +++ b/models/finetuned/sider/merges.txt @@ -0,0 +1,378 @@ +#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 new file mode 100644 index 0000000000000000000000000000000000000000..d5262ada0a1773d2f5142c00c258de47e32fbb41 --- /dev/null +++ b/models/finetuned/sider/model.pt @@ -0,0 +1,3 @@ +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 new file mode 100644 index 0000000000000000000000000000000000000000..06a55849fa69a91e7179d909e373179ff7467d8c --- /dev/null +++ b/models/finetuned/sider/special_tokens_map.json @@ -0,0 +1,51 @@ +{ + "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": 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"vocab_size": 800 +} diff --git a/models/finetuned/tox21/finetuning_optimized_config.json b/models/finetuned/tox21/finetuning_optimized_config.json new file mode 100644 index 0000000000000000000000000000000000000000..94148e5b692c7112f9e9af56617717810eb0cafb --- /dev/null +++ b/models/finetuned/tox21/finetuning_optimized_config.json @@ -0,0 +1,23 @@ +{ + "dataset_meta_csv": "data/finetuning_datasets/classification/tox21/tox21.csv", + "dataset_embs_npz": "data/finetuning_datasets/classification/tox21/tox21_embs.npz", + "use_scaffold": 0, + "seed": 42, + "train_frac": 0.8, + "val_frac": 0.1, + "test_frac": 0.1, + "model_path": "HUBioDataLab/SELFormer", + "tokenizer_path": "HUBioDataLab/SELFormer", + "pretrained_multimodal_dir": "data/models/SELFormerMM", + "task_type": "multilabel", + "num_labels": 0, + "batch_size": 8, + "max_len": 128, + "epochs": 25, + "backbone_lr": 1e-05, + "head_lr": 0.0005, + "weight_decay": 0.001, + "checkpoint_every": 25, + "test_eval_every": 0, + "save_dir": "data/models/finetuned/tox21" +} diff --git a/models/finetuned/tox21/merges.txt b/models/finetuned/tox21/merges.txt new file mode 100644 index 0000000000000000000000000000000000000000..7cd5ec62809503c23f18c80afc0ba3bdf9d253d0 --- /dev/null +++ b/models/finetuned/tox21/merges.txt @@ -0,0 +1,378 @@ +#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 new file mode 100644 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