diff --git a/models/finetuned/bace/checkpoint_epoch_025/config.json b/models/finetuned/bace/checkpoint_epoch_025/config.json new file mode 100644 index 0000000000000000000000000000000000000000..3811e21539577b37e06313eab31ec11e53f0cbbc --- /dev/null +++ b/models/finetuned/bace/checkpoint_epoch_025/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/checkpoint_epoch_025/merges.txt b/models/finetuned/bace/checkpoint_epoch_025/merges.txt new file mode 100644 index 0000000000000000000000000000000000000000..7cd5ec62809503c23f18c80afc0ba3bdf9d253d0 --- /dev/null +++ b/models/finetuned/bace/checkpoint_epoch_025/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 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"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", 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\ No newline at end of file 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/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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"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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+ "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 new file mode 100644 index 0000000000000000000000000000000000000000..03c26b0ae4120b70ae323542a7cffa79f8253ca4 --- /dev/null +++ b/models/finetuned/bace/train_stdout.log @@ -0,0 +1,91 @@ +[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 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+@@ +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 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+@@ +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 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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/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 0000000000000000000000000000000000000000..a27b52e128ed17cabe4cf7875c06eb290f65abe8 --- /dev/null +++ b/models/finetuned/bbbp/model.pt @@ -0,0 +1,3 @@ +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 new file mode 100644 index 0000000000000000000000000000000000000000..06a55849fa69a91e7179d909e373179ff7467d8c --- /dev/null +++ b/models/finetuned/bbbp/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": "", + "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 new file mode 100644 index 0000000000000000000000000000000000000000..3b64b273e6fa9799e2d8375722b9e815de9ebb8f --- /dev/null +++ b/models/finetuned/bbbp/tokenizer.json @@ -0,0 +1,909 @@ +{ + "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", + 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+ "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 new file mode 100644 index 0000000000000000000000000000000000000000..e6f1c4bb9d809523a6881395f093c8192e483169 --- /dev/null +++ b/models/finetuned/bbbp/train_stdout.log @@ -0,0 +1,91 @@ +[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 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\ 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 new file mode 100644 index 0000000000000000000000000000000000000000..3811e21539577b37e06313eab31ec11e53f0cbbc --- /dev/null +++ b/models/finetuned/esol/checkpoint_epoch_025/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/esol/checkpoint_epoch_025/merges.txt b/models/finetuned/esol/checkpoint_epoch_025/merges.txt new file mode 100644 index 0000000000000000000000000000000000000000..7cd5ec62809503c23f18c80afc0ba3bdf9d253d0 --- /dev/null +++ b/models/finetuned/esol/checkpoint_epoch_025/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 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+@@ +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 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800 +} diff --git a/models/finetuned/esol/merges.txt b/models/finetuned/esol/merges.txt new file mode 100644 index 0000000000000000000000000000000000000000..7cd5ec62809503c23f18c80afc0ba3bdf9d253d0 --- /dev/null +++ b/models/finetuned/esol/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/esol/model.pt b/models/finetuned/esol/model.pt new file mode 100644 index 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+ "= 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 new file mode 100644 index 0000000000000000000000000000000000000000..08860954acd34fad07fd77f7635298fa565f3149 --- /dev/null +++ b/models/finetuned/esol/tokenizer_config.json @@ -0,0 +1,65 @@ +{ + "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 new file mode 100644 index 0000000000000000000000000000000000000000..ad7f63f0bfb065ea4587adce57b9b88b02103e03 --- /dev/null +++ b/models/finetuned/esol/train_stdout.log @@ -0,0 +1,84 @@ +[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 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\ 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 new file mode 100644 index 0000000000000000000000000000000000000000..3811e21539577b37e06313eab31ec11e53f0cbbc --- /dev/null +++ b/models/finetuned/freesolv/checkpoint_epoch_025/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/freesolv/checkpoint_epoch_025/merges.txt b/models/finetuned/freesolv/checkpoint_epoch_025/merges.txt new file mode 100644 index 0000000000000000000000000000000000000000..7cd5ec62809503c23f18c80afc0ba3bdf9d253d0 --- /dev/null +++ b/models/finetuned/freesolv/checkpoint_epoch_025/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/checkpoint_epoch_025/model.pt b/models/finetuned/freesolv/checkpoint_epoch_025/model.pt new file mode 100644 index 0000000000000000000000000000000000000000..b4c39ddfaaef7a18c0375b2bd5a792d5f81f38e7 --- /dev/null +++ b/models/finetuned/freesolv/checkpoint_epoch_025/model.pt @@ -0,0 +1,3 @@ +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 new file mode 100644 index 0000000000000000000000000000000000000000..06a55849fa69a91e7179d909e373179ff7467d8c --- /dev/null +++ b/models/finetuned/freesolv/checkpoint_epoch_025/special_tokens_map.json @@ -0,0 +1,51 @@ +{ + "bos_token": { + "content": "", + "lstrip": false, + "normalized": true, + "rstrip": false, + "single_word": 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"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 new file mode 100644 index 0000000000000000000000000000000000000000..7cd5ec62809503c23f18c80afc0ba3bdf9d253d0 --- /dev/null +++ b/models/finetuned/freesolv/checkpoint_epoch_050/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/checkpoint_epoch_050/model.pt b/models/finetuned/freesolv/checkpoint_epoch_050/model.pt new file mode 100644 index 0000000000000000000000000000000000000000..b4db7d8c07d36db777c87860a91fdcbce7b97039 --- /dev/null +++ b/models/finetuned/freesolv/checkpoint_epoch_050/model.pt @@ -0,0 +1,3 @@ +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 new file mode 100644 index 0000000000000000000000000000000000000000..06a55849fa69a91e7179d909e373179ff7467d8c --- /dev/null +++ b/models/finetuned/freesolv/checkpoint_epoch_050/special_tokens_map.json @@ -0,0 +1,51 @@ +{ + "bos_token": { + "content": "", + "lstrip": false, + "normalized": true, + "rstrip": false, + "single_word": 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\ No newline at end of file diff --git a/models/finetuned/freesolv/config.json b/models/finetuned/freesolv/config.json new file mode 100644 index 0000000000000000000000000000000000000000..3811e21539577b37e06313eab31ec11e53f0cbbc --- /dev/null +++ b/models/finetuned/freesolv/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/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 b/models/finetuned/freesolv/model.pt new file mode 100644 index 0000000000000000000000000000000000000000..b4db7d8c07d36db777c87860a91fdcbce7b97039 --- /dev/null +++ b/models/finetuned/freesolv/model.pt @@ -0,0 +1,3 @@ +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 new file mode 100644 index 0000000000000000000000000000000000000000..06a55849fa69a91e7179d909e373179ff7467d8c --- /dev/null +++ b/models/finetuned/freesolv/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": { + 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"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 @@", 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+ "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 new file mode 100644 index 0000000000000000000000000000000000000000..183a4d5663bbb05b5adfeb7778283af490685b3b --- /dev/null +++ b/models/finetuned/freesolv/train_stdout.log @@ -0,0 +1,84 @@ +[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 new file mode 100644 index 0000000000000000000000000000000000000000..f7e4cc22809f4e9035cc450ef189c8a7da8fd03e --- /dev/null +++ b/models/finetuned/freesolv/vocab.json @@ -0,0 +1 @@ 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\ No newline at end of file diff --git a/models/finetuned/hiv/config.json b/models/finetuned/hiv/config.json new file mode 100644 index 0000000000000000000000000000000000000000..3811e21539577b37e06313eab31ec11e53f0cbbc --- /dev/null +++ b/models/finetuned/hiv/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/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 += 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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/lipo/checkpoint_epoch_025/config.json b/models/finetuned/lipo/checkpoint_epoch_025/config.json new file mode 100644 index 0000000000000000000000000000000000000000..3811e21539577b37e06313eab31ec11e53f0cbbc --- /dev/null +++ b/models/finetuned/lipo/checkpoint_epoch_025/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/lipo/checkpoint_epoch_025/merges.txt b/models/finetuned/lipo/checkpoint_epoch_025/merges.txt new file mode 100644 index 0000000000000000000000000000000000000000..7cd5ec62809503c23f18c80afc0ba3bdf9d253d0 --- /dev/null +++ b/models/finetuned/lipo/checkpoint_epoch_025/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 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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, + 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"# 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", + "/ 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\ 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 new file mode 100644 index 0000000000000000000000000000000000000000..3811e21539577b37e06313eab31ec11e53f0cbbc --- /dev/null +++ b/models/finetuned/lipo/checkpoint_epoch_050/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": 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+@@ +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 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+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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+ "= 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 new file mode 100644 index 0000000000000000000000000000000000000000..08860954acd34fad07fd77f7635298fa565f3149 --- /dev/null +++ b/models/finetuned/lipo/tokenizer_config.json @@ -0,0 +1,65 @@ +{ + "add_prefix_space": false, + "bos_token": { + "__type": "AddedToken", + "content": "", + "lstrip": false, + 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+ "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 new file mode 100644 index 0000000000000000000000000000000000000000..acd2e33136a7ff829af04264977e9249e5aaad87 --- /dev/null +++ b/models/finetuned/lipo/train_stdout.log @@ -0,0 +1,84 @@ +[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 new file mode 100644 index 0000000000000000000000000000000000000000..f7e4cc22809f4e9035cc450ef189c8a7da8fd03e --- /dev/null +++ b/models/finetuned/lipo/vocab.json @@ -0,0 +1 @@ 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\ 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 new file mode 100644 index 0000000000000000000000000000000000000000..3811e21539577b37e06313eab31ec11e53f0cbbc --- /dev/null +++ b/models/finetuned/pdbbind_full/checkpoint_epoch_025/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/pdbbind_full/checkpoint_epoch_025/merges.txt b/models/finetuned/pdbbind_full/checkpoint_epoch_025/merges.txt new file mode 100644 index 0000000000000000000000000000000000000000..7cd5ec62809503c23f18c80afc0ba3bdf9d253d0 --- /dev/null +++ b/models/finetuned/pdbbind_full/checkpoint_epoch_025/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/pdbbind_full/checkpoint_epoch_025/model.pt b/models/finetuned/pdbbind_full/checkpoint_epoch_025/model.pt new file mode 100644 index 0000000000000000000000000000000000000000..00970a4febd336802d0db95d26f86cfeb77f132d --- /dev/null +++ b/models/finetuned/pdbbind_full/checkpoint_epoch_025/model.pt @@ -0,0 +1,3 @@ +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 new file mode 100644 index 0000000000000000000000000000000000000000..06a55849fa69a91e7179d909e373179ff7467d8c --- /dev/null +++ b/models/finetuned/pdbbind_full/checkpoint_epoch_025/special_tokens_map.json @@ -0,0 +1,51 @@ +{ + "bos_token": { + "content": "", + "lstrip": false, + "normalized": true, 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"use_cache": true, + "vocab_size": 800 +} 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 +=32 PH1 +NH4 +1 diff --git a/models/finetuned/pdbbind_full/model.pt 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b/models/finetuned/pdbbind_full/tokenizer_config.json @@ -0,0 +1,65 @@ +{ + "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 new file mode 100644 index 0000000000000000000000000000000000000000..311f4ebdcdfc122bcb5a7fd77c685c4193f4a7b6 --- /dev/null +++ b/models/finetuned/pdbbind_full/train_stdout.log @@ -0,0 +1,84 @@ +[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 new file mode 100644 index 0000000000000000000000000000000000000000..f7e4cc22809f4e9035cc450ef189c8a7da8fd03e --- /dev/null +++ b/models/finetuned/pdbbind_full/vocab.json @@ -0,0 +1 @@ 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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 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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 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\ No newline at end of file diff --git a/models/finetuned/sider/config.json b/models/finetuned/sider/config.json new file mode 100644 index 0000000000000000000000000000000000000000..3811e21539577b37e06313eab31ec11e53f0cbbc --- /dev/null +++ b/models/finetuned/sider/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/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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"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 new file mode 100644 index 0000000000000000000000000000000000000000..08860954acd34fad07fd77f7635298fa565f3149 --- /dev/null +++ b/models/finetuned/sider/tokenizer_config.json @@ -0,0 +1,65 @@ +{ + "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 new file mode 100644 index 0000000000000000000000000000000000000000..a523764f132bdef6e1ba601f9f150225da05096f --- /dev/null +++ b/models/finetuned/sider/train_stdout.log @@ -0,0 +1,86 @@ +[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 new file mode 100644 index 0000000000000000000000000000000000000000..f7e4cc22809f4e9035cc450ef189c8a7da8fd03e --- /dev/null +++ b/models/finetuned/sider/vocab.json @@ -0,0 +1 @@ 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\ 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 new file mode 100644 index 0000000000000000000000000000000000000000..3811e21539577b37e06313eab31ec11e53f0cbbc --- /dev/null +++ b/models/finetuned/tox21/checkpoint_epoch_025/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": 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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 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"vocab_size": 800 +} 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 index 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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 new file mode 100644 index 0000000000000000000000000000000000000000..08860954acd34fad07fd77f7635298fa565f3149 --- /dev/null +++ b/models/finetuned/tox21/tokenizer_config.json @@ -0,0 +1,65 @@ +{ + "add_prefix_space": false, + "bos_token": { + "__type": "AddedToken", + "content": "", + "lstrip": 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"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 new file mode 100644 index 0000000000000000000000000000000000000000..3360f20215181e93710f5f5cf87e7964fe267b0f --- /dev/null +++ b/models/finetuned/tox21/train_stdout.log @@ -0,0 +1,92 @@ +[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 new file mode 100644 index 0000000000000000000000000000000000000000..f7e4cc22809f4e9035cc450ef189c8a7da8fd03e --- /dev/null +++ b/models/finetuned/tox21/vocab.json @@ -0,0 +1 @@ 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