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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
+}

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

models/finetuned/bace/checkpoint_epoch_025/model.pt

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:155ae50273d6ae3fb3badd7bd9021a5737165434ae9487d89face60faccb20f6
+size 1022855293

models/finetuned/bace/checkpoint_epoch_025/special_tokens_map.json

@@ -0,0 +1,51 @@
+{
+  "bos_token": {
+    "content": "<s>",
+    "lstrip": false,
+    "normalized": true,
+    "rstrip": false,
+    "single_word": false
+  },
+  "cls_token": {
+    "content": "<s>",
+    "lstrip": false,
+    "normalized": true,
+    "rstrip": false,
+    "single_word": false
+  },
+  "eos_token": {
+    "content": "</s>",
+    "lstrip": false,
+    "normalized": true,
+    "rstrip": false,
+    "single_word": false
+  },
+  "mask_token": {
+    "content": "<mask>",
+    "lstrip": true,
+    "normalized": true,
+    "rstrip": false,
+    "single_word": false
+  },
+  "pad_token": {
+    "content": "<pad>",
+    "lstrip": false,
+    "normalized": true,
+    "rstrip": false,
+    "single_word": false
+  },
+  "sep_token": {
+    "content": "</s>",
+    "lstrip": false,
+    "normalized": true,
+    "rstrip": false,
+    "single_word": false
+  },
+  "unk_token": {
+    "content": "<unk>",
+    "lstrip": false,
+    "normalized": true,
+    "rstrip": false,
+    "single_word": false
+  }
+}

models/finetuned/bace/checkpoint_epoch_025/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": "<pad>"
+  },
+  "added_tokens": [
+    {
+      "id": 0,
+      "content": "<unk>",
+      "single_word": false,
+      "lstrip": false,
+      "rstrip": false,
+      "normalized": true,
+      "special": true
+    },
+    {
+      "id": 1,
+      "content": "<s>",
+      "single_word": false,
+      "lstrip": false,
+      "rstrip": false,
+      "normalized": true,
+      "special": true
+    },
+    {
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+      "content": "</s>",
+      "single_word": false,
+      "lstrip": false,
+      "rstrip": false,
+      "normalized": true,
+      "special": true
+    },
+    {
+      "id": 3,
+      "content": "<pad>",
+      "single_word": false,
+      "lstrip": false,
+      "rstrip": false,
+      "normalized": true,
+      "special": true
+    },
+    {
+      "id": 4,
+      "content": "<mask>",
+      "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": [
+      "</s>",
+      2
+    ],
+    "cls": [
+      "<s>",
+      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": {
+      "<unk>": 0,
+      "<s>": 1,
+      "</s>": 2,
+      "<pad>": 3,
+      "<mask>": 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,
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+      "=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,
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+      "Se-2": 400,
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+      "As-1": 407,
+      "14C@@": 408,
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+      "135I": 414,
+      "131I-1": 415,
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+      "223Ra+2": 421,
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+      "45Ca+2": 423,
+      "47Ca+2": 424,
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+      "=32PH1": 426,
+      "NH4+1": 427
+    },
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+      "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",
+      "@ @",
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+      "# N+1",
+      "B -1",
+      "+ 3",
+      "Cl +3",
+      "\\ NH1",
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+      "18 F",
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+      "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"
+    ]
+  }
+}

models/finetuned/bace/checkpoint_epoch_025/tokenizer_config.json

@@ -0,0 +1,65 @@
+{
+  "add_prefix_space": false,
+  "bos_token": {
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+    "content": "<s>",
+    "lstrip": false,
+    "normalized": true,
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+    "lstrip": false,
+    "normalized": true,
+    "rstrip": false,
+    "single_word": false
+  },
+  "eos_token": {
+    "__type": "AddedToken",
+    "content": "</s>",
+    "lstrip": false,
+    "normalized": true,
+    "rstrip": false,
+    "single_word": false
+  },
+  "errors": "replace",
+  "mask_token": {
+    "__type": "AddedToken",
+    "content": "<mask>",
+    "lstrip": true,
+    "normalized": true,
+    "rstrip": false,
+    "single_word": false
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+  "model_max_length": 1000000000000000019884624838656,
+  "name_or_path": "/home/erva/SELFormerMM/data/pretrained_multimodal_chembl36",
+  "pad_token": {
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+    "content": "<pad>",
+    "lstrip": false,
+    "normalized": true,
+    "rstrip": false,
+    "single_word": false
+  },
+  "sep_token": {
+    "__type": "AddedToken",
+    "content": "</s>",
+    "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": "<unk>",
+    "lstrip": false,
+    "normalized": true,
+    "rstrip": false,
+    "single_word": false
+  }
+}

models/finetuned/bace/checkpoint_epoch_025/vocab.json

@@ -0,0 +1 @@
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models/finetuned/bace/config.json

@@ -0,0 +1,27 @@
+{
+  "_name_or_path": "/home/erva/SELFormerMM/data/pretrained_multimodal_chembl36",
+  "architectures": [
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+  "bos_token_id": 0,
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+  "eos_token_id": 2,
+  "hidden_act": "gelu",
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+  "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
+}

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
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+=S i
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+/ 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 @
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+/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

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models/finetuned/bace/special_tokens_map.json

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models/finetuned/bace/tokenizer.json

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+      "\\123I": 342,
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+      "- /",
+      "\\ 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"
+    ]
+  }
+}

models/finetuned/bace/tokenizer_config.json

@@ -0,0 +1,65 @@
+{
+  "add_prefix_space": false,
+  "bos_token": {
+    "__type": "AddedToken",
+    "content": "<s>",
+    "lstrip": false,
+    "normalized": true,
+    "rstrip": false,
+    "single_word": false
+  },
+  "cls_token": {
+    "__type": "AddedToken",
+    "content": "<s>",
+    "lstrip": false,
+    "normalized": true,
+    "rstrip": false,
+    "single_word": false
+  },
+  "eos_token": {
+    "__type": "AddedToken",
+    "content": "</s>",
+    "lstrip": false,
+    "normalized": true,
+    "rstrip": false,
+    "single_word": false
+  },
+  "errors": "replace",
+  "mask_token": {
+    "__type": "AddedToken",
+    "content": "<mask>",
+    "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": "<pad>",
+    "lstrip": false,
+    "normalized": true,
+    "rstrip": false,
+    "single_word": false
+  },
+  "sep_token": {
+    "__type": "AddedToken",
+    "content": "</s>",
+    "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": "<unk>",
+    "lstrip": false,
+    "normalized": true,
+    "rstrip": false,
+    "single_word": false
+  }
+}

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 [00:00<?, ?it/s]
+ 21%|██▏       | 325/1513 [00:00<00:00, 3239.43it/s]
+ 43%|████▎     | 649/1513 [00:00<00:00, 3235.14it/s]
+ 66%|██████▋   | 1006/1513 [00:00<00:00, 3386.92it/s]
+ 90%|█████████ | 1362/1513 [00:00<00:00, 3454.73it/s]
+100%|██████████| 1513/1513 [00:00<00:00, 3457.01it/s]
+[finetune] split sizes: train=1,210 val=151 test=152
+[finetune] train modality_non_empty: graph=1,210/1,210 text=87/1,210 kg=172/1,210
+[finetune] val   modality_non_empty: graph=151/151 text=2/151 kg=8/151
+[finetune] test  modality_non_empty: graph=152/152 text=23/152 kg=18/152
+[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=76 val_steps=10 test_steps=10
+[finetune] initialized head: in_dim=3072 out=2
+[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=0.6443 val_loss=0.5344 time=20.3s tod=02:28
+[finetune] epoch 2/50: train_loss=0.5351 val_loss=0.4565 time=20.1s tod=02:29
+[finetune] epoch 3/50: train_loss=0.4530 val_loss=0.4736 time=20.2s tod=02:29
+[finetune] epoch 4/50: train_loss=0.4232 val_loss=0.3851 time=20.0s tod=02:29
+[finetune] epoch 5/50: train_loss=0.3725 val_loss=0.5440 time=20.1s tod=02:30
+[finetune] epoch 6/50: train_loss=0.3314 val_loss=0.4757 time=20.1s tod=02:30
+[finetune] epoch 7/50: train_loss=0.3265 val_loss=0.6589 time=20.1s tod=02:30
+[finetune] epoch 8/50: train_loss=0.3003 val_loss=0.4855 time=20.1s tod=02:31
+[finetune] epoch 9/50: train_loss=0.2645 val_loss=0.4110 time=20.0s tod=02:31
+[finetune] epoch 10/50: train_loss=0.2473 val_loss=0.5245 time=20.0s tod=02:31
+[finetune] epoch 11/50: train_loss=0.2134 val_loss=0.4764 time=20.1s tod=02:32
+[finetune] epoch 12/50: train_loss=0.1911 val_loss=0.5448 time=20.1s tod=02:32
+[finetune] epoch 13/50: train_loss=0.1706 val_loss=0.6041 time=20.2s tod=02:32
+[finetune] epoch 14/50: train_loss=0.1543 val_loss=0.6573 time=20.3s tod=02:33
+[finetune] epoch 15/50: train_loss=0.1514 val_loss=0.7120 time=20.2s tod=02:33
+[finetune] epoch 16/50: train_loss=0.1367 val_loss=0.5487 time=20.0s tod=02:33
+[finetune] epoch 17/50: train_loss=0.1170 val_loss=0.6278 time=20.1s tod=02:34
+[finetune] epoch 18/50: train_loss=0.1168 val_loss=0.5940 time=20.0s tod=02:34
+[finetune] epoch 19/50: train_loss=0.0957 val_loss=0.6297 time=20.2s tod=02:34
+[finetune] epoch 20/50: train_loss=0.0911 val_loss=0.7283 time=19.0s tod=02:35
+[finetune] epoch 21/50: train_loss=0.0738 val_loss=0.6790 time=20.2s tod=02:35
+[finetune] epoch 22/50: train_loss=0.0631 val_loss=0.6892 time=20.1s tod=02:35
+[finetune] epoch 23/50: train_loss=0.0577 val_loss=0.7209 time=20.1s tod=02:36
+[finetune] epoch 24/50: train_loss=0.0533 val_loss=0.8518 time=17.3s tod=02:36
+[finetune] epoch 25/50: train_loss=0.0614 val_loss=0.9262 time=13.7s tod=02:36
+[finetune] test_metrics: epoch=25 loss=1.3773 accuracy=0.7961 precision=0.7568 recall=0.8116 f1=0.7832 roc-auc=0.7974 prc-auc=0.8269
+[finetune] saved checkpoint (best roc-auc=0.7974): /media/ubuntu/8TB/erva/selformer-mm/output/new_finetune_sweeps/bace/e0tdguei/checkpoint_epoch_025
+[finetune] epoch 26/50: train_loss=0.0411 val_loss=0.7979 time=15.5s tod=02:37
+[finetune] epoch 27/50: train_loss=0.0465 val_loss=0.8770 time=20.1s tod=02:37
+[finetune] epoch 28/50: train_loss=0.0277 val_loss=0.9220 time=20.1s tod=02:37
+[finetune] epoch 29/50: train_loss=0.0290 val_loss=0.8844 time=20.1s tod=02:38
+[finetune] epoch 30/50: train_loss=0.0214 val_loss=0.9923 time=20.0s tod=02:38
+[finetune] epoch 31/50: train_loss=0.0187 val_loss=0.8791 time=20.2s tod=02:38
+[finetune] epoch 32/50: train_loss=0.0210 val_loss=0.9760 time=20.1s tod=02:39
+[finetune] epoch 33/50: train_loss=0.0211 val_loss=0.9671 time=20.0s tod=02:39
+[finetune] epoch 34/50: train_loss=0.0161 val_loss=1.0266 time=20.1s tod=02:39
+[finetune] epoch 35/50: train_loss=0.0154 val_loss=1.0887 time=20.1s tod=02:40
+[finetune] epoch 36/50: train_loss=0.0117 val_loss=1.0074 time=20.1s tod=02:40
+[finetune] epoch 37/50: train_loss=0.0072 val_loss=0.9916 time=20.1s tod=02:40
+[finetune] epoch 38/50: train_loss=0.0092 val_loss=1.0393 time=20.2s tod=02:41
+[finetune] epoch 39/50: train_loss=0.0090 val_loss=1.1473 time=20.2s tod=02:41
+[finetune] epoch 40/50: train_loss=0.0055 val_loss=1.1209 time=20.0s tod=02:41
+[finetune] epoch 41/50: train_loss=0.0060 val_loss=1.1437 time=20.2s tod=02:42
+[finetune] epoch 42/50: train_loss=0.0039 val_loss=1.2147 time=20.1s tod=02:42
+[finetune] epoch 43/50: train_loss=0.0033 val_loss=1.2128 time=20.1s tod=02:42
+[finetune] epoch 44/50: train_loss=0.0027 val_loss=1.2480 time=20.1s tod=02:43
+[finetune] epoch 45/50: train_loss=0.0019 val_loss=1.2552 time=20.1s tod=02:43
+[finetune] epoch 46/50: train_loss=0.0017 val_loss=1.2641 time=20.1s tod=02:43
+[finetune] epoch 47/50: train_loss=0.0008 val_loss=1.2660 time=20.1s tod=02:44
+[finetune] epoch 48/50: train_loss=0.0008 val_loss=1.2750 time=20.0s tod=02:44
+[finetune] epoch 49/50: train_loss=0.0005 val_loss=1.2843 time=20.1s tod=02:44
+[finetune] epoch 50/50: train_loss=0.0004 val_loss=1.2864 time=20.2s tod=02:45
+[finetune] test_metrics: epoch=50 loss=2.1284 accuracy=0.7697 precision=0.7429 recall=0.7536 f1=0.7482 roc-auc=0.7684 prc-auc=0.8042
+[finetune] checkpoint skipped (current roc-auc=0.7684 vs best=0.7974 at epoch 25)
+[finetune] final evaluation on test split...
+[finetune] test_metrics: loss=2.1284 accuracy=0.7697 precision=0.7429 recall=0.7536 f1=0.7482 roc-auc=0.7684 prc-auc=0.8042
+[finetune] saving model...
+[finetune] saved finetuned model to: /media/ubuntu/8TB/erva/selformer-mm/output/new_finetune_sweeps/bace/e0tdguei
+[finetune] done in 1002.9s

models/finetuned/bace/vocab.json

@@ -0,0 +1 @@
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models/finetuned/bbbp/checkpoint_epoch_025/config.json

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+{
+  "_name_or_path": "/home/erva/SELFormerMM/data/pretrained_multimodal_chembl36",
+  "architectures": [
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+  ],
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+  "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
+}

models/finetuned/bbbp/checkpoint_epoch_025/merges.txt

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+#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
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+\ S
+S +1
+Cl -1
+I -1
+/ C@@H1
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+/ C@H1
+/ S
+=N -1
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+= P
+N -1
+Ring 3
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+K +1
+\ C@@H1
+\ C@H1
+/ N+1
+@ @
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++ 3
+Cl +3
+\ NH1
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+@ +1
+3 H
+P @@
+H 0
+O H0
+1 2
+P @
++ 2
+@@ +1
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+/ 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@
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+H 2
+H1 -1
+=O +1
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+=S +1
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+/ P
+a +2
+/ I
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+C a+2
+\ Br
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+/ F
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+1 3
+I +1
+/ O-1
+-\ Ring1
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+/ NH1
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+= 14C
+/ S+1
+= Ring3
+\ C@@
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+\ C@
+A g
+= As
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+N H2+1
+Se H1
+-/ Ring1
+= Te
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+Na H1
+=Te +1
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+H1 +1
+NH1 -1
+\ P
+14C H2
+13 C
+14C H1
+= 11C
+S @@
+=P @@
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+14C H3
+B H3-1
+S @
+=14C H1
+=P H1
+=P @
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+/ 125I
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+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

models/finetuned/bbbp/checkpoint_epoch_025/model.pt

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models/finetuned/bbbp/checkpoint_epoch_025/special_tokens_map.json

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models/finetuned/bbbp/checkpoint_epoch_025/tokenizer.json

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+    },
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+      "c h",
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+      "Bran ch",
+      "Branch 1",
+      "= C",
+      "R i",
+      "n g",
+      "Ri ng",
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+      "= Branch1",
+      "Branch 2",
+      "= O",
+      "Ring 2",
+      "H 1",
+      "C @",
+      "= N",
+      "# Branch1",
+      "C@ @",
+      "= Branch2",
+      "C@ H1",
+      "C@@ H1",
+      "# Branch2",
+      "# C",
+      "C l",
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+      "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"
+    ]
+  }
+}

models/finetuned/bbbp/checkpoint_epoch_025/tokenizer_config.json

@@ -0,0 +1,65 @@
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+  "name_or_path": "/home/erva/SELFormerMM/data/pretrained_multimodal_chembl36",
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+}

models/finetuned/bbbp/checkpoint_epoch_025/vocab.json

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models/finetuned/bbbp/checkpoint_epoch_050/config.json

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+{
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+  "intermediate_size": 3072,
+  "layer_norm_eps": 1e-12,
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+  "model_type": "roberta",
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+  "num_hidden_layers": 12,
+  "pad_token_id": 1,
+  "position_embedding_type": "absolute",
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models/finetuned/bbbp/checkpoint_epoch_050/merges.txt

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+#version: 0.2 - Trained by `huggingface/tokenizers`
+B r
+a n
+c h
+Br an
+Bran ch
+Branch 1
+= C
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+n g
+Ri ng
+Ring 1
+= Branch1
+Branch 2
+= O
+Ring 2
+H 1
+C @
+= N
+# Branch1
+C@ @
+= Branch2
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+C@@ H1
+# Branch2
+# C
+C l
+/ C
+N H1
+= Ring1
++ 1
+- 1
+O -1
+N +1
+\ C
+# N
+/ N
+= Ring2
+= S
+=N +1
+\ N
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+\ O
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+/ C@@H1
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+/ S
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+= P
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+/ N+1
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++ 2
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+/ Cl
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+=S e
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+1 4
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+=O +1
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+/ S+1
+= Ring3
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+-/ Ring1
+= Te
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+\ P
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+= 11C
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+= Branch3
+N @@
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+/ Si
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+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

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models/finetuned/bbbp/checkpoint_epoch_050/tokenizer.json

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+    },
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+      "c h",
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+      "Bran ch",
+      "Branch 1",
+      "= C",
+      "R i",
+      "n g",
+      "Ri ng",
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+      "= Branch1",
+      "Branch 2",
+      "= O",
+      "Ring 2",
+      "H 1",
+      "C @",
+      "= N",
+      "# Branch1",
+      "C@ @",
+      "= Branch2",
+      "C@ H1",
+      "C@@ H1",
+      "# Branch2",
+      "# C",
+      "C l",
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+      "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"
+    ]
+  }
+}

models/finetuned/bbbp/checkpoint_epoch_050/tokenizer_config.json

@@ -0,0 +1,65 @@
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+}

models/finetuned/bbbp/checkpoint_epoch_050/vocab.json

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models/finetuned/bbbp/config.json

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+{
+  "_name_or_path": "/home/erva/SELFormerMM/data/pretrained_multimodal_chembl36",
+  "architectures": [
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+  ],
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+  "classifier_dropout": null,
+  "eos_token_id": 2,
+  "hidden_act": "gelu",
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+  "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
+}

models/finetuned/bbbp/merges.txt

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+#version: 0.2 - Trained by `huggingface/tokenizers`
+B r
+a n
+c h
+Br an
+Bran ch
+Branch 1
+= C
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+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
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+/ O
+\ O
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+/ C@@H1
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+/ S
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+= P
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+@ +1
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+H 0
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++ 2
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+=S e
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+1 4
+-\ Ring2
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+\ F
+/ C@
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+=O +1
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+/ O-1
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+/ NH1
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+= 14C
+/ S+1
+= Ring3
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+= As
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+-/ Ring1
+= Te
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+=Te +1
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+\ P
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+= 11C
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+Rb +1
+= Branch3
+N @@
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+/ Si
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+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

models/finetuned/bbbp/model.pt

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models/finetuned/bbbp/special_tokens_map.json

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models/finetuned/bbbp/tokenizer.json

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+      "BH2": 188,
+      "BH2-1": 189,
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+      "/NH1": 191,
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+      "BH1-1": 260,
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+      "Bi": 284,
+      "\\125I": 285,
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+      "6Br": 288,
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+      "14C@@H1": 297,
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+      "/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,
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+      "-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,
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+      "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,
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+      "-4": 363,
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+      "/P@@": 365,
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+      "3Se": 371,
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+      "82Rb+1": 379,
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+      "CH2": 383,
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+      "NH0": 385,
+      "NH4": 386,
+      "OH1": 387,
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+      "\\11CH3": 392,
+      "\\C-1": 393,
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+      "Si@": 395,
+      "Si-1": 396,
+      "SiH1-1": 397,
+      "SiH3-1": 398,
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+      "Se-2": 400,
+      "\\NH1-1": 401,
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+      "11C-1": 405,
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+      "As-1": 407,
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+      "Te-1": 409,
+      "Mg+1": 410,
+      "123I-1": 411,
+      "123Te": 412,
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+      "135I": 414,
+      "131I-1": 415,
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+      "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"
+    ]
+  }
+}

models/finetuned/bbbp/tokenizer_config.json

@@ -0,0 +1,65 @@
+{
+  "add_prefix_space": false,
+  "bos_token": {
+    "__type": "AddedToken",
+    "content": "<s>",
+    "lstrip": false,
+    "normalized": true,
+    "rstrip": false,
+    "single_word": false
+  },
+  "cls_token": {
+    "__type": "AddedToken",
+    "content": "<s>",
+    "lstrip": false,
+    "normalized": true,
+    "rstrip": false,
+    "single_word": false
+  },
+  "eos_token": {
+    "__type": "AddedToken",
+    "content": "</s>",
+    "lstrip": false,
+    "normalized": true,
+    "rstrip": false,
+    "single_word": false
+  },
+  "errors": "replace",
+  "mask_token": {
+    "__type": "AddedToken",
+    "content": "<mask>",
+    "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": "<pad>",
+    "lstrip": false,
+    "normalized": true,
+    "rstrip": false,
+    "single_word": false
+  },
+  "sep_token": {
+    "__type": "AddedToken",
+    "content": "</s>",
+    "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": "<unk>",
+    "lstrip": false,
+    "normalized": true,
+    "rstrip": false,
+    "single_word": false
+  }
+}

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 [00:00<?, ?it/s]
+ 21%|██        | 425/2039 [00:00<00:00, 4245.72it/s]
+ 43%|████▎     | 885/2039 [00:00<00:00, 4448.82it/s]
+ 67%|██████▋   | 1358/2039 [00:00<00:00, 4573.64it/s]
+ 94%|█████████▍| 1923/2039 [00:00<00:00, 4995.19it/s]
+100%|██████████| 2039/2039 [00:00<00:00, 4863.36it/s]
+[finetune] split sizes: train=1,631 val=203 test=205
+[finetune] train modality_non_empty: graph=1,631/1,631 text=1,089/1,631 kg=48/1,631
+[finetune] val   modality_non_empty: graph=203/203 text=151/203 kg=3/203
+[finetune] test  modality_non_empty: graph=205/205 text=136/205 kg=4/205
+[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=51 val_steps=7 test_steps=7
+[finetune] initialized head: in_dim=3072 out=2
+[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=0.4502 val_loss=0.3330 time=19.7s tod=11:10
+[finetune] epoch 2/50: train_loss=0.2497 val_loss=0.2723 time=19.6s tod=11:11
+[finetune] epoch 3/50: train_loss=0.1748 val_loss=0.3403 time=19.2s tod=11:11
+[finetune] epoch 4/50: train_loss=0.1205 val_loss=0.3844 time=19.3s tod=11:11
+[finetune] epoch 5/50: train_loss=0.0923 val_loss=0.4908 time=19.4s tod=11:12
+[finetune] epoch 6/50: train_loss=0.0617 val_loss=0.6117 time=19.3s tod=11:12
+[finetune] epoch 7/50: train_loss=0.0374 val_loss=0.5942 time=19.3s tod=11:12
+[finetune] epoch 8/50: train_loss=0.0312 val_loss=0.6833 time=19.4s tod=11:13
+[finetune] epoch 9/50: train_loss=0.0195 val_loss=0.7027 time=19.3s tod=11:13
+[finetune] epoch 10/50: train_loss=0.0168 val_loss=0.9035 time=19.5s tod=11:13
+[finetune] epoch 11/50: train_loss=0.0116 val_loss=0.6633 time=18.6s tod=11:14
+[finetune] epoch 12/50: train_loss=0.0120 val_loss=0.7813 time=19.4s tod=11:14
+[finetune] epoch 13/50: train_loss=0.0076 val_loss=0.7791 time=19.5s tod=11:14
+[finetune] epoch 14/50: train_loss=0.0072 val_loss=0.8010 time=19.4s tod=11:14
+[finetune] epoch 15/50: train_loss=0.0077 val_loss=0.9591 time=19.5s tod=11:15
+[finetune] epoch 16/50: train_loss=0.0062 val_loss=0.9107 time=19.4s tod=11:15
+[finetune] epoch 17/50: train_loss=0.0027 val_loss=0.9619 time=19.3s tod=11:15
+[finetune] epoch 18/50: train_loss=0.0032 val_loss=0.9483 time=19.7s tod=11:16
+[finetune] epoch 19/50: train_loss=0.0032 val_loss=0.9611 time=19.4s tod=11:16
+[finetune] epoch 20/50: train_loss=0.0025 val_loss=0.9530 time=19.3s tod=11:16
+[finetune] epoch 21/50: train_loss=0.0035 val_loss=0.9558 time=19.5s tod=11:17
+[finetune] epoch 22/50: train_loss=0.0024 val_loss=0.9389 time=19.4s tod=11:17
+[finetune] epoch 23/50: train_loss=0.0023 val_loss=0.9919 time=19.4s tod=11:17
+[finetune] epoch 24/50: train_loss=0.0021 val_loss=1.0150 time=19.6s tod=11:18
+[finetune] epoch 25/50: train_loss=0.0021 val_loss=1.0188 time=19.3s tod=11:18
+[finetune] test_metrics: epoch=25 loss=0.5357 accuracy=0.9073 precision=0.9595 recall=0.9161 f1=0.9373 roc-auc=0.8981 prc-auc=0.9695
+[finetune] saved checkpoint (best roc-auc=0.8981): /media/ubuntu/8TB/erva/selformer-mm/output/new_finetune_sweeps/bbbp/9qb82eig/checkpoint_epoch_025
+[finetune] epoch 26/50: train_loss=0.0017 val_loss=1.0293 time=19.4s tod=11:18
+[finetune] epoch 27/50: train_loss=0.0013 val_loss=1.0406 time=19.7s tod=11:19
+[finetune] epoch 28/50: train_loss=0.0017 val_loss=1.0474 time=19.3s tod=11:19
+[finetune] epoch 29/50: train_loss=0.0020 val_loss=1.0570 time=19.4s tod=11:19
+[finetune] epoch 30/50: train_loss=0.0015 val_loss=1.0563 time=19.6s tod=11:20
+[finetune] epoch 31/50: train_loss=0.0014 val_loss=1.0590 time=19.4s tod=11:20
+[finetune] epoch 32/50: train_loss=0.0010 val_loss=1.0643 time=19.2s tod=11:20
+[finetune] epoch 33/50: train_loss=0.0014 val_loss=1.0696 time=19.5s tod=11:21
+[finetune] epoch 34/50: train_loss=0.0012 val_loss=1.0717 time=19.4s tod=11:21
+[finetune] epoch 35/50: train_loss=0.0017 val_loss=1.0735 time=19.4s tod=11:21
+[finetune] epoch 36/50: train_loss=0.0013 val_loss=1.0781 time=19.6s tod=11:22
+[finetune] epoch 37/50: train_loss=0.0014 val_loss=1.0798 time=18.6s tod=11:22
+[finetune] epoch 38/50: train_loss=0.0009 val_loss=1.0833 time=19.5s tod=11:22
+[finetune] epoch 39/50: train_loss=0.0016 val_loss=1.0830 time=19.6s tod=11:23
+[finetune] epoch 40/50: train_loss=0.0012 val_loss=1.0843 time=19.3s tod=11:23
+[finetune] epoch 41/50: train_loss=0.0010 val_loss=1.0882 time=19.6s tod=11:23
+[finetune] epoch 42/50: train_loss=0.0011 val_loss=1.0891 time=19.3s tod=11:24
+[finetune] epoch 43/50: train_loss=0.0014 val_loss=1.0889 time=19.4s tod=11:24
+[finetune] epoch 44/50: train_loss=0.0010 val_loss=1.0939 time=19.4s tod=11:24
+[finetune] epoch 45/50: train_loss=0.0012 val_loss=1.0937 time=19.3s tod=11:25
+[finetune] epoch 46/50: train_loss=0.0010 val_loss=1.0971 time=19.5s tod=11:25
+[finetune] epoch 47/50: train_loss=0.0012 val_loss=1.0984 time=19.5s tod=11:25
+[finetune] epoch 48/50: train_loss=0.0012 val_loss=1.0978 time=19.3s tod=11:26
+[finetune] epoch 49/50: train_loss=0.0011 val_loss=1.0980 time=19.1s tod=11:26
+[finetune] epoch 50/50: train_loss=0.0010 val_loss=1.0982 time=13.3s tod=11:26
+[finetune] test_metrics: epoch=50 loss=0.5324 accuracy=0.9171 precision=0.9726 recall=0.9161 f1=0.9435 roc-auc=0.9181 prc-auc=0.9761
+[finetune] saved checkpoint (best roc-auc=0.9181): /media/ubuntu/8TB/erva/selformer-mm/output/new_finetune_sweeps/bbbp/9qb82eig/checkpoint_epoch_050
+[finetune] final evaluation on test split...
+[finetune] test_metrics: loss=0.5324 accuracy=0.9171 precision=0.9726 recall=0.9161 f1=0.9435 roc-auc=0.9181 prc-auc=0.9761
+[finetune] saving model...
+[finetune] saved finetuned model to: /media/ubuntu/8TB/erva/selformer-mm/output/new_finetune_sweeps/bbbp/9qb82eig
+[finetune] done in 976.9s

models/finetuned/bbbp/vocab.json

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models/finetuned/esol/checkpoint_epoch_025/config.json

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+{
+  "_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
+}

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
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+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
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+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
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+Sr +2
+#C -1
+/C -1
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+/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

models/finetuned/esol/checkpoint_epoch_025/model.pt

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+oid sha256:1b864cf061c5ebe3019c8d724e63bbea3553c915546e126cced40c03803cacf6
+size 1022843005

models/finetuned/esol/checkpoint_epoch_025/special_tokens_map.json

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+{
+  "bos_token": {
+    "content": "<s>",
+    "lstrip": false,
+    "normalized": true,
+    "rstrip": false,
+    "single_word": false
+  },
+  "cls_token": {
+    "content": "<s>",
+    "lstrip": false,
+    "normalized": true,
+    "rstrip": false,
+    "single_word": false
+  },
+  "eos_token": {
+    "content": "</s>",
+    "lstrip": false,
+    "normalized": true,
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+    "single_word": false
+  },
+  "mask_token": {
+    "content": "<mask>",
+    "lstrip": true,
+    "normalized": true,
+    "rstrip": false,
+    "single_word": false
+  },
+  "pad_token": {
+    "content": "<pad>",
+    "lstrip": false,
+    "normalized": true,
+    "rstrip": false,
+    "single_word": false
+  },
+  "sep_token": {
+    "content": "</s>",
+    "lstrip": false,
+    "normalized": true,
+    "rstrip": false,
+    "single_word": false
+  },
+  "unk_token": {
+    "content": "<unk>",
+    "lstrip": false,
+    "normalized": true,
+    "rstrip": false,
+    "single_word": false
+  }
+}

models/finetuned/esol/checkpoint_epoch_025/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": "<pad>"
+  },
+  "added_tokens": [
+    {
+      "id": 0,
+      "content": "<unk>",
+      "single_word": false,
+      "lstrip": false,
+      "rstrip": false,
+      "normalized": true,
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+      "special": true
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+      "C@ H1",
+      "C@@ H1",
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+      "Cl -1",
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+      "S i",
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+      "P +1",
+      "K +1",
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+      "\\ C@H1",
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+      "@ @",
+      "C -1",
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+      "1 1",
+      "5 I",
+      "12 5I",
+      "11 C",
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+      "T e",
+      "H 2",
+      "H1 -1",
+      "=O +1",
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+      "1 3",
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+      "B H2",
+      "BH2 -1",
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+      "13 1",
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+      "H1 +1",
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+      "14C H1",
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+      "S @@",
+      "=P @@",
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+      "H3 -1",
+      "14C H3",
+      "B H3-1",
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+      "P @+1",
+      "R b",
+      "Cl +1",
+      "Si H4",
+      "Rb +1",
+      "= Branch3",
+      "N @@",
+      "As +1",
+      "/ Si",
+      "B H1-1",
+      "S H1",
+      "/ 123I",
+      "3 2",
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+      "H +1",
+      "\\ B",
+      "Si H1",
+      "P@@ +1",
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+      "1 5",
+      "1 7",
+      "3 5",
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+      "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",
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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"
+    ]
+  }
+}

models/finetuned/esol/checkpoint_epoch_025/tokenizer_config.json

@@ -0,0 +1,65 @@
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+    "content": "<unk>",
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+    "rstrip": false,
+    "single_word": false
+  }
+}

models/finetuned/esol/checkpoint_epoch_025/vocab.json

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models/finetuned/esol/checkpoint_epoch_050/config.json

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+{
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models/finetuned/esol/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
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+n g
+Ri ng
+Ring 1
+= Branch1
+Branch 2
+= O
+Ring 2
+H 1
+C @
+= N
+# Branch1
+C@ @
+= Branch2
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+C@@ H1
+# Branch2
+# C
+C l
+/ C
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+= Ring1
++ 1
+- 1
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+/ N
+= Ring2
+= S
+=N +1
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++ 2
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+=S e
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+=O +1
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+= 14C
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+= Ring3
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+= As
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+= Te
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+=Te +1
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+= 11C
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+=14C H1
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+= Branch3
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+/ 123I
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+= Mg
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+1 7
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+= 13CH1
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+=N H2+1
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+/ P+1
+/ 13C
+/ 13CH1
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+1 0B
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+= 18O
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+=P H2
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+- 3
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+8 5Sr+2
+= B-1
+= 13C
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+B @@
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+=S @
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+Te H1
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+15 N
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+- 4
+/ PH1
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+2 Rb+1
+3 Se
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+4 5
+4 7
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+8 2Rb+1
+= 32
+= 32P
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+C H2
+I +2
+N H0
+N H4
+O H1
+P H2+1
+S H0
+S H2
+\ 3H
+\ 11CH3
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+Se -2
+\NH1 -1
+18F H1
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+11 C-1
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+Te -1
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+13 5I
+131 I-1
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+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

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+      "= N",
+      "# Branch1",
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+      "= Branch2",
+      "C@ H1",
+      "C@@ H1",
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+      "# N",
+      "/ N",
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+      "Br -1",
+      "Branch 3",
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+      "S +1",
+      "Cl -1",
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+      "/ C@@H1",
+      "S i",
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+      "/ S",
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+      "P +1",
+      "K +1",
+      "\\ C@@H1",
+      "\\ C@H1",
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+      "-/ Ring2",
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+      "1 1",
+      "5 I",
+      "12 5I",
+      "11 C",
+      "H 3",
+      "\\ N+1",
+      "- \\",
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+      "A s",
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+      "=S e",
+      "S @@+1",
+      "N @+1",
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+      "-\\ Ring2",
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+      "\\ F",
+      "/ C@",
+      "T e",
+      "H 2",
+      "H1 -1",
+      "=O +1",
+      "N @@+1",
+      "C +1",
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+      "Z n",
+      "/ P",
+      "a +2",
+      "/ I",
+      "O H1-1",
+      "C a+2",
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+      "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",
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+      "13C H1",
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+      "B a+2",
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+      "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"
+    ]
+  }
+}

models/finetuned/esol/checkpoint_epoch_050/tokenizer_config.json

@@ -0,0 +1,65 @@
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