ervau commited on
Commit
3768a96
·
verified ·
1 Parent(s): 194d448

Delete models/finetuned

Browse files
This view is limited to 50 files because it contains too many changes.   See raw diff
Files changed (50) hide show
  1. models/finetuned/bace/config.json +0 -28
  2. models/finetuned/bace/finetuning_optimized_config.json +0 -24
  3. models/finetuned/bace/merges.txt +0 -162
  4. models/finetuned/bace/model.pt +0 -3
  5. models/finetuned/bace/special_tokens_map.json +0 -51
  6. models/finetuned/bace/tokenizer.json +0 -473
  7. models/finetuned/bace/tokenizer_config.json +0 -59
  8. models/finetuned/bace/vocab.json +0 -1
  9. models/finetuned/bbbp/config.json +0 -28
  10. models/finetuned/bbbp/finetuning_optimized_config.json +0 -24
  11. models/finetuned/bbbp/merges.txt +0 -162
  12. models/finetuned/bbbp/model.pt +0 -3
  13. models/finetuned/bbbp/special_tokens_map.json +0 -51
  14. models/finetuned/bbbp/tokenizer.json +0 -473
  15. models/finetuned/bbbp/tokenizer_config.json +0 -59
  16. models/finetuned/bbbp/vocab.json +0 -1
  17. models/finetuned/esol/config.json +0 -28
  18. models/finetuned/esol/finetuning_optimized_config.json +0 -24
  19. models/finetuned/esol/merges.txt +0 -162
  20. models/finetuned/esol/model.pt +0 -3
  21. models/finetuned/esol/special_tokens_map.json +0 -51
  22. models/finetuned/esol/tokenizer.json +0 -473
  23. models/finetuned/esol/tokenizer_config.json +0 -59
  24. models/finetuned/esol/vocab.json +0 -1
  25. models/finetuned/freesolv/config.json +0 -28
  26. models/finetuned/freesolv/finetuning_optimized_config.json +0 -24
  27. models/finetuned/freesolv/merges.txt +0 -162
  28. models/finetuned/freesolv/model.pt +0 -3
  29. models/finetuned/freesolv/special_tokens_map.json +0 -51
  30. models/finetuned/freesolv/tokenizer.json +0 -473
  31. models/finetuned/freesolv/tokenizer_config.json +0 -59
  32. models/finetuned/freesolv/vocab.json +0 -1
  33. models/finetuned/hiv/config.json +0 -27
  34. models/finetuned/hiv/finetuning_optimized_config.json +0 -24
  35. models/finetuned/hiv/merges.txt +0 -378
  36. models/finetuned/hiv/model.pt +0 -3
  37. models/finetuned/hiv/special_tokens_map.json +0 -51
  38. models/finetuned/hiv/tokenizer.json +0 -909
  39. models/finetuned/hiv/tokenizer_config.json +0 -65
  40. models/finetuned/hiv/vocab.json +0 -1
  41. models/finetuned/lipo/config.json +0 -28
  42. models/finetuned/lipo/finetuning_optimized_config.json +0 -24
  43. models/finetuned/lipo/merges.txt +0 -162
  44. models/finetuned/lipo/model.pt +0 -3
  45. models/finetuned/lipo/special_tokens_map.json +0 -51
  46. models/finetuned/lipo/tokenizer.json +0 -473
  47. models/finetuned/lipo/tokenizer_config.json +0 -59
  48. models/finetuned/lipo/vocab.json +0 -1
  49. models/finetuned/pdbbind_full/config.json +0 -28
  50. models/finetuned/pdbbind_full/finetuning_optimized_config.json +0 -24
models/finetuned/bace/config.json DELETED
@@ -1,28 +0,0 @@
1
- {
2
- "_name_or_path": "data/epoch_267/hf",
3
- "architectures": [
4
- "RobertaForMaskedLM"
5
- ],
6
- "attention_probs_dropout_prob": 0.1,
7
- "bos_token_id": 0,
8
- "classifier_dropout": null,
9
- "eos_token_id": 2,
10
- "hidden_act": "gelu",
11
- "hidden_dropout_prob": 0.1,
12
- "hidden_size": 768,
13
- "initializer_range": 0.02,
14
- "intermediate_size": 3072,
15
- "layer_norm_eps": 1e-12,
16
- "max_position_embeddings": 514,
17
- "model_type": "roberta",
18
- "num_attention_heads": 4,
19
- "num_hidden_layers": 12,
20
- "output_hidden_states": true,
21
- "pad_token_id": 1,
22
- "position_embedding_type": "absolute",
23
- "torch_dtype": "float32",
24
- "transformers_version": "4.26.1",
25
- "type_vocab_size": 1,
26
- "use_cache": true,
27
- "vocab_size": 800
28
- }
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
models/finetuned/bace/finetuning_optimized_config.json DELETED
@@ -1,24 +0,0 @@
1
- {
2
- "dataset_meta_csv": "data/finetuning_datasets/classification/bace/bace.csv",
3
- "dataset_embs_npz": "data/finetuning_datasets/classification/bace/bace_embs.npz",
4
- "use_scaffold": 1,
5
- "seed": 42,
6
- "train_frac": 0.8,
7
- "val_frac": 0.1,
8
- "test_frac": 0.1,
9
- "model_path": "HUBioDataLab/SELFormer",
10
- "tokenizer_path": "HUBioDataLab/SELFormer",
11
- "pretrained_multimodal_dir": "data/models/SELFormerMM",
12
- "task_type": "binary",
13
- "label_column": "Class",
14
- "num_labels": 2,
15
- "batch_size": 16,
16
- "max_len": 128,
17
- "epochs": 25,
18
- "backbone_lr": 5e-06,
19
- "head_lr": 5e-05,
20
- "weight_decay": 0.001,
21
- "checkpoint_every": 25,
22
- "test_eval_every": 0,
23
- "save_dir": "data/models/finetuned/bace"
24
- }
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
models/finetuned/bace/merges.txt DELETED
@@ -1,162 +0,0 @@
1
- #version: 0.2 - Trained by `huggingface/tokenizers`
2
- B r
3
- a n
4
- c h
5
- Br an
6
- Bran ch
7
- Branch 1
8
- = C
9
- R i
10
- n g
11
- Ri ng
12
- Ring 1
13
- = Branch1
14
- Branch 2
15
- = O
16
- Ring 2
17
- H 1
18
- C @
19
- = N
20
- # Branch1
21
- C@ @
22
- = Branch2
23
- C@ H1
24
- C@@ H1
25
- # Branch2
26
- C l
27
- # C
28
- / C
29
- N H1
30
- + 1
31
- - 1
32
- = Ring1
33
- O -1
34
- N +1
35
- \ C
36
- / N
37
- # N
38
- = Ring2
39
- = S
40
- =N +1
41
- N a
42
- Na +1
43
- \ N
44
- S +1
45
- / O
46
- \ S
47
- \ O
48
- Br -1
49
- I -1
50
- Cl -1
51
- / C@H1
52
- Branch 3
53
- / C@@H1
54
- = P
55
- / S
56
- =N -1
57
- S i
58
- K +1
59
- N -1
60
- S e
61
- L i
62
- Li +1
63
- + 3
64
- Cl +3
65
- \ C@H1
66
- Ring 3
67
- \ C@@H1
68
- / N+1
69
- / P
70
- \ F
71
- P @
72
- 2 H
73
- P H1
74
- / Br
75
- N @
76
- P +1
77
- / Cl
78
- \ NH1
79
- \ Br
80
- @ +1
81
- / I
82
- / C@
83
- T e
84
- \ N+1
85
- P@ @
86
- 1 2
87
- 5 I
88
- \ O-1
89
- 12 5I
90
- / F
91
- # N+1
92
- \ Cl
93
- N@ +1
94
- \ I
95
- - /
96
- / C@@
97
- N@ @
98
- N@ @+1
99
- -/ Ring2
100
- - \
101
- 1 4
102
- B -1
103
- C -1
104
- S @+1
105
- 14 C
106
- H 2
107
- H 4
108
- I +1
109
- S -1
110
- \ P
111
- =S +1
112
- =P @
113
- Si H4
114
- + 2
115
- 3 H
116
- @ @+1
117
- A g
118
- C +1
119
- S @@+1
120
- Cl +1
121
- =S e
122
- -\ Ring1
123
- H 0
124
- O H0
125
- 1 1
126
- = Branch3
127
- = Te
128
- M g
129
- O +1
130
- Z n
131
- \ C@
132
- \ S+1
133
- H1 -1
134
- Se H1
135
- P@ +1
136
- -\ Ring2
137
- 11 C
138
- =Te +1
139
- Zn +2
140
- / NH1
141
- 1 8
142
- A s
143
- B H2
144
- B H1-1
145
- C a
146
- H 3
147
- O H1-1
148
- S H2
149
- =O +1
150
- Se +1
151
- Te H2
152
- 125I H1
153
- -/ Ring1
154
- 14C H2
155
- Ag +1
156
- =Se +1
157
- Mg H2
158
- Mg +2
159
- 11C H3
160
- 18 F
161
- BH2 -1
162
- Ca +2
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
models/finetuned/bace/model.pt DELETED
@@ -1,3 +0,0 @@
1
- version https://git-lfs.github.com/spec/v1
2
- oid sha256:f17ebde0f06fdca997a8be88bb399bd42ff14b293ddc28bd8223fcb9253dfb13
3
- size 1022855293
 
 
 
 
models/finetuned/bace/special_tokens_map.json DELETED
@@ -1,51 +0,0 @@
1
- {
2
- "bos_token": {
3
- "content": "<s>",
4
- "lstrip": false,
5
- "normalized": true,
6
- "rstrip": false,
7
- "single_word": false
8
- },
9
- "cls_token": {
10
- "content": "<s>",
11
- "lstrip": false,
12
- "normalized": true,
13
- "rstrip": false,
14
- "single_word": false
15
- },
16
- "eos_token": {
17
- "content": "</s>",
18
- "lstrip": false,
19
- "normalized": true,
20
- "rstrip": false,
21
- "single_word": false
22
- },
23
- "mask_token": {
24
- "content": "<mask>",
25
- "lstrip": true,
26
- "normalized": true,
27
- "rstrip": false,
28
- "single_word": false
29
- },
30
- "pad_token": {
31
- "content": "<pad>",
32
- "lstrip": false,
33
- "normalized": true,
34
- "rstrip": false,
35
- "single_word": false
36
- },
37
- "sep_token": {
38
- "content": "</s>",
39
- "lstrip": false,
40
- "normalized": true,
41
- "rstrip": false,
42
- "single_word": false
43
- },
44
- "unk_token": {
45
- "content": "<unk>",
46
- "lstrip": false,
47
- "normalized": true,
48
- "rstrip": false,
49
- "single_word": false
50
- }
51
- }
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
models/finetuned/bace/tokenizer.json DELETED
@@ -1,473 +0,0 @@
1
- {
2
- "version": "1.0",
3
- "truncation": {
4
- "direction": "Right",
5
- "max_length": 128,
6
- "strategy": "LongestFirst",
7
- "stride": 0
8
- },
9
- "padding": {
10
- "strategy": {
11
- "Fixed": 128
12
- },
13
- "direction": "Right",
14
- "pad_to_multiple_of": null,
15
- "pad_id": 3,
16
- "pad_type_id": 0,
17
- "pad_token": "<pad>"
18
- },
19
- "added_tokens": [
20
- {
21
- "id": 0,
22
- "content": "<unk>",
23
- "single_word": false,
24
- "lstrip": false,
25
- "rstrip": false,
26
- "normalized": true,
27
- "special": true
28
- },
29
- {
30
- "id": 1,
31
- "content": "<s>",
32
- "single_word": false,
33
- "lstrip": false,
34
- "rstrip": false,
35
- "normalized": true,
36
- "special": true
37
- },
38
- {
39
- "id": 2,
40
- "content": "</s>",
41
- "single_word": false,
42
- "lstrip": false,
43
- "rstrip": false,
44
- "normalized": true,
45
- "special": true
46
- },
47
- {
48
- "id": 3,
49
- "content": "<pad>",
50
- "single_word": false,
51
- "lstrip": false,
52
- "rstrip": false,
53
- "normalized": true,
54
- "special": true
55
- },
56
- {
57
- "id": 4,
58
- "content": "<mask>",
59
- "single_word": false,
60
- "lstrip": true,
61
- "rstrip": false,
62
- "normalized": true,
63
- "special": true
64
- }
65
- ],
66
- "normalizer": null,
67
- "pre_tokenizer": {
68
- "type": "ByteLevel",
69
- "add_prefix_space": false,
70
- "trim_offsets": true,
71
- "use_regex": true
72
- },
73
- "post_processor": {
74
- "type": "RobertaProcessing",
75
- "sep": [
76
- "</s>",
77
- 2
78
- ],
79
- "cls": [
80
- "<s>",
81
- 1
82
- ],
83
- "trim_offsets": true,
84
- "add_prefix_space": false
85
- },
86
- "decoder": {
87
- "type": "ByteLevel",
88
- "add_prefix_space": true,
89
- "trim_offsets": true,
90
- "use_regex": true
91
- },
92
- "model": {
93
- "type": "BPE",
94
- "dropout": null,
95
- "unk_token": null,
96
- "continuing_subword_prefix": "",
97
- "end_of_word_suffix": "",
98
- "fuse_unk": false,
99
- "vocab": {
100
- "<unk>": 0,
101
- "<s>": 1,
102
- "</s>": 2,
103
- "<pad>": 3,
104
- "<mask>": 4,
105
- "\n": 5,
106
- "#": 6,
107
- "+": 7,
108
- "-": 8,
109
- ".": 9,
110
- "/": 10,
111
- "0": 11,
112
- "1": 12,
113
- "2": 13,
114
- "3": 14,
115
- "4": 15,
116
- "5": 16,
117
- "8": 17,
118
- "=": 18,
119
- "@": 19,
120
- "A": 20,
121
- "B": 21,
122
- "C": 22,
123
- "F": 23,
124
- "H": 24,
125
- "I": 25,
126
- "K": 26,
127
- "L": 27,
128
- "M": 28,
129
- "N": 29,
130
- "O": 30,
131
- "P": 31,
132
- "R": 32,
133
- "S": 33,
134
- "T": 34,
135
- "Z": 35,
136
- "\\": 36,
137
- "a": 37,
138
- "c": 38,
139
- "e": 39,
140
- "g": 40,
141
- "h": 41,
142
- "i": 42,
143
- "l": 43,
144
- "n": 44,
145
- "r": 45,
146
- "s": 46,
147
- "Br": 47,
148
- "an": 48,
149
- "ch": 49,
150
- "Bran": 50,
151
- "Branch": 51,
152
- "Branch1": 52,
153
- "=C": 53,
154
- "Ri": 54,
155
- "ng": 55,
156
- "Ring": 56,
157
- "Ring1": 57,
158
- "=Branch1": 58,
159
- "Branch2": 59,
160
- "=O": 60,
161
- "Ring2": 61,
162
- "H1": 62,
163
- "C@": 63,
164
- "=N": 64,
165
- "#Branch1": 65,
166
- "C@@": 66,
167
- "=Branch2": 67,
168
- "C@H1": 68,
169
- "C@@H1": 69,
170
- "#Branch2": 70,
171
- "Cl": 71,
172
- "#C": 72,
173
- "/C": 73,
174
- "NH1": 74,
175
- "+1": 75,
176
- "-1": 76,
177
- "=Ring1": 77,
178
- "O-1": 78,
179
- "N+1": 79,
180
- "\\C": 80,
181
- "/N": 81,
182
- "#N": 82,
183
- "=Ring2": 83,
184
- "=S": 84,
185
- "=N+1": 85,
186
- "Na": 86,
187
- "Na+1": 87,
188
- "\\N": 88,
189
- "S+1": 89,
190
- "/O": 90,
191
- "\\S": 91,
192
- "\\O": 92,
193
- "Br-1": 93,
194
- "I-1": 94,
195
- "Cl-1": 95,
196
- "/C@H1": 96,
197
- "Branch3": 97,
198
- "/C@@H1": 98,
199
- "=P": 99,
200
- "/S": 100,
201
- "=N-1": 101,
202
- "Si": 102,
203
- "K+1": 103,
204
- "N-1": 104,
205
- "Se": 105,
206
- "Li": 106,
207
- "Li+1": 107,
208
- "+3": 108,
209
- "Cl+3": 109,
210
- "\\C@H1": 110,
211
- "Ring3": 111,
212
- "\\C@@H1": 112,
213
- "/N+1": 113,
214
- "/P": 114,
215
- "\\F": 115,
216
- "P@": 116,
217
- "2H": 117,
218
- "PH1": 118,
219
- "/Br": 119,
220
- "N@": 120,
221
- "P+1": 121,
222
- "/Cl": 122,
223
- "\\NH1": 123,
224
- "\\Br": 124,
225
- "@+1": 125,
226
- "/I": 126,
227
- "/C@": 127,
228
- "Te": 128,
229
- "\\N+1": 129,
230
- "P@@": 130,
231
- "12": 131,
232
- "5I": 132,
233
- "\\O-1": 133,
234
- "125I": 134,
235
- "/F": 135,
236
- "#N+1": 136,
237
- "\\Cl": 137,
238
- "N@+1": 138,
239
- "\\I": 139,
240
- "-/": 140,
241
- "/C@@": 141,
242
- "N@@": 142,
243
- "N@@+1": 143,
244
- "-/Ring2": 144,
245
- "-\\": 145,
246
- "14": 146,
247
- "B-1": 147,
248
- "C-1": 148,
249
- "S@+1": 149,
250
- "14C": 150,
251
- "H2": 151,
252
- "H4": 152,
253
- "I+1": 153,
254
- "S-1": 154,
255
- "\\P": 155,
256
- "=S+1": 156,
257
- "=P@": 157,
258
- "SiH4": 158,
259
- "+2": 159,
260
- "3H": 160,
261
- "@@+1": 161,
262
- "Ag": 162,
263
- "C+1": 163,
264
- "S@@+1": 164,
265
- "Cl+1": 165,
266
- "=Se": 166,
267
- "-\\Ring1": 167,
268
- "H0": 168,
269
- "OH0": 169,
270
- "11": 170,
271
- "=Branch3": 171,
272
- "=Te": 172,
273
- "Mg": 173,
274
- "O+1": 174,
275
- "Zn": 175,
276
- "\\C@": 176,
277
- "\\S+1": 177,
278
- "H1-1": 178,
279
- "SeH1": 179,
280
- "P@+1": 180,
281
- "-\\Ring2": 181,
282
- "11C": 182,
283
- "=Te+1": 183,
284
- "Zn+2": 184,
285
- "/NH1": 185,
286
- "18": 186,
287
- "As": 187,
288
- "BH2": 188,
289
- "BH1-1": 189,
290
- "Ca": 190,
291
- "H3": 191,
292
- "OH1-1": 192,
293
- "SH2": 193,
294
- "=O+1": 194,
295
- "Se+1": 195,
296
- "TeH2": 196,
297
- "125IH1": 197,
298
- "-/Ring1": 198,
299
- "14CH2": 199,
300
- "Ag+1": 200,
301
- "=Se+1": 201,
302
- "MgH2": 202,
303
- "Mg+2": 203,
304
- "11CH3": 204,
305
- "18F": 205,
306
- "BH2-1": 206,
307
- "Ca+2": 207
308
- },
309
- "merges": [
310
- "B r",
311
- "a n",
312
- "c h",
313
- "Br an",
314
- "Bran ch",
315
- "Branch 1",
316
- "= C",
317
- "R i",
318
- "n g",
319
- "Ri ng",
320
- "Ring 1",
321
- "= Branch1",
322
- "Branch 2",
323
- "= O",
324
- "Ring 2",
325
- "H 1",
326
- "C @",
327
- "= N",
328
- "# Branch1",
329
- "C@ @",
330
- "= Branch2",
331
- "C@ H1",
332
- "C@@ H1",
333
- "# Branch2",
334
- "C l",
335
- "# C",
336
- "/ C",
337
- "N H1",
338
- "+ 1",
339
- "- 1",
340
- "= Ring1",
341
- "O -1",
342
- "N +1",
343
- "\\ C",
344
- "/ N",
345
- "# N",
346
- "= Ring2",
347
- "= S",
348
- "=N +1",
349
- "N a",
350
- "Na +1",
351
- "\\ N",
352
- "S +1",
353
- "/ O",
354
- "\\ S",
355
- "\\ O",
356
- "Br -1",
357
- "I -1",
358
- "Cl -1",
359
- "/ C@H1",
360
- "Branch 3",
361
- "/ C@@H1",
362
- "= P",
363
- "/ S",
364
- "=N -1",
365
- "S i",
366
- "K +1",
367
- "N -1",
368
- "S e",
369
- "L i",
370
- "Li +1",
371
- "+ 3",
372
- "Cl +3",
373
- "\\ C@H1",
374
- "Ring 3",
375
- "\\ C@@H1",
376
- "/ N+1",
377
- "/ P",
378
- "\\ F",
379
- "P @",
380
- "2 H",
381
- "P H1",
382
- "/ Br",
383
- "N @",
384
- "P +1",
385
- "/ Cl",
386
- "\\ NH1",
387
- "\\ Br",
388
- "@ +1",
389
- "/ I",
390
- "/ C@",
391
- "T e",
392
- "\\ N+1",
393
- "P@ @",
394
- "1 2",
395
- "5 I",
396
- "\\ O-1",
397
- "12 5I",
398
- "/ F",
399
- "# N+1",
400
- "\\ Cl",
401
- "N@ +1",
402
- "\\ I",
403
- "- /",
404
- "/ C@@",
405
- "N@ @",
406
- "N@ @+1",
407
- "-/ Ring2",
408
- "- \\",
409
- "1 4",
410
- "B -1",
411
- "C -1",
412
- "S @+1",
413
- "14 C",
414
- "H 2",
415
- "H 4",
416
- "I +1",
417
- "S -1",
418
- "\\ P",
419
- "=S +1",
420
- "=P @",
421
- "Si H4",
422
- "+ 2",
423
- "3 H",
424
- "@ @+1",
425
- "A g",
426
- "C +1",
427
- "S @@+1",
428
- "Cl +1",
429
- "=S e",
430
- "-\\ Ring1",
431
- "H 0",
432
- "O H0",
433
- "1 1",
434
- "= Branch3",
435
- "= Te",
436
- "M g",
437
- "O +1",
438
- "Z n",
439
- "\\ C@",
440
- "\\ S+1",
441
- "H1 -1",
442
- "Se H1",
443
- "P@ +1",
444
- "-\\ Ring2",
445
- "11 C",
446
- "=Te +1",
447
- "Zn +2",
448
- "/ NH1",
449
- "1 8",
450
- "A s",
451
- "B H2",
452
- "B H1-1",
453
- "C a",
454
- "H 3",
455
- "O H1-1",
456
- "S H2",
457
- "=O +1",
458
- "Se +1",
459
- "Te H2",
460
- "125I H1",
461
- "-/ Ring1",
462
- "14C H2",
463
- "Ag +1",
464
- "=Se +1",
465
- "Mg H2",
466
- "Mg +2",
467
- "11C H3",
468
- "18 F",
469
- "BH2 -1",
470
- "Ca +2"
471
- ]
472
- }
473
- }
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
models/finetuned/bace/tokenizer_config.json DELETED
@@ -1,59 +0,0 @@
1
- {
2
- "add_prefix_space": false,
3
- "added_tokens_decoder": {
4
- "0": {
5
- "content": "<unk>",
6
- "lstrip": false,
7
- "normalized": true,
8
- "rstrip": false,
9
- "single_word": false,
10
- "special": true
11
- },
12
- "1": {
13
- "content": "<s>",
14
- "lstrip": false,
15
- "normalized": true,
16
- "rstrip": false,
17
- "single_word": false,
18
- "special": true
19
- },
20
- "2": {
21
- "content": "</s>",
22
- "lstrip": false,
23
- "normalized": true,
24
- "rstrip": false,
25
- "single_word": false,
26
- "special": true
27
- },
28
- "3": {
29
- "content": "<pad>",
30
- "lstrip": false,
31
- "normalized": true,
32
- "rstrip": false,
33
- "single_word": false,
34
- "special": true
35
- },
36
- "4": {
37
- "content": "<mask>",
38
- "lstrip": true,
39
- "normalized": true,
40
- "rstrip": false,
41
- "single_word": false,
42
- "special": true
43
- }
44
- },
45
- "bos_token": "<s>",
46
- "clean_up_tokenization_spaces": true,
47
- "cls_token": "<s>",
48
- "eos_token": "</s>",
49
- "errors": "replace",
50
- "mask_token": "<mask>",
51
- "model_max_length": 1000000000000000019884624838656,
52
- "name_or_path": "data/epoch_267/hf",
53
- "pad_token": "<pad>",
54
- "sep_token": "</s>",
55
- "special_tokens_map_file": "data/epoch_267/hf/special_tokens_map.json",
56
- "tokenizer_class": "RobertaTokenizer",
57
- "trim_offsets": true,
58
- "unk_token": "<unk>"
59
- }
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
models/finetuned/bace/vocab.json DELETED
@@ -1 +0,0 @@
1
- {"<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,"8":17,"=":18,"@":19,"A":20,"B":21,"C":22,"F":23,"H":24,"I":25,"K":26,"L":27,"M":28,"N":29,"O":30,"P":31,"R":32,"S":33,"T":34,"Z":35,"\\":36,"a":37,"c":38,"e":39,"g":40,"h":41,"i":42,"l":43,"n":44,"r":45,"s":46,"Br":47,"an":48,"ch":49,"Bran":50,"Branch":51,"Branch1":52,"=C":53,"Ri":54,"ng":55,"Ring":56,"Ring1":57,"=Branch1":58,"Branch2":59,"=O":60,"Ring2":61,"H1":62,"C@":63,"=N":64,"#Branch1":65,"C@@":66,"=Branch2":67,"C@H1":68,"C@@H1":69,"#Branch2":70,"Cl":71,"#C":72,"/C":73,"NH1":74,"+1":75,"-1":76,"=Ring1":77,"O-1":78,"N+1":79,"\\C":80,"/N":81,"#N":82,"=Ring2":83,"=S":84,"=N+1":85,"Na":86,"Na+1":87,"\\N":88,"S+1":89,"/O":90,"\\S":91,"\\O":92,"Br-1":93,"I-1":94,"Cl-1":95,"/C@H1":96,"Branch3":97,"/C@@H1":98,"=P":99,"/S":100,"=N-1":101,"Si":102,"K+1":103,"N-1":104,"Se":105,"Li":106,"Li+1":107,"+3":108,"Cl+3":109,"\\C@H1":110,"Ring3":111,"\\C@@H1":112,"/N+1":113,"/P":114,"\\F":115,"P@":116,"2H":117,"PH1":118,"/Br":119,"N@":120,"P+1":121,"/Cl":122,"\\NH1":123,"\\Br":124,"@+1":125,"/I":126,"/C@":127,"Te":128,"\\N+1":129,"P@@":130,"12":131,"5I":132,"\\O-1":133,"125I":134,"/F":135,"#N+1":136,"\\Cl":137,"N@+1":138,"\\I":139,"-/":140,"/C@@":141,"N@@":142,"N@@+1":143,"-/Ring2":144,"-\\":145,"14":146,"B-1":147,"C-1":148,"S@+1":149,"14C":150,"H2":151,"H4":152,"I+1":153,"S-1":154,"\\P":155,"=S+1":156,"=P@":157,"SiH4":158,"+2":159,"3H":160,"@@+1":161,"Ag":162,"C+1":163,"S@@+1":164,"Cl+1":165,"=Se":166,"-\\Ring1":167,"H0":168,"OH0":169,"11":170,"=Branch3":171,"=Te":172,"Mg":173,"O+1":174,"Zn":175,"\\C@":176,"\\S+1":177,"H1-1":178,"SeH1":179,"P@+1":180,"-\\Ring2":181,"11C":182,"=Te+1":183,"Zn+2":184,"/NH1":185,"18":186,"As":187,"BH2":188,"BH1-1":189,"Ca":190,"H3":191,"OH1-1":192,"SH2":193,"=O+1":194,"Se+1":195,"TeH2":196,"125IH1":197,"-/Ring1":198,"14CH2":199,"Ag+1":200,"=Se+1":201,"MgH2":202,"Mg+2":203,"11CH3":204,"18F":205,"BH2-1":206,"Ca+2":207}
 
 
models/finetuned/bbbp/config.json DELETED
@@ -1,28 +0,0 @@
1
- {
2
- "_name_or_path": "data/epoch_267/hf",
3
- "architectures": [
4
- "RobertaForMaskedLM"
5
- ],
6
- "attention_probs_dropout_prob": 0.1,
7
- "bos_token_id": 0,
8
- "classifier_dropout": null,
9
- "eos_token_id": 2,
10
- "hidden_act": "gelu",
11
- "hidden_dropout_prob": 0.1,
12
- "hidden_size": 768,
13
- "initializer_range": 0.02,
14
- "intermediate_size": 3072,
15
- "layer_norm_eps": 1e-12,
16
- "max_position_embeddings": 514,
17
- "model_type": "roberta",
18
- "num_attention_heads": 4,
19
- "num_hidden_layers": 12,
20
- "output_hidden_states": true,
21
- "pad_token_id": 1,
22
- "position_embedding_type": "absolute",
23
- "torch_dtype": "float32",
24
- "transformers_version": "4.26.1",
25
- "type_vocab_size": 1,
26
- "use_cache": true,
27
- "vocab_size": 800
28
- }
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
models/finetuned/bbbp/finetuning_optimized_config.json DELETED
@@ -1,24 +0,0 @@
1
- {
2
- "dataset_meta_csv": "data/finetuning_datasets/classification/bbbp/bbbp.csv",
3
- "dataset_embs_npz": "data/finetuning_datasets/classification/bbbp/bbbp_embs.npz",
4
- "use_scaffold": 1,
5
- "seed": 42,
6
- "train_frac": 0.8,
7
- "val_frac": 0.1,
8
- "test_frac": 0.1,
9
- "model_path": "HUBioDataLab/SELFormer",
10
- "tokenizer_path": "HUBioDataLab/SELFormer",
11
- "pretrained_multimodal_dir": "data/models/SELFormerMM",
12
- "task_type": "binary",
13
- "label_column": "p_np",
14
- "num_labels": 2,
15
- "batch_size": 32,
16
- "max_len": 128,
17
- "epochs": 25,
18
- "backbone_lr": 5e-05,
19
- "head_lr": 1e-05,
20
- "weight_decay": 0.1,
21
- "checkpoint_every": 25,
22
- "test_eval_every": 0,
23
- "save_dir": "data/models/finetuned/bbbp"
24
- }
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
models/finetuned/bbbp/merges.txt DELETED
@@ -1,162 +0,0 @@
1
- #version: 0.2 - Trained by `huggingface/tokenizers`
2
- B r
3
- a n
4
- c h
5
- Br an
6
- Bran ch
7
- Branch 1
8
- = C
9
- R i
10
- n g
11
- Ri ng
12
- Ring 1
13
- = Branch1
14
- Branch 2
15
- = O
16
- Ring 2
17
- H 1
18
- C @
19
- = N
20
- # Branch1
21
- C@ @
22
- = Branch2
23
- C@ H1
24
- C@@ H1
25
- # Branch2
26
- C l
27
- # C
28
- / C
29
- N H1
30
- + 1
31
- - 1
32
- = Ring1
33
- O -1
34
- N +1
35
- \ C
36
- / N
37
- # N
38
- = Ring2
39
- = S
40
- =N +1
41
- N a
42
- Na +1
43
- \ N
44
- S +1
45
- / O
46
- \ S
47
- \ O
48
- Br -1
49
- I -1
50
- Cl -1
51
- / C@H1
52
- Branch 3
53
- / C@@H1
54
- = P
55
- / S
56
- =N -1
57
- S i
58
- K +1
59
- N -1
60
- S e
61
- L i
62
- Li +1
63
- + 3
64
- Cl +3
65
- \ C@H1
66
- Ring 3
67
- \ C@@H1
68
- / N+1
69
- / P
70
- \ F
71
- P @
72
- 2 H
73
- P H1
74
- / Br
75
- N @
76
- P +1
77
- / Cl
78
- \ NH1
79
- \ Br
80
- @ +1
81
- / I
82
- / C@
83
- T e
84
- \ N+1
85
- P@ @
86
- 1 2
87
- 5 I
88
- \ O-1
89
- 12 5I
90
- / F
91
- # N+1
92
- \ Cl
93
- N@ +1
94
- \ I
95
- - /
96
- / C@@
97
- N@ @
98
- N@ @+1
99
- -/ Ring2
100
- - \
101
- 1 4
102
- B -1
103
- C -1
104
- S @+1
105
- 14 C
106
- H 2
107
- H 4
108
- I +1
109
- S -1
110
- \ P
111
- =S +1
112
- =P @
113
- Si H4
114
- + 2
115
- 3 H
116
- @ @+1
117
- A g
118
- C +1
119
- S @@+1
120
- Cl +1
121
- =S e
122
- -\ Ring1
123
- H 0
124
- O H0
125
- 1 1
126
- = Branch3
127
- = Te
128
- M g
129
- O +1
130
- Z n
131
- \ C@
132
- \ S+1
133
- H1 -1
134
- Se H1
135
- P@ +1
136
- -\ Ring2
137
- 11 C
138
- =Te +1
139
- Zn +2
140
- / NH1
141
- 1 8
142
- A s
143
- B H2
144
- B H1-1
145
- C a
146
- H 3
147
- O H1-1
148
- S H2
149
- =O +1
150
- Se +1
151
- Te H2
152
- 125I H1
153
- -/ Ring1
154
- 14C H2
155
- Ag +1
156
- =Se +1
157
- Mg H2
158
- Mg +2
159
- 11C H3
160
- 18 F
161
- BH2 -1
162
- Ca +2
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
models/finetuned/bbbp/model.pt DELETED
@@ -1,3 +0,0 @@
1
- version https://git-lfs.github.com/spec/v1
2
- oid sha256:bfd9b008df03c05aeba73099ed9af31c62e30b961ae1d0946e486465996ae64b
3
- size 1022855293
 
 
 
 
models/finetuned/bbbp/special_tokens_map.json DELETED
@@ -1,51 +0,0 @@
1
- {
2
- "bos_token": {
3
- "content": "<s>",
4
- "lstrip": false,
5
- "normalized": true,
6
- "rstrip": false,
7
- "single_word": false
8
- },
9
- "cls_token": {
10
- "content": "<s>",
11
- "lstrip": false,
12
- "normalized": true,
13
- "rstrip": false,
14
- "single_word": false
15
- },
16
- "eos_token": {
17
- "content": "</s>",
18
- "lstrip": false,
19
- "normalized": true,
20
- "rstrip": false,
21
- "single_word": false
22
- },
23
- "mask_token": {
24
- "content": "<mask>",
25
- "lstrip": true,
26
- "normalized": true,
27
- "rstrip": false,
28
- "single_word": false
29
- },
30
- "pad_token": {
31
- "content": "<pad>",
32
- "lstrip": false,
33
- "normalized": true,
34
- "rstrip": false,
35
- "single_word": false
36
- },
37
- "sep_token": {
38
- "content": "</s>",
39
- "lstrip": false,
40
- "normalized": true,
41
- "rstrip": false,
42
- "single_word": false
43
- },
44
- "unk_token": {
45
- "content": "<unk>",
46
- "lstrip": false,
47
- "normalized": true,
48
- "rstrip": false,
49
- "single_word": false
50
- }
51
- }
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
models/finetuned/bbbp/tokenizer.json DELETED
@@ -1,473 +0,0 @@
1
- {
2
- "version": "1.0",
3
- "truncation": {
4
- "direction": "Right",
5
- "max_length": 128,
6
- "strategy": "LongestFirst",
7
- "stride": 0
8
- },
9
- "padding": {
10
- "strategy": {
11
- "Fixed": 128
12
- },
13
- "direction": "Right",
14
- "pad_to_multiple_of": null,
15
- "pad_id": 3,
16
- "pad_type_id": 0,
17
- "pad_token": "<pad>"
18
- },
19
- "added_tokens": [
20
- {
21
- "id": 0,
22
- "content": "<unk>",
23
- "single_word": false,
24
- "lstrip": false,
25
- "rstrip": false,
26
- "normalized": true,
27
- "special": true
28
- },
29
- {
30
- "id": 1,
31
- "content": "<s>",
32
- "single_word": false,
33
- "lstrip": false,
34
- "rstrip": false,
35
- "normalized": true,
36
- "special": true
37
- },
38
- {
39
- "id": 2,
40
- "content": "</s>",
41
- "single_word": false,
42
- "lstrip": false,
43
- "rstrip": false,
44
- "normalized": true,
45
- "special": true
46
- },
47
- {
48
- "id": 3,
49
- "content": "<pad>",
50
- "single_word": false,
51
- "lstrip": false,
52
- "rstrip": false,
53
- "normalized": true,
54
- "special": true
55
- },
56
- {
57
- "id": 4,
58
- "content": "<mask>",
59
- "single_word": false,
60
- "lstrip": true,
61
- "rstrip": false,
62
- "normalized": true,
63
- "special": true
64
- }
65
- ],
66
- "normalizer": null,
67
- "pre_tokenizer": {
68
- "type": "ByteLevel",
69
- "add_prefix_space": false,
70
- "trim_offsets": true,
71
- "use_regex": true
72
- },
73
- "post_processor": {
74
- "type": "RobertaProcessing",
75
- "sep": [
76
- "</s>",
77
- 2
78
- ],
79
- "cls": [
80
- "<s>",
81
- 1
82
- ],
83
- "trim_offsets": true,
84
- "add_prefix_space": false
85
- },
86
- "decoder": {
87
- "type": "ByteLevel",
88
- "add_prefix_space": true,
89
- "trim_offsets": true,
90
- "use_regex": true
91
- },
92
- "model": {
93
- "type": "BPE",
94
- "dropout": null,
95
- "unk_token": null,
96
- "continuing_subword_prefix": "",
97
- "end_of_word_suffix": "",
98
- "fuse_unk": false,
99
- "vocab": {
100
- "<unk>": 0,
101
- "<s>": 1,
102
- "</s>": 2,
103
- "<pad>": 3,
104
- "<mask>": 4,
105
- "\n": 5,
106
- "#": 6,
107
- "+": 7,
108
- "-": 8,
109
- ".": 9,
110
- "/": 10,
111
- "0": 11,
112
- "1": 12,
113
- "2": 13,
114
- "3": 14,
115
- "4": 15,
116
- "5": 16,
117
- "8": 17,
118
- "=": 18,
119
- "@": 19,
120
- "A": 20,
121
- "B": 21,
122
- "C": 22,
123
- "F": 23,
124
- "H": 24,
125
- "I": 25,
126
- "K": 26,
127
- "L": 27,
128
- "M": 28,
129
- "N": 29,
130
- "O": 30,
131
- "P": 31,
132
- "R": 32,
133
- "S": 33,
134
- "T": 34,
135
- "Z": 35,
136
- "\\": 36,
137
- "a": 37,
138
- "c": 38,
139
- "e": 39,
140
- "g": 40,
141
- "h": 41,
142
- "i": 42,
143
- "l": 43,
144
- "n": 44,
145
- "r": 45,
146
- "s": 46,
147
- "Br": 47,
148
- "an": 48,
149
- "ch": 49,
150
- "Bran": 50,
151
- "Branch": 51,
152
- "Branch1": 52,
153
- "=C": 53,
154
- "Ri": 54,
155
- "ng": 55,
156
- "Ring": 56,
157
- "Ring1": 57,
158
- "=Branch1": 58,
159
- "Branch2": 59,
160
- "=O": 60,
161
- "Ring2": 61,
162
- "H1": 62,
163
- "C@": 63,
164
- "=N": 64,
165
- "#Branch1": 65,
166
- "C@@": 66,
167
- "=Branch2": 67,
168
- "C@H1": 68,
169
- "C@@H1": 69,
170
- "#Branch2": 70,
171
- "Cl": 71,
172
- "#C": 72,
173
- "/C": 73,
174
- "NH1": 74,
175
- "+1": 75,
176
- "-1": 76,
177
- "=Ring1": 77,
178
- "O-1": 78,
179
- "N+1": 79,
180
- "\\C": 80,
181
- "/N": 81,
182
- "#N": 82,
183
- "=Ring2": 83,
184
- "=S": 84,
185
- "=N+1": 85,
186
- "Na": 86,
187
- "Na+1": 87,
188
- "\\N": 88,
189
- "S+1": 89,
190
- "/O": 90,
191
- "\\S": 91,
192
- "\\O": 92,
193
- "Br-1": 93,
194
- "I-1": 94,
195
- "Cl-1": 95,
196
- "/C@H1": 96,
197
- "Branch3": 97,
198
- "/C@@H1": 98,
199
- "=P": 99,
200
- "/S": 100,
201
- "=N-1": 101,
202
- "Si": 102,
203
- "K+1": 103,
204
- "N-1": 104,
205
- "Se": 105,
206
- "Li": 106,
207
- "Li+1": 107,
208
- "+3": 108,
209
- "Cl+3": 109,
210
- "\\C@H1": 110,
211
- "Ring3": 111,
212
- "\\C@@H1": 112,
213
- "/N+1": 113,
214
- "/P": 114,
215
- "\\F": 115,
216
- "P@": 116,
217
- "2H": 117,
218
- "PH1": 118,
219
- "/Br": 119,
220
- "N@": 120,
221
- "P+1": 121,
222
- "/Cl": 122,
223
- "\\NH1": 123,
224
- "\\Br": 124,
225
- "@+1": 125,
226
- "/I": 126,
227
- "/C@": 127,
228
- "Te": 128,
229
- "\\N+1": 129,
230
- "P@@": 130,
231
- "12": 131,
232
- "5I": 132,
233
- "\\O-1": 133,
234
- "125I": 134,
235
- "/F": 135,
236
- "#N+1": 136,
237
- "\\Cl": 137,
238
- "N@+1": 138,
239
- "\\I": 139,
240
- "-/": 140,
241
- "/C@@": 141,
242
- "N@@": 142,
243
- "N@@+1": 143,
244
- "-/Ring2": 144,
245
- "-\\": 145,
246
- "14": 146,
247
- "B-1": 147,
248
- "C-1": 148,
249
- "S@+1": 149,
250
- "14C": 150,
251
- "H2": 151,
252
- "H4": 152,
253
- "I+1": 153,
254
- "S-1": 154,
255
- "\\P": 155,
256
- "=S+1": 156,
257
- "=P@": 157,
258
- "SiH4": 158,
259
- "+2": 159,
260
- "3H": 160,
261
- "@@+1": 161,
262
- "Ag": 162,
263
- "C+1": 163,
264
- "S@@+1": 164,
265
- "Cl+1": 165,
266
- "=Se": 166,
267
- "-\\Ring1": 167,
268
- "H0": 168,
269
- "OH0": 169,
270
- "11": 170,
271
- "=Branch3": 171,
272
- "=Te": 172,
273
- "Mg": 173,
274
- "O+1": 174,
275
- "Zn": 175,
276
- "\\C@": 176,
277
- "\\S+1": 177,
278
- "H1-1": 178,
279
- "SeH1": 179,
280
- "P@+1": 180,
281
- "-\\Ring2": 181,
282
- "11C": 182,
283
- "=Te+1": 183,
284
- "Zn+2": 184,
285
- "/NH1": 185,
286
- "18": 186,
287
- "As": 187,
288
- "BH2": 188,
289
- "BH1-1": 189,
290
- "Ca": 190,
291
- "H3": 191,
292
- "OH1-1": 192,
293
- "SH2": 193,
294
- "=O+1": 194,
295
- "Se+1": 195,
296
- "TeH2": 196,
297
- "125IH1": 197,
298
- "-/Ring1": 198,
299
- "14CH2": 199,
300
- "Ag+1": 200,
301
- "=Se+1": 201,
302
- "MgH2": 202,
303
- "Mg+2": 203,
304
- "11CH3": 204,
305
- "18F": 205,
306
- "BH2-1": 206,
307
- "Ca+2": 207
308
- },
309
- "merges": [
310
- "B r",
311
- "a n",
312
- "c h",
313
- "Br an",
314
- "Bran ch",
315
- "Branch 1",
316
- "= C",
317
- "R i",
318
- "n g",
319
- "Ri ng",
320
- "Ring 1",
321
- "= Branch1",
322
- "Branch 2",
323
- "= O",
324
- "Ring 2",
325
- "H 1",
326
- "C @",
327
- "= N",
328
- "# Branch1",
329
- "C@ @",
330
- "= Branch2",
331
- "C@ H1",
332
- "C@@ H1",
333
- "# Branch2",
334
- "C l",
335
- "# C",
336
- "/ C",
337
- "N H1",
338
- "+ 1",
339
- "- 1",
340
- "= Ring1",
341
- "O -1",
342
- "N +1",
343
- "\\ C",
344
- "/ N",
345
- "# N",
346
- "= Ring2",
347
- "= S",
348
- "=N +1",
349
- "N a",
350
- "Na +1",
351
- "\\ N",
352
- "S +1",
353
- "/ O",
354
- "\\ S",
355
- "\\ O",
356
- "Br -1",
357
- "I -1",
358
- "Cl -1",
359
- "/ C@H1",
360
- "Branch 3",
361
- "/ C@@H1",
362
- "= P",
363
- "/ S",
364
- "=N -1",
365
- "S i",
366
- "K +1",
367
- "N -1",
368
- "S e",
369
- "L i",
370
- "Li +1",
371
- "+ 3",
372
- "Cl +3",
373
- "\\ C@H1",
374
- "Ring 3",
375
- "\\ C@@H1",
376
- "/ N+1",
377
- "/ P",
378
- "\\ F",
379
- "P @",
380
- "2 H",
381
- "P H1",
382
- "/ Br",
383
- "N @",
384
- "P +1",
385
- "/ Cl",
386
- "\\ NH1",
387
- "\\ Br",
388
- "@ +1",
389
- "/ I",
390
- "/ C@",
391
- "T e",
392
- "\\ N+1",
393
- "P@ @",
394
- "1 2",
395
- "5 I",
396
- "\\ O-1",
397
- "12 5I",
398
- "/ F",
399
- "# N+1",
400
- "\\ Cl",
401
- "N@ +1",
402
- "\\ I",
403
- "- /",
404
- "/ C@@",
405
- "N@ @",
406
- "N@ @+1",
407
- "-/ Ring2",
408
- "- \\",
409
- "1 4",
410
- "B -1",
411
- "C -1",
412
- "S @+1",
413
- "14 C",
414
- "H 2",
415
- "H 4",
416
- "I +1",
417
- "S -1",
418
- "\\ P",
419
- "=S +1",
420
- "=P @",
421
- "Si H4",
422
- "+ 2",
423
- "3 H",
424
- "@ @+1",
425
- "A g",
426
- "C +1",
427
- "S @@+1",
428
- "Cl +1",
429
- "=S e",
430
- "-\\ Ring1",
431
- "H 0",
432
- "O H0",
433
- "1 1",
434
- "= Branch3",
435
- "= Te",
436
- "M g",
437
- "O +1",
438
- "Z n",
439
- "\\ C@",
440
- "\\ S+1",
441
- "H1 -1",
442
- "Se H1",
443
- "P@ +1",
444
- "-\\ Ring2",
445
- "11 C",
446
- "=Te +1",
447
- "Zn +2",
448
- "/ NH1",
449
- "1 8",
450
- "A s",
451
- "B H2",
452
- "B H1-1",
453
- "C a",
454
- "H 3",
455
- "O H1-1",
456
- "S H2",
457
- "=O +1",
458
- "Se +1",
459
- "Te H2",
460
- "125I H1",
461
- "-/ Ring1",
462
- "14C H2",
463
- "Ag +1",
464
- "=Se +1",
465
- "Mg H2",
466
- "Mg +2",
467
- "11C H3",
468
- "18 F",
469
- "BH2 -1",
470
- "Ca +2"
471
- ]
472
- }
473
- }
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
models/finetuned/bbbp/tokenizer_config.json DELETED
@@ -1,59 +0,0 @@
1
- {
2
- "add_prefix_space": false,
3
- "added_tokens_decoder": {
4
- "0": {
5
- "content": "<unk>",
6
- "lstrip": false,
7
- "normalized": true,
8
- "rstrip": false,
9
- "single_word": false,
10
- "special": true
11
- },
12
- "1": {
13
- "content": "<s>",
14
- "lstrip": false,
15
- "normalized": true,
16
- "rstrip": false,
17
- "single_word": false,
18
- "special": true
19
- },
20
- "2": {
21
- "content": "</s>",
22
- "lstrip": false,
23
- "normalized": true,
24
- "rstrip": false,
25
- "single_word": false,
26
- "special": true
27
- },
28
- "3": {
29
- "content": "<pad>",
30
- "lstrip": false,
31
- "normalized": true,
32
- "rstrip": false,
33
- "single_word": false,
34
- "special": true
35
- },
36
- "4": {
37
- "content": "<mask>",
38
- "lstrip": true,
39
- "normalized": true,
40
- "rstrip": false,
41
- "single_word": false,
42
- "special": true
43
- }
44
- },
45
- "bos_token": "<s>",
46
- "clean_up_tokenization_spaces": true,
47
- "cls_token": "<s>",
48
- "eos_token": "</s>",
49
- "errors": "replace",
50
- "mask_token": "<mask>",
51
- "model_max_length": 1000000000000000019884624838656,
52
- "name_or_path": "data/epoch_267/hf",
53
- "pad_token": "<pad>",
54
- "sep_token": "</s>",
55
- "special_tokens_map_file": "data/epoch_267/hf/special_tokens_map.json",
56
- "tokenizer_class": "RobertaTokenizer",
57
- "trim_offsets": true,
58
- "unk_token": "<unk>"
59
- }
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
models/finetuned/bbbp/vocab.json DELETED
@@ -1 +0,0 @@
1
- {"<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,"8":17,"=":18,"@":19,"A":20,"B":21,"C":22,"F":23,"H":24,"I":25,"K":26,"L":27,"M":28,"N":29,"O":30,"P":31,"R":32,"S":33,"T":34,"Z":35,"\\":36,"a":37,"c":38,"e":39,"g":40,"h":41,"i":42,"l":43,"n":44,"r":45,"s":46,"Br":47,"an":48,"ch":49,"Bran":50,"Branch":51,"Branch1":52,"=C":53,"Ri":54,"ng":55,"Ring":56,"Ring1":57,"=Branch1":58,"Branch2":59,"=O":60,"Ring2":61,"H1":62,"C@":63,"=N":64,"#Branch1":65,"C@@":66,"=Branch2":67,"C@H1":68,"C@@H1":69,"#Branch2":70,"Cl":71,"#C":72,"/C":73,"NH1":74,"+1":75,"-1":76,"=Ring1":77,"O-1":78,"N+1":79,"\\C":80,"/N":81,"#N":82,"=Ring2":83,"=S":84,"=N+1":85,"Na":86,"Na+1":87,"\\N":88,"S+1":89,"/O":90,"\\S":91,"\\O":92,"Br-1":93,"I-1":94,"Cl-1":95,"/C@H1":96,"Branch3":97,"/C@@H1":98,"=P":99,"/S":100,"=N-1":101,"Si":102,"K+1":103,"N-1":104,"Se":105,"Li":106,"Li+1":107,"+3":108,"Cl+3":109,"\\C@H1":110,"Ring3":111,"\\C@@H1":112,"/N+1":113,"/P":114,"\\F":115,"P@":116,"2H":117,"PH1":118,"/Br":119,"N@":120,"P+1":121,"/Cl":122,"\\NH1":123,"\\Br":124,"@+1":125,"/I":126,"/C@":127,"Te":128,"\\N+1":129,"P@@":130,"12":131,"5I":132,"\\O-1":133,"125I":134,"/F":135,"#N+1":136,"\\Cl":137,"N@+1":138,"\\I":139,"-/":140,"/C@@":141,"N@@":142,"N@@+1":143,"-/Ring2":144,"-\\":145,"14":146,"B-1":147,"C-1":148,"S@+1":149,"14C":150,"H2":151,"H4":152,"I+1":153,"S-1":154,"\\P":155,"=S+1":156,"=P@":157,"SiH4":158,"+2":159,"3H":160,"@@+1":161,"Ag":162,"C+1":163,"S@@+1":164,"Cl+1":165,"=Se":166,"-\\Ring1":167,"H0":168,"OH0":169,"11":170,"=Branch3":171,"=Te":172,"Mg":173,"O+1":174,"Zn":175,"\\C@":176,"\\S+1":177,"H1-1":178,"SeH1":179,"P@+1":180,"-\\Ring2":181,"11C":182,"=Te+1":183,"Zn+2":184,"/NH1":185,"18":186,"As":187,"BH2":188,"BH1-1":189,"Ca":190,"H3":191,"OH1-1":192,"SH2":193,"=O+1":194,"Se+1":195,"TeH2":196,"125IH1":197,"-/Ring1":198,"14CH2":199,"Ag+1":200,"=Se+1":201,"MgH2":202,"Mg+2":203,"11CH3":204,"18F":205,"BH2-1":206,"Ca+2":207}
 
 
models/finetuned/esol/config.json DELETED
@@ -1,28 +0,0 @@
1
- {
2
- "_name_or_path": "data/epoch_267/hf",
3
- "architectures": [
4
- "RobertaForMaskedLM"
5
- ],
6
- "attention_probs_dropout_prob": 0.1,
7
- "bos_token_id": 0,
8
- "classifier_dropout": null,
9
- "eos_token_id": 2,
10
- "hidden_act": "gelu",
11
- "hidden_dropout_prob": 0.1,
12
- "hidden_size": 768,
13
- "initializer_range": 0.02,
14
- "intermediate_size": 3072,
15
- "layer_norm_eps": 1e-12,
16
- "max_position_embeddings": 514,
17
- "model_type": "roberta",
18
- "num_attention_heads": 4,
19
- "num_hidden_layers": 12,
20
- "output_hidden_states": true,
21
- "pad_token_id": 1,
22
- "position_embedding_type": "absolute",
23
- "torch_dtype": "float32",
24
- "transformers_version": "4.26.1",
25
- "type_vocab_size": 1,
26
- "use_cache": true,
27
- "vocab_size": 800
28
- }
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
models/finetuned/esol/finetuning_optimized_config.json DELETED
@@ -1,24 +0,0 @@
1
- {
2
- "dataset_meta_csv": "data/finetuning_datasets/regression/esol/esol.csv",
3
- "dataset_embs_npz": "data/finetuning_datasets/regression/esol/esol_embs.npz",
4
- "use_scaffold": 0,
5
- "seed": 42,
6
- "train_frac": 0.8,
7
- "val_frac": 0.1,
8
- "test_frac": 0.1,
9
- "model_path": "HUBioDataLab/SELFormer",
10
- "tokenizer_path": "HUBioDataLab/SELFormer",
11
- "pretrained_multimodal_dir": "data/models/SELFormerMM",
12
- "task_type": "regression",
13
- "label_column": "measured log solubility in mols per litre",
14
- "num_labels": 1,
15
- "batch_size": 8,
16
- "max_len": 128,
17
- "epochs": 100,
18
- "backbone_lr": 5e-05,
19
- "head_lr": 5e-05,
20
- "weight_decay": 0.1,
21
- "checkpoint_every": 25,
22
- "test_eval_every": 0,
23
- "save_dir": "data/models/finetuned/esol"
24
- }
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
models/finetuned/esol/merges.txt DELETED
@@ -1,162 +0,0 @@
1
- #version: 0.2 - Trained by `huggingface/tokenizers`
2
- B r
3
- a n
4
- c h
5
- Br an
6
- Bran ch
7
- Branch 1
8
- = C
9
- R i
10
- n g
11
- Ri ng
12
- Ring 1
13
- = Branch1
14
- Branch 2
15
- = O
16
- Ring 2
17
- H 1
18
- C @
19
- = N
20
- # Branch1
21
- C@ @
22
- = Branch2
23
- C@ H1
24
- C@@ H1
25
- # Branch2
26
- C l
27
- # C
28
- / C
29
- N H1
30
- + 1
31
- - 1
32
- = Ring1
33
- O -1
34
- N +1
35
- \ C
36
- / N
37
- # N
38
- = Ring2
39
- = S
40
- =N +1
41
- N a
42
- Na +1
43
- \ N
44
- S +1
45
- / O
46
- \ S
47
- \ O
48
- Br -1
49
- I -1
50
- Cl -1
51
- / C@H1
52
- Branch 3
53
- / C@@H1
54
- = P
55
- / S
56
- =N -1
57
- S i
58
- K +1
59
- N -1
60
- S e
61
- L i
62
- Li +1
63
- + 3
64
- Cl +3
65
- \ C@H1
66
- Ring 3
67
- \ C@@H1
68
- / N+1
69
- / P
70
- \ F
71
- P @
72
- 2 H
73
- P H1
74
- / Br
75
- N @
76
- P +1
77
- / Cl
78
- \ NH1
79
- \ Br
80
- @ +1
81
- / I
82
- / C@
83
- T e
84
- \ N+1
85
- P@ @
86
- 1 2
87
- 5 I
88
- \ O-1
89
- 12 5I
90
- / F
91
- # N+1
92
- \ Cl
93
- N@ +1
94
- \ I
95
- - /
96
- / C@@
97
- N@ @
98
- N@ @+1
99
- -/ Ring2
100
- - \
101
- 1 4
102
- B -1
103
- C -1
104
- S @+1
105
- 14 C
106
- H 2
107
- H 4
108
- I +1
109
- S -1
110
- \ P
111
- =S +1
112
- =P @
113
- Si H4
114
- + 2
115
- 3 H
116
- @ @+1
117
- A g
118
- C +1
119
- S @@+1
120
- Cl +1
121
- =S e
122
- -\ Ring1
123
- H 0
124
- O H0
125
- 1 1
126
- = Branch3
127
- = Te
128
- M g
129
- O +1
130
- Z n
131
- \ C@
132
- \ S+1
133
- H1 -1
134
- Se H1
135
- P@ +1
136
- -\ Ring2
137
- 11 C
138
- =Te +1
139
- Zn +2
140
- / NH1
141
- 1 8
142
- A s
143
- B H2
144
- B H1-1
145
- C a
146
- H 3
147
- O H1-1
148
- S H2
149
- =O +1
150
- Se +1
151
- Te H2
152
- 125I H1
153
- -/ Ring1
154
- 14C H2
155
- Ag +1
156
- =Se +1
157
- Mg H2
158
- Mg +2
159
- 11C H3
160
- 18 F
161
- BH2 -1
162
- Ca +2
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
models/finetuned/esol/model.pt DELETED
@@ -1,3 +0,0 @@
1
- version https://git-lfs.github.com/spec/v1
2
- oid sha256:eed86c02f896cfdf36e8f5e519d66ae82d7eae4a0993911ee8f89ceb76e8b07b
3
- size 1022843005
 
 
 
 
models/finetuned/esol/special_tokens_map.json DELETED
@@ -1,51 +0,0 @@
1
- {
2
- "bos_token": {
3
- "content": "<s>",
4
- "lstrip": false,
5
- "normalized": true,
6
- "rstrip": false,
7
- "single_word": false
8
- },
9
- "cls_token": {
10
- "content": "<s>",
11
- "lstrip": false,
12
- "normalized": true,
13
- "rstrip": false,
14
- "single_word": false
15
- },
16
- "eos_token": {
17
- "content": "</s>",
18
- "lstrip": false,
19
- "normalized": true,
20
- "rstrip": false,
21
- "single_word": false
22
- },
23
- "mask_token": {
24
- "content": "<mask>",
25
- "lstrip": true,
26
- "normalized": true,
27
- "rstrip": false,
28
- "single_word": false
29
- },
30
- "pad_token": {
31
- "content": "<pad>",
32
- "lstrip": false,
33
- "normalized": true,
34
- "rstrip": false,
35
- "single_word": false
36
- },
37
- "sep_token": {
38
- "content": "</s>",
39
- "lstrip": false,
40
- "normalized": true,
41
- "rstrip": false,
42
- "single_word": false
43
- },
44
- "unk_token": {
45
- "content": "<unk>",
46
- "lstrip": false,
47
- "normalized": true,
48
- "rstrip": false,
49
- "single_word": false
50
- }
51
- }
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
models/finetuned/esol/tokenizer.json DELETED
@@ -1,473 +0,0 @@
1
- {
2
- "version": "1.0",
3
- "truncation": {
4
- "direction": "Right",
5
- "max_length": 128,
6
- "strategy": "LongestFirst",
7
- "stride": 0
8
- },
9
- "padding": {
10
- "strategy": {
11
- "Fixed": 128
12
- },
13
- "direction": "Right",
14
- "pad_to_multiple_of": null,
15
- "pad_id": 3,
16
- "pad_type_id": 0,
17
- "pad_token": "<pad>"
18
- },
19
- "added_tokens": [
20
- {
21
- "id": 0,
22
- "content": "<unk>",
23
- "single_word": false,
24
- "lstrip": false,
25
- "rstrip": false,
26
- "normalized": true,
27
- "special": true
28
- },
29
- {
30
- "id": 1,
31
- "content": "<s>",
32
- "single_word": false,
33
- "lstrip": false,
34
- "rstrip": false,
35
- "normalized": true,
36
- "special": true
37
- },
38
- {
39
- "id": 2,
40
- "content": "</s>",
41
- "single_word": false,
42
- "lstrip": false,
43
- "rstrip": false,
44
- "normalized": true,
45
- "special": true
46
- },
47
- {
48
- "id": 3,
49
- "content": "<pad>",
50
- "single_word": false,
51
- "lstrip": false,
52
- "rstrip": false,
53
- "normalized": true,
54
- "special": true
55
- },
56
- {
57
- "id": 4,
58
- "content": "<mask>",
59
- "single_word": false,
60
- "lstrip": true,
61
- "rstrip": false,
62
- "normalized": true,
63
- "special": true
64
- }
65
- ],
66
- "normalizer": null,
67
- "pre_tokenizer": {
68
- "type": "ByteLevel",
69
- "add_prefix_space": false,
70
- "trim_offsets": true,
71
- "use_regex": true
72
- },
73
- "post_processor": {
74
- "type": "RobertaProcessing",
75
- "sep": [
76
- "</s>",
77
- 2
78
- ],
79
- "cls": [
80
- "<s>",
81
- 1
82
- ],
83
- "trim_offsets": true,
84
- "add_prefix_space": false
85
- },
86
- "decoder": {
87
- "type": "ByteLevel",
88
- "add_prefix_space": true,
89
- "trim_offsets": true,
90
- "use_regex": true
91
- },
92
- "model": {
93
- "type": "BPE",
94
- "dropout": null,
95
- "unk_token": null,
96
- "continuing_subword_prefix": "",
97
- "end_of_word_suffix": "",
98
- "fuse_unk": false,
99
- "vocab": {
100
- "<unk>": 0,
101
- "<s>": 1,
102
- "</s>": 2,
103
- "<pad>": 3,
104
- "<mask>": 4,
105
- "\n": 5,
106
- "#": 6,
107
- "+": 7,
108
- "-": 8,
109
- ".": 9,
110
- "/": 10,
111
- "0": 11,
112
- "1": 12,
113
- "2": 13,
114
- "3": 14,
115
- "4": 15,
116
- "5": 16,
117
- "8": 17,
118
- "=": 18,
119
- "@": 19,
120
- "A": 20,
121
- "B": 21,
122
- "C": 22,
123
- "F": 23,
124
- "H": 24,
125
- "I": 25,
126
- "K": 26,
127
- "L": 27,
128
- "M": 28,
129
- "N": 29,
130
- "O": 30,
131
- "P": 31,
132
- "R": 32,
133
- "S": 33,
134
- "T": 34,
135
- "Z": 35,
136
- "\\": 36,
137
- "a": 37,
138
- "c": 38,
139
- "e": 39,
140
- "g": 40,
141
- "h": 41,
142
- "i": 42,
143
- "l": 43,
144
- "n": 44,
145
- "r": 45,
146
- "s": 46,
147
- "Br": 47,
148
- "an": 48,
149
- "ch": 49,
150
- "Bran": 50,
151
- "Branch": 51,
152
- "Branch1": 52,
153
- "=C": 53,
154
- "Ri": 54,
155
- "ng": 55,
156
- "Ring": 56,
157
- "Ring1": 57,
158
- "=Branch1": 58,
159
- "Branch2": 59,
160
- "=O": 60,
161
- "Ring2": 61,
162
- "H1": 62,
163
- "C@": 63,
164
- "=N": 64,
165
- "#Branch1": 65,
166
- "C@@": 66,
167
- "=Branch2": 67,
168
- "C@H1": 68,
169
- "C@@H1": 69,
170
- "#Branch2": 70,
171
- "Cl": 71,
172
- "#C": 72,
173
- "/C": 73,
174
- "NH1": 74,
175
- "+1": 75,
176
- "-1": 76,
177
- "=Ring1": 77,
178
- "O-1": 78,
179
- "N+1": 79,
180
- "\\C": 80,
181
- "/N": 81,
182
- "#N": 82,
183
- "=Ring2": 83,
184
- "=S": 84,
185
- "=N+1": 85,
186
- "Na": 86,
187
- "Na+1": 87,
188
- "\\N": 88,
189
- "S+1": 89,
190
- "/O": 90,
191
- "\\S": 91,
192
- "\\O": 92,
193
- "Br-1": 93,
194
- "I-1": 94,
195
- "Cl-1": 95,
196
- "/C@H1": 96,
197
- "Branch3": 97,
198
- "/C@@H1": 98,
199
- "=P": 99,
200
- "/S": 100,
201
- "=N-1": 101,
202
- "Si": 102,
203
- "K+1": 103,
204
- "N-1": 104,
205
- "Se": 105,
206
- "Li": 106,
207
- "Li+1": 107,
208
- "+3": 108,
209
- "Cl+3": 109,
210
- "\\C@H1": 110,
211
- "Ring3": 111,
212
- "\\C@@H1": 112,
213
- "/N+1": 113,
214
- "/P": 114,
215
- "\\F": 115,
216
- "P@": 116,
217
- "2H": 117,
218
- "PH1": 118,
219
- "/Br": 119,
220
- "N@": 120,
221
- "P+1": 121,
222
- "/Cl": 122,
223
- "\\NH1": 123,
224
- "\\Br": 124,
225
- "@+1": 125,
226
- "/I": 126,
227
- "/C@": 127,
228
- "Te": 128,
229
- "\\N+1": 129,
230
- "P@@": 130,
231
- "12": 131,
232
- "5I": 132,
233
- "\\O-1": 133,
234
- "125I": 134,
235
- "/F": 135,
236
- "#N+1": 136,
237
- "\\Cl": 137,
238
- "N@+1": 138,
239
- "\\I": 139,
240
- "-/": 140,
241
- "/C@@": 141,
242
- "N@@": 142,
243
- "N@@+1": 143,
244
- "-/Ring2": 144,
245
- "-\\": 145,
246
- "14": 146,
247
- "B-1": 147,
248
- "C-1": 148,
249
- "S@+1": 149,
250
- "14C": 150,
251
- "H2": 151,
252
- "H4": 152,
253
- "I+1": 153,
254
- "S-1": 154,
255
- "\\P": 155,
256
- "=S+1": 156,
257
- "=P@": 157,
258
- "SiH4": 158,
259
- "+2": 159,
260
- "3H": 160,
261
- "@@+1": 161,
262
- "Ag": 162,
263
- "C+1": 163,
264
- "S@@+1": 164,
265
- "Cl+1": 165,
266
- "=Se": 166,
267
- "-\\Ring1": 167,
268
- "H0": 168,
269
- "OH0": 169,
270
- "11": 170,
271
- "=Branch3": 171,
272
- "=Te": 172,
273
- "Mg": 173,
274
- "O+1": 174,
275
- "Zn": 175,
276
- "\\C@": 176,
277
- "\\S+1": 177,
278
- "H1-1": 178,
279
- "SeH1": 179,
280
- "P@+1": 180,
281
- "-\\Ring2": 181,
282
- "11C": 182,
283
- "=Te+1": 183,
284
- "Zn+2": 184,
285
- "/NH1": 185,
286
- "18": 186,
287
- "As": 187,
288
- "BH2": 188,
289
- "BH1-1": 189,
290
- "Ca": 190,
291
- "H3": 191,
292
- "OH1-1": 192,
293
- "SH2": 193,
294
- "=O+1": 194,
295
- "Se+1": 195,
296
- "TeH2": 196,
297
- "125IH1": 197,
298
- "-/Ring1": 198,
299
- "14CH2": 199,
300
- "Ag+1": 200,
301
- "=Se+1": 201,
302
- "MgH2": 202,
303
- "Mg+2": 203,
304
- "11CH3": 204,
305
- "18F": 205,
306
- "BH2-1": 206,
307
- "Ca+2": 207
308
- },
309
- "merges": [
310
- "B r",
311
- "a n",
312
- "c h",
313
- "Br an",
314
- "Bran ch",
315
- "Branch 1",
316
- "= C",
317
- "R i",
318
- "n g",
319
- "Ri ng",
320
- "Ring 1",
321
- "= Branch1",
322
- "Branch 2",
323
- "= O",
324
- "Ring 2",
325
- "H 1",
326
- "C @",
327
- "= N",
328
- "# Branch1",
329
- "C@ @",
330
- "= Branch2",
331
- "C@ H1",
332
- "C@@ H1",
333
- "# Branch2",
334
- "C l",
335
- "# C",
336
- "/ C",
337
- "N H1",
338
- "+ 1",
339
- "- 1",
340
- "= Ring1",
341
- "O -1",
342
- "N +1",
343
- "\\ C",
344
- "/ N",
345
- "# N",
346
- "= Ring2",
347
- "= S",
348
- "=N +1",
349
- "N a",
350
- "Na +1",
351
- "\\ N",
352
- "S +1",
353
- "/ O",
354
- "\\ S",
355
- "\\ O",
356
- "Br -1",
357
- "I -1",
358
- "Cl -1",
359
- "/ C@H1",
360
- "Branch 3",
361
- "/ C@@H1",
362
- "= P",
363
- "/ S",
364
- "=N -1",
365
- "S i",
366
- "K +1",
367
- "N -1",
368
- "S e",
369
- "L i",
370
- "Li +1",
371
- "+ 3",
372
- "Cl +3",
373
- "\\ C@H1",
374
- "Ring 3",
375
- "\\ C@@H1",
376
- "/ N+1",
377
- "/ P",
378
- "\\ F",
379
- "P @",
380
- "2 H",
381
- "P H1",
382
- "/ Br",
383
- "N @",
384
- "P +1",
385
- "/ Cl",
386
- "\\ NH1",
387
- "\\ Br",
388
- "@ +1",
389
- "/ I",
390
- "/ C@",
391
- "T e",
392
- "\\ N+1",
393
- "P@ @",
394
- "1 2",
395
- "5 I",
396
- "\\ O-1",
397
- "12 5I",
398
- "/ F",
399
- "# N+1",
400
- "\\ Cl",
401
- "N@ +1",
402
- "\\ I",
403
- "- /",
404
- "/ C@@",
405
- "N@ @",
406
- "N@ @+1",
407
- "-/ Ring2",
408
- "- \\",
409
- "1 4",
410
- "B -1",
411
- "C -1",
412
- "S @+1",
413
- "14 C",
414
- "H 2",
415
- "H 4",
416
- "I +1",
417
- "S -1",
418
- "\\ P",
419
- "=S +1",
420
- "=P @",
421
- "Si H4",
422
- "+ 2",
423
- "3 H",
424
- "@ @+1",
425
- "A g",
426
- "C +1",
427
- "S @@+1",
428
- "Cl +1",
429
- "=S e",
430
- "-\\ Ring1",
431
- "H 0",
432
- "O H0",
433
- "1 1",
434
- "= Branch3",
435
- "= Te",
436
- "M g",
437
- "O +1",
438
- "Z n",
439
- "\\ C@",
440
- "\\ S+1",
441
- "H1 -1",
442
- "Se H1",
443
- "P@ +1",
444
- "-\\ Ring2",
445
- "11 C",
446
- "=Te +1",
447
- "Zn +2",
448
- "/ NH1",
449
- "1 8",
450
- "A s",
451
- "B H2",
452
- "B H1-1",
453
- "C a",
454
- "H 3",
455
- "O H1-1",
456
- "S H2",
457
- "=O +1",
458
- "Se +1",
459
- "Te H2",
460
- "125I H1",
461
- "-/ Ring1",
462
- "14C H2",
463
- "Ag +1",
464
- "=Se +1",
465
- "Mg H2",
466
- "Mg +2",
467
- "11C H3",
468
- "18 F",
469
- "BH2 -1",
470
- "Ca +2"
471
- ]
472
- }
473
- }
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
models/finetuned/esol/tokenizer_config.json DELETED
@@ -1,59 +0,0 @@
1
- {
2
- "add_prefix_space": false,
3
- "added_tokens_decoder": {
4
- "0": {
5
- "content": "<unk>",
6
- "lstrip": false,
7
- "normalized": true,
8
- "rstrip": false,
9
- "single_word": false,
10
- "special": true
11
- },
12
- "1": {
13
- "content": "<s>",
14
- "lstrip": false,
15
- "normalized": true,
16
- "rstrip": false,
17
- "single_word": false,
18
- "special": true
19
- },
20
- "2": {
21
- "content": "</s>",
22
- "lstrip": false,
23
- "normalized": true,
24
- "rstrip": false,
25
- "single_word": false,
26
- "special": true
27
- },
28
- "3": {
29
- "content": "<pad>",
30
- "lstrip": false,
31
- "normalized": true,
32
- "rstrip": false,
33
- "single_word": false,
34
- "special": true
35
- },
36
- "4": {
37
- "content": "<mask>",
38
- "lstrip": true,
39
- "normalized": true,
40
- "rstrip": false,
41
- "single_word": false,
42
- "special": true
43
- }
44
- },
45
- "bos_token": "<s>",
46
- "clean_up_tokenization_spaces": true,
47
- "cls_token": "<s>",
48
- "eos_token": "</s>",
49
- "errors": "replace",
50
- "mask_token": "<mask>",
51
- "model_max_length": 1000000000000000019884624838656,
52
- "name_or_path": "data/epoch_267/hf",
53
- "pad_token": "<pad>",
54
- "sep_token": "</s>",
55
- "special_tokens_map_file": "data/epoch_267/hf/special_tokens_map.json",
56
- "tokenizer_class": "RobertaTokenizer",
57
- "trim_offsets": true,
58
- "unk_token": "<unk>"
59
- }
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
models/finetuned/esol/vocab.json DELETED
@@ -1 +0,0 @@
1
- {"<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,"8":17,"=":18,"@":19,"A":20,"B":21,"C":22,"F":23,"H":24,"I":25,"K":26,"L":27,"M":28,"N":29,"O":30,"P":31,"R":32,"S":33,"T":34,"Z":35,"\\":36,"a":37,"c":38,"e":39,"g":40,"h":41,"i":42,"l":43,"n":44,"r":45,"s":46,"Br":47,"an":48,"ch":49,"Bran":50,"Branch":51,"Branch1":52,"=C":53,"Ri":54,"ng":55,"Ring":56,"Ring1":57,"=Branch1":58,"Branch2":59,"=O":60,"Ring2":61,"H1":62,"C@":63,"=N":64,"#Branch1":65,"C@@":66,"=Branch2":67,"C@H1":68,"C@@H1":69,"#Branch2":70,"Cl":71,"#C":72,"/C":73,"NH1":74,"+1":75,"-1":76,"=Ring1":77,"O-1":78,"N+1":79,"\\C":80,"/N":81,"#N":82,"=Ring2":83,"=S":84,"=N+1":85,"Na":86,"Na+1":87,"\\N":88,"S+1":89,"/O":90,"\\S":91,"\\O":92,"Br-1":93,"I-1":94,"Cl-1":95,"/C@H1":96,"Branch3":97,"/C@@H1":98,"=P":99,"/S":100,"=N-1":101,"Si":102,"K+1":103,"N-1":104,"Se":105,"Li":106,"Li+1":107,"+3":108,"Cl+3":109,"\\C@H1":110,"Ring3":111,"\\C@@H1":112,"/N+1":113,"/P":114,"\\F":115,"P@":116,"2H":117,"PH1":118,"/Br":119,"N@":120,"P+1":121,"/Cl":122,"\\NH1":123,"\\Br":124,"@+1":125,"/I":126,"/C@":127,"Te":128,"\\N+1":129,"P@@":130,"12":131,"5I":132,"\\O-1":133,"125I":134,"/F":135,"#N+1":136,"\\Cl":137,"N@+1":138,"\\I":139,"-/":140,"/C@@":141,"N@@":142,"N@@+1":143,"-/Ring2":144,"-\\":145,"14":146,"B-1":147,"C-1":148,"S@+1":149,"14C":150,"H2":151,"H4":152,"I+1":153,"S-1":154,"\\P":155,"=S+1":156,"=P@":157,"SiH4":158,"+2":159,"3H":160,"@@+1":161,"Ag":162,"C+1":163,"S@@+1":164,"Cl+1":165,"=Se":166,"-\\Ring1":167,"H0":168,"OH0":169,"11":170,"=Branch3":171,"=Te":172,"Mg":173,"O+1":174,"Zn":175,"\\C@":176,"\\S+1":177,"H1-1":178,"SeH1":179,"P@+1":180,"-\\Ring2":181,"11C":182,"=Te+1":183,"Zn+2":184,"/NH1":185,"18":186,"As":187,"BH2":188,"BH1-1":189,"Ca":190,"H3":191,"OH1-1":192,"SH2":193,"=O+1":194,"Se+1":195,"TeH2":196,"125IH1":197,"-/Ring1":198,"14CH2":199,"Ag+1":200,"=Se+1":201,"MgH2":202,"Mg+2":203,"11CH3":204,"18F":205,"BH2-1":206,"Ca+2":207}
 
 
models/finetuned/freesolv/config.json DELETED
@@ -1,28 +0,0 @@
1
- {
2
- "_name_or_path": "data/epoch_267/hf",
3
- "architectures": [
4
- "RobertaForMaskedLM"
5
- ],
6
- "attention_probs_dropout_prob": 0.1,
7
- "bos_token_id": 0,
8
- "classifier_dropout": null,
9
- "eos_token_id": 2,
10
- "hidden_act": "gelu",
11
- "hidden_dropout_prob": 0.1,
12
- "hidden_size": 768,
13
- "initializer_range": 0.02,
14
- "intermediate_size": 3072,
15
- "layer_norm_eps": 1e-12,
16
- "max_position_embeddings": 514,
17
- "model_type": "roberta",
18
- "num_attention_heads": 4,
19
- "num_hidden_layers": 12,
20
- "output_hidden_states": true,
21
- "pad_token_id": 1,
22
- "position_embedding_type": "absolute",
23
- "torch_dtype": "float32",
24
- "transformers_version": "4.26.1",
25
- "type_vocab_size": 1,
26
- "use_cache": true,
27
- "vocab_size": 800
28
- }
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
models/finetuned/freesolv/finetuning_optimized_config.json DELETED
@@ -1,24 +0,0 @@
1
- {
2
- "dataset_meta_csv": "data/finetuning_datasets/regression/freesolv/freesolv.csv",
3
- "dataset_embs_npz": "data/finetuning_datasets/regression/freesolv/freesolv_embs.npz",
4
- "use_scaffold": 0,
5
- "seed": 42,
6
- "train_frac": 0.8,
7
- "val_frac": 0.1,
8
- "test_frac": 0.1,
9
- "model_path": "HUBioDataLab/SELFormer",
10
- "tokenizer_path": "HUBioDataLab/SELFormer",
11
- "pretrained_multimodal_dir": "data/models/SELFormerMM",
12
- "task_type": "regression",
13
- "label_column": "freesolv",
14
- "num_labels": 1,
15
- "batch_size": 4,
16
- "max_len": 128,
17
- "epochs": 25,
18
- "backbone_lr": 5e-05,
19
- "head_lr": 0.0002,
20
- "weight_decay": 0.001,
21
- "checkpoint_every": 25,
22
- "test_eval_every": 0,
23
- "save_dir": "data/models/finetuned/freesolv"
24
- }
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
models/finetuned/freesolv/merges.txt DELETED
@@ -1,162 +0,0 @@
1
- #version: 0.2 - Trained by `huggingface/tokenizers`
2
- B r
3
- a n
4
- c h
5
- Br an
6
- Bran ch
7
- Branch 1
8
- = C
9
- R i
10
- n g
11
- Ri ng
12
- Ring 1
13
- = Branch1
14
- Branch 2
15
- = O
16
- Ring 2
17
- H 1
18
- C @
19
- = N
20
- # Branch1
21
- C@ @
22
- = Branch2
23
- C@ H1
24
- C@@ H1
25
- # Branch2
26
- C l
27
- # C
28
- / C
29
- N H1
30
- + 1
31
- - 1
32
- = Ring1
33
- O -1
34
- N +1
35
- \ C
36
- / N
37
- # N
38
- = Ring2
39
- = S
40
- =N +1
41
- N a
42
- Na +1
43
- \ N
44
- S +1
45
- / O
46
- \ S
47
- \ O
48
- Br -1
49
- I -1
50
- Cl -1
51
- / C@H1
52
- Branch 3
53
- / C@@H1
54
- = P
55
- / S
56
- =N -1
57
- S i
58
- K +1
59
- N -1
60
- S e
61
- L i
62
- Li +1
63
- + 3
64
- Cl +3
65
- \ C@H1
66
- Ring 3
67
- \ C@@H1
68
- / N+1
69
- / P
70
- \ F
71
- P @
72
- 2 H
73
- P H1
74
- / Br
75
- N @
76
- P +1
77
- / Cl
78
- \ NH1
79
- \ Br
80
- @ +1
81
- / I
82
- / C@
83
- T e
84
- \ N+1
85
- P@ @
86
- 1 2
87
- 5 I
88
- \ O-1
89
- 12 5I
90
- / F
91
- # N+1
92
- \ Cl
93
- N@ +1
94
- \ I
95
- - /
96
- / C@@
97
- N@ @
98
- N@ @+1
99
- -/ Ring2
100
- - \
101
- 1 4
102
- B -1
103
- C -1
104
- S @+1
105
- 14 C
106
- H 2
107
- H 4
108
- I +1
109
- S -1
110
- \ P
111
- =S +1
112
- =P @
113
- Si H4
114
- + 2
115
- 3 H
116
- @ @+1
117
- A g
118
- C +1
119
- S @@+1
120
- Cl +1
121
- =S e
122
- -\ Ring1
123
- H 0
124
- O H0
125
- 1 1
126
- = Branch3
127
- = Te
128
- M g
129
- O +1
130
- Z n
131
- \ C@
132
- \ S+1
133
- H1 -1
134
- Se H1
135
- P@ +1
136
- -\ Ring2
137
- 11 C
138
- =Te +1
139
- Zn +2
140
- / NH1
141
- 1 8
142
- A s
143
- B H2
144
- B H1-1
145
- C a
146
- H 3
147
- O H1-1
148
- S H2
149
- =O +1
150
- Se +1
151
- Te H2
152
- 125I H1
153
- -/ Ring1
154
- 14C H2
155
- Ag +1
156
- =Se +1
157
- Mg H2
158
- Mg +2
159
- 11C H3
160
- 18 F
161
- BH2 -1
162
- Ca +2
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
models/finetuned/freesolv/model.pt DELETED
@@ -1,3 +0,0 @@
1
- version https://git-lfs.github.com/spec/v1
2
- oid sha256:bc69910d6e2d4ebf7f440f7737b3c3360533076dea6d985b22f8882bc795237a
3
- size 1022843005
 
 
 
 
models/finetuned/freesolv/special_tokens_map.json DELETED
@@ -1,51 +0,0 @@
1
- {
2
- "bos_token": {
3
- "content": "<s>",
4
- "lstrip": false,
5
- "normalized": true,
6
- "rstrip": false,
7
- "single_word": false
8
- },
9
- "cls_token": {
10
- "content": "<s>",
11
- "lstrip": false,
12
- "normalized": true,
13
- "rstrip": false,
14
- "single_word": false
15
- },
16
- "eos_token": {
17
- "content": "</s>",
18
- "lstrip": false,
19
- "normalized": true,
20
- "rstrip": false,
21
- "single_word": false
22
- },
23
- "mask_token": {
24
- "content": "<mask>",
25
- "lstrip": true,
26
- "normalized": true,
27
- "rstrip": false,
28
- "single_word": false
29
- },
30
- "pad_token": {
31
- "content": "<pad>",
32
- "lstrip": false,
33
- "normalized": true,
34
- "rstrip": false,
35
- "single_word": false
36
- },
37
- "sep_token": {
38
- "content": "</s>",
39
- "lstrip": false,
40
- "normalized": true,
41
- "rstrip": false,
42
- "single_word": false
43
- },
44
- "unk_token": {
45
- "content": "<unk>",
46
- "lstrip": false,
47
- "normalized": true,
48
- "rstrip": false,
49
- "single_word": false
50
- }
51
- }
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
models/finetuned/freesolv/tokenizer.json DELETED
@@ -1,473 +0,0 @@
1
- {
2
- "version": "1.0",
3
- "truncation": {
4
- "direction": "Right",
5
- "max_length": 128,
6
- "strategy": "LongestFirst",
7
- "stride": 0
8
- },
9
- "padding": {
10
- "strategy": {
11
- "Fixed": 128
12
- },
13
- "direction": "Right",
14
- "pad_to_multiple_of": null,
15
- "pad_id": 3,
16
- "pad_type_id": 0,
17
- "pad_token": "<pad>"
18
- },
19
- "added_tokens": [
20
- {
21
- "id": 0,
22
- "content": "<unk>",
23
- "single_word": false,
24
- "lstrip": false,
25
- "rstrip": false,
26
- "normalized": true,
27
- "special": true
28
- },
29
- {
30
- "id": 1,
31
- "content": "<s>",
32
- "single_word": false,
33
- "lstrip": false,
34
- "rstrip": false,
35
- "normalized": true,
36
- "special": true
37
- },
38
- {
39
- "id": 2,
40
- "content": "</s>",
41
- "single_word": false,
42
- "lstrip": false,
43
- "rstrip": false,
44
- "normalized": true,
45
- "special": true
46
- },
47
- {
48
- "id": 3,
49
- "content": "<pad>",
50
- "single_word": false,
51
- "lstrip": false,
52
- "rstrip": false,
53
- "normalized": true,
54
- "special": true
55
- },
56
- {
57
- "id": 4,
58
- "content": "<mask>",
59
- "single_word": false,
60
- "lstrip": true,
61
- "rstrip": false,
62
- "normalized": true,
63
- "special": true
64
- }
65
- ],
66
- "normalizer": null,
67
- "pre_tokenizer": {
68
- "type": "ByteLevel",
69
- "add_prefix_space": false,
70
- "trim_offsets": true,
71
- "use_regex": true
72
- },
73
- "post_processor": {
74
- "type": "RobertaProcessing",
75
- "sep": [
76
- "</s>",
77
- 2
78
- ],
79
- "cls": [
80
- "<s>",
81
- 1
82
- ],
83
- "trim_offsets": true,
84
- "add_prefix_space": false
85
- },
86
- "decoder": {
87
- "type": "ByteLevel",
88
- "add_prefix_space": true,
89
- "trim_offsets": true,
90
- "use_regex": true
91
- },
92
- "model": {
93
- "type": "BPE",
94
- "dropout": null,
95
- "unk_token": null,
96
- "continuing_subword_prefix": "",
97
- "end_of_word_suffix": "",
98
- "fuse_unk": false,
99
- "vocab": {
100
- "<unk>": 0,
101
- "<s>": 1,
102
- "</s>": 2,
103
- "<pad>": 3,
104
- "<mask>": 4,
105
- "\n": 5,
106
- "#": 6,
107
- "+": 7,
108
- "-": 8,
109
- ".": 9,
110
- "/": 10,
111
- "0": 11,
112
- "1": 12,
113
- "2": 13,
114
- "3": 14,
115
- "4": 15,
116
- "5": 16,
117
- "8": 17,
118
- "=": 18,
119
- "@": 19,
120
- "A": 20,
121
- "B": 21,
122
- "C": 22,
123
- "F": 23,
124
- "H": 24,
125
- "I": 25,
126
- "K": 26,
127
- "L": 27,
128
- "M": 28,
129
- "N": 29,
130
- "O": 30,
131
- "P": 31,
132
- "R": 32,
133
- "S": 33,
134
- "T": 34,
135
- "Z": 35,
136
- "\\": 36,
137
- "a": 37,
138
- "c": 38,
139
- "e": 39,
140
- "g": 40,
141
- "h": 41,
142
- "i": 42,
143
- "l": 43,
144
- "n": 44,
145
- "r": 45,
146
- "s": 46,
147
- "Br": 47,
148
- "an": 48,
149
- "ch": 49,
150
- "Bran": 50,
151
- "Branch": 51,
152
- "Branch1": 52,
153
- "=C": 53,
154
- "Ri": 54,
155
- "ng": 55,
156
- "Ring": 56,
157
- "Ring1": 57,
158
- "=Branch1": 58,
159
- "Branch2": 59,
160
- "=O": 60,
161
- "Ring2": 61,
162
- "H1": 62,
163
- "C@": 63,
164
- "=N": 64,
165
- "#Branch1": 65,
166
- "C@@": 66,
167
- "=Branch2": 67,
168
- "C@H1": 68,
169
- "C@@H1": 69,
170
- "#Branch2": 70,
171
- "Cl": 71,
172
- "#C": 72,
173
- "/C": 73,
174
- "NH1": 74,
175
- "+1": 75,
176
- "-1": 76,
177
- "=Ring1": 77,
178
- "O-1": 78,
179
- "N+1": 79,
180
- "\\C": 80,
181
- "/N": 81,
182
- "#N": 82,
183
- "=Ring2": 83,
184
- "=S": 84,
185
- "=N+1": 85,
186
- "Na": 86,
187
- "Na+1": 87,
188
- "\\N": 88,
189
- "S+1": 89,
190
- "/O": 90,
191
- "\\S": 91,
192
- "\\O": 92,
193
- "Br-1": 93,
194
- "I-1": 94,
195
- "Cl-1": 95,
196
- "/C@H1": 96,
197
- "Branch3": 97,
198
- "/C@@H1": 98,
199
- "=P": 99,
200
- "/S": 100,
201
- "=N-1": 101,
202
- "Si": 102,
203
- "K+1": 103,
204
- "N-1": 104,
205
- "Se": 105,
206
- "Li": 106,
207
- "Li+1": 107,
208
- "+3": 108,
209
- "Cl+3": 109,
210
- "\\C@H1": 110,
211
- "Ring3": 111,
212
- "\\C@@H1": 112,
213
- "/N+1": 113,
214
- "/P": 114,
215
- "\\F": 115,
216
- "P@": 116,
217
- "2H": 117,
218
- "PH1": 118,
219
- "/Br": 119,
220
- "N@": 120,
221
- "P+1": 121,
222
- "/Cl": 122,
223
- "\\NH1": 123,
224
- "\\Br": 124,
225
- "@+1": 125,
226
- "/I": 126,
227
- "/C@": 127,
228
- "Te": 128,
229
- "\\N+1": 129,
230
- "P@@": 130,
231
- "12": 131,
232
- "5I": 132,
233
- "\\O-1": 133,
234
- "125I": 134,
235
- "/F": 135,
236
- "#N+1": 136,
237
- "\\Cl": 137,
238
- "N@+1": 138,
239
- "\\I": 139,
240
- "-/": 140,
241
- "/C@@": 141,
242
- "N@@": 142,
243
- "N@@+1": 143,
244
- "-/Ring2": 144,
245
- "-\\": 145,
246
- "14": 146,
247
- "B-1": 147,
248
- "C-1": 148,
249
- "S@+1": 149,
250
- "14C": 150,
251
- "H2": 151,
252
- "H4": 152,
253
- "I+1": 153,
254
- "S-1": 154,
255
- "\\P": 155,
256
- "=S+1": 156,
257
- "=P@": 157,
258
- "SiH4": 158,
259
- "+2": 159,
260
- "3H": 160,
261
- "@@+1": 161,
262
- "Ag": 162,
263
- "C+1": 163,
264
- "S@@+1": 164,
265
- "Cl+1": 165,
266
- "=Se": 166,
267
- "-\\Ring1": 167,
268
- "H0": 168,
269
- "OH0": 169,
270
- "11": 170,
271
- "=Branch3": 171,
272
- "=Te": 172,
273
- "Mg": 173,
274
- "O+1": 174,
275
- "Zn": 175,
276
- "\\C@": 176,
277
- "\\S+1": 177,
278
- "H1-1": 178,
279
- "SeH1": 179,
280
- "P@+1": 180,
281
- "-\\Ring2": 181,
282
- "11C": 182,
283
- "=Te+1": 183,
284
- "Zn+2": 184,
285
- "/NH1": 185,
286
- "18": 186,
287
- "As": 187,
288
- "BH2": 188,
289
- "BH1-1": 189,
290
- "Ca": 190,
291
- "H3": 191,
292
- "OH1-1": 192,
293
- "SH2": 193,
294
- "=O+1": 194,
295
- "Se+1": 195,
296
- "TeH2": 196,
297
- "125IH1": 197,
298
- "-/Ring1": 198,
299
- "14CH2": 199,
300
- "Ag+1": 200,
301
- "=Se+1": 201,
302
- "MgH2": 202,
303
- "Mg+2": 203,
304
- "11CH3": 204,
305
- "18F": 205,
306
- "BH2-1": 206,
307
- "Ca+2": 207
308
- },
309
- "merges": [
310
- "B r",
311
- "a n",
312
- "c h",
313
- "Br an",
314
- "Bran ch",
315
- "Branch 1",
316
- "= C",
317
- "R i",
318
- "n g",
319
- "Ri ng",
320
- "Ring 1",
321
- "= Branch1",
322
- "Branch 2",
323
- "= O",
324
- "Ring 2",
325
- "H 1",
326
- "C @",
327
- "= N",
328
- "# Branch1",
329
- "C@ @",
330
- "= Branch2",
331
- "C@ H1",
332
- "C@@ H1",
333
- "# Branch2",
334
- "C l",
335
- "# C",
336
- "/ C",
337
- "N H1",
338
- "+ 1",
339
- "- 1",
340
- "= Ring1",
341
- "O -1",
342
- "N +1",
343
- "\\ C",
344
- "/ N",
345
- "# N",
346
- "= Ring2",
347
- "= S",
348
- "=N +1",
349
- "N a",
350
- "Na +1",
351
- "\\ N",
352
- "S +1",
353
- "/ O",
354
- "\\ S",
355
- "\\ O",
356
- "Br -1",
357
- "I -1",
358
- "Cl -1",
359
- "/ C@H1",
360
- "Branch 3",
361
- "/ C@@H1",
362
- "= P",
363
- "/ S",
364
- "=N -1",
365
- "S i",
366
- "K +1",
367
- "N -1",
368
- "S e",
369
- "L i",
370
- "Li +1",
371
- "+ 3",
372
- "Cl +3",
373
- "\\ C@H1",
374
- "Ring 3",
375
- "\\ C@@H1",
376
- "/ N+1",
377
- "/ P",
378
- "\\ F",
379
- "P @",
380
- "2 H",
381
- "P H1",
382
- "/ Br",
383
- "N @",
384
- "P +1",
385
- "/ Cl",
386
- "\\ NH1",
387
- "\\ Br",
388
- "@ +1",
389
- "/ I",
390
- "/ C@",
391
- "T e",
392
- "\\ N+1",
393
- "P@ @",
394
- "1 2",
395
- "5 I",
396
- "\\ O-1",
397
- "12 5I",
398
- "/ F",
399
- "# N+1",
400
- "\\ Cl",
401
- "N@ +1",
402
- "\\ I",
403
- "- /",
404
- "/ C@@",
405
- "N@ @",
406
- "N@ @+1",
407
- "-/ Ring2",
408
- "- \\",
409
- "1 4",
410
- "B -1",
411
- "C -1",
412
- "S @+1",
413
- "14 C",
414
- "H 2",
415
- "H 4",
416
- "I +1",
417
- "S -1",
418
- "\\ P",
419
- "=S +1",
420
- "=P @",
421
- "Si H4",
422
- "+ 2",
423
- "3 H",
424
- "@ @+1",
425
- "A g",
426
- "C +1",
427
- "S @@+1",
428
- "Cl +1",
429
- "=S e",
430
- "-\\ Ring1",
431
- "H 0",
432
- "O H0",
433
- "1 1",
434
- "= Branch3",
435
- "= Te",
436
- "M g",
437
- "O +1",
438
- "Z n",
439
- "\\ C@",
440
- "\\ S+1",
441
- "H1 -1",
442
- "Se H1",
443
- "P@ +1",
444
- "-\\ Ring2",
445
- "11 C",
446
- "=Te +1",
447
- "Zn +2",
448
- "/ NH1",
449
- "1 8",
450
- "A s",
451
- "B H2",
452
- "B H1-1",
453
- "C a",
454
- "H 3",
455
- "O H1-1",
456
- "S H2",
457
- "=O +1",
458
- "Se +1",
459
- "Te H2",
460
- "125I H1",
461
- "-/ Ring1",
462
- "14C H2",
463
- "Ag +1",
464
- "=Se +1",
465
- "Mg H2",
466
- "Mg +2",
467
- "11C H3",
468
- "18 F",
469
- "BH2 -1",
470
- "Ca +2"
471
- ]
472
- }
473
- }
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
models/finetuned/freesolv/tokenizer_config.json DELETED
@@ -1,59 +0,0 @@
1
- {
2
- "add_prefix_space": false,
3
- "added_tokens_decoder": {
4
- "0": {
5
- "content": "<unk>",
6
- "lstrip": false,
7
- "normalized": true,
8
- "rstrip": false,
9
- "single_word": false,
10
- "special": true
11
- },
12
- "1": {
13
- "content": "<s>",
14
- "lstrip": false,
15
- "normalized": true,
16
- "rstrip": false,
17
- "single_word": false,
18
- "special": true
19
- },
20
- "2": {
21
- "content": "</s>",
22
- "lstrip": false,
23
- "normalized": true,
24
- "rstrip": false,
25
- "single_word": false,
26
- "special": true
27
- },
28
- "3": {
29
- "content": "<pad>",
30
- "lstrip": false,
31
- "normalized": true,
32
- "rstrip": false,
33
- "single_word": false,
34
- "special": true
35
- },
36
- "4": {
37
- "content": "<mask>",
38
- "lstrip": true,
39
- "normalized": true,
40
- "rstrip": false,
41
- "single_word": false,
42
- "special": true
43
- }
44
- },
45
- "bos_token": "<s>",
46
- "clean_up_tokenization_spaces": true,
47
- "cls_token": "<s>",
48
- "eos_token": "</s>",
49
- "errors": "replace",
50
- "mask_token": "<mask>",
51
- "model_max_length": 1000000000000000019884624838656,
52
- "name_or_path": "data/epoch_267/hf",
53
- "pad_token": "<pad>",
54
- "sep_token": "</s>",
55
- "special_tokens_map_file": "data/epoch_267/hf/special_tokens_map.json",
56
- "tokenizer_class": "RobertaTokenizer",
57
- "trim_offsets": true,
58
- "unk_token": "<unk>"
59
- }
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
models/finetuned/freesolv/vocab.json DELETED
@@ -1 +0,0 @@
1
- {"<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,"8":17,"=":18,"@":19,"A":20,"B":21,"C":22,"F":23,"H":24,"I":25,"K":26,"L":27,"M":28,"N":29,"O":30,"P":31,"R":32,"S":33,"T":34,"Z":35,"\\":36,"a":37,"c":38,"e":39,"g":40,"h":41,"i":42,"l":43,"n":44,"r":45,"s":46,"Br":47,"an":48,"ch":49,"Bran":50,"Branch":51,"Branch1":52,"=C":53,"Ri":54,"ng":55,"Ring":56,"Ring1":57,"=Branch1":58,"Branch2":59,"=O":60,"Ring2":61,"H1":62,"C@":63,"=N":64,"#Branch1":65,"C@@":66,"=Branch2":67,"C@H1":68,"C@@H1":69,"#Branch2":70,"Cl":71,"#C":72,"/C":73,"NH1":74,"+1":75,"-1":76,"=Ring1":77,"O-1":78,"N+1":79,"\\C":80,"/N":81,"#N":82,"=Ring2":83,"=S":84,"=N+1":85,"Na":86,"Na+1":87,"\\N":88,"S+1":89,"/O":90,"\\S":91,"\\O":92,"Br-1":93,"I-1":94,"Cl-1":95,"/C@H1":96,"Branch3":97,"/C@@H1":98,"=P":99,"/S":100,"=N-1":101,"Si":102,"K+1":103,"N-1":104,"Se":105,"Li":106,"Li+1":107,"+3":108,"Cl+3":109,"\\C@H1":110,"Ring3":111,"\\C@@H1":112,"/N+1":113,"/P":114,"\\F":115,"P@":116,"2H":117,"PH1":118,"/Br":119,"N@":120,"P+1":121,"/Cl":122,"\\NH1":123,"\\Br":124,"@+1":125,"/I":126,"/C@":127,"Te":128,"\\N+1":129,"P@@":130,"12":131,"5I":132,"\\O-1":133,"125I":134,"/F":135,"#N+1":136,"\\Cl":137,"N@+1":138,"\\I":139,"-/":140,"/C@@":141,"N@@":142,"N@@+1":143,"-/Ring2":144,"-\\":145,"14":146,"B-1":147,"C-1":148,"S@+1":149,"14C":150,"H2":151,"H4":152,"I+1":153,"S-1":154,"\\P":155,"=S+1":156,"=P@":157,"SiH4":158,"+2":159,"3H":160,"@@+1":161,"Ag":162,"C+1":163,"S@@+1":164,"Cl+1":165,"=Se":166,"-\\Ring1":167,"H0":168,"OH0":169,"11":170,"=Branch3":171,"=Te":172,"Mg":173,"O+1":174,"Zn":175,"\\C@":176,"\\S+1":177,"H1-1":178,"SeH1":179,"P@+1":180,"-\\Ring2":181,"11C":182,"=Te+1":183,"Zn+2":184,"/NH1":185,"18":186,"As":187,"BH2":188,"BH1-1":189,"Ca":190,"H3":191,"OH1-1":192,"SH2":193,"=O+1":194,"Se+1":195,"TeH2":196,"125IH1":197,"-/Ring1":198,"14CH2":199,"Ag+1":200,"=Se+1":201,"MgH2":202,"Mg+2":203,"11CH3":204,"18F":205,"BH2-1":206,"Ca+2":207}
 
 
models/finetuned/hiv/config.json DELETED
@@ -1,27 +0,0 @@
1
- {
2
- "_name_or_path": "/home/erva/SELFormerMM/data/pretrained_multimodal_chembl36",
3
- "architectures": [
4
- "RobertaForMaskedLM"
5
- ],
6
- "attention_probs_dropout_prob": 0.1,
7
- "bos_token_id": 0,
8
- "classifier_dropout": null,
9
- "eos_token_id": 2,
10
- "hidden_act": "gelu",
11
- "hidden_dropout_prob": 0.1,
12
- "hidden_size": 768,
13
- "initializer_range": 0.02,
14
- "intermediate_size": 3072,
15
- "layer_norm_eps": 1e-12,
16
- "max_position_embeddings": 514,
17
- "model_type": "roberta",
18
- "num_attention_heads": 4,
19
- "num_hidden_layers": 12,
20
- "pad_token_id": 1,
21
- "position_embedding_type": "absolute",
22
- "torch_dtype": "float32",
23
- "transformers_version": "4.26.1",
24
- "type_vocab_size": 1,
25
- "use_cache": true,
26
- "vocab_size": 800
27
- }
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
models/finetuned/hiv/finetuning_optimized_config.json DELETED
@@ -1,24 +0,0 @@
1
- {
2
- "dataset_meta_csv": "data/finetuning_datasets/classification/hiv/hiv.csv",
3
- "dataset_embs_npz": "data/finetuning_datasets/classification/hiv/hiv_embs.npz",
4
- "use_scaffold": 1,
5
- "seed": 42,
6
- "train_frac": 0.8,
7
- "val_frac": 0.1,
8
- "test_frac": 0.1,
9
- "model_path": "HUBioDataLab/SELFormer",
10
- "tokenizer_path": "HUBioDataLab/SELFormer",
11
- "pretrained_multimodal_dir": "data/models/SELFormerMM",
12
- "task_type": "binary",
13
- "label_column": "HIV_active",
14
- "num_labels": 2,
15
- "batch_size": 16,
16
- "max_len": 128,
17
- "epochs": 50,
18
- "backbone_lr": 5e-5,
19
- "head_lr": 5e-5,
20
- "weight_decay": 0.0,
21
- "checkpoint_every": 25,
22
- "test_eval_every": 0,
23
- "save_dir": "data/models/finetuned/hiv"
24
- }
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
models/finetuned/hiv/merges.txt DELETED
@@ -1,378 +0,0 @@
1
- #version: 0.2 - Trained by `huggingface/tokenizers`
2
- B r
3
- a n
4
- c h
5
- Br an
6
- Bran ch
7
- Branch 1
8
- = C
9
- R i
10
- n g
11
- Ri ng
12
- Ring 1
13
- = Branch1
14
- Branch 2
15
- = O
16
- Ring 2
17
- H 1
18
- C @
19
- = N
20
- # Branch1
21
- C@ @
22
- = Branch2
23
- C@ H1
24
- C@@ H1
25
- # Branch2
26
- # C
27
- C l
28
- / C
29
- N H1
30
- = Ring1
31
- + 1
32
- - 1
33
- O -1
34
- N +1
35
- \ C
36
- # N
37
- / N
38
- = Ring2
39
- = S
40
- =N +1
41
- \ N
42
- N a
43
- Na +1
44
- / O
45
- \ O
46
- Br -1
47
- Branch 3
48
- \ S
49
- S +1
50
- Cl -1
51
- I -1
52
- / C@@H1
53
- S i
54
- / C@H1
55
- / S
56
- =N -1
57
- S e
58
- = P
59
- N -1
60
- Ring 3
61
- 2 H
62
- P +1
63
- K +1
64
- \ C@@H1
65
- \ C@H1
66
- / N+1
67
- @ @
68
- C -1
69
- # N+1
70
- B -1
71
- + 3
72
- Cl +3
73
- \ NH1
74
- L i
75
- Li +1
76
- P H1
77
- 1 8
78
- 18 F
79
- @ +1
80
- 3 H
81
- P @@
82
- H 0
83
- O H0
84
- 1 2
85
- P @
86
- + 2
87
- @@ +1
88
- S -1
89
- / Br
90
- - /
91
- \ Cl
92
- -/ Ring2
93
- \ O-1
94
- 1 1
95
- 5 I
96
- 12 5I
97
- 11 C
98
- H 3
99
- \ N+1
100
- - \
101
- / C@@
102
- S @+1
103
- A s
104
- / Cl
105
- 11C H3
106
- =S e
107
- S @@+1
108
- N @+1
109
- 1 4
110
- -\ Ring2
111
- 14 C
112
- \ F
113
- / C@
114
- T e
115
- H 2
116
- H1 -1
117
- =O +1
118
- N @@+1
119
- C +1
120
- =S +1
121
- Z n
122
- / P
123
- a +2
124
- / I
125
- O H1-1
126
- C a+2
127
- \ Br
128
- M g
129
- Zn +2
130
- A l
131
- / F
132
- Mg +2
133
- 12 3
134
- 123 I
135
- 1 3
136
- I +1
137
- / O-1
138
- -\ Ring1
139
- B H2
140
- BH2 -1
141
- \ I
142
- / NH1
143
- O +1
144
- 13 1
145
- 131 I
146
- = 14C
147
- / S+1
148
- = Ring3
149
- \ C@@
150
- H2 +1
151
- \ C@
152
- A g
153
- = As
154
- =Se +1
155
- N H2+1
156
- Se H1
157
- -/ Ring1
158
- = Te
159
- Al +3
160
- Na H1
161
- =Te +1
162
- NH1 +1
163
- Ag +1
164
- H1 +1
165
- NH1 -1
166
- \ P
167
- 14C H2
168
- 13 C
169
- 14C H1
170
- = 11C
171
- S @@
172
- =P @@
173
- Si H2
174
- H3 -1
175
- 14C H3
176
- B H3-1
177
- S @
178
- =14C H1
179
- =P H1
180
- =P @
181
- =N H1+1
182
- \S +1
183
- 12 4
184
- C H1-1
185
- S r
186
- =S i
187
- 124 I
188
- Sr +2
189
- #C -1
190
- /C -1
191
- N @
192
- /N -1
193
- 13C H1
194
- / B
195
- 1 9
196
- B a+2
197
- H 4
198
- S H1+1
199
- Se +1
200
- 19 F
201
- / 125I
202
- P @+1
203
- R b
204
- Cl +1
205
- Si H4
206
- Rb +1
207
- = Branch3
208
- N @@
209
- As +1
210
- / Si
211
- B H1-1
212
- S H1
213
- / 123I
214
- 3 2
215
- = Mg
216
- H +1
217
- \ B
218
- Si H1
219
- P@@ +1
220
- - 2
221
- 1 5
222
- 1 7
223
- 3 5
224
- = 13CH1
225
- C s
226
- =N H2+1
227
- =S H1
228
- Mg H2
229
- 32 P
230
- 17 F
231
- 35 S
232
- Cs +1
233
- # 11C
234
- / 131I
235
- B i
236
- \ 125I
237
- =S @@
238
- \S -1
239
- 6 Br
240
- 7 I
241
- 7 6Br
242
- = B
243
- e H1
244
- \N -1
245
- 18 O
246
- 12 7I
247
- 11C H2
248
- 14 C@@H1
249
- Te H2
250
- 15 NH1
251
- Bi +3
252
- / P+1
253
- / 13C
254
- / 13CH1
255
- 0 B
256
- 1 0B
257
- = Al
258
- = 18O
259
- B H0
260
- F -1
261
- N H3
262
- S -2
263
- Br +2
264
- Cl +2
265
- \S i
266
- /S -1
267
- =P H2
268
- 14 C@H1
269
- NH3 +1
270
- # 14C
271
- # O+1
272
- - 3
273
- 2 2
274
- 4 H
275
- 5 Se
276
- 5 Sr+2
277
- 7 5Se
278
- 8 5Sr+2
279
- = B-1
280
- = 13C
281
- @ -1
282
- B e
283
- B @@
284
- B @-1
285
- C a
286
- C H1
287
- I +3
288
- K H1
289
- O H1+1
290
- R a+2
291
- S H1-1
292
- \ PH1
293
- \ 123I
294
- =C a
295
- \C H1-1
296
- =S @
297
- \S eH1
298
- /S eH1
299
- Se -1
300
- Li H1
301
- 18F -1
302
- 125I H1
303
- 11C H1
304
- Te H1
305
- Zn +1
306
- Zn -2
307
- Al -3
308
- 13C H3
309
- 15 N
310
- Be +2
311
- B@@ -1
312
- # P
313
- # S
314
- - 4
315
- / PH1
316
- / P@@
317
- / As
318
- / 14C
319
- / 14CH1
320
- 2 K+1
321
- 2 Rb+1
322
- 3 Se
323
- 3 Ra+2
324
- 4 5
325
- 4 7
326
- 4 2K+1
327
- 5 I-1
328
- 7 3Se
329
- 8 9
330
- 8 2Rb+1
331
- = 32
332
- = 32P
333
- C H0
334
- C H2
335
- I +2
336
- N H0
337
- N H4
338
- O H1
339
- P H2+1
340
- S H0
341
- S H2
342
- \ 3H
343
- \ 11CH3
344
- \C -1
345
- \S e
346
- Si @
347
- Si -1
348
- Si H1-1
349
- Si H3-1
350
- /S e
351
- Se -2
352
- \NH1 -1
353
- 18F H1
354
- 12 5I-1
355
- 11 C@@H1
356
- 11 C-1
357
- As H1
358
- As -1
359
- 14 C@@
360
- Te -1
361
- Mg +1
362
- 123 I-1
363
- 123 Te
364
- 123I H1
365
- 13 5I
366
- 131 I-1
367
- Ag -4
368
- 124 I-1
369
- 76Br H1
370
- 18O H1
371
- 22 Na+1
372
- 22 3Ra+2
373
- Ca H2
374
- 45 Ca+2
375
- 47 Ca+2
376
- 89 Sr+2
377
- =32 PH1
378
- NH4 +1
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
models/finetuned/hiv/model.pt DELETED
@@ -1,3 +0,0 @@
1
- version https://git-lfs.github.com/spec/v1
2
- oid sha256:e256d9c1f34dc1d3521586b383cb58b01238a2d5229e4383cb7a0cae792fb7a8
3
- size 1022855293
 
 
 
 
models/finetuned/hiv/special_tokens_map.json DELETED
@@ -1,51 +0,0 @@
1
- {
2
- "bos_token": {
3
- "content": "<s>",
4
- "lstrip": false,
5
- "normalized": true,
6
- "rstrip": false,
7
- "single_word": false
8
- },
9
- "cls_token": {
10
- "content": "<s>",
11
- "lstrip": false,
12
- "normalized": true,
13
- "rstrip": false,
14
- "single_word": false
15
- },
16
- "eos_token": {
17
- "content": "</s>",
18
- "lstrip": false,
19
- "normalized": true,
20
- "rstrip": false,
21
- "single_word": false
22
- },
23
- "mask_token": {
24
- "content": "<mask>",
25
- "lstrip": true,
26
- "normalized": true,
27
- "rstrip": false,
28
- "single_word": false
29
- },
30
- "pad_token": {
31
- "content": "<pad>",
32
- "lstrip": false,
33
- "normalized": true,
34
- "rstrip": false,
35
- "single_word": false
36
- },
37
- "sep_token": {
38
- "content": "</s>",
39
- "lstrip": false,
40
- "normalized": true,
41
- "rstrip": false,
42
- "single_word": false
43
- },
44
- "unk_token": {
45
- "content": "<unk>",
46
- "lstrip": false,
47
- "normalized": true,
48
- "rstrip": false,
49
- "single_word": false
50
- }
51
- }
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
models/finetuned/hiv/tokenizer.json DELETED
@@ -1,909 +0,0 @@
1
- {
2
- "version": "1.0",
3
- "truncation": {
4
- "direction": "Right",
5
- "max_length": 128,
6
- "strategy": "LongestFirst",
7
- "stride": 0
8
- },
9
- "padding": {
10
- "strategy": {
11
- "Fixed": 128
12
- },
13
- "direction": "Right",
14
- "pad_to_multiple_of": null,
15
- "pad_id": 3,
16
- "pad_type_id": 0,
17
- "pad_token": "<pad>"
18
- },
19
- "added_tokens": [
20
- {
21
- "id": 0,
22
- "content": "<unk>",
23
- "single_word": false,
24
- "lstrip": false,
25
- "rstrip": false,
26
- "normalized": true,
27
- "special": true
28
- },
29
- {
30
- "id": 1,
31
- "content": "<s>",
32
- "single_word": false,
33
- "lstrip": false,
34
- "rstrip": false,
35
- "normalized": true,
36
- "special": true
37
- },
38
- {
39
- "id": 2,
40
- "content": "</s>",
41
- "single_word": false,
42
- "lstrip": false,
43
- "rstrip": false,
44
- "normalized": true,
45
- "special": true
46
- },
47
- {
48
- "id": 3,
49
- "content": "<pad>",
50
- "single_word": false,
51
- "lstrip": false,
52
- "rstrip": false,
53
- "normalized": true,
54
- "special": true
55
- },
56
- {
57
- "id": 4,
58
- "content": "<mask>",
59
- "single_word": false,
60
- "lstrip": true,
61
- "rstrip": false,
62
- "normalized": true,
63
- "special": true
64
- }
65
- ],
66
- "normalizer": null,
67
- "pre_tokenizer": {
68
- "type": "ByteLevel",
69
- "add_prefix_space": false,
70
- "trim_offsets": true,
71
- "use_regex": true
72
- },
73
- "post_processor": {
74
- "type": "RobertaProcessing",
75
- "sep": [
76
- "</s>",
77
- 2
78
- ],
79
- "cls": [
80
- "<s>",
81
- 1
82
- ],
83
- "trim_offsets": true,
84
- "add_prefix_space": false
85
- },
86
- "decoder": {
87
- "type": "ByteLevel",
88
- "add_prefix_space": true,
89
- "trim_offsets": true,
90
- "use_regex": true
91
- },
92
- "model": {
93
- "type": "BPE",
94
- "dropout": null,
95
- "unk_token": null,
96
- "continuing_subword_prefix": "",
97
- "end_of_word_suffix": "",
98
- "fuse_unk": false,
99
- "vocab": {
100
- "<unk>": 0,
101
- "<s>": 1,
102
- "</s>": 2,
103
- "<pad>": 3,
104
- "<mask>": 4,
105
- "\n": 5,
106
- "#": 6,
107
- "+": 7,
108
- "-": 8,
109
- ".": 9,
110
- "/": 10,
111
- "0": 11,
112
- "1": 12,
113
- "2": 13,
114
- "3": 14,
115
- "4": 15,
116
- "5": 16,
117
- "6": 17,
118
- "7": 18,
119
- "8": 19,
120
- "9": 20,
121
- "=": 21,
122
- "@": 22,
123
- "A": 23,
124
- "B": 24,
125
- "C": 25,
126
- "F": 26,
127
- "H": 27,
128
- "I": 28,
129
- "K": 29,
130
- "L": 30,
131
- "M": 31,
132
- "N": 32,
133
- "O": 33,
134
- "P": 34,
135
- "R": 35,
136
- "S": 36,
137
- "T": 37,
138
- "Z": 38,
139
- "\\": 39,
140
- "a": 40,
141
- "b": 41,
142
- "c": 42,
143
- "e": 43,
144
- "g": 44,
145
- "h": 45,
146
- "i": 46,
147
- "l": 47,
148
- "n": 48,
149
- "r": 49,
150
- "s": 50,
151
- "Br": 51,
152
- "an": 52,
153
- "ch": 53,
154
- "Bran": 54,
155
- "Branch": 55,
156
- "Branch1": 56,
157
- "=C": 57,
158
- "Ri": 58,
159
- "ng": 59,
160
- "Ring": 60,
161
- "Ring1": 61,
162
- "=Branch1": 62,
163
- "Branch2": 63,
164
- "=O": 64,
165
- "Ring2": 65,
166
- "H1": 66,
167
- "C@": 67,
168
- "=N": 68,
169
- "#Branch1": 69,
170
- "C@@": 70,
171
- "=Branch2": 71,
172
- "C@H1": 72,
173
- "C@@H1": 73,
174
- "#Branch2": 74,
175
- "#C": 75,
176
- "Cl": 76,
177
- "/C": 77,
178
- "NH1": 78,
179
- "=Ring1": 79,
180
- "+1": 80,
181
- "-1": 81,
182
- "O-1": 82,
183
- "N+1": 83,
184
- "\\C": 84,
185
- "#N": 85,
186
- "/N": 86,
187
- "=Ring2": 87,
188
- "=S": 88,
189
- "=N+1": 89,
190
- "\\N": 90,
191
- "Na": 91,
192
- "Na+1": 92,
193
- "/O": 93,
194
- "\\O": 94,
195
- "Br-1": 95,
196
- "Branch3": 96,
197
- "\\S": 97,
198
- "S+1": 98,
199
- "Cl-1": 99,
200
- "I-1": 100,
201
- "/C@@H1": 101,
202
- "Si": 102,
203
- "/C@H1": 103,
204
- "/S": 104,
205
- "=N-1": 105,
206
- "Se": 106,
207
- "=P": 107,
208
- "N-1": 108,
209
- "Ring3": 109,
210
- "2H": 110,
211
- "P+1": 111,
212
- "K+1": 112,
213
- "\\C@@H1": 113,
214
- "\\C@H1": 114,
215
- "/N+1": 115,
216
- "@@": 116,
217
- "C-1": 117,
218
- "#N+1": 118,
219
- "B-1": 119,
220
- "+3": 120,
221
- "Cl+3": 121,
222
- "\\NH1": 122,
223
- "Li": 123,
224
- "Li+1": 124,
225
- "PH1": 125,
226
- "18": 126,
227
- "18F": 127,
228
- "@+1": 128,
229
- "3H": 129,
230
- "P@@": 130,
231
- "H0": 131,
232
- "OH0": 132,
233
- "12": 133,
234
- "P@": 134,
235
- "+2": 135,
236
- "@@+1": 136,
237
- "S-1": 137,
238
- "/Br": 138,
239
- "-/": 139,
240
- "\\Cl": 140,
241
- "-/Ring2": 141,
242
- "\\O-1": 142,
243
- "11": 143,
244
- "5I": 144,
245
- "125I": 145,
246
- "11C": 146,
247
- "H3": 147,
248
- "\\N+1": 148,
249
- "-\\": 149,
250
- "/C@@": 150,
251
- "S@+1": 151,
252
- "As": 152,
253
- "/Cl": 153,
254
- "11CH3": 154,
255
- "=Se": 155,
256
- "S@@+1": 156,
257
- "N@+1": 157,
258
- "14": 158,
259
- "-\\Ring2": 159,
260
- "14C": 160,
261
- "\\F": 161,
262
- "/C@": 162,
263
- "Te": 163,
264
- "H2": 164,
265
- "H1-1": 165,
266
- "=O+1": 166,
267
- "N@@+1": 167,
268
- "C+1": 168,
269
- "=S+1": 169,
270
- "Zn": 170,
271
- "/P": 171,
272
- "a+2": 172,
273
- "/I": 173,
274
- "OH1-1": 174,
275
- "Ca+2": 175,
276
- "\\Br": 176,
277
- "Mg": 177,
278
- "Zn+2": 178,
279
- "Al": 179,
280
- "/F": 180,
281
- "Mg+2": 181,
282
- "123": 182,
283
- "123I": 183,
284
- "13": 184,
285
- "I+1": 185,
286
- "/O-1": 186,
287
- "-\\Ring1": 187,
288
- "BH2": 188,
289
- "BH2-1": 189,
290
- "\\I": 190,
291
- "/NH1": 191,
292
- "O+1": 192,
293
- "131": 193,
294
- "131I": 194,
295
- "=14C": 195,
296
- "/S+1": 196,
297
- "=Ring3": 197,
298
- "\\C@@": 198,
299
- "H2+1": 199,
300
- "\\C@": 200,
301
- "Ag": 201,
302
- "=As": 202,
303
- "=Se+1": 203,
304
- "NH2+1": 204,
305
- "SeH1": 205,
306
- "-/Ring1": 206,
307
- "=Te": 207,
308
- "Al+3": 208,
309
- "NaH1": 209,
310
- "=Te+1": 210,
311
- "NH1+1": 211,
312
- "Ag+1": 212,
313
- "H1+1": 213,
314
- "NH1-1": 214,
315
- "\\P": 215,
316
- "14CH2": 216,
317
- "13C": 217,
318
- "14CH1": 218,
319
- "=11C": 219,
320
- "S@@": 220,
321
- "=P@@": 221,
322
- "SiH2": 222,
323
- "H3-1": 223,
324
- "14CH3": 224,
325
- "BH3-1": 225,
326
- "S@": 226,
327
- "=14CH1": 227,
328
- "=PH1": 228,
329
- "=P@": 229,
330
- "=NH1+1": 230,
331
- "\\S+1": 231,
332
- "124": 232,
333
- "CH1-1": 233,
334
- "Sr": 234,
335
- "=Si": 235,
336
- "124I": 236,
337
- "Sr+2": 237,
338
- "#C-1": 238,
339
- "/C-1": 239,
340
- "N@": 240,
341
- "/N-1": 241,
342
- "13CH1": 242,
343
- "/B": 243,
344
- "19": 244,
345
- "Ba+2": 245,
346
- "H4": 246,
347
- "SH1+1": 247,
348
- "Se+1": 248,
349
- "19F": 249,
350
- "/125I": 250,
351
- "P@+1": 251,
352
- "Rb": 252,
353
- "Cl+1": 253,
354
- "SiH4": 254,
355
- "Rb+1": 255,
356
- "=Branch3": 256,
357
- "N@@": 257,
358
- "As+1": 258,
359
- "/Si": 259,
360
- "BH1-1": 260,
361
- "SH1": 261,
362
- "/123I": 262,
363
- "32": 263,
364
- "=Mg": 264,
365
- "H+1": 265,
366
- "\\B": 266,
367
- "SiH1": 267,
368
- "P@@+1": 268,
369
- "-2": 269,
370
- "15": 270,
371
- "17": 271,
372
- "35": 272,
373
- "=13CH1": 273,
374
- "Cs": 274,
375
- "=NH2+1": 275,
376
- "=SH1": 276,
377
- "MgH2": 277,
378
- "32P": 278,
379
- "17F": 279,
380
- "35S": 280,
381
- "Cs+1": 281,
382
- "#11C": 282,
383
- "/131I": 283,
384
- "Bi": 284,
385
- "\\125I": 285,
386
- "=S@@": 286,
387
- "\\S-1": 287,
388
- "6Br": 288,
389
- "7I": 289,
390
- "76Br": 290,
391
- "=B": 291,
392
- "eH1": 292,
393
- "\\N-1": 293,
394
- "18O": 294,
395
- "127I": 295,
396
- "11CH2": 296,
397
- "14C@@H1": 297,
398
- "TeH2": 298,
399
- "15NH1": 299,
400
- "Bi+3": 300,
401
- "/P+1": 301,
402
- "/13C": 302,
403
- "/13CH1": 303,
404
- "0B": 304,
405
- "10B": 305,
406
- "=Al": 306,
407
- "=18O": 307,
408
- "BH0": 308,
409
- "F-1": 309,
410
- "NH3": 310,
411
- "S-2": 311,
412
- "Br+2": 312,
413
- "Cl+2": 313,
414
- "\\Si": 314,
415
- "/S-1": 315,
416
- "=PH2": 316,
417
- "14C@H1": 317,
418
- "NH3+1": 318,
419
- "#14C": 319,
420
- "#O+1": 320,
421
- "-3": 321,
422
- "22": 322,
423
- "4H": 323,
424
- "5Se": 324,
425
- "5Sr+2": 325,
426
- "75Se": 326,
427
- "85Sr+2": 327,
428
- "=B-1": 328,
429
- "=13C": 329,
430
- "@-1": 330,
431
- "Be": 331,
432
- "B@@": 332,
433
- "B@-1": 333,
434
- "Ca": 334,
435
- "CH1": 335,
436
- "I+3": 336,
437
- "KH1": 337,
438
- "OH1+1": 338,
439
- "Ra+2": 339,
440
- "SH1-1": 340,
441
- "\\PH1": 341,
442
- "\\123I": 342,
443
- "=Ca": 343,
444
- "\\CH1-1": 344,
445
- "=S@": 345,
446
- "\\SeH1": 346,
447
- "/SeH1": 347,
448
- "Se-1": 348,
449
- "LiH1": 349,
450
- "18F-1": 350,
451
- "125IH1": 351,
452
- "11CH1": 352,
453
- "TeH1": 353,
454
- "Zn+1": 354,
455
- "Zn-2": 355,
456
- "Al-3": 356,
457
- "13CH3": 357,
458
- "15N": 358,
459
- "Be+2": 359,
460
- "B@@-1": 360,
461
- "#P": 361,
462
- "#S": 362,
463
- "-4": 363,
464
- "/PH1": 364,
465
- "/P@@": 365,
466
- "/As": 366,
467
- "/14C": 367,
468
- "/14CH1": 368,
469
- "2K+1": 369,
470
- "2Rb+1": 370,
471
- "3Se": 371,
472
- "3Ra+2": 372,
473
- "45": 373,
474
- "47": 374,
475
- "42K+1": 375,
476
- "5I-1": 376,
477
- "73Se": 377,
478
- "89": 378,
479
- "82Rb+1": 379,
480
- "=32": 380,
481
- "=32P": 381,
482
- "CH0": 382,
483
- "CH2": 383,
484
- "I+2": 384,
485
- "NH0": 385,
486
- "NH4": 386,
487
- "OH1": 387,
488
- "PH2+1": 388,
489
- "SH0": 389,
490
- "SH2": 390,
491
- "\\3H": 391,
492
- "\\11CH3": 392,
493
- "\\C-1": 393,
494
- "\\Se": 394,
495
- "Si@": 395,
496
- "Si-1": 396,
497
- "SiH1-1": 397,
498
- "SiH3-1": 398,
499
- "/Se": 399,
500
- "Se-2": 400,
501
- "\\NH1-1": 401,
502
- "18FH1": 402,
503
- "125I-1": 403,
504
- "11C@@H1": 404,
505
- "11C-1": 405,
506
- "AsH1": 406,
507
- "As-1": 407,
508
- "14C@@": 408,
509
- "Te-1": 409,
510
- "Mg+1": 410,
511
- "123I-1": 411,
512
- "123Te": 412,
513
- "123IH1": 413,
514
- "135I": 414,
515
- "131I-1": 415,
516
- "Ag-4": 416,
517
- "124I-1": 417,
518
- "76BrH1": 418,
519
- "18OH1": 419,
520
- "22Na+1": 420,
521
- "223Ra+2": 421,
522
- "CaH2": 422,
523
- "45Ca+2": 423,
524
- "47Ca+2": 424,
525
- "89Sr+2": 425,
526
- "=32PH1": 426,
527
- "NH4+1": 427
528
- },
529
- "merges": [
530
- "B r",
531
- "a n",
532
- "c h",
533
- "Br an",
534
- "Bran ch",
535
- "Branch 1",
536
- "= C",
537
- "R i",
538
- "n g",
539
- "Ri ng",
540
- "Ring 1",
541
- "= Branch1",
542
- "Branch 2",
543
- "= O",
544
- "Ring 2",
545
- "H 1",
546
- "C @",
547
- "= N",
548
- "# Branch1",
549
- "C@ @",
550
- "= Branch2",
551
- "C@ H1",
552
- "C@@ H1",
553
- "# Branch2",
554
- "# C",
555
- "C l",
556
- "/ C",
557
- "N H1",
558
- "= Ring1",
559
- "+ 1",
560
- "- 1",
561
- "O -1",
562
- "N +1",
563
- "\\ C",
564
- "# N",
565
- "/ N",
566
- "= Ring2",
567
- "= S",
568
- "=N +1",
569
- "\\ N",
570
- "N a",
571
- "Na +1",
572
- "/ O",
573
- "\\ O",
574
- "Br -1",
575
- "Branch 3",
576
- "\\ S",
577
- "S +1",
578
- "Cl -1",
579
- "I -1",
580
- "/ C@@H1",
581
- "S i",
582
- "/ C@H1",
583
- "/ S",
584
- "=N -1",
585
- "S e",
586
- "= P",
587
- "N -1",
588
- "Ring 3",
589
- "2 H",
590
- "P +1",
591
- "K +1",
592
- "\\ C@@H1",
593
- "\\ C@H1",
594
- "/ N+1",
595
- "@ @",
596
- "C -1",
597
- "# N+1",
598
- "B -1",
599
- "+ 3",
600
- "Cl +3",
601
- "\\ NH1",
602
- "L i",
603
- "Li +1",
604
- "P H1",
605
- "1 8",
606
- "18 F",
607
- "@ +1",
608
- "3 H",
609
- "P @@",
610
- "H 0",
611
- "O H0",
612
- "1 2",
613
- "P @",
614
- "+ 2",
615
- "@@ +1",
616
- "S -1",
617
- "/ Br",
618
- "- /",
619
- "\\ Cl",
620
- "-/ Ring2",
621
- "\\ O-1",
622
- "1 1",
623
- "5 I",
624
- "12 5I",
625
- "11 C",
626
- "H 3",
627
- "\\ N+1",
628
- "- \\",
629
- "/ C@@",
630
- "S @+1",
631
- "A s",
632
- "/ Cl",
633
- "11C H3",
634
- "=S e",
635
- "S @@+1",
636
- "N @+1",
637
- "1 4",
638
- "-\\ Ring2",
639
- "14 C",
640
- "\\ F",
641
- "/ C@",
642
- "T e",
643
- "H 2",
644
- "H1 -1",
645
- "=O +1",
646
- "N @@+1",
647
- "C +1",
648
- "=S +1",
649
- "Z n",
650
- "/ P",
651
- "a +2",
652
- "/ I",
653
- "O H1-1",
654
- "C a+2",
655
- "\\ Br",
656
- "M g",
657
- "Zn +2",
658
- "A l",
659
- "/ F",
660
- "Mg +2",
661
- "12 3",
662
- "123 I",
663
- "1 3",
664
- "I +1",
665
- "/ O-1",
666
- "-\\ Ring1",
667
- "B H2",
668
- "BH2 -1",
669
- "\\ I",
670
- "/ NH1",
671
- "O +1",
672
- "13 1",
673
- "131 I",
674
- "= 14C",
675
- "/ S+1",
676
- "= Ring3",
677
- "\\ C@@",
678
- "H2 +1",
679
- "\\ C@",
680
- "A g",
681
- "= As",
682
- "=Se +1",
683
- "N H2+1",
684
- "Se H1",
685
- "-/ Ring1",
686
- "= Te",
687
- "Al +3",
688
- "Na H1",
689
- "=Te +1",
690
- "NH1 +1",
691
- "Ag +1",
692
- "H1 +1",
693
- "NH1 -1",
694
- "\\ P",
695
- "14C H2",
696
- "13 C",
697
- "14C H1",
698
- "= 11C",
699
- "S @@",
700
- "=P @@",
701
- "Si H2",
702
- "H3 -1",
703
- "14C H3",
704
- "B H3-1",
705
- "S @",
706
- "=14C H1",
707
- "=P H1",
708
- "=P @",
709
- "=N H1+1",
710
- "\\S +1",
711
- "12 4",
712
- "C H1-1",
713
- "S r",
714
- "=S i",
715
- "124 I",
716
- "Sr +2",
717
- "#C -1",
718
- "/C -1",
719
- "N @",
720
- "/N -1",
721
- "13C H1",
722
- "/ B",
723
- "1 9",
724
- "B a+2",
725
- "H 4",
726
- "S H1+1",
727
- "Se +1",
728
- "19 F",
729
- "/ 125I",
730
- "P @+1",
731
- "R b",
732
- "Cl +1",
733
- "Si H4",
734
- "Rb +1",
735
- "= Branch3",
736
- "N @@",
737
- "As +1",
738
- "/ Si",
739
- "B H1-1",
740
- "S H1",
741
- "/ 123I",
742
- "3 2",
743
- "= Mg",
744
- "H +1",
745
- "\\ B",
746
- "Si H1",
747
- "P@@ +1",
748
- "- 2",
749
- "1 5",
750
- "1 7",
751
- "3 5",
752
- "= 13CH1",
753
- "C s",
754
- "=N H2+1",
755
- "=S H1",
756
- "Mg H2",
757
- "32 P",
758
- "17 F",
759
- "35 S",
760
- "Cs +1",
761
- "# 11C",
762
- "/ 131I",
763
- "B i",
764
- "\\ 125I",
765
- "=S @@",
766
- "\\S -1",
767
- "6 Br",
768
- "7 I",
769
- "7 6Br",
770
- "= B",
771
- "e H1",
772
- "\\N -1",
773
- "18 O",
774
- "12 7I",
775
- "11C H2",
776
- "14 C@@H1",
777
- "Te H2",
778
- "15 NH1",
779
- "Bi +3",
780
- "/ P+1",
781
- "/ 13C",
782
- "/ 13CH1",
783
- "0 B",
784
- "1 0B",
785
- "= Al",
786
- "= 18O",
787
- "B H0",
788
- "F -1",
789
- "N H3",
790
- "S -2",
791
- "Br +2",
792
- "Cl +2",
793
- "\\S i",
794
- "/S -1",
795
- "=P H2",
796
- "14 C@H1",
797
- "NH3 +1",
798
- "# 14C",
799
- "# O+1",
800
- "- 3",
801
- "2 2",
802
- "4 H",
803
- "5 Se",
804
- "5 Sr+2",
805
- "7 5Se",
806
- "8 5Sr+2",
807
- "= B-1",
808
- "= 13C",
809
- "@ -1",
810
- "B e",
811
- "B @@",
812
- "B @-1",
813
- "C a",
814
- "C H1",
815
- "I +3",
816
- "K H1",
817
- "O H1+1",
818
- "R a+2",
819
- "S H1-1",
820
- "\\ PH1",
821
- "\\ 123I",
822
- "=C a",
823
- "\\C H1-1",
824
- "=S @",
825
- "\\S eH1",
826
- "/S eH1",
827
- "Se -1",
828
- "Li H1",
829
- "18F -1",
830
- "125I H1",
831
- "11C H1",
832
- "Te H1",
833
- "Zn +1",
834
- "Zn -2",
835
- "Al -3",
836
- "13C H3",
837
- "15 N",
838
- "Be +2",
839
- "B@@ -1",
840
- "# P",
841
- "# S",
842
- "- 4",
843
- "/ PH1",
844
- "/ P@@",
845
- "/ As",
846
- "/ 14C",
847
- "/ 14CH1",
848
- "2 K+1",
849
- "2 Rb+1",
850
- "3 Se",
851
- "3 Ra+2",
852
- "4 5",
853
- "4 7",
854
- "4 2K+1",
855
- "5 I-1",
856
- "7 3Se",
857
- "8 9",
858
- "8 2Rb+1",
859
- "= 32",
860
- "= 32P",
861
- "C H0",
862
- "C H2",
863
- "I +2",
864
- "N H0",
865
- "N H4",
866
- "O H1",
867
- "P H2+1",
868
- "S H0",
869
- "S H2",
870
- "\\ 3H",
871
- "\\ 11CH3",
872
- "\\C -1",
873
- "\\S e",
874
- "Si @",
875
- "Si -1",
876
- "Si H1-1",
877
- "Si H3-1",
878
- "/S e",
879
- "Se -2",
880
- "\\NH1 -1",
881
- "18F H1",
882
- "12 5I-1",
883
- "11 C@@H1",
884
- "11 C-1",
885
- "As H1",
886
- "As -1",
887
- "14 C@@",
888
- "Te -1",
889
- "Mg +1",
890
- "123 I-1",
891
- "123 Te",
892
- "123I H1",
893
- "13 5I",
894
- "131 I-1",
895
- "Ag -4",
896
- "124 I-1",
897
- "76Br H1",
898
- "18O H1",
899
- "22 Na+1",
900
- "22 3Ra+2",
901
- "Ca H2",
902
- "45 Ca+2",
903
- "47 Ca+2",
904
- "89 Sr+2",
905
- "=32 PH1",
906
- "NH4 +1"
907
- ]
908
- }
909
- }
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
models/finetuned/hiv/tokenizer_config.json DELETED
@@ -1,65 +0,0 @@
1
- {
2
- "add_prefix_space": false,
3
- "bos_token": {
4
- "__type": "AddedToken",
5
- "content": "<s>",
6
- "lstrip": false,
7
- "normalized": true,
8
- "rstrip": false,
9
- "single_word": false
10
- },
11
- "cls_token": {
12
- "__type": "AddedToken",
13
- "content": "<s>",
14
- "lstrip": false,
15
- "normalized": true,
16
- "rstrip": false,
17
- "single_word": false
18
- },
19
- "eos_token": {
20
- "__type": "AddedToken",
21
- "content": "</s>",
22
- "lstrip": false,
23
- "normalized": true,
24
- "rstrip": false,
25
- "single_word": false
26
- },
27
- "errors": "replace",
28
- "mask_token": {
29
- "__type": "AddedToken",
30
- "content": "<mask>",
31
- "lstrip": true,
32
- "normalized": true,
33
- "rstrip": false,
34
- "single_word": false
35
- },
36
- "model_max_length": 1000000000000000019884624838656,
37
- "name_or_path": "/home/erva/SELFormerMM/data/pretrained_multimodal_chembl36",
38
- "pad_token": {
39
- "__type": "AddedToken",
40
- "content": "<pad>",
41
- "lstrip": false,
42
- "normalized": true,
43
- "rstrip": false,
44
- "single_word": false
45
- },
46
- "sep_token": {
47
- "__type": "AddedToken",
48
- "content": "</s>",
49
- "lstrip": false,
50
- "normalized": true,
51
- "rstrip": false,
52
- "single_word": false
53
- },
54
- "special_tokens_map_file": null,
55
- "tokenizer_class": "RobertaTokenizer",
56
- "trim_offsets": true,
57
- "unk_token": {
58
- "__type": "AddedToken",
59
- "content": "<unk>",
60
- "lstrip": false,
61
- "normalized": true,
62
- "rstrip": false,
63
- "single_word": false
64
- }
65
- }
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
models/finetuned/hiv/vocab.json DELETED
@@ -1 +0,0 @@
1
- {"<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,"=PH1":228,"=P@":229,"=NH1+1":230,"\\S+1":231,"124":232,"CH1-1":233,"Sr":234,"=Si":235,"124I":236,"Sr+2":237,"#C-1":238,"/C-1":239,"N@":240,"/N-1":241,"13CH1":242,"/B":243,"19":244,"Ba+2":245,"H4":246,"SH1+1":247,"Se+1":248,"19F":249,"/125I":250,"P@+1":251,"Rb":252,"Cl+1":253,"SiH4":254,"Rb+1":255,"=Branch3":256,"N@@":257,"As+1":258,"/Si":259,"BH1-1":260,"SH1":261,"/123I":262,"32":263,"=Mg":264,"H+1":265,"\\B":266,"SiH1":267,"P@@+1":268,"-2":269,"15":270,"17":271,"35":272,"=13CH1":273,"Cs":274,"=NH2+1":275,"=SH1":276,"MgH2":277,"32P":278,"17F":279,"35S":280,"Cs+1":281,"#11C":282,"/131I":283,"Bi":284,"\\125I":285,"=S@@":286,"\\S-1":287,"6Br":288,"7I":289,"76Br":290,"=B":291,"eH1":292,"\\N-1":293,"18O":294,"127I":295,"11CH2":296,"14C@@H1":297,"TeH2":298,"15NH1":299,"Bi+3":300,"/P+1":301,"/13C":302,"/13CH1":303,"0B":304,"10B":305,"=Al":306,"=18O":307,"BH0":308,"F-1":309,"NH3":310,"S-2":311,"Br+2":312,"Cl+2":313,"\\Si":314,"/S-1":315,"=PH2":316,"14C@H1":317,"NH3+1":318,"#14C":319,"#O+1":320,"-3":321,"22":322,"4H":323,"5Se":324,"5Sr+2":325,"75Se":326,"85Sr+2":327,"=B-1":328,"=13C":329,"@-1":330,"Be":331,"B@@":332,"B@-1":333,"Ca":334,"CH1":335,"I+3":336,"KH1":337,"OH1+1":338,"Ra+2":339,"SH1-1":340,"\\PH1":341,"\\123I":342,"=Ca":343,"\\CH1-1":344,"=S@":345,"\\SeH1":346,"/SeH1":347,"Se-1":348,"LiH1":349,"18F-1":350,"125IH1":351,"11CH1":352,"TeH1":353,"Zn+1":354,"Zn-2":355,"Al-3":356,"13CH3":357,"15N":358,"Be+2":359,"B@@-1":360,"#P":361,"#S":362,"-4":363,"/PH1":364,"/P@@":365,"/As":366,"/14C":367,"/14CH1":368,"2K+1":369,"2Rb+1":370,"3Se":371,"3Ra+2":372,"45":373,"47":374,"42K+1":375,"5I-1":376,"73Se":377,"89":378,"82Rb+1":379,"=32":380,"=32P":381,"CH0":382,"CH2":383,"I+2":384,"NH0":385,"NH4":386,"OH1":387,"PH2+1":388,"SH0":389,"SH2":390,"\\3H":391,"\\11CH3":392,"\\C-1":393,"\\Se":394,"Si@":395,"Si-1":396,"SiH1-1":397,"SiH3-1":398,"/Se":399,"Se-2":400,"\\NH1-1":401,"18FH1":402,"125I-1":403,"11C@@H1":404,"11C-1":405,"AsH1":406,"As-1":407,"14C@@":408,"Te-1":409,"Mg+1":410,"123I-1":411,"123Te":412,"123IH1":413,"135I":414,"131I-1":415,"Ag-4":416,"124I-1":417,"76BrH1":418,"18OH1":419,"22Na+1":420,"223Ra+2":421,"CaH2":422,"45Ca+2":423,"47Ca+2":424,"89Sr+2":425,"=32PH1":426,"NH4+1":427}
 
 
models/finetuned/lipo/config.json DELETED
@@ -1,28 +0,0 @@
1
- {
2
- "_name_or_path": "data/epoch_267/hf",
3
- "architectures": [
4
- "RobertaForMaskedLM"
5
- ],
6
- "attention_probs_dropout_prob": 0.1,
7
- "bos_token_id": 0,
8
- "classifier_dropout": null,
9
- "eos_token_id": 2,
10
- "hidden_act": "gelu",
11
- "hidden_dropout_prob": 0.1,
12
- "hidden_size": 768,
13
- "initializer_range": 0.02,
14
- "intermediate_size": 3072,
15
- "layer_norm_eps": 1e-12,
16
- "max_position_embeddings": 514,
17
- "model_type": "roberta",
18
- "num_attention_heads": 4,
19
- "num_hidden_layers": 12,
20
- "output_hidden_states": true,
21
- "pad_token_id": 1,
22
- "position_embedding_type": "absolute",
23
- "torch_dtype": "float32",
24
- "transformers_version": "4.26.1",
25
- "type_vocab_size": 1,
26
- "use_cache": true,
27
- "vocab_size": 800
28
- }
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
models/finetuned/lipo/finetuning_optimized_config.json DELETED
@@ -1,24 +0,0 @@
1
- {
2
- "dataset_meta_csv": "data/finetuning_datasets/regression/lipo/lipo.csv",
3
- "dataset_embs_npz": "data/finetuning_datasets/regression/lipo/lipo_embs.npz",
4
- "use_scaffold": 0,
5
- "seed": 42,
6
- "train_frac": 0.8,
7
- "val_frac": 0.1,
8
- "test_frac": 0.1,
9
- "model_path": "HUBioDataLab/SELFormer",
10
- "tokenizer_path": "HUBioDataLab/SELFormer",
11
- "pretrained_multimodal_dir": "data/models/SELFormerMM",
12
- "task_type": "regression",
13
- "label_column": "lipo",
14
- "num_labels": 1,
15
- "batch_size": 32,
16
- "max_len": 128,
17
- "epochs": 100,
18
- "backbone_lr": 5e-05,
19
- "head_lr": 5e-06,
20
- "weight_decay": 0.1,
21
- "checkpoint_every": 25,
22
- "test_eval_every": 0,
23
- "save_dir": "data/models/finetuned/lipo"
24
- }
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
models/finetuned/lipo/merges.txt DELETED
@@ -1,162 +0,0 @@
1
- #version: 0.2 - Trained by `huggingface/tokenizers`
2
- B r
3
- a n
4
- c h
5
- Br an
6
- Bran ch
7
- Branch 1
8
- = C
9
- R i
10
- n g
11
- Ri ng
12
- Ring 1
13
- = Branch1
14
- Branch 2
15
- = O
16
- Ring 2
17
- H 1
18
- C @
19
- = N
20
- # Branch1
21
- C@ @
22
- = Branch2
23
- C@ H1
24
- C@@ H1
25
- # Branch2
26
- C l
27
- # C
28
- / C
29
- N H1
30
- + 1
31
- - 1
32
- = Ring1
33
- O -1
34
- N +1
35
- \ C
36
- / N
37
- # N
38
- = Ring2
39
- = S
40
- =N +1
41
- N a
42
- Na +1
43
- \ N
44
- S +1
45
- / O
46
- \ S
47
- \ O
48
- Br -1
49
- I -1
50
- Cl -1
51
- / C@H1
52
- Branch 3
53
- / C@@H1
54
- = P
55
- / S
56
- =N -1
57
- S i
58
- K +1
59
- N -1
60
- S e
61
- L i
62
- Li +1
63
- + 3
64
- Cl +3
65
- \ C@H1
66
- Ring 3
67
- \ C@@H1
68
- / N+1
69
- / P
70
- \ F
71
- P @
72
- 2 H
73
- P H1
74
- / Br
75
- N @
76
- P +1
77
- / Cl
78
- \ NH1
79
- \ Br
80
- @ +1
81
- / I
82
- / C@
83
- T e
84
- \ N+1
85
- P@ @
86
- 1 2
87
- 5 I
88
- \ O-1
89
- 12 5I
90
- / F
91
- # N+1
92
- \ Cl
93
- N@ +1
94
- \ I
95
- - /
96
- / C@@
97
- N@ @
98
- N@ @+1
99
- -/ Ring2
100
- - \
101
- 1 4
102
- B -1
103
- C -1
104
- S @+1
105
- 14 C
106
- H 2
107
- H 4
108
- I +1
109
- S -1
110
- \ P
111
- =S +1
112
- =P @
113
- Si H4
114
- + 2
115
- 3 H
116
- @ @+1
117
- A g
118
- C +1
119
- S @@+1
120
- Cl +1
121
- =S e
122
- -\ Ring1
123
- H 0
124
- O H0
125
- 1 1
126
- = Branch3
127
- = Te
128
- M g
129
- O +1
130
- Z n
131
- \ C@
132
- \ S+1
133
- H1 -1
134
- Se H1
135
- P@ +1
136
- -\ Ring2
137
- 11 C
138
- =Te +1
139
- Zn +2
140
- / NH1
141
- 1 8
142
- A s
143
- B H2
144
- B H1-1
145
- C a
146
- H 3
147
- O H1-1
148
- S H2
149
- =O +1
150
- Se +1
151
- Te H2
152
- 125I H1
153
- -/ Ring1
154
- 14C H2
155
- Ag +1
156
- =Se +1
157
- Mg H2
158
- Mg +2
159
- 11C H3
160
- 18 F
161
- BH2 -1
162
- Ca +2
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
models/finetuned/lipo/model.pt DELETED
@@ -1,3 +0,0 @@
1
- version https://git-lfs.github.com/spec/v1
2
- oid sha256:1b92b270751c67da0e55692cd40d5d0aa33e73b669f41e5f1e920b4ca1e3735a
3
- size 1022843005
 
 
 
 
models/finetuned/lipo/special_tokens_map.json DELETED
@@ -1,51 +0,0 @@
1
- {
2
- "bos_token": {
3
- "content": "<s>",
4
- "lstrip": false,
5
- "normalized": true,
6
- "rstrip": false,
7
- "single_word": false
8
- },
9
- "cls_token": {
10
- "content": "<s>",
11
- "lstrip": false,
12
- "normalized": true,
13
- "rstrip": false,
14
- "single_word": false
15
- },
16
- "eos_token": {
17
- "content": "</s>",
18
- "lstrip": false,
19
- "normalized": true,
20
- "rstrip": false,
21
- "single_word": false
22
- },
23
- "mask_token": {
24
- "content": "<mask>",
25
- "lstrip": true,
26
- "normalized": true,
27
- "rstrip": false,
28
- "single_word": false
29
- },
30
- "pad_token": {
31
- "content": "<pad>",
32
- "lstrip": false,
33
- "normalized": true,
34
- "rstrip": false,
35
- "single_word": false
36
- },
37
- "sep_token": {
38
- "content": "</s>",
39
- "lstrip": false,
40
- "normalized": true,
41
- "rstrip": false,
42
- "single_word": false
43
- },
44
- "unk_token": {
45
- "content": "<unk>",
46
- "lstrip": false,
47
- "normalized": true,
48
- "rstrip": false,
49
- "single_word": false
50
- }
51
- }
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
models/finetuned/lipo/tokenizer.json DELETED
@@ -1,473 +0,0 @@
1
- {
2
- "version": "1.0",
3
- "truncation": {
4
- "direction": "Right",
5
- "max_length": 128,
6
- "strategy": "LongestFirst",
7
- "stride": 0
8
- },
9
- "padding": {
10
- "strategy": {
11
- "Fixed": 128
12
- },
13
- "direction": "Right",
14
- "pad_to_multiple_of": null,
15
- "pad_id": 3,
16
- "pad_type_id": 0,
17
- "pad_token": "<pad>"
18
- },
19
- "added_tokens": [
20
- {
21
- "id": 0,
22
- "content": "<unk>",
23
- "single_word": false,
24
- "lstrip": false,
25
- "rstrip": false,
26
- "normalized": true,
27
- "special": true
28
- },
29
- {
30
- "id": 1,
31
- "content": "<s>",
32
- "single_word": false,
33
- "lstrip": false,
34
- "rstrip": false,
35
- "normalized": true,
36
- "special": true
37
- },
38
- {
39
- "id": 2,
40
- "content": "</s>",
41
- "single_word": false,
42
- "lstrip": false,
43
- "rstrip": false,
44
- "normalized": true,
45
- "special": true
46
- },
47
- {
48
- "id": 3,
49
- "content": "<pad>",
50
- "single_word": false,
51
- "lstrip": false,
52
- "rstrip": false,
53
- "normalized": true,
54
- "special": true
55
- },
56
- {
57
- "id": 4,
58
- "content": "<mask>",
59
- "single_word": false,
60
- "lstrip": true,
61
- "rstrip": false,
62
- "normalized": true,
63
- "special": true
64
- }
65
- ],
66
- "normalizer": null,
67
- "pre_tokenizer": {
68
- "type": "ByteLevel",
69
- "add_prefix_space": false,
70
- "trim_offsets": true,
71
- "use_regex": true
72
- },
73
- "post_processor": {
74
- "type": "RobertaProcessing",
75
- "sep": [
76
- "</s>",
77
- 2
78
- ],
79
- "cls": [
80
- "<s>",
81
- 1
82
- ],
83
- "trim_offsets": true,
84
- "add_prefix_space": false
85
- },
86
- "decoder": {
87
- "type": "ByteLevel",
88
- "add_prefix_space": true,
89
- "trim_offsets": true,
90
- "use_regex": true
91
- },
92
- "model": {
93
- "type": "BPE",
94
- "dropout": null,
95
- "unk_token": null,
96
- "continuing_subword_prefix": "",
97
- "end_of_word_suffix": "",
98
- "fuse_unk": false,
99
- "vocab": {
100
- "<unk>": 0,
101
- "<s>": 1,
102
- "</s>": 2,
103
- "<pad>": 3,
104
- "<mask>": 4,
105
- "\n": 5,
106
- "#": 6,
107
- "+": 7,
108
- "-": 8,
109
- ".": 9,
110
- "/": 10,
111
- "0": 11,
112
- "1": 12,
113
- "2": 13,
114
- "3": 14,
115
- "4": 15,
116
- "5": 16,
117
- "8": 17,
118
- "=": 18,
119
- "@": 19,
120
- "A": 20,
121
- "B": 21,
122
- "C": 22,
123
- "F": 23,
124
- "H": 24,
125
- "I": 25,
126
- "K": 26,
127
- "L": 27,
128
- "M": 28,
129
- "N": 29,
130
- "O": 30,
131
- "P": 31,
132
- "R": 32,
133
- "S": 33,
134
- "T": 34,
135
- "Z": 35,
136
- "\\": 36,
137
- "a": 37,
138
- "c": 38,
139
- "e": 39,
140
- "g": 40,
141
- "h": 41,
142
- "i": 42,
143
- "l": 43,
144
- "n": 44,
145
- "r": 45,
146
- "s": 46,
147
- "Br": 47,
148
- "an": 48,
149
- "ch": 49,
150
- "Bran": 50,
151
- "Branch": 51,
152
- "Branch1": 52,
153
- "=C": 53,
154
- "Ri": 54,
155
- "ng": 55,
156
- "Ring": 56,
157
- "Ring1": 57,
158
- "=Branch1": 58,
159
- "Branch2": 59,
160
- "=O": 60,
161
- "Ring2": 61,
162
- "H1": 62,
163
- "C@": 63,
164
- "=N": 64,
165
- "#Branch1": 65,
166
- "C@@": 66,
167
- "=Branch2": 67,
168
- "C@H1": 68,
169
- "C@@H1": 69,
170
- "#Branch2": 70,
171
- "Cl": 71,
172
- "#C": 72,
173
- "/C": 73,
174
- "NH1": 74,
175
- "+1": 75,
176
- "-1": 76,
177
- "=Ring1": 77,
178
- "O-1": 78,
179
- "N+1": 79,
180
- "\\C": 80,
181
- "/N": 81,
182
- "#N": 82,
183
- "=Ring2": 83,
184
- "=S": 84,
185
- "=N+1": 85,
186
- "Na": 86,
187
- "Na+1": 87,
188
- "\\N": 88,
189
- "S+1": 89,
190
- "/O": 90,
191
- "\\S": 91,
192
- "\\O": 92,
193
- "Br-1": 93,
194
- "I-1": 94,
195
- "Cl-1": 95,
196
- "/C@H1": 96,
197
- "Branch3": 97,
198
- "/C@@H1": 98,
199
- "=P": 99,
200
- "/S": 100,
201
- "=N-1": 101,
202
- "Si": 102,
203
- "K+1": 103,
204
- "N-1": 104,
205
- "Se": 105,
206
- "Li": 106,
207
- "Li+1": 107,
208
- "+3": 108,
209
- "Cl+3": 109,
210
- "\\C@H1": 110,
211
- "Ring3": 111,
212
- "\\C@@H1": 112,
213
- "/N+1": 113,
214
- "/P": 114,
215
- "\\F": 115,
216
- "P@": 116,
217
- "2H": 117,
218
- "PH1": 118,
219
- "/Br": 119,
220
- "N@": 120,
221
- "P+1": 121,
222
- "/Cl": 122,
223
- "\\NH1": 123,
224
- "\\Br": 124,
225
- "@+1": 125,
226
- "/I": 126,
227
- "/C@": 127,
228
- "Te": 128,
229
- "\\N+1": 129,
230
- "P@@": 130,
231
- "12": 131,
232
- "5I": 132,
233
- "\\O-1": 133,
234
- "125I": 134,
235
- "/F": 135,
236
- "#N+1": 136,
237
- "\\Cl": 137,
238
- "N@+1": 138,
239
- "\\I": 139,
240
- "-/": 140,
241
- "/C@@": 141,
242
- "N@@": 142,
243
- "N@@+1": 143,
244
- "-/Ring2": 144,
245
- "-\\": 145,
246
- "14": 146,
247
- "B-1": 147,
248
- "C-1": 148,
249
- "S@+1": 149,
250
- "14C": 150,
251
- "H2": 151,
252
- "H4": 152,
253
- "I+1": 153,
254
- "S-1": 154,
255
- "\\P": 155,
256
- "=S+1": 156,
257
- "=P@": 157,
258
- "SiH4": 158,
259
- "+2": 159,
260
- "3H": 160,
261
- "@@+1": 161,
262
- "Ag": 162,
263
- "C+1": 163,
264
- "S@@+1": 164,
265
- "Cl+1": 165,
266
- "=Se": 166,
267
- "-\\Ring1": 167,
268
- "H0": 168,
269
- "OH0": 169,
270
- "11": 170,
271
- "=Branch3": 171,
272
- "=Te": 172,
273
- "Mg": 173,
274
- "O+1": 174,
275
- "Zn": 175,
276
- "\\C@": 176,
277
- "\\S+1": 177,
278
- "H1-1": 178,
279
- "SeH1": 179,
280
- "P@+1": 180,
281
- "-\\Ring2": 181,
282
- "11C": 182,
283
- "=Te+1": 183,
284
- "Zn+2": 184,
285
- "/NH1": 185,
286
- "18": 186,
287
- "As": 187,
288
- "BH2": 188,
289
- "BH1-1": 189,
290
- "Ca": 190,
291
- "H3": 191,
292
- "OH1-1": 192,
293
- "SH2": 193,
294
- "=O+1": 194,
295
- "Se+1": 195,
296
- "TeH2": 196,
297
- "125IH1": 197,
298
- "-/Ring1": 198,
299
- "14CH2": 199,
300
- "Ag+1": 200,
301
- "=Se+1": 201,
302
- "MgH2": 202,
303
- "Mg+2": 203,
304
- "11CH3": 204,
305
- "18F": 205,
306
- "BH2-1": 206,
307
- "Ca+2": 207
308
- },
309
- "merges": [
310
- "B r",
311
- "a n",
312
- "c h",
313
- "Br an",
314
- "Bran ch",
315
- "Branch 1",
316
- "= C",
317
- "R i",
318
- "n g",
319
- "Ri ng",
320
- "Ring 1",
321
- "= Branch1",
322
- "Branch 2",
323
- "= O",
324
- "Ring 2",
325
- "H 1",
326
- "C @",
327
- "= N",
328
- "# Branch1",
329
- "C@ @",
330
- "= Branch2",
331
- "C@ H1",
332
- "C@@ H1",
333
- "# Branch2",
334
- "C l",
335
- "# C",
336
- "/ C",
337
- "N H1",
338
- "+ 1",
339
- "- 1",
340
- "= Ring1",
341
- "O -1",
342
- "N +1",
343
- "\\ C",
344
- "/ N",
345
- "# N",
346
- "= Ring2",
347
- "= S",
348
- "=N +1",
349
- "N a",
350
- "Na +1",
351
- "\\ N",
352
- "S +1",
353
- "/ O",
354
- "\\ S",
355
- "\\ O",
356
- "Br -1",
357
- "I -1",
358
- "Cl -1",
359
- "/ C@H1",
360
- "Branch 3",
361
- "/ C@@H1",
362
- "= P",
363
- "/ S",
364
- "=N -1",
365
- "S i",
366
- "K +1",
367
- "N -1",
368
- "S e",
369
- "L i",
370
- "Li +1",
371
- "+ 3",
372
- "Cl +3",
373
- "\\ C@H1",
374
- "Ring 3",
375
- "\\ C@@H1",
376
- "/ N+1",
377
- "/ P",
378
- "\\ F",
379
- "P @",
380
- "2 H",
381
- "P H1",
382
- "/ Br",
383
- "N @",
384
- "P +1",
385
- "/ Cl",
386
- "\\ NH1",
387
- "\\ Br",
388
- "@ +1",
389
- "/ I",
390
- "/ C@",
391
- "T e",
392
- "\\ N+1",
393
- "P@ @",
394
- "1 2",
395
- "5 I",
396
- "\\ O-1",
397
- "12 5I",
398
- "/ F",
399
- "# N+1",
400
- "\\ Cl",
401
- "N@ +1",
402
- "\\ I",
403
- "- /",
404
- "/ C@@",
405
- "N@ @",
406
- "N@ @+1",
407
- "-/ Ring2",
408
- "- \\",
409
- "1 4",
410
- "B -1",
411
- "C -1",
412
- "S @+1",
413
- "14 C",
414
- "H 2",
415
- "H 4",
416
- "I +1",
417
- "S -1",
418
- "\\ P",
419
- "=S +1",
420
- "=P @",
421
- "Si H4",
422
- "+ 2",
423
- "3 H",
424
- "@ @+1",
425
- "A g",
426
- "C +1",
427
- "S @@+1",
428
- "Cl +1",
429
- "=S e",
430
- "-\\ Ring1",
431
- "H 0",
432
- "O H0",
433
- "1 1",
434
- "= Branch3",
435
- "= Te",
436
- "M g",
437
- "O +1",
438
- "Z n",
439
- "\\ C@",
440
- "\\ S+1",
441
- "H1 -1",
442
- "Se H1",
443
- "P@ +1",
444
- "-\\ Ring2",
445
- "11 C",
446
- "=Te +1",
447
- "Zn +2",
448
- "/ NH1",
449
- "1 8",
450
- "A s",
451
- "B H2",
452
- "B H1-1",
453
- "C a",
454
- "H 3",
455
- "O H1-1",
456
- "S H2",
457
- "=O +1",
458
- "Se +1",
459
- "Te H2",
460
- "125I H1",
461
- "-/ Ring1",
462
- "14C H2",
463
- "Ag +1",
464
- "=Se +1",
465
- "Mg H2",
466
- "Mg +2",
467
- "11C H3",
468
- "18 F",
469
- "BH2 -1",
470
- "Ca +2"
471
- ]
472
- }
473
- }
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
models/finetuned/lipo/tokenizer_config.json DELETED
@@ -1,59 +0,0 @@
1
- {
2
- "add_prefix_space": false,
3
- "added_tokens_decoder": {
4
- "0": {
5
- "content": "<unk>",
6
- "lstrip": false,
7
- "normalized": true,
8
- "rstrip": false,
9
- "single_word": false,
10
- "special": true
11
- },
12
- "1": {
13
- "content": "<s>",
14
- "lstrip": false,
15
- "normalized": true,
16
- "rstrip": false,
17
- "single_word": false,
18
- "special": true
19
- },
20
- "2": {
21
- "content": "</s>",
22
- "lstrip": false,
23
- "normalized": true,
24
- "rstrip": false,
25
- "single_word": false,
26
- "special": true
27
- },
28
- "3": {
29
- "content": "<pad>",
30
- "lstrip": false,
31
- "normalized": true,
32
- "rstrip": false,
33
- "single_word": false,
34
- "special": true
35
- },
36
- "4": {
37
- "content": "<mask>",
38
- "lstrip": true,
39
- "normalized": true,
40
- "rstrip": false,
41
- "single_word": false,
42
- "special": true
43
- }
44
- },
45
- "bos_token": "<s>",
46
- "clean_up_tokenization_spaces": true,
47
- "cls_token": "<s>",
48
- "eos_token": "</s>",
49
- "errors": "replace",
50
- "mask_token": "<mask>",
51
- "model_max_length": 1000000000000000019884624838656,
52
- "name_or_path": "data/epoch_267/hf",
53
- "pad_token": "<pad>",
54
- "sep_token": "</s>",
55
- "special_tokens_map_file": "data/epoch_267/hf/special_tokens_map.json",
56
- "tokenizer_class": "RobertaTokenizer",
57
- "trim_offsets": true,
58
- "unk_token": "<unk>"
59
- }
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
models/finetuned/lipo/vocab.json DELETED
@@ -1 +0,0 @@
1
- {"<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,"8":17,"=":18,"@":19,"A":20,"B":21,"C":22,"F":23,"H":24,"I":25,"K":26,"L":27,"M":28,"N":29,"O":30,"P":31,"R":32,"S":33,"T":34,"Z":35,"\\":36,"a":37,"c":38,"e":39,"g":40,"h":41,"i":42,"l":43,"n":44,"r":45,"s":46,"Br":47,"an":48,"ch":49,"Bran":50,"Branch":51,"Branch1":52,"=C":53,"Ri":54,"ng":55,"Ring":56,"Ring1":57,"=Branch1":58,"Branch2":59,"=O":60,"Ring2":61,"H1":62,"C@":63,"=N":64,"#Branch1":65,"C@@":66,"=Branch2":67,"C@H1":68,"C@@H1":69,"#Branch2":70,"Cl":71,"#C":72,"/C":73,"NH1":74,"+1":75,"-1":76,"=Ring1":77,"O-1":78,"N+1":79,"\\C":80,"/N":81,"#N":82,"=Ring2":83,"=S":84,"=N+1":85,"Na":86,"Na+1":87,"\\N":88,"S+1":89,"/O":90,"\\S":91,"\\O":92,"Br-1":93,"I-1":94,"Cl-1":95,"/C@H1":96,"Branch3":97,"/C@@H1":98,"=P":99,"/S":100,"=N-1":101,"Si":102,"K+1":103,"N-1":104,"Se":105,"Li":106,"Li+1":107,"+3":108,"Cl+3":109,"\\C@H1":110,"Ring3":111,"\\C@@H1":112,"/N+1":113,"/P":114,"\\F":115,"P@":116,"2H":117,"PH1":118,"/Br":119,"N@":120,"P+1":121,"/Cl":122,"\\NH1":123,"\\Br":124,"@+1":125,"/I":126,"/C@":127,"Te":128,"\\N+1":129,"P@@":130,"12":131,"5I":132,"\\O-1":133,"125I":134,"/F":135,"#N+1":136,"\\Cl":137,"N@+1":138,"\\I":139,"-/":140,"/C@@":141,"N@@":142,"N@@+1":143,"-/Ring2":144,"-\\":145,"14":146,"B-1":147,"C-1":148,"S@+1":149,"14C":150,"H2":151,"H4":152,"I+1":153,"S-1":154,"\\P":155,"=S+1":156,"=P@":157,"SiH4":158,"+2":159,"3H":160,"@@+1":161,"Ag":162,"C+1":163,"S@@+1":164,"Cl+1":165,"=Se":166,"-\\Ring1":167,"H0":168,"OH0":169,"11":170,"=Branch3":171,"=Te":172,"Mg":173,"O+1":174,"Zn":175,"\\C@":176,"\\S+1":177,"H1-1":178,"SeH1":179,"P@+1":180,"-\\Ring2":181,"11C":182,"=Te+1":183,"Zn+2":184,"/NH1":185,"18":186,"As":187,"BH2":188,"BH1-1":189,"Ca":190,"H3":191,"OH1-1":192,"SH2":193,"=O+1":194,"Se+1":195,"TeH2":196,"125IH1":197,"-/Ring1":198,"14CH2":199,"Ag+1":200,"=Se+1":201,"MgH2":202,"Mg+2":203,"11CH3":204,"18F":205,"BH2-1":206,"Ca+2":207}
 
 
models/finetuned/pdbbind_full/config.json DELETED
@@ -1,28 +0,0 @@
1
- {
2
- "_name_or_path": "data/epoch_267/hf",
3
- "architectures": [
4
- "RobertaForMaskedLM"
5
- ],
6
- "attention_probs_dropout_prob": 0.1,
7
- "bos_token_id": 0,
8
- "classifier_dropout": null,
9
- "eos_token_id": 2,
10
- "hidden_act": "gelu",
11
- "hidden_dropout_prob": 0.1,
12
- "hidden_size": 768,
13
- "initializer_range": 0.02,
14
- "intermediate_size": 3072,
15
- "layer_norm_eps": 1e-12,
16
- "max_position_embeddings": 514,
17
- "model_type": "roberta",
18
- "num_attention_heads": 4,
19
- "num_hidden_layers": 12,
20
- "output_hidden_states": true,
21
- "pad_token_id": 1,
22
- "position_embedding_type": "absolute",
23
- "torch_dtype": "float32",
24
- "transformers_version": "4.26.1",
25
- "type_vocab_size": 1,
26
- "use_cache": true,
27
- "vocab_size": 800
28
- }
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
models/finetuned/pdbbind_full/finetuning_optimized_config.json DELETED
@@ -1,24 +0,0 @@
1
- {
2
- "dataset_meta_csv": "data/finetuning_datasets/regression/pdbbind_full/pdbbind_full.csv",
3
- "dataset_embs_npz": "data/finetuning_datasets/regression/pdbbind_full/pdbbind_full_embs.npz",
4
- "use_scaffold": 0,
5
- "seed": 42,
6
- "train_frac": 0.8,
7
- "val_frac": 0.1,
8
- "test_frac": 0.1,
9
- "model_path": "HUBioDataLab/SELFormer",
10
- "tokenizer_path": "HUBioDataLab/SELFormer",
11
- "pretrained_multimodal_dir": "data/models/SELFormerMM",
12
- "task_type": "regression",
13
- "label_column": "-logKd/Ki",
14
- "num_labels": 1,
15
- "batch_size": 32,
16
- "max_len": 128,
17
- "epochs": 75,
18
- "backbone_lr": 5e-05,
19
- "head_lr": 1e-06,
20
- "weight_decay": 0.01,
21
- "checkpoint_every": 25,
22
- "test_eval_every": 0,
23
- "save_dir": "data/models/finetuned/pdbbind_full"
24
- }