as-cle-bert commited on
Commit
dd1068c
1 Parent(s): 2e92ded

Upload folder using huggingface_hub

Browse files
README.md ADDED
@@ -0,0 +1,37 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+
2
+ ---
3
+ tags:
4
+ - autotrain
5
+ - text-classification
6
+ widget:
7
+ - text: "I love AutoTrain"
8
+ datasets:
9
+ - as-cle-bert/AMR-Gene-Families
10
+ ---
11
+
12
+ # Model Trained Using AutoTrain
13
+
14
+ - Problem type: Text Classification
15
+
16
+ ## Validation Metrics
17
+ loss: 0.08235077559947968
18
+
19
+ f1_macro: 0.986759581881533
20
+
21
+ f1_micro: 0.99
22
+
23
+ f1_weighted: 0.9899790940766551
24
+
25
+ precision_macro: 0.9871615312791784
26
+
27
+ precision_micro: 0.99
28
+
29
+ precision_weighted: 0.9901213818860879
30
+
31
+ recall_macro: 0.986574074074074
32
+
33
+ recall_micro: 0.99
34
+
35
+ recall_weighted: 0.99
36
+
37
+ accuracy: 0.99
checkpoint-450/config.json ADDED
@@ -0,0 +1,55 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "_name_or_path": "Rostlab/prot_bert",
3
+ "_num_labels": 12,
4
+ "architectures": [
5
+ "BertForSequenceClassification"
6
+ ],
7
+ "attention_probs_dropout_prob": 0.0,
8
+ "classifier_dropout": null,
9
+ "hidden_act": "gelu",
10
+ "hidden_dropout_prob": 0.0,
11
+ "hidden_size": 1024,
12
+ "id2label": {
13
+ "0": "PDC beta-lactamase",
14
+ "1": "CTX-M beta-lactamase",
15
+ "2": "SHV beta-lactamase",
16
+ "3": "CMY beta-lactamase",
17
+ "4": "resistance-nodulation-cell division (RND) antibiotic efflux pump",
18
+ "5": "major facilitator superfamily (MFS) antibiotic efflux pump",
19
+ "6": "quinolone resistance protein (qnr)",
20
+ "7": "IMP beta-lactamase",
21
+ "8": "KPC beta-lactamase",
22
+ "9": "ACT beta-lactamase",
23
+ "10": "MCR phosphoethanolamine transferase",
24
+ "11": "VIM beta-lactamase"
25
+ },
26
+ "initializer_range": 0.02,
27
+ "intermediate_size": 4096,
28
+ "label2id": {
29
+ "ACT beta-lactamase": 9,
30
+ "CMY beta-lactamase": 3,
31
+ "CTX-M beta-lactamase": 1,
32
+ "IMP beta-lactamase": 7,
33
+ "KPC beta-lactamase": 8,
34
+ "MCR phosphoethanolamine transferase": 10,
35
+ "PDC beta-lactamase": 0,
36
+ "SHV beta-lactamase": 2,
37
+ "VIM beta-lactamase": 11,
38
+ "major facilitator superfamily (MFS) antibiotic efflux pump": 5,
39
+ "quinolone resistance protein (qnr)": 6,
40
+ "resistance-nodulation-cell division (RND) antibiotic efflux pump": 4
41
+ },
42
+ "layer_norm_eps": 1e-12,
43
+ "max_position_embeddings": 40000,
44
+ "model_type": "bert",
45
+ "num_attention_heads": 16,
46
+ "num_hidden_layers": 30,
47
+ "pad_token_id": 0,
48
+ "position_embedding_type": "absolute",
49
+ "problem_type": "single_label_classification",
50
+ "torch_dtype": "float32",
51
+ "transformers_version": "4.39.0",
52
+ "type_vocab_size": 2,
53
+ "use_cache": true,
54
+ "vocab_size": 30
55
+ }
checkpoint-450/model.safetensors ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:7b482ed0644cc263571f364d2f8c163134071cf2e1f377000fdb9576dad99882
3
+ size 1679832496
checkpoint-450/optimizer.pt ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:9309b9d765925a9e41447d54c63767cfe3285429cae7a8e089794f2e91b70bb1
3
+ size 3359943437
checkpoint-450/rng_state.pth ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:5e721764cfe6d7ef80d19a2ff27d723d65ac25eb377b60bb6e4c10a66202a1bf
3
+ size 13990
checkpoint-450/scheduler.pt ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:7f2295262c8b0cd31776d8d5f370bfd4d7da47a787dc53758a73b3dbb54b80f3
3
+ size 1064
checkpoint-450/trainer_state.json ADDED
@@ -0,0 +1,523 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "best_metric": 0.08235077559947968,
3
+ "best_model_checkpoint": "autotrain-fzudm-korrh/checkpoint-450",
4
+ "epoch": 3.0,
5
+ "eval_steps": 500,
6
+ "global_step": 450,
7
+ "is_hyper_param_search": false,
8
+ "is_local_process_zero": true,
9
+ "is_world_process_zero": true,
10
+ "log_history": [
11
+ {
12
+ "epoch": 0.05,
13
+ "grad_norm": 1.8473684787750244,
14
+ "learning_rate": 7.777777777777777e-06,
15
+ "loss": 2.4944,
16
+ "step": 7
17
+ },
18
+ {
19
+ "epoch": 0.09,
20
+ "grad_norm": 2.497635841369629,
21
+ "learning_rate": 1.5555555555555555e-05,
22
+ "loss": 2.461,
23
+ "step": 14
24
+ },
25
+ {
26
+ "epoch": 0.14,
27
+ "grad_norm": 2.6727840900421143,
28
+ "learning_rate": 2.3333333333333336e-05,
29
+ "loss": 2.3714,
30
+ "step": 21
31
+ },
32
+ {
33
+ "epoch": 0.19,
34
+ "grad_norm": 3.3866329193115234,
35
+ "learning_rate": 3.111111111111111e-05,
36
+ "loss": 2.3521,
37
+ "step": 28
38
+ },
39
+ {
40
+ "epoch": 0.23,
41
+ "grad_norm": 3.0266103744506836,
42
+ "learning_rate": 3.888888888888889e-05,
43
+ "loss": 2.2204,
44
+ "step": 35
45
+ },
46
+ {
47
+ "epoch": 0.28,
48
+ "grad_norm": 5.708084583282471,
49
+ "learning_rate": 4.666666666666667e-05,
50
+ "loss": 2.0935,
51
+ "step": 42
52
+ },
53
+ {
54
+ "epoch": 0.33,
55
+ "grad_norm": 2.413567543029785,
56
+ "learning_rate": 4.950617283950618e-05,
57
+ "loss": 1.9364,
58
+ "step": 49
59
+ },
60
+ {
61
+ "epoch": 0.37,
62
+ "grad_norm": 2.816483497619629,
63
+ "learning_rate": 4.864197530864198e-05,
64
+ "loss": 1.7083,
65
+ "step": 56
66
+ },
67
+ {
68
+ "epoch": 0.42,
69
+ "grad_norm": 3.948235273361206,
70
+ "learning_rate": 4.7777777777777784e-05,
71
+ "loss": 1.6135,
72
+ "step": 63
73
+ },
74
+ {
75
+ "epoch": 0.47,
76
+ "grad_norm": 3.652134418487549,
77
+ "learning_rate": 4.691358024691358e-05,
78
+ "loss": 1.4522,
79
+ "step": 70
80
+ },
81
+ {
82
+ "epoch": 0.51,
83
+ "grad_norm": 3.7319400310516357,
84
+ "learning_rate": 4.604938271604938e-05,
85
+ "loss": 1.2261,
86
+ "step": 77
87
+ },
88
+ {
89
+ "epoch": 0.56,
90
+ "grad_norm": 2.1848716735839844,
91
+ "learning_rate": 4.518518518518519e-05,
92
+ "loss": 1.1589,
93
+ "step": 84
94
+ },
95
+ {
96
+ "epoch": 0.61,
97
+ "grad_norm": 2.331566572189331,
98
+ "learning_rate": 4.432098765432099e-05,
99
+ "loss": 0.9291,
100
+ "step": 91
101
+ },
102
+ {
103
+ "epoch": 0.65,
104
+ "grad_norm": 2.437225818634033,
105
+ "learning_rate": 4.345679012345679e-05,
106
+ "loss": 0.882,
107
+ "step": 98
108
+ },
109
+ {
110
+ "epoch": 0.7,
111
+ "grad_norm": 3.426419734954834,
112
+ "learning_rate": 4.259259259259259e-05,
113
+ "loss": 0.8062,
114
+ "step": 105
115
+ },
116
+ {
117
+ "epoch": 0.75,
118
+ "grad_norm": 27.056604385375977,
119
+ "learning_rate": 4.17283950617284e-05,
120
+ "loss": 0.8794,
121
+ "step": 112
122
+ },
123
+ {
124
+ "epoch": 0.79,
125
+ "grad_norm": 2.7623507976531982,
126
+ "learning_rate": 4.0864197530864204e-05,
127
+ "loss": 0.7981,
128
+ "step": 119
129
+ },
130
+ {
131
+ "epoch": 0.84,
132
+ "grad_norm": 1.0507307052612305,
133
+ "learning_rate": 4e-05,
134
+ "loss": 0.6203,
135
+ "step": 126
136
+ },
137
+ {
138
+ "epoch": 0.89,
139
+ "grad_norm": 6.599649429321289,
140
+ "learning_rate": 3.91358024691358e-05,
141
+ "loss": 0.5586,
142
+ "step": 133
143
+ },
144
+ {
145
+ "epoch": 0.93,
146
+ "grad_norm": 1.9725279808044434,
147
+ "learning_rate": 3.82716049382716e-05,
148
+ "loss": 0.4613,
149
+ "step": 140
150
+ },
151
+ {
152
+ "epoch": 0.98,
153
+ "grad_norm": 0.9860884547233582,
154
+ "learning_rate": 3.740740740740741e-05,
155
+ "loss": 0.4811,
156
+ "step": 147
157
+ },
158
+ {
159
+ "epoch": 1.0,
160
+ "eval_accuracy": 0.9866666666666667,
161
+ "eval_f1_macro": 0.9824074074074073,
162
+ "eval_f1_micro": 0.9866666666666668,
163
+ "eval_f1_weighted": 0.9866666666666667,
164
+ "eval_loss": 0.47558584809303284,
165
+ "eval_precision_macro": 0.9824074074074073,
166
+ "eval_precision_micro": 0.9866666666666667,
167
+ "eval_precision_weighted": 0.9866666666666667,
168
+ "eval_recall_macro": 0.9824074074074073,
169
+ "eval_recall_micro": 0.9866666666666667,
170
+ "eval_recall_weighted": 0.9866666666666667,
171
+ "eval_runtime": 226.8158,
172
+ "eval_samples_per_second": 1.323,
173
+ "eval_steps_per_second": 0.084,
174
+ "step": 150
175
+ },
176
+ {
177
+ "epoch": 1.03,
178
+ "grad_norm": 1.572788953781128,
179
+ "learning_rate": 3.654320987654321e-05,
180
+ "loss": 0.4706,
181
+ "step": 154
182
+ },
183
+ {
184
+ "epoch": 1.07,
185
+ "grad_norm": 1.8391231298446655,
186
+ "learning_rate": 3.567901234567901e-05,
187
+ "loss": 0.4863,
188
+ "step": 161
189
+ },
190
+ {
191
+ "epoch": 1.12,
192
+ "grad_norm": 1.4992858171463013,
193
+ "learning_rate": 3.481481481481482e-05,
194
+ "loss": 0.3355,
195
+ "step": 168
196
+ },
197
+ {
198
+ "epoch": 1.17,
199
+ "grad_norm": 16.52165412902832,
200
+ "learning_rate": 3.395061728395062e-05,
201
+ "loss": 0.4208,
202
+ "step": 175
203
+ },
204
+ {
205
+ "epoch": 1.21,
206
+ "grad_norm": 0.8345728516578674,
207
+ "learning_rate": 3.308641975308642e-05,
208
+ "loss": 0.3104,
209
+ "step": 182
210
+ },
211
+ {
212
+ "epoch": 1.26,
213
+ "grad_norm": 1.0207165479660034,
214
+ "learning_rate": 3.222222222222223e-05,
215
+ "loss": 0.2553,
216
+ "step": 189
217
+ },
218
+ {
219
+ "epoch": 1.31,
220
+ "grad_norm": 4.886829853057861,
221
+ "learning_rate": 3.135802469135803e-05,
222
+ "loss": 0.3013,
223
+ "step": 196
224
+ },
225
+ {
226
+ "epoch": 1.35,
227
+ "grad_norm": 0.7672041654586792,
228
+ "learning_rate": 3.0493827160493827e-05,
229
+ "loss": 0.2357,
230
+ "step": 203
231
+ },
232
+ {
233
+ "epoch": 1.4,
234
+ "grad_norm": 1.1569510698318481,
235
+ "learning_rate": 2.962962962962963e-05,
236
+ "loss": 0.2197,
237
+ "step": 210
238
+ },
239
+ {
240
+ "epoch": 1.45,
241
+ "grad_norm": 0.44843003153800964,
242
+ "learning_rate": 2.8765432098765432e-05,
243
+ "loss": 0.1555,
244
+ "step": 217
245
+ },
246
+ {
247
+ "epoch": 1.49,
248
+ "grad_norm": 0.48682141304016113,
249
+ "learning_rate": 2.7901234567901235e-05,
250
+ "loss": 0.1917,
251
+ "step": 224
252
+ },
253
+ {
254
+ "epoch": 1.54,
255
+ "grad_norm": 0.6816083788871765,
256
+ "learning_rate": 2.7037037037037037e-05,
257
+ "loss": 0.1292,
258
+ "step": 231
259
+ },
260
+ {
261
+ "epoch": 1.59,
262
+ "grad_norm": 0.38534966111183167,
263
+ "learning_rate": 2.617283950617284e-05,
264
+ "loss": 0.1009,
265
+ "step": 238
266
+ },
267
+ {
268
+ "epoch": 1.63,
269
+ "grad_norm": 0.5634031891822815,
270
+ "learning_rate": 2.5308641975308646e-05,
271
+ "loss": 0.1725,
272
+ "step": 245
273
+ },
274
+ {
275
+ "epoch": 1.68,
276
+ "grad_norm": 1.3090158700942993,
277
+ "learning_rate": 2.4444444444444445e-05,
278
+ "loss": 0.1355,
279
+ "step": 252
280
+ },
281
+ {
282
+ "epoch": 1.73,
283
+ "grad_norm": 0.2513110041618347,
284
+ "learning_rate": 2.3580246913580247e-05,
285
+ "loss": 0.077,
286
+ "step": 259
287
+ },
288
+ {
289
+ "epoch": 1.77,
290
+ "grad_norm": 4.024202346801758,
291
+ "learning_rate": 2.271604938271605e-05,
292
+ "loss": 0.0972,
293
+ "step": 266
294
+ },
295
+ {
296
+ "epoch": 1.82,
297
+ "grad_norm": 0.8751043677330017,
298
+ "learning_rate": 2.1851851851851852e-05,
299
+ "loss": 0.087,
300
+ "step": 273
301
+ },
302
+ {
303
+ "epoch": 1.87,
304
+ "grad_norm": 0.2541038990020752,
305
+ "learning_rate": 2.0987654320987655e-05,
306
+ "loss": 0.0759,
307
+ "step": 280
308
+ },
309
+ {
310
+ "epoch": 1.91,
311
+ "grad_norm": 0.29228782653808594,
312
+ "learning_rate": 2.0123456790123457e-05,
313
+ "loss": 0.0715,
314
+ "step": 287
315
+ },
316
+ {
317
+ "epoch": 1.96,
318
+ "grad_norm": 0.42550790309906006,
319
+ "learning_rate": 1.925925925925926e-05,
320
+ "loss": 0.0689,
321
+ "step": 294
322
+ },
323
+ {
324
+ "epoch": 2.0,
325
+ "eval_accuracy": 0.99,
326
+ "eval_f1_macro": 0.986759581881533,
327
+ "eval_f1_micro": 0.99,
328
+ "eval_f1_weighted": 0.9899790940766551,
329
+ "eval_loss": 0.10256664454936981,
330
+ "eval_precision_macro": 0.9871615312791784,
331
+ "eval_precision_micro": 0.99,
332
+ "eval_precision_weighted": 0.9901213818860879,
333
+ "eval_recall_macro": 0.986574074074074,
334
+ "eval_recall_micro": 0.99,
335
+ "eval_recall_weighted": 0.99,
336
+ "eval_runtime": 229.5963,
337
+ "eval_samples_per_second": 1.307,
338
+ "eval_steps_per_second": 0.083,
339
+ "step": 300
340
+ },
341
+ {
342
+ "epoch": 2.01,
343
+ "grad_norm": 0.2770730257034302,
344
+ "learning_rate": 1.8395061728395062e-05,
345
+ "loss": 0.1148,
346
+ "step": 301
347
+ },
348
+ {
349
+ "epoch": 2.05,
350
+ "grad_norm": 0.2336236983537674,
351
+ "learning_rate": 1.7530864197530865e-05,
352
+ "loss": 0.1179,
353
+ "step": 308
354
+ },
355
+ {
356
+ "epoch": 2.1,
357
+ "grad_norm": 0.32252636551856995,
358
+ "learning_rate": 1.6666666666666667e-05,
359
+ "loss": 0.0629,
360
+ "step": 315
361
+ },
362
+ {
363
+ "epoch": 2.15,
364
+ "grad_norm": 0.2286107987165451,
365
+ "learning_rate": 1.580246913580247e-05,
366
+ "loss": 0.112,
367
+ "step": 322
368
+ },
369
+ {
370
+ "epoch": 2.19,
371
+ "grad_norm": 0.34691134095191956,
372
+ "learning_rate": 1.4938271604938272e-05,
373
+ "loss": 0.0633,
374
+ "step": 329
375
+ },
376
+ {
377
+ "epoch": 2.24,
378
+ "grad_norm": 0.25500062108039856,
379
+ "learning_rate": 1.4074074074074075e-05,
380
+ "loss": 0.0512,
381
+ "step": 336
382
+ },
383
+ {
384
+ "epoch": 2.29,
385
+ "grad_norm": 0.44312888383865356,
386
+ "learning_rate": 1.3209876543209876e-05,
387
+ "loss": 0.0604,
388
+ "step": 343
389
+ },
390
+ {
391
+ "epoch": 2.33,
392
+ "grad_norm": 0.3760792016983032,
393
+ "learning_rate": 1.2345679012345678e-05,
394
+ "loss": 0.0595,
395
+ "step": 350
396
+ },
397
+ {
398
+ "epoch": 2.38,
399
+ "grad_norm": 0.2281612902879715,
400
+ "learning_rate": 1.1481481481481482e-05,
401
+ "loss": 0.0619,
402
+ "step": 357
403
+ },
404
+ {
405
+ "epoch": 2.43,
406
+ "grad_norm": 0.2144249677658081,
407
+ "learning_rate": 1.0617283950617285e-05,
408
+ "loss": 0.0448,
409
+ "step": 364
410
+ },
411
+ {
412
+ "epoch": 2.47,
413
+ "grad_norm": 0.16961945593357086,
414
+ "learning_rate": 9.753086419753086e-06,
415
+ "loss": 0.0524,
416
+ "step": 371
417
+ },
418
+ {
419
+ "epoch": 2.52,
420
+ "grad_norm": 0.21082834899425507,
421
+ "learning_rate": 8.88888888888889e-06,
422
+ "loss": 0.0417,
423
+ "step": 378
424
+ },
425
+ {
426
+ "epoch": 2.57,
427
+ "grad_norm": 0.21366652846336365,
428
+ "learning_rate": 8.02469135802469e-06,
429
+ "loss": 0.0473,
430
+ "step": 385
431
+ },
432
+ {
433
+ "epoch": 2.61,
434
+ "grad_norm": 0.19165301322937012,
435
+ "learning_rate": 7.160493827160494e-06,
436
+ "loss": 0.039,
437
+ "step": 392
438
+ },
439
+ {
440
+ "epoch": 2.66,
441
+ "grad_norm": 0.14223778247833252,
442
+ "learning_rate": 6.296296296296296e-06,
443
+ "loss": 0.0362,
444
+ "step": 399
445
+ },
446
+ {
447
+ "epoch": 2.71,
448
+ "grad_norm": 0.22010144591331482,
449
+ "learning_rate": 5.432098765432099e-06,
450
+ "loss": 0.112,
451
+ "step": 406
452
+ },
453
+ {
454
+ "epoch": 2.75,
455
+ "grad_norm": 0.2625073492527008,
456
+ "learning_rate": 4.567901234567902e-06,
457
+ "loss": 0.0441,
458
+ "step": 413
459
+ },
460
+ {
461
+ "epoch": 2.8,
462
+ "grad_norm": 0.13207264244556427,
463
+ "learning_rate": 3.7037037037037037e-06,
464
+ "loss": 0.0393,
465
+ "step": 420
466
+ },
467
+ {
468
+ "epoch": 2.85,
469
+ "grad_norm": 0.14408986270427704,
470
+ "learning_rate": 2.8395061728395062e-06,
471
+ "loss": 0.047,
472
+ "step": 427
473
+ },
474
+ {
475
+ "epoch": 2.89,
476
+ "grad_norm": 0.26891738176345825,
477
+ "learning_rate": 1.9753086419753087e-06,
478
+ "loss": 0.048,
479
+ "step": 434
480
+ },
481
+ {
482
+ "epoch": 2.94,
483
+ "grad_norm": 0.28397634625434875,
484
+ "learning_rate": 1.1111111111111112e-06,
485
+ "loss": 0.0439,
486
+ "step": 441
487
+ },
488
+ {
489
+ "epoch": 2.99,
490
+ "grad_norm": 0.14882226288318634,
491
+ "learning_rate": 2.469135802469136e-07,
492
+ "loss": 0.0495,
493
+ "step": 448
494
+ },
495
+ {
496
+ "epoch": 3.0,
497
+ "eval_accuracy": 0.99,
498
+ "eval_f1_macro": 0.986759581881533,
499
+ "eval_f1_micro": 0.99,
500
+ "eval_f1_weighted": 0.9899790940766551,
501
+ "eval_loss": 0.08235077559947968,
502
+ "eval_precision_macro": 0.9871615312791784,
503
+ "eval_precision_micro": 0.99,
504
+ "eval_precision_weighted": 0.9901213818860879,
505
+ "eval_recall_macro": 0.986574074074074,
506
+ "eval_recall_micro": 0.99,
507
+ "eval_recall_weighted": 0.99,
508
+ "eval_runtime": 236.6057,
509
+ "eval_samples_per_second": 1.268,
510
+ "eval_steps_per_second": 0.08,
511
+ "step": 450
512
+ }
513
+ ],
514
+ "logging_steps": 7,
515
+ "max_steps": 450,
516
+ "num_input_tokens_seen": 0,
517
+ "num_train_epochs": 3,
518
+ "save_steps": 500,
519
+ "total_flos": 1044230397530112.0,
520
+ "train_batch_size": 8,
521
+ "trial_name": null,
522
+ "trial_params": null
523
+ }
checkpoint-450/training_args.bin ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:a181d426a846aed31d185c1c8e7462bde216a5de70b47a96fc82542bdb87ea9d
3
+ size 4920
config.json ADDED
@@ -0,0 +1,55 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "_name_or_path": "Rostlab/prot_bert",
3
+ "_num_labels": 12,
4
+ "architectures": [
5
+ "BertForSequenceClassification"
6
+ ],
7
+ "attention_probs_dropout_prob": 0.0,
8
+ "classifier_dropout": null,
9
+ "hidden_act": "gelu",
10
+ "hidden_dropout_prob": 0.0,
11
+ "hidden_size": 1024,
12
+ "id2label": {
13
+ "0": "PDC beta-lactamase",
14
+ "1": "CTX-M beta-lactamase",
15
+ "2": "SHV beta-lactamase",
16
+ "3": "CMY beta-lactamase",
17
+ "4": "resistance-nodulation-cell division (RND) antibiotic efflux pump",
18
+ "5": "major facilitator superfamily (MFS) antibiotic efflux pump",
19
+ "6": "quinolone resistance protein (qnr)",
20
+ "7": "IMP beta-lactamase",
21
+ "8": "KPC beta-lactamase",
22
+ "9": "ACT beta-lactamase",
23
+ "10": "MCR phosphoethanolamine transferase",
24
+ "11": "VIM beta-lactamase"
25
+ },
26
+ "initializer_range": 0.02,
27
+ "intermediate_size": 4096,
28
+ "label2id": {
29
+ "ACT beta-lactamase": 9,
30
+ "CMY beta-lactamase": 3,
31
+ "CTX-M beta-lactamase": 1,
32
+ "IMP beta-lactamase": 7,
33
+ "KPC beta-lactamase": 8,
34
+ "MCR phosphoethanolamine transferase": 10,
35
+ "PDC beta-lactamase": 0,
36
+ "SHV beta-lactamase": 2,
37
+ "VIM beta-lactamase": 11,
38
+ "major facilitator superfamily (MFS) antibiotic efflux pump": 5,
39
+ "quinolone resistance protein (qnr)": 6,
40
+ "resistance-nodulation-cell division (RND) antibiotic efflux pump": 4
41
+ },
42
+ "layer_norm_eps": 1e-12,
43
+ "max_position_embeddings": 40000,
44
+ "model_type": "bert",
45
+ "num_attention_heads": 16,
46
+ "num_hidden_layers": 30,
47
+ "pad_token_id": 0,
48
+ "position_embedding_type": "absolute",
49
+ "problem_type": "single_label_classification",
50
+ "torch_dtype": "float32",
51
+ "transformers_version": "4.39.0",
52
+ "type_vocab_size": 2,
53
+ "use_cache": true,
54
+ "vocab_size": 30
55
+ }
model.safetensors ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:7b482ed0644cc263571f364d2f8c163134071cf2e1f377000fdb9576dad99882
3
+ size 1679832496
special_tokens_map.json ADDED
@@ -0,0 +1,7 @@
 
 
 
 
 
 
 
 
1
+ {
2
+ "cls_token": "[CLS]",
3
+ "mask_token": "[MASK]",
4
+ "pad_token": "[PAD]",
5
+ "sep_token": "[SEP]",
6
+ "unk_token": "[UNK]"
7
+ }
tokenizer.json ADDED
@@ -0,0 +1,194 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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": 0,
16
+ "pad_type_id": 0,
17
+ "pad_token": "[PAD]"
18
+ },
19
+ "added_tokens": [
20
+ {
21
+ "id": 0,
22
+ "content": "[PAD]",
23
+ "single_word": false,
24
+ "lstrip": false,
25
+ "rstrip": false,
26
+ "normalized": false,
27
+ "special": true
28
+ },
29
+ {
30
+ "id": 1,
31
+ "content": "[UNK]",
32
+ "single_word": false,
33
+ "lstrip": false,
34
+ "rstrip": false,
35
+ "normalized": false,
36
+ "special": true
37
+ },
38
+ {
39
+ "id": 2,
40
+ "content": "[CLS]",
41
+ "single_word": false,
42
+ "lstrip": false,
43
+ "rstrip": false,
44
+ "normalized": false,
45
+ "special": true
46
+ },
47
+ {
48
+ "id": 3,
49
+ "content": "[SEP]",
50
+ "single_word": false,
51
+ "lstrip": false,
52
+ "rstrip": false,
53
+ "normalized": false,
54
+ "special": true
55
+ },
56
+ {
57
+ "id": 4,
58
+ "content": "[MASK]",
59
+ "single_word": false,
60
+ "lstrip": false,
61
+ "rstrip": false,
62
+ "normalized": false,
63
+ "special": true
64
+ }
65
+ ],
66
+ "normalizer": {
67
+ "type": "BertNormalizer",
68
+ "clean_text": true,
69
+ "handle_chinese_chars": true,
70
+ "strip_accents": null,
71
+ "lowercase": false
72
+ },
73
+ "pre_tokenizer": {
74
+ "type": "BertPreTokenizer"
75
+ },
76
+ "post_processor": {
77
+ "type": "TemplateProcessing",
78
+ "single": [
79
+ {
80
+ "SpecialToken": {
81
+ "id": "[CLS]",
82
+ "type_id": 0
83
+ }
84
+ },
85
+ {
86
+ "Sequence": {
87
+ "id": "A",
88
+ "type_id": 0
89
+ }
90
+ },
91
+ {
92
+ "SpecialToken": {
93
+ "id": "[SEP]",
94
+ "type_id": 0
95
+ }
96
+ }
97
+ ],
98
+ "pair": [
99
+ {
100
+ "SpecialToken": {
101
+ "id": "[CLS]",
102
+ "type_id": 0
103
+ }
104
+ },
105
+ {
106
+ "Sequence": {
107
+ "id": "A",
108
+ "type_id": 0
109
+ }
110
+ },
111
+ {
112
+ "SpecialToken": {
113
+ "id": "[SEP]",
114
+ "type_id": 0
115
+ }
116
+ },
117
+ {
118
+ "Sequence": {
119
+ "id": "B",
120
+ "type_id": 1
121
+ }
122
+ },
123
+ {
124
+ "SpecialToken": {
125
+ "id": "[SEP]",
126
+ "type_id": 1
127
+ }
128
+ }
129
+ ],
130
+ "special_tokens": {
131
+ "[CLS]": {
132
+ "id": "[CLS]",
133
+ "ids": [
134
+ 2
135
+ ],
136
+ "tokens": [
137
+ "[CLS]"
138
+ ]
139
+ },
140
+ "[SEP]": {
141
+ "id": "[SEP]",
142
+ "ids": [
143
+ 3
144
+ ],
145
+ "tokens": [
146
+ "[SEP]"
147
+ ]
148
+ }
149
+ }
150
+ },
151
+ "decoder": {
152
+ "type": "WordPiece",
153
+ "prefix": "##",
154
+ "cleanup": true
155
+ },
156
+ "model": {
157
+ "type": "WordPiece",
158
+ "unk_token": "[UNK]",
159
+ "continuing_subword_prefix": "##",
160
+ "max_input_chars_per_word": 100,
161
+ "vocab": {
162
+ "[PAD]": 0,
163
+ "[UNK]": 1,
164
+ "[CLS]": 2,
165
+ "[SEP]": 3,
166
+ "[MASK]": 4,
167
+ "L": 5,
168
+ "A": 6,
169
+ "G": 7,
170
+ "V": 8,
171
+ "E": 9,
172
+ "S": 10,
173
+ "I": 11,
174
+ "K": 12,
175
+ "R": 13,
176
+ "D": 14,
177
+ "T": 15,
178
+ "P": 16,
179
+ "N": 17,
180
+ "Q": 18,
181
+ "F": 19,
182
+ "Y": 20,
183
+ "M": 21,
184
+ "H": 22,
185
+ "C": 23,
186
+ "W": 24,
187
+ "X": 25,
188
+ "U": 26,
189
+ "B": 27,
190
+ "Z": 28,
191
+ "O": 29
192
+ }
193
+ }
194
+ }
tokenizer_config.json ADDED
@@ -0,0 +1,58 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "added_tokens_decoder": {
3
+ "0": {
4
+ "content": "[PAD]",
5
+ "lstrip": false,
6
+ "normalized": false,
7
+ "rstrip": false,
8
+ "single_word": false,
9
+ "special": true
10
+ },
11
+ "1": {
12
+ "content": "[UNK]",
13
+ "lstrip": false,
14
+ "normalized": false,
15
+ "rstrip": false,
16
+ "single_word": false,
17
+ "special": true
18
+ },
19
+ "2": {
20
+ "content": "[CLS]",
21
+ "lstrip": false,
22
+ "normalized": false,
23
+ "rstrip": false,
24
+ "single_word": false,
25
+ "special": true
26
+ },
27
+ "3": {
28
+ "content": "[SEP]",
29
+ "lstrip": false,
30
+ "normalized": false,
31
+ "rstrip": false,
32
+ "single_word": false,
33
+ "special": true
34
+ },
35
+ "4": {
36
+ "content": "[MASK]",
37
+ "lstrip": false,
38
+ "normalized": false,
39
+ "rstrip": false,
40
+ "single_word": false,
41
+ "special": true
42
+ }
43
+ },
44
+ "clean_up_tokenization_spaces": true,
45
+ "cls_token": "[CLS]",
46
+ "do_basic_tokenize": true,
47
+ "do_lower_case": false,
48
+ "full_tokenizer_file": null,
49
+ "mask_token": "[MASK]",
50
+ "model_max_length": 1000000000000000019884624838656,
51
+ "never_split": null,
52
+ "pad_token": "[PAD]",
53
+ "sep_token": "[SEP]",
54
+ "strip_accents": null,
55
+ "tokenize_chinese_chars": true,
56
+ "tokenizer_class": "BertTokenizer",
57
+ "unk_token": "[UNK]"
58
+ }
training_args.bin ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:a181d426a846aed31d185c1c8e7462bde216a5de70b47a96fc82542bdb87ea9d
3
+ size 4920
training_params.json ADDED
@@ -0,0 +1,30 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "data_path": "as-cle-bert/AMR-Gene-Families",
3
+ "model": "Rostlab/prot_bert",
4
+ "lr": 5e-05,
5
+ "epochs": 3,
6
+ "max_seq_length": 128,
7
+ "batch_size": 8,
8
+ "warmup_ratio": 0.1,
9
+ "gradient_accumulation": 1,
10
+ "optimizer": "adamw_torch",
11
+ "scheduler": "linear",
12
+ "weight_decay": 0.0,
13
+ "max_grad_norm": 1.0,
14
+ "seed": 42,
15
+ "train_split": "train",
16
+ "valid_split": "test",
17
+ "text_column": "text",
18
+ "target_column": "label",
19
+ "logging_steps": -1,
20
+ "project_name": "autotrain-fzudm-korrh",
21
+ "auto_find_batch_size": false,
22
+ "mixed_precision": "no",
23
+ "save_total_limit": 1,
24
+ "save_strategy": "epoch",
25
+ "push_to_hub": true,
26
+ "repo_id": "as-cle-bert/autotrain-fzudm-korrh",
27
+ "evaluation_strategy": "epoch",
28
+ "username": "as-cle-bert",
29
+ "log": "none"
30
+ }
vocab.txt ADDED
@@ -0,0 +1,30 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ [PAD]
2
+ [UNK]
3
+ [CLS]
4
+ [SEP]
5
+ [MASK]
6
+ L
7
+ A
8
+ G
9
+ V
10
+ E
11
+ S
12
+ I
13
+ K
14
+ R
15
+ D
16
+ T
17
+ P
18
+ N
19
+ Q
20
+ F
21
+ Y
22
+ M
23
+ H
24
+ C
25
+ W
26
+ X
27
+ U
28
+ B
29
+ Z
30
+ O