Chenghao-Qiu commited on
Commit
04e388d
·
verified ·
1 Parent(s): 1cd1285

Upload folder using huggingface_hub

Browse files
config.json ADDED
@@ -0,0 +1,34 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "_name_or_path": "zhihan1996/DNABERT-2-117M",
3
+ "alibi_starting_size": 512,
4
+ "architectures": [
5
+ "BertForSequenceClassification"
6
+ ],
7
+ "attention_probs_dropout_prob": 0.0,
8
+ "auto_map": {
9
+ "AutoConfig": "zhihan1996/DNABERT-2-117M--configuration_bert.BertConfig",
10
+ "AutoModel": "zhihan1996/DNABERT-2-117M--bert_layers.BertModel",
11
+ "AutoModelForMaskedLM": "zhihan1996/DNABERT-2-117M--bert_layers.BertForMaskedLM",
12
+ "AutoModelForSequenceClassification": "zhihan1996/DNABERT-2-117M--bert_layers.BertForSequenceClassification"
13
+ },
14
+ "classifier_dropout": null,
15
+ "gradient_checkpointing": false,
16
+ "hidden_act": "gelu",
17
+ "hidden_dropout_prob": 0.1,
18
+ "hidden_size": 768,
19
+ "initializer_range": 0.02,
20
+ "intermediate_size": 3072,
21
+ "layer_norm_eps": 1e-12,
22
+ "max_position_embeddings": 512,
23
+ "model_type": "bert",
24
+ "num_attention_heads": 12,
25
+ "num_hidden_layers": 12,
26
+ "pad_token_id": 0,
27
+ "position_embedding_type": "absolute",
28
+ "problem_type": "single_label_classification",
29
+ "torch_dtype": "float32",
30
+ "transformers_version": "4.45.2",
31
+ "type_vocab_size": 2,
32
+ "use_cache": true,
33
+ "vocab_size": 4096
34
+ }
model.safetensors ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:c7e21f9b600d586eeb4db064201ebde43796f70adc7ce707805ccbeb52a3ebb8
3
+ size 468296408
optimizer_state_dict.pth ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:9881afd7df4d60c0b9c2c445b26faf26ce6ee4c3b1b19da1f9da47ee3ecae84c
3
+ size 936682546
special_tokens_map.json ADDED
@@ -0,0 +1,37 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "cls_token": {
3
+ "content": "[CLS]",
4
+ "lstrip": false,
5
+ "normalized": false,
6
+ "rstrip": false,
7
+ "single_word": false
8
+ },
9
+ "mask_token": {
10
+ "content": "[MASK]",
11
+ "lstrip": false,
12
+ "normalized": false,
13
+ "rstrip": false,
14
+ "single_word": false
15
+ },
16
+ "pad_token": {
17
+ "content": "[PAD]",
18
+ "lstrip": false,
19
+ "normalized": false,
20
+ "rstrip": false,
21
+ "single_word": false
22
+ },
23
+ "sep_token": {
24
+ "content": "[SEP]",
25
+ "lstrip": false,
26
+ "normalized": false,
27
+ "rstrip": false,
28
+ "single_word": false
29
+ },
30
+ "unk_token": {
31
+ "content": "[UNK]",
32
+ "lstrip": false,
33
+ "normalized": false,
34
+ "rstrip": false,
35
+ "single_word": false
36
+ }
37
+ }
tokenizer.json ADDED
The diff for this file is too large to render. See raw diff
 
tokenizer_config.json ADDED
@@ -0,0 +1,53 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "added_tokens_decoder": {
3
+ "0": {
4
+ "content": "[UNK]",
5
+ "lstrip": false,
6
+ "normalized": false,
7
+ "rstrip": false,
8
+ "single_word": false,
9
+ "special": true
10
+ },
11
+ "1": {
12
+ "content": "[CLS]",
13
+ "lstrip": false,
14
+ "normalized": false,
15
+ "rstrip": false,
16
+ "single_word": false,
17
+ "special": true
18
+ },
19
+ "2": {
20
+ "content": "[SEP]",
21
+ "lstrip": false,
22
+ "normalized": false,
23
+ "rstrip": false,
24
+ "single_word": false,
25
+ "special": true
26
+ },
27
+ "3": {
28
+ "content": "[PAD]",
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": false,
45
+ "cls_token": "[CLS]",
46
+ "mask_token": "[MASK]",
47
+ "model_max_length": 256,
48
+ "pad_token": "[PAD]",
49
+ "padding_side": "right",
50
+ "sep_token": "[SEP]",
51
+ "tokenizer_class": "PreTrainedTokenizerFast",
52
+ "unk_token": "[UNK]"
53
+ }
trainer_state.json ADDED
@@ -0,0 +1,265 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "best_metric": 0.5052554607391357,
3
+ "best_model_checkpoint": "output_pipe/tf3/origin/checkpoint-800",
4
+ "epoch": 4.0,
5
+ "eval_steps": 200,
6
+ "global_step": 1708,
7
+ "is_hyper_param_search": false,
8
+ "is_local_process_zero": true,
9
+ "is_world_process_zero": true,
10
+ "log_history": [
11
+ {
12
+ "epoch": 0.234192037470726,
13
+ "grad_norm": 2.7039601802825928,
14
+ "learning_rate": 2.9113389626055487e-05,
15
+ "loss": 0.6654,
16
+ "step": 100
17
+ },
18
+ {
19
+ "epoch": 0.468384074941452,
20
+ "grad_norm": 3.1499617099761963,
21
+ "learning_rate": 2.730398069963812e-05,
22
+ "loss": 0.596,
23
+ "step": 200
24
+ },
25
+ {
26
+ "epoch": 0.468384074941452,
27
+ "eval_accuracy": 0.717,
28
+ "eval_f1": 0.7164257621683909,
29
+ "eval_loss": 0.5442966222763062,
30
+ "eval_matthews_correlation": 0.4329679728858218,
31
+ "eval_precision": 0.7166597799182416,
32
+ "eval_recall": 0.7163083356029414,
33
+ "eval_runtime": 0.1542,
34
+ "eval_samples_per_second": 6484.289,
35
+ "eval_steps_per_second": 103.749,
36
+ "step": 200
37
+ },
38
+ {
39
+ "epoch": 0.702576112412178,
40
+ "grad_norm": 7.257410526275635,
41
+ "learning_rate": 2.551266586248492e-05,
42
+ "loss": 0.5642,
43
+ "step": 300
44
+ },
45
+ {
46
+ "epoch": 0.936768149882904,
47
+ "grad_norm": 2.4942615032196045,
48
+ "learning_rate": 2.3703256936067552e-05,
49
+ "loss": 0.5347,
50
+ "step": 400
51
+ },
52
+ {
53
+ "epoch": 0.936768149882904,
54
+ "eval_accuracy": 0.739,
55
+ "eval_f1": 0.73370580511142,
56
+ "eval_loss": 0.5310949683189392,
57
+ "eval_matthews_correlation": 0.48433190369826334,
58
+ "eval_precision": 0.7496817401892955,
59
+ "eval_recall": 0.7348763998141592,
60
+ "eval_runtime": 0.1461,
61
+ "eval_samples_per_second": 6845.049,
62
+ "eval_steps_per_second": 109.521,
63
+ "step": 400
64
+ },
65
+ {
66
+ "epoch": 1.17096018735363,
67
+ "grad_norm": 2.8709988594055176,
68
+ "learning_rate": 2.1911942098914357e-05,
69
+ "loss": 0.5004,
70
+ "step": 500
71
+ },
72
+ {
73
+ "epoch": 1.405152224824356,
74
+ "grad_norm": 4.1638407707214355,
75
+ "learning_rate": 2.0102533172496985e-05,
76
+ "loss": 0.4955,
77
+ "step": 600
78
+ },
79
+ {
80
+ "epoch": 1.405152224824356,
81
+ "eval_accuracy": 0.734,
82
+ "eval_f1": 0.7339904236552517,
83
+ "eval_loss": 0.5175114870071411,
84
+ "eval_matthews_correlation": 0.4705750950456619,
85
+ "eval_precision": 0.7354063762909744,
86
+ "eval_recall": 0.7351687787372435,
87
+ "eval_runtime": 0.1445,
88
+ "eval_samples_per_second": 6918.485,
89
+ "eval_steps_per_second": 110.696,
90
+ "step": 600
91
+ },
92
+ {
93
+ "epoch": 1.639344262295082,
94
+ "grad_norm": 2.644895553588867,
95
+ "learning_rate": 1.8293124246079617e-05,
96
+ "loss": 0.4805,
97
+ "step": 700
98
+ },
99
+ {
100
+ "epoch": 1.8735362997658078,
101
+ "grad_norm": 2.8720955848693848,
102
+ "learning_rate": 1.6483715319662242e-05,
103
+ "loss": 0.4715,
104
+ "step": 800
105
+ },
106
+ {
107
+ "epoch": 1.8735362997658078,
108
+ "eval_accuracy": 0.746,
109
+ "eval_f1": 0.7451426599079303,
110
+ "eval_loss": 0.5052554607391357,
111
+ "eval_matthews_correlation": 0.491011015471221,
112
+ "eval_precision": 0.7461352657004832,
113
+ "eval_recall": 0.7448773610599337,
114
+ "eval_runtime": 0.1451,
115
+ "eval_samples_per_second": 6890.491,
116
+ "eval_steps_per_second": 110.248,
117
+ "step": 800
118
+ },
119
+ {
120
+ "epoch": 2.107728337236534,
121
+ "grad_norm": 3.5036978721618652,
122
+ "learning_rate": 1.4674306393244874e-05,
123
+ "loss": 0.447,
124
+ "step": 900
125
+ },
126
+ {
127
+ "epoch": 2.34192037470726,
128
+ "grad_norm": 3.8766090869903564,
129
+ "learning_rate": 1.2864897466827504e-05,
130
+ "loss": 0.3976,
131
+ "step": 1000
132
+ },
133
+ {
134
+ "epoch": 2.34192037470726,
135
+ "eval_accuracy": 0.739,
136
+ "eval_f1": 0.738999738999739,
137
+ "eval_loss": 0.533879280090332,
138
+ "eval_matthews_correlation": 0.4800256364380334,
139
+ "eval_precision": 0.7400306041924539,
140
+ "eval_recall": 0.7399950335634984,
141
+ "eval_runtime": 0.1465,
142
+ "eval_samples_per_second": 6824.012,
143
+ "eval_steps_per_second": 109.184,
144
+ "step": 1000
145
+ },
146
+ {
147
+ "epoch": 2.576112412177986,
148
+ "grad_norm": 4.963836669921875,
149
+ "learning_rate": 1.1055488540410132e-05,
150
+ "loss": 0.3976,
151
+ "step": 1100
152
+ },
153
+ {
154
+ "epoch": 2.810304449648712,
155
+ "grad_norm": 5.53127384185791,
156
+ "learning_rate": 9.246079613992762e-06,
157
+ "loss": 0.3951,
158
+ "step": 1200
159
+ },
160
+ {
161
+ "epoch": 2.810304449648712,
162
+ "eval_accuracy": 0.754,
163
+ "eval_f1": 0.7527180905815749,
164
+ "eval_loss": 0.5216661095619202,
165
+ "eval_matthews_correlation": 0.5074068589508701,
166
+ "eval_precision": 0.7550306778261644,
167
+ "eval_recall": 0.7523830884826735,
168
+ "eval_runtime": 0.1477,
169
+ "eval_samples_per_second": 6769.341,
170
+ "eval_steps_per_second": 108.309,
171
+ "step": 1200
172
+ },
173
+ {
174
+ "epoch": 3.0444964871194378,
175
+ "grad_norm": 6.315124034881592,
176
+ "learning_rate": 7.436670687575392e-06,
177
+ "loss": 0.3806,
178
+ "step": 1300
179
+ },
180
+ {
181
+ "epoch": 3.278688524590164,
182
+ "grad_norm": 6.265092372894287,
183
+ "learning_rate": 5.627261761158022e-06,
184
+ "loss": 0.3164,
185
+ "step": 1400
186
+ },
187
+ {
188
+ "epoch": 3.278688524590164,
189
+ "eval_accuracy": 0.747,
190
+ "eval_f1": 0.7469977229795068,
191
+ "eval_loss": 0.5834727883338928,
192
+ "eval_matthews_correlation": 0.495624205103108,
193
+ "eval_precision": 0.7477629866880192,
194
+ "eval_recall": 0.7478612281516845,
195
+ "eval_runtime": 0.141,
196
+ "eval_samples_per_second": 7094.176,
197
+ "eval_steps_per_second": 113.507,
198
+ "step": 1400
199
+ },
200
+ {
201
+ "epoch": 3.51288056206089,
202
+ "grad_norm": 3.3670613765716553,
203
+ "learning_rate": 3.817852834740652e-06,
204
+ "loss": 0.322,
205
+ "step": 1500
206
+ },
207
+ {
208
+ "epoch": 3.747072599531616,
209
+ "grad_norm": 3.348931312561035,
210
+ "learning_rate": 2.0084439083232813e-06,
211
+ "loss": 0.3142,
212
+ "step": 1600
213
+ },
214
+ {
215
+ "epoch": 3.747072599531616,
216
+ "eval_accuracy": 0.746,
217
+ "eval_f1": 0.7455929487179487,
218
+ "eval_loss": 0.6034936904907227,
219
+ "eval_matthews_correlation": 0.491209820260192,
220
+ "eval_precision": 0.7456836435338816,
221
+ "eval_recall": 0.7455262019577372,
222
+ "eval_runtime": 0.144,
223
+ "eval_samples_per_second": 6943.522,
224
+ "eval_steps_per_second": 111.096,
225
+ "step": 1600
226
+ },
227
+ {
228
+ "epoch": 3.981264637002342,
229
+ "grad_norm": 5.6311235427856445,
230
+ "learning_rate": 1.9903498190591076e-07,
231
+ "loss": 0.3161,
232
+ "step": 1700
233
+ },
234
+ {
235
+ "epoch": 4.0,
236
+ "step": 1708,
237
+ "total_flos": 2164148938566432.0,
238
+ "train_loss": 0.4461390853486519,
239
+ "train_runtime": 82.1619,
240
+ "train_samples_per_second": 1328.791,
241
+ "train_steps_per_second": 20.788
242
+ }
243
+ ],
244
+ "logging_steps": 100,
245
+ "max_steps": 1708,
246
+ "num_input_tokens_seen": 0,
247
+ "num_train_epochs": 4,
248
+ "save_steps": 200,
249
+ "stateful_callbacks": {
250
+ "TrainerControl": {
251
+ "args": {
252
+ "should_epoch_stop": false,
253
+ "should_evaluate": false,
254
+ "should_log": false,
255
+ "should_save": true,
256
+ "should_training_stop": true
257
+ },
258
+ "attributes": {}
259
+ }
260
+ },
261
+ "total_flos": 2164148938566432.0,
262
+ "train_batch_size": 64,
263
+ "trial_name": null,
264
+ "trial_params": null
265
+ }
training_args.bin ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:ab1010cc30d040e025f20270dccc788d1ba283b2bc779c0608781cb8d9e23077
3
+ size 5368