joneill
commited on
Commit
·
876243b
1
Parent(s):
709adc1
Added model files and documentation
Browse files- README.md +69 -0
- checkpoint-10595/config.json +48 -0
- checkpoint-10595/model.safetensors +3 -0
- checkpoint-10595/optimizer.pt +3 -0
- checkpoint-10595/rng_state.pth +3 -0
- checkpoint-10595/scheduler.pt +3 -0
- checkpoint-10595/trainer_state.json +228 -0
- checkpoint-10595/training_args.bin +3 -0
- checkpoint-3204/config.json +50 -0
- checkpoint-3204/model.safetensors +3 -0
- checkpoint-3204/optimizer.pt +3 -0
- checkpoint-3204/rng_state.pth +3 -0
- checkpoint-3204/scheduler.pt +3 -0
- checkpoint-3204/trainer_state.json +87 -0
- checkpoint-3204/training_args.bin +3 -0
- checkpoint-8010/config.json +50 -0
- checkpoint-8010/model.safetensors +3 -0
- checkpoint-8010/optimizer.pt +3 -0
- checkpoint-8010/rng_state.pth +3 -0
- checkpoint-8010/scheduler.pt +3 -0
- checkpoint-8010/trainer_state.json +193 -0
- checkpoint-8010/training_args.bin +3 -0
- config.json +48 -0
- model.safetensors +3 -0
- runs/Apr25_14-35-27_hpcf/events.out.tfevents.1714080930.hpcf.137937.0 +3 -0
- runs/Apr26_09-58-52_hpcf/events.out.tfevents.1714150736.hpcf.183226.0 +3 -0
- runs/Apr26_10-20-51_hpcf/events.out.tfevents.1714152055.hpcf.183659.0 +3 -0
- runs/Apr26_10-21-30_hpcf/events.out.tfevents.1714152093.hpcf.186484.0 +3 -0
- special_tokens_map.json +7 -0
- tokenizer.json +0 -0
- tokenizer_config.json +61 -0
- training_args.bin +3 -0
- vocab.txt +0 -0
README.md
ADDED
@@ -0,0 +1,69 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
1 |
+
# CarD-T: Carcinogen Detection via Transformers
|
2 |
+
|
3 |
+
## Overview
|
4 |
+
|
5 |
+
CarD-T (Carcinogen Detection via Transformers) is a novel text analytics approach that combines transformer-based machine learning with probabilistic statistical analysis to efficiently nominate carcinogens from scientific texts. This model is designed to address the challenges faced by current systems in managing the burgeoning biomedical literature related to carcinogen identification and classification.
|
6 |
+
|
7 |
+
## Model Details
|
8 |
+
|
9 |
+
- **Architecture**: Based on Bio-ELECTRA, a 335 million parameter language model
|
10 |
+
- **Training Data**: PubMed abstracts featuring known carcinogens from International Agency for Research on Cancer (IARC) groups G1 and G2A
|
11 |
+
- **Task**: Named Entity Recognition (NER) for carcinogen identification
|
12 |
+
- **Performance**:
|
13 |
+
- Precision: 0.894
|
14 |
+
- Recall: 0.857
|
15 |
+
- F1 Score: 0.875
|
16 |
+
|
17 |
+
## Features
|
18 |
+
|
19 |
+
- Efficient nomination of potential carcinogens from scientific literature
|
20 |
+
- Context classifier to enhance accuracy and manage computational demands
|
21 |
+
- Capable of identifying both chemical and non-chemical carcinogenic factors
|
22 |
+
- Trained on a comprehensive dataset of carcinogen-related abstracts from 2000-2024
|
23 |
+
|
24 |
+
## Use Cases
|
25 |
+
|
26 |
+
- Streamlining toxicogenomic literature reviews
|
27 |
+
- Identifying potential carcinogens for further investigation
|
28 |
+
- Augmenting existing carcinogen databases with emerging candidates
|
29 |
+
|
30 |
+
## Limitations
|
31 |
+
|
32 |
+
- Identifies potential candidates, not confirmed carcinogens
|
33 |
+
- Analysis limited to abstract-level information
|
34 |
+
- May be influenced by publication trends and research focus shifts
|
35 |
+
|
36 |
+
|
37 |
+
## Citation
|
38 |
+
|
39 |
+
If you use this model in your research, please cite:
|
40 |
+
|
41 |
+
O'Neill, J., Reddy, G.A., Dhillon, N., Tripathi, O., Alexandrov, L., & Katira, P. (2024). CarD-T: Interpreting Carcinomic Lexicon via Transformers. BioRxiv.
|
42 |
+
|
43 |
+
## License
|
44 |
+
|
45 |
+
MIT License
|
46 |
+
|
47 |
+
Copyright (c) 2024 Jamey O'Neill
|
48 |
+
|
49 |
+
Permission is hereby granted, free of charge, to any person obtaining a copy
|
50 |
+
of this software and associated documentation files (the "Software"), to deal
|
51 |
+
in the Software without restriction, including without limitation the rights
|
52 |
+
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
|
53 |
+
copies of the Software, and to permit persons to whom the Software is
|
54 |
+
furnished to do so, subject to the following conditions:
|
55 |
+
|
56 |
+
The above copyright notice and this permission notice shall be included in all
|
57 |
+
copies or substantial portions of the Software.
|
58 |
+
|
59 |
+
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
|
60 |
+
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
|
61 |
+
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
|
62 |
+
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
|
63 |
+
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
|
64 |
+
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
|
65 |
+
SOFTWARE.
|
66 |
+
|
67 |
+
## Contact
|
68 |
+
|
69 |
+
For questions and feedback, please contact Jamey ONeill at [email protected].
|
checkpoint-10595/config.json
ADDED
@@ -0,0 +1,48 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
1 |
+
{
|
2 |
+
"_name_or_path": "sultan/BioM-ELECTRA-Large-SQuAD2",
|
3 |
+
"architectures": [
|
4 |
+
"ElectraForTokenClassification"
|
5 |
+
],
|
6 |
+
"attention_probs_dropout_prob": 0.1,
|
7 |
+
"classifier_dropout": null,
|
8 |
+
"embedding_size": 1024,
|
9 |
+
"hidden_act": "gelu",
|
10 |
+
"hidden_dropout_prob": 0.1,
|
11 |
+
"hidden_size": 1024,
|
12 |
+
"id2label": {
|
13 |
+
"0": "O",
|
14 |
+
"1": "B-cancertype",
|
15 |
+
"2": "B-carcinogen",
|
16 |
+
"3": "B-negative",
|
17 |
+
"4": "I-cancertype",
|
18 |
+
"5": "I-carcinogen",
|
19 |
+
"6": "I-negative"
|
20 |
+
},
|
21 |
+
"initializer_range": 0.02,
|
22 |
+
"intermediate_size": 4096,
|
23 |
+
"label2id": {
|
24 |
+
"B-cancertype": 1,
|
25 |
+
"B-carcinogen": 2,
|
26 |
+
"B-negative": 3,
|
27 |
+
"I-cancertype": 4,
|
28 |
+
"I-carcinogen": 5,
|
29 |
+
"I-negative": 6,
|
30 |
+
"O": 0
|
31 |
+
},
|
32 |
+
"layer_norm_eps": 1e-12,
|
33 |
+
"max_position_embeddings": 512,
|
34 |
+
"model_type": "electra",
|
35 |
+
"num_attention_heads": 16,
|
36 |
+
"num_hidden_layers": 24,
|
37 |
+
"pad_token_id": 0,
|
38 |
+
"position_embedding_type": "absolute",
|
39 |
+
"summary_activation": "gelu",
|
40 |
+
"summary_last_dropout": 0.1,
|
41 |
+
"summary_type": "first",
|
42 |
+
"summary_use_proj": true,
|
43 |
+
"torch_dtype": "float32",
|
44 |
+
"transformers_version": "4.40.1",
|
45 |
+
"type_vocab_size": 2,
|
46 |
+
"use_cache": true,
|
47 |
+
"vocab_size": 28895
|
48 |
+
}
|
checkpoint-10595/model.safetensors
ADDED
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
1 |
+
version https://git-lfs.github.com/spec/v1
|
2 |
+
oid sha256:1152dab87a3cb1cf2d6d8812b793cf31390c77c430ba4c20736601390303770a
|
3 |
+
size 1329781612
|
checkpoint-10595/optimizer.pt
ADDED
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
1 |
+
version https://git-lfs.github.com/spec/v1
|
2 |
+
oid sha256:15a0c6be3b8cad9cacda15dab0ad3bfb05a3f313d063e536180c0ccf651b85f1
|
3 |
+
size 2659794471
|
checkpoint-10595/rng_state.pth
ADDED
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
1 |
+
version https://git-lfs.github.com/spec/v1
|
2 |
+
oid sha256:17024af815d4eee454cd54e1c9d6acbc87c00976e22d68b0fae1dc0f611fdbe4
|
3 |
+
size 14244
|
checkpoint-10595/scheduler.pt
ADDED
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
1 |
+
version https://git-lfs.github.com/spec/v1
|
2 |
+
oid sha256:cc25d54a6f628bcee11085d2055063ab51e6a482a0b0a73494d5bd691588b7b4
|
3 |
+
size 1064
|
checkpoint-10595/trainer_state.json
ADDED
@@ -0,0 +1,228 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
1 |
+
{
|
2 |
+
"best_metric": 0.0534161813557148,
|
3 |
+
"best_model_checkpoint": "/storage/BioM-ELECTRA-Large-SQuAD2_carDB_5e_neg_lg_SGD/checkpoint-4238",
|
4 |
+
"epoch": 5.0,
|
5 |
+
"eval_steps": 500,
|
6 |
+
"global_step": 10595,
|
7 |
+
"is_hyper_param_search": false,
|
8 |
+
"is_local_process_zero": true,
|
9 |
+
"is_world_process_zero": true,
|
10 |
+
"log_history": [
|
11 |
+
{
|
12 |
+
"epoch": 0.23596035865974516,
|
13 |
+
"grad_norm": 1.2747831344604492,
|
14 |
+
"learning_rate": 1.9063709296838132e-05,
|
15 |
+
"loss": 0.1626,
|
16 |
+
"step": 500
|
17 |
+
},
|
18 |
+
{
|
19 |
+
"epoch": 0.4719207173194903,
|
20 |
+
"grad_norm": 0.4436088800430298,
|
21 |
+
"learning_rate": 1.8119867862199152e-05,
|
22 |
+
"loss": 0.0822,
|
23 |
+
"step": 1000
|
24 |
+
},
|
25 |
+
{
|
26 |
+
"epoch": 0.7078810759792354,
|
27 |
+
"grad_norm": 1.6280406713485718,
|
28 |
+
"learning_rate": 1.7176026427560172e-05,
|
29 |
+
"loss": 0.0789,
|
30 |
+
"step": 1500
|
31 |
+
},
|
32 |
+
{
|
33 |
+
"epoch": 0.9438414346389806,
|
34 |
+
"grad_norm": 2.336548089981079,
|
35 |
+
"learning_rate": 1.6232184992921192e-05,
|
36 |
+
"loss": 0.0706,
|
37 |
+
"step": 2000
|
38 |
+
},
|
39 |
+
{
|
40 |
+
"epoch": 1.0,
|
41 |
+
"eval_accuracy_score": 0.9812832660700708,
|
42 |
+
"eval_f1": 0.8218279984573852,
|
43 |
+
"eval_loss": 0.05883064866065979,
|
44 |
+
"eval_precision": 0.8056710775047259,
|
45 |
+
"eval_recall": 0.8386462022825659,
|
46 |
+
"eval_runtime": 5.2595,
|
47 |
+
"eval_samples_per_second": 358.209,
|
48 |
+
"eval_steps_per_second": 44.871,
|
49 |
+
"step": 2119
|
50 |
+
},
|
51 |
+
{
|
52 |
+
"epoch": 1.1798017932987257,
|
53 |
+
"grad_norm": 2.0369768142700195,
|
54 |
+
"learning_rate": 1.528834355828221e-05,
|
55 |
+
"loss": 0.0496,
|
56 |
+
"step": 2500
|
57 |
+
},
|
58 |
+
{
|
59 |
+
"epoch": 1.415762151958471,
|
60 |
+
"grad_norm": 0.6217797994613647,
|
61 |
+
"learning_rate": 1.4344502123643229e-05,
|
62 |
+
"loss": 0.0487,
|
63 |
+
"step": 3000
|
64 |
+
},
|
65 |
+
{
|
66 |
+
"epoch": 1.651722510618216,
|
67 |
+
"grad_norm": 0.8187075257301331,
|
68 |
+
"learning_rate": 1.3400660689004247e-05,
|
69 |
+
"loss": 0.0455,
|
70 |
+
"step": 3500
|
71 |
+
},
|
72 |
+
{
|
73 |
+
"epoch": 1.8876828692779613,
|
74 |
+
"grad_norm": 1.2321038246154785,
|
75 |
+
"learning_rate": 1.2456819254365267e-05,
|
76 |
+
"loss": 0.0439,
|
77 |
+
"step": 4000
|
78 |
+
},
|
79 |
+
{
|
80 |
+
"epoch": 2.0,
|
81 |
+
"eval_accuracy_score": 0.9828429938975649,
|
82 |
+
"eval_f1": 0.8423466462832028,
|
83 |
+
"eval_loss": 0.0534161813557148,
|
84 |
+
"eval_precision": 0.8187221396731055,
|
85 |
+
"eval_recall": 0.867375049193231,
|
86 |
+
"eval_runtime": 5.2808,
|
87 |
+
"eval_samples_per_second": 356.764,
|
88 |
+
"eval_steps_per_second": 44.69,
|
89 |
+
"step": 4238
|
90 |
+
},
|
91 |
+
{
|
92 |
+
"epoch": 2.1236432279377064,
|
93 |
+
"grad_norm": 1.0647934675216675,
|
94 |
+
"learning_rate": 1.1512977819726287e-05,
|
95 |
+
"loss": 0.0337,
|
96 |
+
"step": 4500
|
97 |
+
},
|
98 |
+
{
|
99 |
+
"epoch": 2.3596035865974514,
|
100 |
+
"grad_norm": 0.07234682887792587,
|
101 |
+
"learning_rate": 1.0569136385087306e-05,
|
102 |
+
"loss": 0.0247,
|
103 |
+
"step": 5000
|
104 |
+
},
|
105 |
+
{
|
106 |
+
"epoch": 2.595563945257197,
|
107 |
+
"grad_norm": 2.0315685272216797,
|
108 |
+
"learning_rate": 9.625294950448326e-06,
|
109 |
+
"loss": 0.0263,
|
110 |
+
"step": 5500
|
111 |
+
},
|
112 |
+
{
|
113 |
+
"epoch": 2.831524303916942,
|
114 |
+
"grad_norm": 0.034490641206502914,
|
115 |
+
"learning_rate": 8.681453515809346e-06,
|
116 |
+
"loss": 0.027,
|
117 |
+
"step": 6000
|
118 |
+
},
|
119 |
+
{
|
120 |
+
"epoch": 3.0,
|
121 |
+
"eval_accuracy_score": 0.9833888986371878,
|
122 |
+
"eval_f1": 0.853031465848043,
|
123 |
+
"eval_loss": 0.06263311207294464,
|
124 |
+
"eval_precision": 0.832272557094721,
|
125 |
+
"eval_recall": 0.8748524203069658,
|
126 |
+
"eval_runtime": 5.3057,
|
127 |
+
"eval_samples_per_second": 355.091,
|
128 |
+
"eval_steps_per_second": 44.481,
|
129 |
+
"step": 6357
|
130 |
+
},
|
131 |
+
{
|
132 |
+
"epoch": 3.067484662576687,
|
133 |
+
"grad_norm": 0.1344643086194992,
|
134 |
+
"learning_rate": 7.739499764039643e-06,
|
135 |
+
"loss": 0.0254,
|
136 |
+
"step": 6500
|
137 |
+
},
|
138 |
+
{
|
139 |
+
"epoch": 3.303445021236432,
|
140 |
+
"grad_norm": 0.07355394959449768,
|
141 |
+
"learning_rate": 6.795658329400662e-06,
|
142 |
+
"loss": 0.0163,
|
143 |
+
"step": 7000
|
144 |
+
},
|
145 |
+
{
|
146 |
+
"epoch": 3.5394053798961775,
|
147 |
+
"grad_norm": 0.7838532328605652,
|
148 |
+
"learning_rate": 5.85181689476168e-06,
|
149 |
+
"loss": 0.016,
|
150 |
+
"step": 7500
|
151 |
+
},
|
152 |
+
{
|
153 |
+
"epoch": 3.7753657385559225,
|
154 |
+
"grad_norm": 3.0708000659942627,
|
155 |
+
"learning_rate": 4.9079754601227e-06,
|
156 |
+
"loss": 0.0138,
|
157 |
+
"step": 8000
|
158 |
+
},
|
159 |
+
{
|
160 |
+
"epoch": 4.0,
|
161 |
+
"eval_accuracy_score": 0.9838763135832798,
|
162 |
+
"eval_f1": 0.8535911602209945,
|
163 |
+
"eval_loss": 0.06983982026576996,
|
164 |
+
"eval_precision": 0.8559556786703602,
|
165 |
+
"eval_recall": 0.8512396694214877,
|
166 |
+
"eval_runtime": 5.271,
|
167 |
+
"eval_samples_per_second": 357.425,
|
168 |
+
"eval_steps_per_second": 44.773,
|
169 |
+
"step": 8476
|
170 |
+
},
|
171 |
+
{
|
172 |
+
"epoch": 4.011326097215668,
|
173 |
+
"grad_norm": 0.10571020096540451,
|
174 |
+
"learning_rate": 3.966021708352997e-06,
|
175 |
+
"loss": 0.0144,
|
176 |
+
"step": 8500
|
177 |
+
},
|
178 |
+
{
|
179 |
+
"epoch": 4.247286455875413,
|
180 |
+
"grad_norm": 0.029509373009204865,
|
181 |
+
"learning_rate": 3.0221802737140165e-06,
|
182 |
+
"loss": 0.0086,
|
183 |
+
"step": 9000
|
184 |
+
},
|
185 |
+
{
|
186 |
+
"epoch": 4.483246814535158,
|
187 |
+
"grad_norm": 1.1270127296447754,
|
188 |
+
"learning_rate": 2.0783388390750357e-06,
|
189 |
+
"loss": 0.0066,
|
190 |
+
"step": 9500
|
191 |
+
},
|
192 |
+
{
|
193 |
+
"epoch": 4.719207173194903,
|
194 |
+
"grad_norm": 0.010910986922681332,
|
195 |
+
"learning_rate": 1.134497404436055e-06,
|
196 |
+
"loss": 0.0097,
|
197 |
+
"step": 10000
|
198 |
+
},
|
199 |
+
{
|
200 |
+
"epoch": 4.955167531854649,
|
201 |
+
"grad_norm": 1.0645971298217773,
|
202 |
+
"learning_rate": 1.906559697970741e-07,
|
203 |
+
"loss": 0.0076,
|
204 |
+
"step": 10500
|
205 |
+
},
|
206 |
+
{
|
207 |
+
"epoch": 5.0,
|
208 |
+
"eval_accuracy_score": 0.9837593339962176,
|
209 |
+
"eval_f1": 0.8539891556932611,
|
210 |
+
"eval_loss": 0.07769417762756348,
|
211 |
+
"eval_precision": 0.8406404879908502,
|
212 |
+
"eval_recall": 0.8677685950413223,
|
213 |
+
"eval_runtime": 5.252,
|
214 |
+
"eval_samples_per_second": 358.721,
|
215 |
+
"eval_steps_per_second": 44.935,
|
216 |
+
"step": 10595
|
217 |
+
}
|
218 |
+
],
|
219 |
+
"logging_steps": 500,
|
220 |
+
"max_steps": 10595,
|
221 |
+
"num_input_tokens_seen": 0,
|
222 |
+
"num_train_epochs": 5,
|
223 |
+
"save_steps": 500,
|
224 |
+
"total_flos": 1.7692937221754256e+16,
|
225 |
+
"train_batch_size": 8,
|
226 |
+
"trial_name": null,
|
227 |
+
"trial_params": null
|
228 |
+
}
|
checkpoint-10595/training_args.bin
ADDED
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
1 |
+
version https://git-lfs.github.com/spec/v1
|
2 |
+
oid sha256:07af839673be954537faf350c212a49f3f745cf8247da4cb4f9a1d9f73b78ed7
|
3 |
+
size 5048
|
checkpoint-3204/config.json
ADDED
@@ -0,0 +1,50 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
1 |
+
{
|
2 |
+
"_name_or_path": "sultan/BioM-ELECTRA-Large-SQuAD2",
|
3 |
+
"architectures": [
|
4 |
+
"ElectraForTokenClassification"
|
5 |
+
],
|
6 |
+
"attention_probs_dropout_prob": 0.1,
|
7 |
+
"classifier_dropout": null,
|
8 |
+
"embedding_size": 1024,
|
9 |
+
"hidden_act": "gelu",
|
10 |
+
"hidden_dropout_prob": 0.1,
|
11 |
+
"hidden_size": 1024,
|
12 |
+
"id2label": {
|
13 |
+
"0": "O",
|
14 |
+
"1": "B-antineoplastic",
|
15 |
+
"2": "B-cancertype",
|
16 |
+
"3": "B-carcinogen",
|
17 |
+
"4": "B-negative",
|
18 |
+
"5": "I-cancertype",
|
19 |
+
"6": "I-carcinogen",
|
20 |
+
"7": "I-negative"
|
21 |
+
},
|
22 |
+
"initializer_range": 0.02,
|
23 |
+
"intermediate_size": 4096,
|
24 |
+
"label2id": {
|
25 |
+
"B-antineoplastic": 1,
|
26 |
+
"B-cancertype": 2,
|
27 |
+
"B-carcinogen": 3,
|
28 |
+
"B-negative": 4,
|
29 |
+
"I-cancertype": 5,
|
30 |
+
"I-carcinogen": 6,
|
31 |
+
"I-negative": 7,
|
32 |
+
"O": 0
|
33 |
+
},
|
34 |
+
"layer_norm_eps": 1e-12,
|
35 |
+
"max_position_embeddings": 512,
|
36 |
+
"model_type": "electra",
|
37 |
+
"num_attention_heads": 16,
|
38 |
+
"num_hidden_layers": 24,
|
39 |
+
"pad_token_id": 0,
|
40 |
+
"position_embedding_type": "absolute",
|
41 |
+
"summary_activation": "gelu",
|
42 |
+
"summary_last_dropout": 0.1,
|
43 |
+
"summary_type": "first",
|
44 |
+
"summary_use_proj": true,
|
45 |
+
"torch_dtype": "float32",
|
46 |
+
"transformers_version": "4.40.1",
|
47 |
+
"type_vocab_size": 2,
|
48 |
+
"use_cache": true,
|
49 |
+
"vocab_size": 28895
|
50 |
+
}
|
checkpoint-3204/model.safetensors
ADDED
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
1 |
+
version https://git-lfs.github.com/spec/v1
|
2 |
+
oid sha256:3ca26bb96ef03d72f27f204e9972313d8190bf4c74542e7b5ba3c035bd9011e4
|
3 |
+
size 1329785712
|
checkpoint-3204/optimizer.pt
ADDED
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
1 |
+
version https://git-lfs.github.com/spec/v1
|
2 |
+
oid sha256:f27b65e1ecc59b25c4d7e5c7daf5576fa34b0dfa99c71f5de7be4333aec324da
|
3 |
+
size 2659802663
|
checkpoint-3204/rng_state.pth
ADDED
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
1 |
+
version https://git-lfs.github.com/spec/v1
|
2 |
+
oid sha256:223e37654453351bb53133440aabdb815af7d246c62afead675019647840ae7f
|
3 |
+
size 14244
|
checkpoint-3204/scheduler.pt
ADDED
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
1 |
+
version https://git-lfs.github.com/spec/v1
|
2 |
+
oid sha256:a90c28e7909084a367599a7cdab33ed7a9cb38d9886e04e2a407c17d10355fba
|
3 |
+
size 1064
|
checkpoint-3204/trainer_state.json
ADDED
@@ -0,0 +1,87 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
1 |
+
{
|
2 |
+
"best_metric": 0.07832363992929459,
|
3 |
+
"best_model_checkpoint": "/storage/BioM-ELECTRA-Large-SQuAD2_carDB_5e_neg_lg_SGD/checkpoint-3204",
|
4 |
+
"epoch": 2.0,
|
5 |
+
"eval_steps": 500,
|
6 |
+
"global_step": 3204,
|
7 |
+
"is_hyper_param_search": false,
|
8 |
+
"is_local_process_zero": true,
|
9 |
+
"is_world_process_zero": true,
|
10 |
+
"log_history": [
|
11 |
+
{
|
12 |
+
"epoch": 0.3121098626716604,
|
13 |
+
"grad_norm": 3.2046010494232178,
|
14 |
+
"learning_rate": 4.690387016229713e-05,
|
15 |
+
"loss": 0.1789,
|
16 |
+
"step": 500
|
17 |
+
},
|
18 |
+
{
|
19 |
+
"epoch": 0.6242197253433208,
|
20 |
+
"grad_norm": 1.161939263343811,
|
21 |
+
"learning_rate": 4.378277153558052e-05,
|
22 |
+
"loss": 0.1113,
|
23 |
+
"step": 1000
|
24 |
+
},
|
25 |
+
{
|
26 |
+
"epoch": 0.9363295880149812,
|
27 |
+
"grad_norm": 2.1341910362243652,
|
28 |
+
"learning_rate": 4.066167290886392e-05,
|
29 |
+
"loss": 0.1054,
|
30 |
+
"step": 1500
|
31 |
+
},
|
32 |
+
{
|
33 |
+
"epoch": 1.0,
|
34 |
+
"eval_accuracy_score": 0.9690997325938397,
|
35 |
+
"eval_f1": 0.7794316644113668,
|
36 |
+
"eval_loss": 0.08875501155853271,
|
37 |
+
"eval_precision": 0.7747886241352806,
|
38 |
+
"eval_recall": 0.7841306884480747,
|
39 |
+
"eval_runtime": 4.093,
|
40 |
+
"eval_samples_per_second": 348.153,
|
41 |
+
"eval_steps_per_second": 43.733,
|
42 |
+
"step": 1602
|
43 |
+
},
|
44 |
+
{
|
45 |
+
"epoch": 1.2484394506866416,
|
46 |
+
"grad_norm": 0.97569340467453,
|
47 |
+
"learning_rate": 3.754057428214732e-05,
|
48 |
+
"loss": 0.079,
|
49 |
+
"step": 2000
|
50 |
+
},
|
51 |
+
{
|
52 |
+
"epoch": 1.5605493133583022,
|
53 |
+
"grad_norm": 0.8073092699050903,
|
54 |
+
"learning_rate": 3.441947565543071e-05,
|
55 |
+
"loss": 0.0685,
|
56 |
+
"step": 2500
|
57 |
+
},
|
58 |
+
{
|
59 |
+
"epoch": 1.8726591760299627,
|
60 |
+
"grad_norm": 2.6909968852996826,
|
61 |
+
"learning_rate": 3.129837702871411e-05,
|
62 |
+
"loss": 0.0671,
|
63 |
+
"step": 3000
|
64 |
+
},
|
65 |
+
{
|
66 |
+
"epoch": 2.0,
|
67 |
+
"eval_accuracy_score": 0.973506982271962,
|
68 |
+
"eval_f1": 0.814260389994091,
|
69 |
+
"eval_loss": 0.07832363992929459,
|
70 |
+
"eval_precision": 0.8248204309656824,
|
71 |
+
"eval_recall": 0.8039673278879813,
|
72 |
+
"eval_runtime": 4.1937,
|
73 |
+
"eval_samples_per_second": 339.796,
|
74 |
+
"eval_steps_per_second": 42.683,
|
75 |
+
"step": 3204
|
76 |
+
}
|
77 |
+
],
|
78 |
+
"logging_steps": 500,
|
79 |
+
"max_steps": 8010,
|
80 |
+
"num_input_tokens_seen": 0,
|
81 |
+
"num_train_epochs": 5,
|
82 |
+
"save_steps": 500,
|
83 |
+
"total_flos": 4245597826238592.0,
|
84 |
+
"train_batch_size": 8,
|
85 |
+
"trial_name": null,
|
86 |
+
"trial_params": null
|
87 |
+
}
|
checkpoint-3204/training_args.bin
ADDED
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
1 |
+
version https://git-lfs.github.com/spec/v1
|
2 |
+
oid sha256:36534a66cd54fa62d55a78ae7da66791486f97dbf75f55360327b517cd4e0be3
|
3 |
+
size 5048
|
checkpoint-8010/config.json
ADDED
@@ -0,0 +1,50 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
1 |
+
{
|
2 |
+
"_name_or_path": "sultan/BioM-ELECTRA-Large-SQuAD2",
|
3 |
+
"architectures": [
|
4 |
+
"ElectraForTokenClassification"
|
5 |
+
],
|
6 |
+
"attention_probs_dropout_prob": 0.1,
|
7 |
+
"classifier_dropout": null,
|
8 |
+
"embedding_size": 1024,
|
9 |
+
"hidden_act": "gelu",
|
10 |
+
"hidden_dropout_prob": 0.1,
|
11 |
+
"hidden_size": 1024,
|
12 |
+
"id2label": {
|
13 |
+
"0": "O",
|
14 |
+
"1": "B-antineoplastic",
|
15 |
+
"2": "B-cancertype",
|
16 |
+
"3": "B-carcinogen",
|
17 |
+
"4": "B-negative",
|
18 |
+
"5": "I-cancertype",
|
19 |
+
"6": "I-carcinogen",
|
20 |
+
"7": "I-negative"
|
21 |
+
},
|
22 |
+
"initializer_range": 0.02,
|
23 |
+
"intermediate_size": 4096,
|
24 |
+
"label2id": {
|
25 |
+
"B-antineoplastic": 1,
|
26 |
+
"B-cancertype": 2,
|
27 |
+
"B-carcinogen": 3,
|
28 |
+
"B-negative": 4,
|
29 |
+
"I-cancertype": 5,
|
30 |
+
"I-carcinogen": 6,
|
31 |
+
"I-negative": 7,
|
32 |
+
"O": 0
|
33 |
+
},
|
34 |
+
"layer_norm_eps": 1e-12,
|
35 |
+
"max_position_embeddings": 512,
|
36 |
+
"model_type": "electra",
|
37 |
+
"num_attention_heads": 16,
|
38 |
+
"num_hidden_layers": 24,
|
39 |
+
"pad_token_id": 0,
|
40 |
+
"position_embedding_type": "absolute",
|
41 |
+
"summary_activation": "gelu",
|
42 |
+
"summary_last_dropout": 0.1,
|
43 |
+
"summary_type": "first",
|
44 |
+
"summary_use_proj": true,
|
45 |
+
"torch_dtype": "float32",
|
46 |
+
"transformers_version": "4.40.1",
|
47 |
+
"type_vocab_size": 2,
|
48 |
+
"use_cache": true,
|
49 |
+
"vocab_size": 28895
|
50 |
+
}
|
checkpoint-8010/model.safetensors
ADDED
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
1 |
+
version https://git-lfs.github.com/spec/v1
|
2 |
+
oid sha256:28ff692670e07e3443424d23688d7f8c5f7ab04b3a81f11285f1ae8c826d24d3
|
3 |
+
size 1329785712
|
checkpoint-8010/optimizer.pt
ADDED
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
1 |
+
version https://git-lfs.github.com/spec/v1
|
2 |
+
oid sha256:75b61d9f1a1c4a763eefe45bc88b93a6caaff5621848dba6693e1c84f9e02b5f
|
3 |
+
size 2659802663
|
checkpoint-8010/rng_state.pth
ADDED
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
1 |
+
version https://git-lfs.github.com/spec/v1
|
2 |
+
oid sha256:24255887216b6ed59d1dea7f442c2bf9f0d4baf66cc6133b44860e5e7a22bdb9
|
3 |
+
size 14244
|
checkpoint-8010/scheduler.pt
ADDED
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
1 |
+
version https://git-lfs.github.com/spec/v1
|
2 |
+
oid sha256:3b119d907611dd4a92192cad349abbf6251e9f178cd9bdccbc47a3fd72a25015
|
3 |
+
size 1064
|
checkpoint-8010/trainer_state.json
ADDED
@@ -0,0 +1,193 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
1 |
+
{
|
2 |
+
"best_metric": 0.07832363992929459,
|
3 |
+
"best_model_checkpoint": "/storage/BioM-ELECTRA-Large-SQuAD2_carDB_5e_neg_lg_SGD/checkpoint-3204",
|
4 |
+
"epoch": 5.0,
|
5 |
+
"eval_steps": 500,
|
6 |
+
"global_step": 8010,
|
7 |
+
"is_hyper_param_search": false,
|
8 |
+
"is_local_process_zero": true,
|
9 |
+
"is_world_process_zero": true,
|
10 |
+
"log_history": [
|
11 |
+
{
|
12 |
+
"epoch": 0.3121098626716604,
|
13 |
+
"grad_norm": 3.2046010494232178,
|
14 |
+
"learning_rate": 4.690387016229713e-05,
|
15 |
+
"loss": 0.1789,
|
16 |
+
"step": 500
|
17 |
+
},
|
18 |
+
{
|
19 |
+
"epoch": 0.6242197253433208,
|
20 |
+
"grad_norm": 1.161939263343811,
|
21 |
+
"learning_rate": 4.378277153558052e-05,
|
22 |
+
"loss": 0.1113,
|
23 |
+
"step": 1000
|
24 |
+
},
|
25 |
+
{
|
26 |
+
"epoch": 0.9363295880149812,
|
27 |
+
"grad_norm": 2.1341910362243652,
|
28 |
+
"learning_rate": 4.066167290886392e-05,
|
29 |
+
"loss": 0.1054,
|
30 |
+
"step": 1500
|
31 |
+
},
|
32 |
+
{
|
33 |
+
"epoch": 1.0,
|
34 |
+
"eval_accuracy_score": 0.9690997325938397,
|
35 |
+
"eval_f1": 0.7794316644113668,
|
36 |
+
"eval_loss": 0.08875501155853271,
|
37 |
+
"eval_precision": 0.7747886241352806,
|
38 |
+
"eval_recall": 0.7841306884480747,
|
39 |
+
"eval_runtime": 4.093,
|
40 |
+
"eval_samples_per_second": 348.153,
|
41 |
+
"eval_steps_per_second": 43.733,
|
42 |
+
"step": 1602
|
43 |
+
},
|
44 |
+
{
|
45 |
+
"epoch": 1.2484394506866416,
|
46 |
+
"grad_norm": 0.97569340467453,
|
47 |
+
"learning_rate": 3.754057428214732e-05,
|
48 |
+
"loss": 0.079,
|
49 |
+
"step": 2000
|
50 |
+
},
|
51 |
+
{
|
52 |
+
"epoch": 1.5605493133583022,
|
53 |
+
"grad_norm": 0.8073092699050903,
|
54 |
+
"learning_rate": 3.441947565543071e-05,
|
55 |
+
"loss": 0.0685,
|
56 |
+
"step": 2500
|
57 |
+
},
|
58 |
+
{
|
59 |
+
"epoch": 1.8726591760299627,
|
60 |
+
"grad_norm": 2.6909968852996826,
|
61 |
+
"learning_rate": 3.129837702871411e-05,
|
62 |
+
"loss": 0.0671,
|
63 |
+
"step": 3000
|
64 |
+
},
|
65 |
+
{
|
66 |
+
"epoch": 2.0,
|
67 |
+
"eval_accuracy_score": 0.973506982271962,
|
68 |
+
"eval_f1": 0.814260389994091,
|
69 |
+
"eval_loss": 0.07832363992929459,
|
70 |
+
"eval_precision": 0.8248204309656824,
|
71 |
+
"eval_recall": 0.8039673278879813,
|
72 |
+
"eval_runtime": 4.1937,
|
73 |
+
"eval_samples_per_second": 339.796,
|
74 |
+
"eval_steps_per_second": 42.683,
|
75 |
+
"step": 3204
|
76 |
+
},
|
77 |
+
{
|
78 |
+
"epoch": 2.184769038701623,
|
79 |
+
"grad_norm": 0.14074726402759552,
|
80 |
+
"learning_rate": 2.818352059925094e-05,
|
81 |
+
"loss": 0.0534,
|
82 |
+
"step": 3500
|
83 |
+
},
|
84 |
+
{
|
85 |
+
"epoch": 2.4968789013732833,
|
86 |
+
"grad_norm": 0.8002931475639343,
|
87 |
+
"learning_rate": 2.5062421972534333e-05,
|
88 |
+
"loss": 0.043,
|
89 |
+
"step": 4000
|
90 |
+
},
|
91 |
+
{
|
92 |
+
"epoch": 2.808988764044944,
|
93 |
+
"grad_norm": 1.326310157775879,
|
94 |
+
"learning_rate": 2.194132334581773e-05,
|
95 |
+
"loss": 0.0433,
|
96 |
+
"step": 4500
|
97 |
+
},
|
98 |
+
{
|
99 |
+
"epoch": 3.0,
|
100 |
+
"eval_accuracy_score": 0.9748935327324948,
|
101 |
+
"eval_f1": 0.8186646433990896,
|
102 |
+
"eval_loss": 0.09053385257720947,
|
103 |
+
"eval_precision": 0.7989633469085524,
|
104 |
+
"eval_recall": 0.839362115908207,
|
105 |
+
"eval_runtime": 4.09,
|
106 |
+
"eval_samples_per_second": 348.41,
|
107 |
+
"eval_steps_per_second": 43.765,
|
108 |
+
"step": 4806
|
109 |
+
},
|
110 |
+
{
|
111 |
+
"epoch": 3.1210986267166043,
|
112 |
+
"grad_norm": 0.9473728537559509,
|
113 |
+
"learning_rate": 1.8820224719101125e-05,
|
114 |
+
"loss": 0.0318,
|
115 |
+
"step": 5000
|
116 |
+
},
|
117 |
+
{
|
118 |
+
"epoch": 3.4332084893882646,
|
119 |
+
"grad_norm": 0.391970157623291,
|
120 |
+
"learning_rate": 1.569912609238452e-05,
|
121 |
+
"loss": 0.0228,
|
122 |
+
"step": 5500
|
123 |
+
},
|
124 |
+
{
|
125 |
+
"epoch": 3.7453183520599254,
|
126 |
+
"grad_norm": 5.073329448699951,
|
127 |
+
"learning_rate": 1.258426966292135e-05,
|
128 |
+
"loss": 0.0224,
|
129 |
+
"step": 6000
|
130 |
+
},
|
131 |
+
{
|
132 |
+
"epoch": 4.0,
|
133 |
+
"eval_accuracy_score": 0.9751906506883232,
|
134 |
+
"eval_f1": 0.8262295081967214,
|
135 |
+
"eval_loss": 0.09821399301290512,
|
136 |
+
"eval_precision": 0.819433817903596,
|
137 |
+
"eval_recall": 0.8331388564760793,
|
138 |
+
"eval_runtime": 4.1062,
|
139 |
+
"eval_samples_per_second": 347.04,
|
140 |
+
"eval_steps_per_second": 43.593,
|
141 |
+
"step": 6408
|
142 |
+
},
|
143 |
+
{
|
144 |
+
"epoch": 4.057428214731585,
|
145 |
+
"grad_norm": 0.055937759578228,
|
146 |
+
"learning_rate": 9.463171036204745e-06,
|
147 |
+
"loss": 0.0204,
|
148 |
+
"step": 6500
|
149 |
+
},
|
150 |
+
{
|
151 |
+
"epoch": 4.369538077403246,
|
152 |
+
"grad_norm": 0.6860196590423584,
|
153 |
+
"learning_rate": 6.342072409488139e-06,
|
154 |
+
"loss": 0.0116,
|
155 |
+
"step": 7000
|
156 |
+
},
|
157 |
+
{
|
158 |
+
"epoch": 4.681647940074907,
|
159 |
+
"grad_norm": 0.6975510716438293,
|
160 |
+
"learning_rate": 3.2209737827715358e-06,
|
161 |
+
"loss": 0.011,
|
162 |
+
"step": 7500
|
163 |
+
},
|
164 |
+
{
|
165 |
+
"epoch": 4.9937578027465666,
|
166 |
+
"grad_norm": 0.33860084414482117,
|
167 |
+
"learning_rate": 9.987515605493134e-08,
|
168 |
+
"loss": 0.0091,
|
169 |
+
"step": 8000
|
170 |
+
},
|
171 |
+
{
|
172 |
+
"epoch": 5.0,
|
173 |
+
"eval_accuracy_score": 0.9755125284738041,
|
174 |
+
"eval_f1": 0.8289676425269646,
|
175 |
+
"eval_loss": 0.11285488307476044,
|
176 |
+
"eval_precision": 0.8210606638687524,
|
177 |
+
"eval_recall": 0.8370283936211591,
|
178 |
+
"eval_runtime": 4.1141,
|
179 |
+
"eval_samples_per_second": 346.37,
|
180 |
+
"eval_steps_per_second": 43.509,
|
181 |
+
"step": 8010
|
182 |
+
}
|
183 |
+
],
|
184 |
+
"logging_steps": 500,
|
185 |
+
"max_steps": 8010,
|
186 |
+
"num_input_tokens_seen": 0,
|
187 |
+
"num_train_epochs": 5,
|
188 |
+
"save_steps": 500,
|
189 |
+
"total_flos": 1.064813249753856e+16,
|
190 |
+
"train_batch_size": 8,
|
191 |
+
"trial_name": null,
|
192 |
+
"trial_params": null
|
193 |
+
}
|
checkpoint-8010/training_args.bin
ADDED
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
1 |
+
version https://git-lfs.github.com/spec/v1
|
2 |
+
oid sha256:36534a66cd54fa62d55a78ae7da66791486f97dbf75f55360327b517cd4e0be3
|
3 |
+
size 5048
|
config.json
ADDED
@@ -0,0 +1,48 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
1 |
+
{
|
2 |
+
"_name_or_path": "sultan/BioM-ELECTRA-Large-SQuAD2",
|
3 |
+
"architectures": [
|
4 |
+
"ElectraForTokenClassification"
|
5 |
+
],
|
6 |
+
"attention_probs_dropout_prob": 0.1,
|
7 |
+
"classifier_dropout": null,
|
8 |
+
"embedding_size": 1024,
|
9 |
+
"hidden_act": "gelu",
|
10 |
+
"hidden_dropout_prob": 0.1,
|
11 |
+
"hidden_size": 1024,
|
12 |
+
"id2label": {
|
13 |
+
"0": "O",
|
14 |
+
"1": "B-cancertype",
|
15 |
+
"2": "B-carcinogen",
|
16 |
+
"3": "B-negative",
|
17 |
+
"4": "I-cancertype",
|
18 |
+
"5": "I-carcinogen",
|
19 |
+
"6": "I-negative"
|
20 |
+
},
|
21 |
+
"initializer_range": 0.02,
|
22 |
+
"intermediate_size": 4096,
|
23 |
+
"label2id": {
|
24 |
+
"B-cancertype": 1,
|
25 |
+
"B-carcinogen": 2,
|
26 |
+
"B-negative": 3,
|
27 |
+
"I-cancertype": 4,
|
28 |
+
"I-carcinogen": 5,
|
29 |
+
"I-negative": 6,
|
30 |
+
"O": 0
|
31 |
+
},
|
32 |
+
"layer_norm_eps": 1e-12,
|
33 |
+
"max_position_embeddings": 512,
|
34 |
+
"model_type": "electra",
|
35 |
+
"num_attention_heads": 16,
|
36 |
+
"num_hidden_layers": 24,
|
37 |
+
"pad_token_id": 0,
|
38 |
+
"position_embedding_type": "absolute",
|
39 |
+
"summary_activation": "gelu",
|
40 |
+
"summary_last_dropout": 0.1,
|
41 |
+
"summary_type": "first",
|
42 |
+
"summary_use_proj": true,
|
43 |
+
"torch_dtype": "float32",
|
44 |
+
"transformers_version": "4.40.1",
|
45 |
+
"type_vocab_size": 2,
|
46 |
+
"use_cache": true,
|
47 |
+
"vocab_size": 28895
|
48 |
+
}
|
model.safetensors
ADDED
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
1 |
+
version https://git-lfs.github.com/spec/v1
|
2 |
+
oid sha256:2fc3d970de77d2af227efab4238d737a8226de685bea1a93bc42848c723b9e9a
|
3 |
+
size 1329781612
|
runs/Apr25_14-35-27_hpcf/events.out.tfevents.1714080930.hpcf.137937.0
ADDED
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
1 |
+
version https://git-lfs.github.com/spec/v1
|
2 |
+
oid sha256:64afb7a940a161fa73270408d5c7bdfd08cd268948f591dde724000e76873b33
|
3 |
+
size 11444
|
runs/Apr26_09-58-52_hpcf/events.out.tfevents.1714150736.hpcf.183226.0
ADDED
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
1 |
+
version https://git-lfs.github.com/spec/v1
|
2 |
+
oid sha256:de80d861e08c3f13afa8fec93cdc5f4e42c442309baa5f920daa4b9cdaa03721
|
3 |
+
size 12443
|
runs/Apr26_10-20-51_hpcf/events.out.tfevents.1714152055.hpcf.183659.0
ADDED
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
1 |
+
version https://git-lfs.github.com/spec/v1
|
2 |
+
oid sha256:78ad061897c41c39551a6a3fb59cf510f60d389690b2792b223efbe66fc4cf5b
|
3 |
+
size 5268
|
runs/Apr26_10-21-30_hpcf/events.out.tfevents.1714152093.hpcf.186484.0
ADDED
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
1 |
+
version https://git-lfs.github.com/spec/v1
|
2 |
+
oid sha256:7036534514f03fdd01de11863b01a94b6e43cbfeba22e6d634a073eeb2b2b5a4
|
3 |
+
size 12443
|
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
The diff for this file is too large to render.
See raw diff
|
|
tokenizer_config.json
ADDED
@@ -0,0 +1,61 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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": true,
|
48 |
+
"ignore_mismatched_sizes": true,
|
49 |
+
"mask_token": "[MASK]",
|
50 |
+
"max_len": 512,
|
51 |
+
"model_max_length": 512,
|
52 |
+
"never_split": null,
|
53 |
+
"pad_token": "[PAD]",
|
54 |
+
"padding": true,
|
55 |
+
"sep_token": "[SEP]",
|
56 |
+
"strip_accents": null,
|
57 |
+
"tokenize_chinese_chars": true,
|
58 |
+
"tokenizer_class": "ElectraTokenizer",
|
59 |
+
"truncation": true,
|
60 |
+
"unk_token": "[UNK]"
|
61 |
+
}
|
training_args.bin
ADDED
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
1 |
+
version https://git-lfs.github.com/spec/v1
|
2 |
+
oid sha256:07af839673be954537faf350c212a49f3f745cf8247da4cb4f9a1d9f73b78ed7
|
3 |
+
size 5048
|
vocab.txt
ADDED
The diff for this file is too large to render.
See raw diff
|
|