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add the trained bert model

Browse files
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+ "_name_or_path": "bionlp/bluebert_pubmed_mimic_uncased_L-12_H-768_A-12",
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+ "_name_or_path": "emilyalsentzer/Bio_ClinicalBERT",
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+ "BertForSequenceClassification"
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+ "_name_or_path": "microsoft/BiomedNLP-PubMedBERT-base-uncased-abstract-fulltext",
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+ {
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+ "cells": [
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+ {
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+ "cell_type": "code",
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+ "execution_count": 4,
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+ "metadata": {},
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+ "outputs": [],
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+ "source": [
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+ "# import the package\n",
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+ "import numpy as np\n",
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+ "import pandas as pd\n",
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+ "import datasets\n",
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+ "import evaluate\n",
14
+ "from datasets import DatasetDict, Dataset\n",
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+ "from transformers import AutoTokenizer, Trainer, BertForSequenceClassification\n",
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+ "import torch\n",
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+ "from accelerate import Accelerator"
18
+ ]
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+ },
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+ {
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+ "attachments": {},
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+ "cell_type": "markdown",
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+ "metadata": {},
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+ "source": [
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+ "# Attention: \n",
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+ "\n",
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+ "This file is used to ranking the response. It will calculate the probability for each sample_answer and return the most probability one and the index of it. \n",
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+ "\n",
29
+ "The file only contains answers to one question is recommended or we need to split the dataframe manually.\n",
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+ "\n",
31
+ "The input of the function is the path of the file and the file of the pretrained model and corresponding tokenizer."
32
+ ]
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+ },
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+ {
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+ "cell_type": "code",
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+ "execution_count": 14,
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+ "metadata": {},
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+ "outputs": [],
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+ "source": [
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+ "# load the data\n",
41
+ "\n",
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+ "path = 'C:/Users/cxz55/Desktop/UCL/term2/COMP087/cw/data_nlp_porject' #!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n",
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+ "file_name = 'five_responses.csv' #!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n",
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+ "\n",
45
+ "def load_data(path,file_name):\n",
46
+ "\n",
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+ " path = '/'.join([path,file_name])\n",
48
+ " test_response = pd.read_csv(path)\n",
49
+ " return test_response"
50
+ ]
51
+ },
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+ {
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+ "cell_type": "code",
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+ "execution_count": 6,
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+ "metadata": {},
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+ "outputs": [
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+ {
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+ "name": "stderr",
59
+ "output_type": "stream",
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+ "text": [
61
+ "Some weights of BertForSequenceClassification were not initialized from the model checkpoint at dmis-lab/biobert-v1.1 and are newly initialized: ['classifier.bias', 'classifier.weight']\n",
62
+ "You should probably TRAIN this model on a down-stream task to be able to use it for predictions and inference.\n"
63
+ ]
64
+ }
65
+ ],
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+ "source": [
67
+ "# give the model and corresponfing tokenizer\n",
68
+ "\n",
69
+ "# the base models we used are:\n",
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+ "# \"emilyalsentzer/Bio_ClinicalBERT\" \n",
71
+ "# \"dmis-lab/biobert-v1.1\"\n",
72
+ "# \"microsoft/BiomedNLP-PubMedBERT-base-uncased-abstract-fulltext\"\n",
73
+ "# \"allenai/scibert_scivocab_uncased\"\n",
74
+ "# \"bionlp/bluebert_pubmed_mimic_uncased_L-12_H-768_A-12\"\n",
75
+ "\n",
76
+ "# model_name = 'dmis-lab/biobert-v1.1' #!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n",
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+ "# model = BertForSequenceClassification.from_pretrained(model_name, num_labels=2)\n",
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+ "\n",
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+ "# tokenizer_name = 'dmis-lab/biobert-v1.1' #!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n",
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+ "# tokenizer = AutoTokenizer.from_pretrained(tokenizer_name)"
81
+ ]
82
+ },
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+ {
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+ "cell_type": "code",
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+ "execution_count": 18,
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+ "metadata": {},
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+ "outputs": [],
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+ "source": [
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+ "# def tokenize_function(data):\n",
90
+ "# return tokenizer(data['Question'],data['Answer'],padding='max_length',truncation=True,max_length=128)\n",
91
+ "\n",
92
+ "# def compute_metrics(eval_preds):\n",
93
+ "# metric = evaluate.load(\"accuracy\")\n",
94
+ "# x,y = eval_preds\n",
95
+ "# preds = np.argmax(x, -1)\n",
96
+ "# return metric.compute(predictions=preds, references=y)"
97
+ ]
98
+ },
99
+ {
100
+ "cell_type": "code",
101
+ "execution_count": 8,
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+ "metadata": {},
103
+ "outputs": [],
104
+ "source": [
105
+ "# # add device\n",
106
+ "# accelerator = Accelerator()\n",
107
+ "# device = accelerator.device"
108
+ ]
109
+ },
110
+ {
111
+ "cell_type": "code",
112
+ "execution_count": 9,
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+ "metadata": {},
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+ "outputs": [],
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+ "source": [
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+ "# build the model\n",
117
+ "# trainer = Trainer(\n",
118
+ "# model=model.to(device),\n",
119
+ "# # args=training_args,\n",
120
+ "# # data_collator=data_collator,\n",
121
+ "# tokenizer=tokenizer,\n",
122
+ "# compute_metrics=compute_metrics,\n",
123
+ "# )"
124
+ ]
125
+ },
126
+ {
127
+ "cell_type": "code",
128
+ "execution_count": 19,
129
+ "metadata": {},
130
+ "outputs": [],
131
+ "source": [
132
+ "# # dealing with data: from dataframe transform into DatasetDict\n",
133
+ "# data_set = load_data(path,file_name)\n",
134
+ "# data_dict = Dataset.from_pandas(data_set)\n",
135
+ "# data_dict_token = data_dict.map(tokenize_function, batched=8)\n",
136
+ "# # make prediction\n",
137
+ "# prediction = trainer.predict(data_dict_token)\n",
138
+ "# logits = torch.tensor(prediction.predictions)\n",
139
+ "# prob = torch.softmax(logits,dim=1)\n",
140
+ "# right_prob = prob[:,1]\n",
141
+ "# prob_list = right_prob.tolist()\n"
142
+ ]
143
+ },
144
+ {
145
+ "cell_type": "code",
146
+ "execution_count": 29,
147
+ "metadata": {},
148
+ "outputs": [],
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+ "source": [
150
+ "def prob_position(path, file_name, model_name,tokenizer_name):\n",
151
+ "\n",
152
+ " # the list of model name:\n",
153
+ " # the base models we used are:\n",
154
+ " # \"emilyalsentzer/Bio_ClinicalBERT\" \n",
155
+ " # \"dmis-lab/biobert-v1.1\"\n",
156
+ " # \"microsoft/BiomedNLP-PubMedBERT-base-uncased-abstract-fulltext\"\n",
157
+ " # \"allenai/scibert_scivocab_uncased\"\n",
158
+ " # \"bionlp/bluebert_pubmed_mimic_uncased_L-12_H-768_A-12\"\n",
159
+ "\n",
160
+ " model = BertForSequenceClassification.from_pretrained(model_name, num_labels=2)\n",
161
+ " tokenizer = AutoTokenizer.from_pretrained(tokenizer_name)\n",
162
+ "\n",
163
+ " # define the tokenizing map and the metrics\n",
164
+ " def tokenize_function(data):\n",
165
+ " return tokenizer(data['Question'],data['Answer'],padding='max_length',truncation=True,max_length=128)\n",
166
+ " def compute_metrics(eval_preds):\n",
167
+ " metric = evaluate.load(\"accuracy\")\n",
168
+ " x,y = eval_preds\n",
169
+ " preds = np.argmax(x, -1)\n",
170
+ " return metric.compute(predictions=preds, references=y)\n",
171
+ "\n",
172
+ " # add device\n",
173
+ " accelerator = Accelerator()\n",
174
+ " device = accelerator.device\n",
175
+ "\n",
176
+ " # build trainer\n",
177
+ " trainer = Trainer(\n",
178
+ " model=model.to(device),\n",
179
+ " # args=training_args,\n",
180
+ " # data_collator=data_collator,\n",
181
+ " tokenizer=tokenizer,\n",
182
+ " compute_metrics=compute_metrics,\n",
183
+ " )\n",
184
+ "\n",
185
+ " # dealing with data: from dataframe transform into DatasetDict\n",
186
+ " data_set = load_data(path,file_name)\n",
187
+ " data_dict = Dataset.from_pandas(data_set)\n",
188
+ " data_dict_token = data_dict.map(tokenize_function, batched=8)\n",
189
+ " \n",
190
+ " # make prediction\n",
191
+ " prediction = trainer.predict(data_dict_token)\n",
192
+ "\n",
193
+ " # transform it into probability\n",
194
+ " logits = torch.tensor(prediction.predictions)\n",
195
+ " prob = torch.softmax(logits,dim=1)\n",
196
+ "\n",
197
+ " # the probability the answer is correct\n",
198
+ " right_prob = prob[:,1]\n",
199
+ " prob_list = right_prob.tolist()\n",
200
+ "\n",
201
+ " max_value = max(prob_list)\n",
202
+ " max_index = prob_list.index(max_value) + 1\n",
203
+ "\n",
204
+ " print(f'\\n##############RESULT####################\\nThe index of the most proper answer is: {max_index}\\nThe probability it is correct is: {max_value}')\n",
205
+ "\n",
206
+ " return max_value,max_index"
207
+ ]
208
+ },
209
+ {
210
+ "cell_type": "code",
211
+ "execution_count": 30,
212
+ "metadata": {},
213
+ "outputs": [
214
+ {
215
+ "name": "stderr",
216
+ "output_type": "stream",
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+ "text": [
218
+ "loading configuration file config.json from cache at C:\\Users\\cxz55/.cache\\huggingface\\hub\\models--dmis-lab--biobert-v1.1\\snapshots\\551ca18efd7f052c8dfa0b01c94c2a8e68bc5488\\config.json\n",
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+ "Model config BertConfig {\n",
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+ " \"architectures\": [\n",
221
+ " \"BertModel\"\n",
222
+ " ],\n",
223
+ " \"attention_probs_dropout_prob\": 0.1,\n",
224
+ " \"classifier_dropout\": null,\n",
225
+ " \"gradient_checkpointing\": false,\n",
226
+ " \"hidden_act\": \"gelu\",\n",
227
+ " \"hidden_dropout_prob\": 0.1,\n",
228
+ " \"hidden_size\": 768,\n",
229
+ " \"initializer_range\": 0.02,\n",
230
+ " \"intermediate_size\": 3072,\n",
231
+ " \"layer_norm_eps\": 1e-12,\n",
232
+ " \"max_position_embeddings\": 512,\n",
233
+ " \"model_type\": \"bert\",\n",
234
+ " \"num_attention_heads\": 12,\n",
235
+ " \"num_hidden_layers\": 12,\n",
236
+ " \"pad_token_id\": 0,\n",
237
+ " \"position_embedding_type\": \"absolute\",\n",
238
+ " \"transformers_version\": \"4.24.0\",\n",
239
+ " \"type_vocab_size\": 2,\n",
240
+ " \"use_cache\": true,\n",
241
+ " \"vocab_size\": 28996\n",
242
+ "}\n",
243
+ "\n",
244
+ "loading weights file pytorch_model.bin from cache at C:\\Users\\cxz55/.cache\\huggingface\\hub\\models--dmis-lab--biobert-v1.1\\snapshots\\551ca18efd7f052c8dfa0b01c94c2a8e68bc5488\\pytorch_model.bin\n",
245
+ "All model checkpoint weights were used when initializing BertForSequenceClassification.\n",
246
+ "\n",
247
+ "Some weights of BertForSequenceClassification were not initialized from the model checkpoint at dmis-lab/biobert-v1.1 and are newly initialized: ['classifier.bias', 'classifier.weight']\n",
248
+ "You should probably TRAIN this model on a down-stream task to be able to use it for predictions and inference.\n",
249
+ "loading configuration file config.json from cache at C:\\Users\\cxz55/.cache\\huggingface\\hub\\models--dmis-lab--biobert-v1.1\\snapshots\\551ca18efd7f052c8dfa0b01c94c2a8e68bc5488\\config.json\n",
250
+ "Model config BertConfig {\n",
251
+ " \"_name_or_path\": \"dmis-lab/biobert-v1.1\",\n",
252
+ " \"architectures\": [\n",
253
+ " \"BertModel\"\n",
254
+ " ],\n",
255
+ " \"attention_probs_dropout_prob\": 0.1,\n",
256
+ " \"classifier_dropout\": null,\n",
257
+ " \"gradient_checkpointing\": false,\n",
258
+ " \"hidden_act\": \"gelu\",\n",
259
+ " \"hidden_dropout_prob\": 0.1,\n",
260
+ " \"hidden_size\": 768,\n",
261
+ " \"initializer_range\": 0.02,\n",
262
+ " \"intermediate_size\": 3072,\n",
263
+ " \"layer_norm_eps\": 1e-12,\n",
264
+ " \"max_position_embeddings\": 512,\n",
265
+ " \"model_type\": \"bert\",\n",
266
+ " \"num_attention_heads\": 12,\n",
267
+ " \"num_hidden_layers\": 12,\n",
268
+ " \"pad_token_id\": 0,\n",
269
+ " \"position_embedding_type\": \"absolute\",\n",
270
+ " \"transformers_version\": \"4.24.0\",\n",
271
+ " \"type_vocab_size\": 2,\n",
272
+ " \"use_cache\": true,\n",
273
+ " \"vocab_size\": 28996\n",
274
+ "}\n",
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+ "\n",
276
+ "loading file vocab.txt from cache at C:\\Users\\cxz55/.cache\\huggingface\\hub\\models--dmis-lab--biobert-v1.1\\snapshots\\551ca18efd7f052c8dfa0b01c94c2a8e68bc5488\\vocab.txt\n",
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+ "loading file tokenizer.json from cache at None\n",
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+ "loading file added_tokens.json from cache at None\n",
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+ "loading file special_tokens_map.json from cache at C:\\Users\\cxz55/.cache\\huggingface\\hub\\models--dmis-lab--biobert-v1.1\\snapshots\\551ca18efd7f052c8dfa0b01c94c2a8e68bc5488\\special_tokens_map.json\n",
280
+ "loading file tokenizer_config.json from cache at C:\\Users\\cxz55/.cache\\huggingface\\hub\\models--dmis-lab--biobert-v1.1\\snapshots\\551ca18efd7f052c8dfa0b01c94c2a8e68bc5488\\tokenizer_config.json\n",
281
+ "loading configuration file config.json from cache at C:\\Users\\cxz55/.cache\\huggingface\\hub\\models--dmis-lab--biobert-v1.1\\snapshots\\551ca18efd7f052c8dfa0b01c94c2a8e68bc5488\\config.json\n",
282
+ "Model config BertConfig {\n",
283
+ " \"_name_or_path\": \"dmis-lab/biobert-v1.1\",\n",
284
+ " \"architectures\": [\n",
285
+ " \"BertModel\"\n",
286
+ " ],\n",
287
+ " \"attention_probs_dropout_prob\": 0.1,\n",
288
+ " \"classifier_dropout\": null,\n",
289
+ " \"gradient_checkpointing\": false,\n",
290
+ " \"hidden_act\": \"gelu\",\n",
291
+ " \"hidden_dropout_prob\": 0.1,\n",
292
+ " \"hidden_size\": 768,\n",
293
+ " \"initializer_range\": 0.02,\n",
294
+ " \"intermediate_size\": 3072,\n",
295
+ " \"layer_norm_eps\": 1e-12,\n",
296
+ " \"max_position_embeddings\": 512,\n",
297
+ " \"model_type\": \"bert\",\n",
298
+ " \"num_attention_heads\": 12,\n",
299
+ " \"num_hidden_layers\": 12,\n",
300
+ " \"pad_token_id\": 0,\n",
301
+ " \"position_embedding_type\": \"absolute\",\n",
302
+ " \"transformers_version\": \"4.24.0\",\n",
303
+ " \"type_vocab_size\": 2,\n",
304
+ " \"use_cache\": true,\n",
305
+ " \"vocab_size\": 28996\n",
306
+ "}\n",
307
+ "\n",
308
+ "loading configuration file config.json from cache at C:\\Users\\cxz55/.cache\\huggingface\\hub\\models--dmis-lab--biobert-v1.1\\snapshots\\551ca18efd7f052c8dfa0b01c94c2a8e68bc5488\\config.json\n",
309
+ "Model config BertConfig {\n",
310
+ " \"_name_or_path\": \"dmis-lab/biobert-v1.1\",\n",
311
+ " \"architectures\": [\n",
312
+ " \"BertModel\"\n",
313
+ " ],\n",
314
+ " \"attention_probs_dropout_prob\": 0.1,\n",
315
+ " \"classifier_dropout\": null,\n",
316
+ " \"gradient_checkpointing\": false,\n",
317
+ " \"hidden_act\": \"gelu\",\n",
318
+ " \"hidden_dropout_prob\": 0.1,\n",
319
+ " \"hidden_size\": 768,\n",
320
+ " \"initializer_range\": 0.02,\n",
321
+ " \"intermediate_size\": 3072,\n",
322
+ " \"layer_norm_eps\": 1e-12,\n",
323
+ " \"max_position_embeddings\": 512,\n",
324
+ " \"model_type\": \"bert\",\n",
325
+ " \"num_attention_heads\": 12,\n",
326
+ " \"num_hidden_layers\": 12,\n",
327
+ " \"pad_token_id\": 0,\n",
328
+ " \"position_embedding_type\": \"absolute\",\n",
329
+ " \"transformers_version\": \"4.24.0\",\n",
330
+ " \"type_vocab_size\": 2,\n",
331
+ " \"use_cache\": true,\n",
332
+ " \"vocab_size\": 28996\n",
333
+ "}\n",
334
+ "\n",
335
+ "No `TrainingArguments` passed, using `output_dir=tmp_trainer`.\n",
336
+ "PyTorch: setting up devices\n",
337
+ "The default value for the training argument `--report_to` will change in v5 (from all installed integrations to none). In v5, you will need to use `--report_to all` to get the same behavior as now. You should start updating your code and make this info disappear :-).\n",
338
+ "The following columns in the test set don't have a corresponding argument in `BertForSequenceClassification.forward` and have been ignored: Unnamed: 0, Context, Label, Question, Answer. If Unnamed: 0, Context, Label, Question, Answer are not expected by `BertForSequenceClassification.forward`, you can safely ignore this message.\n",
339
+ "***** Running Prediction *****\n",
340
+ " Num examples = 300\n",
341
+ " Batch size = 8\n",
342
+ "You're using a BertTokenizerFast tokenizer. Please note that with a fast tokenizer, using the `__call__` method is faster than using a method to encode the text followed by a call to the `pad` method to get a padded encoding.\n",
343
+ "100%|β–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆβ–ˆ| 38/38 [00:01<00:00, 25.79it/s]"
344
+ ]
345
+ },
346
+ {
347
+ "name": "stdout",
348
+ "output_type": "stream",
349
+ "text": [
350
+ "\n",
351
+ "##############RESULT####################\n",
352
+ "The index of the most proper answer is: 54\n",
353
+ "The probability it is correct is: 0.6013683676719666\n"
354
+ ]
355
+ },
356
+ {
357
+ "name": "stderr",
358
+ "output_type": "stream",
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+ "text": [
360
+ "\n"
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+ ]
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+ },
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+ {
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+ "data": {
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+ "text/plain": [
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+ "(0.6013683676719666, 54)"
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+ ]
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+ },
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+ "execution_count": 30,
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+ "metadata": {},
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+ "output_type": "execute_result"
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+ }
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+ ],
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+ "source": [
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+ "prob_position(path,file_name,\"dmis-lab/biobert-v1.1\",\"dmis-lab/biobert-v1.1\")"
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+ ]
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+ }
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+ "name": "python3"
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+ "name": "ipython",
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+ "version": 3
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+ "file_extension": ".py",
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+ "mimetype": "text/x-python",
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+ "name": "python",
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+ "nbconvert_exporter": "python",
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+ "pygments_lexer": "ipython3",
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+ "version": "3.8.5 (default, Sep 3 2020, 21:29:08) [MSC v.1916 64 bit (AMD64)]"
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+ "nbformat": 4,
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+ "nbformat_minor": 2
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