Rodrigo1771 commited on
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Training in progress, epoch 1

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README.md ADDED
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+ ---
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+ library_name: transformers
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+ license: apache-2.0
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+ base_model: PlanTL-GOB-ES/bsc-bio-ehr-es
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+ tags:
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+ - token-classification
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+ - generated_from_trainer
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+ datasets:
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+ - Rodrigo1771/combined-train-distemist-dev-85-ner
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+ metrics:
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+ - precision
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+ - recall
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+ - f1
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+ - accuracy
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+ model-index:
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+ - name: output
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+ results:
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+ - task:
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+ name: Token Classification
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+ type: token-classification
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+ dataset:
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+ name: Rodrigo1771/combined-train-distemist-dev-85-ner
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+ type: Rodrigo1771/combined-train-distemist-dev-85-ner
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+ config: CombinedTrainDisTEMISTDevNER
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+ split: validation
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+ args: CombinedTrainDisTEMISTDevNER
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+ metrics:
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+ - name: Precision
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+ type: precision
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+ value: 0.3152508603513856
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+ - name: Recall
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+ type: recall
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+ value: 0.8144595226953674
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+ - name: F1
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+ type: f1
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+ value: 0.45455732567249935
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+ - name: Accuracy
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+ type: accuracy
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+ value: 0.8564886649182308
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+ ---
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+
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+ <!-- This model card has been generated automatically according to the information the Trainer had access to. You
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+ should probably proofread and complete it, then remove this comment. -->
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+
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+ # output
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+
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+ This model is a fine-tuned version of [PlanTL-GOB-ES/bsc-bio-ehr-es](https://huggingface.co/PlanTL-GOB-ES/bsc-bio-ehr-es) on the Rodrigo1771/combined-train-distemist-dev-85-ner dataset.
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+ It achieves the following results on the evaluation set:
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+ - Loss: 0.7006
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+ - Precision: 0.3153
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+ - Recall: 0.8145
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+ - F1: 0.4546
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+ - Accuracy: 0.8565
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+
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+ ## Model description
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+
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+ More information needed
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+
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+ ## Intended uses & limitations
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+
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+ More information needed
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+
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+ ## Training and evaluation data
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+
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+ More information needed
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+
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+ ## Training procedure
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+
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+ ### Training hyperparameters
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+
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+ The following hyperparameters were used during training:
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+ - learning_rate: 5e-05
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+ - train_batch_size: 32
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+ - eval_batch_size: 8
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+ - seed: 42
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+ - gradient_accumulation_steps: 2
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+ - total_train_batch_size: 64
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+ - optimizer: Adam with betas=(0.9,0.999) and epsilon=1e-08
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+ - lr_scheduler_type: linear
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+ - num_epochs: 10.0
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+
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+ ### Training results
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+
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+ | Training Loss | Epoch | Step | Validation Loss | Precision | Recall | F1 | Accuracy |
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+ |:-------------:|:-----:|:----:|:---------------:|:---------:|:------:|:------:|:--------:|
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+ | 0.3191 | 1.0 | 541 | 0.4772 | 0.2725 | 0.8074 | 0.4075 | 0.8443 |
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+ | 0.1619 | 2.0 | 1082 | 0.4584 | 0.3041 | 0.7941 | 0.4398 | 0.8553 |
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+ | 0.11 | 3.0 | 1623 | 0.6447 | 0.2976 | 0.8000 | 0.4338 | 0.8435 |
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+ | 0.0764 | 4.0 | 2164 | 0.7413 | 0.2896 | 0.7871 | 0.4234 | 0.8399 |
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+ | 0.0567 | 5.0 | 2705 | 0.7006 | 0.3153 | 0.8145 | 0.4546 | 0.8565 |
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+ | 0.0428 | 6.0 | 3246 | 0.8112 | 0.3071 | 0.8210 | 0.4470 | 0.8504 |
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+ | 0.0332 | 7.0 | 3787 | 0.9046 | 0.3114 | 0.8070 | 0.4494 | 0.8533 |
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+ | 0.0257 | 8.0 | 4328 | 0.9723 | 0.3060 | 0.8109 | 0.4444 | 0.8482 |
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+ | 0.022 | 9.0 | 4869 | 1.0028 | 0.3087 | 0.8077 | 0.4467 | 0.8502 |
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+ | 0.0181 | 10.0 | 5410 | 1.0023 | 0.3116 | 0.8119 | 0.4504 | 0.8533 |
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+
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+
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+ ### Framework versions
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+
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+ - Transformers 4.44.2
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+ - Pytorch 2.4.0+cu121
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+ - Datasets 2.21.0
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+ - Tokenizers 0.19.1
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  10%|█ | 541/5410 [02:16<25:28, 3.18it/s][INFO|trainer.py:811] 2024-09-06 00:11:24,745 >> The following columns in the evaluation set don't have a corresponding argument in `RobertaForTokenClassification.forward` and have been ignored: tokens, ner_tags, id. If tokens, ner_tags, id are not expected by `RobertaForTokenClassification.forward`, you can safely ignore this message.
 
 
 
 
 
 
 
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+ 2024-09-06 00:08:37.934804: I tensorflow/core/util/port.cc:153] oneDNN custom operations are on. You may see slightly different numerical results due to floating-point round-off errors from different computation orders. To turn them off, set the environment variable `TF_ENABLE_ONEDNN_OPTS=0`.
2
+ 2024-09-06 00:08:37.953090: E external/local_xla/xla/stream_executor/cuda/cuda_fft.cc:485] Unable to register cuFFT factory: Attempting to register factory for plugin cuFFT when one has already been registered
3
+ 2024-09-06 00:08:37.974597: E external/local_xla/xla/stream_executor/cuda/cuda_dnn.cc:8454] Unable to register cuDNN factory: Attempting to register factory for plugin cuDNN when one has already been registered
4
+ 2024-09-06 00:08:37.981013: E external/local_xla/xla/stream_executor/cuda/cuda_blas.cc:1452] Unable to register cuBLAS factory: Attempting to register factory for plugin cuBLAS when one has already been registered
5
+ 2024-09-06 00:08:37.996733: I tensorflow/core/platform/cpu_feature_guard.cc:210] This TensorFlow binary is optimized to use available CPU instructions in performance-critical operations.
6
+ To enable the following instructions: AVX2 AVX512F AVX512_VNNI FMA, in other operations, rebuild TensorFlow with the appropriate compiler flags.
7
+ 2024-09-06 00:08:39.252831: W tensorflow/compiler/tf2tensorrt/utils/py_utils.cc:38] TF-TRT Warning: Could not find TensorRT
8
+ /usr/local/lib/python3.10/dist-packages/transformers/training_args.py:1525: FutureWarning: `evaluation_strategy` is deprecated and will be removed in version 4.46 of 🤗 Transformers. Use `eval_strategy` instead
9
+ warnings.warn(
10
+ 09/06/2024 00:08:40 - WARNING - __main__ - Process rank: 0, device: cuda:0, n_gpu: 1distributed training: True, 16-bits training: False
11
+ 09/06/2024 00:08:40 - INFO - __main__ - Training/evaluation parameters TrainingArguments(
12
+ _n_gpu=1,
13
+ accelerator_config={'split_batches': False, 'dispatch_batches': None, 'even_batches': True, 'use_seedable_sampler': True, 'non_blocking': False, 'gradient_accumulation_kwargs': None, 'use_configured_state': False},
14
+ adafactor=False,
15
+ adam_beta1=0.9,
16
+ adam_beta2=0.999,
17
+ adam_epsilon=1e-08,
18
+ auto_find_batch_size=False,
19
+ batch_eval_metrics=False,
20
+ bf16=False,
21
+ bf16_full_eval=False,
22
+ data_seed=None,
23
+ dataloader_drop_last=False,
24
+ dataloader_num_workers=0,
25
+ dataloader_persistent_workers=False,
26
+ dataloader_pin_memory=True,
27
+ dataloader_prefetch_factor=None,
28
+ ddp_backend=None,
29
+ ddp_broadcast_buffers=None,
30
+ ddp_bucket_cap_mb=None,
31
+ ddp_find_unused_parameters=None,
32
+ ddp_timeout=1800,
33
+ debug=[],
34
+ deepspeed=None,
35
+ disable_tqdm=False,
36
+ dispatch_batches=None,
37
+ do_eval=True,
38
+ do_predict=True,
39
+ do_train=True,
40
+ eval_accumulation_steps=None,
41
+ eval_delay=0,
42
+ eval_do_concat_batches=True,
43
+ eval_on_start=False,
44
+ eval_steps=None,
45
+ eval_strategy=epoch,
46
+ eval_use_gather_object=False,
47
+ evaluation_strategy=epoch,
48
+ fp16=False,
49
+ fp16_backend=auto,
50
+ fp16_full_eval=False,
51
+ fp16_opt_level=O1,
52
+ fsdp=[],
53
+ fsdp_config={'min_num_params': 0, 'xla': False, 'xla_fsdp_v2': False, 'xla_fsdp_grad_ckpt': False},
54
+ fsdp_min_num_params=0,
55
+ fsdp_transformer_layer_cls_to_wrap=None,
56
+ full_determinism=False,
57
+ gradient_accumulation_steps=2,
58
+ gradient_checkpointing=False,
59
+ gradient_checkpointing_kwargs=None,
60
+ greater_is_better=True,
61
+ group_by_length=False,
62
+ half_precision_backend=auto,
63
+ hub_always_push=False,
64
+ hub_model_id=None,
65
+ hub_private_repo=False,
66
+ hub_strategy=every_save,
67
+ hub_token=<HUB_TOKEN>,
68
+ ignore_data_skip=False,
69
+ include_inputs_for_metrics=False,
70
+ include_num_input_tokens_seen=False,
71
+ include_tokens_per_second=False,
72
+ jit_mode_eval=False,
73
+ label_names=None,
74
+ label_smoothing_factor=0.0,
75
+ learning_rate=5e-05,
76
+ length_column_name=length,
77
+ load_best_model_at_end=True,
78
+ local_rank=0,
79
+ log_level=passive,
80
+ log_level_replica=warning,
81
+ log_on_each_node=True,
82
+ logging_dir=/content/dissertation/scripts/ner/output/tb,
83
+ logging_first_step=False,
84
+ logging_nan_inf_filter=True,
85
+ logging_steps=500,
86
+ logging_strategy=steps,
87
+ lr_scheduler_kwargs={},
88
+ lr_scheduler_type=linear,
89
+ max_grad_norm=1.0,
90
+ max_steps=-1,
91
+ metric_for_best_model=f1,
92
+ mp_parameters=,
93
+ neftune_noise_alpha=None,
94
+ no_cuda=False,
95
+ num_train_epochs=10.0,
96
+ optim=adamw_torch,
97
+ optim_args=None,
98
+ optim_target_modules=None,
99
+ output_dir=/content/dissertation/scripts/ner/output,
100
+ overwrite_output_dir=True,
101
+ past_index=-1,
102
+ per_device_eval_batch_size=8,
103
+ per_device_train_batch_size=32,
104
+ prediction_loss_only=False,
105
+ push_to_hub=True,
106
+ push_to_hub_model_id=None,
107
+ push_to_hub_organization=None,
108
+ push_to_hub_token=<PUSH_TO_HUB_TOKEN>,
109
+ ray_scope=last,
110
+ remove_unused_columns=True,
111
+ report_to=['tensorboard'],
112
+ restore_callback_states_from_checkpoint=False,
113
+ resume_from_checkpoint=None,
114
+ run_name=/content/dissertation/scripts/ner/output,
115
+ save_on_each_node=False,
116
+ save_only_model=False,
117
+ save_safetensors=True,
118
+ save_steps=500,
119
+ save_strategy=epoch,
120
+ save_total_limit=None,
121
+ seed=42,
122
+ skip_memory_metrics=True,
123
+ split_batches=None,
124
+ tf32=None,
125
+ torch_compile=False,
126
+ torch_compile_backend=None,
127
+ torch_compile_mode=None,
128
+ torch_empty_cache_steps=None,
129
+ torchdynamo=None,
130
+ tpu_metrics_debug=False,
131
+ tpu_num_cores=None,
132
+ use_cpu=False,
133
+ use_ipex=False,
134
+ use_legacy_prediction_loop=False,
135
+ use_mps_device=False,
136
+ warmup_ratio=0.0,
137
+ warmup_steps=0,
138
+ weight_decay=0.0,
139
+ )
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+
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+
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+
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+
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+
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+
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+
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+ [INFO|configuration_utils.py:733] 2024-09-06 00:08:59,880 >> loading configuration file config.json from cache at /root/.cache/huggingface/hub/models--PlanTL-GOB-ES--bsc-bio-ehr-es/snapshots/1e543adb2d21f19d85a89305eebdbd64ab656b99/config.json
148
+ [INFO|configuration_utils.py:800] 2024-09-06 00:08:59,883 >> Model config RobertaConfig {
149
+ "_name_or_path": "PlanTL-GOB-ES/bsc-bio-ehr-es",
150
+ "architectures": [
151
+ "RobertaForMaskedLM"
152
+ ],
153
+ "attention_probs_dropout_prob": 0.1,
154
+ "bos_token_id": 0,
155
+ "classifier_dropout": null,
156
+ "eos_token_id": 2,
157
+ "finetuning_task": "ner",
158
+ "gradient_checkpointing": false,
159
+ "hidden_act": "gelu",
160
+ "hidden_dropout_prob": 0.1,
161
+ "hidden_size": 768,
162
+ "id2label": {
163
+ "0": "O",
164
+ "1": "B-ENFERMEDAD",
165
+ "2": "I-ENFERMEDAD",
166
+ "3": "B-PROCEDIMIENTO",
167
+ "4": "I-PROCEDIMIENTO",
168
+ "5": "B-SINTOMA",
169
+ "6": "I-SINTOMA",
170
+ "7": "B-FARMACO",
171
+ "8": "I-FARMACO"
172
+ },
173
+ "initializer_range": 0.02,
174
+ "intermediate_size": 3072,
175
+ "label2id": {
176
+ "B-ENFERMEDAD": 1,
177
+ "B-FARMACO": 7,
178
+ "B-PROCEDIMIENTO": 3,
179
+ "B-SINTOMA": 5,
180
+ "I-ENFERMEDAD": 2,
181
+ "I-FARMACO": 8,
182
+ "I-PROCEDIMIENTO": 4,
183
+ "I-SINTOMA": 6,
184
+ "O": 0
185
+ },
186
+ "layer_norm_eps": 1e-05,
187
+ "max_position_embeddings": 514,
188
+ "model_type": "roberta",
189
+ "num_attention_heads": 12,
190
+ "num_hidden_layers": 12,
191
+ "pad_token_id": 1,
192
+ "position_embedding_type": "absolute",
193
+ "transformers_version": "4.44.2",
194
+ "type_vocab_size": 1,
195
+ "use_cache": true,
196
+ "vocab_size": 50262
197
+ }
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+
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+ [INFO|configuration_utils.py:733] 2024-09-06 00:09:00,140 >> loading configuration file config.json from cache at /root/.cache/huggingface/hub/models--PlanTL-GOB-ES--bsc-bio-ehr-es/snapshots/1e543adb2d21f19d85a89305eebdbd64ab656b99/config.json
200
+ [INFO|configuration_utils.py:800] 2024-09-06 00:09:00,140 >> Model config RobertaConfig {
201
+ "_name_or_path": "PlanTL-GOB-ES/bsc-bio-ehr-es",
202
+ "architectures": [
203
+ "RobertaForMaskedLM"
204
+ ],
205
+ "attention_probs_dropout_prob": 0.1,
206
+ "bos_token_id": 0,
207
+ "classifier_dropout": null,
208
+ "eos_token_id": 2,
209
+ "gradient_checkpointing": false,
210
+ "hidden_act": "gelu",
211
+ "hidden_dropout_prob": 0.1,
212
+ "hidden_size": 768,
213
+ "initializer_range": 0.02,
214
+ "intermediate_size": 3072,
215
+ "layer_norm_eps": 1e-05,
216
+ "max_position_embeddings": 514,
217
+ "model_type": "roberta",
218
+ "num_attention_heads": 12,
219
+ "num_hidden_layers": 12,
220
+ "pad_token_id": 1,
221
+ "position_embedding_type": "absolute",
222
+ "transformers_version": "4.44.2",
223
+ "type_vocab_size": 1,
224
+ "use_cache": true,
225
+ "vocab_size": 50262
226
+ }
227
+
228
+ [INFO|tokenization_utils_base.py:2269] 2024-09-06 00:09:00,153 >> loading file vocab.json from cache at /root/.cache/huggingface/hub/models--PlanTL-GOB-ES--bsc-bio-ehr-es/snapshots/1e543adb2d21f19d85a89305eebdbd64ab656b99/vocab.json
229
+ [INFO|tokenization_utils_base.py:2269] 2024-09-06 00:09:00,153 >> loading file merges.txt from cache at /root/.cache/huggingface/hub/models--PlanTL-GOB-ES--bsc-bio-ehr-es/snapshots/1e543adb2d21f19d85a89305eebdbd64ab656b99/merges.txt
230
+ [INFO|tokenization_utils_base.py:2269] 2024-09-06 00:09:00,153 >> loading file tokenizer.json from cache at None
231
+ [INFO|tokenization_utils_base.py:2269] 2024-09-06 00:09:00,153 >> loading file added_tokens.json from cache at None
232
+ [INFO|tokenization_utils_base.py:2269] 2024-09-06 00:09:00,153 >> loading file special_tokens_map.json from cache at /root/.cache/huggingface/hub/models--PlanTL-GOB-ES--bsc-bio-ehr-es/snapshots/1e543adb2d21f19d85a89305eebdbd64ab656b99/special_tokens_map.json
233
+ [INFO|tokenization_utils_base.py:2269] 2024-09-06 00:09:00,153 >> loading file tokenizer_config.json from cache at /root/.cache/huggingface/hub/models--PlanTL-GOB-ES--bsc-bio-ehr-es/snapshots/1e543adb2d21f19d85a89305eebdbd64ab656b99/tokenizer_config.json
234
+ [INFO|configuration_utils.py:733] 2024-09-06 00:09:00,153 >> loading configuration file config.json from cache at /root/.cache/huggingface/hub/models--PlanTL-GOB-ES--bsc-bio-ehr-es/snapshots/1e543adb2d21f19d85a89305eebdbd64ab656b99/config.json
235
+ [INFO|configuration_utils.py:800] 2024-09-06 00:09:00,154 >> Model config RobertaConfig {
236
+ "_name_or_path": "PlanTL-GOB-ES/bsc-bio-ehr-es",
237
+ "architectures": [
238
+ "RobertaForMaskedLM"
239
+ ],
240
+ "attention_probs_dropout_prob": 0.1,
241
+ "bos_token_id": 0,
242
+ "classifier_dropout": null,
243
+ "eos_token_id": 2,
244
+ "gradient_checkpointing": false,
245
+ "hidden_act": "gelu",
246
+ "hidden_dropout_prob": 0.1,
247
+ "hidden_size": 768,
248
+ "initializer_range": 0.02,
249
+ "intermediate_size": 3072,
250
+ "layer_norm_eps": 1e-05,
251
+ "max_position_embeddings": 514,
252
+ "model_type": "roberta",
253
+ "num_attention_heads": 12,
254
+ "num_hidden_layers": 12,
255
+ "pad_token_id": 1,
256
+ "position_embedding_type": "absolute",
257
+ "transformers_version": "4.44.2",
258
+ "type_vocab_size": 1,
259
+ "use_cache": true,
260
+ "vocab_size": 50262
261
+ }
262
+
263
+ /usr/local/lib/python3.10/dist-packages/transformers/tokenization_utils_base.py:1601: FutureWarning: `clean_up_tokenization_spaces` was not set. It will be set to `True` by default. This behavior will be depracted in transformers v4.45, and will be then set to `False` by default. For more details check this issue: https://github.com/huggingface/transformers/issues/31884
264
+ warnings.warn(
265
+ [INFO|configuration_utils.py:733] 2024-09-06 00:09:00,236 >> loading configuration file config.json from cache at /root/.cache/huggingface/hub/models--PlanTL-GOB-ES--bsc-bio-ehr-es/snapshots/1e543adb2d21f19d85a89305eebdbd64ab656b99/config.json
266
+ [INFO|configuration_utils.py:800] 2024-09-06 00:09:00,238 >> Model config RobertaConfig {
267
+ "_name_or_path": "PlanTL-GOB-ES/bsc-bio-ehr-es",
268
+ "architectures": [
269
+ "RobertaForMaskedLM"
270
+ ],
271
+ "attention_probs_dropout_prob": 0.1,
272
+ "bos_token_id": 0,
273
+ "classifier_dropout": null,
274
+ "eos_token_id": 2,
275
+ "gradient_checkpointing": false,
276
+ "hidden_act": "gelu",
277
+ "hidden_dropout_prob": 0.1,
278
+ "hidden_size": 768,
279
+ "initializer_range": 0.02,
280
+ "intermediate_size": 3072,
281
+ "layer_norm_eps": 1e-05,
282
+ "max_position_embeddings": 514,
283
+ "model_type": "roberta",
284
+ "num_attention_heads": 12,
285
+ "num_hidden_layers": 12,
286
+ "pad_token_id": 1,
287
+ "position_embedding_type": "absolute",
288
+ "transformers_version": "4.44.2",
289
+ "type_vocab_size": 1,
290
+ "use_cache": true,
291
+ "vocab_size": 50262
292
+ }
293
+
294
+ [INFO|modeling_utils.py:3678] 2024-09-06 00:09:00,573 >> loading weights file pytorch_model.bin from cache at /root/.cache/huggingface/hub/models--PlanTL-GOB-ES--bsc-bio-ehr-es/snapshots/1e543adb2d21f19d85a89305eebdbd64ab656b99/pytorch_model.bin
295
+ [INFO|modeling_utils.py:4497] 2024-09-06 00:09:00,651 >> Some weights of the model checkpoint at PlanTL-GOB-ES/bsc-bio-ehr-es were not used when initializing RobertaForTokenClassification: ['lm_head.bias', 'lm_head.decoder.bias', 'lm_head.decoder.weight', 'lm_head.dense.bias', 'lm_head.dense.weight', 'lm_head.layer_norm.bias', 'lm_head.layer_norm.weight']
296
+ - This IS expected if you are initializing RobertaForTokenClassification from the checkpoint of a model trained on another task or with another architecture (e.g. initializing a BertForSequenceClassification model from a BertForPreTraining model).
297
+ - This IS NOT expected if you are initializing RobertaForTokenClassification from the checkpoint of a model that you expect to be exactly identical (initializing a BertForSequenceClassification model from a BertForSequenceClassification model).
298
+ [WARNING|modeling_utils.py:4509] 2024-09-06 00:09:00,651 >> Some weights of RobertaForTokenClassification were not initialized from the model checkpoint at PlanTL-GOB-ES/bsc-bio-ehr-es and are newly initialized: ['classifier.bias', 'classifier.weight']
299
+ You should probably TRAIN this model on a down-stream task to be able to use it for predictions and inference.
300
+
301
+
302
+
303
+ /content/dissertation/scripts/ner/run_ner_train.py:397: FutureWarning: load_metric is deprecated and will be removed in the next major version of datasets. Use 'evaluate.load' instead, from the new library 🤗 Evaluate: https://huggingface.co/docs/evaluate
304
+ metric = load_metric("seqeval", trust_remote_code=True)
305
+ [INFO|trainer.py:811] 2024-09-06 00:09:07,817 >> The following columns in the training set don't have a corresponding argument in `RobertaForTokenClassification.forward` and have been ignored: tokens, ner_tags, id. If tokens, ner_tags, id are not expected by `RobertaForTokenClassification.forward`, you can safely ignore this message.
306
+ [INFO|trainer.py:2134] 2024-09-06 00:09:08,371 >> ***** Running training *****
307
+ [INFO|trainer.py:2135] 2024-09-06 00:09:08,371 >> Num examples = 34,604
308
+ [INFO|trainer.py:2136] 2024-09-06 00:09:08,371 >> Num Epochs = 10
309
+ [INFO|trainer.py:2137] 2024-09-06 00:09:08,371 >> Instantaneous batch size per device = 32
310
+ [INFO|trainer.py:2140] 2024-09-06 00:09:08,371 >> Total train batch size (w. parallel, distributed & accumulation) = 64
311
+ [INFO|trainer.py:2141] 2024-09-06 00:09:08,371 >> Gradient Accumulation steps = 2
312
+ [INFO|trainer.py:2142] 2024-09-06 00:09:08,371 >> Total optimization steps = 5,410
313
+ [INFO|trainer.py:2143] 2024-09-06 00:09:08,372 >> Number of trainable parameters = 124,059,657
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+ ***** Running Evaluation *****
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