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--- |
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license: apache-2.0 |
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tags: |
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- generated_from_trainer |
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model-index: |
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- name: biolinkbert-mednli |
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results: [] |
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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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# biolinkbert-mednli |
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This model is a fine-tuned version of [michiyasunaga/BioLinkBERT-large](https://huggingface.co/michiyasunaga/BioLinkBERT-large) on [MedNLI](https://physionet.org/content/mednli/1.0.0/). |
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It achieves the following results on the evaluation set: |
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``` |
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{ |
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"eval_accuracy": 0.8788530230522156, |
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"eval_loss": 0.7843484878540039, |
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"eval_runtime": 39.7009, |
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"eval_samples": 1395, |
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"eval_samples_per_second": 35.138, |
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"eval_steps_per_second": 1.108 |
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} |
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``` |
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The accuracy for the test set is |
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``` |
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{ |
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"eval_accuracy": 0.8607594966888428, |
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"eval_loss": 0.879707932472229, |
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"eval_runtime": 27.4404, |
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"eval_samples": 1395, |
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"eval_samples_per_second": 51.821, |
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"eval_steps_per_second": 1.64 |
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} |
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``` |
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The labels are |
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``` |
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"id2label": { |
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"0": "entailment", |
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"1": "neutral", |
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"2": "contradiction" |
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}, |
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``` |
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## Training procedure |
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This model checkpoint is made by [mednli.py](https://huggingface.co/cnut1648/biolinkbert-mednli/blob/main/mednli.py) by the following command: |
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```shell |
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root=/path/to/mednli/; |
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python mednli.py \ |
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--model_name_or_path michiyasunaga/BioLinkBERT-large \ |
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--do_train --train_file ${root}/mli_train_v1.jsonl \ |
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--do_eval --validation_file ${root}/mli_dev_v1.jsonl \ |
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--do_predict --test_file ${root}/mli_test_v1.jsonl \ |
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--max_seq_length 512 --fp16 --per_device_train_batch_size 16 --gradient_accumulation_steps 2 \ |
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--learning_rate 3e-5 --warmup_ratio 0.5 --num_train_epochs 10 \ |
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--output_dir ./biolinkbert_mednli |
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``` |
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### Training hyperparameters |
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The following hyperparameters were used during training: |
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- learning_rate: 3e-05 |
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- train_batch_size: 16 |
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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: 32 |
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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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- lr_scheduler_warmup_ratio: 0.5 |
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- num_epochs: 10.0 |
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- mixed_precision_training: Native AMP |
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### Framework versions |
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- Transformers 4.22.2 |
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- Pytorch 1.13.0+cu117 |
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- Datasets 2.4.0 |
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- Tokenizers 0.12.1 |
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