---
license: apache-2.0
tags:
- generated_from_trainer
model-index:
- name: biolinkbert-mednli
  results: []
---

<!-- This model card has been generated automatically according to the information the Trainer had access to. You
should probably proofread and complete it, then remove this comment. -->

# biolinkbert-mednli

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/).
It achieves the following results on the evaluation set:
```
{
    "eval_accuracy": 0.8788530230522156,
    "eval_loss": 0.7843484878540039,
    "eval_runtime": 39.7009,
    "eval_samples": 1395,
    "eval_samples_per_second": 35.138,
    "eval_steps_per_second": 1.108
}
```

The accuracy for the test set is
```
{
    "eval_accuracy": 0.8607594966888428,
    "eval_loss": 0.879707932472229,
    "eval_runtime": 27.4404,
    "eval_samples": 1395,
    "eval_samples_per_second": 51.821,
    "eval_steps_per_second": 1.64
}
```
The labels are
```
"id2label": {
    "0": "entailment",
    "1": "neutral",
    "2": "contradiction"
  },
```

## Training procedure

This model checkpoint is made by [mednli.py](https://huggingface.co/cnut1648/biolinkbert-mednli/blob/main/mednli.py) by the following command:
```shell
root=/path/to/mednli/;
python mednli.py \
    --model_name_or_path michiyasunaga/BioLinkBERT-large \
    --do_train --train_file ${root}/mli_train_v1.jsonl \
    --do_eval --validation_file ${root}/mli_dev_v1.jsonl \
    --do_predict --test_file ${root}/mli_test_v1.jsonl \
    --max_seq_length 512 --fp16 --per_device_train_batch_size 16 --gradient_accumulation_steps 2 \
    --learning_rate 3e-5 --warmup_ratio 0.5 --num_train_epochs 10 \
    --output_dir ./biolinkbert_mednli
```

### Training hyperparameters

The following hyperparameters were used during training:
- learning_rate: 3e-05
- train_batch_size: 16
- eval_batch_size: 8
- seed: 42
- gradient_accumulation_steps: 2
- total_train_batch_size: 32
- optimizer: Adam with betas=(0.9,0.999) and epsilon=1e-08
- lr_scheduler_type: linear
- lr_scheduler_warmup_ratio: 0.5
- num_epochs: 10.0
- mixed_precision_training: Native AMP

### Framework versions

- Transformers 4.22.2
- Pytorch 1.13.0+cu117
- Datasets 2.4.0
- Tokenizers 0.12.1