BACKGROUND CONCLUSIONS METHODS OBJECTIVE RESULTS
---
tags:
- generated_from_trainer
metrics:
- accuracy
widget:
- text: "SAMPLE 32,441 archived appendix samples fixed in formalin and embedded in paraffin and tested for the presence of abnormal prion protein (PrP)."
model-index:
- name: BioBert-PubMed200kRCT
  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. -->

# best_model

This model is a fine-tuned version of [dmis-lab/biobert-base-cased-v1.1](https://huggingface.co/dmis-lab/biobert-base-cased-v1.1) on the [PubMed200kRCT](https://github.com/Franck-Dernoncourt/pubmed-rct/tree/master/PubMed_200k_RCT) dataset.
It achieves the following results on the evaluation set:
- Loss: 0.2832
- Accuracy: 0.8934

## Model description

More information needed

## Intended uses & limitations

The model can be used for text classification tasks of Randomized Controlled Trials that does not have any structure. The text can be classified as one of the following:
* BACKGROUND
* CONCLUSIONS
* METHODS
* OBJECTIVE
* RESULTS

The model can be directly used like this:

```python
from transformers import TextClassificationPipeline
from transformers import AutoTokenizer, AutoModelForSequenceClassification
model = AutoModelForSequenceClassification.from_pretrained("pritamdeka/BioBert-PubMed200kRCT")
tokenizer = AutoTokenizer.from_pretrained("pritamdeka/BioBert-PubMed200kRCT")
pipe = TextClassificationPipeline(model=model, tokenizer=tokenizer, return_all_scores=True)
pipe("Treatment of 12 healthy female subjects with CDCA for 2 days resulted in increased BAT activity.")
```
Results will be shown as follows:

```python
[[{'label': 'BACKGROUND', 'score': 0.0027583304326981306},
  {'label': 'CONCLUSIONS', 'score': 0.044541116803884506},
  {'label': 'METHODS', 'score': 0.19493348896503448},
  {'label': 'OBJECTIVE', 'score': 0.003996663726866245},
  {'label': 'RESULTS', 'score': 0.7537703514099121}]]
```

More information needed

## Training and evaluation data

More information needed

## Training procedure

### Training hyperparameters

The following hyperparameters were used during training:
- learning_rate: 5e-05
- train_batch_size: 64
- eval_batch_size: 64
- seed: 42
- optimizer: Adam with betas=(0.9,0.999) and epsilon=1e-08
- lr_scheduler_type: linear
- num_epochs: 2.0
- mixed_precision_training: Native AMP

### Training results

| Training Loss | Epoch | Step  | Validation Loss | Accuracy |
|:-------------:|:-----:|:-----:|:---------------:|:--------:|
| 0.3587        | 0.14  | 5000  | 0.3137          | 0.8834   |
| 0.3318        | 0.29  | 10000 | 0.3100          | 0.8831   |
| 0.3286        | 0.43  | 15000 | 0.3033          | 0.8864   |
| 0.3236        | 0.58  | 20000 | 0.3037          | 0.8862   |
| 0.3182        | 0.72  | 25000 | 0.2939          | 0.8876   |
| 0.3129        | 0.87  | 30000 | 0.2910          | 0.8885   |
| 0.3078        | 1.01  | 35000 | 0.2914          | 0.8887   |
| 0.2791        | 1.16  | 40000 | 0.2975          | 0.8874   |
| 0.2723        | 1.3   | 45000 | 0.2913          | 0.8906   |
| 0.2724        | 1.45  | 50000 | 0.2879          | 0.8904   |
| 0.27          | 1.59  | 55000 | 0.2874          | 0.8911   |
| 0.2681        | 1.74  | 60000 | 0.2848          | 0.8928   |
| 0.2672        | 1.88  | 65000 | 0.2832          | 0.8934   |


### Framework versions

- Transformers 4.18.0.dev0
- Pytorch 1.10.0+cu111
- Datasets 1.18.4
- Tokenizers 0.11.6
