transformers pytorch bert token-classification generated_from_trainer medical en license:mit autotrain_compatible endpoints_compatible region:us
---
language:
- en
license: mit
metrics:
- f1
- recall
- precision
pipeline_tag: token-classification
tags:
- generated_from_trainer
- medical
widget:
- text: I have a cyst in the corner of my right eye and it grows bigger and bigger.
model-index:
- name: models
  results: []
---

# Model

This model is a fine-tuned version of [microsoft/BiomedNLP-PubMedBERT-base-uncased-abstract-fulltext](https://huggingface.co/microsoft/BiomedNLP-PubMedBERT-base-uncased-abstract-fulltext) on BC5CDR dataset.
It achieves the following results on the evaluation set:
- Loss: 0.0876
- Precision: 0.8882
- Recall: 0.9258
- F1: 0.9066

## Examples from BC5CDR (Test Set)

All the entities in following examples are correctly predicted by the model:

- The authors report on six cases of famotidine - associated delirium in hospitalized patients who cleared completely upon removal of famotidine . The pharmacokinetics of famotidine are reviewed , with no change in its metabolism in the elderly population seen . The implications of using famotidine in elderly persons are discussed.
- Scleroderma renal crisis ( SRC ) is a rare complication of systemic sclerosis ( SSc ) but can be severe enough to require temporary or permanent renal replacement therapy . Moderate to high dose corticosteroid use is recognized as a major risk factor for SRC.

Model fails to extract all the entities from the following examples (correct Chemical entities are highlighted with lime colour and Disease entities with yellow colour):

- <span style="background-color: lime">Famotidine</span> is a histamine H2 - receptor antagonist used in inpatient settings for prevention of stress <span style="background-color: yellow">ulcers</span> and is showing increasing popularity because of its low cost.
- We used high - resolution MRI and surface - based computational image analyses to map regional <span style="background-color: yellow">abnormalities in the cortex , hippocampus , white matter , and ventricles</span> in 22 human subjects who used <span style="background-color: lime">MA</span> and 21 age - matched , healthy controls . Cortical maps revealed severe gray - matter deficits in the cingulate , limbic , and paralimbic cortices of <span style="background-color: lime">MA</span>  abusers had 7.8% smaller hippocampal volumes than control subjects and significant white - matter <span style="background-color: yellow">hypertrophy</span>.



### Training hyperparameters

The following hyperparameters were used during training:
- learning_rate: 5e-05
- train_batch_size: 16
- eval_batch_size: 16
- seed: 42
- optimizer: Adam with betas=(0.9,0.999) and epsilon=1e-08
- lr_scheduler_type: linear
- lr_scheduler_warmup_steps: 42
- num_epochs: 6


### Framework versions

- Transformers 4.25.1
- Pytorch 1.13.1+cu117
- Tokenizers 0.13.2