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