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