Table 3 Comparison metrics of biomedically related pre-trained BERT-based models
From: Precision information extraction for rare disease epidemiology at scale
Model | Overall token-level precision | Overall entity-level precision |
|---|---|---|
BioBERT large cased v1.1 | 0.834 | 0.720 |
BioBERT base cased v1.2 | 0.825 | 0.698 |
PubMedBERT base | 0.824 | 0.713 |
PubMedBERT + PMC base | 0.824 | 0.715 |
BlueBERT base | 0.829 | 0.722 |
BlueBERT large | 0.818 | 0.690 |