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Table 3 Performance of BlueBERT model on the PPI, ChemProt, and DDI tasks before and after removing MIMIC-III from the domain adaptation data

From: Investigation of improving the pre-training and fine-tuning of BERT model for biomedical relation extraction

Model PPI DDI ChemProt
P R F P R F P R F
BlueBERT 69.3 75.0 71.9 76.2 77.4 76.8 70.9 71.5 71.2
BlueBERT (-M) 76.6 83.1 79.6 80.0 78.5 79.2 74.7 75.8 75.2
  1. Bold values indicate better results
  2. P: Precision; R: Recall; F: F1 Score; -M: Subtract the MIMIC-III clinical notes