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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
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BMC Bioinformatics

ISSN: 1471-2105

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