Model/Dataset | NCBI | BC5 CDR | BC4 CHEMD | BC2 GM | JNL PBA | i2b2-clinical | i2b2-2012 | Our data |
---|---|---|---|---|---|---|---|---|
BiLSTM-based | ||||||||
BiLSTM-CRF [63] | 85.80 | 85.92 | 89.48 | 80.60 | 74.29 | 85.66 | 86.10 | 88.10 |
BILSTM-CNN-Char [71] | 89.73 | 87.73 | 88.06 | 87.51 | 77.29 | 84.08 | 83.10 | 89.20 |
BiLSTM-CRF-MTL [72] | 88.85 | 84.93 | 89.42 | 82.12 | 77.03 | 83.25 | 83.24 | 87.10 |
Att-BiLSTM-CRF [73] | 84.50 | 88.93 | 91.08 | 84.37 | 77.10 | 88.60 | 85.83 | 88.10 |
Doc-Att-BiLSTM-CRF [16] | 88.60 | 87.30 | 85.10 | 81.80 | 76.23 | 85.18 | 85.17 | 86.94 |
BiLSTM-contextualized [74] | 85.17 | 87.83 | 87.12 | 80.51 | 73.52 | 85.26 | 84.22 | 85.18 |
CollaboNet [75] | 84.08 | 84.08 | 87.12 | 79.73 | 78.58 | 85.61 | 84.29 | 86.70 |
BERT-based | ||||||||
SciBERT [76] | 86.88 | 87.94 | 88.06 | 84.08 | 75.77 | 79.19 | 79.10 | 81.95 |
BLUE [77] | 86.37 | 86.60 | 90.19 | 80.93 | 75.27 | 84.06 | 83.45 | 89.95 |
BioBERT-Base v1.0 [13] | 87.71 | 85.80 | 90.77 | 84.72 | 77.59 | 85.64 | 86.00 | 90.10 |
BioBERT-Base v1.1 [13] | 88.30 | 84.67 | 90.78 | 88.41 | 77.21 | 86.73 | 86.23 | 90.39 |
BioBERT-Base v1.2Â [13] | 88.15 | 86.70 | 92.20 | 88.72 | 79.10 | 88.95 | 87.40 | 92.34 |
Our approach | 90.58 | 89.90 | 91.58 | 89.15 | 79.92 | 89.10 | 90.10 | 94.78 |