Table 10.
F1 score results for detection of discontinuous spans for all algorithms tested against the core evaluation annotation set of the 30 held-out articles
Ontology | Support | CRF | BiLSTM | BiLSTM-CRF | Char-Embeddings | BiLSTM-ELMo | BioBERT |
---|---|---|---|---|---|---|---|
ChEBI | 14 | 0 | 0 | 0 | 0 | 0 | 0 |
CL | 175 | 0.1176 | 0.1158 | 0.1171 | 0 | 0.0107 | 0.1818 |
GO_BP | 272 | 0.0952 | 0 | 0.014 | 0 | 0.007 | 0.2742 |
GO_CC | 14 | 0.1053 | 0 | 0 | 0.0526 | 0 | 0.3 |
PR | 44 | 0 | 0 | 0 | 0 | 0 | 0.08 |
SO | 45 | 0.0408 | 0 | 0 | 0 | 0 | 0.3 |
UBERON | 118 | 0.04 | 0 | 0 | 0 | 0 | 0.0915 |
Note that there are no discontinuous spans in the GO_MF, MOP, and NCBITaxon sets