Parallel sequence tagging for concept recognition
Table 3: Results for our current BioBERT system, best system reported in the shared-task paper (Furrer et al., 2019a), and the official baseline.
['Annotation set', 'System', 'proper SER', 'proper F-score', 'extended SER', 'extended F-score']
Our system consistently achieves better scores than the baseline, which is a pipeline with a CRF-based span tagger and a BiLSTM-based concept classifier that were also trained on the CRAFT corpus alone. For most annotation sets, our current system performed better than the best system presented in the shared-task paper, with the exception of GO_MF_EXT and PR_EXT. For NCBITaxon_EXT and PR, the comparison is inconclusive, as SER and F-score give contradictory rankings.