Biomedical Named Entity Recognition via Reference-Set Augmented Bootstrapping

Joel Mathew, Shobeir Fakhraei, Jose Luis Ambite

Keywords: Name Entity Recognition, Bootstrapping, Neural Networks, Reference Set, Biomedicine

TL;DR: Augmented bootstrapping approach combining information from a reference set with iterative refinements of soft labels to improve Name Entity Recognition from biomedical literature.

Abstract: We present a weakly-supervised data augmentation approach to improve Named Entity Recognition (NER) in a challenging domain: extracting biomedical entities (e.g., proteins) from the scientific literature. First, we train a neural NER (NNER) model over a small seed of fully-labeled examples. Second, we use a reference set of entity names (e.g., proteins in UniProt) to identify entity mentions with high precision, but low recall, on an unlabeled corpus. Third, we use the NNER model to assign weak labels to the corpus. Finally, we retrain our NNER model iteratively over the augmented training set, including the seed, the reference-set examples, and the weakly-labeled examples, which results in refined labels. We show empirically that this augmented bootstrapping process significantly improves NER performance, and discuss the factors impacting the efficacy of the approach.