Knowledge Guided Named Entity Recognition for BioMedical Text

In this work, we formulate the NER task as a multi-answer knowledge guided QA task (KGQA) which helps to predict entities only by assigning B, I and O tags without associating entity types with the tags. We provide different knowledge contexts, such as, entity types, questions, definitions and examples along with the text and train on a combined dataset of 18 biomedical corpora. This formulation (a) enables systems to jointly learn NER specific features from varied NER datasets, (b) can use knowledge-text attention to identify words having higher similarity to provided knowledge, improving performance, (c) reduces system confusion by reducing the prediction classes to B, I, O only, and (d) makes detection of nested entities easier. We perform extensive experiments of this KGQA formulation on 18 biomedical NER datasets, and through experiments we note that knowledge helps in achieving better performance. Our problem formulation is able to achieve state-of-the-art results in 12 datasets.