Biomedical Named Entity Recognition via Knowledge Guidance and Question Answering

Pratyay Banerjee, Kuntal Kumar Pal, Murthy Devarakonda, Chitta Baral

Research output: Contribution to journalArticlepeer-review

9 Scopus citations


In this work, we formulated the named entity recognition (NER) task as a multi-answer knowledge guided question-answer task (KGQA) and showed that the knowledge guidance helps to achieve state-of-the-art results for 11 of 18 biomedical NER datasets. We prepended five different knowledge contexts -entity types, questions, definitions, and examples -to the input text and trained and tested BERT-based neural models on such input sequences from a combined dataset of the 18 different datasets. This novel formulation of the task (a) improved named entity recognition and illustrated the impact of different knowledge contexts, (b) reduced system confusion by limiting prediction to a single entity-class for each input token (i.e., B, I, O only) compared to multiple entity-classes in traditional NER (i.e., Bentity1, Bentity2, Ientity1, I, O), (c) made detection of nested entities easier, and (d) enabled the models to jointly learn NER-specific features from a large number of datasets. We performed extensive experiments of this KGQA formulation on the biomedical datasets, and through the experiments, we showed when knowledge improved named entity recognition. We analyzed the effect of the task formulation, the impact of the different knowledge contexts, the multi-task aspect of the generic format, and the generalization ability of KGQA. We also probed the model to better understand the key contributors for these improvements.

Original languageEnglish (US)
Article number3465221
JournalACM Transactions on Computing for Healthcare
Issue number4
StatePublished - Oct 2021


  • BIO tagging
  • NER
  • Named entity recognition
  • biomedical
  • multitask training
  • question answering
  • text tagging
  • transfer learning

ASJC Scopus subject areas

  • Software
  • Medicine (miscellaneous)
  • Information Systems
  • Biomedical Engineering
  • Computer Science Applications
  • Health Informatics
  • Health Information Management


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