A generate-and-rank framework with semantic type regularization for biomedical concept normalization

Dongfang Xu, Zeyu Zhang, Steven Bethard

Research output: Chapter in Book/Report/Conference proceedingConference contribution

22 Scopus citations

Abstract

Concept normalization, the task of linking textual mentions of concepts to concepts in an ontology, is challenging because ontologies are large. In most cases, annotated datasets cover only a small sample of the concepts, yet concept normalizers are expected to predict all concepts in the ontology. In this paper, we propose an architecture consisting of a candidate generator and a list-wise ranker based on BERT. The ranker considers pairings of concept mentions and candidate concepts, allowing it to make predictions for any concept, not just those seen during training. We further enhance this list-wise approach with a semantic type regularizer that allows the model to incorporate semantic type information from the ontology during training. Our proposed concept normalization framework achieves state-of-the-art performance on multiple datasets.

Original languageEnglish (US)
Title of host publicationACL 2020 - 58th Annual Meeting of the Association for Computational Linguistics, Proceedings of the Conference
PublisherAssociation for Computational Linguistics (ACL)
Pages8452-8464
Number of pages13
ISBN (Electronic)9781952148255
StatePublished - 2020
Event58th Annual Meeting of the Association for Computational Linguistics, ACL 2020 - Virtual, Online, United States
Duration: Jul 5 2020Jul 10 2020

Publication series

NameProceedings of the Annual Meeting of the Association for Computational Linguistics
ISSN (Print)0736-587X

Conference

Conference58th Annual Meeting of the Association for Computational Linguistics, ACL 2020
Country/TerritoryUnited States
CityVirtual, Online
Period7/5/207/10/20

ASJC Scopus subject areas

  • Computer Science Applications
  • Linguistics and Language
  • Language and Linguistics

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