Clinical concept linking with contextualized neural representations

Elliot Schumacher, Andriy Mulyar, Mark Dredze

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

Abstract

In traditional approaches to entity linking, linking decisions are based on three sources of information - the similarity of the mention string to an entity's name, the similarity of the context of the document to the entity, and broader information about the knowledge base (KB). In some domains, there is little contextual information present in the KB and thus we rely more heavily on mention string similarity. We consider one example of this, concept linking, which seeks to link mentions of medical concepts to a medical concept ontology. We propose an approach to concept linking that leverages recent work in contextualized neural models, such as ELMo (Peters et al., 2018), which create a token representation that integrates the surrounding context of the mention and concept name. We find a neural ranking approach paired with contextualized embeddings provides gains over a competitive baseline (Leaman et al., 2013). Additionally, we find that a pre-training step using synonyms from the ontology offers a useful initialization for the ranker.

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)
Pages8585-8592
Number of pages8
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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