TY - GEN
T1 - Clinical concept linking with contextualized neural representations
AU - Schumacher, Elliot
AU - Mulyar, Andriy
AU - Dredze, Mark
N1 - Funding Information:
Contribution performed during an internship at Johns Hopkins University.
Publisher Copyright:
© 2020 Association for Computational Linguistics
PY - 2020
Y1 - 2020
N2 - 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.
AB - 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.
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M3 - Conference contribution
AN - SCOPUS:85095681591
T3 - Proceedings of the Annual Meeting of the Association for Computational Linguistics
SP - 8585
EP - 8592
BT - ACL 2020 - 58th Annual Meeting of the Association for Computational Linguistics, Proceedings of the Conference
PB - Association for Computational Linguistics (ACL)
T2 - 58th Annual Meeting of the Association for Computational Linguistics, ACL 2020
Y2 - 5 July 2020 through 10 July 2020
ER -