Implicit entity recognition in clinical documents

Sujan Perera, Pablo Mendes, Amit Sheth, Krishnaprasad Thirunarayan, Adarsh Alex, Christopher Heid, Greg Mott

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

8 Scopus citations


With the increasing automation of health care information processing, it has become crucial to extract meaningful information from textual notes in electronic medical records. One of the key challenges is to extract and normalize entity mentions. State-of-the-art approaches have focused on the recognition of entities that are explicitly mentioned in a sentence. However, clinical documents often contain phrases that indicate the entities but do not contain their names. We term those implicit entity mentions and introduce the problem of implicit entity recognition (IER) in clinical documents. We propose a solution to IER that leverages entity definitions from a knowledge base to create entity models, projects sentences to the entity models and identifies implicit entity mentions by evaluating semantic similarity between sentences and entity models. The evaluation with 857 sentences selected for 8 different entities shows that our algorithm outperforms the most closely related unsupervised solution. The similarity value calculated by our algorithm proved to be an effective feature in a supervised learning setting, helping it to improve over the baselines, and achieving F1 scores of .81 and .73 for different classes of implicit mentions. Our gold standard annotations are made available to encourage further research in the area of IER.

Original languageEnglish (US)
Title of host publicationProceedings of the 4th Joint Conference on Lexical and Computational Semantics, *SEM 2015
PublisherAssociation for Computational Linguistics (ACL)
Number of pages11
ISBN (Electronic)9781941643396
StatePublished - 2015
Externally publishedYes
Event4th Joint Conference on Lexical and Computational Semantics, *SEM 2015 - Denver, United States
Duration: Jun 4 2015Jun 5 2015

Publication series

NameProceedings of the 4th Joint Conference on Lexical and Computational Semantics, *SEM 2015


Conference4th Joint Conference on Lexical and Computational Semantics, *SEM 2015
Country/TerritoryUnited States

ASJC Scopus subject areas

  • Computer Networks and Communications
  • Computer Science Applications
  • Information Systems


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