Explainable prediction of medical codes from clinical text

James Mullenbach, Sarah Wiegreffe, Jon Duke, Jimeng Sun, Jacob Eisenstein

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

Abstract

Clinical notes are text documents that are created by clinicians for each patient encounter. They are typically accompanied by medical codes, which describe the diagnosis and treatment. Annotating these codes is labor intensive and error prone; furthermore, the connection between the codes and the text is not annotated, obscuring the reasons and details behind specific diagnoses and treatments. We present an attentional convolutional network that predicts medical codes from clinical text. Our method aggregates information across the document using a convolutional neural network, and uses an attention mechanism to select the most relevant segments for each of the thousands of possible codes. The method is accurate, achieving precision@8 of 0.71 and a Micro-F1 of 0.54, which are both better than the prior state of the art. Furthermore, through an interpretability evaluation by a physician, we show that the attention mechanism identifies meaningful explanations for each code assignment.

Original languageEnglish (US)
Title of host publicationLong Papers
PublisherAssociation for Computational Linguistics (ACL)
Pages1101-1111
Number of pages11
ISBN (Electronic)9781948087278
StatePublished - 2018
Externally publishedYes
Event2018 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies, NAACL HLT 2018 - New Orleans, United States
Duration: Jun 1 2018Jun 6 2018

Publication series

NameNAACL HLT 2018 - 2018 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies - Proceedings of the Conference
Volume1

Conference

Conference2018 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies, NAACL HLT 2018
Country/TerritoryUnited States
CityNew Orleans
Period6/1/186/6/18

ASJC Scopus subject areas

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

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