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Deep learning in clinical natural language processing: a methodical review

Journal of the American Medical Informatics Association : JAMIA, 2020-03, Vol.27 (3), p.457-470 [Peer Reviewed Journal]

The Author(s) 2019. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved. For permissions, please email: journals.permissions@oup.com. ;The Author(s) 2019. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved. For permissions, please email: journals.permissions@oup.com 2019 ;ISSN: 1527-974X ;ISSN: 1067-5027 ;EISSN: 1527-974X ;DOI: 10.1093/jamia/ocz200 ;PMID: 31794016

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  • Title:
    Deep learning in clinical natural language processing: a methodical review
  • Author: Wu, Stephen ; Roberts, Kirk ; Datta, Surabhi ; Du, Jingcheng ; Ji, Zongcheng ; Si, Yuqi ; Soni, Sarvesh ; Wang, Qiong ; Wei, Qiang ; Xiang, Yang ; Zhao, Bo ; Xu, Hua
  • Subjects: Bibliometrics ; Deep Learning - statistics & numerical data ; Deep Learning - trends ; Electronic Health Records ; Humans ; Natural Language Processing ; Reviews
  • Is Part Of: Journal of the American Medical Informatics Association : JAMIA, 2020-03, Vol.27 (3), p.457-470
  • Description: This article methodically reviews the literature on deep learning (DL) for natural language processing (NLP) in the clinical domain, providing quantitative analysis to answer 3 research questions concerning methods, scope, and context of current research. We searched MEDLINE, EMBASE, Scopus, the Association for Computing Machinery Digital Library, and the Association for Computational Linguistics Anthology for articles using DL-based approaches to NLP problems in electronic health records. After screening 1,737 articles, we collected data on 25 variables across 212 papers. DL in clinical NLP publications more than doubled each year, through 2018. Recurrent neural networks (60.8%) and word2vec embeddings (74.1%) were the most popular methods; the information extraction tasks of text classification, named entity recognition, and relation extraction were dominant (89.2%). However, there was a "long tail" of other methods and specific tasks. Most contributions were methodological variants or applications, but 20.8% were new methods of some kind. The earliest adopters were in the NLP community, but the medical informatics community was the most prolific. Our analysis shows growing acceptance of deep learning as a baseline for NLP research, and of DL-based NLP in the medical community. A number of common associations were substantiated (eg, the preference of recurrent neural networks for sequence-labeling named entity recognition), while others were surprisingly nuanced (eg, the scarcity of French language clinical NLP with deep learning). Deep learning has not yet fully penetrated clinical NLP and is growing rapidly. This review highlighted both the popular and unique trends in this active field.
  • Publisher: England: Oxford University Press
  • Language: English
  • Identifier: ISSN: 1527-974X
    ISSN: 1067-5027
    EISSN: 1527-974X
    DOI: 10.1093/jamia/ocz200
    PMID: 31794016
  • Source: GFMER Free Medical Journals
    MEDLINE
    PubMed Central
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