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Artificial Intelligence in MedicineVolume 151, May 2024, Article number 102845

De-identification of clinical free text using natural language processing: A systematic review of current approaches(Review)(Open Access)

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  • aThe University of Novi Sad, Faculty of Technical Sciences, Trg Dositeja Obradovića 6, Novi Sad, 21002, Serbia
  • bThe Institute for Artificial Intelligence Research and Development of Serbia, Fruškogorska 1, Novi Sad, 21000, Serbia
  • cBayer A.G., Research and Development, Mullerstrasse 173, Berlin, 13342, Germany
  • dThe University of Manchester, Department of Computer Science, Manchester, United Kingdom

Abstract

Background: Electronic health records (EHRs) are a valuable resource for data-driven medical research. However, the presence of protected health information (PHI) makes EHRs unsuitable to be shared for research purposes. De-identification, i.e. the process of removing PHI is a critical step in making EHR data accessible. Natural language processing has repeatedly demonstrated its feasibility in automating the de-identification process. Objectives: Our study aims to provide systematic evidence on how the de-identification of clinical free text written in English has evolved in the last thirteen years, and to report on the performances and limitations of the current state-of-the-art systems for the English language. In addition, we aim to identify challenges and potential research opportunities in this field. Methods: A systematic search in PubMed, Web of Science, and the DBLP was conducted for studies published between January 2010 and February 2023. Titles and abstracts were examined to identify the relevant studies. Selected studies were then analysed in-depth, and information was collected on de-identification methodologies, data sources, and measured performance. Results: A total of 2125 publications were identified for the title and abstract screening. 69 studies were found to be relevant. Machine learning (37 studies) and hybrid (26 studies) approaches are predominant, while six studies relied only on rules. The majority of the approaches were trained and evaluated on public corpora. The 2014 i2b2/UTHealth corpus is the most frequently used (36 studies), followed by the 2006 i2b2 (18 studies) and 2016 CEGS N-GRID (10 studies) corpora. Conclusion: Earlier de-identification approaches aimed at English were mainly rule and machine learning hybrids with extensive feature engineering and post-processing, while more recent performance improvements are due to feature-inferring recurrent neural networks. Current leading performance is achieved using attention-based neural models. Recent studies report state-of-the-art F1-scores (over 98 %) when evaluated in the manner usually adopted by the clinical natural language processing community. However, their performance needs to be more thoroughly assessed with different measures to judge their reliability to safely de-identify data in a real-world setting. Without additional manually labeled training data, state-of-the-art systems fail to generalise well across a wide range of clinical sub-domains. © 2024 Elsevier B.V.

Author keywords

de-identificationEnglish clinical free textnatural language processing

Indexed keywords

Engineering controlled terms:AbstractingDiagnosisLearning algorithmsNatural language processing systems
Engineering uncontrolled terms'currentDe-identificationElectronic healthEnglish clinical free textFree textsHealth recordsLanguage processingNatural language processingNatural languagesPerformance
Engineering main heading:Recurrent neural networks
EMTREE medical terms:biological modelelectronic health recordEnglish (language)humanmachine learningmedical informationnatural language processingrecurrent neural networkreliabilityreviewsystematic reviewWeb of Scienceelectronic health record
MeSH:Electronic Health RecordsHumansMachine LearningNatural Language Processing

Funding details

Funding sponsor Funding number Acronym
Engineering and Physical Sciences Research Council
See opportunities by EPSRC
EPSRC
EP/N027280/1
451-03-47/2023-01/200156
  • 1

    This work was supported by the Engineering and Physical Sciences Research Council for HealTex—UK Healthcare Text Analytics Research Network [grant number EP/N027280/1 ]; and the Serbian Ministry of Science, Technological Development, and Innovation through project “Innovative scientific and artistic research from the FTS (activity) domain” [project number 451-03-47/2023-01/200156 ].

  • 2

    This work was supported by the Engineering and Physical Sciences Research Council for HealTex—UK Healthcare Text Analytics Research Network [grant number EP/N027280/1]; and the Republic of Serbia Ministry of Science, Technological Development, and Innovation through project “Innovative scientific and artistic research from the FTS (activity) domain” [project number 451-03-47/2023-01/200156].

  • ISSN: 09333657
  • CODEN: AIMEE
  • Source Type: Journal
  • Original language: English
  • DOI: 10.1016/j.artmed.2024.102845
  • PubMed ID: 38555848
  • Document Type: Review
  • Publisher: Elsevier B.V.

  Bašaragin, B.; The Institute for Artificial Intelligence Research and Development of Serbia, Fruškogorska 1, Novi Sad, Serbia;
© Copyright 2024 Elsevier B.V., All rights reserved.

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