Opportunities and challenges in developing deep learning models using electronic health records data: a systematic review
Open accessAbstract
Objective: To conduct a systematic review of deep learning models for electronic health record (EHR) data, and illustrate various deep learning architectures for analyzing different data sources and their target applications. We also highlight ongoing research and identify open challenges in building deep learning models of EHRs. Design/method: We searched PubMed and Google Scholar for papers on deep learning studies using EHR data published between January 1, 2010, and January 31, 2018. We summarize them according to these axes: types of analytics tasks, types of deep learning model architectures, special challenges arising from health data and tasks and their potential solutions, as well as evaluation strategies. Results: We surveyed and analyzed multiple aspects of the 98 articles we found and identified the following analytics tasks: disease detection/classification, sequential prediction of clinical events, concept embedding, data augmentation, and EHR data privacy. We then studied how deep architectures were applied to these tasks. We also discussed some special challenges arising from modeling EHR data and reviewed a few popular approaches. Finally, we summarized how performance evaluations were conducted for each task. Discussion: Despite the early success in using deep learning for health analytics applications, there still exist a number of issues to be addressed. We discuss them in detail including data and label availability, the interpretability and transparency of the model, and ease of deployment.
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Deep neural network models have the potential to identify important diagnostic indicators from raw data and encapsulate clinical patterns.
“By leveraging a large set of patient data, deep neural network models have the potential to identify important diagnostic indicators from the raw data and encapsulate clinical patterns8–10.”
From Early prediction of diagnostic-related groups and estimation of hospital cost by processing clinical notes (2021) · cites this paper as [10]
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- Authors
- Xiao, C., Choi, E., & Sun, J.
- Affiliations
- IBM Research - Cambridge (United States) (US)
- Georgia Institute of Technology (US)
- Corresponding author
- Sun, Jimeng
- Venue
- Journal of the American Medical Informatics Association
- Publisher
- Oxford University Press (OUP)
- Published
- 2018-06-08
- Volume
- 25
- Issue
- 10
- Pages
- 1419-1428
- ISSN
- 1067-5027 (ISSN-L)
- 1527-974X
- PMC
- PMC6188527
- OpenAlex
- W2805089815
- Cited by
- 792
- References
- 92
- Citations by year
- 2026: 70 · 2025: 112 · 2024: 112 · 2023: 112 · 2022: 100 · 2021: 137 · 2020: 81 · 2019: 60 · 2018: 8
- FWCI
- 8.36
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Journal of the American Medical Informatics Association (publishedVersion, cc-by-nc)
- Europe PMC (PubMed Central) (publishedVersion, cc-by-nc)
- PubMed Central (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- Funders
- National Science Foundation (IIS-#1418511, CCF-#1533768)
- National Institutes of Health (1R01MD011682-01, R56HL138415)
- Children’s Healthcare of Atlanta
- Topics
- Physical Sciences › Computer Science › Artificial Intelligence › Machine Learning in Healthcare
- Health Sciences › Health Professions › Health Information Management › Electronic Health Records Systems
- Health Sciences › Medicine › Health Informatics › Artificial Intelligence in Healthcare and Education
- Keywords
- deep learning, electronic health records, deep learning architectures, clinical event prediction, concept embeddings, data augmentation, model interpretability, model deployment
- MeSH terms
- Data Anonymization, Deep Learning, Disease, Humans, Prognosis, Neural Networks, Computer, Electronic Health Records
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