Learning vector representation of medical objects via EMR-driven nonnegative restricted Boltzmann machines (eNRBM)
Open accessAbstract
Electronic medical record (EMR) offers promises for novel analytics. However, manual feature engineering from EMR is labor intensive because EMR is complex - it contains temporal, mixed-type and multimodal data packed in irregular episodes. We present a computational framework to harness EMR with minimal human supervision via restricted Boltzmann machine (RBM). The framework derives a new representation of medical objects by embedding them in a low-dimensional vector space. This new representation facilitates algebraic and statistical manipulations such as projection onto 2D plane (thereby offering intuitive visualization), object grouping (hence enabling automated phenotyping), and risk stratification. To enhance model interpretability, we introduced two constraints into model parameters: (a) nonnegative coefficients, and (b) structural smoothness. These result in a novel model called eNRBM (EMR-driven nonnegative RBM). We demonstrate the capability of the eNRBM on a cohort of 7578 mental health patients under suicide risk assessment. The derived representation not only shows clinically meaningful feature grouping but also facilitates short-term risk stratification. The F-scores, 0.21 for moderate-risk and 0.36 for high-risk, are significantly higher than those obtained by clinicians and competitive with the results obtained by support vector machines.
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Among 37 studies learning from structured codes, the frequency of a given code was used in 5 studies.
“Among 37 studies learning from structured codes, the majority (n = 27) generate one-hot vectors for the input data, and the frequency of a given code is used in 5 studies [11,48,58–60].”
From Deep representation learning of patient data from Electronic Health Records (EHR): A systematic review (2021) · cites this paper as [60]
The earliest attempt of learning patient representations with deep learning used Restricted Boltzmann Machines, proposed in 2015.
“The earliest attempt of learning patient representations with deep learning used Restricted Boltzmann Machines, proposed in 2015 [60].”
From Deep representation learning of patient data from Electronic Health Records (EHR): A systematic review (2021) · cites this paper as [60]
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- Authors
- Tran, T., Nguyen, T. D., Phung, D., & Venkatesh, S.
- Affiliations
- Deakin University (AU)
- Corresponding author
- Tran, Truyen
- Venue
- Journal of Biomedical Informatics
- Publisher
- Elsevier BV
- Published
- 2015-04
- Volume
- 54
- Pages
- 96-105
- ISSN
- 1532-0464 (ISSN-L)
- OpenAlex
- W2027106132
- Cited by
- 172
- References
- 48
- Citations by year
- 2026: 1 · 2025: 9 · 2024: 16 · 2023: 18 · 2022: 16 · 2021: 17 · 2020: 25 · 2019: 29 · 2018: 17 · 2017: 12 · 2016: 9 · 2015: 3
- FWCI
- 13.41
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Journal of Biomedical Informatics (publishedVersion)
- PubMed (publishedVersion)
- eSpace (Curtin University) (submittedVersion)
- Figshare (submittedVersion, cc-by)
- Topics
- Physical Sciences › Computer Science › Artificial Intelligence › Machine Learning in Healthcare
- Health Sciences › Health Professions › Health Information Management › Artificial Intelligence in Healthcare
- Social Sciences › Psychology › Social Psychology › Mental Health via Writing
- Keywords
- electronic health records, restricted Boltzmann machine, automated phenotyping, suicide risk assessment, psychiatric patients, risk stratification, model interpretability, low-dimensional embedding, multimodal medical data
- MeSH terms
- Mental Disorders, Female, Humans, Male, Markov Chains, Medical Informatics, Neoplasms, Suicide, Models, Statistical, Neural Networks, Computer, Risk Assessment, Electronic Health Records, Support Vector Machine
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