Learning latent space representations to predict patient outcomes: Model development and validation

Subendhu Rongali, Adam J. Rose, David D. McManus, Adarsha S. Bajracharya, Alok Kapoor, Edgard Granillo, Hong Yu*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

9 Scopus citations


Background: Scalable and accurate health outcome prediction using electronic health record (EHR) data has gained much attention in research recently. Previous machine learning models mostly ignore relations between different types of clinical data (ie, laboratory components, International Classification of Diseases codes, and medications). Objective: This study aimed to model such relations and build predictive models using the EHR data from intensive care units. We developed innovative neural network models and compared them with the widely used logistic regression model and other state-of-the-art neural network models to predict the patient’s mortality using their longitudinal EHR data. Methods: We built a set of neural network models that we collectively called as long short-term memory (LSTM) outcome prediction using comprehensive feature relations or in short, CLOUT. Our CLOUT models use a correlational neural network model to identify a latent space representation between different types of discrete clinical features during a patient’s encounter and integrate the latent representation into an LSTM-based predictive model framework. In addition, we designed an ablation experiment to identify risk factors from our CLOUT models. Using physicians’ input as the gold standard, we compared the risk factors identified by both CLOUT and logistic regression models. Results: Experiments on the Medical Information Mart for Intensive Care-III dataset (selected patient population: 7537) show that CLOUT (area under the receiver operating characteristic curve=0.89) has surpassed logistic regression (0.82) and other baseline NN models (<0.86). In addition, physicians’ agreement with the CLOUT-derived risk factor rankings was statistically significantly higher than the agreement with the logistic regression model. Conclusions: Our results support the applicability of CLOUT for real-world clinical use in identifying patients at high risk of mortality.

Original languageAmerican English
Article numbere16374
JournalJournal of Medical Internet Research
Issue number3
StatePublished - Mar 2020
Externally publishedYes

Bibliographical note

Funding Information:
This work was supported in part by the grant R01HL137794 from the National Institutes of Health (NIH). The content is solely the responsibility of the authors and does not necessarily represent the official views of the NIH. HY’s time was also supported by grants 5R01HL125089, R01HL135129, R01DA045816, and R01LM012817. DM’s time was also supported by grants R01HL137734, R01HL126911, R01HL13660, and R01HL141434 from the National Heart, Lung, and Blood Institute.

Funding Information:
DM has received research grant support from Apple Computer, Bristol-Myers Squibb, Boehringher-Ingelheim, Pfizer, Samsung, Philips Healthcare, Care Evolution, and Biotronik; has received consultancy fees from Bristol-Myers Squibb, Pfizer, Flexcon, and Boston Biomedical Associates; and has inventor equity in Mobile Sense Technologies, Inc, Connecticut.

Publisher Copyright:
©Subendhu Rongali, Adam J Rose, David D McManus, Adarsha S Bajracharya, Alok Kapoor, Edgard Granillo, Hong Yu.


  • Ablation
  • Neural networks
  • Patient mortality
  • Predictive modeling


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