Supervised multi-specialist topic model with applications on large-scale electronic health record data

TL;DR

This paper introduces MixEHR-S, a novel supervised hierarchical Bayesian topic model for EHR data that jointly infers disease and specialist topics, enabling accurate disease prediction and patient risk stratification.

Contribution

The paper presents a new unified model for EHR data that captures disease and specialist topics simultaneously, with an efficient inference algorithm, applied successfully to large-scale datasets.

Findings

Achieved superior prediction accuracy over existing methods.

Identified clinically meaningful latent topics.

Demonstrated effectiveness in three disease prediction tasks.

Abstract

Motivation: Electronic health record (EHR) data provides a new venue to elucidate disease comorbidities and latent phenotypes for precision medicine. To fully exploit its potential, a realistic data generative process of the EHR data needs to be modelled. We present MixEHR-S to jointly infer specialist-disease topics from the EHR data. As the key contribution, we model the specialist assignments and ICD-coded diagnoses as the latent topics based on patient's underlying disease topic mixture in a novel unified supervised hierarchical Bayesian topic model. For efficient inference, we developed a closed-form collapsed variational inference algorithm to learn the model distributions of MixEHR-S. We applied MixEHR-S to two independent large-scale EHR databases in Quebec with three targeted applications: (1) Congenital Heart Disease (CHD) diagnostic prediction among 154,775 patients; (2) Chronic obstructive pulmonary disease (COPD) diagnostic prediction among 73,791 patients; (3) future insulin treatment prediction among 78,712 patients diagnosed with diabetes as a mean to assess the disease exacerbation. In all three applications, MixEHR-S conferred clinically meaningful latent topics among the most predictive latent topics and achieved superior target prediction accuracy compared to the existing methods, providing opportunities for prioritizing high-risk patients for healthcare services. MixEHR-S source code and scripts of the experiments are freely available at https://github.com/li-lab-mcgill/mixehrS