This program is designed to provide decision-makers, policymakers and professional working in policy with a foundational understanding of AI technology.
We use cookies to analyze the browsing and usage of our website and to personalize your experience. You can disable these technologies at any time, but this may limit certain functionalities of the site. Read our Privacy Policy for more information.
Setting cookies
You can enable and disable the types of cookies you wish to accept. However certain choices you make could affect the services offered on our sites (e.g. suggestions, personalised ads, etc.).
Essential cookies
These cookies are necessary for the operation of the site and cannot be deactivated. (Still active)
Analytics cookies
Do you accept the use of cookies to measure the audience of our sites?
Multimedia Player
Do you accept the use of cookies to display and allow you to watch the video content hosted by our partners (YouTube, etc.)?
Electronic health records (EHRs) provide rich clinical information and the opportunities to extract epidemiological patterns to understand a… (see more)nd predict patient disease risks with suitable machine learning methods such as topic models. However, existing topic models do not generate identifiable topics each predicting a unique phenotype. One promising direction is to use known phenotype concepts to guide topic inference. We present a seed-guided Bayesian topic model called MixEHR-Seed with 3 contributions: (1) for each phenotype, we infer a dual-form of topic distribution: a seed-topic distribution over a small set of key EHR codes and a regular topic distribution over the entire EHR vocabulary; (2) we model age-dependent disease progression as Markovian dynamic topic priors; (3) we infer seed-guided multi-modal topics over distinct EHR data types. For inference, we developed a variational inference algorithm. Using MixEHR-Seed, we inferred 1569 PheCode-guided phenotype topics from an EHR database in Quebec, Canada covering 1.3 million patients for up to 20-year follow-up with 122 million records for 8539 and 1126 unique diagnostic and drug codes, respectively. We observed (1) accurate phenotype prediction by the guided topics, (2) clinically relevant PheCode-guided disease topics, (3) meaningful age-dependent disease prevalence. Source code is available at GitHub: https://github.com/li-lab-mcgill/MixEHR-Seed.
Motivation: Electronic health record (EHR) data provides a new venue to elucidate disease comorbidities and latent phenotypes for precision … (see more)medicine. To fully exploit its potential, a realistic data generative process of the EHR data needs to be modelled. Materials and Methods: 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. Results: 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. Availability and implementation: MixEHR-S source code and scripts of the experiments are freely available at https://github.com/li-lab-mcgill/mixehrS
2021-08-01
Proceedings of the 12th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (published)