Development and validation of phenotype classifiers across multiple sites in the observational health data sciences and informatics network

J Am Med Inform Assoc. 2020 Jun 1;27(6):877-883. doi: 10.1093/jamia/ocaa032.


Objective: Accurate electronic phenotyping is essential to support collaborative observational research. Supervised machine learning methods can be used to train phenotype classifiers in a high-throughput manner using imperfectly labeled data. We developed 10 phenotype classifiers using this approach and evaluated performance across multiple sites within the Observational Health Data Sciences and Informatics (OHDSI) network.

Materials and methods: We constructed classifiers using the Automated PHenotype Routine for Observational Definition, Identification, Training and Evaluation (APHRODITE) R-package, an open-source framework for learning phenotype classifiers using datasets in the Observational Medical Outcomes Partnership Common Data Model. We labeled training data based on the presence of multiple mentions of disease-specific codes. Performance was evaluated on cohorts derived using rule-based definitions and real-world disease prevalence. Classifiers were developed and evaluated across 3 medical centers, including 1 international site.

Results: Compared to the multiple mentions labeling heuristic, classifiers showed a mean recall boost of 0.43 with a mean precision loss of 0.17. Performance decreased slightly when classifiers were shared across medical centers, with mean recall and precision decreasing by 0.08 and 0.01, respectively, at a site within the USA, and by 0.18 and 0.10, respectively, at an international site.

Discussion and conclusion: We demonstrate a high-throughput pipeline for constructing and sharing phenotype classifiers across sites within the OHDSI network using APHRODITE. Classifiers exhibit good portability between sites within the USA, however limited portability internationally, indicating that classifier generalizability may have geographic limitations, and, consequently, sharing the classifier-building recipe, rather than the pretrained classifiers, may be more useful for facilitating collaborative observational research.

Keywords: cohort identification; electronic health records; electronic phenotyping; machine learning; phenotype.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Validation Study

MeSH terms

  • Classification / methods
  • Data Science
  • Electronic Health Records / classification*
  • Humans
  • Medical Informatics*
  • Observational Studies as Topic
  • Supervised Machine Learning*