Semi-supervised ROC analysis for reliable and streamlined evaluation of phenotyping algorithms

• Published in: Journal of the American Medical Informatics Association : JAMIA Vol. 31; no. 3; pp. 640 - 650
• Main Authors: Gao, Jianhui, Bonzel, Clara-Lea, Hong, Chuan, Varghese, Paul, Zakir, Karim, Gronsbell, Jessica
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 16-02-2024
• Subjects: semi-supervised; electronic health records; phenotyping; ROC analysis
• ISSN: 1067-5027; 1527-974X; 1527-974X
• DOI: 10.1093/jamia/ocad226

Abstract
Objective
High-throughput phenotyping will accelerate the use of electronic health records (EHRs) for translational research. A critical roadblock is the extensive medical supervision required for phenotyping algorithm (PA) estimation and evaluation. To address this challenge, numerous weakly-supervised learning methods have been proposed. However, there is a paucity of methods for reliably evaluating the predictive performance of PAs when a very small proportion of the data is labeled. To fill this gap, we introduce a semi-supervised approach (ssROC) for estimation of the receiver operating characteristic (ROC) parameters of PAs (eg, sensitivity, specificity).
Materials and Methods
ssROC uses a small labeled dataset to nonparametrically impute missing labels. The imputations are then used for ROC parameter estimation to yield more precise estimates of PA performance relative to classical supervised ROC analysis (supROC) using only labeled data. We evaluated ssROC with synthetic, semi-synthetic, and EHR data from Mass General Brigham (MGB).
Results
ssROC produced ROC parameter estimates with minimal bias and significantly lower variance than supROC in the simulated and semi-synthetic data. For the 5 PAs from MGB, the estimates from ssROC are 30% to 60% less variable than supROC on average.
Discussion
ssROC enables precise evaluation of PA performance without demanding large volumes of labeled data. ssROC is also easily implementable in open-source R software.
Conclusion
When used in conjunction with weakly-supervised PAs, ssROC facilitates the reliable and streamlined phenotyping necessary for EHR-based research.