A Semiparametric Approach for Robust Modeling of Electronic Health Record Linked Biobank Data

With the increasing availability of electronic health records (EHR) linked to biobank data for translational research, a critical step to realize its potential is to accurately classify phenotypes for patients. Existing approaches to achieve this goal are based on error‐prone EHR surrogate outcomes, assisted and validated by a small set of labels obtained via medical chart review, which may also be subject to misclassification. Ignoring the noise in these outcomes can induce severe estimation and validation bias in both EHR phenotyping and risk modeling with biomarkers collected in the biobank. To overcome this challenge, we propose a novel unsupervised and semiparametric approach to jointly model multiple noisy EHR outcomes with their linked biobank features. Our approach primarily aims at disease risk modeling with the baseline biomarkers, and is also able to produce a predictive EHR phenotyping model and validate its performance without observations of the true disease outcome. It consists of composite and nonparametric regression steps free of any parametric model specification, followed by a parametric projection step to reduce the variance of the estimator. We show that our method is robust to violations of the parametric assumptions while attaining the desirable root‐ convergence rates in risk modeling. Our developed method outperforms existing methods in extensive simulation studies, as well as in a real‐world application in the phenotyping and genetic risk modeling of type II diabetes.