A simplified and robust proxy-based approach for overcoming unmeasured confounding in EHR studies

Abstract: Electronic health records (EHR) are used to study treatment effects in clinical settings, yet unmeasured confounding remains a persistent challenge. Indirect measurements of the unmeasured confounder (proxies) offer a potential solution, but existing approaches -- such as proximal inference or full joint modeling -- can be difficult to implement. We propose a two-stage, proxy-based method that is practical, broadly applicable, and robust. In the first stage, we apply factor analysis to proxy and treatment variables, extracting information on latent factors that serve as a surrogate for the unmeasured confounder. In the second stage, we use this model to build covariates that improve causal effect estimation in a standard outcome regression model. Through simulations, we test the method's performance under assumption violations, including non-normal errors, model misspecification, and scenarios where instruments or confounders are incorrectly treated as proxies. We also apply the method to estimate the effect of hospital admission for older adults presenting to the emergency department with chest pain, a setting where standard analyses may fail to recover plausible effects. Our results show that this simplified strategy recovers more reliable estimates than conventional adjustment methods, offering applied researchers a practical tool for addressing unmeasured confounding with proxy variables.