The Medical Deconfounder: Assessing Treatment Effect with Electronic Health Records (EHRs)

Causal estimation of treatment effect has an important role in guiding physicians' decision process for drug prescription. While treatment effect is classically assessed with randomized controlled trials (RCTs), the availability of electronic health records (EHRs) bring an unprecedented opportunity for more efficient estimation. However, the presence of unobserved confounders makes treatment effect assessment from EHRs a challenging task. Confounders are the variables that affect both drug prescription and the patient's outcome; examples include a patient's gender, race, social economic status and comorbidities. When these confounders are unobserved, they bias the estimation. To adjust for unobserved confounders, we develop the medical deconfounder, a machine learning algorithm that unbiasedly estimates treatment effect from EHRs. The medical deconfounder first constructs a substitute confounder by modeling which drugs were prescribed to each patient; this substitute confounder is guaranteed to capture all multi-drug confounders, observed or unobserved (Wang and Blei, 2018). It then uses this substitute confounder to adjust for the confounding bias in the analysis. We validate the medical deconfounder on simulations and two medical data sets. The medical deconfounder produces closer-to-truth estimates in simulations and identifies effective medications that are more consistent with the findings reported in the medical literature compared to classical approaches.