Variational Temporal Deconfounder for Individualized Treatment Effect Estimation with Longitudinal Observational Data

PURPOSE: This paper proposes a new approach, Variational Temporal Deconfounder (VTD), for estimating individualized treatment effects (ITE) from longitudinal observational data, where we address the hidden confounding issues by using proxies (i.e., surrogate variables that serve for unobservable variables). METHODS: We build VTD by incorporating a variational recurrent autoencoder that learns the latent encodings of hidden confounders from observed proxies and an ITE estimation network that takes the learned hidden encodings to predict the probability of receiving treatments and potential outcomes. RESULTS: We test VTD on both synthetic and real-world clinical data, and the results from synthetic data experiments demonstrate VTD’s effectiveness in deconfounding by outperforming existing methods, while results from two real-world datasets (i.e., Medical Information Mart for Intensive Care version III [MIMIC-III] and the National Alzheimer’s Coordinating Center [NACC] database) suggest that the performance of the VTD model outperforms existing baseline models, however, varies depending on the assumptions of underlying causal structures and availability of proxies for hidden confounders. CONCLUSION: The VTD offers a unique solution to address the confounding bias without the “unconfoundedness” assumption when estimating the ITE from longitudinal observational data. The elimination of the requirement for the “unconfoundedness” assumption makes the VTD more versatile and practical in real-world clinical applications of personalized medicine.