Variational temporal deconfounder network for individualized treatment effect estimation with longitudinal observational data

Objective

By leveraging real-world electronic health record (EHR) data, this study set out to estimate individualized treatment effects (ITE) in longitudinal observational settings to advance personalized medicine, addressing key challenges that are often observed in real-world clinical scenarios and pose statistical challenges, including hidden confounding and dynamic treatment regimens.

Methods

We propose the Variational Temporal Deconfounder Network (VTDNet), a novel framework designed to account for time-varying hidden confounding using a variational recurrent transformer-based autoencoder. Specifically, VTDNet comprises three critical components: a temporal Encoder-Decoder structure to capture hidden representation, a Treatment Block that captures interdependencies among multiple treatments, and a Potential Outcome Block that predicts both factual and counterfactual outcomes. We assess the effectiveness of the proposed framework using a synthetic dataset and two real-world datasets: MIMIC-III, an EHR dataset focusing on intensive care settings, and NACC, emphasizing neurodegenerative disease, collected using a standardized protocol from participants enrolled in Alzheimer’s Disease Research Center (ADRC) clinical cores.

Results

Experimental results on the synthetic dataset demonstrate superior accuracy under varying levels of confounding. On real-world EHR datasets, VTDNet achieves lower root mean squared error, mean absolute error, and influence function precision in the estimation of heterogeneous effects compared to existing state-of-the-art methods.

Conclusion

The proposed VTDNet offers a robust framework for estimating individualized treatment effects in longitudinal settings, effectively accommodating irregular time points and high-dimensional data while addressing hidden confounders through a deep generative approach. It holds significant potential to advance personalized medicine and support real-world evidence generation. Future work will aim to extend VTDNet to continuous treatment scenarios, such as dose–response analysis, to further broaden its applicability in clinical practice.