G-Transformer: Counterfactual Outcome Prediction under Dynamic and Time-varying Treatment Regimes

In the context of medical decision making, counterfactual prediction enables clinicians to predict treatment outcomes of interest under alternative courses of therapeutic actions given observed patient history. Prior machine learning approaches for counterfactual predictions under time-varying treatments focus on static time-varying treatment regimes where treatments do not depend on previous covariate history. In this work, we present G-Transformer, a Transformer-based framework supporting g-computation for counterfactual prediction under dynamic and time-varying treatment strategies. G-Transfomer captures complex, long-range dependencies in time-varying covariates using a Transformer architecture. G-Transformer estimates the conditional distribution of relevant covariates given covariate and treatment history at each time point using an encoder architecture, then produces Monte Carlo estimates of counterfactual outcomes by simulating forward patient trajectories under treatment strategies of interest. We evaluate G-Transformer extensively using two simulated longitudinal datasets from mechanistic models, and a real-world sepsis ICU dataset from MIMIC-IV. G-Transformer outperforms both classical and state-of-the-art counterfactual prediction models in these settings. To the best of our knowledge, this is the first Transformer-based architecture for counterfactual outcome prediction under dynamic and time-varying treatment strategies. Code will be released upon publication of the paper.