A Foundation Model for Policy In-Context Longitudinal Causal Effect Estimation

Comparative evaluation of multiple dynamic treatment policies is essential for healthcare and policy decisions, yet conventional longitudinal causal inference methods estimate each in isolation, preventing information sharing across counterfactuals. We demonstrate that this separate estimation paradigm induces a structurally uncontrolled second-order bias, inflating finite-sample variance even after standard debiasing with longitudinal targeted maximum likelihood estimation(LTMLE). To address this, we propose a policy-aware reparameterization of Iterative Conditional Expectation (ICE) Q-functions that enables joint estimation through shared representations. We implement this approach in the Policy-Encoded Q Network (PEQ-Net), an architecture centered on a shared policy encoder. The encoder is trained using kernel mean embeddings, ensuring that the learned representation space reflects population-level policy dissimilarities. After applying an LTMLE correction step, we prove this design imposes a structural constraint on the second-order remainder, thereby stabilizing finite-sample variance. Experiments on semi-synthetic datasets demonstrate that PEQ-Net consistently outperforms existing ICE-based methods, achieving substantial reductions in root-mean-square error, particularly when evaluating closely related policies.

Longitudinal treatment decisions from multivariate time-series data require predicting potential outcomes under future treatment sequences in the presence of time-varying confounding, heterogeneous patient dynamics, and limited domain-specific data. Existing longitudinal causal estimators typically address this problem by training a new model for each cohort or simulator. We introduce Causal Longitudinal Prior-Fitted Networks (CausalLongPFN), a prior-fitted network for time-series causal inference in longitudinal treatment-response data and zero-shot in-context counterfactual outcome prediction. The model is pretrained entirely on synthetic episodes sampled from a broad prior over temporal structural causal models, exposing it to treatment-confounder feedback, latent heterogeneity, nonlinear state evolution, delayed effects, and cumulative treatment responses. At test time, CausalLongPFN remains frozen and is used zero-shot: it conditions on support trajectories, a query history, and a planned future treatment sequence, and returns a predictive distribution over future outcomes without gradient updates or propensity-model fitting. Multi-step predictions are obtained by recursively applying the one-step predictor under the specified treatment sequence. We evaluate the model on branchable cancer, HIV, and warfarin benchmarks with ground-truth counterfactual labels, and on factual-only rolling-origin prediction in MIMIC-III ICU trajectories. CausalLongPFN is competitive with domain-trained longitudinal baselines on counterfactual benchmarks and performs strongly on factual MIMIC-III prediction, suggesting that broad synthetic causal pretraining can provide a frozen, amortized alternative for zero-shot longitudinal treatment-response prediction when repeated domain-specific training is costly or impractical.

Prior-data fitted networks (PFNs) have emerged as powerful foundation models for tabular causal inference, yet their extension to time series remains limited by the absence of synthetic data generators that provide interventional targets. Existing time series benchmarks generate observational data with ground-truth causal graphs but lack the interventional data required for training causal foundation models. To address this, we propose CausalTimePrior, a principled framework for generating synthetic temporal structural causal models (TSCMs) with paired observational and interventional time series. Our prior supports configurable causal graph structures, nonlinear autoregressive mechanisms, regime-switching dynamics, and multiple intervention types (hard, soft, time-varying). We demonstrate that PFNs trained on CausalTimePrior can perform in-context causal effect estimation on held-out TSCMs, establishing a pathway toward foundation models for time series causal inference.