# Causal Longitudinal Prior-Fitted Networks for Counterfactual Outcome Prediction

arXiv: https://arxiv.org/abs/2606.05797 · HTML: https://mlsanity.com/paper/2606.05797/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Builds on 13 of its 36 references that are in the map.
- First posted on arXiv 4 Jun 2026.

## Builds on (most cited first, 13 of 13)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [TabPFN: A Transformer That Solves Small Tabular Classification Problems in a Second](https://mlsanity.com/paper/2207.01848/) (2022)
- [Transformers Can Do Bayesian Inference](https://mlsanity.com/paper/2112.10510/) (2021)
- [Multitask learning and benchmarking with clinical time series data](https://mlsanity.com/paper/1703.07771/) (2017)
- [Estimating Counterfactual Treatment Outcomes over Time Through Adversarially Balanced Representations](https://mlsanity.com/paper/2002.04083/) (2020)
- [Causal Transformer for Estimating Counterfactual Outcomes](https://mlsanity.com/paper/2204.07258/) (2022)
- [MIMIC-Extract: A Data Extraction, Preprocessing, and Representation Pipeline for MIMIC-III](https://mlsanity.com/paper/1907.08322/) (2019)
- [Statistical Foundations of Prior-Data Fitted Networks](https://mlsanity.com/paper/2305.11097/) (2023)
- [CausalPFN: Amortized Causal Effect Estimation via In-Context Learning](https://mlsanity.com/paper/2506.07918/) (2025)
- [Foundation Models for Causal Inference via Prior-Data Fitted Networks](https://mlsanity.com/paper/2506.10914/) (2025)
- [TimePFN: Effective Multivariate Time Series Forecasting with Synthetic Data](https://mlsanity.com/paper/2502.16294/) (2025)
- [G-Transformer: Counterfactual Outcome Prediction under Dynamic and Time-varying Treatment Regimes](https://mlsanity.com/paper/2406.05504/) (2024)
- [Interventional Time Series Priors for Causal Foundation Models](https://mlsanity.com/paper/2603.11090/) (2026)

## Built on by (most cited first, 1 of 1)

- [Causal Foundation Models](https://mlsanity.com/paper/2609.03003/) (2026)

## Abstract (arXiv)

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.