Foundation models based on prior-data fitted networks (PFNs) have shown strong empirical performance in causal inference by framing the task as an in-context learning problem. However, it is unclear whether PFN-based causal estimators provide uncertainty quantification that is consistent with classical frequentist estimators. In this work, we address this gap by analyzing the frequentist consistency of PFN-based estimators for the average treatment effect (ATE). (1) We show that existing PFNs, when interpreted as Bayesian ATE estimators, can exhibit prior-induced confounding bias: the prior is not asymptotically overwritten by data, which, in turn, prevents frequentist consistency. (2) As a remedy, we suggest employing a calibration procedure based on a one-step posterior correction (OSPC). We show that the OSPC helps to restore frequentist consistency and can yield a semi-parametric Bernstein-von Mises theorem for calibrated PFNs (i.e., both the calibrated PFN-based estimators and the classical semi-parametric efficient estimators converge in distribution with growing data size). (3) Finally, we implement OSPC through tailoring martingale posteriors on top of the PFNs. In this way, we are able to recover functional nuisance posteriors from PFNs, required by the OSPC. In multiple (semi-)synthetic experiments, PFNs calibrated with our martingale posterior OSPC produce ATE uncertainty that (i) asymptotically matches frequentist uncertainty and (ii) is well calibrated in finite samples in comparison to other Bayesian ATE estimators.
Table 1: Overview of prior-data fitted networks (PFNs) that are suitable for ATE estimation.
Figure 1: Recovering functional posteriors from TabPFN. In (a) , we show a PPD P(y∣D,x) , where D={(xi,yi)}i=150 . Then, in (b) - (d) , we draw PPD samples from different functional posteriors μ~∼Π(μ∣D) (recovered with martingale posteriors), where μ(x)=E(Y∣x) . Notably, the same PPD P(y∣D,x) (a) can encompass different functional posteriors (in the causal setting, those, in turn, lead to different ATE posteriors): (b) x -independent posterior, (c) x -parallel posterior, (d) smooth posterior.
Figure 2: Prior-induced confounding bias of different PFNs. High values of Δ correspond to a high degree of the observed confounding. Thus, when Δ is concentrated around zero, the prior might induce the confounding bias which does not vanish asymptotically / vanishes very slowly with growing data. Here, we sample B=512 causal datasets with n=10000 each. Δ was computed from the prior causal datasets used to train PFNs: for CausalPFN/CausalFM, these are directly available in code or from the authors; for TabPFN, we additionally sampled treatment assignments in the same spirit as its synthetic classification data generation.
Figure 3: L2 -concentration check based on the synthetic data with varying size of the train data, ntrain (here: dx=25 ). Reported: mean R^2± se over 10 runs (lower is better). Note that both x- and y-axes are log-scaled.
Figure 4: Quality of the asymptotic uncertainty for Bayesian ATE estimators based on the synthetic data with (a) varying size of the train data, ntrain , and (b) varying dimensionality of covariates, dx . Reported: mean d^TV± se over 40 runs (lower is better).
(i) %TV
(ii) %KS
μa model
π model
ATE estimator
CausalPFN ( T = 0.5)
—
Naïve plug-in
54.16
30.95
TabPFN+copula (smooth; ρ = 0.25)
MP-OSPC
18.70
45.24
TabPFN+copula (smooth; ρ = 0.5)
MP-OSPC
27.14
23.81
CausalPFN ( T = 0.1)
—
Naïve plug-in
39.74
31.65
TabPFN+copula (smooth; ρ = 0.25)
MP-OSPC
34.94
49.37
Table 2: Quality of (i) asymptotic and (ii) finite-sample uncertainties of Bayesian ATE estimators based on 77 ACIC-2016 datasets. Reported: (i) % of runs with the best performance wrt. dTV over 77 datasets times 10 runs each ( %TV ), and (ii) % of runs with the best performance wrt. dKS over 77 datasets each evaluated with 10 runs ( %KS ). Both percentages of (i) and (ii) are grouped wrt. the underlying PFN.
Appendix figures & tables14 assets
Supplementary material from the paper’s appendix.
Appendix
Figure 5: Overview of connections between different posterior distributions, PPDs, and the underlying PFNs.
Figure 6: Overview of our MP-OSPC calibration procedure. Here, N is the number of MP steps and B is the number of posterior draws from the functional posteriors. Our MP-OSPC with PFNs thus yields the OSPC ATE posterior and serves as a Bayesian ATE estimator.
Figure 7: Convergence of different MP variants wrt. increasing number of MP steps N for every nuisance function based on the synthetic data with varying size of the train data, ntrain (here dx=25 ). Reported: mean posterior standard deviation sd[⋄~∣D,x]± se over 10 runs, where ⋄ corresponds to different nuisance functions: (top row) ⋄=μ0 , (middle row) ⋄=μ1 , and (bottom row) ⋄=π .
Figure 8: L2 -concentration check for every nuisance function based on the synthetic data with varying size of the train data, ntrain (here dx=25 ). Reported: mean L2 error E^⋄± se over 10 runs (lower is better), where ⋄ corresponds to different nuisance functions: (a) ⋄=μ0 , (b) ⋄=μ1 , and (c) ⋄=π−1 .
Figure 9: L2 -concentration check for every nuisance function (a)-(b) and for the second-order remainder R2 (c) based on the synthetic data with varying size of the train data, ntrain (here dx=25 ). Reported: mean L2 error E^⋄/R^2± se over 10 runs (lower is better), where ⋄ corresponds to different nuisance functions: (a) ⋄=μ0 , (b) ⋄=μ1 (note that propensity score is not available for CausalPFN).
Figure 10: Quality of the asymptotic uncertainty for Bayesian ATE estimators based on the synthetic data with (a) varying number of posterior draws, B , and (b) varying number of MP steps, N (here ntrain=500,dx=25 ). Reported: mean d^TV± se over 40 runs (lower is better).
Figure 11: Quality of the asymptotic uncertainty for Bayesian ATE estimators based on the synthetic data with varying copula types, (a) Gaussian and (b) Gumbel, and corresponding hyperparameters, (a) ρ∈(0,1) and (b) θ≥1 ( ntrain=500,dx=25 , B=100,N=100 ). Reported: mean d^TV± se over 40 runs (lower is better).
ntrain
100
500
1000
5000
10000
μa model
π model
ATE estimator
CausalPFN ( T = 1.0)
—
Naïve plug-in
0.965
1.000
1.000
1.000
1.000
TabPFN-only
MP-OSPC
0.685
0.485
0.585
0.890
0.980
TabPFN+copula (smooth; ρ = 0.25)
MP-OSPC
0.735
0.520
0.610
0.865
0.970
TabPFN+copula (smooth; ρ = 0.5)
MP-OSPC
0.695
0.510
0.600
0.865
0.970
CausalPFN ( T = 0.5)
—
Naïve plug-in
1.000
1.000
1.000
1.000
1.000
Appendix
Table 3: Quality of the (ii) finite-sample uncertainty for Bayesian ATE estimators based on the synthetic data with (a) varying size of the train data, ntrain . Reported: mean dKS evaluated with 40 runs, grouped wrt. the underlying PFN. Here: dx=25 .
dx
15
25
50
100
μa model
π model
ATE estimator
CausalPFN ( T = 1.0)
—
Naïve plug-in
0.990
1.000
1.000
1.000
TabPFN-only
MP-OSPC
0.500
0.485
0.560
0.575
TabPFN+copula (smooth; ρ = 0.25)
MP-OSPC
0.540
0.520
0.575
0.585
TabPFN+copula (smooth; ρ = 0.5)
MP-OSPC
0.555
0.510
0.560
0.585
CausalPFN ( T = 0.5)
—
Naïve plug-in
1.000
1.000
1.000
1.000
Appendix
Table 4: Quality of the (ii) finite-sample uncertainty for Bayesian ATE estimators based on the synthetic data with (b) varying dimensionality of covariates, dx . Reported: mean dKS evaluated with 40 runs, grouped wrt. the underlying PFN. Here: ntrain=500 .
(i) dTV
(ii) dKS
μa model
π model
ATE estimator
CausalPFN ( T = 1.0)
—
Naïve plug-in
0.239 ± 0.014
0.14
TabPFN-only
MP-OSPC
0.319 ± 0.015
0.09
TabPFN+copula (smooth; ρ = 0.25)
MP-OSPC
0.303 ± 0.013
0.13
TabPFN+copula (smooth; ρ = 0.5)
MP-OSPC
0.311 ± 0.013
0.14
CausalPFN ( T = 0.5)
—
Naïve plug-in
0.271 ± 0.015
0.10
Appendix
Table 5: Quality of the (i) asymptotic and (ii) finite-sample uncertainties of ATE estimators based on the IHDP dataset. Reported: (i) mean dTV± se over 100 splits, and (ii) mean dKS evaluated with 100 splits. Both (i) and (ii) are grouped wrt. the underlying PFN.
Figure 12: Full (i) asymptotic and (ii) finite-sample results of ATE estimation with TabPFN-based estimators for 77 semi-synthetic ACIC 2016 datasets. Datasets are sorted wrt. the absolute degree of measured confounding, ∣Δ∣ ; and the median inverse propensity score is provided for reference. Reported: (i) mean d^TV and (ii) d^KS over 10 runs (lower is better).
Figure 13: Full (i) asymptotic and (ii) finite-sample results of ATE estimation with CausalPFN-based/combined estimators for 77 semi-synthetic ACIC 2016 datasets. Datasets are sorted wrt. the absolute degree of measured confounding, ∣Δ∣ ; and the median inverse propensity score is provided for reference. Reported: (i) mean d^TV and (ii) d^KS over 10 runs (lower is better).
Figure 14: Peak GPU memory usage (top figure, in gigibytes (GiB)) and total runtime (bottom figure, in minutes) of ATE experiments for our MP-OSPC with different MP variants and varying number of MP steps based on the synthetic data with varying size of the train data, ntrain (here dx=25 ). Experiments are carried out on AMD EPYC 9455 48-Core CPU and 1 H200 Nvidia GPU.
Figure 15: Uncertainty of frequentist and Bayesian ATE estimators based on different PFNs: (a) TabPFN-based and (b) CausalPFN-based/combined estimators. Reported: (i) density of an A-IPTW-based asymptotic normal distribution for frequentist estimators (in black); and (ii) posterior densities for Bayesian estimators (in colors). Both (i) and (ii) are based on 5-fold cross-fitting.
Prior-data fitted networks (PFNs) have recently gained popularity as an end-to-end approach to amortized Bayesian inference. Yet, their statistical behavior for semi-parametric targets, such as means under missingness or causal effects, remains poorly understood. In this work, we develop theoretical foundations for debiased PFNs to perform inference on finite-dimensional targets in general semi-parametric settings. First, we show that, despite being Bayes-optimal with respect to the target, an idealized PFN can exhibit a posterior concentration rate that implicitly depends on the concentration rates of (latent) nuisance functions and can become slower as the prior becomes more diverse. Then, to speed up the target posterior concentration rates, we introduce two generic debiasing strategies based on efficient influence functions: (i) a label correction and (ii) a prior correction. Finally, we show that the debiased PFNs (i) & (ii) possess concentration rates that asymptotically match a convergence rate given by traditional frequentist bias-corrected estimators. In this way, we establish a novel connection between amortized Bayesian inference with PFNs and frequentist semi-parametric efficiency theory. Under additional assumptions, this allows us to guarantee local and global optimality of PFN-based estimators (namely, the Bernstein-von Mises property and minimax optimality, respectively). Therefore, our work provides guidelines for designing debiased PFNs for semi-parametric inference with principled and provable asymptotic guarantees.
Valentyn Melnychuk, Emil Javurek, Stefan Feuerriegel
LMU Munich & Munich Center for Machine Learning, Munich, Germany
Standard causal identification methods often assume no unmeasured confounding and can fail when relevant confounders are unobserved. Proximal causal inference instead uses proxy variables to identify effects under hidden confounding. However, nonparametric proximal estimation can be challenging in practice: recovering causal estimands such as the conditional average treatment effect (CATE) requires solving an ill-posed integral equation that is data-hungry, hyperparameter-sensitive, and optimization-unstable. Bayesian inference for such models provides a desirable alternative, mitigating these difficulties by regularizing through the prior. However, computing a posterior is itself challenging, as a typical likelihood function will include latent variables. Following the recent success of tabular foundation models in backdoor, instrumental variable, and frontdoor settings, we propose that prior-data fitted networks (PFNs) are uniquely suited to resolve this bottleneck. Indeed, by training on synthetic data sampled from compliant structural causal models with access to oracle counterfactuals, we simplify the task substantially, amortizing the implied Bayesian operator inversion into a single transformer forward pass. Compared to prior literature that focuses primarily on point estimation, our model, ProximalFM, explicitly targets the Bayesian posterior distribution of the CATE. One unique aspect of this problem is that we need to provide Monte Carlo estimates of the oracle CATEs, leading to a novel variation of PFNs that accounts for the added stochastic error. Across a diverse suite of proximal regimes, ProximalFM achieves consistently strong CATE-estimation performance without dataset-specific tuning, with its largest advantage when latent confounding is substantial and the proxies are weakly informative; it also provides fast inference through a single amortized forward pass.
Christophe Muller, Ayub Kharel, Alex Luedtke +6
University of Oxford · Harvard University · University of Illinois Urbana-Champaign +5
Uncertainty quantification is central to many applications of causal machine learning, yet principled Bayesian inference for causal effects remains challenging. Standard Bayesian approaches typically require specifying a probabilistic model for the data-generating process, including high-dimensional nuisance components such as propensity scores and outcome regressions. Standard posteriors are thus vulnerable to strong modeling choices, including complex prior elicitation. In this paper, we propose a generalized Bayesian framework for causal inference. Our framework avoids explicit likelihood modeling; instead, we place priors directly on the causal estimands and update these using an identification-driven loss function, which yields generalized posteriors for causal effects. As a result, our framework turns existing loss-based causal estimators into estimators with full uncertainty quantification. Our framework is flexible and applicable to a broad range of causal estimands (e.g., ATE, CATE). Further, our framework can be applied on top of state-of-the-art causal machine learning pipelines (e.g., Neyman-orthogonal meta-learners). For Neyman-orthogonal losses, we show that the generalized posteriors converge to their oracle counterparts and remain robust to first-stage nuisance estimation error. With calibration, we thus obtain valid frequentist uncertainty even when nuisance estimators converge at slower-than-parametric rates. Empirically, we demonstrate that our proposed framework offers causal effect estimation with calibrated uncertainty across several causal inference settings. To the best of our knowledge, this is the first flexible framework for constructing generalized Bayesian posteriors for causal machine learning.