High Performance, Low Reliability: Uncertainty Benchmarking for Tabular Foundation Models

Foundation models (FMs) have achieved substantial success in generalizing across tasks without problemspecific training or fine-tuning. However, many critical applications in mechanics and computational science require not only accurate predictions but also reliable uncertainty quantification (UQ). Herein we investigate the UQ capabilities of tabular FMs in regression tasks through a comprehensive empirical study comparing Tabular Prior-Data Fitted Networks (TabPFN) against Gaussian processes (GPs). We systematically evaluate these two methods across a host of regression problems with varying complexity, dataset sizes, and input dimensionalities. We use a default setting to build all the GPs and for a fair comparison against TabPFN v2.5. Our findings highlight an important trade-off between explicit and learned priors: while TabPFN achieves highly competitive performance for complex, high-dimensional problems with sufficient data, GPs often provide superior predictive accuracy and UQ in data-scarce settings. Moreover, when the chosen kernel constitutes a good prior for the underlying function, GP performance can substantially exceed that of TabPFN. Our results can be reproduced from https://github.com/kianswarehouse/GPvsPFN.

Tabular Foundation Models (TFMs) are currently the best approach to tabular prediction problems. They are constructed as transformers that approximate the Bayesian posterior predictive distribution based on a pre-training prior. These univariate predictors can be converted into multivariate ones autoregressively by sampling one target and adding it to the features. However, the faithfulness of the resulting joint has not been investigated. Furthermore, TFMs cannot be evaluated against the posterior itself, at least not on real-world datasets, because the ground-truth distribution is unknown. We therefore propose asking a different question: could a model's predictions result from any joint distribution? To answer this question, we pose two requirements that any such model must satisfy. The first is marginalization consistency, which demands that marginalized conditionals are equal to directly predicted marginals. The second is factorization consistency, which demands that different factorization orders result in equal joint distributions. Every TFM that we evaluate violates both of these requirements for both classification and regression across all datasets.

Tabular foundation models (TFMs) now match or beat tuned gradient-boosted trees on a growing fraction of tabular tasks, but no single TFM wins on every dataset. Ensembling is the go to fix here, and it works less well than expected. Six modern TFMs form a near-redundant pool: their mean pairwise Q-statistic is $0.961$, close enough to $1$ that any convex combination is bounded above. We benchmark six ensemble strategies over six TFMs on 153 OpenML classification tasks. The best ensemble, two-level cascade stacking, buys $+0.18\%$ accuracy over the strongest single TFM at $253\times$ the compute. A Friedman and Nemenyi analysis places three ensembles and the best base TFM in a single equivalence group; three other ensembles are significantly \emph{worse} than the best base. Stacking with a logistic-regression meta-learner is the most striking case: competitive accuracy and ROC-AUC, the worst log-loss rank among the ensembles. The meta-learner improves accuracy by sharpening class boundaries, which destroys calibration. We recommend greedy selection as the practical default.