Beyond Point Estimates: Benchmarking Uncertainty Quantification Methods on the AION-1 Astronomical Foundation Model

Accurate uncertainty estimation is essential for machine learning systems de- ployed in high-stakes domains such as medicine. Traditional approaches primarily rely on probability outputs from trained models (point predictions), which provide no formal guarantees on prediction coverage and often require additional calibra- tion techniques to improve reliability. In contrast, conformal prediction (region prediction) offers a principled alternative by generating prediction sets with finite- sample validity guarantees, ensuring that the ground truth is contained within the set at a specified confidence level. In this study, we explore the impact of pre-training approach, dataset scale and domain on both point and region-level uncertainty quantification, by studying domain-specific vision medical foundation models vs. general domain vision foundation models. We conduct a comprehensive evaluation across foundation models trained on retinal, histopathological, and Chest X-Rays data, applying various calibration techniques. Our results demonstrate that (1) pre-training on higher-quality domain-specific datasets along with self-supervised learning leads to better-calibrated point predictions than general domain pre-training, (2) stan- dard re-calibration methods alone cannot fully mitigate uncertainty discrepancies across models trained on different data sources, (3) domain-specific foundation model can lead to more efficient conformal prediction. These findings highlight the importance of careful model selection and the inte- gration of both point and region prediction to enhance the reliability and trust- worthiness of medical AI systems. Our work underscores the need for a holistic approach to uncertainty quantification in recent development of medical vision foundation model, ensuring robust and interpretable AI-driven decision-making.

Conformal Prediction provides distribution-free prediction intervals with guaranteed coverage, but its reliance on a single global calibration threshold obscures the sources of uncertainty at the instance level. In particular, it conflates irreducible noise with uncertainty induced by heterogeneous training data (aleatoric), model limitations, or calibration mismatch (epistemic), offering little insight into why an interval is wide or whether it could be reduced. We introduce an uncertainty-aware explainability framework that analyses the reducibility of calibration-induced epistemic conformal uncertainty via progressive calibration localisation for regression tasks. The approach is diagnostic rather than causal: it does not estimate true aleatoric or epistemic uncertainty, but explains how conformal intervals contract and stabilise as calibration support is localised around a test instance. Across benchmarks and real-world data, absolute reducible uncertainty aligns with epistemic proxies, while its relative contribution varies by task, revealing regimes hidden by interval width. This instance-level view complements conformal uncertainty, enhancing interpretability without altering the predictor or coverage.

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.