Tyler R. Johnson | Searcharxiv

arXiv2026

On the Brittleness of Maximum Likelihood Estimation for Gaussian Process Hyperparameter Optimization

Machine learning (ML) has become an indispensable part of modern engineering design workflows. A crucial step in training an ML model is the selection of the loss function which can be systematically formulated via various techniques such as maximum likelihood estimation (MLE) and cross-validation . While MLE is one of the most popular, effective, and intuitive mechanisms for training ML models, it is brittle: if the assumptions underpinning it are not met, the trained ML model may generalize poorly. This brittleness affects even Gaussian processes (GPs) which are widely used in engineering design and are often (incorrectly) presumed to be very robust to overfitting. In this paper, we fundamentally evaluate the brittleness of MLE in the context of training GPs for probabilistic regression or classification tasks. We compare theoretically grounded metrics against MLE and propose practical solutions. Our extensive studies demonstrate the effectiveness of our solutions in downstream design tasks such as Bayesian optimization and provide a blueprint for practitioners to build accurate and robust GPs that can even outperform tabular foundation models in terms of prediction accuracy, uncertainty quantification, and inference cost. Our contributions are publicly available via GitHub at https://github.com/Bostanabad-Research-Group/GP-vs-TabPFN-vs-GPyTorch.

stat.ML↗

arXiv2026

On the Uncertainty Quantification Ability of 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.

stat.ML↗