A unified framework, KENDO (Kernel ENsemble Disagreement-aware Operator), is proposed that integrates Ensemble Gaussian Processes (EGP) with disagreement-aware acquisition strategies and extends the approach to multi-objective optimization via random scalarization that preserves the single-optimizer conditioning structure.
Abstract
Hyperparameter selection remains a key challenge in Bayesian optimization (BO) and Bayesian active learning (AL), as model misspecification can lead to suboptimal performance, while more accurate fully Bayesian treatments typically rely on computationally expensive MCMC sampling. This paper proposes a unified framework, KENDO (Kernel ENsemble Disagreement-aware Operator), that integrates Ensemble Gaussian Processes (EGP) with disagreement-aware acquisition strategies. The central idea is to replace hyperparameter sampling with a kernel ensemble and adaptive Bayesian weighting, combined with disagreement-aware acquisition strategies. Within this unified framework, we instantiate KENDO-BO for BO and KENDO-AL for Bayesian AL, demonstrating that both arise from a common self-correcting mechanism with task-specific acquisition objectives. We further extend the approach to multi-objective optimization via random scalarization that preserves the single-optimizer conditioning structure. Thorough numerical tests on synthetic and real-world benchmarks across single-objective optimization, multi-objective optimization, and active learning demonstrate that (i) KENDO-BO achieves competitive or superior optimization performance compared to state-of-the-art methods while reducing computational overhead by up to $5\times$ and (ii) KENDO-AL achieves superior predictive calibration over MCMC-based active learning baselines with up to $27\times$ speedup.
This work introduces agentic Bayesian optimization: a paradigm in which an LLM agent is the central decision maker in the BO loop while a Bayesian backend provides the uncertainty-aware optimization substrate, and demonstrates the practical value of agentic BO in dynamic settings.
Paul Brunzema, Louis C. Tiao, Nhat Le et al.· 0 citations
Bayesian optimization is increasingly used to guide data-efficient experimentation in chemistry, materials science, and related laboratory settings, but its practical performance depends strongly on how well surrogate-model assumptions match the geometry and noise structure of the underlying objective. We introduce tidyHEBO, a robust Bayesian optimization model inspired by heteroskedastic evolutionary Bayesian optimization (HEBO) for single-objective, sequential optimization. tidyHEBO reconstructs the HEBO design philosophy in BoTorch and revises surrogate training, output-warping selection, acquisition function evaluation, and Pareto-front search. We benchmarked tidyHEBO on synthetic functions, Olympus emulators, fully experimental reaction-optimization datasets, needle-in-a-haystack (NIAH) materials problems, and Bayesmark hyperparameter optimization tasks. On these tasks tidyHEBO achieved competitive to superior performance and improvement in robustness across repeated optimization runs. We therefore propose tidyHEBO as a practical tool for sequential experimentations and a strong general-purpose benchmark for future Bayesian optimization research.
Evaluating large generative models across benchmarks is time-consuming and computationally expensive. This drives the need for methods that can estimate full benchmark performance by evaluating models on only a subset of items, known as a coreset. Current literature mostly requires the practitioner to input a coreset size. However, when reliable performance estimation takes priority over efficiency, an evaluation method should also be capable of automatically determining a coreset size that reflects this priority. We introduce BayesAME, a sequential Bayesian framework specifically targeting automatic determination of the coreset size. BayesAME models performance as a random variable by defining a latent ability for each group of items sharing the same historical model performances, with a joint prior distribution encoding the belief that the target model behaves similarly to these historical models. The posterior distribution over these abilities is used to derive performance estimators, quantify performance uncertainty, and select items to add to the coreset via an information-gain criterion. The coreset is iteratively augmented until the performance estimate fluctuation and the performance uncertainty fall below their respective user-defined thresholds. We propose a multi-target extension that captures performance correlations across multiple target models to further reduce the coreset size. Through extensive experiments across diverse benchmarks, we demonstrate that BayesAME consistently outperforms sequential adaptations of existing methods. Crucially, our comprehensive analysis addresses recent skepticism in the literature, establishing that non-random coreset selection is advantageous over random selection. Finally, we highlight that leveraging continuous response log-likelihoods over traditional binary scores significantly enhances estimation accuracy.
Paula Cordero Encinar, taylan. cemgil, Arnaud Doucet et al.· 0 citations
A surrogate-recommendation framework is introduced that predicts the most suitable BO surrogate from inexpensive dataset characteristics and establishes FruBO as a reproducible, compute-aware baseline for Bayesian Optimization and provides practical guidance for surrogate selection under limited computational and experimental budgets.
P. Krokidas, C. Rekatsinas, Vassilis Sioros et al.· 1 citation
Bayesian online learning promises uncertainty-aware prediction on data streams, but its performance hinges on inferential choices, including learning rates, prior distributions and variational families, which are usually fixed before seeing the stream. We address this by treating Bayesian update rules as experts and aggregating the Bayesian experts according to sequential predictive losses. We prove that the resulting aggregate competes with the best expert in hindsight at an aggregation cost determined by how each expert's per-round performance is evaluated. We instantiate the framework in online conformal inference and Gaussian process regression. The conformal inference application yields a smoothed Bayesian counterpart of adaptive conformal inference with long-run randomized coverage, while the Gaussian process application gives an oracle inequality in cumulative predictive Kullback-Leibler risk and adaptation to unknown H\"older smoothness up to logarithmic factors. Experiments show that the aggregate tracks strong experts without oracle expert selection.
Bayesian optimization routinely warm-starts a target experiment with data from related source tasks, and the multi-task Gaussian process is the textbook surrogate for the job, but it is found that it misestimates the cross-task correlation even in the simplest non-trivial case.
Carl Hvarfner, Sam Daulton, M. Balandat et al.· 0 citations
A new machine-learning framework aims to improve the success rate of computational protein design while moving away from results that reproduce sequences found in nature.
MIT News · Artificial Intelligence· news.mit.eduAug 24, 2026
