In this paper, we address the problem of cost-sensitive hyperparameter optimization (HPO) built upon freeze-thaw Bayesian optimization (BO). Specifically, we assume a scenario where users want to early-stop the HPO process when the expected performance improvement is not satisfactory with respect to the additional computational cost. Motivated by this scenario, we introduce utility in the freezethaw framework, a function describing the trade-off between the cost and performance that can be estimated from the user's preference data. This utility function, combined with our novel acquisition function and stopping criterion, allows us to dynamically continue training the configuration that we expect to maximally improve the utility in the future, and also automatically stop the HPO process around the maximum utility. Further, we improve the sample efficiency of existing freezethaw methods with transfer learning to develop a specialized surrogate model for the cost-sensitive HPO problem. We validate our algorithm on established multifidelity HPO benchmarks and show that it outperforms all the previous freezethaw BO and transfer-BO baselines we consider, while achieving a significantly better trade-off between the cost and performance. Our code is publicly available at https://github.com/db-Lee/CFBO.

Protein fitness optimization involves finding a protein sequence that maximizes desired quantitative properties in a combinatorially large design space of possible sequences. Recent advances in steering protein generative models (e.g., diffusion models and language models) with labeled data offer a promising approach. However, most previous studies have optimized surrogate rewards and/or utilized large amounts of labeled data for steering, making it unclear how well existing methods perform and compare to each other in real-world optimization campaigns where fitness is measured through low-throughput wet-lab assays. In this study, we explore fitness optimization using small amounts (hundreds) of labeled sequencefitness pairs and comprehensively evaluate strategies such as classifier guidance and posterior sampling for guiding generation from different discrete diffusion models of protein sequences. We also demonstrate how guidance can be integrated into adaptive sequence selection akin to Thompson sampling in Bayesian optimization, showing that plug-and-play guidance strategies offer advantages over alternatives such as reinforcement learning with protein language models. Overall, we provide practical insights into how to effectively steer modern generative models for next-generation protein fitness optimization.

However, these methods often suffer from a significant one-step bias, which may lead to convergence towards local optima and poor performance in complex or high-dimensional tasks. Recently, Black-Box Optimization (BBO) has achieved success across various scientific and engineering domains, particularly when function evaluations are costly and gradients are unavailable. Motivated by this, we propose the Reinforced EnergyBased Model for Bayesian Optimization (REBMBO), which integrates Gaussian Processes (GP) for local guidance with an Energy-Based Model (EBM) to capture global structural information. Notably, we define each Bayesian Optimization iteration as a Markov Decision Process (MDP) and use Proximal Policy Optimization (PPO) for adaptive multi-step lookahead, dynamically adjusting the depth and direction of exploration to effectively overcome the limitations of traditional BO methods. We conduct extensive experiments on synthetic and real-world benchmarks, confirming the superior performance of REBMBO.

Many real-world black-box optimization problems have multiple conflicting objectives. Rather than attempting to approximate the entire set of Pareto-optimal solutions, interactive preference learning, i.e., optimization with a decision maker in the loop, allows us to focus the search on the most relevant subset. However, few previous studies have exploited the fact that utility functions are typically monotonic. In this paper, we address the Bayesian Optimization with Preference Exploration (BOPE) problem and propose using a neural network ensemble as a utility surrogate model. This approach naturally integrates monotonicity and allows learning the decision maker's preferences from pairwise comparisons. Our experiments demonstrate that the proposed method outperforms state-of-the-art approaches and is robust to noise in utility evaluations. An ablation study highlights the critical role of monotonicity in enhancing performance.

Constrained Bayesian optimization (CBO) methods have seen significant success in black-box optimization with constraints. One of the most commonly used CBO methods is the constrained expected improvement (CEI) algorithm. CEI is a natural extension of expected improvement (EI) when constraints are incorporated. However, the theoretical convergence rate of CEI has not been established. In this work, we study the convergence rate of CEI by analyzing its simple regret upper bound.

This work presents an extension to Pareto Front Guided Sampling (PFGS), a Human-in-the-Loop (HitL) Bayesian Optimization (BO) framework in which Gaussian process (GP) surrogate-derived quantities are reformulated as objectives of a multi-objective optimization problem, and the resulting Pareto front is exposed to a domain expert for interactive candidate selection rather than returning a single automated recommendation. The framework is extended in two directions: constrained optimization is addressed by incorporating the posterior probability of satisfying output specification limits as an explicit Pareto objective, computed analytically from the GP posterior distribution; robust optimization is addressed by a Monte Carlo sampling strategy that estimates expected lower-confidence performance over a user-defined variability of input perturbations, capturing performance degradation under likely implementation deviations. The resulting multi-dimensional Pareto representation renders trade-offs between predicted performance, model uncertainty, probabilistic constraint satisfaction, and input robustness simultaneously visible through pairwise two-dimensional projections on an interactive dashboard, enabling selection criteria to be iteratively refined as the surrogate model improves and development objectives evolve. The framework is showcased on an eight-dimensional fed-batch Chinese Hamster Ovary (CHO) cell culture simulator demonstrating systematic identification of high-performing, feasibility-compliant, and perturbation-resilient operating conditions, and illustrating how expert-defined requirements provide a principled stopping criterion and support informed allocation of experimental resources.

Bayesian Optimization is a widely used method for optimizing expensive black-box functions, relying on probabilistic surrogate models such as Gaussian Processes. The quality of the surrogate model is crucial for good optimization performance, especially in the few-shot setting where only a small number of batches of points can be evaluated. In this setting, the initialization plays a critical role in shaping the surrogate's predictive quality and guiding subsequent optimization. Despite this, practitioners typically rely on (quasi-)random designs to cover the input space. However, such approaches neglect two key factors: (a) space-filling designs may not be desirable to reduce predictive uncertainty, and (b) efficient hyperparameter learning during initialization is essential for high-quality prediction, which may conflict with space-filling designs. To address these limitations, we propose Hyperparameter-Informed Predictive Exploration (HIPE), a novel acquisition strategy that balances predictive uncertainty reduction with hyperparameter learning using information-theoretic principles. We derive a closed-form expression for HIPE in the Gaussian Process setting and demonstrate its effectiveness through extensive experiments in active learning and few-shot BO. Our results show that HIPE outperforms standard initialization strategies in terms of predictive accuracy, hyperparameter identification, and subsequent optimization performance, particularly in large-batch, few-shot settings relevant to many real-world Bayesian Optimization applications.

We introduce BayeSQP, a novel algorithm for general black-box optimization that merges the structure of sequential quadratic programming with concepts from Bayesian optimization. BayeSQP employs second-order Gaussian process surrogates for both the objective and constraints to jointly model the function values, gradients, and Hessian from only zero-order information. At each iteration, a local subproblem is constructed using the GP posterior estimates and solved to obtain a search direction. Crucially, the formulation of the subproblem explicitly incorporates uncertainty in both the function and derivative estimates, resulting in a tractable second-order cone program for high probability improvements under model uncertainty. A subsequent one-dimensional line search via constrained Thompson sampling selects the next evaluation point. Empirical results show that BayeSQPoutperforms state-of-the-art methods in specific high-dimensional settings. Our algorithm offers a principled and flexible framework that bridges classical optimization techniques with modern approaches to black-box optimization.

We address the problem of Gaussian Process (GP) optimization in the presence of unknown and potentially varying adversarial perturbations. Unlike traditional robust optimization approaches that focus on maximizing performance under worstcase scenarios, we consider a robust satisficing objective, where the goal is to consistently achieve a predefined performance threshold τ, even under adversarial conditions. We propose two novel algorithms based on distinct formulations of robust satisficing, and show that they are instances of a general robust satisficing framework. Further, each algorithm offers different guarantees depending on the nature of the adversary. Specifically, we derive two regret bounds: one that is sublinear over time, assuming certain conditions on the adversary and the satisficing threshold τ, and another that scales with the perturbation magnitude but requires no assumptions on the adversary. Through extensive experiments, we demonstrate that our approach outperforms the established robust optimization methods in achieving the satisficing objective, particularly when the ambiguity set of the robust optimization framework is inaccurately specified.

We propose an extension of Thompson sampling to optimization problems over function spaces where the objective is a known functional of an unknown operator's output. We assume that queries to the operator (such as running a high-fidelity simulator or physical experiment) are costly, while functional evaluations on the operator's output are inexpensive. Our algorithm employs a sample-then-optimize approach using neural operator surrogates. This strategy avoids explicit uncertainty quantification by treating trained neural operators as approximate samples from a Gaussian process (GP) posterior. We derive regret bounds and theoretical results connecting neural operators with GPs in infinite-dimensional settings.