Antibody lead optimization is inherently a multi-objective challenge in drug discovery. Achieving a balance between different drug-like properties is crucial for the development of viable candidates, and this search becomes exponentially challenging as desired properties grow. The ever-growing zoo of sophisticated in silico tools for predicting antibody properties calls for an efficient joint optimization procedure to overcome resource-intensive sequential filtering pipelines. We present BOAT, a versatile Bayesian optimization framework for multi-property antibody engineering. Our `plug-and-play' framework couples uncertainty-aware surrogate modeling with a genetic algorithm to jointly optimize various predicted antibody traits while enabling efficient exploration of sequence space. Through systematic benchmarking against genetic algorithms and newer generative learning approaches, we demonstrate competitive performance with state-of-the-art methods for multi-objective protein optimization. We identify clear regimes where surrogate-driven optimization outperforms expensive generative approaches and establish practical limits imposed by sequence dimensionality and oracle costs.

We present mlr3mbo, a comprehensive and modular toolbox for Bayesian optimization in R. mlr3mbo supports single- and multi-objective optimization, multi-point proposals, batch and asynchronous parallelization, input and output transformations, and robust error handling. While it can be used for many standard Bayesian optimization variants in applied settings, researchers can also construct custom BO algorithms from its flexible building blocks. In addition to an introduction to the software, its design principles, and its building blocks, the paper presents two extensive empirical evaluations of the software on the surrogate-based benchmark suite YAHPO Gym. To identify robust default configurations for both numeric and mixed-hierarchical optimization regimes, and to gain further insights into the respective impacts of individual settings, we run a coordinate descent search over the mlr3mbo configuration space and analyze its results. Furthermore, we demonstrate that mlr3mbo achieves state-of-the-art performance by benchmarking it against a wide range of optimizers, including HEBO, SMAC3, Ax, and Optuna.

Constrained optimization in high-dimensional black-box settings is difficult due to expensive evaluations, the lack of gradient information, and complex feasibility regions. In this work, we propose a Bayesian optimization method that combines a penalty formulation, a surrogate model, and a trust region strategy. The constrained problem is converted to an unconstrained form by penalizing constraint violations, which provides a unified modeling framework. A trust region restricts the search to a local region around the current best solution, which improves stability and efficiency in high dimensions. Within this region, we use the Expected Improvement acquisition function to select evaluation points by balancing improvement and uncertainty. The proposed Trust Region method integrates penalty-based constraint handling with local surrogate modeling. This combination enables efficient exploration of feasible regions while maintaining sample efficiency. We compare the proposed method with state-of-the-art methods on synthetic and real-world high-dimensional constrained optimization problems. The results show that the method identifies high-quality feasible solutions with fewer evaluations and maintains stable performance across different settings.

We present the first general purpose framework for marginal maximum a posteriori estimation of probabilistic program variables.

Recent advances in computationally efficient non-myopic Bayesian optimization offer improved query efficiency over traditional myopic methods like expected improvement, with only a modest increase in computational cost. These advances have been largely limited to unconstrained BO methods with only a few exceptions which require heavy computation. For instance, one existing multi-step lookahead constrained BO method (Lam & Willcox, 2017) relies on computationally expensive unreliable brute force derivative-free optimization of a Monte Carlo rollout acquisition function. Methods that use the reparameterization trick for more efficient derivative-based optimization of non-myopic acquisition functions in the unconstrained setting, like sample average approximation and infinitesimal perturbation analysis, do not extend: constraints introduce discontinuities in the sampled acquisition function surface. Moreover, we argue here that being non-myopic is even more important in constrained problems because fear of violating constraints pushes myopic methods away from sampling the boundary between feasible and infeasible regions, slowing the discovery of optimal solutions with tight constraints. In this paper, we propose a computationally efficient two-step lookahead constrained Bayesian optimization acquisition function (2-OPT-C) supporting both sequential and batch settings. To enable fast acquisition function optimization, we develop a novel likelihood ratio-based unbiased estimator of the gradient of the two-step optimal acquisition function that does not use the reparameterization trick. In numerical experiments, 2-OPT-C typically improves query efficiency by 2x or more over previous methods, and in some cases by 10x or more.

Trust and ethical concerns due to the widespread deployment of opaque machine learning (ML) models motivating the need for reliable model explanations. Post-hoc model-agnostic explanation methods addresses this challenge by learning a surrogate model that approximates the behavior of the deployed black-box ML model in the locality of a sample of interest. In post-hoc scenarios, neither the underlying model parameters nor the training are available, and hence, this local neighborhood must be constructed by generating perturbed inputs in the neighborhood of the sample of interest, and its corresponding model predictions. We propose \emph{Expected Active Gain for Local Explanations} (\texttt{EAGLE}), a post-hoc model-agnostic explanation framework that formulates perturbation selection as an information-theoretic active learning problem. By adaptively sampling perturbations that maximize the expected information gain, \texttt{EAGLE} efficiently learns a linear surrogate explainable model while producing feature importance scores along with the uncertainty/confidence estimates. Theoretically, we establish that cumulative information gain scales as $\mathcal{O}(d \log t)$, where $d$ is the feature dimension and $t$ represents the number of samples, and that the sample complexity grows linearly with $d$ and logarithmically with the confidence parameter $1/δ$. Empirical results on tabular and image datasets corroborate our theoretical findings and demonstrate that \texttt{EAGLE} improves explanation reproducibility across runs, achieves higher neighborhood stability, and improves perturbation sample quality as compared to state-of-the-art baselines such as Tilia, US-LIME, GLIME and BayesLIME.

Asynchronous Bayesian optimization is widely used for gradient-free optimization in domains with independent parallel experiments and varying evaluation times. Existing methods posit that standard acquisitions lead to redundant and repeated queries, proposing complex solutions to enforce diversity in queries. Challenging this fundamental premise, we show that methods, like the Upper Confidence Bound, can in fact achieve theoretical guarantees essentially equivalent to those of sequential Thompson sampling. A conceptual analysis of asynchronous Bayesian optimization reveals that existing works neglect intermediate posterior updates, which we find to be generally sufficient to avoid redundant queries. Further investigation shows that by penalizing busy locations, diversity-enforcing methods can over-explore in asynchronous settings, reducing their performance. Our extensive experiments demonstrate that simple standard acquisition functions match or outperform purpose-built asynchronous methods across synthetic and real-world tasks.

Bayesian optimization is a sample-efficient approach to global optimization that relies on theoretically motivated value heuristics (acquisition functions) to guide its search process. Fully maximizing acquisition functions produces the Bayes' decision rule, but this ideal is difficult to achieve since these functions are frequently non-trivial to optimize. This statement is especially true when evaluating queries in parallel, where acquisition functions are routinely non-convex, high-dimensional, and intractable. We first show that acquisition functions estimated via Monte Carlo integration are consistently amenable to gradient-based optimization. Subsequently, we identify a common family of acquisition functions, including EI and UCB, whose characteristics not only facilitate but justify use of greedy approaches for their maximization.

Global optimization of expensive, potentially gradient-free functions has long been a critical component of many complex problems in science and engineering.