Bayesian Optimization

Model merging combines trained models directly in weight space, offering a compute-efficient alternative to additional fine-tuning. Selecting merge parameters is nevertheless difficult because downstream evaluations are expensive, gradients are unavailable, and source capabilities can conflict. We formulate merge-parameter selection as a black-box multi-objective optimization problem and introduce MOBO-Merge, a merge-operator agnostic framework that uses multi-objective Bayesian optimization to approximate the Pareto front under a limited evaluation budget. We evaluate Qwen3-4B and Llama-3.1-8B in two-model instruction-math and three-model instruction-math-code settings using Linear, SLERP, TIES, and block-wise merge operators. On held-out benchmark partitions, MOBO-Merge obtains higher mean hypervolume than random search in 11 of 12 reported comparisons. The gain is small for one-dimensional Linear interpolation but substantially larger for several TIES, block-wise, and three-objective searches. No merge operator is uniformly best: TIES leads in three of four family-setting combinations, whereas Block-Linear 4x is strongest for the Llama three-model merge. These results show that multi-objective Bayesian optimization is valuable as a search layer for expressive merge parameterizations.

Bayesian optimization (BO) is a sample-efficient framework for analog circuit topology search, where evaluating each candidate topology can require costly simulation. However, representation-based BO methods typically treat circuit embeddings as fixed after encoder training. This creates a mismatch between representation learning and optimization: embeddings learned to encode or reconstruct circuit structure are not necessarily organized according to the figure of merit (FoM) being optimized. This paper introduces Test-Time Analog Representation Adaptation for Bayesian Optimization (TTARO), an online deep-kernel BO framework that adapts circuit representations throughout the search process. Starting from pretrained circuit embeddings, TTARO jointly learns a nonlinear feature transformation and a Gaussian-process surrogate using the FoM labels of the circuits evaluated so far. Following each new evaluation, TTARO updates the representation and surrogate before selecting the next candidate. We compare TTARO with conventional Gaussian Process-based BO over fixed embeddings and with Deep Kernel Learning (DKL), which learns the representation only from the initial evaluated designs and keeps it fixed throughout the remainder of the search. By continually incorporating newly observed FoM labels into representation learning, TTARO aligns the search space with the optimization objective as BO progresses. In our experiments, TTARO reduces regret AUC by 15.2% on average relative to BO and by 20.7% relative to DKL across 40 encoder/kernel/acquisition settings, outperforming prior art in most settings with reductions as large as 46.7%.

Multi-objective Bayesian optimization (MOBO) is effective in identifying the Pareto fronts for expensive black-box problems. However, most current MOBO approaches are limited to low-dimensional decision space due to its exponential sampling complexity. This paper presents decision variable interaction analysis-based MOBO, ViaMOBO, a generic framework for expensive multi-objective problems with high-dimensional decision space. The key idea of ViaMOBO is that it utilizes a variable interaction analysis model to determine whether the decision space can be completely or partially divided, and then performs local Bayesian optimization in the divided decision subspaces. Through the variable analysis model, it can be derived whether the objectives in black-box problems are separable, partially separable, or non-separable based on the potential independent or interdependent relationships among decision variables without any strong assumptions. We compare ViaMOBO with the state-of-the-art MOBO methods on both synthetic and real-world benchmarks. The experimental results demonstrate that ViaMOBO outperforms other related MOBO baselines in approximating the Pareto front of high-dimensional expensive multi-objective problems.

Track seeding strongly affects both the quality and computational cost of charged-particle reconstruction, yet its many configuration parameters are commonly tuned through expert intuition and repeated trial and error. ACTS reduces this burden with an Optuna Tree-structured Parzen Estimator auto-tuner, but expensive evaluations, a restricted search space, and a scalarized objective can limit evaluation efficiency, exclude promising configurations, and obscure performance trade-offs. We investigate whether Bayesian optimization can address these limitations using ACTS with the Open Data Detector (ODD). Under identical search ranges and a common 100-trial budget, we compare Expected Improvement and Upper Confidence Bound with TPE and random search on the existing eight-parameter problem, extend the best-performing Bayesian method to fifteen parameters, and apply Expected Hypervolume Improvement to optimize efficiency, fake rate, duplicate rate, and runtime without fixed scalar weights. Candidate configurations are evaluated through the full ACTS reconstruction chain and validated on disjoint held-out events. The Bayesian acquisition methods identify strong configurations earlier than TPE, and their advantage persists in held-out validation. Expanding the search further improves performance, while multi-objective optimization reveals competitive non-dominated solutions spanning distinct trade-offs. These results indicate that Bayesian optimization can strengthen ACTS auto-tuning through efficient evaluation, broader parameter searches, and post-hoc expert selection among non-dominated alternatives.

Gradient-free post-training has emerged as a compelling alternative to gradient-based optimization for large language models (LLMs), but existing approaches remain costly. We ask whether structured search can identify a strong single expert under a modest evaluation budget. Motivated by evidence that useful weight updates lie in low-dimensional subspaces, we apply Bayesian optimization within a random linear embedding of weight space. Our method requires no backpropagation and uses a Gaussian process surrogate to guide candidate evaluations efficiently. Across several reasoning benchmarks with Qwen2.5-Instruct models from 0.5B to 3B parameters, Bayesian optimization using five times less candidate evaluations matches or exceeds RandOpt. These results show that surrogate-guided search can substantially reduce the evaluation cost of gradient-free post-training while producing stronger deployable single experts.

A significant challenge in exoskeleton robotics is the need to dynamically adapt control profiles to individual motion preferences, thereby ensuring both efficient and comfortable assistance. Currently, since user experience can serve as a comprehensive metric for evaluating the effectiveness of assistance, user preference-based optimization methods have been widely studied for parameter tuning. However, the existing methods rely heavily on extensive human-robot online interactions and suffer from slow optimization speed, which not only induces user fatigue but also compromises optimization effectiveness. Therefore, this paper aims to explore an efficient preference-based optimization framework for personalized exoskeleton assistance that can learn optimal parameters with minimal interaction. We propose a preference-based Bayesian optimization (PbBO) approach that can improve sample efficiency by leveraging knowledge about the sampling distribution of candidate sets. For optimizing six control parameters, PbBO can converge to user-preferred parameters with 90.7% validation accuracy via 20 iterations. Moreover, the hierarchical controller is designed to generate personalized torque for different tasks and achieve interaction torque tracking in real time. The results of treadmill and outdoor experiments demonstrate that the optimized parameters can reduce metabolic rate by 14.5%-15.4%, heart rate by 6.3%-7.6%, and muscle activation by 6.7%-31.5% compared to unassisted walking.

Preferential Bayesian optimization (PBO) optimizes objectives accessible only through pairwise user comparisons. The standard approach fits a Gaussian process surrogate for observed pairwise comparisons (PairwiseGP) using the Laplace approximation and selects queries with the Expected Utility of Best Option (EUBO) acquisition function. EUBO queries new candidates at each step, producing pairs that share no candidates with previous queries. Each such pair forms an isolated component in the comparison graph, removing one degree of freedom from the likelihood Hessian and making it rank-deficient. This deficiency is structural and cannot be resolved by changing the surrogate modeling approach. Existing approaches to remedy this issue either waste query budget by forcing comparisons to stay connected, or apply uniform regularization that also perturbs directions already well-constrained by the observed comparisons. We propose KappaSharp that enables a diagonal correction to the Hessian to reduce its condition number, with larger corrections where the prior uncertainty is higher. The correction is only applied in the model fitting step, not query selection. An adaptive variant of KappaSharp is also presented that activates the correction only when the surrogate is confident about recent comparisons, avoiding unnecessary corrections when the problem is well-conditioned. On 11 benchmarks (5--20 dimensions), including a 16-dimensional controller tuning problem in plasma medicine, Adaptive KappaSharp outperforms the standard PBO baseline, with up to +10.9% ($p{=}0.003$).

Advanced materials discovery increasingly relies on machine learning and Bayesian optimization to explore large discrete design spaces under limited evaluation budgets. However, conventional Bayesian optimization (BO) can become inefficient as candidate spaces grow, often evaluating low-value regions before reaching informative areas. We propose an active-learning (AL)-guided adaptive search-space refinement framework combined with multi-objective BO to accelerate materials optimization while preserving Pareto-relevant regions. We evaluate the approach on CH4/N2 separation in covalent-organic frameworks and pressure-vessel design with material-direction stress components and thickness objectives. Results show that the AL-guided refinement reduces the candidate space by approximately half while preserving more than 99 percent of the original hypervolume. The reduced-space strategy improves early convergence and cumulative Pareto-front discovery from the BO, demonstrating efficient large-scale materials optimization across constrained autonomous materials discovery settings.

Black-box optimization is a ubiquitous problem in science and engineering, often dealing with expensive objective functions with cheaper lower-fidelity proxies available. Multi-fidelity Bayesian optimization (MF-BO) is a principled approach to this problem, leveraging correlations across different fidelities when querying the objective. However, for many important MF-BO tasks, the true highest-fidelity function is prohibitively expensive to be part of the optimization loop. Nevertheless, practitioners often have gold standard data (observations of the highest-fidelity function) obtained from previous experiments that might provide information for the current task. For instance, in molecular optimization, chemists often pick the top-$k$ candidate molecules using various computer simulations, and later reveal their true objective function values. In this work, we demonstrate the suboptimality of standard MF-BO algorithms in the real-world scenarios above, even under ideal assumptions. Next, we mitigate this problem by incorporating historical high-fidelity data accompanied by task descriptors---which can be explicitly given or extracted from unstructured metadata. We demonstrate the effectiveness of our methods on synthetic functions, as well as real-world problems in chemistry and hyperparameter optimization.

We consider grey-box optimization problems where the decision variables naturally partition into black-box variables (as arguments to an expensive black-box function) and white-box variables, governed by a set of explicit, closed-form equations that also depend on the output of the black-box function. We exploit this separability through a bilevel reformulation: an outer Bayesian optimization (BO) to optimize the scalar objective as a function of black-box variables alone, while an inner problem solves the white-box subproblem via global optimization. The Gaussian process surrogate used in BO is therefore defined rather than and white-box constraints are satisfied exactly whenever the inner optimizer converges to a feasible point---without penalty functions, chance constraints, or moment approximations. On a suite of 13 benchmark problems, bilevel BO achieves lower regret, with fewer iterations and wall clock time. This advantage is robust to initialization set size, exploration parameters, and inner-solver choice.

Natural disasters frequently inflict severe damage to the built environment, which demands a rapid, reliable, and cost-effective damage assessment for emergency response. However, traditional methods for post-disaster damage assessment often rely on static, labor-intensive data collection strategies that can be prohibitively expensive and struggle to adapt to dynamic post-disaster conditions. In this study, we propose a cost-aware Bayesian optimization framework combined with level-set estimation that continuously guides autonomous data collectors, e.g., an unmanned aerial vehicle (UAV), toward the most informative regions. By dynamically updating damage estimates across different geographic zones, our approach systematically reduces uncertainty while minimizing operational costs. The proposed framework is first validated using a controlled synthetic toy study, demonstrating the agent's ability to efficiently trace damage boundaries, recover the underlying damage map, and rapidly reduce predictive uncertainty. Furthermore, the approach is evaluated using high-fidelity disaster data generated by the Regional Resilience Determination (R2D) software. The results of the algorithm provide accurate and timely damage estimates that support informative and fast emergency response.

Bayesian optimization (BO) relies on a surrogate model and an acquisition function, yet the most suitable choices vary across tasks and optimization stages. Automated Bayesian optimization (AutoBO) addresses this variability by adapting BO components online. However, existing AutoBO methods either adapt one component, leaving the other mismatched and creating a bottleneck, or jointly select surrogate--acquisition pairs under a shared criterion, overlooking their distinct roles: surrogate selection depends on predictive reliability, whereas acquisition adaptation should respond to campaign context.In this paper, we propose DASH, a Decoupled Adaptive Surrogate--Acquisition Harness for large-language- model (LLM)-enhanced AutoBO. DASH selects surrogates by predictive reliability, uncertainty calibration, and ranking consistency; its two-stage acquisition controller periodically reallocates quotas across acquisition functions, builds a BO shortlist accordingly, and delegates final selection to an LLM. DASH also incorporates an integrated harness, consisting of knowledge-guided warm start and structured memory, to ground optimization in domain knowledge and accumulated feedback. Across four chemical optimization tasks, DASH outperforms the best AutoBO baseline by 12.51% in trajectory-level Acceleration Factor and 5.00% in endpoint Enhancement Factor. Results remain strong across LLM backbones, and ablations verify the complementary contributions of all components. Full-table and behavioral contamination checks find no detectable evidence that direct benchmark memorization or source-cell leakage explains these gains.

Bayesian optimization (BO) has become the standard tool for sample-efficient optimization and owes its efficiency to uncertainty-aware search driven by generic statistical priors. Richer domain priors can improve BO in principle, but encoding them through tailored kernels or problem structure is difficult and rarely done in practice. LLMs can help sidestep this difficulty by making informal priors from natural language, code, and documentation directly available to the optimizer. However, existing LLM-based BO methods either insert the LLM into a fixed role (surrogate, acquisition proxy, or configuration interface) or hand it broad control, sacrificing the systematic exploration that makes BO reliable. We introduce 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. The agent configures the problem, queries the backend, selects and commits evaluations, and can revise the optimization strategy during the run by tightening bounds, switching acquisition functions, proposing targeted evaluations, or even reframing the problem following new instructions or observed evidence. We instantiate this idea in Sara, a surrogate-augmented autoresearch agent, and lenz, a modular BoTorch-based backend that the agent can inspect and modify through a structured interface. Across synthetic and real-world benchmarks, Sara preserves the reliability of state-of-the-art BO without prior knowledge, outperforms LLM-based baselines, and uses natural-language priors to improve beyond standard BO. We further demonstrate the practical value of agentic BO in dynamic settings, where Sara reconfigures the full optimization problem on the fly as requirements change, a capability not previously available in standard BO.

We study expected improvement (EI) for minimizing a deterministic function $f$ in the RKHS $\mathcal H_k$ of a continuous positive-semidefinite kernel $k$ on a nonempty compact set $\mathcal X\subset\mathbb R^d$. Function values are observed exactly, and EI is computed from a fixed zero-mean Gaussian-process model with covariance $σ^2k$, $σ>0$. A weak-EI policy queries a point whose EI is at least a fixed positive fraction of its maximum. We introduce a notion of sequential separation radius relating ranked selected-point innovation norms to Kolmogorov widths, drawing on greedy approximation. Standard power-function estimates from scattered-data approximation and a finite-budget regret argument yield the rates. After $N$ post-initial queries, every weak-EI policy has simple regret $O(N^{-ν/d})$ for isotropic Matérn kernels of smoothness $ν>0$ and $O(\exp[-c_1\min\{N,N^{1/d}\log(eN)\}])$ for the isotropic squared-exponential kernel, with $c_1>0$. For $d=1$, the sharper bound $O(\exp[-c_2N\log(eN)])$ holds for exact EI, with $c_2>0$. These bounds are uniform over each fixed RKHS ball. If $\mathcal X$ has nonempty interior and $B>0$, the exact EI policy is minimax-rate optimal over the RKHS ball of radius $B$ for Matérn kernels, even among randomized strategies whose final recommendation need not be a query point. For the squared-exponential kernel, it is minimax-rate optimal up to constants in the exponent among deterministic methods whose final recommendation may be any point of $\mathcal X$.

Bayesian Optimization (BO) is widely adopted for data-efficient optimization in scientific and engineering applications, yet its computational cost is rarely evaluated alongside optimization performance. Here we present a systematic, compute-aware study of BO that evaluates surrogate models along two axes: optimization quality and computational frugality. Across eight benchmark functions and nine real-world datasets spanning materials science, mechanics, robotics, chemistry, and machine learning, we benchmark four surrogate models: Gaussian Processes, Random Forests, NGBoost, and Bayesian Adaptive Spline Surfaces. We show that Gaussian Process-based BO consistently incurs the highest time and memory overhead without delivering superior optimization or sample efficiency. In contrast, scalable alternatives achieve equal or better performance at a fraction of the computational cost. Motivated by these findings, we introduce a surrogate-recommendation framework that predicts the most suitable BO surrogate from inexpensive dataset characteristics. Together, these results establish FruBO as a reproducible, compute-aware baseline for Bayesian Optimization and provide practical guidance for surrogate selection under limited computational and experimental budgets.

Wavelength selection is one of the important preprocessing methods in near-infrared spectroscopy to improve prediction accuracy and interpretability of spectral data. We formulate wavelength-region selection for sugar content estimation as a binary black-box optimization problem and propose a method based on Bayesian optimization. The proposed method constructs a sparse quadratic surrogate model and sequentially extracts interested wavelength regions by Thompson sampling. Minimizing an acquisition function is performed as a quadratic unconstrained binary optimization problem by simulated or quantum annealing. Experiments show that the proposed method improves the prediction accuracy of partial least squares regression and yields more consistent wavelength regions than genetic-algorithm-based selection and simulated annealing. Under one-bit local perturbations, the selected wavelength regions show minimal fluctuations in root mean square errors between observed and predicted values of a validation set. This local stability suggests that our method converges to a smoother error landscape and avoids isolated overfitted solutions. These results indicate that combinatorial Bayesian optimization is a useful framework for robust feature selection in spectroscopic prediction tasks.

Reinforcement learning (RL) has shown remarkable success across a wide range of complex tasks. However, RL outcomes can be highly stochastic, and both expected performance and variability often depend on hyperparameter (HP) configurations. We propose efficient and risk-averse heteroscedastic Bayesian Optimization (ERAHBO), a Bayesian optimization method that models both the mean and variance of learning outcomes as functions of the HP configurations. ERAHBO aims to identify HP configurations that achieve high average return while reducing variability across training runs, and it improves the sample efficiency of the HP optimization via adaptive re-sampling rather than a fixed budget per HP. Empirical evaluations across diverse RL algorithms and environments demonstrate that ERAHBO generally outperforms both risk-neutral and risk-averse baselines, delivering improved sample efficiency for risk-averse returns.

Autonomous laboratories automate experimental execution, but a campaign must also decide which recovery pathway merits optimization. We formulate this as a sequential decision problem with a discrete pathway-identification stage and a continuous within-pathway optimization stage under heterogeneous experimental costs. Our implementation, Coactive learning, combines a cost-sensitive Bayesian hypothesis-discrimination policy motivated by EC2 (Golovin et al., 2010) with Gaussian-process Bayesian optimization (Srinivas et al., 2010). Under explicitly stated assumptions, the expected spend of one fixed-budget campaign attempt is bounded by the expected pathway-identification cost plus the capped within-pathway optimization budget. We evaluate the method on synthetic benchmarks constrained by selected results reported for PNNL's CICERO selective-precipitation study (Ritchhart et al., 2026). The method performs comparably to an oracle-pathway Bayesian-optimization reference and to a strong split-plate baseline that discriminates pathways with its first plate, without receiving an oracle label for the correct pathway. It is given a candidate hypothesis space and a diagnostic likelihood model. On an NdFeB-inspired instance, it avoids the simulated penalty of a commit-first baseline that initially selects a plausible but inferior hydroxide pathway. This hypothetical wrong-first-commitment scenario is motivated by the hydroxide-oxalate performance contrast reported by CICERO. We characterize the sensitivity of these conclusions to the assumed cost model. The code and benchmark are open source.

Expensive constrained optimization problems in real-world industry design often involve constraint thresholds that are difficult to determine in advance. Engineers may need to adjust constraint thresholds to explore different feasibility-performance trade-offs, requiring solutions under a wide range of threshold settings. However, existing constrained Bayesian optimization methods treat each threshold configuration independently, leading to repeated optimization and failing to exploit the shared relationship among continuously varying thresholds. To address this challenge, we propose constraint-bound agnostic Bayesian optimization (CBA-BO), a learning-based framework that learns a parametric constraint model mapping thresholds to optimal solutions. Once learned, CBA-BO directly predicts solutions for arbitrary unseen threshold configurations without additional optimization, with a one-step Bayesian optimization refinement further improving solution quality. Experiments on benchmark and engineering problems demonstrate that CBA-BO learns a transferable threshold-solution mapping, enabling efficient prediction and optimization for arbitrary threshold queries. An intent-guided constraint-bound recommendation mechanism is further developed to improve objective performance while satisfying user-specified constraint preferences.

Self-driving laboratories increasingly rely on multi-fidelity Bayesian optimization (MFBO) to balance cheap, approximate evaluations against scarce, expensive ones, with a predictive surrogate at its core. Gaussian processes (GPs) are the default choice, but they scale poorly as data accumulate and assume a smooth landscape that molecular and materials search spaces routinely violate. Transfer learning offers an alternative suited to this regime: it learns a representation from abundant cheap data and adapts it to sparse expensive data. Despite its use in property prediction, transfer learning has not been tested as the engine of a closed-loop optimization. Here we benchmark eleven transfer-learning surrogates against four GP methods under an identical selection rule, fidelity budget, and model size, across nine tasks spanning synthetic functions to real chemistry and materials problems. GPs win on smooth, low-dimensional functions but perform worst on molecular and materials problems, where transfer-learning surrogates reach substantially better solutions using far less computation. Because acquisition policy is held fixed across surrogates, this advantage is attributable to the surrogate itself. Uncertainty-driven exploration is not reliably beneficial, and calibration does not predict optimization performance, so greedy exploitation of the transfer-learned mean is the more robust default. Transfer learning is therefore the surrogate of choice for molecular and materials MFBO.

Bayesian optimization (BO) is an optimization method that sequentially proposes the next candidate explainable variables for optimizing target variables by balancing exploration and exploitation. BO is often used under a limited evaluation budget, such as hyperparameter tuning of deep learning. Despite its effectiveness, conventional BO may have poor convergence in practical experimental science where each evaluation is often costly and time-consuming. Recently, BO methods have been proposed that accelerate optimization by using pseudo-experimental data that simulate experimental data. However, when only a limited number of experimental data are available, the generated pseudo-experimental data may be of insufficient quality. In this study, we developed PolyBO to improve optimization time by generating high-quality pseudo-experimental data even when the number of trials is limited. PolyBO performs BO efficiently by generating pseudo-experimental data with an adaptively updated versatile parametric model. This low-capacity polynomial regression model is intended to enable efficient BO even with limited experimental data. PolyBO updates the BO surrogate model with a combined dataset consisting of experimental data and pseudo-experimental data and then performs optimization. Using synthetic benchmark functions with diverse landscapes, we found that PolyBO reduced the optimization time by a median of 42%. For a real-world material composition optimization problem, PolyBO reduced the optimization time by a median of 96% compared with conventional methods. Overall, PolyBO achieves efficient optimization in settings where each experiment requires a long time.

Near 1310 nm photonic-crystal surface-emitting lasers (PCSELs) are attractive narrow-beam sources for optical communication and sensing, but their final design refinement is costly. Small geometry changes simultaneously shift the band-edge resonance, cavity leakage, far-field divergence, and the numerical stability of a high-$Q$ decay fit, while every full-wave trial requires a time-domain simulation. We couple a commercial finite-difference time-domain solver to a reliability-aware Bayesian optimization (BO) loop over eight local design variables. Each completed simulation updates the surrogate used to choose the next geometry. Candidate ranking combines wavelength and beam-quality requirements with a reliability-adjusted metric $Q_{\mathrm{eff}}$ derived from the solver-reported relative fit-error estimate $dQ/Q$. Across three 80-evaluation runs from the same reference model, BO produced 5--15 candidates per run that passed the joint filter. Designs reconstructed from fresh model copies retained $Q_{\mathrm{eff}}=4.33\times10^6$--$7.76\times10^6$, a 60--108-fold increase over the baseline metric, at 1308.23--1310.90~nm with approximately $0.84^{\circ}$ divergence. Under equal budgets, BO gave the highest mean strict-filter yield (9.0 candidates), compared with differential evolution (7.0) and Latin-hypercube sampling (1.5), although the controls occasionally matched the peak $Q_{\mathrm{eff}}$. Field maps, resonance spectra, and local perturbations further identify an index-related wavelength handle and a hole-size-related leakage handle. The resulting FDTD budget produces a pool of wavelength-compatible, narrow-beam, and reproducible high-$Q$ PCSEL candidates without trusting a single optimistic decay fit.

Many design tasks can be cast as black-box function optimization, enabling use of Bayesian optimization to find an ideal design with minimal number of trials. However, often we do not actually need the optimum but instead a sufficiently good solution is enough, for instance a material that is durable enough for its intended use. In most cases there are multiple satisfactory solutions, forming a superlevel set of the function, raising a key question of which one to prefer. We answer this by explaining why robustness to input perturbations that may occur when the solution is deployed is a good criterion and by introduce a Bayesian optimization method that efficiently finds satisficing solutions that are robust to maximally large perturbations. In contrast to previous works, we assume the inputs can be accurately controlled during optimization, but will be perturbed after the deployment.

Molecular optimization in drug discovery, materials design, and catalysis requires searching vast chemical spaces under tight evaluation budgets, since high-fidelity oracles and experimental measurements are costly. The practical impact of an optimization method therefore hinges on its sample efficiency: how few evaluations it needs to find strong candidates. We introduce Sample Efficient Generative Optimization (SEGO), a framework for Bayesian optimization on adaptively generated molecules. In SEGO, a probabilistic surrogate model forms a hypothesis about where hits lie in chemical space, a generative model is steered to propose candidates in that region, the most promising candidate is selected via an acquisition function, and the resulting oracle call is used both to sharpen the surrogate and to anchor the generator in real reward. SEGO attains state-of-the-art performance on the practical molecular optimization (PMO) benchmark using only one tenth of the oracle calls consumed by other methods, and on a multiparameter docking task it reaches ten hits in roughly half the oracle calls of existing approaches. These gains move molecular optimization closer to campaigns driven by direct experimental feedback.

We propose a collaborative meta-learning framework for distributed Bayesian optimization matching centralized performance without raw-data exchange. We show gradient sharing leaks client observations, with leakage worsening as the search converges and queries concentrate near the optimum. We evaluate a differentially private defense and characterize its privacy-utility trade-off.

Bayesian optimization is widely used for expensive black-box optimization problems. While methodological advances often focus on individual components, practical performance depends on how these components work together. We present tidyHEBO, a Bayesian optimization model. tidyHEBO jointly learns output warping and Gaussian-process parameters, evaluates acquisition functions on the original objective scale, and preserves promising novel candidates throughout evolutionary search. On the Olympus benchmark, tidyHEBO ranked first among the evaluated methods, achieving the best average ranks for typical optimization quality, worst-tail outcomes, and run-to-run variability. It also obtained results comparable to specialized optimizers on Needle-in-a-Haystack problems. On the Bayesmark benchmark, tidyHEBO also demonstrated strong results in hyperparameter tuning. Across these benchmarks, tidyHEBO combines strong optimization results with robustness across diverse black-box problems.

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. We revisit this default in a controlled setting and find that it misestimates the cross-task correlation even in the simplest non-trivial case, affinely related source and target tasks, where a working transfer learning method should obviously succeed. We trace the failure to two independent structural mechanisms. Per-task standardization, the textbook fix for the affine slice ambiguity, propagates a finite-sample alignment error into the recovered correlation. The marginal likelihood itself identifies the correlation only at a per-sample rate that a Gaussian process at non-overlapping designs further dilutes. We propose three conservative remedies that follow from the analysis: promoting per-task means and scales to model parameters, restricting the task covariance to non-negative correlations, and co-locating part of the source and target designs. Across synthetic multi-task problems and surrogate-based hyperparameter tuning transfer, these remedies recover the target-only baseline on the simple instances, while the broader failure persists on harder instances and across most rank-based and latent-context variants.

This study presents a multi-fidelity framework for the systematic optimization of genetic algorithm (GA) hyperparameters. The framework integrates three fidelity levels: high-fidelity Fast Fourier Transform (FFT) homogenization for validation, a medium-fidelity 3D convolutional neural network surrogate for rapid property evaluation, and a low-fidelity Gaussian process (GP) surrogate within a Bayesian optimization (BO) framework to guide the hyperparameter search. Various acquisition functions are evaluated, with logNEI achieving the best performance by effectively accounting for the noise inherent in GA evaluations. The proposed framework identifies hyperparameter configurations that enable a 25-generation GA run to achieve elastic modulus values comparable to those obtained in a full 75-generation optimization. Furthermore, introducing a penalized BO objective significantly reduces the number of required lattices with only minor decreases in absolute achieved elastic modulus, revealing a practical trade-off between performance and the number of structures that must be evaluated. High-fidelity FFT validation verifies the effectiveness of the surrogate-driven optimization strategy. The optimized hyperparameters allow for rapid convergence, eliminate the need for lattice mutation, and reduce the overall computational cost by 24% (from 225 to 171 hours) while preserving mechanical performance. These results demonstrate the potential of multi-fidelity optimization as an efficient and practical approach for GA hyperparameter tuning and future experimental lattice design studies.

Designing effective multi-objective Bayesian optimization (MOBO) algorithms requires balancing many interdependent design choices whose optimal configuration is problem-dependent and typically demands deep expertise. We extend the LLaMEA framework to MOBO, using large language models as mutation and crossover operators within evolutionary strategies to generate complete algorithm implementations, with SMAC hyperparameter optimization integrated into the evolutionary loop. Across nine evolutionary runs we generated approximately 900 algorithms and benchmarked them on twelve synthetic problems (ZDT, DTLZ, WFG) and three real-world engineering problems (RE), using a BoFire qParEGO implementation as a state-of-the-art Bayesian-optimization baseline. On the synthetic suite the strongest generated algorithm attains the highest mean normalized hypervolume (0.971, vs. 0.869 for qParEGO) while requiring roughly 60x less wall-clock time; a Friedman test with post-hoc analysis places the two in a single top-performing group, and per-problem tests find the generated algorithm significantly better than qParEGO on 7 of the 12 problems and never worse, matching state-of-the-art accuracy at an order-of-magnitude lower cost. On the three unseen real-world engineering problems a generated algorithm attains the best mean normalized hypervolume (0.985, vs. 0.971 for qParEGO)--significantly better than qParEGO on two of the three problems--at roughly 3.4x lower wall-clock cost, confirming that the gains transfer beyond the synthetic regime. LLM-driven evolutionary search can thus discover algorithm designs that achieve Pareto-efficient trade-offs difficult to reach through manual design.

Bayesian Optimization (BO) generally begins with an initialization phase: a batch of $n_0$ uninformed evaluations. The choice of $n_0$ remains largely heuristic, and we empirically observe that the total cost (random initial points plus BO iterations needed to find the global optimum) is U-shaped in $n_0$, i.e., a practitioner wastes resources by selecting either too low or too high a value of $n_0$. We find this tradeoff persists across MLE, Bayesian MCMC, and exact GP hyperparameters, as well as across acquisition functions. Toward the latter, Thompson Sampling appears an exception, with both total cost and simple regret essentially $n_0$-agnostic, though higher in our experiments. We attribute this U-shape to the known boundary issue of variance-driven BO: BO burns early budget on corners of the hypercube before turning inward. We demonstrate this effect using a 3D BO trajectory where the exact hyperparameters are known. We conclude with practical recommendations: use multi-step lookahead BO where possible; otherwise use Thompson Sampling when $n_0$ cannot be tuned, and a generously large $n_0$ when it can.