Bayesian Optimization

LLM benchmarks are increasingly dynamic: instead of containing a fixed set of questions, they define templates and parameters that can generate an effectively unlimited number of question variants. This flexibility is valuable, but it makes evaluation expensive -- especially when the goal is not just determining an average score, but reliably identifying a model's weak spots. This paper introduces a new methodology for identifying hard questions in dynamic benchmarks. It leverages COUP, a recent Bayesian optimization algorithm (Graham, Velez & Leyton-Brown, 2026), after introducing several substantive modifications to make the algorithm suitable for practical LLM pipelines. We also wrap it in a tool that supports flexible choices of datasets and utility functions, enabling users to target the kinds of questions they care about (e.g., low-accuracy questions; questions that are unusually hard relative to their measured complexity). In experiments across a range of benchmarks, we show that our method, dubbed $\texttt{QuickScope}$, discovers truly difficult questions more sample efficiently than standard baselines, while also reducing false positives from noisy outcomes.

Multi-objective Bayesian optimization (MOBO) provides a principled framework for optimizing multiple expensive black-box functions. However, existing MOBO methods often struggle with coverage, scalability, and handling constraints and preferences. In this work we propose STAGE-BO, Sequential Targeting Adaptive Gap-Filling $\varepsilon$-Constraint Bayesian Optimization: by analyzing the coverage of the surrogate Pareto front, our method identifies the Pareto front point with the largest uncovered gap, and uses its coordinates to define adaptive constraints in $\varepsilon$-constraint method, which transforms the problem into a sequence of inequality-constrained subproblems, efficiently solved via constrained expected improvement acquisition. Our approach provides uniform Pareto coverage without hypervolume computation and naturally handles constraints and preferences. Experiments on synthetic and real-world benchmarks demonstrate superior coverage and competitive hypervolume performance against state-of-the-art baselines. Our code implementation can be found at https://github.com/YangYaohong1/STAGE-BO.

The L infinity star discrepancy is a measure for how uniformly a point set is distributed in a given space. Point sets of low star discrepancy are used as designs of experiments, as initial designs for Bayesian optimization algorithms, for quasi-Monte Carlo integration methods, and many other applications. Recent work has shown that classical constructions such as Sobol', Halton, or Hammersley sequences can be outperformed by large margins when considering point sets of fixed sizes rather than their convergence behavior. These results, highly relevant to the aforementioned applications, raise the question of how much existing constructions can be improved through size-specific optimization. In this work, we study this question for the so-called Kronecker construction. Focusing on the 3-dimensional setting, we show that optimizing the two configurable parameters of its construction yields point sets outperforming the state-of-the-art value for sets of at least 500 points. Using the algorithm configuration technique irace, we then derive parameters that yield new state-of-the-art discrepancy values for whole ranges of set sizes.

We propose an Expected Free Energy-based acquisition function for Bayesian optimization to solve the joint learning and optimization problem, i.e., optimize and learn the underlying function simultaneously. We show that, under specific assumptions, Expected Free Energy reduces to Upper Confidence Bound, Lower Confidence Bound, and Expected Information Gain. We prove that Expected Free Energy has unbiased convergence guarantees for concave functions. Using the results from these derivations, we introduce a curvature-aware update law for Expected Free Energy and show its proof of concept using a system identification problem on a Van der Pol oscillator. On a two-dimensional benchmark with an oscillatory landscape, our adaptive Expected Free Energy acquisition achieves competitive performance in both regret and mean squared error, unlike the typical acquisition functions that perform well in only one metric.

Efficient selection among multiple generative models is increasingly important in modern generative AI, where sampling from suboptimal models is costly. This problem can be viewed as a multi-armed bandit (MAB) task. Under diversity-aware evaluation scores, a non-degenerate mixture of generators can outperform any individual model, distinguishing this MAB setting from classical best-arm identification. Prior approaches incorporate an Upper Confidence Bound (UCB) exploration bonus into the mixture objective. However, across multiple datasets and evaluation metrics, we observe that the UCB term consistently slows convergence and reduces sample efficiency. In contrast, a simple Mixture-Greedy strategy without explicit UCB-type optimism converges faster and achieves even better performance, particularly for widely used metrics such as FID and Vendi where tight confidence bounds are difficult to construct. We provide theoretical insight explaining this behavior: under structural conditions, diversity-aware objectives induce implicit exploration by favoring interior mixtures, leading to sampling of all arms and sublinear regret guarantees for diversity-based objectives. These results suggest that in diversity-aware multi-armed bandits, e.g., for generative model selection, exploration can arise intrinsically from the objective's geometry.

Bayesian optimization (BO) for high-dimensional constrained problems remains a significant challenge due to the curse of dimensionality. We propose Local Constrained Bayesian Optimization (LCBO), a novel framework tailored for such settings. Unlike trust-region methods that are prone to premature shrinking when confronting tight or complex constraints, LCBO leverages the differentiable landscape of constraint-penalized surrogates to alternate between rapid local descent and uncertainty-driven exploration. Theoretically, we prove that LCBO achieves a convergence rate for the Karush-Kuhn-Tucker (KKT) residual that depends polynomially on the dimension $d$ for common kernels under mild assumptions, offering a rigorous alternative to global BO where regret bounds typically scale exponentially. Extensive evaluations on high-dimensional benchmarks (up to 100D) demonstrate that LCBO consistently outperforms state-of-the-art baselines.

We consider the optimization problem of an expensive-to-evaluate black-box function, in which we can obtain noisy function values in parallel. For this problem, parallel Bayesian optimization (PBO) is a promising approach, which aims to optimize with fewer function evaluations by selecting a diverse input set for parallel evaluation. However, existing PBO methods suffer from poor practical performance or lack theoretical guarantees. In this study, we propose a PBO method, called randomized kriging believer (KB), based on a well-known KB heuristic and inheriting the advantages of the original KB: low computational complexity, a simple implementation, versatility across various BO methods, and applicability to asynchronous parallelization. Furthermore, we show that our randomized KB achieves Bayesian expected regret guarantees. We demonstrate the effectiveness of the proposed method through experiments, including those on real-data emulators.

Categorizing events using discriminant observables is central to many high-energy physics analyses. Yet, bin boundaries are often chosen manually. A simple, popular choice in multi-classification tasks is to assign events according to the largest per-class score ("argmax") and to apply equidistant binning to the resulting one-dimensional discriminants. We propose a binning optimization for signal significance directly in multi-dimensional discriminants. We use a Gaussian Mixture Model (GMM) to define flexible regions in the score space, which can be interpreted either as bins or as analysis categories. While this GMM-based strategy is applicable in both one and multiple dimensions, we also study a direct bin-boundary optimization in one dimension as a simpler alternative for binary discriminants. On this binning model, we study two optimization strategies: a differentiable and a Bayesian optimization approach. We study two toy setups: a binary classification and a three-class problem with two signals and backgrounds. In the one-dimensional case, both approaches achieve similar gains in signal sensitivity compared to equidistant binning for a given number of bins, while in the multi-dimensional case the differentiable approach performs best. We show that the GMM-based optimization can outperform argmax classification even after optimized binning is applied to the one-dimensional projections. We further study the performance of our methods on the FAIR Universe $H\rightarrowττ$ dataset, where the GMM-based optimization gives the highest signal significance. Both methods are released as lightweight Python plugins intended for straightforward integration into existing analyses.

Vision Language Models (VLMs) have demonstrated remarkable potential in multimodal reasoning. However, they can have spatial blindness and logical hallucinations when interpreting densely structured engineering content, such as analog circuit schematics. To address these challenges, we propose a Vision Language Model-Optimized Collaborative Agent Design Workflow for Analog Circuit Sizing (VLM-CAD) designed to support step-by-step reasoning over multimodal evidence. VLM-CAD bridges the modality gap by integrating a neuro-symbolic structural parsing module, Image2Net, which transforms raw pixels into explicit topological graphs and structured JSON representations to anchor VLM interpretation in deterministic facts. To ensure the reliability required for engineering decisions, we further propose ExTuRBO, an Explainable Trust Region Bayesian Optimization method. ExTuRBO employs agent-generated semantic seeds to warm-start local searches and uses Automatic Relevance Determination to provide sensitivity evidence for the final design report. Experimental results on 12 sizing tasks covering six circuits and four technology platforms show that VLM-CAD achieves a pooled Strict Pass@1 of 23.3% and a Relaxed Pass@1 of 91.7%, while providing sensitivity evidence for final design reports.

Quantum circuit design is a key bottleneck for practical quantum machine learning on complex, real-world data. We present an automated framework that discovers and refines variational quantum circuits (VQCs) using graph-based Bayesian optimization with a graph neural network (GNN) surrogate. Circuits are represented as graphs and mutated and selected via an expected improvement acquisition function informed by surrogate uncertainty with Monte Carlo dropout. Candidate circuits are evaluated with a hybrid quantum-classical variational classifier on the next generation firewall telemetry and network internet of things (NF-ToN-IoT-V2) cybersecurity dataset, after feature selection and scaling for quantum embedding. We benchmark our pipeline against an MLP-based surrogate, random search, and greedy GNN selection. The GNN-guided optimizer consistently finds circuits with lower complexity and competitive or superior classification accuracy compared to all baselines. Robustness is assessed via a noise study across standard quantum noise channels, including amplitude damping, phase damping, thermal relaxation, depolarizing, and readout bit flip noise. The implementation is fully reproducible, with time benchmarking and export of best found circuits, providing a scalable and interpretable route to automated quantum circuit discovery.

Sequential optimization of black-box functions from noisy evaluations has been widely studied, with Gaussian Process bandit algorithms such as GP-UCB guaranteeing no-regret in stationary settings. However, for time-varying objectives, no-regret is unattainable under pure bandit feedback unless strong and often unrealistic assumptions are imposed. We propose a novel method for optimizing time-varying rewards in the frequentist setting, where the objective has bounded RKHS norm almost surely. Time variations are captured through uncertainty injection, enabling heteroscedastic Gaussian process regression that adapts past observations to the current time step. As no-regret is unattainable in general in the strict bandit setting, we relax the latter allowing additional queries on previously observed points. Building on sparse inference and the effect of uncertainty injection on regret, we propose W-SparQ-GP-UCB, an online algorithm that achieves no-regret with a vanishing number of additional queries per iteration. To assess the theoretical limits of this approach, we establish a lower bound on the number of additional queries required for no-regret, proving the efficiency of our method. Finally, we provide a comprehensive analysis linking the temporal regime of the function to achievable regret rates, together with upper and lower bounds on the number of additional queries needed in each regime.

Efficient Gaussian process (GP) inference is critical for sequential decision-making tasks such as active learning, online prediction, and Bayesian optimization. Iterative approaches of approximating the GP posterior using solvers like conjugate gradients, stochastic gradient descent, or alternating projections avoid cubic costs, but often require many iterations to converge, limiting their efficacy when the posterior is updated frequently with new data. To address this, we introduce three warm-start strategies that exploit solutions of smaller linear systems to substantially speed-up convergence when updating the posterior with new data. Our methods are supported by theoretical analysis showing reduced initialization error in reproducing kernel Hilbert space (RKHS) distance, and by empirical results on regression benchmarks and Bayesian optimization tasks. Across solvers, warm-starting achieves speed-ups of up to 19x when solving to tolerance, and produces more accurate posterior estimates under fixed compute budgets, directly improving optimization performance. These results establish warm-starting as a simple, effective, and broadly applicable tool for scaling Gaussian processes in sequential settings.

General chemical reaction conditions that achieve consistently high performance across multiple substrates are important for practical applications such as library synthesis and high-throughput experimentation. However, identifying such conditions efficiently has been a longstanding challenge, as it requires decision making under uncertainty with respect to both conditions and substrates, while minimizing the number of required experiments. Here, we introduce CurryBO, a high-level framework for generality-oriented optimization. By formalizing the problem as Bayesian optimization over curried functions, CurryBO provides a unified framework that accommodates different generality definitions (e.g., mean yield across substrates), and supports a range of substrate and condition selection strategies. We evaluate this framework on four benchmark tasks in experimental reaction optimization, and systematically analyze key algorithmic components. Our results show that efficient experiment planning can be achieved by emphasizing exploration when selecting reaction conditions, followed by the uncertainty-guided prioritization of substrates in a sequential decison-making scheme. Based on these insights, we design and validate an optimization policy that substantially improves sample efficiency relative to previously reported approaches across all benchmarks. Overall, the flexibility and modularity of CurryBO facilitate the integration of generality-oriented optimization into experimental settings, enabling more efficient identification of solutions that perform robustly across diverse tasks.

Novelty search (NS) aims to uncover diverse system behaviors through simulation or experiment without requiring a pre-specified scalar objective. This capability is especially relevant to modern discovery problems in chemistry, materials science, and molecular design, where researchers often seek broad coverage of attainable property space rather than a single optimum and where each evaluation may require a costly computation or experiment. For such expensive black-box settings, we propose BEACON, a sample-efficient NS strategy inspired by Bayesian optimization principles. BEACON models the input-to-outcome mapping using multi-output Gaussian processes and selects new inputs by scoring how far plausible posterior outcomes lie from a denoised archive of previously observed outcomes. This gives a distance-based novelty acquisition that accounts for predictive uncertainty and observational noise while operating directly in continuous outcome space, rather than requiring direct optimization over a discretized partition of behaviors. By leveraging efficient posterior sampling together with scalable high-dimensional Gaussian process models, the proposed framework can be extended to settings with large data sets and high-dimensional design variables. We demonstrate BEACON on established benchmark problems together with real-world case studies in materials and molecular discovery. Across these settings, BEACON consistently discovers broader sets of distinct behaviors than several competing baselines under limited evaluation budgets.

Bayesian optimisation (BO) enables sample-efficient global optimisation of expensive black-box functions but remains challenging in high dimensions. We investigate nonlinear dimensionality reduction to a sequence of low-dimensional latent-space BO (LSBO) problems. Early LSBO used linear random and supervised embeddings; building on Grosnit et al., we employ variational autoencoders (VAEs), deep metric loss for structured latent manifolds, and retraining to adapt the encoder-decoder pair to newly sampled regions. We couple LSBO with sequential domain reduction (SDR) directly in latent space (SDR-LSBO), narrowing search domains as evidence accumulates. Implemented in GPU-accelerated BoTorch with Mat'ern-5/2 Gaussian-process surrogates, our methods improve benchmark optimisation quality, and retraining can enhance BO performance. Comparisons with adaptive supervised linear random embeddings demonstrate the effectiveness of VAE-based BO for nonlinear low-dimensional structures. We analyse BO-VAE with a fixed pretrained representation, decomposing ambient-space simple regret into latent BO error and a fixed VAE-induced representation gap. Under a PAC-Bayes-certified reconstruction condition and standard fixed-prior assumptions for expected improvement with a Mat'ern-5/2 kernel, latent BO error vanishes as the evaluation budget increases, whereas the representation gap remains fixed and may impose a non-vanishing error floor. Visualisations empirically assess accessibility of the ambient optimum through the learned decoder. To our knowledge, this is the first study combining SDR with VAE-based LSBO. Our analysis clarifies metric shaping and retraining choices critical for scalable latent-space BO. For reproducibility, source code is available at https://github.com/L-Lok/Nonlinear-Dimensionality-Reduction-Techniques-for-Bayesian-Optimization.git.

Practical molecular inverse design is rarely a one-shot generation problem; it often takes the form of closed-loop candidate-pool enrichment, where under a limited oracle budget the goal is to increase the fraction of generated molecules that match a desired property profile. Bayesian optimization (BO) offers a natural framework for this setting, yet standard Gaussian-process surrogates typically operate in compressed continuous embeddings, which discard the substructural and reference-similarity signals that chemists naturally use to decide where to look next. We propose BoMolLLM, a closed-loop framework in which the surrogate, rather than the generator, is treated as the locus of design choice, and instantiate it with a frozen large language model that reasons directly over the task instruction, SMILES-level optimization history, and oracle feedback in their native textual form. At each iteration, the surrogate returns a structured decision signal that selects informative reference molecules under an exploration and exploitation principle, optionally with a concise guidance sentence. This signal is converted into next-round conditioning text for a frozen molecular generator, yielding an inspectable optimization trace in natural language. Experiments on MolQA drug and material design tasks show that BoMolLLM improves over one-shot prompting, is competitive with or stronger than GP-based BO baselines, and reveals a domain-dependent interface: reference-only transfer works best for binary drug targets, while adding a concise surrogate summary is more beneficial for continuous material