Improving Bayesian Optimization via Training-Aware Conditional Diffusion Models

Guided-diffusion black-box optimization (BO) has shown strong empirical performance on structured design problems such as molecules and crystals, but its regret behavior remains poorly understood. Existing BO regret analyses typically rely on maximum information gain, non-pretrained surrogate models, or exact acquisition maximization -- assumptions that break down in modern diffusion -- BO pipelines, where pretrained diffusion models serve as powerful priors over valid structures and acquisition maximization is replaced by approximate sampling over astronomically large discrete spaces. We develop a first certificate-based expected simple-regret framework for guided-diffusion BO that avoids maximum-information-gain bounds, RKHS assumptions, and exact acquisition maximization. The central quantity in our analysis is mass lift: the increase in probability mass assigned to near-optimal designs relative to the pretrained generator. This view explains how exponential-looking finite-budget convergence and polynomial acceleration can all arise from the same mechanism. We also give practical diagnostics for estimating search exponents from finite candidate pools and a proposal-corrected resampling construction that provides a fully certified sampler instance.

Constant Liar (CL), Kriging Believer (KB), and fantasy models are widely used for batch selection in parallel Bayesian Optimization, yet a unified theory explaining their effectiveness and conditions under which they fail has been lacking. We identify efficient conditioning as the key surrogate property the ability to update predictions in closed form when data is augmented. We prove that Gaussian Processes satisfy this requirement, producing provably distinct batch points with separation of order l, and that this holds for any acquisition function monotonically non decreasing in posterior uncertainty (EI, UCB, PI), with qualitatively similar behavior for Thompson Sampling. We unify CL, KB, and fantasy models as instances of a single conditioning mechanism differing only in the lie value distribution, and draw quantitative connections to Local Penalization (LP) and qualitative connections to Determinantal Point Processes (DPPs). To disentangle model structure from optimizer randomness, we introduce the Structural Diversity Diagnostic (SDD), a reusable methodology for testing surrogate compatibility. Experiments on Hartmann6D, Ackley 8D, Levy10D, and SVM hyperparameter tuning validate all theoretical predictions: CL or KBs implicit penalty matches or outperforms explicit LP greedy conditioning achieves convergence on par with joint qEI efficient conditioning extends to Multiquadric RBF networks; and parametric surrogates produce degenerate batches even when fully retrained (random forests), while neural networks regain diversity only at 15x the wall clock cost of GP conditioning. Robustness is confirmed across multiple initial datasets and under observation noise.

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.