arXiv subjects

Donney Fan

Publications and source records attributed to Donney Fan.

3 recordsLinked to original sources

arXiv2026

Search at the Cost of Sampling: Nearly-Instant Latent Space Bayesian Optimization

Generative models are increasingly central to many de novo discovery pipelines, in which designs are generated at scale and filtered through virtual screens to determine a set of candidates to experimentally validate. While Bayesian optimization (BO) is a natural fit for this setting, as it uses past evaluations to guide future proposals, the computational overhead required for its sequential decision-making becomes a bottleneck when virtual screens are relatively cheap. We make BO practical in this regime by exploiting the unique combination of a linear model constrained to a spherical domain where high-dimensional latents concentrate. We build off recent work justifying the use of linear surrogates, while deriving nearly closed-form solutions to the surrogate modelling and acquisition problems that exploit spherical symmetry. The result is at least a 100x speedup over state-of-the art baselines, with matching or improved performance across molecular and image generation benchmarks. Altogether, our method makes BO a practical drop-in for de novo pipelines where it was previously too slow to consider.

cs.LG↗

arXiv2026

Adaptive Candidate Point Thompson Sampling for High-Dimensional Bayesian Optimization

In Bayesian optimization, Thompson sampling selects the evaluation point by sampling from the posterior distribution over the objective function maximizer. Because this sampling problem is intractable for Gaussian process (GP) surrogates, the posterior distribution is typically restricted to fixed discretizations (i.e., candidate points) that become exponentially sparse as dimensionality increases. While previous works aim to increase candidate point density through scalable GP approximations, our orthogonal approach increases density by adaptively reducing the search space during sampling. Specifically, we introduce Adaptive Candidate Thompson Sampling (ACTS), which generates candidate points in subspaces guided by the gradient of a surrogate model sample. ACTS is a simple drop-in replacement for existing TS methods -- including those that use trust regions or other local approximations -- producing better samples of maxima and improved optimization across synthetic and real-world benchmarks.

cs.LG↗

arXiv2026

We Still Don't Understand High-Dimensional Bayesian Optimization

Existing high-dimensional Bayesian optimization (BO) methods aim to overcome the curse of dimensionality by carefully encoding structural assumptions, from locality to sparsity to smoothness, into the optimization procedure. Surprisingly, we demonstrate that these approaches are outperformed by arguably the simplest method imaginable: Bayesian linear regression. After applying a geometric transformation to avoid boundary-seeking behavior, Gaussian processes with linear kernels match state-of-the-art performance on tasks with 60- to 6,000-dimensional search spaces. Linear models offer numerous advantages over their non-parametric counterparts: they afford closed-form sampling and their computation scales linearly with data, a fact we exploit on molecular optimization tasks with >20,000 observations. Coupled with empirical analyses, our results suggest the need to depart from past intuitions about BO methods in high-dimensions.

cs.LG↗