Time-Aware Latent Space Bayesian Optimization

Bayesian optimization (BO) is a central tool for sample-efficient design, and latent-space Bayesian optimization (LSBO) extends it to structured objects such as molecules and proteins. In parallel, tabular foundation models such as TabPFN and TabICL now achieve state-of-the-art regression performance and are increasingly used as BO surrogates. Because their Bayesian behavior is induced by large synthetic pretraining collections, the composition of this pretraining distribution is crucial. LSBO creates a distinctive mismatch: the induced map from latent code to objective value differs markedly from the regression tasks used to train current in-context models. We address this mismatch by complementing the pretraining stage of tabular foundation model surrogates with synthetic optimization tasks defined on the latent space of a molecular VAE. The continued-pretraining objective features a regularizer that anchors the model to the original checkpoint, preserving its broad regression prior while avoiding overspecialization to the adaptation tasks. On held-out molecular optimization benchmarks, the resulting model achieves strong performance, supporting the relevance of LSBO-specific adaptation for in-context surrogates.

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.

Black-box optimization problems are ubiquitous across science and engineering, often dealing with expensive objective functions. This objective latency has two consequences during optimization: (i) the objective evaluation dominates execution time, and (ii) sample-efficient algorithms are crucial to accelerate development and avoid wasting resources. Bayesian optimization (BO) methods are the de facto choice of planners for suggesting the next point to try. Standard BO fits the surrogate model's hyperparameters with a point estimate. Alternatively, a fully Bayesian approach uses model averaging to account for uncertainty over the hyperparameters, leading to better uncertainty estimates---useful in the low-data regime that is pervasive in BO. However, it is often prohibitively expensive and thus rarely used. In this work, we propose ELF-BO, an algorithm that uses the objective evaluation latency to headstart the computation of the next suggestion, allowing for fully Bayesian optimization without incurring substantial decision-time costs. This is done by sampling from the hyperparameter posterior while the objective is being evaluated, only requiring reweighting of the samples once the objective value is observed. Across synthetic functions and real-world applications, we show that ELF-BO matches the performance of fully Bayesian methods while only incurring decision latency on par with or better than standard BO. Thus, ELF-BO makes fully Bayesian optimization practical in real-world use cases.