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Life sciences · Preprint
arXiv · October 8, 2026
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Bayesian Optimization (BO) is a popular method for efficiently optimizing expensive black-box objectives. However, BO utilizing standard Gaussian Processes is ill-suited for doubly stochastic Cox Processes that are often used in spatio-temporal problem spaces. We introduce INLA-SPDE Spatio-Temporal Bayesian Optimization (ISBO): the first scalable BO framework for spatio-temporal data, that models the log-intensity with a Log-Gaussian Cox Process(LGCP) and performs inference via Integrated Nested Laplace Approximation and Stochastic Partial Differential Equations (INLA-SPDE) approach. Using a Matern field on meshes yields a sparse Gaussian Markov Random Field, where INLA provides fast and accurate posterior inference throughout sequential optimization. ISBO stably locates high-intensity regions and the peak of the latent intensity with minimal evaluations. A time-varying Upper Confidence Bound acquisition with masking avoids revisits, while penalized-complexity priors regularize early rounds. Experiments on synthetic and real-world spatio-temporal datasets show accurate peak discovery, intensity recovery, and substantial speedups over an RKHS-based baseline, positioning ISBO as a practical choice for BO with point-process data.