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arXiv · 2508.14072

Multi-Objective Bayesian Optimization with Independent Tanimoto Kernel Gaussian Processes for Diverse Pareto Front Exploration

Anabel Yong
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Abstract

We present GP-MOBO, a novel multi-objective Bayesian Optimization algorithm that advances the state-of-the-art in molecular optimization. Our approach integrates a fast minimal package for Exact Gaussian Processes (GPs) capable of efficiently handling the full dimensionality of sparse molecular fingerprints without the need for extensive computational resources. GP-MOBO consistently outperforms traditional methods like GP-BO by fully leveraging fingerprint dimensionality, leading to the identification of higher-quality and valid SMILES. Moreover, our model achieves a broader exploration of the chemical search space, as demonstrated by its superior proximity to the Pareto front in all tested scenarios. Empirical results from the DockSTRING dataset reveal that GP-MOBO yields higher geometric mean values across 20 Bayesian optimization iterations, underscoring its effectiveness and efficiency in addressing complex multi-objective optimization challenges with minimal computational overhead.

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Anabel Yong. 2025-08-12. Multi-Objective Bayesian Optimization with Independent Tanimoto Kernel Gaussian Processes for Diverse Pareto Front Exploration. https://arxiv.org/abs/2508.14072

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