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Diagnosing and fixing common problems in Bayesian optimization for molecule design

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arxiv 2406.07709 v2 pith:CAS53RSX submitted 2024-06-11 cs.LG physics.chem-phstat.ML

Diagnosing and fixing common problems in Bayesian optimization for molecule design

classification cs.LG physics.chem-phstat.ML
keywords designbayesianmoleculeoptimizationperformanceableachieveacquisition
verification ladder T0 review T1 audit T2 compute T3 formal T4 reserved
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Bayesian optimization (BO) is a principled approach to molecular design tasks. In this paper we explain three pitfalls of BO which can cause poor empirical performance: an incorrect prior width, over-smoothing, and inadequate acquisition function maximization. We show that with these issues addressed, even a basic BO setup is able to achieve the highest overall performance on the PMO benchmark for molecule design (Gao et al 2022). These results suggest that BO may benefit from more attention in the machine learning for molecules community.

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