Covering Multiple Objectives with a Small Set of Solutions Using Bayesian Optimization

Natalie Maus; Kyurae Kim; Yimeng Zeng; Haydn Thomas Jones; Fangping Wan; Marcelo Der Torossian Torres; Cesar de la Fuente-Nunez; Jacob R. Gardner

arXiv · 2501.19342

Covering Multiple Objectives with a Small Set of Solutions Using Bayesian Optimization

Natalie Maus·Kyurae Kim·Yimeng Zeng·Haydn Thomas Jones·Fangping Wan·Marcelo Der Torossian Torres·Cesar de la Fuente-Nunez·Jacob R. Gardner

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Abstract

In multi-objective black-box optimization, the goal is typically to find solutions that optimize a set of $T$ black-box objective functions, $f_1, \ldots f_T$, simultaneously. Traditional approaches often seek a single Pareto-optimal set that balances trade-offs among all objectives. In contrast, we consider a problem setting that departs from this paradigm: finding a small set of $K < T$ solutions, that collectively "cover" the $T$ objectives. A set of solutions is defined as "covering" if, for each objective $f_1, \ldots f_T$, there is at least one good solution. A motivating example for this problem setting occurs in drug design. For example, we may have $T$ pathogens and aim to identify a set of $K < T$ antibiotics such that at least one antibiotic can be used to treat each pathogen. This problem, known as coverage optimization, has yet to be tackled with the Bayesian optimization (BO) framework. To fill this void, we develop Multi-Objective Coverage Bayesian Optimization (MOCOBO), a BO algorithm for solving coverage optimization. Our approach is based on a new acquisition function reminiscent of expected improvement in the vanilla BO setup. We demonstrate the performance of our method on high-dimensional black-box optimization tasks, including applications in peptide and molecular design. Results show that the coverage of the $K < T$ solutions found by MOCOBO matches or nearly matches the coverage of $T$ solutions obtained by optimizing each objective individually. Furthermore, in in vitro experiments, the peptides found by MOCOBO exhibited high potency against drug-resistant pathogens, further demonstrating the potential of MOCOBO for drug discovery. All of our code is publicly available at the following link: https://github.com/nataliemaus/mocobo.

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Natalie Maus, Kyurae Kim, Yimeng Zeng, Haydn Thomas Jones, Fangping Wan, Marcelo Der Torossian Torres, Cesar de la Fuente-Nunez, Jacob R. Gardner. 2025-01-31. Covering Multiple Objectives with a Small Set of Solutions Using Bayesian Optimization. https://arxiv.org/abs/2501.19342

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