Constrained Bayesian Optimization for Automatic Chemical Design

Ryan-Rhys Griffiths, José Miguel Hernández-Lobato

Abstract: Automatic Chemical Design provides a framework for generating novel molecules with optimized molecular properties. The current model suffers from the pathology that it tends to produce invalid molecular structures. By reformulating the search procedure as a constrained Bayesian optimization problem, we showcase improvements in both the validity and quality of the generated molecules. We demonstrate that the model consistently produces novel molecules ranking above the 90th percentile of the distribution over training set scores across a range of objective functions. Importantly, our method suffers no degradation in the complexity or the diversity of the generated molecules.

Keywords: Bayesian Optimization, Generative Models

Community Implementations: [ 1 code implementation](https://www.catalyzex.com/paper/arxiv:1709.05501/code)