MGCVAE: Multi-Objective Inverse Design via Molecular Graph Conditional Variational Autoencoder

Abstract

The ultimate goal of various fields is to directly generate molecules with desired properties, such as water-soluble molecules in drug development and molecules suitable for organic light-emitting diodes or photosensitizers in the field of development of new organic materials. This study proposes a molecular graph generative model based on an autoencoder for the de novo design. The performance of the molecular graph conditional variational autoencoder (MGCVAE) for generating molecules with specific desired properties was investigated by comparing it to a molecular graph variational autoencoder (MGVAE). Furthermore, multi-objective optimization for MGCVAE was applied to satisfy the two selected properties simultaneously. In this study, two physical properties, calculated log(P) and molar refractivity, were used as optimization targets for designing de novo molecules. Consequently, it was confirmed that among the generated molecules, 25.89% of the optimized molecules were generated in MGCVAE compared to 0.66% in MGVAE. This demonstrates that MGCVAE effectively produced drug-like molecules with two target properties. The results of this study suggest that these graph-based data-driven models are an effective method for designing new molecules that fulfill various physical properties.