NeVAE: A Deep Generative Model for Molecular Graphs
This work addresses the challenge of generating and optimizing molecular structures for drug discovery or materials science, representing a domain-specific advancement.
The paper tackled the problem of generating molecular graphs with unique structural properties, proposing a variational autoencoder that can generate molecules with spatial coordinates and optimize them for specific properties, achieving property values 121% higher than state-of-the-art methods.
Deep generative models have been praised for their ability to learn smooth latent representation of images, text, and audio, which can then be used to generate new, plausible data. However, current generative models are unable to work with molecular graphs due to their unique characteristics-their underlying structure is not Euclidean or grid-like, they remain isomorphic under permutation of the nodes labels, and they come with a different number of nodes and edges. In this paper, we first propose a novel variational autoencoder for molecular graphs, whose encoder and decoder are specially designed to account for the above properties by means of several technical innovations. Moreover, in contrast with the state of the art, our decoder is able to provide the spatial coordinates of the atoms of the molecules it generates. Then, we develop a gradient-based algorithm to optimize the decoder of our model so that it learns to generate molecules that maximize the value of certain property of interest and, given a molecule of interest, it is able to optimize the spatial configuration of its atoms for greater stability. Experiments reveal that our variational autoencoder can discover plausible, diverse and novel molecules more effectively than several state of the art models. Moreover, for several properties of interest, our optimized decoder is able to identify molecules with property values 121% higher than those identified by several state of the art methods based on Bayesian optimization and reinforcement learning