Molecule Generation by Principal Subgraph Mining and Assembling

Part of Advances in Neural Information Processing Systems 35 (NeurIPS 2022) Main Conference Track

Bibtex Paper Supplemental


Xiangzhe Kong, Wenbing Huang, Zhixing Tan, Yang Liu


Molecule generation is central to a variety of applications. Current attention has been paid to approaching the generation task as subgraph prediction and assembling. Nevertheless, these methods usually rely on hand-crafted or external subgraph construction, and the subgraph assembling depends solely on local arrangement. In this paper, we define a novel notion, principal subgraph that is closely related to the informative pattern within molecules. Interestingly, our proposed merge-and-update subgraph extraction method can automatically discover frequent principal subgraphs from the dataset, while previous methods are incapable of. Moreover, we develop a two-step subgraph assembling strategy, which first predicts a set of subgraphs in a sequence-wise manner and then assembles all generated subgraphs globally as the final output molecule. Built upon graph variational auto-encoder, our model is demonstrated to be effective in terms of several evaluation metrics and efficiency, compared with state-of-the-art methods on distribution learning and (constrained) property optimization tasks.