Equivariant Flow Matching with Hybrid Probability Transport for 3D Molecule Generation

Yuxuan Song, Jingjing Gong, Minkai Xu, Ziyao Cao, Yanyan Lan, Stefano Ermon, Hao Zhou, Wei-Ying Ma

Keywords: Drug Design, Molecule Generation, Deep Learning, Computational Biology

Abstract:

The generation of 3D molecules requires simultaneously deciding the categorical features (atom types) and continuous features (atom coordinates). Deep generative models, especially Diffusion Models (DMs), have demonstrated effectiveness in generating feature-rich geometries. However, existing DMs typically suffer from unstable probability dynamics with inefficient sampling speed. In this paper, we introduce geometric flow matching, which enjoys the advantages of both equivariant modeling and stabilized probability dynamics.
More specifically, we propose a hybrid probability path where the coordinates probability path is regularized by an equivariant optimal transport, and the information between different modalities is aligned. Experimentally, the proposed method could consistently achieve better performance on multiple molecule generation benchmarks with 4.75$\times$ speed up of sampling on average.

Submission Number: 5224