Enhancing Generalizability in Molecular Conformation Generation with METRIZATION-Informed Geometric Diffusion Pretraining

Abstract

Diffusion-based generative models have recently excelled in generating molecular conformations but struggled with the generalization issue -- models trained on one dataset may produce meaningless conformations on out-of-distribution molecules. On the other hand, distance geometry serves as a generalizable tool for the traditional computational chemistry methods of molecular conformation, which is predicated on the assumption that it is possible to adequately define the set of all potential conformations of any non-rigid molecular system using purely geometric constraints. In this work, we for the first time explicitly incorporate distance geometry constraints into pretraining phase of diffusion-based molecular generation models to improve the generalizability. Inspired by the classical distance geometry solution designed for solving the molecular distance geometry problem, we propose MiGDiff, a Metrization-Informed Geometric Diffusion framework. MiGDiff injects distance geometry constraints by pretraining the deep geometric diffusion backbone within the Metrization sampling approach, yielding a "Metrization-driven pretraining + Data-driven finetuning" paradigm. Experimental results demonstrate that MiGDiff outperforms state-of-the-art methods and possesses strong generalization capabilities, particularly on generating previously unseen molecules, revealing the vast untapped potential of combining traditional computational methods with deep generative models for 3D molecular generation.