On Accelerating Diffusion-based Molecular Conformation Generation in SE(3)-invariant Space
Abstract
Diffusion-based generative models in SE(3)-invariant space have demonstrated promising performance in molecular conformation generation, but typically require solving stochastic differential equations (SDEs) with thousands of update steps. Till now, it remains unclear how to effectively accelerate this procedure explicitly in SE(3)-invariant space, which greatly hinders its wide application in the real world. In this paper, we systematically study the diffusion mechanism in SE(3)-invariant space via the lens of approximate errors induced by existing methods. Thereby, we develop more precise approximate in SE(3) in the context of projected differential equations. Theoretical analysis is further provided as well as empirical proof relating hyper-parameters with such errors. Altogether, we propose a novel acceleration scheme for generating molecular conformations in SE(3)-invariant space. Experimentally, our scheme can generate high-quality conformations with 50x--100x speedup compared to existing methods.
Cite
@article{arxiv.2310.04915,
title = {On Accelerating Diffusion-based Molecular Conformation Generation in SE(3)-invariant Space},
author = {Zihan Zhou and Ruiying Liu and Tianshu Yu},
journal= {arXiv preprint arXiv:2310.04915},
year = {2024}
}
Comments
We are currently developing a new manuscript that significantly expands upon and integrates the research presented here. The forthcoming paper includes broader analyses and more comprehensive findings, rendering the current version obsolete. We believe this decision will contribute to a clearer and more consolidated presentation of our research findings