3D Equivariant Molecular Graph Pretraining

• URL: http://arxiv.org/abs/2207.08824v2
• Date: Wed, 20 Jul 2022 14:41:17 GMT
• Title: 3D Equivariant Molecular Graph Pretraining
• Authors: Rui Jiao, Jiaqi Han, Wenbing Huang, Yu Rong, Yang Liu
• Abstract summary: We tackle 3D molecular pretraining in a complete and novel sense. We first propose to adopt an equivariant energy-based model as the backbone for pretraining, which enjoys the merit of fulfilling the symmetry of 3D space. We evaluate our model pretrained from a large-scale 3D dataset GEOM-QM9 on two challenging 3D benchmarks: MD17 and QM9.
• Score: 42.957880677779556
• License: http://creativecommons.org/licenses/by-sa/4.0/
• Abstract: Pretraining molecular representation models without labels is fundamental to various applications. Conventional methods mainly process 2D molecular graphs and focus solely on 2D tasks, making their pretrained models incapable of characterizing 3D geometry and thus defective for downstream 3D tasks. In this work, we tackle 3D molecular pretraining in a complete and novel sense. In particular, we first propose to adopt an equivariant energy-based model as the backbone for pretraining, which enjoys the merit of fulfilling the symmetry of 3D space. Then we develop a node-level pretraining loss for force prediction, where we further exploit the Riemann-Gaussian distribution to ensure the loss to be E(3)-invariant, enabling more robustness. Moreover, a graph-level noise scale prediction task is also leveraged to further promote the eventual performance. We evaluate our model pretrained from a large-scale 3D dataset GEOM-QM9 on two challenging 3D benchmarks: MD17 and QM9. The experimental results support the better efficacy of our method against current state-of-the-art pretraining approaches, and verify the validity of our design for each proposed component.

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