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Symphony: Symmetry-Equivariant Point-Centered Spherical Harmonics for 3D Molecule Generation

About

We present Symphony, an $E(3)$-equivariant autoregressive generative model for 3D molecular geometries that iteratively builds a molecule from molecular fragments. Existing autoregressive models such as G-SchNet and G-SphereNet for molecules utilize rotationally invariant features to respect the 3D symmetries of molecules. In contrast, Symphony uses message-passing with higher-degree $E(3)$-equivariant features. This allows a novel representation of probability distributions via spherical harmonic signals to efficiently model the 3D geometry of molecules. We show that Symphony is able to accurately generate small molecules from the QM9 dataset, outperforming existing autoregressive models and approaching the performance of diffusion models.

Ameya Daigavane, Song Kim, Mario Geiger, Tess Smidt• 2023

Related benchmarks

TaskDatasetResultRank
3D Molecule GenerationQM9 (test)
Validity83.5
55
Molecule GenerationQM9 (test)
Uniqueness97.98
11
Fragment CompletionQM9 (train)
VCR98.53
4
Fragment CompletionQM9 (test)
Valid Completion Rate98.66
4
3D Molecular Generative ModelingQM9
All Atoms Connected99.92
4
Molecular GenerationQM9
MMD Bond Lengths (C-H: 1.0)0.0739
4
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