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

Machine Learning 2024-09-24 v3 Biomolecules

Abstract

We present Symphony, an E(3)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)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.

Cite

@article{arxiv.2311.16199,
  title  = {Symphony: Symmetry-Equivariant Point-Centered Spherical Harmonics for 3D Molecule Generation},
  author = {Ameya Daigavane and Song Kim and Mario Geiger and Tess Smidt},
  journal= {arXiv preprint arXiv:2311.16199},
  year   = {2024}
}

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Published at ICLR 2024

R2 v1 2026-06-28T13:33:14.483Z