Geometric Deep Learning

Many problems in chemistry and biology involve data with geometric structure: molecules have 3D coordinates, proteins have orientations, and physical forces transform predictably under rotation. Geometric deep learning addresses this by building symmetries directly into model architectures. Notes in this section cover equivariant networks, focusing on SO(3) and SE(3) equivariance achieved through group representation theory and spherical harmonics. The goal is to understand how these models work and why the symmetry constraints matter for data efficiency and physical correctness.

Machine Learning Fundamentals

SE(3)-Transformer architecture showing invariant attention weights modulating equivariant value messages on a 3D point cloud

SE(3)-Transformers: Equivariant Attention for 3D Data

Fuchs et al. introduce the SE(3)-Transformer, which combines self-attention with SE(3)-equivariance for 3D point clouds and graphs. Invariant attention weights modulate equivariant value messages from tensor field networks, resolving angular filter constraints while enabling data-adaptive, anisotropic processing.

Machine Learning Fundamentals

Comparison of planar CNN (translation only) versus spherical CNN (SO(3)-equivariant) showing how filters rotate on the sphere

Spherical CNNs: Rotation-Equivariant Networks on the Sphere

Cohen et al. introduce Spherical CNNs that achieve SO(3)-equivariance by defining cross-correlation on the sphere and rotation group, computed efficiently via generalized FFT algorithms from non-commutative harmonic analysis.

Machine Learning Fundamentals

Comparison of standard 3D CNN versus 3D Steerable CNN for handling rotational symmetry

3D Steerable CNNs: Rotationally Equivariant Features

Weiler et al.’s NeurIPS 2018 paper introducing 3D Steerable CNNs that achieve SE(3) equivariance through group representation theory and spherical harmonic convolution kernels, eliminating the need for rotational data augmentation and improving data efficiency for scientific applications with rotational symmetry like molecular and protein structures.