Do we need equivariant models for molecule generation?

Ewa Nowara, Joshua A Rackers, Patricia Adriana Suriana, Pan Kessel, Max W Shen, Andrew Martin Watkins, Michael Maser

Keywords: Machine Learning, Equivariant Models, Drug Discovery, Generative Models, 3D Generation, Voxel Structures, Molecules

TL;DR: We evaluate whether data augmentation is sufficient to learn equivariance in 3D molecular generation, finding that while CNNs can learn equivariance for denoising, robust equivariant generation requires larger models, more data, and longer training.

Abstract:

Deep generative models are increasingly used for molecular discovery, with most recent approaches relying on equivariant graph neural networks (GNNs) under the assumption that explicit equivariance is essential for generating high-quality 3D molecules. However, these models are complex, difficult to train, and scale poorly.

We investigate whether non-equivariant convolutional neural networks (CNNs) trained with rotation augmentations can learn equivariance and match the performance of equivariant models. We derive a loss decomposition that separates prediction error from equivariance error, and evaluate how model size, dataset size, and training duration affect performance across denoising, molecule generation, and property prediction. To our knowledge, this is the first study to analyze learned equivariance in generative tasks.

Submission Number: 16