Pushing the Limits of All-Atom Geometric Graph Neural Networks: Pre-Training, Scaling, and Zero-Shot Transfer

Abstract

The ability to construct transferable descriptors for molecular and biological systems has broad applications in drug discovery, molecular dynamics, and protein analysis. Geometric graph neural networks (Geom-GNNs) utilizing all-atom information have revolutionized atomistic simulations by enabling the prediction of interatomic potentials and molecular properties. Despite these advances, the application of all-atom Geom-GNNs in protein modeling remains limited due to computational constraints. In this work, we first demonstrate the potential of pre-trained Geom-GNNs as zero-shot transfer learners, effectively modeling protein systems with all-atom granularity. Through extensive experimentation to evaluate their expressive power, we characterize the scaling behaviors of Geom-GNNs across self-supervised, supervised, and unsupervised setups. Interestingly, we find that Geom-GNNs deviate from conventional power-law scaling observed in other domains, with no predictable scaling principles for molecular representation learning. Furthermore, we show how pre-trained graph embeddings can be directly used for analysis and synergize with other architectures to enhance expressive power for protein modeling.