Enhancing Graph Contrastive Learning for Protein Graphs from Perspective of Invariance

Graph Contrastive Learning (GCL) improves Graph Neural Network (GNN)-based protein representation learning by enhancing its generalization and robustness. Existing GCL approaches for protein representation learning rely on 2D topology, where graph augmentation is solely based on topological features, ignoring the intrinsic biological properties of proteins. Besides, 3D structure-based protein graph augmentation remains unexplored, despite proteins inherently exhibiting 3D structures. To bridge this gap, we propose novel biology-aware graph augmentation strategies from the perspective of invariance and integrate them into the protein GCL framework. Specifically, we introduce Functional Community Invariance (FCI)-based graph augmentation, which employs spectral constraints to preserve topology-driven community structures while incorporating residue-level chemical similarity as edge weights to guide edge sampling and maintain functional communities. Furthermore, we propose 3D Protein Structure Invariance (3-PSI)based graph augmentation, leveraging dihedral angle perturbations and secondary structure rotations to retain critical 3D structural information of proteins while diversifying graph views. Extensive experiments on four different protein-related tasks demonstrate the superiority of our proposed GCL protein representation learning framework.