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.

Fine-tuning large pre-trained foundation models, such as the 175B GPT-3, has become the prevailing approach for downstream tasks. While parameter-efficient fine-tuning methods have been proposed and proven effective without retraining all model parameters, their performance is limited by the capacity of incremental modules, especially under constrained parameter budgets. To overcome this challenge, we propose CAPABOOST, a simple yet effective strategy that enhances model capacity by leveraging low-rank updates through parallel weight modules in target layers. By applying static random masks to the shared weight matrix, CAPABOOST constructs a diverse set of weight matrices, effectively increasing the rank of incremental weights without adding parameters. Notably, our approach can be seamlessly integrated into various existing parameter-efficient fine-tuning methods. We extensively validate the efficacy of CAPABOOST through experiments on diverse downstream tasks, including natural language understanding, question answering, and image classification. Our results demonstrate significant improvements over baselines, without incurring additional computation or storage costs. We will make our code and benchmark publicly available.