GTPLM-GO: Enhancing Protein Function Prediction Through Dual-Branch Graph Transformer and Protein Language Model Fusing Sequence and Local–Global PPI Information

Currently, protein-protein interaction (PPI) networks have become an essential data source for protein function prediction. However, methods utilizing graph neural networks (GNNs) face significant challenges in modeling PPI networks. A primary issue is over-smoothing, which occurs when multiple GNN layers are stacked to capture global information. This architectural limitation inherently impairs the integration of local and global information within PPI networks, thereby limiting the accuracy of protein function prediction. To effectively utilize information within PPI networks, we propose GTPLM-GO, a protein function prediction method based on a dual-branch Graph Transformer and protein language model. The dual-branch Graph Transformer achieves the collaborative modeling of local and global information in PPI networks through two branches: a graph neural network and a linear attention-based Transformer encoder. GTPLM-GO integrates local-global PPI information with the functional semantic encoding constructed by the protein language model, overcoming the issue of inadequate information extraction in existing methods. Experimental results demonstrate that GTPLM-GO outperforms advanced network-based and sequence-based methods on PPI network datasets of varying scales.