SGAC: A Graph Neural Network Framework for Imbalanced and Structure-Aware AMP Classification

Abstract

Classifying antimicrobial peptides(AMPs) from the vast array of peptides mined from metagenomic sequencing data is a significant approach to addressing the issue of antibiotic resistance. However, current AMP classification methods, primarily relying on sequence-based data, neglect the spatial structure of peptides, thereby limiting the accurate classification of AMPs. Additionally, the number of known AMPs is significantly lower than that of non-AMPs, leading to imbalanced datasets that reduce predictive accuracy for AMPs. To alleviate these two limitations, we first employ Omegafold to predict the three-dimensional spatial structures of AMPs and non-AMPs, constructing peptide graphs based on the amino acids' C$_α$ positions. Building upon this, we propose a novel classification model named Spatial GNN-based AMP Classifier (SGAC). Our SGAC model employs a graph encoder based on Graph Neural Networks (GNNs) to process peptide graphs, generating high-dimensional representations that capture essential features from the three-dimensional spatial structure of amino acids. Then, to address the inherent imbalanced datasets, SGAC first incorporates Weight-enhanced Contrastive Learning, which clusters similar peptides while ensuring separation between dissimilar ones, using weighted contributions to emphasize AMP-specific features. Furthermore, SGAC employs Weight-enhanced Pseudo-label Distillation to dynamically generate high-confidence pseudo labels for ambiguous peptides, further refining predictions and promoting balanced learning between AMPs and non-AMPs. Experiments on publicly available AMP and non-AMP datasets demonstrate that SGAC significantly outperforms traditional sequence-based methods and achieves state-of-the-art performance among graph-based models, validating its effectiveness in AMP classification.