Glycan immunogenicity prediction based on Graph neural network

Glycans play important roles in a great variety of biological processes, and these roles are closely determined by the details of their structures. It becomes possible to acquire hidden features from glycan structures using deep learning method with the great progress in recent years. Unlike the linear chain of proteins and DNAs, branching is a unique feature of glycan structures, which makes it very difficult to directly apply deep learning models on glycans. Thus, how to comprehensively and efficiently describe glycans and use them as input to deep learning models still remains challenging. Here, a graph neural network (GNN) called GlyNet was used to obtain high-dimensional representation of glycans and predict their immunogenicity. Our method was applied in SugarBase, and it works more superiorly than the state-of-art method with accuracy increased from 91.7% to 95.6%.