Transformer and Snowball Graph Convolution Learning for Biomedical Graph Classification

Graph or network has been widely used for describing and modeling complex systems in biomedicine. Deep learning methods, especially graph neural networks (GNNs), have been developed to learn and predict with such structured data. In this paper, we proposed a novel transformer and snowball encoding networks (TSEN) for biomedical graph classification, which introduced transformer architecture with graph snowball connection into GNNs for learning whole-graph representation. TSEN combined graph snowball connection with graph transformer by snowball encoding layers, which enhanced the power to capture multi-scale information and global patterns to learn the whole-graph features. On the other hand, TSEN also used snowball graph convolution as position embedding in transformer structure, which was a simple yet effective method for capturing local patterns naturally. Results of experiments using four graph classification datasets demonstrated that TSEN outperformed the state-of-the-art typical GNN models and the graph-transformer based GNN models.