Brain Network Analysis with Graph Neural Network

Mapping the connectome of the human brain using structural or functional connectivity has become one of the most pervasive paradigms for neuroimaging analysis. Recently, Graph Neural Networks (GNNs) motivated by geometric deep learning have attracted broad interest due to their established power for modeling complex networked data. Despite their superior performance in many fields, there has not yet been a systematic tutorial on practical GNNs for brain network analysis. In this tutorial, we will cover (1) the summarization of brain network construction pipelines for both structural and functional neuroimaging modalities; (2) the modularization of fundamental GNN designs for brain networks, and a set of recommendations on general effective recipes based on empirical observations; (3) hands-on instructions on our out-of-box Python package BrainGB, which is available at https://braingb.us with models, tutorials, and examples; (4) more advanced GNN designs and training strategies for brain network analysis and future directions. We believe this tutorial can bridge researchers in neuroscience and machine learning/deep learning and offer insights for future research in this novel and promising direction.