Graph Neural Network approaches for single-cell data: A recent overview

Abstract

Graph Neural Networks (GNN) are reshaping our understanding of biomedicine and diseases by revealing the deep connections among genes and cells. As both algorithmic and biomedical technologies have advanced significantly, we're entering a transformative phase of personalized medicine. While pioneering tools like Graph Attention Networks (GAT) and Graph Convolutional Neural Networks (Graph CNN) are advancing graph-based learning, the rise of single-cell sequencing techniques is reshaping our insights on cellular diversity and function. Numerous studies have combined GNNs with single-cell data, showing promising results. In this work, we highlight the GNN methodologies tailored for single-cell data over the recent years. We outline the diverse range of graph deep learning architectures that center on GAT methodologies. Furthermore, we underscore the several objectives of GNN strategies in single-cell data contexts, ranging from cell-type annotation, data integration and imputation, gene regulatory network reconstruction, clustering and many others. This review anticipates a future where GNNs become central to single-cell analysis efforts, particularly as vast omics datasets are continuously generated and the interconnectedness of cells and genes enhances our depth of knowledge in biomedicine.