CellSpatialGraph: Integrate hierarchical phenotyping and graph modeling to characterize spatial architecture in tumor microenvironment on digital pathology

We present CellSpatialGraph, an integrated clustering and graph-based framework, to investigate the cellular spatial structure. Due to the lack of a clear understanding of the cell subtypes in the tumor microenvironment, unsupervised learning is applied to uncover cell phenotypes. Then, we build local cell graphs, referred to as supercells, to model the cell-to-cell relationships at a local scale. After that, we apply clustering again to identify the subtypes of supercells. In the end, we build a global graph to summarize supercell-to-supercell interactions, from which we extract features to classify different disease subtypes.