HyperNiche: Learning Heterophilic Cellular Niches with Hypergraph Neural Networks (opens in new tab)

We propose HyperNiche, a hypergraph-based framework for modeling higher-order, heterogeneous cellular niches from spatial transcriptomics data. Unlike conventional graph-based methods that rely on pairwise similarity and tend to produce homogeneous clusters, HyperNiche learns anchor-centered hyperedges through a compatibility-driven mechanism that captures both homophilic and heterophilic relationships among cells. By decoupling node roles into anchor and member representations and integratin...