Boosting Spatially Resolved Transcriptomics Data Clustering via Multi-View Information Rebalance Learning

Spatially resolved transcriptomics (SRT) facilitates the simultaneous acquisition of gene expression profiles, spatial location, and histology images for spatial clustering analysis, providing transformative insights into cellular interactions and the underlying mechanisms of disease progression. Despite the success of existing research in spatial clustering tasks, most methods overlook the information imbalance arising among spots in intra- and inter-modal communication due to insufficient sequencing depth and modality discrepancies. To this end, we propose a novel multi-view information rebalance learning method for SRT data clustering, referred to as MIRL. Specifically, we construct hypergraphs for the gene and histological image modalities and leverage hypergraph neural networks to learn the hypergraph features, which helps mitigate the propagation of intra-modal information imbalance by capturing higher-order interactions among multiple spots, rather than relying solely on pairwise relationships in traditional feature graphs. To enhance the global coordination among spots and the interrelations between features across modalities, we perform intra-modal adaptive fusion of modality-specific hypergraph features and spatial features, followed by cross-modal integration. Furthermore, adaptive reconstruction of the cross-modal heterogeneous graph is employed to rebalance inter-modal information flow associated with pseudo-labels, ensuring more reliable information extraction by alleviating the impact of incorrect heterogeneous negative edges connections through the construction of hypergraph edges. Extensive experimental results demonstrate that the proposed MIRL achieves competitive performance in spatial domain identification compared to other state-of-the-art ones.