Spatially Resolved Transcriptomics Data Clustering with Tailored Spatial-scale Modulation

Abstract

Spatial transcriptomics, comprising spatial location and high-throughput gene expression information, provides revolutionary insights into disease discovery and cellular evolution. Spatial transcriptomic clustering, which pinpoints distinct spatial domains within tissues, reveals cellular interactions and enhances our understanding of the intricate architecture of tissues. Existing methods typically construct spatial graphs using a static radius based on spatial coordinates, which hinders the accurate identification of spatial domains and complicates the precise partitioning of boundary nodes within clusters. To address this issue, we introduce a novel spatially resolved transcriptomics data clustering network (TSstc). Specifically, we employ a tailored spatial-scale modulation approach, constructing different spatial graphs incrementally as the radius of the spatial domain expands, and a Spatiality-Aware Sampling (SAS) strategy is proposed to aggregate node representations by considering the spatial dependencies between spots. We then use GCN encoders to learn gene embedding with gene graph and multiple spatial embeddings with spatial graphs. During training, we incorporate cross-view correlation-based tailored spatial regularization constraints to preserve high-quality neighbor relationships across spatial embeddings at different scales. Finally, a zero-inflated negative binomial model is utilized to capture the global probability distribution of gene expression profiles. Extensive experimental results demonstrate that our approach surpasses existing state-of-the-art methods in clustering tasks and related downstream applications.