Unveiling Fine-scale Spatial Structures and Amplifying Gene Expression Signals in Ultra-Large ST slices with HERGAST

Abstract We propose HERGAST, a system for spatial structure identification and signal amplification in ultra-large-scale and ultra-high-resolution spatial transcriptomics data. To handle ultra-large data, we devise a Divide-Iterate-Conque strategy and construct a heterogeneous graph network to incorporate both local and global spatial relationships. HERGAST's high-precision spatial clustering enabled finding SPP1+ macrophages intermingled in tumors in colorectal cancer, while the enhanced gene expression signal enabled discovering unique spatial expression pattern of key genes in breast cancer.