A graph neural network-based spatial multi-omics data integration method for deciphering spatial domains.

Recent advancements of spatial sequencing technologies enable measurements of transcriptomic and epigenomic profiles within the same tissue slice, providing an unprecedented opportunity to understand cellular microenvironments. However, effective approaches for the integrative analysis of such spatial multi-omics data are lacking. Here, we propose SpaMI, a graph neural network-based model which extract features by contrastive learning strategy for each omics and integrate different omics by an attention mechanism to integrate spatial multi-omics data. We applied SpaMI to both simulated data and three real spatial multi-omics datasets derived from the same tissue slices, including spatial epigenome-transcriptome and transcriptome-proteome data. By comparing SpaMI with the state-of-the-art methods on simulation and real datasets, we demonstrate the superior performance of SpaMI in identifying spatial domain and data denoising.