StereoMM: a graph fusion model for integrating spatial transcriptomic data and pathological images.

Spatial omics technologies, generating high-throughput and multimodal data, have necessitated the development of advanced data integration methods to facilitate comprehensive biological and clinical treatment discoveries. Based on the cross-attention concept, we developed an AI learning based toolchain called StereoMM, a graph based fusion model that can incorporate omics data such as gene expression, histological images, and spatial location. StereoMM uses an attention module for omics data interaction and a graph autoencoder to integrate spatial positions and omics data in a self-supervised manner. Applying StereoMM across various cancer types and platforms has demonstrated its robust capability. StereoMM outperforms competitors in identifying spatial regions reflecting tumour progression and shows promise in classifying colorectal cancer patients into deficient mismatch repair and proficient mismatch repair groups. The comprehensive inter-modal integration and efficiency of StereoMM enable researchers to construct spatial views of integrated multimodal features efficiently, advancing thorough tissue and patient characterization.