Elucidating Spatial Complex Structures from Mass Spectrometry Imaging with Deep Multimodal Model

Spatial mass spectrometry imaging (SMSI) technology has enabled the characterization of biomolecule patterns within the tissue microenvironment, yet its analyses suffer from substantial noise. The lack of effective methods for exploiting multi-view features (e.g., spatial location) has hindered their elucidation ability for tissue heterogeneity. Here, we propose MSG, a multimodal modal that integrates histology, spatial location, and MSI data, in deciphering tissue structure by graph neural network. Specifically, MSG learns low-dimensional representations by aggregating histomorphological features from neighboring tiles via graph attention autoencoder. MSG outperforms other methods in identifying spatial domains and denoising data. The subsequent domain-guided differential expression analysis of the denoised data enables the identification of ions with significantly enriched patterns within the recognized domains. MSG exhibits its versatility in handling SMSI data from various platforms.