Identifying batch-integrated domains from spatial transcriptomics via graph autoencoder with contrastive learning based on cross-modality and data augmentation

Spatially resolved transcriptomics (SRT) allows for the comprehensive profiling of gene expression while preserving spatial context, advancing the study of tissue architecture. However, existing computational approaches still face key limitations, particularly the insufficient exploitation of histology information and the lack of cross-modal meaningful contrastive strategies for biological analyses. To overcome these challenges, we propose GCAST, a graph contrastive autoencoder framework for spatial transcriptomics that seamlessly integrates multimodal SRT data. GCAST adopts a self-supervised strategy to derive biologically meaningful representations directly from histology images when available. GCAST constructs dual graph views based on data augmentation and introduces a novel contrastive learning designed to leverage histology-weighted and gene-weighted features and improve biological interpretability. In addition, GCAST employs a block-diagonal graph construction to automatically align multiple datasets, achieving batch-effect correction without manual intervention. The framework not only captures spatial gene expression patterns to identify tissue domains but also adapts to datasets with or without histological images and supports the integration of multiple datasets for joint analyses. Overall, GCAST provides a unified and biologically informed framework that has the potential to facilitate deeper analyses of spatial transcriptomics.