A masked generative graph representation learning framework empowering precise spatial domain identification

However, the sparsity of ST data leads to poor usage of gene expression and spatial information, resulting in the embeddings that are not well represented and challenging for downstream analyses. Here, we introduced GSG, a generative self-supervised representation learning framework for ST data that leverages a masking mechanism to learn informative representations.

For spatial domain identification, GSG consistently outperformed state-of-the-art methods across benchmarking datasets, regardless of sequencing platforms. In addition, we applied GSG to an in-house human fetal heart dataset, revealing anatomically coherent spatial domains and identifying APCDD1 as an endocardial-specific marker potentially involved in congenital heart disease. Our results showcase GSG's superiority and underscore its valuable contributions to advancing ST analysis.