STAHD: a scalable and accurate method to detect spatial domains in high-resolution spatial transcriptomics data

Motivation Spatial transcriptomics (ST) enables the study of spatial heterogeneity in tissues. How- ever, current methods struggle with large-scale, high-resolution data, leading to reduced efficiency and accuracy in detecting spatial domains. A scalable, precise solution is urgently needed. Results We present STAHD, a scalable and efficient framework for spatial domain detection in ST data. Combining a graph attention autoencoder with multilevel k-way graph partitioning, STAHD de- composes large graphs into compact subgraphs and generates low-dimensional embeddings. This improves computational efficiency and clustering accuracy. Benchmarks on human and mouse da- tasets show STAHD outperforms existing methods and accurately reveals spatially distinct tumor microenvironments and functional regions. Availability Source code and data are available at: [https://github.com/Little-Eel/STAHD]. Supplementary information Supplementary data are available at Bioinformatics online.