Integrating multiple spatial transcriptomics data using community-enhanced graph contrastive learning.

Abstract

Due to the rapid development of spatial sequencing technologies, large amounts of spatial transcriptomic datasets have been generated across various technological platforms or different biological conditions (e.g., control vs. treatment). Spatial transcriptomics data coming from different platforms usually has different resolutions. Moreover, current methods do not consider the heterogeneity of spatial structures within and across slices when modeling spatial transcriptomics data with graph-based methods. In this study, we propose a community-enhanced graph contrastive learning-based method named Tacos to integrate multiple spatial transcriptomics data. We applied Tacos to several real datasets coming from different platforms under different scenarios. Systematic benchmark analyses demonstrate Tacos's superior performance in integrating different slices. Furthermore, Tacos can accurately denoise the spatially resolved transcriptomics data.