Spatially contrastive variational autoencoder for deciphering tissue heterogeneity from spatially resolved transcriptomics

• Published in: Briefings in bioinformatics 2024-01, Vol.25 (2)
• Main Authors: Hu, Yaofeng, Xiao, Kai, Yang, Hengyu, Liu, Xiaoping, Zhang, Chuanchao, Shi, Qianqian
• Format: Article
• Language: English
• Subjects: Embedding; Gene Expression Profiling; Graph neural networks; Heterogeneity; Machine learning; Neural networks; Neural Networks, Computer; Problem Solving Protocol; Self-supervised learning; Spatial discrimination learning; Transcriptome; Transcriptomics
• ISSN: 1467-5463; 1477-4054
• DOI: 10.1093/bib/bbae016

Abstract Recent advances in spatially resolved transcriptomics (SRT) have brought ever-increasing opportunities to characterize expression landscape in the context of tissue spatiality. Nevertheless, there still exist multiple challenges to accurately detect spatial functional regions in tissue. Here, we present a novel contrastive learning framework, SPAtially Contrastive variational AutoEncoder (SpaCAE), which contrasts transcriptomic signals of each spot and its spatial neighbors to achieve fine-grained tissue structures detection. By employing a graph embedding variational autoencoder and incorporating a deep contrastive strategy, SpaCAE achieves a balance between spatial local information and global information of expression, enabling effective learning of representations with spatial constraints. Particularly, SpaCAE provides a graph deconvolutional decoder to address the smoothing effect of local spatial structure on expression’s self-supervised learning, an aspect often overlooked by current graph neural networks. We demonstrated that SpaCAE could achieve effective performance on SRT data generated from multiple technologies for spatial domains identification and data denoising, making it a remarkable tool to obtain novel insights from SRT studies.