Article · PLoS Computational Biology · October 17, 2025

Spatial domain identification method based on multi-view graph convolutional network and contrastive learning

Xikeng Liang, Shutong Xiao, Lu Ba, Yuhui Feng, Zhicheng Ma, Fatima Аdilova

Abstract

Spatial transcriptomics is a rapidly developing field of single-cell genomics that quantitatively measures gene expression while providing spatial information within tissues. A key challenge in spatial transcriptomics is identifying spatially structured domains, which involves analyzing transcriptomic data to find clusters of cells with similar expression patterns and their spatial distribution. To address these challenges, we propose a novel deep-learning method called DMGCN for domain identification. The process begins with preprocessing that constructs two types of graphs: a spatial graph based on Euclidean distance and a feature graph based on Cosine distance. These graphs represent spatial positions and gene expressions, respectively. The embeddings of both graphs are generated using a multi-view graph convolutional encoder with an attention mechanism, enabling separate and co-convolution of the graphs, as well as corrupted feature convolution for contrastive learning. Finally, a fully connected network (FCN) decoder is employed to generate domain labels and reconstruct gene expressions for downstream analysis. Experimental results demonstrate that DMGCN consistently outperforms state-of-the-art methods in various tasks, including spatial clustering, trajectory inference, and gene expression broadcasting.

Single-cell and spatial transcriptomicsGene expression and cancer classificationGene Regulatory Network Analysisspatial transcriptomicsspatial domain identificationcontrastive learning

Spatial domain identification method based on multi-view graph convolutional network and contrastive learning

Abstract

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