SpaMWGDA: Identifying spatial domains of spatial transcriptomes using multi-view weighted fusion graph convolutional network and data augmentation

Lin Yuan, Boyuan Meng, Qingxiang Wang, Chunyu Hu, Cuihong Wang and Huang De-Shuang

PLOS Computational Biology, 2025, vol. 21, issue 11, 1-19

Abstract: The rapid development of spatial transcriptomics (ST) has made it possible to effectively integrate gene expression and spatial information of cells and accurately identify spatial domains. A large number of deep learning (DL)-based methods have been proposed to perform spatial domain identification and achieved impressive results. However, these methods have some limitations. First, these methods rely on a fixed similarity metric and cannot fully utilize neighborhood information. Second, they cannot efficiently and adaptively integrate key information when fusing and reconstructing gene expression using purely additive methods. Finally, these methods ignore key nonlinear features and introduce noise during clustering. To address these limitations, we propose a novel DL model SpaMWGDA based on multi-view weighted fused graph convolutional network (GCN) and data augmentation. By modeling spatial information using different similarity metrics, the model is able to successfully capture comprehensive neighborhood information of the spot features. By combining data augmentation and contrastive learning, SpaMWGDA is able to learn key gene expressions. SpaMWGDA uses a multi-view GCN encoder to model the similarities between spatial information and gene features, and uses a view-level attention mechanism for weighted fusion to adaptively learn the dependencies between them and learn the key features of each view. Experimental results not only demonstrate that SpaMWGDA outperforms competing methods in spatial domain identification and trajectory inference but also show the ability of SpaMWGDA to analyse tissue structure and function. The source code for SpaMWGDA is available at https://github.com/nathanyl/SpaMWGDA .Author summary: DL-based methods have some limitations. First, these methods rely on a fixed similarity metric and cannot fully utilize neighborhood information. Second, they cannot efficiently and adaptively integrate key information when fusing and reconstructing gene expression using purely additive methods. Finally, these methods ignore key nonlinear features and introduce noise during clustering. We propose a novel DL model SpaMWGDA based on multi-view weighted fused graph convolutional network (GCN) and data augmentation. SpaMWGDA uses a multi-view GCN encoder to model the similarities between spatial information and gene features, and uses a view-level attention mechanism for weighted fusion to adaptively learn the dependencies between them and learn the key features of each view. Experimental results not only demonstrate that SpaMWGDA outperforms competing methods in spatial domain identification and trajectory inference but also show the ability of SpaMWGDA to analyse tissue structure and function.

Date: 2025
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Persistent link: https://EconPapers.repec.org/RePEc:plo:pcbi00:1013667

DOI: 10.1371/journal.pcbi.1013667

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