Zhongning Jiang, Wei Huang, Raymond H W Lam, Wei Zhang
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引用次数: 0
Abstract
Recent developments in spatially resolved transcriptomics (SRT) enable the characterization of spatial structures for different tissues. Many decomposition methods have been proposed to depict the cellular distribution within tissues. However, existing computational methods struggle to balance spatial continuity in cell distribution with the preservation of cell-specific characteristics. To address this, we propose Spall, a novel decomposition network that integrates scRNA-seq data with SRT data to accurately infer cell type proportions. Spall introduced the GATv2 module, featuring a flexible dynamic attention mechanism to capture relationships between spots. This improves the identification of cellular distribution patterns in spatial analysis. Additionally, Spall incorporates skip connections to address the loss of cell-specific information, thereby enhancing the prediction capability for rare cell types. Experimental results show that Spall outperforms the state-of-the-art methods in reconstructing cell distribution patterns on multiple datasets. Notably, Spall reveals tumor heterogeneity in human pancreatic ductal adenocarcinoma samples and delineates complex tissue structures, such as the laminar organization of the mouse cerebral cortex and the mouse cerebellum. These findings highlight the ability of Spall to provide reliable low-dimensional embeddings for downstream analyses, offering new opportunities for deciphering tissue structures.
期刊介绍:
BMC Bioinformatics is an open access, peer-reviewed journal that considers articles on all aspects of the development, testing and novel application of computational and statistical methods for the modeling and analysis of all kinds of biological data, as well as other areas of computational biology.
BMC Bioinformatics is part of the BMC series which publishes subject-specific journals focused on the needs of individual research communities across all areas of biology and medicine. We offer an efficient, fair and friendly peer review service, and are committed to publishing all sound science, provided that there is some advance in knowledge presented by the work.