用超图神经网络解析单细胞转录组的空间域,捕捉复杂细胞关联。
Hypergraph Neural Networks Reveal Spatial Domains from Single-cell Transcriptomics Data
- 引入超图结构建模多细胞非成对关系,突破传统图网络局限。
- iLISI达1.843,识别细胞类型多样性最优;ARI达0.51,聚类效果领先。
- 适合研究组织空间结构、细胞互作的生物学家和计算研究人员。
空间转录组数据的聚类任务至关重要,可将组织样本划分为不同细胞亚群,用于分析生物学功能、组织重建及细胞间相互作用。现有方法结合基因表达、空间位置与组织学图像检测空间域,但主流图神经网络(GNN)受限于节点间仅能建立成对连接的假设。在空间转录组中,部分细胞虽无直接关联却同属一个域,表明传统GNN难以捕捉隐含联系。超图神经网络(HGNN)通过超边连接任意数量节点,能更丰富地建模复杂结构信息。我们采用自编码器解决缺乏真实标签的问题,适用于无监督学习。模型在多项指标上表现卓越:iLISI得分最高达1.843,表明识别出的细胞类型多样性最优;下游聚类中,ARI达0.51,Leiden分数达0.60,优于其他方法。
原文摘要 · Abstract (English)
The task of spatial clustering of transcriptomics data is of paramount importance. It enables the classification of tissue samples into diverse subpopulations of cells, which, in turn, facilitates the analysis of the biological functions of clusters, tissue reconstruction, and cell-cell interactions. Many approaches leverage gene expressions, spatial locations, and histological images to detect spatial domains; however, Graph Neural Networks (GNNs) as state of the art models suffer from a limitation in the assumption of pairwise connections between nodes. In the case of domain detection in spatial transcriptomics, some cells are found to be not directly related. Still, they are grouped as the same domain, which shows the incapability of GNNs for capturing implicit connections among the cells. While graph edges connect only two nodes, hyperedges connect an arbitrary number of nodes along their edges, which lets Hypergraph Neural Networks (HGNNs) capture and utilize richer and more complex structural information than traditional GNNs. We use autoencoders to address the limitation of not having the actual labels, which are well-suited for unsupervised learning. Our model has demonstrated exceptional performance, achieving the highest iLISI score of 1.843 compared to other methods. This score indicates the greatest diversity of cell types identified by our method. Furthermore, our model outperforms other methods in downstream clustering, achieving the highest ARI values of 0.51 and Leiden score of 0.60.
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