Suppr超能文献

BiGATAE:一种二部图注意自动编码器,可从单切片增强到多切片的空间域识别。

BiGATAE: a bipartite graph attention auto-encoder enhancing spatial domain identification from single-slice to multi-slices.

机构信息

Shanghai Key Lab of Intelligent Information Processing, Handan Street, 200433 Shanghai, China.

School of Computer Science and Technology, Fudan University  Handan Street, 200433 Shanghai, China.

出版信息

Brief Bioinform. 2024 Jan 22;25(2). doi: 10.1093/bib/bbae045.

Abstract

Recent advancements in spatial transcriptomics technology have revolutionized our ability to comprehensively characterize gene expression patterns within the tissue microenvironment, enabling us to grasp their functional significance in a spatial context. One key field of research in spatial transcriptomics is the identification of spatial domains, which refers to distinct regions within the tissue where specific gene expression patterns are observed. Diverse methodologies have been proposed, each with its unique characteristics. As the availability of spatial transcriptomics data continues to expand, there is a growing need for methods that can integrate information from multiple slices to discover spatial domains. To extend the applicability of existing single-slice analysis methods to multi-slice clustering, we introduce BiGATAE (Bipartite Graph Attention Auto Encoder) that leverages gene expression information from adjacent tissue slices to enhance spatial transcriptomics data. BiGATAE comprises two steps: aligning slices to generate an adjacency matrix for different spots in consecutive slices and constructing a bipartite graph. Subsequently, it utilizes a graph attention network to integrate information across different slices. Then it can seamlessly integrate with pre-existing techniques. To evaluate the performance of BiGATAE, we conducted benchmarking analyses on three different datasets. The experimental results demonstrate that for existing single-slice clustering methods, the integration of BiGATAE significantly enhances their performance. Moreover, single-slice clustering methods integrated with BiGATAE outperform methods specifically designed for multi-slice integration. These results underscore the proficiency of BiGATAE in facilitating information transfer across multiple slices and its capacity to broaden the applicability and sustainability of pre-existing methods.

摘要

近年来,空间转录组学技术的进步彻底改变了我们全面描述组织微环境中基因表达模式的能力,使我们能够在空间背景下理解它们的功能意义。空间转录组学的一个关键研究领域是识别空间域,这是指在组织中观察到特定基因表达模式的不同区域。已经提出了多种方法,每种方法都有其独特的特点。随着空间转录组学数据的可用性不断扩大,人们越来越需要能够整合来自多个切片的信息以发现空间域的方法。为了将现有的单切片分析方法的适用性扩展到多切片聚类,我们引入了 BiGATAE(二部图注意自动编码器),它利用相邻组织切片中的基因表达信息来增强空间转录组学数据。BiGATAE 包括两个步骤:对齐切片以生成连续切片中不同点的邻接矩阵,以及构建二部图。然后,它利用图注意网络来整合不同切片之间的信息。然后,它可以与现有的技术无缝集成。为了评估 BiGATAE 的性能,我们在三个不同的数据集上进行了基准分析。实验结果表明,对于现有的单切片聚类方法,BiGATAE 的集成显著提高了它们的性能。此外,与 BiGATAE 集成的单切片聚类方法优于专门为多切片集成设计的方法。这些结果突出了 BiGATAE 在促进跨多个切片的信息传递方面的有效性,以及它扩展现有方法的适用性和可持续性的能力。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ac5e/10883416/3aad41502d0b/bbae045f1.jpg

文献AI研究员

20分钟写一篇综述,助力文献阅读效率提升50倍。

立即体验

用中文搜PubMed

大模型驱动的PubMed中文搜索引擎

马上搜索

文档翻译

学术文献翻译模型,支持多种主流文档格式。

立即体验