Search citation statements
Paper Sections
Citation Types
Year Published
Publication Types
Relationship
Authors
Journals
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.
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.
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.
hi@scite.ai
10624 S. Eastern Ave., Ste. A-614
Henderson, NV 89052, USA
Copyright © 2024 scite LLC. All rights reserved.
Made with 💙 for researchers
Part of the Research Solutions Family.