Multi-Manifolds fusing hyperbolic graph network balanced by pareto optimization for identifying spatial domains of spatial transcriptomics Article Swipe
Minghao Yin
,
Qifeng Hu
,
Siyu Han
,
Rui Wang‐Sattler
,
Wei Du
·
YOU?
·
· 2025
· Open Access
·
· DOI: https://doi.org/10.1093/bib/bbaf162
YOU?
·
· 2025
· Open Access
·
· DOI: https://doi.org/10.1093/bib/bbaf162
Identifying spatial domains for spatial transcriptomics is crucial for achieving comprehensive insights into the pathogenesis of gene expression. Increasingly, computational methods based on graph neural networks are being developed for spatial transcriptomics. However, previous methods have solely focused on the Euclidean manifold. To effectively exploit and explore the informative and deeper topological structures of inherent manifolds, we presented a Multi-Manifolds fusing hyperbolic graph network, balanced by Pareto optimization, for identifying spatial domains in Spatial Transcriptomics (MManiST). First, we developed multi-manifolds encoders for distinct manifolds using the hyperbolic neural network. Features from different manifolds were then combined using an attention mechanism, with multiple reconstruction losses balanced by Pareto optimization. Extensive experiments on commonly used benchmark datasets show that our method consistently outperforms seven state-of-the-art methods. Additionally, we investigated the validity of each component and the impact of fusion methods in ablation experiments.
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- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.1093/bib/bbaf162
- https://academic.oup.com/bib/article-pdf/26/2/bbaf162/62921939/bbaf162.pdf
- OA Status
- gold
- References
- 39
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4409387690
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W4409387690Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.1093/bib/bbaf162Digital Object Identifier
- Title
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Multi-Manifolds fusing hyperbolic graph network balanced by pareto optimization for identifying spatial domains of spatial transcriptomicsWork title
- Type
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articleOpenAlex work type
- Language
-
enPrimary language
- Publication year
-
2025Year of publication
- Publication date
-
2025-03-01Full publication date if available
- Authors
-
Minghao Yin, Qifeng Hu, Siyu Han, Rui Wang‐Sattler, Wei DuList of authors in order
- Landing page
-
https://doi.org/10.1093/bib/bbaf162Publisher landing page
- PDF URL
-
https://academic.oup.com/bib/article-pdf/26/2/bbaf162/62921939/bbaf162.pdfDirect link to full text PDF
- Open access
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YesWhether a free full text is available
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-
goldOpen access status per OpenAlex
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https://academic.oup.com/bib/article-pdf/26/2/bbaf162/62921939/bbaf162.pdfDirect OA link when available
- Concepts
-
Pareto principle, Computer science, Graph, Spatial network, Multi-objective optimization, Mathematical optimization, Theoretical computer science, Mathematics, Machine learning, CombinatoricsTop concepts (fields/topics) attached by OpenAlex
- Cited by
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0Total citation count in OpenAlex
- References (count)
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39Number of works referenced by this work
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10Other works algorithmically related by OpenAlex
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