stDyer enables spatial domain clustering with dynamic graph embedding Article Swipe
Ke Xu
,
Yu Xu
,
Zirui Wang
,
Xin Zhou
,
Lu Zhang
·
YOU?
·
· 2025
· Open Access
·
· DOI: https://doi.org/10.1186/s13059-025-03503-y
YOU?
·
· 2025
· Open Access
·
· DOI: https://doi.org/10.1186/s13059-025-03503-y
Spatially resolved transcriptomics (SRT) data provide critical insights into gene expression patterns within tissue contexts, necessitating effective methods for identifying spatial domains. We introduce stDyer, an end-to-end deep learning framework for spatial domain clustering in SRT data. stDyer combines Gaussian Mixture Variational AutoEncoder with graph attention networks to learn embeddings and perform clustering. Its dynamic graphs adaptively link units based on Gaussian Mixture assignments, improving clustering and producing smoother domain boundaries. stDyer's mini-batch strategy and multi-GPU support facilitate scalability to large datasets. Benchmarking against state-of-the-art tools, stDyer demonstrates superior performance in spatial domain clustering, multi-slice analysis, and large-scale dataset handling.
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- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.1186/s13059-025-03503-y
- OA Status
- gold
- Cited By
- 3
- References
- 37
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4407772831
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https://openalex.org/W4407772831Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.1186/s13059-025-03503-yDigital Object Identifier
- Title
-
stDyer enables spatial domain clustering with dynamic graph embeddingWork title
- Type
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articleOpenAlex work type
- Language
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enPrimary language
- Publication year
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2025Year of publication
- Publication date
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2025-02-20Full publication date if available
- Authors
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Ke Xu, Yu Xu, Zirui Wang, Xin Zhou, Lu ZhangList of authors in order
- Landing page
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https://doi.org/10.1186/s13059-025-03503-yPublisher landing page
- Open access
-
YesWhether a free full text is available
- OA status
-
goldOpen access status per OpenAlex
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https://doi.org/10.1186/s13059-025-03503-yDirect OA link when available
- Concepts
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Biology, Human genetics, Cluster analysis, Computational biology, Genome Biology, Evolutionary biology, Embedding, Computer science, Genetics, Genomics, Genome, Artificial intelligence, GeneTop concepts (fields/topics) attached by OpenAlex
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3Total citation count in OpenAlex
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2025: 3Per-year citation counts (last 5 years)
- References (count)
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37Number of works referenced by this work
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10Other works algorithmically related by OpenAlex
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