Academic Journal
Attention-guided variational graph autoencoders reveal heterogeneity in spatial transcriptomics
| العنوان: | Attention-guided variational graph autoencoders reveal heterogeneity in spatial transcriptomics |
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| المؤلفون: | Lei, Lixin, Han, Kaitai, Wang, Zijun, Shi, Chaojing, Wang, Zhenghui, Dai, Ruoyan, Zhang, Zhiwei, Wang, Mengqiu, Guo, Qianjin |
| المساهمون: | NSFCs, Beijing Municipal Education Commission, Climbing Program Foundation from Beijing Institute of Petrochemical Technology |
| المصدر: | Briefings in Bioinformatics ; volume 25, issue 3 ; ISSN 1467-5463 1477-4054 |
| بيانات النشر: | Oxford University Press (OUP) |
| سنة النشر: | 2024 |
| مصطلحات موضوعية: | Molecular Biology, Information Systems |
| الوصف: | The latest breakthroughs in spatially resolved transcriptomics technology offer comprehensive opportunities to delve into gene expression patterns within the tissue microenvironment. However, the precise identification of spatial domains within tissues remains challenging. In this study, we introduce AttentionVGAE (AVGN), which integrates slice images, spatial information and raw gene expression while calibrating low-quality gene expression. By combining the variational graph autoencoder with multi-head attention blocks (MHA blocks), AVGN captures spatial relationships in tissue gene expression, adaptively focusing on key features and alleviating the need for prior knowledge of cluster numbers, thereby achieving superior clustering performance. Particularly, AVGN attempts to balance the model’s attention focus on local and global structures by utilizing MHA blocks, an aspect that current graph neural networks have not extensively addressed. Benchmark testing demonstrates its significant efficacy in elucidating tissue anatomy and interpreting tumor heterogeneity, indicating its potential in advancing spatial transcriptomics research and understanding complex biological phenomena. |
| نوع الوثيقة: | article in journal/newspaper |
| اللغة: | English |
| DOI: | 10.1093/bib/bbae173 |
| الاتاحة: | http://dx.doi.org/10.1093/bib/bbae173 https://academic.oup.com/bib/article-pdf/25/3/bbae173/57240776/bbae173.pdf |
| Rights: | https://creativecommons.org/licenses/by/4.0/ |
| رقم الانضمام: | edsbas.777513C3 |
| قاعدة البيانات: | BASE |
| DOI: | 10.1093/bib/bbae173 |
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