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ScSiameseClu: A Siamese Clustering Framework for Interpreting single-cell RNA Sequencing Data

Created by
  • Haebom

Author

Ping Xu, Zhiyuan Ning, Pengjiang Li, Wenhao Liu, Pengyang Wang, Jiaxu Cui, Yuanchun Zhou, Pengfei Wang

Outline

This paper proposes scSiameseClu, a novel Siamese Clustering framework for interpreting single-cell RNA sequencing (scRNA-seq) data. scSiameseClu was developed to address the challenges of scRNA-seq data analysis, such as noise, sparsity, and high dimensionality. scSiameseClu comprises three main steps: (1) Dual Augmentation Module (enhancing the robustness of representation learning through biologically informative perturbations), (2) Siamese Fusion Module (mitigating over-smoothing through cross-correlation improvement and adaptive information fusion), and (3) Optimal Transport Clustering (efficiently aligning cluster assignments to a predefined ratio using Sinkhorn distance). Evaluation results on seven real-world datasets show that scSiameseClu outperforms existing state-of-the-art methods.

Takeaways, Limitations

Takeaways:
It outperforms existing methods in clustering, cell type annotation, and cell type classification of scRNA-seq data.
Increase data robustness through Dual Augmentation Module utilizing biological knowledge.
Recognize complex cellular relationships by mitigating over-smoothing with the Siamese Fusion Module.
Optimal Transport Clustering enables efficient cluster allocation while maintaining cluster balance.
Providing powerful tools for interpreting scRNA-seq data.
Limitations:
No specific mention of Limitations in the paper. (No mention of Limitations in the abstract.)
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