NDLI: Clustering of cancer data based on Stiefel manifold for multiple views

Content Provider	Springer Nature : BioMed Central
Author	Tian, Jing Zhao, Jianping Zheng, Chunhou
Abstract	Background In recent years, various sequencing techniques have been used to collect biomedical omics datasets. It is usually possible to obtain multiple types of omics data from a single patient sample. Clustering of omics data plays an indispensable role in biological and medical research, and it is helpful to reveal data structures from multiple collections. Nevertheless, clustering of omics data consists of many challenges. The primary challenges in omics data analysis come from high dimension of data and small size of sample. Therefore, it is difficult to find a suitable integration method for structural analysis of multiple datasets. Results In this paper, a multi-view clustering based on Stiefel manifold method (MCSM) is proposed. The MCSM method comprises three core steps. Firstly, we established a binary optimization model for the simultaneous clustering problem. Secondly, we solved the optimization problem by linear search algorithm based on Stiefel manifold. Finally, we integrated the clustering results obtained from three omics by using k-nearest neighbor method. We applied this approach to four cancer datasets on TCGA. The result shows that our method is superior to several state-of-art methods, which depends on the hypothesis that the underlying omics cluster class is the same. Conclusion Particularly, our approach has better performance than compared approaches when the underlying clusters are inconsistent. For patients with different subtypes, both consistent and differential clusters can be identified at the same time.
Related Links	https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-021-04195-4.pdf
Ending Page	15
Page Count	15
Starting Page	1
File Format	HTM / HTML
ISSN	14712105
DOI	10.1186/s12859-021-04195-4
Journal	BMC Bioinformatics
Issue Number	1
Volume Number	22
Language	English
Publisher	BioMed Central
Publisher Date	2021-05-25
Access Restriction	Open
Subject Keyword	Bioinformatics Microarrays Computational Biology Computer Appl. in Life Sciences Algorithms Stiefel manifold Multi-view clustering Cancer data Optimization model Linear search algorithm Computational Biology/Bioinformatics
Content Type	Text
Resource Type	Article
Subject	Molecular Biology Biochemistry Computer Science Applications Applied Mathematics Structural Biology
Journal Impact Factor	2.9/2023
5-Year Journal Impact Factor	3.6/2023

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