HTRPCA: Hypergraph Regularized Tensor Robust Principal Component Analysis for Sample Clustering in Tumor Omics Data.

Interdisciplinary Sciences, Computational Life Sciences
Yu-Ying ZhaoChun-Hou Zheng

Abstract

In recent years, clustering analysis of cancer genomics data has gained widespread attention. However, limited by the dimensions of the matrix, the traditional methods cannot fully mine the underlying geometric structure information in the data. Besides, noise and outliers inevitably exist in the data. To solve the above two problems, we come up with a new method which uses tensor to represent cancer omics data and applies hypergraph to save the geometric structure information in original data. This model is called hypergraph regularized tensor robust principal component analysis (HTRPCA). The data processed by HTRPCA becomes two parts, one of which is a low-rank component that contains pure underlying structure information between samples, and the other is some sparse interference points. So we can use the low-rank component for clustering. This model can retain complex geometric information between more sample points due to the addition of the hypergraph regularization. Through clustering, we can demonstrate the effectiveness of HTRPCA, and the experimental results on TCGA datasets demonstrate that HTRPCA precedes other advanced methods. This paper proposes a new method of using tensors to represent cancer omics data and intr...Continue Reading

References

Dec 22, 2010·IEEE Transactions on Pattern Analysis and Machine Intelligence·Deng CaiThomas S Huang
Apr 11, 2012·IEEE Transactions on Pattern Analysis and Machine Intelligence·Guangcan LiuYi Ma
Apr 4, 2013·IEEE Transactions on Image Processing : a Publication of the IEEE Signal Processing Society·Weifeng Liu, Dacheng Tao
Jul 17, 2013·BMC Bioinformatics·Jin-Xing LiuYong Xu
Nov 8, 2013·IEEE Transactions on Cybernetics·Jinhui Chen, Jian Yang
Sep 10, 2015·IEEE Transactions on Pattern Analysis and Machine Intelligence·Tae-Hyun OhIn So Kweon
May 5, 2017·BioMed Research International·Chun-Mei FengChang-Gang Wen
Jan 11, 2019·IEEE Transactions on Pattern Analysis and Machine Intelligence·Canyi LuShuicheng Yan

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.

Related Papers

IEEE Transactions on Image Processing : a Publication of the IEEE Signal Processing Society
Taisong JinDacheng Tao
IEEE Transactions on Pattern Analysis and Machine Intelligence
Yue GaoChangqing Zou
IEEE/ACM Transactions on Computational Biology and Bioinformatics
Chuan-Yuan WangJuan Wang
© 2021 Meta ULC. All rights reserved