Hyper-graph Robust Non-negative Matrix Factorization Method for Cancer Sample Clustering and Feature Selection

2020 ◽  
pp. 112-125
Author(s):  
Cui-Na Jiao ◽  
Tian-Ru Wu ◽  
Jin-Xing Liu ◽  
Xiang-Zhen Kong
Keyword(s):  
Feature Selection ◽  
Matrix Factorization ◽  
Factorization Method ◽  
Cancer Sample ◽  
Non Negative Matrix Factorization

scholarly journals Robust hypergraph regularized non-negative matrix factorization for sample clustering and feature selection in multi-view gene expression data

2019 ◽  
Vol 13 (S1) ◽  
Author(s):  
Na Yu ◽  
Ying-Lian Gao ◽  
Jin-Xing Liu ◽  
Juan Wang ◽  
Junliang Shang
Keyword(s):  
Feature Selection ◽  
Matrix Factorization ◽  
Gene Selection ◽  
Matrix Decomposition ◽  
Original Data ◽  
Data Representation ◽  
Abnormal Expression ◽  
Sample Points ◽  
Laplacian Regularization ◽  
Non Negative Matrix Factorization

Abstract Background As one of the most popular data representation methods, non-negative matrix decomposition (NMF) has been widely concerned in the tasks of clustering and feature selection. However, most of the previously proposed NMF-based methods do not adequately explore the hidden geometrical structure in the data. At the same time, noise and outliers are inevitably present in the data. Results To alleviate these problems, we present a novel NMF framework named robust hypergraph regularized non-negative matrix factorization (RHNMF). In particular, the hypergraph Laplacian regularization is imposed to capture the geometric information of original data. Unlike graph Laplacian regularization which captures the relationship between pairwise sample points, it captures the high-order relationship among more sample points. Moreover, the robustness of the RHNMF is enhanced by using the L2,1-norm constraint when estimating the residual. This is because the L2,1-norm is insensitive to noise and outliers. Conclusions Clustering and common abnormal expression gene (com-abnormal expression gene) selection are conducted to test the validity of the RHNMF model. Extensive experimental results on multi-view datasets reveal that our proposed model outperforms other state-of-the-art methods.

An Improved Non-negative Matrix Factorization Method for Dynamic Industrial Fault Diagnosis

2020 ◽  
Vol 53 (7) ◽  
pp. 321-326
Author(s):  
XiaoFeng Gong ◽  
Dongdong Sun ◽  
Zuodong Tang ◽  
Kai Zhou ◽  
RuiSen Luo
Keyword(s):  
Fault Diagnosis ◽  
Matrix Factorization ◽  
Factorization Method ◽  
Non Negative Matrix Factorization

scholarly journals Indicator Regularized Non-Negative Matrix Factorization Method-Based Drug Repurposing for COVID-19

2021 ◽  
Vol 11 ◽  
Author(s):  
Xianfang Tang ◽  
Lijun Cai ◽  
Yajie Meng ◽  
JunLin Xu ◽  
Changcheng Lu ◽  
...  
Keyword(s):  
Matrix Factorization ◽  
De Novo ◽  
Characteristic Curve ◽  
Drug Repurposing ◽  
Factorization Method ◽  
Therapeutic Drugs ◽  
Indicator Matrix ◽  
Novel Coronavirus ◽  
Approved Drugs ◽  
Non Negative Matrix Factorization

A novel coronavirus, named COVID-19, has become one of the most prevalent and severe infectious diseases in human history. Currently, there are only very few vaccines and therapeutic drugs against COVID-19, and their efficacies are yet to be tested. Drug repurposing aims to explore new applications of approved drugs, which can significantly reduce time and cost compared with de novo drug discovery. In this study, we built a virus-drug dataset, which included 34 viruses, 210 drugs, and 437 confirmed related virus-drug pairs from existing literature. Besides, we developed an Indicator Regularized non-negative Matrix Factorization (IRNMF) method, which introduced the indicator matrix and Karush-Kuhn-Tucker condition into the non-negative matrix factorization algorithm. According to the 5-fold cross-validation on the virus-drug dataset, the performance of IRNMF was better than other methods, and its Area Under receiver operating characteristic Curve (AUC) value was 0.8127. Additionally, we analyzed the case on COVID-19 infection, and our results suggested that the IRNMF algorithm could prioritize unknown virus-drug associations.

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