Hessian regularization based symmetric nonnegative matrix factorization for clustering gene expression and microbiome data

Methods ◽  
2016 ◽  
Vol 111 ◽  
pp. 80-84 ◽  
Author(s):  
Yuanyuan Ma ◽  
Xiaohua Hu ◽  
Tingting He ◽  
Xingpeng Jiang
Keyword(s):  
Gene Expression ◽  
Matrix Factorization ◽  
Nonnegative Matrix Factorization ◽  
Nonnegative Matrix ◽  
Microbiome Data ◽  
Symmetric Nonnegative Matrix Factorization

scholarly journals MHSNMF: multi-view hessian regularization based symmetric nonnegative matrix factorization for microbiome data analysis

2020 ◽  
Vol 21 (S6) ◽  
Author(s):  
Yuanyuan Ma ◽  
Junmin Zhao ◽  
Yingjun Ma
Keyword(s):  
Data Analysis ◽  
Matrix Factorization ◽  
Nonnegative Matrix Factorization ◽  
Rapid Development ◽  
Nonnegative Matrix ◽  
Metabolomics Data ◽  
Normalized Mutual Information ◽  
Microbiome Data ◽  
Symmetric Nonnegative Matrix Factorization ◽  
Microbiome Data Analysis

Abstract Background With the rapid development of high-throughput technique, multiple heterogeneous omics data have been accumulated vastly (e.g., genomics, proteomics and metabolomics data). Integrating information from multiple sources or views is challenging to obtain a profound insight into the complicated relations among micro-organisms, nutrients and host environment. In this paper we propose a multi-view Hessian regularization based symmetric nonnegative matrix factorization algorithm (MHSNMF) for clustering heterogeneous microbiome data. Compared with many existing approaches, the advantages of MHSNMF lie in: (1) MHSNMF combines multiple Hessian regularization to leverage the high-order information from the same cohort of instances with multiple representations; (2) MHSNMF utilities the advantages of SNMF and naturally handles the complex relationship among microbiome samples; (3) uses the consensus matrix obtained by MHSNMF, we also design a novel approach to predict the classification of new microbiome samples. Results We conduct extensive experiments on two real-word datasets (Three-source dataset and Human Microbiome Plan dataset), the experimental results show that the proposed MHSNMF algorithm outperforms other baseline and state-of-the-art methods. Compared with other methods, MHSNMF achieves the best performance (accuracy: 95.28%, normalized mutual information: 91.79%) on microbiome data. It suggests the potential application of MHSNMF in microbiome data analysis. Conclusions Results show that the proposed MHSNMF algorithm can effectively combine the phylogenetic, transporter, and metabolic profiles into a unified paradigm to analyze the relationships among different microbiome samples. Furthermore, the proposed prediction method based on MHSNMF has been shown to be effective in judging the types of new microbiome samples.

scholarly journals A Robust Symmetric Nonnegative Matrix Factorization Framework for Clustering Multiple Heterogeneous Microbiome Data

2017 ◽  
Author(s):  
Yuanyuan Ma ◽  
Xiaohua Hu ◽  
Tingting He ◽  
Xingpeng Jiang
Keyword(s):  
Matrix Factorization ◽  
Nonnegative Matrix Factorization ◽  
Human Microbiome ◽  
Nonnegative Matrix ◽  
Data Types ◽  
Robust Clustering ◽  
Phylogenetic Profiles ◽  
Leibler Divergence ◽  
Microbiome Data ◽  
Symmetric Nonnegative Matrix Factorization

Integration of multi-view datasets which are comprised of heterogeneous sources or different representations is challenging to understand the subtle and complex relationship in data. Such data integration methods attempt to combine efficiently the complementary information of multiple data types to construct a comprehensive view of underlying data. Nonnegative matrix factorization (NMF), an approach that can be used for signal compression and noise reduction, has aroused widespread attention in the last two decades. The Kullback–Leibler divergence (or relative entropy) information distance can be used to measure the loss function of NMF. In this article, we propose a fast and robust framework (RSNMF) based on symmetric nonnegative matrix factorization (SNMF) and similarity network fusion (SNF) for clustering human microbiome data including functional, metabolic and phylogenetic profiles. Many existing methods typically utilize all the information provided by each view to create a consensus representation, which often suffers a lot from noise in data and cannot provide a precise representation of the latent data structures. In contrast, RSNMF combines the strength of SNMF and the advantage of SNF to form a robust clustering indicator matrix thus can reduce the noise influence. We conduct experiments on one synthetic and two real dataset (microbiome data, text data) and the results show that the proposed RSNMF has better performance over the baseline and the state-of-art methods, which demonstrates the potential application of RSNMF for microbiome data analysis.

scholarly journals An Accelerated Symmetric Nonnegative Matrix Factorization Algorithm Using Extrapolation

Symmetry ◽  
2020 ◽  
Vol 12 (7) ◽  
pp. 1187
Author(s):  
Peitao Wang ◽  
Zhaoshui He ◽  
Jun Lu ◽  
Beihai Tan ◽  
YuLei Bai ◽  
...  
Keyword(s):  
Real World ◽  
Matrix Factorization ◽  
Nonnegative Matrix Factorization ◽  
Nonnegative Matrix ◽  
Low Rank ◽  
Tensor Factorization ◽  
Real World Data ◽  
Restart Strategy ◽  
Extrapolation Scheme ◽  
Symmetric Nonnegative Matrix Factorization

Symmetric nonnegative matrix factorization (SNMF) approximates a symmetric nonnegative matrix by the product of a nonnegative low-rank matrix and its transpose. SNMF has been successfully used in many real-world applications such as clustering. In this paper, we propose an accelerated variant of the multiplicative update (MU) algorithm of He et al. designed to solve the SNMF problem. The accelerated algorithm is derived by using the extrapolation scheme of Nesterov and a restart strategy. The extrapolation scheme plays a leading role in accelerating the MU algorithm of He et al. and the restart strategy ensures that the objective function of SNMF is monotonically decreasing. We apply the accelerated algorithm to clustering problems and symmetric nonnegative tensor factorization (SNTF). The experiment results on both synthetic and real-world data show that it is more than four times faster than the MU algorithm of He et al. and performs favorably compared to recent state-of-the-art algorithms.

Sign in / Sign up

Export Citation Format

Share Document