scholarly journals Accelerated Multiplicative Updates and Hierarchical ALS Algorithms for Nonnegative Matrix Factorization

2012 ◽  
Vol 24 (4) ◽  
pp. 1085-1105 ◽  
Author(s):  
Nicolas Gillis ◽  
François Glineur
Keyword(s):  
Data Analysis ◽  
Least Squares ◽  
Matrix Factorization ◽  
Nonnegative Matrix Factorization ◽  
Computational Cost ◽  
Nonnegative Matrix ◽  
Careful Analysis ◽  
Hyperspectral Data ◽  
Projected Gradient Method ◽  
Multiplicative Updates

Nonnegative matrix factorization (NMF) is a data analysis technique used in a great variety of applications such as text mining, image processing, hyperspectral data analysis, computational biology, and clustering. In this letter, we consider two well-known algorithms designed to solve NMF problems: the multiplicative updates of Lee and Seung and the hierarchical alternating least squares of Cichocki et al. We propose a simple way to significantly accelerate these schemes, based on a careful analysis of the computational cost needed at each iteration, while preserving their convergence properties. This acceleration technique can also be applied to other algorithms, which we illustrate on the projected gradient method of Lin. The efficiency of the accelerated algorithms is empirically demonstrated on image and text data sets and compares favorably with a state-of-the-art alternating nonnegative least squares algorithm.

scholarly journals Maximum Likelihood Estimation Based Nonnegative Matrix Factorization for Hyperspectral Unmixing

2021 ◽  
Vol 13 (13) ◽  
pp. 2637
Author(s):  
Qin Jiang ◽  
Yifei Dong ◽  
Jiangtao Peng ◽  
Mei Yan ◽  
Yi Sun
Keyword(s):  
Maximum Likelihood ◽  
Maximum Likelihood Estimation ◽  
Objective Function ◽  
Least Squares ◽  
Matrix Factorization ◽  
Nonnegative Matrix Factorization ◽  
Nonnegative Matrix ◽  
Likelihood Estimation ◽  
Hyperspectral Data ◽  
Hyperspectral Unmixing

Hyperspectral unmixing (HU) is a research hotspot of hyperspectral remote sensing technology. As a classical HU method, the nonnegative matrix factorization (NMF) unmixing method can decompose an observed hyperspectral data matrix into the product of two nonnegative matrices, i.e., endmember and abundance matrices. Because the objective function of NMF is the traditional least-squares function, NMF is sensitive to noise. In order to improve the robustness of NMF, this paper proposes a maximum likelihood estimation (MLE) based NMF model (MLENMF) for unmixing of hyperspectral images (HSIs), which substitutes the least-squares objective function in traditional NMF by a robust MLE-based loss function. Experimental results on a simulated and two widely used real hyperspectral data sets demonstrate the superiority of our MLENMF over existing NMF methods.

scholarly journals Retinal vessel segmentation with constrained-based nonnegative matrix factorization and 3D modified attention U-Net

2021 ◽  
Vol 2021 (1) ◽  
Author(s):  
Yang Yu ◽  
Hongqing Zhu
Keyword(s):  
Matrix Factorization ◽  
Nonnegative Matrix Factorization ◽  
Computational Cost ◽  
Three Dimensional ◽  
Nonnegative Matrix ◽  
Retinal Vessel ◽  
Classification Problem ◽  
Image Resolution ◽  
Retinal Vessels ◽  
Segmentation Task

AbstractDue to the complex morphology and characteristic of retinal vessels, it remains challenging for most of the existing algorithms to accurately detect them. This paper proposes a supervised retinal vessels extraction scheme using constrained-based nonnegative matrix factorization (NMF) and three dimensional (3D) modified attention U-Net architecture. The proposed method detects the retinal vessels by three major steps. First, we perform Gaussian filter and gamma correction on the green channel of retinal images to suppress background noise and adjust the contrast of images. Then, the study develops a new within-class and between-class constrained NMF algorithm to extract neighborhood feature information of every pixel and reduce feature data dimension. By using these constraints, the method can effectively gather similar features within-class and discriminate features between-class to improve feature description ability for each pixel. Next, this study formulates segmentation task as a classification problem and solves it with a more contributing 3D modified attention U-Net as a two-label classifier for reducing computational cost. This proposed network contains an upsampling to raise image resolution before encoding and revert image to its original size with a downsampling after three max-pooling layers. Besides, the attention gate (AG) set in these layers contributes to more accurate segmentation by maintaining details while suppressing noises. Finally, the experimental results on three publicly available datasets DRIVE, STARE, and HRF demonstrate better performance than most existing methods.

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 Parameterized Nonlinear Least Squares for Unsupervised Nonlinear Spectral Unmixing

2019 ◽  
Vol 11 (2) ◽  
pp. 148 ◽  
Author(s):  
Risheng Huang ◽  
Xiaorun Li ◽  
Haiqiang Lu ◽  
Jing Li ◽  
Liaoying Zhao
Keyword(s):  
Least Squares ◽  
Optimization Problem ◽  
Nonnegative Matrix Factorization ◽  
Optimization Problems ◽  
State Of The Art ◽  
Synthetic Data ◽  
Nonnegative Matrix ◽  
Nonlinear Least Squares ◽  
Hyperspectral Data ◽  
Spectral Unmixing

This paper presents a new parameterized nonlinear least squares (PNLS) algorithm for unsupervised nonlinear spectral unmixing (UNSU). The PNLS-based algorithms transform the original optimization problem with respect to the endmembers, abundances, and nonlinearity coefficients estimation into separate alternate parameterized nonlinear least squares problems. Owing to the Sigmoid parameterization, the PNLS-based algorithms are able to thoroughly relax the additional nonnegative constraint and the nonnegative constraint in the original optimization problems, which facilitates finding a solution to the optimization problems . Subsequently, we propose to solve the PNLS problems based on the Gauss–Newton method. Compared to the existing nonnegative matrix factorization (NMF)-based algorithms for UNSU, the well-designed PNLS-based algorithms have faster convergence speed and better unmixing accuracy. To verify the performance of the proposed algorithms, the PNLS-based algorithms and other state-of-the-art algorithms are applied to synthetic data generated by the Fan model and the generalized bilinear model (GBM), as well as real hyperspectral data. The results demonstrate the superiority of the PNLS-based algorithms.

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