Search · four archives
Search · four archives
20 papers · ranked by Valyu relevance
Volkan Sevinç, Nikolas Kontemeniotis, Theodoros Perdikis, Michail Tsagris
Non--negative matrix factorization (NMF) has become an established dimensionality reduction technique for extracting latent structures from non--negative data and has found widespread applications in fields such as bioinformatics, text mining, image analysis, and recommender systems. As the popularity of NMF has…
Michael R. Lindstrom, Xiaofu Ding, Feng Liu, Anand Somayajula + 1 more
'Deanna Needell'] Nonnegative matrix factorization can be used to automatically detect topics within a corpus in an unsupervised fashion. The technique amounts to an approximation of a nonnegative matrix as the product of two nonnegative matrices of lower rank. In this paper, we show this factorization can be combined…
Sajad Fathi Hafshejani, Devanshi Gaur, S. Hossain, R. Benkoczi
We propose a method for computing binary orthogonal nonnegative matrix factorization (BONMF) for clustering and classification. The method is tested on several representative real-world data sets. The numerical results confirm that the method has improved accuracy compared to the related techniques. The proposed method…
Mahbod Nouri, David Rotermund, Alberto Garcia-Ortiz, Klaus R. Pawelzik
Considering biological constraints in artificial neural networks has led to dramatic improvements in performance. Nevertheless, to date, the positivity of long-range signals in the cortex has not been shown to yield improvements. While Non-negative matrix factorization (NMF) captures biological constraints of positive…
János Abonyi, Ádám Ipkovich, Gyula Dörgő, Károly Héberger + 1 more
'Majid Soleimani-damaneh'] Non-negative matrix factorization (NMF) efficiently reduces high dimensionality for many-objective ranking problems. In multi-objective optimization, as long as only three or four conflicting viewpoints are present, an optimal solution can be determined by finding the Pareto front. When the…
Denis Kleverov, Ekaterina Aladyeva, Alexey Serdyukov, Maxim N. Artyomov
Non-negative matrix factorization (NMF) is one of the most powerful linear algebra tools, which has found application in various areas of data analysis, including computational biology. Despite numerous optimization methods devised for NMF, our comprehension of the inherent topological structure within factorizable…
Ling Zhong, Haiyan Gao, Friedhelm Schwenker
Clustering algorithms based on non-negative matrix factorization (NMF) have garnered significant attention in data mining due to their strong interpretability and computational simplicity. However, traditional NMF often struggles to effectively capture and preserve topological structure information between data during…
Jens Sjölund, Maria Bånkestad
We describe a graph-based neural acceleration technique for nonnegative matrix factorization that builds upon a connection between matrices and bipartite graphs that is well-known in certain fields, e.g., sparse linear algebra, but has not yet been exploited to design graph neural networks for matrix computations. We…
Rachid Hedjam, Abdelhamid Abdesselam, Abderrahmane Rahiche, Mohamed Cheriet
'Mohamed Cheriet'] The model described in this paper belongs to the family of non-negative matrix factorization methods designed for data representation and dimension reduction. In addition to preserving the data positivity property, it aims also to preserve the structure of data during matrix factorization. The idea…
Jeanette Johnson, Ashley Tsang, Jacob T. Mitchell, Emily Davis-Marcisak + 12 more
Non-negative matrix factorization (NMF) is an unsupervised learning method well suited to high-throughput biology. Still, inferring biological processes requires additional post hoc statistics and annotation for interpretation of features learned from software packages developed for NMF implementation. Here, we aim to…
Mengyang Wang, Wenbao Zhang, Mingzhen Shao, Guang Wang + 1 more
'Ernestina Menasalvas'] To solve the separation of multi-source signals and detect their features from a single channel, a signal separation method using multi-constraint non-negative matrix factorization (NMF) is proposed. In view of the existing NMF algorithm not performing well in the underdetermined blind source…
Lara Kassab, Erin George, Deanna Needell, Haowen Geng + 2 more
There has been a recent critical need to study fairness and bias in machine learning (ML) algorithms. Since there is clearly no one-size-fits-all solution to fairness, ML methods should be developed alongside bias mitigation strategies that are practical and approachable to the practitioner. Motivated by recent work on…
Steven E. Pav
Factorizations Authors: ['Steven E. Pav'] We generalize the non-negative matrix factorization algorithm of Lee and Seung [3] to accept a weighted norm, and to support ridge and Lasso regularization. We recast the Lee and Seung multiplicative update as an additive update which does not get stuck on zero values. We apply…
Eric Weine, Peter Carbonetto, Rafael A. Irizarry, Matthew Stephens
Poisson non-negative matrix factorization (NMF) is a widely used method to find interpretable "parts-based" decompositions of count data. While many variants of Poisson NMF exist, existing methods assume that the "parts" in the decomposition combine additively. This assumption may be natural in some settings, but not…
Emine Güven
There is a great need to develop a computational approach to analyze and exploit the information contained in gene expression data. Recent utilization of non-negative matrix factorization (NMF) in computational biology has served its capability to derive essential details from a high amount of data in particular gene…
Wei Wang, Matthew Stephens
Matrix factorization methods, which include Factor analysis (FA) and Principal Components Analysis (PCA), are widely used for inferring and summarizing structure in multivariate data. Many such methods use a penalty or prior distribution to achieve sparse representations (“Sparse FA/PCA”), and a key question is how…
Ko Abe, Shintaro Yuki, Teppei Shimamura
Combinatorial indexing-based single-cell RNA sequencing methods such as sci-RNA-seq and sci-RNA-seq3 now enable the profiling of millions of cells, producing expression matrices that are both extremely sparse and high-dimensional. Conventional nonnegative matrix factorization (NMF) provides an interpretable framework…
Ragunathan Mariappan, Aishwarya Jayagopal, Ho Zong Sien, Vaibhav Rajan
In many biomedical studies, there arises the need to integrate data from multiple directly or indirectly related sources. Collective matrix factorization (CMF) and its variants are models designed to collectively learn from arbitrary collections of matrices. The latent factors learnt are rich integrative…
Stuti Jain, Emilie Chouzenoux, Kriti Kumar, Angshul Majumdar
Co-administration of two or more drugs simultaneously can result in adverse drug reactions. Identifying drug-drug interactions (DDIs) is necessary, especially for drug development and for repurposing old drugs. DDI prediction can be viewed as a matrix completion task, for which matrix factorization (MF) appears as a…
Diba Behnoudfar, Cory Simon, Joshua Schrier
Aqueous, two-phase systems (ATPSs) may form upon mixing two solutions of independently water-soluble compounds. Many separation, purification, and extraction processes rely on ATPSs. Predicting the miscibility of solutions can accelerate and reduce the cost of the discovery of new ATPSs for these applications. Whereas…