Related papers: Model selection and robust inference of mutational…
Mutational signatures are patterns of somatic mutations in tumor genomes that provide insights into underlying mutagenic processes and cancer origin. Developing reliable methods for their estimation is of growing importance in cancer…
Somatic mutations, or alterations in DNA of a somatic cell, are key markers of cancer. In recent years, mutational signature analysis has become a prominent field of study within cancer research, commonly with Nonnegative Matrix…
Mutational signatures are powerful summaries of the mutational processes altering the DNA of cancer cells. The usual approach to mutational signature analysis consists of decomposing the matrix of mutation counts from a sample of patients…
Non-negative matrix factorization (NMF) is widely used in many applications for dimensionality reduction. Inferring an appropriate number of factors for NMF is a challenging problem, and several approaches based on information criteria or…
Non-negative matrix factorization (NMF) is widely used as a feature extraction technique for matrices with non-negative entries, such as image data, purchase histories, and other types of count data. In NMF, a non-negative matrix is…
Non-negative Matrix Factorization (NMF) is a useful method to extract features from multivariate data, but an important and sometimes neglected concern is that NMF can result in non-unique solutions. Often, there exist a Set of Feasible…
Non-negative matrix factorization (NMF) is a fundamental matrix decomposition technique that is used primarily for dimensionality reduction and is increasing in popularity in the biological domain. Although finding a unique NMF is generally…
Bayesian Poisson Non-Negative Matrix Factorization (NMF) is widely used to model count data, including in cancer mutational signature analysis. However, standard Gibbs samplers rely on computationally expensive Poisson augmentation, and…
We introduce negative binomial matrix factorization (NBMF), a matrix factorization technique specially designed for analyzing over-dispersed count data. It can be viewed as an extension of Poisson matrix factorization (PF) perturbed by a…
Extracting genetic information from a full range of sequencing data is important for understanding diseases. We propose a novel method to effectively explore the landscape of genetic mutations and aggregate them to predict cancer type. We…
Non-Negative Matrix Factorization (NMF) is a widely used dimension reduction method that factorizes a non-negative data matrix into two lower dimensional non-negative matrices: One is the basis or feature matrix which consists of the…
Non-negative matrix factorisation (NMF) is a widely used tool for unsupervised learning and feature extraction, with applications ranging from genomics to text analysis and signal processing. Standard formulations of NMF are typically…
We present a novel method for extracting cancer signatures by applying statistical risk models (http://ssrn.com/abstract=2732453) from quantitative finance to cancer genome data. Using 1389 whole genome sequenced samples from 14 cancers, we…
The aim of this study is to provide a foundation to understand the relationship between non-negative matrix factorization (NMF) and non-negative autoencoders enabling proper interpretation and understanding of autoencoder-based alternatives…
Somatic mutations in cancer can be viewed as a mixture distribution of several mutational signatures, which can be inferred using non-negative matrix factorization (NMF). Mutational signatures have previously been parametrized using either…
Nonnegative matrix factorization (NMF) has an established reputation as a useful data analysis technique in numerous applications. However, its usage in practical situations is undergoing challenges in recent years. The fundamental factor…
Non-negative matrix factorization (NMF) is a prob- lem with many applications, ranging from facial recognition to document clustering. However, due to the variety of algorithms that solve NMF, the randomness involved in these algorithms,…
Understanding the association between dietary patterns and health outcomes, such as the cancer risk, is crucial to inform public health guidelines and shaping future dietary interventions. However, dietary intake data present several…
Over the past few years, there has been a considerable spread of microarray technology in many biological patterns, particularly in those pertaining to cancer diseases like leukemia, prostate, colon cancer, etc. The primary bottleneck that…
Binary data matrices can represent many types of data such as social networks, votes, or gene expression. In some cases, the analysis of binary matrices can be tackled with nonnegative matrix factorization (NMF), where the observed data…