Related papers: Doubly Non-Central Beta Matrix Factorization for D…
Identifying differentially methylated cytosine-guanine dinucleotide (CpG) sites between benign and tumour samples can assist in understanding disease. However, differential analysis of bounded DNA methylation data often requires data…
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…
We introduce a probabilistic model with implicit norm regularization for learning nonnegative matrix factorization (NMF) that is commonly used for predicting missing values and finding hidden patterns in the data, in which the matrix…
Background: The analysis of DNA methylation is a key component in the development of personalized treatment approaches. A common way to measure DNA methylation is the calculation of beta values, which are bounded variables of the form M =…
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…
Biological signals of interest in high-dimensional data are often masked by dominant variation shared across conditions. This variation, arising from baseline biological structure or technical effects, can prevent standard dimensionality…
Many researches demonstrated that the DNA methylation, which occurs in the context of a CpG, has strong correlation with diseases, including cancer. There is a strong interest in analyzing the DNA methylation data to find how to distinguish…
The objective of this study is to predict suicidal and non-suicidal deaths from DNA methylation data using a modern machine learning algorithm. We used support vector machines to classify existing secondary data consisting of normalized…
We show how to incorporate information from labeled examples into nonnegative matrix factorization (NMF), a popular unsupervised learning algorithm for dimensionality reduction. In addition to mapping the data into a space of lower…
Beta process is the standard nonparametric Bayesian prior for latent factor model. In this paper, we derive a structured mean-field variational inference algorithm for a beta process non-negative matrix factorization (NMF) model with…
We propose a deep generative factor analysis model with beta process prior that can approximate complex non-factorial distributions over the latent codes. We outline a stochastic EM algorithm for scalable inference in a specific…
Nonnegative Matrix Factorization (NMF) is a widely used technique for data representation. Inspired by the expressive power of deep learning, several NMF variants equipped with deep architectures have been proposed. However, these methods…
Semi-Non-negative Matrix Factorization is a technique that learns a low-dimensional representation of a dataset that lends itself to a clustering interpretation. It is possible that the mapping between this new representation and our…
Non-negative matrix factorization (NMF) has become a popular machine learning approach to many problems in text mining, speech and image processing, bio-informatics and seismic data analysis to name a few. In NMF, a matrix of non-negative…
Deep Nonnegative Matrix Factorization (deep NMF) has recently emerged as a valuable technique for extracting multiple layers of features across different scales. However, all existing deep NMF models and algorithms have primarily centered…
Nonnegative matrix factorization (NMF) is a popular method used to reduce dimensionality in data sets whose elements are nonnegative. It does so by decomposing the data set of interest, $\mathbf{X}$, into two lower rank nonnegative matrices…
DNA methylation is a significant driver of cell-type heterogeneity and has been implicated in various regulatory processes ranging from cell differentiation to imprinting. As the methyl group is embedded in the DNA molecule, assessing DNA…
Epigenetic alterations have an important role in the development of several types of cancer. Epigenetic studies generate a large amount of data, which makes it essential to develop novel models capable of dealing with large-scale data. In…
Accurate computational identification of DNA methylation is essential for understanding epigenetic regulation. Although deep learning excels in this binary classification task, its "black-box" nature impedes biological insight. We address…
This paper describes algorithms for nonnegative matrix factorization (NMF) with the beta-divergence (beta-NMF). The beta-divergence is a family of cost functions parametrized by a single shape parameter beta that takes the Euclidean…