Related papers: Doubly Non-Central Beta Matrix Factorization for D…
We develop Bayesian inference methods for a recently-emerging type of epigenetic data to study the transmission fidelity of DNA methylation patterns over cell divisions. The data consist of parent-daughter double-stranded DNA methylation…
Nonnegative matrix factorization is usually powerful for learning the "shallow" parts-based representation, but it clearly fails to discover deep hierarchical information within both the basis and representation spaces. In this paper, we…
The beta distribution is the best-known distribution for modelling doubly-bounded data, \eg percentage data or probabilities. A new generalization of the beta distribution is proposed, which uses a cubic transformation of the beta random…
We perform differential expression analysis of high-throughput sequencing count data under a Bayesian nonparametric framework, removing sophisticated ad-hoc pre-processing steps commonly required in existing algorithms. We propose to use…
This paper explores the transgenerational DNA methylation pattern (DNA methylation transmitted from one generation to the next) via a clustering approach. Beta regression is employed to model the transmission pattern from parents to their…
In this paper, we determine the density functions of nonsymmetrised doubly noncentral matrix variate beta type I and II distributions. The nonsymetrised density functions of doubly noncentral and noncentral bimatrix variate generalised beta…
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…
In many fields, researchers are interested in large and complex biological processes. Two important examples are gene expression and DNA methylation in genetics. One key problem is to identify aberrant patterns of these processes and…
How DNA-binding proteins locate specific genomic targets remains a central challenge in molecular biology. Traditional protein-centric approaches, which rely on wet-lab experiments and visualization techniques, often lack genome-wide…
Non-negative matrix factorization with the generalized Kullback-Leibler divergence (NMF) and latent Dirichlet allocation (LDA) are two popular approaches for dimensionality reduction of non-negative data. Here, we show that NMF with…
Non-negative matrix factorization (NMF) approximates a non-negative endogenous data matrix as $Y_1 \approx XB$, with non-negative latent components $X$ and coefficients $B$. Standard covariate-aware NMF is feedforward: $B$ depends only on…
Batch Normalization (BN) and its variants have delivered tremendous success in combating the covariate shift induced by the training step of deep learning methods. While these techniques normalize feature distributions by standardizing with…
We introduce a novel Bayesian hybrid matrix factorisation model (HMF) for data integration, based on combining multiple matrix factorisation methods, that can be used for in- and out-of-matrix prediction of missing values. The model is very…
This paper introduces a robust mixing model to describe hyperspectral data resulting from the mixture of several pure spectral signatures. This new model not only generalizes the commonly used linear mixing model, but also allows for…
Non-negative Matrix Factorization (NMF) is an intensively used technique for obtaining parts-based, lower dimensional and non-negative representation. Researchers in biology, medicine, pharmacy and other fields often prefer NMF over other…
Non-negative matrix factorization (NMF) is an important technique for obtaining low dimensional representations of datasets. However, classical NMF does not take into account data that is collected at different times or in different…
Non-negative matrix factorization (NMF) and non-negative tensor factorization (NTF) decompose non-negative high-dimensional data into non-negative low-rank components. NMF and NTF methods are popular for their intrinsic interpretability and…
In this paper, we determine the density functions of doubly noncentral singular matrix variate beta type I and II distributions.
We make use of ideas from the theory of complex networks to implement a machine learning classification of human DNA methylation data, that carry signatures of cancer development. The data were obtained from patients with various kinds of…
Cell-free DNA (cfDNA) analysis is a powerful, minimally invasive tool for monitoring disease progression, treatment response, and early detection. A major challenge, however, is accurately determining the tissue of origin, especially in…