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Non-negative Matrix Factorization (NMF) has proven to be a powerful unsupervised learning method for uncovering hidden features in complex and noisy data sets with applications in data mining, text recognition, dimension reduction, face…
Latent Dirichlet allocation (LDA) is useful in document analysis, image processing, and many information systems; however, its generalization performance has been left unknown because it is a singular learning machine to which regular…
Deep Generative Models (DGMs) are versatile tools for learning data representations while adequately incorporating domain knowledge such as the specification of conditional probability distributions. Recently proposed DGMs tackle the…
Boolean matrix factorisation aims to decompose a binary data matrix into an approximate Boolean product of two low rank, binary matrices: one containing meaningful patterns, the other quantifying how the observations can be expressed as a…
Matrix factorization is a fundamental method in statistics and machine learning for inferring and summarizing structure in multivariate data. Modern data sets often come with "side information" of various forms (images, text, graphs) that…
DNA methylation is an important biological mechanism to regulate gene expression and control cell development. Mechanistic modeling has become a popular approach to enhance our understanding of the dynamics of methylation pattern formation…
In this paper, we describe centering and noncentering methodology as complementary techniques for use in parametrization of broad classes of hierarchical models, with a view to the construction of effective MCMC algorithms for exploring…
Nonnegative matrix factorization (NMF) is a powerful tool in data exploratory analysis by discovering the hidden features and part-based patterns from high-dimensional data. NMF and its variants have been successfully applied into diverse…
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…
Nonnegative matrix factorization (NMF) has attracted much attention in the last decade as a dimension reduction method in many applications. Due to the explosion in the size of data, naturally the samples are collected and stored…
To generalize deepfake detectors to future unseen forgeries, most existing methods attempt to simulate the dynamically evolving forgery types using available source domain data. However, predicting an unbounded set of future manipulations…
Non-negative matrix factorization (NMF) is widely used for dimensionality reduction and interpretable analysis, but standard formulations are unsupervised and cannot directly exploit class labels. Existing supervised or semi-supervised…
DNA Methylation has been the most extensively studied epigenetic mark. Usually a change in the genotype, DNA sequence, leads to a change in the phenotype, observable characteristics of the individual. But DNA methylation, which happens in…
We introduce a model of DNA sequence evolution which can account for biases in mutation rates that depend on the identity of the neighboring bases. An analytic solution for this class of non-equilibrium models is developed by adopting…
A common approach to analyze a covariate-sample count matrix, an element of which represents how many times a covariate appears in a sample, is to factorize it under the Poisson likelihood. We show its limitation in capturing the tendency…
Nonnegative matrix factorization (NMF) has been successfully applied to many areas for classification and clustering. Commonly-used NMF algorithms mainly target on minimizing the $l_2$ distance or Kullback-Leibler (KL) divergence, which may…
Recently, many improved naive Bayes methods have been developed with enhanced discrimination capabilities. Among them, regularized naive Bayes (RNB) produces excellent performance by balancing the discrimination power and generalization…
From a systems biology perspective the majority of cancer models, although interesting and providing a qualitative explanation of some problems, have a major disadvantage in that they usually miss a genuine connection with experimental…
Non-negative matrix factorization (NMF) has proved effective in many clustering and classification tasks. The classic ways to measure the errors between the original and the reconstructed matrix are $l_2$ distance or Kullback-Leibler (KL)…
Identifying differentially expressed genes from RNA sequencing data remains a challenging task because of the considerable uncertainties in parameter estimation and the small sample sizes in typical applications. Here we introduce Bayesian…