Related papers: NBLDA: Negative Binomial Linear Discriminant Analy…

The seemingly disjoint problems of count and mixture modeling are united under the negative binomial (NB) process. A gamma process is employed to model the rate measure of a Poisson process, whose normalization provides a random probability…

We propose data thinning, an approach for splitting an observation into two or more independent parts that sum to the original observation, and that follow the same distribution as the original observation, up to a (known) scaling of a…

Recently, ultra high-throughput sequencing of RNA (RNA-Seq) has been developed as an approach for analysis of gene expression. By obtaining tens or even hundreds of millions of reads of transcribed sequences, an RNA-Seq experiment can offer…

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…

We propose a Bayesian approach to learn discriminative dictionaries for sparse representation of data. The proposed approach infers probability distributions over the atoms of a discriminative dictionary using a Beta Process. It also…

This paper proposes a new generalized linear model with the fractional binomial distribution. Zero-inflated Poisson/negative binomial distributions are used for count data with many zeros. To analyze the association of such a count variable…

RNA-Seq is a widely-used method for studying the behavior of genes under different biological conditions. An essential step in an RNA-Seq study is normalization, in which raw data are adjusted to account for factors that prevent direct…

The advancement of single-cell RNA-sequencing (scRNA-seq) technologies allow us to study the individual level cell-type-specific gene expression networks by direct inference of genes' conditional independence structures. scRNA-seq data…

We introduce the Poisson Log-Normal Graphical Model for count data, and present a normality transformation for data arising from this distribution. The model and transformation are feasible for high-throughput microRNA (miRNA) sequencing…

We consider the problem of choosing between parametric models for a discrete observable, taking a Bayesian approach in which the within-model prior distributions are allowed to be improper. In order to avoid the ambiguity in the marginal…

The analysis of multivariate discrete data is crucial in various scientific research areas, such as epidemiology, the social sciences, genomics, and environmental studies. As the availability of such data increases, developing robust…

Regression for count data is widely performed by models such as Poisson, negative binomial (NB) and zero-inflated regression. A challenge often faced by practitioners is the selection of the right model to take into account dispersion,…

Ultra high-throughput sequencing of transcriptomes (RNA-Seq) has enabled the accurate estimation of gene expression at individual isoform level. However, systematic biases introduced during the sequencing and mapping processes as well as…

RNA-sequencing (RNA-seq) has become an exemplar technology in modern biology and clinical applications over the past decade. It has gained immense popularity in the recent years driven by continuous efforts of the bioinformatics community…

Next-generation sequencing technologies now constitute a method of choice to measure gene expression. Data to analyze are read counts, commonly modeled using Negative Binomial distributions. A relevant issue associated with this…

We propose a modification of linear discriminant analysis, referred to as compressive regularized discriminant analysis (CRDA), for analysis of high-dimensional datasets. CRDA is specially designed for feature elimination purpose and can be…

In behavioral and psychiatric research, data consisting of a per-subject proportion of "successes" and "failures" over a finite number of trials often arise. This kind of clustered binary data are usually non-normally distributed, which can…

The analysis of count data is commonly done using Poisson models. Negative binomial models are a straightforward and readily motivated generalization for the case of overdispersed data, i.e., when the observed variance is greater than…

The use of deep learning models in computational biology has increased massively in recent years, and it is expected to continue with the current advances in the fields such as Natural Language Processing. These models, although able to…

Gene regulatory network inference is crucial for understanding the complex molecular interactions in various genetic and environmental conditions. The rapid development of single-cell RNA sequencing (scRNA-seq) technologies unprecedentedly…