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Single-cell gene expression data are often characterized by large matrices, where the number of cells may be lower than the number of genes of interest. Factorization models have emerged as powerful tools to condense the available…

Gaussian factor models have proven widely useful for parsimoniously characterizing dependence in multivariate data. There is a rich literature on their extension to mixed categorical and continuous variables, using latent Gaussian variables…

Network models provide a powerful framework for analysing single-cell count data, facilitating the characterisation of cellular identities, disease mechanisms, and developmental trajectories. However, uncertainty modeling in unsupervised…

Next-generation sequencing technologies provide a revolutionary tool for generating gene expression data. Starting with a fixed RNA sample, they construct a library of millions of differentially abundant short sequence tags or "reads",…

Sequencing-based technologies provide an abundance of high-dimensional biological datasets with skewed and zero-inflated measurements. Classification of such data with linear discriminant analysis leads to poor performance due to the…

Background: Single-cell RNA sequencing (scRNA-seq) is a powerful profiling technique at the single-cell resolution. Appropriate analysis of scRNA-seq data can characterize molecular heterogeneity and shed light into the underlying cellular…

In recent years, the field of single-cell data analysis has seen a marked advancement in the development of clustering methods. Despite advancements, most of these algorithms still concentrate on analyzing the provided single-cell matrix…

Sequencing technologies have revolutionised the field of molecular biology. We now have the ability to routinely capture the complete RNA profile in tissue samples. This wealth of data allows for comparative analyses of RNA levels at…

Missing data is a common issue in various fields such as medicine, social sciences, and natural sciences, and it poses significant challenges for accurate statistical analysis. Although numerous imputation methods have been proposed to…

We propose a novel approach to estimating the precision matrix of multivariate Gaussian data that relies on decomposing them into a low-rank and a diagonal component. Such decompositions are very popular for modeling large covariance…

We propose a probabilistic model for interpreting gene expression levels that are observed through single-cell RNA sequencing. In the model, each cell has a low-dimensional latent representation. Additional latent variables account for…

We propose a probabilistic model for interpreting gene expression levels that are observed through single-cell RNA sequencing. In the model, each cell has a low-dimensional latent representation. Additional latent variables account for…

The location, timing, and abundance of gene expression (both mRNA and proteins) within a tissue define the molecular mechanisms of cell functions. Recent technology breakthroughs in spatial molecular profiling, including imaging-based…

This paper presents a new modeling strategy for joint unsupervised analysis of multiple high-throughput biological studies. As in Multi-study Factor Analysis, our goals are to identify both common factors shared across studies and…

Bayesian computation for filtering and forecasting analysis is developed for a broad class of dynamic models. The ability to scale-up such analyses in non-Gaussian, nonlinear multivariate time series models is advanced through the…

One important problem in genome science is to determine sets of co-regulated genes based on measurements of gene expression levels across samples, where the quantification of expression levels includes substantial technical and biological…

Models with latent factors recently attract a lot of attention. However, most investigations focus on linear regression models and thus cannot capture nonlinearity. To address this issue, we propose a novel Factor Augmented Single-Index…

Motivation: Modelling methods that find structure in data are necessary with the current large volumes of genomic data, and there have been various efforts to find subsets of genes exhibiting consistent patterns over subsets of treatments.…

Single-cell RNA sequencing (scRNA-seq) is powerful technology that allows researchers to understand gene expression patterns at the single-cell level. However, analysing scRNA-seq data is challenging due to issues and biases in data…

Dimension reduction techniques are among the most essential analytical tools in the analysis of high-dimensional data. Generalized principal component analysis (PCA) is an extension to standard PCA that has been widely used to identify…