Related papers: Multi-sample estimation of centered log-ratio matr…

Metagenomics sequencing is routinely applied to quantify bacterial abundances in microbiome studies, where the bacterial composition is estimated based on the sequencing read counts. Due to limited sequencing depth and DNA dropouts, many…

Discrete data such as counts of microbiome taxa resulting from next-generation sequencing are routinely encountered in bioinformatics. Taxa count data in microbiome studies are typically high-dimensional, over-dispersed, and can only reveal…

Compositional data, where only relative abundances are available, are common in microbiome and other high-throughput sequencing studies. Log ratios between groups of variables serve as key biomarkers in these settings. However, selecting…

In microbiome and genomic studies, the regression of compositional data has been a crucial tool for identifying microbial taxa or genes that are associated with clinical phenotypes. To account for the variation in sequencing depth, the…

Microbial communities analysis is drawing growing attention due to the rapid development of high-throughput sequencing techniques nowadays. The observed data has the following typical characteristics: it is high-dimensional, compositional…

In current applied research the most-used route to an analysis of composition is through log-ratios -- that is, contrasts among log-transformed measurements. Here we argue instead for a more direct approach, using a statistical model for…

High-throughput sequencing technology allows us to test the compositional difference of bacteria in different populations. One important feature of human microbiome data is that it often includes a large number of zeros. Such data can be…

Compositional data arise in many areas of research in the natural and biomedical sciences. One prominent example is in the study of the human gut microbiome, where one can measure the relative abundance of many distinct microorganisms in a…

Human microbiome studies based on genetic sequencing techniques produce compositional longitudinal data of the relative abundances of microbial taxa over time, allowing to understand, through mixed-effects modeling, how microbial…

This paper investigates the computational and statistical limits in clustering matrix-valued observations. We propose a low-rank mixture model (LrMM), adapted from the classical Gaussian mixture model (GMM) to treat matrix-valued…

Clustering analysis by nonnegative low-rank approximations has achieved remarkable progress in the past decade. However, most approximation approaches in this direction are still restricted to matrix factorization. We propose a new low-rank…

In natural language processing (NLP), the likelihood ratios (LRs) of N-grams are often estimated from the frequency information. However, a corpus contains only a fraction of the possible N-grams, and most of them occur infrequently. Hence,…

The interactions between microbial taxa in microbiome data has been under great research interest in the science community. In particular, several methods such as SPIEC-EASI, gCoda, and CD-trace have been proposed to model the conditional…

Compositional data sets are ubiquitous in science, including geology, ecology, and microbiology. In microbiome research, compositional data primarily arise from high-throughput sequence-based profiling experiments. These data comprise…

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…

CUR matrix decomposition computes the low rank approximation of a given matrix by using the actual rows and columns of the matrix. It has been a very useful tool for handling large matrices. One limitation with the existing algorithms for…

The human microbiome plays an important role in human health and disease status. Next generating sequencing technologies allow for quantifying the composition of the human microbiome. Clustering these microbiome data can provide valuable…

The interpretation of count data originating from the current generation of DNA sequencing platforms requires special attention. In particular, the per-sample library sizes often vary by orders of magnitude from the same sequencing run, and…

With the development of next generation sequencing technology, researchers have now been able to study the microbiome composition using direct sequencing, whose output are bacterial taxa counts for each microbiome sample. One goal of…

In human microbiome studies, sequencing reads data are often summarized as counts of bacterial taxa at various taxonomic levels specified by a taxonomic tree. This paper considers the problem of analyzing two repeated measurements of…