Related papers: A New Approach to Compositional Data Analysis usin…
Microbiome data are complex in nature, involving high dimensionality, compositionally, zero inflation, and taxonomic hierarchy. Compositional data reside in a simplex that does not admit the standard Euclidean geometry. Most existing…
This paper introduces a rectified and renormalized Fisher-Bingham model for compositional data with zeros, motivated in part by the presence of zeros in microbiota studies. The approach represents compositions through a square-root…
High-dimensional compositional data, such as those from human microbiome studies, pose unique statistical challenges due to the simplex constraint and excess zeros. While dimension reduction is indispensable for analyzing such data,…
In real world applications dealing with compositional datasets, it is easy to face the presence of structural zeros. The latter arise when, due to physical limitations, one or more variables are intrinsically zero for a subset of the…
In compositional data analysis an observation is a vector containing non-negative values, only the relative sizes of which are considered to be of interest. Without loss of generality, a compositional vector can be taken to be a vector of…
This paper is motivated by the recent interest in the analysis of high dimen- sional microbiome data. A key feature of this data is the presence of `structural zeros' which are microbes missing from an observation vector due to an…
The growing use of high-throughput sequencing (HTS) has enabled the large-scale production of compositional count data, driving progress in microbiome research. However, such count data are often high-dimensional, over-dispersed, and…
Compositional data, such as human gut microbiomes, consist of non-negative variables whose only the relative values to other variables are available. Analyzing compositional data such as human gut microbiomes needs a careful treatment of…
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, also referred to as simplicial data, naturally arise in many scientific domains such as geochemistry, microbiology, and economics. In such domains, obtaining sensible lower-dimensional representations and modes of…
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…
Compositional data have two unique characteristics compared to typical multivariate data: the observed values are nonnegative and their summand is exactly one. To reflect these characteristics, a specific regularized regression model with…
Compositional data analysis is carried out either by neglecting the compositional constraint and applying standard multivariate data analysis, or by transforming the data using the logs of the ratios of the components. In this work we…
Many scientific datasets are compositional in nature. Important biological examples include species abundances in ecology, cell-type compositions derived from single-cell sequencing data, and amplicon abundance data in microbiome research.…
Applications such as the analysis of microbiome data have led to renewed interest in statistical methods for compositional data, i.e., multivariate data in the form of probability vectors that contain relative proportions. In particular,…
High-dimensional compositional data are prevalent in many applications. The simplex constraint poses intrinsic challenges to inferring the conditional dependence relationships among the components forming a composition, as encoded by a…
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…
Compositional data, representing proportions constrained to the simplex, arise in diverse fields such as geosciences, ecology, genomics, and microbiome research. Existing nonparametric density estimation methods often rely on…
For the Bio+Med-Vis Challenge 2024, we propose a visual analytics system as a redesign for the scatter pie chart visualization of cell type proportions of spatial transcriptomics data. Our design uses three linked views: a view of the…
A key challenge in differential abundance analysis of microbial samples is that the counts for each sample are compositional, resulting in biased comparisons of the absolute abundance across study groups. Normalization-based differential…