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

We propose Subsampling MCMC, a Markov Chain Monte Carlo (MCMC) framework where the likelihood function for $n$ observations is estimated from a random subset of $m$ observations. We introduce a highly efficient unbiased estimator of the…

Feature quality is paramount for classification performance, particularly in few-shot scenarios. Contrastive learning, a widely adopted technique for enhancing feature quality, leverages sample relations to extract intrinsic features that…

When estimating a proportion and only a sample of triplets is given, dependencies within the triplets are to be accounted for. Without assuming a distribution for the success count of the triplet, together with the proportion, as second and…

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…

This study reveals the inherent tolerance of contrastive learning (CL) towards sampling bias, wherein negative samples may encompass similar semantics (\eg labels). However, existing theories fall short in providing explanations for this…

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…

Single-cell RNA sequencing (scRNA-seq) enables researchers to analyze gene expression at single-cell level. One important task in scRNA-seq data analysis is unsupervised clustering, which helps identify distinct cell types, laying down the…

The Plackett-Luce (PL) model is ubiquitous in learning-to-rank (LTR) because it provides a useful and intuitive probabilistic model for sampling ranked lists. Counterfactual offline evaluation and optimization of ranking metrics are pivotal…

RNA-Seq data characteristically exhibits large variances, which need to be appropriately accounted for in the model. We first explore the effects of this variability on the maximum likelihood estimator (MLE) of the overdispersion parameter…

Generalized linear mixed models (GLMM) are commonly used to analyze clustered data, but when the number of clusters is small to moderate, standard statistical tests may produce elevated type I error rates. Small-sample corrections have been…

High-dimensional compositional covariates, often derived from count data, are subject to measurement error and are frequently analyzed after aggregation along a prespecified tree to improve interpretability in applications such as…

Objective: The objective of this study is to develop a machine learning (ML)-based framework for early risk stratification of clinical trials (CTs) according to their likelihood of exhibiting a high rate of dosing errors, using information…

The so-called gut-brain axis has stimulated extensive research on microbiomes. One focus is to assess the association between certain clinical outcomes and the relative abundances of gut microbes, which can be presented as sub-compositional…

Modern computational advances have enabled easy parallel implementations of Markov chain Monte Carlo (MCMC). However, almost all work in estimating the variance of Monte Carlo averages, including the efficient batch means (BM) estimator,…

Contrastive Analysis is a sub-field of Representation Learning that aims at separating common factors of variation between two datasets, a background (i.e., healthy subjects) and a target (i.e., diseased subjects), from the salient factors…

Bacterial biofilm segmentation poses significant challenges due to lack of apparent structure, poor imaging resolution, limited contrast between conterminous cells and high density of cells that overlap. Although there exist bacterial…

Trace norm regularization is a widely used approach for learning low rank matrices. A standard optimization strategy is based on formulating the problem as one of low rank matrix factorization which, however, leads to a non-convex problem.…

Predictive models trained on observational data often fail to generalise to the distributions they encounter when deployed, especially when the training data is a product of the system being optimised. Recommender systems are a canonical…

Motivated by regression analysis for microbiome compositional data, this paper considers generalized linear regression analysis with compositional covariates, where a group of linear constraints on regression coefficients are imposed to…

Microbiome compositional data are often high-dimensional, sparse, and exhibit pervasive cross-sample heterogeneity. Generative modeling is a popular approach to analyze such data, and effective generative models must accurately characterize…