Related papers: Inference for microbe--metabolite association netw…

Selecting relevant features associated with a given response variable is an important issue in many scientific fields. Quantifying quality and uncertainty of a selection result via false discovery rate (FDR) control has been of recent…

In recent years, multiple hypothesis testing has come to the forefront of statistical research, ostensibly in relation to applications in genomics and some other emerging fields. The false discovery rate (FDR) and its variants provide very…

We introduce Mercator, a reliable embedding method to map real complex networks into their hyperbolic latent geometry. The method assumes that the structure of networks is well described by the Popularity$\times$Similarity…

In microbiome studies, it is often of great interest to identify clusters or partitions of microbiome profiles within a study population and to characterize the distinctive attributes of each resulting microbial community. While raw counts…

Extracting associations that recur across multiple studies while controlling the false discovery rate is a fundamental challenge. Here, we consider an extension of Efron's single-study two-groups model to allow joint analysis of multiple…

This paper explores the intrinsic connections between the Bayesian false discovery rate (FDR) control procedures and their counterpart of frequentist procedures. We attempt to offer a unified view of FDR control within and beyond the…

Simultaneously performing variable selection and inference in high-dimensional regression models is an open challenge in statistics and machine learning. The increasing availability of vast amounts of variables requires the adoption of…

A fundamental problem associated with the task of network reconstruction from dynamical or behavioral data consists in determining the most appropriate model complexity in a manner that prevents overfitting, and produces an inferred network…

Efforts to develop more efficient multiple hypothesis testing procedures for false discovery rate (FDR) control have focused on incorporating an estimate of the proportion of true null hypotheses (such procedures are called adaptive) or…

In many applications, the process of identifying a specific feature of interest often involves testing multiple hypotheses for their joint statistical significance. Examples include mediation analysis which simultaneously examines the…

The genetic basis of multiple phenotypes such as gene expression, metabolite levels, or imaging features is often investigated by testing a large collection of hypotheses, probing the existence of association between each of the traits and…

The intricate interplay between host organisms and their gut microbiota has catalyzed research into the microbiome's role in disease, shedding light on novel aspects of disease pathogenesis. However, the mechanisms through which the…

Complex systems are often driven by higher-order interactions among multiple units, naturally represented as hypergraphs. Understanding dependency structures within these hypergraphs is crucial for understanding and predicting the behavior…

Many statistical problems can be addressed by applying a multiple testing procedure (MTP) that controls either the Family-wise Error Rate (FWER) or False Discovery Rate (FDR) under unknown arbitrarily-interdependent $p$-values, without…

We consider a system of binary interacting chains describing the dynamics of a group of $N$ components that, at each time unit, either send some signal to the others or remain silent otherwise. The interactions among the chains are encoded…

The analysis of biological networks is characterized by the definition of precise linear constraints used to cumulatively reduce the solution space of the computed states of a multi-omic (for instance metabolic, transcriptomic and…

Conventional multiple testing procedures often assume hypotheses for different features are exchangeable. However, in many scientific applications, additional covariate information regarding the patterns of signals and nulls are available.…

Machine-learning methods in biochemistry commonly represent molecules as graphs of pairwise intermolecular interactions for property and structure predictions. Most methods operate on a single graph, typically the minimal free energy (MFE)…

Models of networks play a major role in explaining and reproducing empirically observed patterns. Suitable models can be used to randomize an observed network while preserving some of its features, or to generate synthetic graphs whose…

Predicting the ground-state 3D molecular conformations from 2D molecular graphs is critical in computational chemistry due to its profound impact on molecular properties. Deep learning (DL) approaches have recently emerged as promising…