Related papers: Towards a Taxonomical Consensus: Diversity and Ric…
We describe the Microbial Community Reconstruction ({\bf MCR}) Problem, which is fundamental for microbiome analysis. In this problem, the goal is to reconstruct the identity and frequency of species comprising a microbial community, using…
Clustering of single-cell RNA sequencing (scRNA-seq) datasets can give key insights into the biological functions of cells. Therefore, it is not surprising that network-based community detection methods (one of the better clustering…
The assessment of diversity and similarity is relevant in monitoring the status of ecosystems. The respective indicators are based on the taxonomic composition of biological communities of interest, currently estimated through the…
High-throughput shotgun sequence data makes it possible in principle to accurately estimate population genetic parameters without confounding by SNP ascertainment bias. One such statistic of interest is the proportion of heterozygous sites…
Multicellular systems play a key role in bioprocess and biomedical engineering. Cell ensembles encountered in these setups show phenotypic variability like size and biochemical composition. As this variability may result in undesired…
The paper presents the investigation and implementation of the relationship between diversity and the performance of multiple classifiers on classification accuracy. The study is critical as to build classifiers that are strong and can…
We wish to estimate the total number of classes in a population based on sample counts, especially in the presence of high latent diversity. Drawing on probability theory that characterizes distributions on the integers by ratios of…
The increasing volumes of data produced by high-throughput instruments coupled with advanced computational infrastructures for scientific computing have enabled what is often called a {\em Fourth Paradigm} for scientific research based on…
This paper studies the sample complexity of searching over multiple populations. We consider a large number of populations, each corresponding to either distribution P0 or P1. The goal of the search problem studied here is to find one…
Network Intrusion Detection System is a critical means of ensuring cybersecurity. However, existing Genetic Algorithm-based feature selection methods face several limitations when dealing with high-dimensional redundant traffic features.…
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…
Training population selection for genomic selection has captured a great deal of interest in animal and plant breeding. In this article, we derive a computationally efficient statistic to measure the reliability of estimates of genetic…
Accurate sample classification using transcriptomics data is crucial for advancing personalized medicine. Achieving this goal necessitates determining a suitable sample size that ensures adequate statistical power without undue resource…
The diversity of virus populations within single infected hosts presents a major difficulty for the natural immune response as well as for vaccine design and antiviral drug therapy. Recently developed pyrophosphate based sequencing…
The problem of community detection in networks is usually formulated as finding a single partition of the network into some "correct" number of communities. We argue that it is more interpretable and in some regimes more accurate to…
There are many instances in genetics in which we wish to determine whether two candidate populations are distinguishable on the basis of their genetic structure. Examples include populations which are geographically separated, case--control…
Insects comprise millions of species, many experiencing severe population declines under environmental and habitat changes. High-throughput approaches are crucial for accelerating our understanding of insect diversity, with DNA barcoding…
Cluster analysis of biological samples using gene expression measurements is a common task which aids the discovery of heterogeneous biological sub-populations having distinct mRNA profiles. Several model-based clustering algorithms have…
In this paper entropy based methods are compared and used to measure structural diversity of an ensemble of 21 classifiers. This measure is mostly applied in ecology, whereby species counts are used as a measure of diversity. The measures…
Background: Microbiota have evolved to acclimate themselves to many environments. Humanity is become ever increasingly medicated and many of those medications are antibiotics. Sadly, Microbiota are adapting to medication and with each…