Related papers: Robust estimation of microbial diversity in theory…
Capture-recapture methods aim to estimate the size of a closed population on the basis of multiple incomplete enumerations of individuals. In many applications, the individual probability of being recorded is heterogeneous in the…
Advances in next-generation sequencing technology have enabled the high-throughput profiling of metagenomes and accelerated the microbiome study. Recently, there has been a rise in quantitative studies that aim to decipher the microbiome…
Source-sink systems are metapopulations of patches that can be of variable habitat quality. They can be seen as graphs, where vertices represent the patches, and the weighted oriented edges give the probability of dispersal from one patch…
Motivation: Estimation of bacterial community composition from a high-throughput sequenced sample is an important task in metagenomics applications. Since the sample sequence data typically harbors reads of variable lengths and different…
A key unresolved question in microbial ecology is how the extraordinary diversity of microbiomes emerges from the behaviour of individual populations. This process is driven by the cross-feeding networks that structure these communities,…
Species-rich communities, such as the microbiota or microbial ecosystems, provide key functions for human health and climatic resilience. Increasing effort is being dedicated to design experimental protocols for selecting community-level…
We propose a truncation model for abundance distribution in the species richness estimation. This model is inherently semiparametric and incorporates an unknown truncation threshold between rare and abundant counts observations. Using the…
Why, contrary to theoretical predictions, do marine microbe communities harbor tremendous phenotypic heterogeneity? How can so many marine microbe species competing in the same niche coexist? We discovered a unifying explanation for both…
It is generally accepted that "diversity" is associated with success in evolutionary algorithms. However, diversity is a broad concept that can be measured and defined in a multitude of ways. To date, most evolutionary computation research…
Source-sink systems are metapopulations of habitat patches with different, and possibly temporally varying, habitat qualities, which are commonly used in ecology to study the fate of spatially extended natural populations. We propose new…
Topical discussion networks (TDNs) are networks centered around a discourse concerning a particular concept, whether in real life or online. This paper analogises the population of such networks to populations encountered in mathematical…
Measuring diversity accurately is important for many scientific fields, including machine learning (ML), ecology, and chemistry. The Vendi Score was introduced as a generic similarity-based diversity metric that extends the Hill number of…
Phytoplankton plays an important role in marine ecosystem. It is defined as a biological factor to assess marine quality. The identification of phytoplankton species has a high potential for monitoring environmental, climate changes and for…
Frequently one has to search within a finite population for a single particular individual or item with a rare characteristic. Whether an item possesses the characteristic can only be determined by close inspection. The availability of…
Complex contagions describe systems where the probability or rate of contagious transmission is a nonlinear function of the exposure to contagious agents. These models were first studied theoretically but have since been used to capture…
Complementarity among species with different traits is one of the basic processes affecting biodiversity, defined as the number of species in the ecosystem. We present here a soluble model ecosystem in which the species are characterized by…
In this paper, we advocate a novel measure for the purpose of checking the quality of a cluster partition for a sample into several distinct classes, and thus, determine the unknown value for the true number of clusters prevailing the…
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…
Surveys of microbial biodiversity such as the Earth Microbiome Project (EMP) and the Human Microbiome Project (HMP) have revealed robust ecological patterns across different environments. A major goal in ecology is to leverage these…
The goal of metagenomics is to study the composition of microbial communities, typically using high-throughput shotgun sequencing. In the metagenomic binning problem, we observe random substrings (called contigs) from a mixture of genomes…