Related papers: Robust estimation of microbial diversity in theory…
We consider the estimation of the total number $N$ of species based on the abundances of species that have been observed. We adopt a non parametric approach where the true abundance distribution $p$ is only supposed to be convex. From this…
Variation and selection are the core principles of Darwinian evolution, yet quantitatively relating the diversity of a population to its capacity to respond to selection is challenging. Here, we examine this problem at a molecular level in…
Microbial communities are ubiquitous in nature and come in a multitude of forms, ranging from communities dominated by a handful of species to communities containing a wide variety of metabolically distinct organisms. This huge range in…
Evolution has fascinated quantitative and physical scientists for decades: how can the random process of mutation, recombination, and duplication of genetic information generate the diversity of life? What determines the rate of evolution?…
Socio-diversity, the variety of human opinions, ideas, behaviors and styles, has profound implications for social systems. While it fuels innovation, productivity, and collective intelligence, it can also complicate communication and erode…
Richness estimation of an interesting area is always a challenge statistical work due to small sample size or species identity error. In the literatures, most richness estimators were only proposed to tackle the underestimation of the…
A major challenge for community ecology is using spatio-temporal data to infer parameters of dynamical models without conducting laborious experiments. We present a novel framework from statistical physics -- Maximum Caliber -- to…
The advent of high-throughput sequencing technologies has made data from DNA material readily available, leading to a surge of microbiome-related research establishing links between markers of microbiome health and specific outcomes.…
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 number density and correlation function of galaxies are two key quantities to characterize the distribution of the observed galaxy population. High-$z$ spectroscopic surveys, which usually involve complex target selection and are…
Estimating the density of a continuous random variable X has been studied extensively in statistics, in the setting where n independent observations of X are given a priori and one wishes to estimate the density from that. Popular methods…
Microorganisms live in environments that inevitably fluctuate between mild and harsh conditions. As harsh conditions may cause extinctions, the rate at which fluctuations occur can shape microbial communities and their diversity, but we…
A central issue in ecology today is that of the factors determining the relative abundance of species within a natural community. The proper application of the principles of statistical physics to the problem of species abundance…
Antibiotic resistance is a major threat to global health. It emerges in multispecies microbial communities under antibiotic exposure. This makes antibiotic spectrum -- a drug's distribution of effects across species -- a potential key…
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…
Microbial communities assemble through a complex set of interactions between microbes and their environment, and the resulting metabolic impact on the host ecosystem can be profound. Microbial activity is known to impact human health, plant…
The analysis of benthic assemblages is a valuable tool to describe the ecological status of transitional water ecosystems, but species are extremely sensitive and respond to both microhabitat and seasonal differences. The identification of…
Classic concepts of genetic (gene) diversity (heterozygosity) such as Nei (1973: PNAS) and Nei and Li (1979: PNAS) nucleotide diversity were defined within the context of populations. Although variations are often measured in population…
Ranking populations such as institutions based on certain characteristics is often of interest, and these ranks are typically estimated using samples drawn from the populations. Due to sample randomness, it is important to quantify the…
Reliable data-driven estimation of Shannon entropy from small data sets, where the number of examples is potentially smaller than the number of possible outcomes, is a critical matter in several applications. In this paper, we introduce a…