相关论文: Quantitative Comparison of Abundance Structures of…

By creating networks of biochemical pathways, communities of micro-organisms are able to modulate the properties of their environment and even the metabolic processes within their hosts. Next-generation high-throughput sequencing has led to…

We present a non-equilibrium statistical mechanics description of rank abundance relations (RAR) in random community models of ecology. Specifically, we study a multi-species replicator system with quenched random interaction matrices. We…

Studies on distribution, abundance and diversity of species revealed fascinating universalities in macroecology. Many of these patterns, like the species-area and range-abundance relationship or the year-to-year fluctuations in population…

We build a general framework which establishes a one-to-one correspondence between species abundance distribution (SAD) and species accumulation curve (SAC). The appearance rates of the species and the appearance times of individuals of…

The mainstream crowd counting methods regress density map and integrate it to obtain counting results. Since the density representation to one head accords to its adjacent distribution, it embeds the same category objects with variant…

Flow based models such as Real NVP are an extremely powerful approach to density estimation. However, existing flow based models are restricted to transforming continuous densities over a continuous input space into similarly continuous…

The competition for resources is a defining feature of microbial communities. In many contexts, from soils to host-associated communities, highly diverse microbes are organized into metabolic groups or guilds with similar resource…

Population analysis is persistently challenging but important, leading to the determination of diversity and function prediction of microbial community members. Here we detail our bioinformatics methods for analyzing population distribution…

Microbial ecosystems are remarkably diverse, stable, and often consist of a balanced mixture of core and peripheral species. Here we propose a conceptual model exhibiting all these emergent properties in quantitative agreement with real…

Renormalization group (RG) methods are emerging as tools in biology and computer science to support the search for simplifying structure in distributions over high-dimensional spaces. We show that mixture models can be thought of as having…

The microbiome constitutes a complex microbial ecology of interacting components that regulates important pathways in the host. Measurements of microbial abundances are key to learning the intricate network of interactions amongst microbes.…

Recently there has been growing interest in the use of Maximum Relative Entropy (MaxREnt) as a tool for statistical inference in ecology. In contrast, here we propose MaxREnt as a tool for applying statistical mechanics to ecology. We use…

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…

A key challenge in differential abundance analysis of microbial samples is that the counts for each sample are compositional, resulting in biased comparisons of the absolute abundance across study groups. Normalization-based differential…

Raking is widely used in categorical data modeling and survey practice but faced with methodological and computational challenges. We develop a Bayesian paradigm for raking by incorporating the marginal constraints as a prior distribution…

An analytical approximation is derived for the Zero Sum Multinomial distribution which gives the Species Abundance Distribution in Neutral Community Models. The obtained distribution function describes well computer simulation results on…

Many natural patterns, such as the distributions of blood particles in a blood sample, proteins on cell surfaces, biological populations in their habitat, galaxies in the universe, the sequence of human genes, and the fitness in…

One of the central questions of metacommunity theory is how dispersal of organisms affects species diversity. Here we show that the diversity-dispersal relationship should not be studied in isolation of other abiotic and biotic flows in the…

Quantifying diversity is of central importance for the study of structure, function and evolution of microbial communities. The estimation of microbial diversity has received renewed attention with the advent of large-scale metagenomic…

The growth of complex populations, such as microbial communities, forests, and cities, occurs over vastly different spatial and temporal scales. Although research in different fields has developed detailed, system-specific models to…