Related papers: Robust estimation of microbial diversity in theory…
We revisit the well-studied problem of estimating the Shannon entropy of a probability distribution, now given access to a probability-revealing conditional sampling oracle. In this model, the oracle takes as input the representation of a…
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…
Diversity indices have been traditionally used to capture the biodiversity of ecosystems by measuring the effective number of species or groups of species. In contrast to abundance, which is correlated with the amount of data available,…
For measuring the strength of visually-observed subpopulation differences, the Population Difference Criterion is proposed to assess the statistical significance of visually observed subpopulation differences. It addresses the following…
Assume in a sample of size M one finds M_i representatives of species i with i=1...N^*. The normalized frequency p^*_i=M_i/M, based on the finite sample, may deviate considerably from the true probabilities p_i. We propose a method to infer…
Selective sweeps are typically associated with a local reduction of genetic diversity around the adaptive site. However, selective sweeps can also quickly carry neutral mutations to observable population frequencies if they arise early in a…
Evolutionary and ecosystem dynamics are often treated as different processes --operating at separate timescales-- even if evidence reveals that rapid evolutionary changes can feed back into ecological interactions. A recent long-term field…
Many microbes associate with higher eukaryotes and impact their vitality. In order to engineer microbiomes for host benefit, we must understand the rules of community assembly and maintenence, which in large part, demands an understanding…
Phylodynamics seeks to estimate effective population size fluctuations from molecular sequences of individuals sampled from a population of interest. One way to accomplish this task formulates an observed sequence data likelihood exploiting…
The notion of information pervades informal descriptions of biological systems, but formal treatments face the problem of defining a quantitative measure of information rooted in a concept of fitness, which is itself an elusive notion.…
Microbiomes, which are collections of interacting microbes in an environment, often substantially impact the environmental patches or living hosts that they occupy. In microbiome models, it is important to consider both the local dynamics…
The commonly observed negative correlation between the number of species in an ecological community and disease risk, typically referred to as "the dilution effect", has received a substantial amount of attention over the past decade.…
A neutral ecology model is simulated on an island chain, in which neighbouring islands can exchange individuals but only the first island is able to receive immigrants from a metacommunity. It is found by several measures that biodiversity…
Human associated microbial communities exert tremendous influence over human health and disease. With modern metagenomic sequencing methods it is possible to follow the relative abundance of microbes in a community over time. These…
Diversity plays a crucial role in multiple contexts such as team formation, representation of minority groups and generally when allocating resources fairly. Given a community composed by individuals of different types, we study the problem…
We are losing biodiversity at an unprecedented scale and in many cases, we do not even know the basic data for the species. Traditional methods for wildlife monitoring are inadequate. Development of new computer vision tools enables the use…
Many empirical networks have community structure, in which nodes are densely interconnected within each community (i.e., a group of nodes) and sparsely across different communities. Like other local and meso-scale structure of networks,…
Due to the recent advances in high-throughput sequencing technologies, it becomes possible to directly analyze microbial communities in the human body and in the environment. Knowledge of how microbes interact with each other and form…
Analysis of a probabilistic system often requires to learn the joint probability distribution of its random variables. The computation of the exact distribution is usually an exhaustive precise analysis on all executions of the system. To…
It is not obvious how to extend Shannon's original information entropy to higher dimensions, and many different approaches have been tried. We replace the English text symbol sequence originally used to illustrate the theory by a discrete,…