Related papers: Phylogenetic effective sample size
The phylogenetic effective sample size is a parameter that has as its goal the quantification of the amount of independent signal in a phylogenetically correlated sample. It was studied for Brownian motion and Ornstein-Uhlenbeck models of…
Phylogenetic comparative methods are well established tools for using inter-species variation to analyse phenotypic evolution and adaptation. They are generally hampered, however, by predominantly univariate approaches and failure to…
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…
Phylogenetic comparative analysis is an approach to inferring evolutionary process from a combination of phylogenetic and phenotypic data. The last few years have seen increasingly sophisticated models employed in the evaluation of more and…
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…
We consider a stochastic evolutionary model for a phenotype developing amongst n related species with unknown phylogeny. The unknown tree is modelled by a Yule process conditioned on n contemporary nodes. The trait value is assumed to…
Coalescent theory combined with statistical modeling allows us to estimate effective population size fluctuations from molecular sequences of individuals sampled from a population of interest. When sequences are sampled serially through…
Phylogenetic diversity is a measure for describing how much of an evolutionary tree is spanned by a subset of species. If one applies this to the (unknown) subset of current species that will still be present at some future time, then this…
A phylogenetic tree is an important way in Bioinformatics to find the evolutionary relationship among biological species. In this research, a proposed model is described for the estimation of a phylogenetic tree for a given set of data. To…
The quality of the inferences we make from pathogen sequence data is determined by the number and composition of pathogen sequences that make up the sample used to drive that inference. However, there remains limited guidance on how to best…
Biological phenotypes are products of complex evolutionary processes in which selective forces influence multiple biological trait measurements in unknown ways. Phylogenetic factor analysis disentangles these relationships across the…
Clinical prediction models are estimated using a sample of limited size from the target population, leading to uncertainty in predictions, even when the model is correctly specified. Generally, not all patient profiles are observed…
The use of Bayesian information criterion (BIC) in the model selection procedure is under the assumption that the observations are independent and identically distributed (i.i.d.). However, in practice, we do not always have i.i.d. samples.…
Many biological studies involve inferring the evolutionary history of a sample of individuals from a large population and interpreting the reconstructed tree. Such an ascertained tree typically represents only a small part of a…
Biological data objects often have both of the following features: (i) they are functions rather than single numbers or vectors, and (ii) they are correlated due to phylogenetic relationships. In this paper we give a flexible statistical…
Importance sampling approximates expectations with respect to a target measure by using samples from a proposal measure. The performance of the method over large classes of test functions depends heavily on the closeness between both…
Phylogenies are commonly used to represent the evolutionary relationships between species, and often these phylogenies are equipped with edge lengths that indicate degrees of evolutionary difference. Given such a phylogeny, a popular…
Estimating the effective sample size (ESS) is fundamental in Bayesian phylogenetic inference to properly account for autocorrelation in MCMC samples. While methods for continuous parameters are well established, the discrete and…
Variation in a sample of molecular sequence data informs about the past evolutionary history of the sample's population. Traditionally, Bayesian modeling coupled with the standard coalescent, is used to infer the sample's bifurcating…
The modeling and analysis of networks and network data has seen an explosion of interest in recent years and represents an exciting direction for potential growth in statistics. Despite the already substantial amount of work done in this…