Related papers: Detecting adaptive evolution in phylogenetic compa…
Understanding which phenotypic traits are consistently correlated throughout evolution is a highly pertinent problem in modern evolutionary biology. Here, we propose a multivariate phylogenetic latent liability model for assessing the…
A phylogeny describes the evolutionary history of an evolving population. Evolutionary search algorithms can perfectly track the ancestry of candidate solutions, illuminating a population's trajectory through the search space. However,…
Phylogenetic mixture models are statistical models of character evolution allowing for heterogeneity. Each of the classes in some unknown partition of the characters may evolve by different processes, or even along different trees. The…
Sudden changes in environmental conditions can lead to evolutionary shifts not only in the optimal trait value, but also in the diffusion variance under the Ornstein-Uhlenbeck (OU) model. While several methods have been developed to detect…
Hierarchical autocorrelation in the error term of linear models arises when sampling units are related to each other according to a tree. The residual covariance is parametrized using the tree-distance between sampling units. When…
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…
In this paper we address the use of rare event computation techniques to estimate small over-threshold probabilities of observables in determin-istic dynamical systems. We demonstrate that the genealogical particle analysis algorithms can…
Phylogenetic trees are simple models of evolutionary processes. They describe conditionally independent divergent evolution of taxa from common ancestors. Phylogenetic trees commonly do not have enough flexibility to adequately model all…
Many biological systems regulate phenotypic heterogeneity as a fitness-maximising strategy in uncertain and dynamic environments. Analysis of such strategies is typically confined both to a discrete set of environmental conditions, and to a…
Phylogenetic comparative methods for real-valued traits usually make use of stochastic process whose trajectories are continuous. This is despite biological intuition that evolution is rather punctuated than gradual. On the other hand,…
The linking genotype to phenotype is the fundamental aim of modern genetics. We focus on study of links between gene expression data and phenotype data through integrative analysis. We propose three approaches. 1) The inherent complexity of…
Identifying subtle phenotypic variations in cellular images is critical for advancing biological research and accelerating drug discovery. These variations are often masked by the inherent cellular heterogeneity, making it challenging to…
Phylogenies (ancestry trees) depict the evolutionary history of an evolving population. In evolutionary computing, a phylogeny can reveal how an evolutionary algorithm steers a population through a search space, illuminating the…
A methodology is introduced which uses three simple objective function features to predict effective control parameters for differential evolution. This is achieved using cluster analysis techniques to classify objective functions using…
Inferring dependencies between complex biological traits while accounting for evolutionary relationships between specimens is of great scientific interest yet remains infeasible when trait and specimen counts grow large. The…
1. Abrupt environmental changes can lead to evolutionary shifts in trait evolution. Identifying these shifts is an important step in understanding the evolutionary history of phenotypes. 2. We propose an ensemble variable selection method…
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…
Phylogenetic comparative methods correct for shared evolutionary history among a set of non-independent organisms by modeling sample traits as arising from a diffusion process along on the branches of a possibly unknown history. To…
In this paper, we analyze the use of the Ornstein-Uhlenbeck process to model dynamical systems subjected to bounded noisy perturbations. In order to discuss the main characteristics of this new approach we consider some basic models in…
The use of an Ornstein-Uhlenbeck (OU) process is ubiquitous in business, economics and finance to capture various price processes and evolution of economic indicators exhibiting mean-reverting properties. When structural changes happen,…