Related papers: Detecting adaptive evolution in phylogenetic compa…
Comparing allele frequencies among populations that differ in environment has long been a tool for detecting loci involved in local adaptation. However, such analyses are complicated by an imperfect knowledge of population allele…
Phylogenetic inference-the derivation of a hypothesis for the common evolutionary history of a group of species- is an active area of research at the intersection of biology, computer science, mathematics, and statistics. One assumes the…
Phenotypically structured equations arise in population biology to describe the interaction of species with their environment that brings the nutrients. This interaction usually leads to selection of the fittest individuals. Models used in…
The prediction of phenotypic traits using high-density genomic data has many applications such as the selection of plants and animals of commercial interest; and it is expected to play an increasing role in medical diagnostics. Statistical…
The reconstruction of phylogenies from DNA or protein sequences is a major task of computational evolutionary biology. Common phenomena, notably variations in mutation rates across genomes and incongruences between gene lineage histories,…
Rapid advancements in genome sequencing have led to the collection of vast amounts of genomics data. Researchers may be interested in using machine learning models on such data to predict the pathogenicity or clinical significance of a…
In the era of big data, analysts usually explore various statistical models or machine learning methods for observed data in order to facilitate scientific discoveries or gain predictive power. Whatever data and fitting procedures are…
The combination of multiple classifiers using ensemble methods is increasingly important for making progress in a variety of difficult prediction problems. We present a comparative analysis of several ensemble methods through two case…
Complex Ornstein-Uhlenbeck (OU) processes have various applications in statistical modelling. They play role e.g. in the description of the motion of a charged test particle in a constant magnetic field or in the study of rotating waves in…
Motivation: Gene selection has become a common task in most gene expression studies. The objective of such research is often to identify the smallest possible set of genes that can still achieve good predictive performance. The problem of…
Evolvability is defined as the ability of a population to generate heritable variation to facilitate its adaptation to new environments or selection pressures. In this article, we consider evolvability as a phenotypic trait subject to…
Pest phenological models describe the cumulative flux of the individuals into each stage of the life cycle of a stage-structured population. Phenological models are widely used tools in pest control decision making. Despite the fact that…
The advances in variational inference are providing promising paths in Bayesian estimation problems. These advances make variational phylogenetic inference an alternative approach to Markov Chain Monte Carlo methods for approximating the…
Given the increasing complexity of omics datasets, a key challenge is not only improving classification performance but also enhancing the transparency and reliability of model decisions. Effective model performance and feature selection…
We introduce a model for the evolution of species triggered by generation of novel features and exhaustive combination with other available traits. Under the assumption that innovations are rare, we obtain a bursty branching process of…
Branch-specific substitution models are popular for detecting evolutionary change-points, such as shifts in selective pressure. However, applying such models typically requires prior knowledge of change-point locations on the phylogeny or…
Most theories of evolutionary diversification are based on equilibrium assumptions: they are either based on optimality arguments involving static fitness landscapes, or they assume that populations first evolve to an equilibrium state…
As an alternative to parsimony analyses, stochastic models have been proposed (Lewis, 2001), (Nylander, et al., 2004) for morphological characters, so that maximum likelihood or Bayesian analyses may be used for phylogenetic inference. A…
In molecular phylogeny, relationships among organisms are reconstructed using DNA or protein sequences and are displayed as trees. A linear increase in the number of sequences results in an exponential increase of possible trees. Thus,…
We evaluated whether model explanations could efficiently detect bias in image classification by highlighting discriminating features, thereby removing the reliance on sensitive attributes for fairness calculations. To this end, we…