Related papers: Multiple-line inference of selection on quantitati…

We review recent progress on ancestral processes related to mutation-selection models, both in the deterministic and the stochastic setting. We mainly rely on two concepts, namely, the killed ancestral selection graph and the pruned…

Selective inference is considered for testing trees and edges in phylogenetic tree selection from molecular sequences. This improves the previously proposed approximately unbiased test by adjusting the selection bias when testing many trees…

One approach to estimating a species tree from a collection of gene trees is to first estimate probabilities of clades from the gene trees, and then to construct the species tree from the estimated clade probabilities. While a greedy…

Plant breeding programs use data obtained from multi-environment selection experiments to produce improved varieties with the ultimate aim of maintaining high levels of genetic gain. Selection accuracy can be improved with the use of…

The advent of accessible ancient DNA technology now allows the direct ascertainment of allele frequencies in ancestral populations, thereby enabling the use of allele frequency time series to detect and estimate natural selection. Such…

Feature selection plays a pivotal role in the data preprocessing and model-building pipeline, significantly enhancing model performance, interpretability, and resource efficiency across diverse domains. In population-based optimization…

In this paper, we address the question of comparison between populations of trees. We study an statistical test based on the distance between empirical mean trees, as an analog of the two sample z statistic for comparing two means. Despite…

We propose a statistical method to test whether two phylogenetic trees with given alignments are significantly incongruent. Our method compares the two distributions of phylogenetic trees given by the input alignments, instead of comparing…

The delimitation of biological species, i.e., deciding which individuals belong to the same species and whether and how many different species are represented in a data set, is key to the conservation of biodiversity. Much existing work…

The problem of multiple hypothesis testing arises when there are more than one hypothesis to be tested simultaneously for statistical significance. This is a very common situation in many data mining applications. For instance, assessing…

Multiple hypothesis testing is widely used to evaluate scientific studies involving statistical tests. However, for many of these tests, p-values are not available and are thus often approximated using Monte Carlo tests such as permutation…

Conjoint analysis is a popular experimental design used to measure multidimensional preferences. Researchers examine how varying a factor of interest, while controlling for other relevant factors, influences decision-making. Currently,…

We develop a model-based methodology for integrating gene-set information with an experimentally-derived gene list. The methodology uses a previously reported sampling model, but takes advantage of natural constraints in the…

Background: Heritability is a central measure in genetics quantifying how much of the variability observed in a trait is attributable to genetic differences. Existing methods for estimating heritability are most often based on random-effect…

Phylogenetics uses alignments of molecular sequence data to learn about evolutionary trees relating species. Along branches, sequence evolution is modelled using a continuous-time Markov process characterised by an instantaneous rate…

High-dimensional tests are applied to find relevant sets of variables and relevant models. If variables are selected by analyzing the sums of products matrices and a corresponding mean-value test is performed, there is the danger that the…

We are interested in the evolving genealogy of a birth and death process with trait structure and ecological interactions. Traits are hereditarily transmitted from a parent to its offspring unless a mutation occurs. The dynamics may depend…

We consider the mutation--selection differential equation with pairwise interaction (or, equivalently, the diploid mutation--selection equation) and establish the corresponding ancestral process, which is a random tree and a variant of the…

Social networks play an important role in analyzing the impact of individual-level interactions on societal or economic outcomes. We model interactive decision making for a community of individuals with different traits, represented by a…

We consider the long-term behaviour of critical multitype branching processes conditioned on non-extinction, both with respect to the forward and the ancestral processes. Forward in time, we prove a functional limit theorem in the space of…