Related papers: Lines of descent in the deterministic mutation-sel…
We review models of biological evolution in which the population frequency changes deterministically with time. If the population is self-replicating, although the equations for simple prototypes can be linearised, nonlinear equations arise…
Species tree estimation is a complex problem, due to the fact that different parts of the genome can have different evolutionary histories than the genome itself. One of the causes for this discord is incomplete lineage sorting (also called…
The evolution of aligned DNA sequence sites is generally modeled by a Markov process operating along the edges of a phylogenetic tree. It is well known that the probability distribution on the site patterns at the tips of the tree…
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…
Neural Networks and Decision Trees: two popular techniques for supervised learning that are seemingly disconnected in their formulation and optimization method, have recently been combined in a single construct. The connection pivots on…
In this article, we focus on Bienaym\'e-Galton-Watson processes with linear-fractional offspring distributions. At a fixed generation, we consider a sample of the individuals alive, drawn in two different ways: either through Bernoulli…
Understanding the decisions of tree-based ensembles and their relationships is pivotal for machine learning model interpretation. Recent attempts to mitigate the human-in-the-loop interpretation challenge have explored the extraction of the…
Do ecosystems primarily reflect evolutionary history or current environment? Predicting land-atmosphere exchange hinges on this unresolved question. Plant traits adapt to particular environments over evolutionary timescales, yet their…
The coupled Wright-Fisher diffusion is a multi-dimensional Wright-Fisher diffusion for multi-locus and multi-allelic genetic frequencies, expressed as the strong solution to a system of stochastic differential equations that are coupled in…
In genetics the Moran model describes the neutral evolution of a bi-allelic gene in a population of haploid individuals subjected to mutations. We show in this paper that this model can be mapped into an influence dynamical process on…
This article is a presentation of specific recent results describing scaling limits of individual-based models. Thanks to them, we wish to relate the time-scales typical of demographic dynamics and natural selection to the parameters of the…
We describe a duality mapping between STRIPS planning tasks. By exchanging the initial and goal conditions, taking their respective complements, and swapping for every action its precondition and delete list, one obtains for every STRIPS…
We consider a fitness-structured population model with competition and migration between nearest neighbors. Under a combination of large population and rare migration limits we are particularly interested in the asymptotic behavior of the…
Random intersection graphs model networks with communities, assuming an underlying bipartite structure of groups and individuals, where these groups may overlap. Group memberships are generated through the bipartite configuration model.…
The role of the selection pressure and mutation amplitude on the behavior of a single-species population evolving on a two-dimensional lattice, in a periodically changing environment, is studied both analytically and numerically. The…
Decision trees are a popular family of models due to their attractive properties such as interpretability and ability to handle heterogeneous data. Concurrently, missing data is a prevalent occurrence that hinders performance of machine…
Wright-Fisher diffusions and their dual ancestral graphs occupy a central role in the study of allele frequency change and genealogical structure, and they provide expressions, explicit in some special cases but generally implicit, for the…
We consider a class of Crump-Mode-Jagers processes with interaction, constructed by removing a newly born offspring with a probability that depends on the age structure of the population at its birth time. We prove a law of large numbers…
Ancestral sequence reconstruction is a key task in computational biology. It consists in inferring a molecular sequence at an ancestral species of a known phylogeny, given descendant sequences at the tip of the tree. In addition to its many…
We are interested in a stochastic model of trait and age-structured population undergoing mutation and selection. We start with a continuous time, discrete individual-centered population process. Taking the large population and rare…