Related papers: Markovian simulation for ancestors trees
A Markovian model of group-structured (two-level) population dynamics features births, deaths, and migrations of individuals, and fission and extinction of groups. These models are useful for studying group selection and other evolutionary…
In this work we model the dynamics of a population that evolves as a continuous time branching process with a trait structure and ecological interactions in form of mutations and competition between individuals. We generalize existing…
We apply genetic programming techniques to the `shepherding' problem, in which a group of one type of animal (sheep dogs) attempts to control the movements of a second group of animals (sheep) obeying flocking behavior. Our genetic…
Data structures known as $k$-d trees have numerous applications in scientific computing, particularly in areas of modern statistics and data science such as range search in decision trees, clustering, nearest neighbors search, local…
Reconstructing a parsimonious phylogenetic network that displays multiple phylogenetic trees is an important problem in theory of phylogenetics, where the complexity of the inferred networks is measured by reticulation numbers. The…
In this research, we investigate the possibility of applying a search strategy to genetic algorithms to explore the entire genetic tree structure. Several methods aid in performing tree searches; however, simpler algorithms such as…
The multispecies coalescent process models the genealogical relationships of genes sampled from several species, enabling useful predictions about phenomena such as the discordance between the gene tree and the species phylogeny due to…
Background: Continuous traits evolution of a group of taxa that are correlated through a phylogenetic tree is commonly modelled using parametric stochastic differential equations to represent deterministic change of trait through time,…
Sweepstakes reproduction may be generated by chance matching of reproduction with favorable environmental conditions. Gene genealogies generated by sweepstakes reproduction are in the domain of attraction of multiple-merger coalescents…
Since the advent of modern bioinformatics, the challenging, multifaceted problem of reconstructing phylogenetic history from biological sequences has hatched perennial statistical and algorithmic innovation. Studies of the phylogenetic…
The evolution of molecular and phenotypic traits is commonly modelled using Markov processes along a phylogeny. This phylogeny can be a tree, or a network if it includes reticulations, representing events such as hybridization or admixture.…
In this paper we present the simplest individual level model of predator-prey dynamics and show, via direct calculation, that it exhibits cycling behavior. The deterministic analogue of our model, recovered when the number of individuals is…
A discrete time branching process where the offspring distribution is generation-dependent, and the number of reproductive individuals is controlled by a random mechanism is considered. This model is a Markov chain but, in general, the…
The forest-of-octrees approach to parallel adaptive mesh refinement and coarsening (AMR) has recently been demonstrated in the context of a number of large-scale PDE-based applications. Although linear octrees, which store only leaf…
The varying-coefficient model is a strong tool for the modelling of interactions in generalized regression. It is easy to apply if both the variables that are modified as well as the effect modifiers are known. However, in general one has a…
Deep generative models have been shown powerful in generating novel molecules with desired chemical properties via their representations such as strings, trees or graphs. However, these models are limited in recommending synthetic routes…
We consider Markov jump processes describing structured populations with interactions via density dependance. We propose a Markov construction with a distinguished individual which allows to describe the random tree and random sample at a…
Simulation of population dynamics is a central research theme in computational biology, which contributes to understanding the interactions between predators and preys. Conventional mathematical tools of this theme, however, are incapable…
In a population with haploid reproduction any individual has a single parent in the previous generation. If all genealogical distances among pairs of individuals (generations from the closest common ancestor) are known it is possible to…
The class of self-nested trees presents remarkable compression properties because of the systematic repetition of subtrees in their structure. In this paper, we provide a better combinatorial characterization of this specific family of…