Related papers: Selection and Coalescence in a Finite State Model
We consider an extension of the noisy $N$-Branching Random Walk that models the evolution of a population subject to natural selection. We show the existence of a critical value for the noise which separates the limiting genealogical…
There has been great interest in identifying tractable subclasses of NP complete problems and designing efficient algorithms for these tractable classes. Constraint satisfaction and Bayesian network inference are two examples of such…
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…
Phylodynamics seeks to estimate effective population size fluctuations from molecular sequences of individuals sampled from a population of interest. One way to accomplish this task formulates an observed sequence data likelihood exploiting…
Within machine learning, the supervised learning field aims at modeling the input-output relationship of a system, from past observations of its behavior. Decision trees characterize the input-output relationship through a series of nested…
We reconsider the Moran model in continuous time with population size $N$, two allelic types, and selection. We introduce a new particle representation, which we call the labelled Moran model, and which has the same distribution of type…
Consider a population where individuals give birth at constant rate during their lifetimes to i.i.d. copies of themselves. Individuals bear clonally inherited types, but (neutral) mutations may happen at the birth events. The smallest…
Using molecular dynamics simulations and scaling arguments, we investigate the coalescence preference dynamics of liquid droplets in a phase-segregating off-critical, single-component fluid. It is observed that the preferential distance of…
Phylogenetic trees capture evolutionary relationships among species and reflect the forces that shaped them. While many studies rely on branch length information, the topology of phylogenetic trees (particularly their degree of imbalance)…
We ask the question "when will natural selection on a gene in a spatially structured population cause a detectable trace in the patterns of genetic variation observed in the contemporary population?". We focus on the situation in which…
We investigate the evolutionary dynamics of an age-structured population under weak frequency-dependent selection. It turns out that the weak selection is affected in a non-trivial way by the life-history trait. We can disentangle the…
We analyse the motion of a system of particles subjected a random force fluctuating in both space and time, and experiencing viscous damping. When the damping exceeds a certain threshold, the system undergoes a phase transition: the…
Representations of population models in terms of countable systems of particles are constructed, in which each particle has a `type', typically recording both spatial position and genetic type, and a level. For finite intensity models, the…
Eliciting preferences from human judgements is inherently imprecise, yet most decision analysis methods force a single priority vector from pairwise comparisons, discarding the information embedded in inconsistencies. We instead leverage…
Partition refinement is a method for minimizing automata and transition systems of various types. Recently, we have developed a partition refinement algorithm that is generic in the transition type of the given system and matches the run…
Several groups have recently modeled evolutionary transitions from an ancestral allele to a beneficial allele separated by one or more intervening mutants. The beneficial allele can become fixed if a succession of intermediate mutants are…
Linear mixed effects models are highly flexible in handling a broad range of data types and are therefore widely used in applications. A key part in the analysis of data is model selection, which often aims to choose a parsimonious 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…
The problem of estimating the growth rate of a birth and death processes based on the coalescence times of a sample of $n$ individuals has been considered by several authors (\cite{stadler2009incomplete, williams2022life,…
The goal of this paper is to prove rigorous results for the behavior of genealogies in a one-dimensional long range biased voter model introduced by Hallatschek and Nelson [25]. The first step, which is easily accomplished using results of…