Related papers: Trees within trees: Simple nested coalescents
The assembly of RecA on single-stranded DNA is measured and interpreted as a stochastic finite-state machine that is able to discriminate fine differences between sequences, a basic computational operation. RecA filaments efficiently scan…
We consider a stochastic model, called the replicator coalescent, describing a system of blocks of $k$ different types which undergo pairwise mergers at rates depending on the block types: with rate $C_{i,j}$ blocks of type $i$ and $j$…
This article introduces new tools to study self-organisation in a family of simple cellular automata which contain some particle-like objects with good collision properties (coalescence) in their time evolution. We draw an initial…
Semi-labeled trees are phylogenies whose internal nodes may be labeled by higher-order taxa. Thus, a leaf labeled Mus musculus could nest within a subtree whose root node is labeled Rodentia, which itself could nest within a subtree whose…
Begin continuous time random walks from every vertex of a graph and have particles coalesce when they collide. We use a duality relation with the voter model to prove the process is site recurrent on bounded degree graphs, and for…
Neural networks and tree ensembles are state-of-the-art learners, each with its unique statistical and computational advantages. We aim to combine these advantages by introducing a new layer for neural networks, composed of an ensemble of…
The sequence of so-called signature moments describes the laws of many stochastic processes in analogy with how the sequence of moments describes the laws of vector-valued random variables. However, even for vector-valued random variables,…
We consider a stochastic process that describes several particles interacting by either merging or annihilation. When two particles merge, they combine their masses; when annihilation occurs, only the particle of smallest mass survives.…
There have been many studies to examine whether one trait is correlated with another trait across a group of present-day species (for example, do species with larger brains tend to have longer gestation times. Since the introduction of the…
We study stochastic processes that generate non-growing complex networks without self-loops and multiple edges (simple graphs). The work concentrates on understanding and formulation of constraints which keep the rewiring stochastic…
We present a two channel driven lattice gas model with oppositely directed species moving on two parallel lanes with lane switching processes. We study correlated lane switching mechanism for particles so that switching may occur with…
We consider the process of uncovering the vertices of a random labeled tree according to their labels. First, a labeled tree with $n$ vertices is generated uniformly at random. Thereafter, the vertices are uncovered one by one, in order of…
Percolation of fine particles (fines) in a static bed of larger particles is central to many industrial and natural processes. Non-cohesive fines either pass through the bed or become trapped depending on multiple factors including particle…
In this paper, we study a two-species model in the form of a coupled system of nonlinear stochastic differential equations (SDEs) that arises from a variety of applications such as aggregation of biological cells and pedestrian movements.…
A microscopic understanding of low-temperature thermodynamics and its relation to dynamical features such as a fragile-to-strong crossover (FSC) remains a central challenge in glass physics. Using swap Monte Carlo combined with a full…
We consider a general class of branching processes in discrete time, where particles have types belonging to a Polish space and reproduce independently according to their type. If the process is critical and the mean distribution of types…
Conditional sampling distributions (CSDs), sometimes referred to as copying models, underlie numerous practical tools in population genomic analyses. Though an important application that has received much attention is the inference of…
Inference of species networks from genomic data under the Network Multispecies Coalescent Model is currently severely limited by heavy computational demands. It also remains unclear how complicated networks can be for consistent inference…
Statistics of distinguishable particles has become relevant in systems of colloidal particles and in the context of applications of statistical mechanics to complex networks. When studying these type of systems with the standard textbook…
Consider a haploid population which has evolved through an exchangeable reproduction dynamics, and in which all individuals alive at time $t$ have a most recent common ancestor (MRCA) who lived at time $A_t$, say. As time goes on, not only…