Related papers: Coalescence in Markov chains
The method of 'coupling from the past' permits exact sampling from the invariant distribution of a Markov chain on a finite state space. The coupling is successful whenever the stochastic dynamics are such that there is coalescence of all…
I show how to run an N-time-step Markov chain simulation in a circular fashion, so that the state at time 0 follows the state at time N-1 in the same way as states at times t follow those at times t-1 for 0<t<N. This wrap-around of the…
We consider finite state, discrete-time, mixing Markov chains $(V,P)$, where $V$ is the state space and $P$ is transition matrix. To each such chain $(V,P)$, we associate a sequence of chains $(V_n,P_n)$ by coding trajectories of $(V,P)$…
Consider a continuous-state branching population constructed as a flow of nested subordinators. Inverting the subordinators and reversing time give rise to a flow of coalescing Markov processes (with negative jumps) which correspond to the…
The Kingman coalescent is a fundamental process in population genetics modelling the ancestry of a sample of individuals backwards in time. In this paper, in a large-sample-size regime, we study asymptotic properties of the coalescent under…
Kingman's coalescent is a widely used process to model sample genealogies in population genetics. Recently there have been studies on the inference of quantities related to the genealogy of additional individuals given a known sample. This…
A $k$-height on a graph $G=(V, E)$ is an assignment $V\to\{0, \ldots, k\}$ such that the value on ajacent vertices differs by at most $1$. We study the Markov chain on $k$-heights that in each step selects a vertex at random, and, if…
A lumping of a Markov chain is a coordinate-wise projection of the chain. We characterise the entropy rate preservation of a lumping of an aperiodic and irreducible Markov chain on a finite state space by the random growth rate of the…
This simple note lays out a few observations which are well known in many ways but may not have been said in quite this way before. The basic idea is that when comparing two different Markov chains it is useful to couple them is such a way…
In this paper, we study consistent and partially exchangeable sequences of Markov chains on a finite state space. We provide a characterisation of the admissible transition rates via a decomposition into individual and coordinated motion of…
We present a novel approach to quantizing Markov chains. The approach is based on the Markov chain coupling method, which is frequently used to prove fast mixing. Given a particular coupling, e.g., a grand coupling, we construct a…
The sequentially Markov coalescent (SMC) is a Markov jump process which models correlations in local genealogies across a chromosome. It has been used as a theoretical tool for studying linkage disequilibrium and identity-by-descent, and it…
We analyse sequential Markov coalescent algorithms for populations with demographic structure: for a bottleneck model, a population-divergence model, and for a two-island model with migration. The sequential Markov coalescent method is an…
We study infinite systems of particles which undergo coalescence and fragmentation, in a manner determined solely by their masses. A pair of particles having masses $x$ and $y$ coalesces at a given rate $K(x,y)$. A particle of mass $x$…
We study the loop clusters induced by Poissonian ensembles of Markov loops on a finite or countable graph (Markov loops can be viewed as excursions of Markov chains with a random starting point, up to re-rooting). Poissonian ensembles are…
We consider continuous-time Markov chain on a finite state space X. We assume X can be clustered into several subsets such that the intra-transition rates within these subsets are of order $\mathcal{O}(\frac{1}{\epsilon})$ comparing to the…
Consider a structured population consisting of $d$ colonies, with migration rates proportional to a positive parameter $K$. We sample $N_K$ individuals, distributed evenly across the $d$ colonies, and trace their ancestral lineages backward…
We study a Markov chain with very different mixing rates depending on how mixing is measured. The chain is the "Burnside process on the hypercube $C_2^n$." Started at the all-zeros state, it mixes in a bounded number of steps, no matter how…
Consider the Markov process taking values in the partitions of N such that each pair of blocks merges at rate one, and each integer is eroded, i.e., becomes a singleton block, at rate d. This is a special case of exchangeable…
Two sequentially Markov coalescent models (SMC and SMC') are available as tractable approximations to the ancestral recombination graph (ARG). We present a Markov process describing coalescence at two fixed points along a pair of sequences…