We revisit the classical problem of approximating a stochastic differential equation by a discrete-time and discrete-space Markov chain. Our construction iterates Caratheodory's theorem over time to match the moments of the increments locally. This allows to construct a Markov chain with a sparse transition matrix where the number of attainable states grows at most polynomially as time increases. Moreover, the MC evolves on a tree whose nodes lie on a "universal lattice" in the sense that an arbitrary number of different SDEs can be approximated on the same tree. The construction is not tailored to specific models, we discuss both the case of uni-variate and multi-variate case SDEs, and provide an implementation and numerical experiments.
Recombination in discrete and continuous time from the viewpoint of Markov embedding
Technische Fakultät, Universität Bielefeld（比勒费尔德大学技术学院）；Fakultät für Mathematik, Universität Bielefeld（比勒费尔德大学数学学院）；School of Natural Sciences, Discipline of Mathematics, University of Tasmania（塔斯马尼亚大学自然科学学院数学系）
The genealogy at a single locus of a constant size $N$ population in equilibrium is given by the well-known Kingman's coalescent. When considering multiple loci under recombination, the ancestral recombination graph encodes the genealogies at all loci in one graph. For a continuous genome $G$, we study the tree-valued process $(T^N_u)_{u\in G}$ of genealogies along the genome in the limit $N\to\infty$. Encoding trees as metric measure spaces, we show convergence to a tree-valued process with cadlag paths. In addition, we study mixing properties of the resulting process for loci which are far a…
We consider the Wright-Fisher model for a population of $N$ individuals, each identified with a sequence of a finite number of sites, and single-crossover recombination between them. We trace back the ancestry of single individuals from the present population. In the $N \to \infty$ limit without rescaling of parameters or time, this ancestral process is described by a random tree, whose branching events correspond to the splitting of the sequence due to recombination. With the help of a decomposition of the trees into subtrees, we calculate the probabilities of the topologies of the ancestral …
We construct the non-linear Markov process connected with biological model of bacterial genome recombination. The description of invariant measures of this process gives us the solution of one problem in elementary probability theory.
We study the continuous-time evolution of the recombination equation of population genetics. This evolution is given by a differential equation that acts on a product probability space, and its solution can be described by a Markov chain on a set of partitions that converges to the finest partition. We study an explicit form of the law of this process by using a family of trees. We also describe the geometric decay rate to the finest partition and the quasi-stationary behavior of the Markov chain when conditioned on the event that the chain does not hit the limit.
Bacteria are known to exchange genetic information by horizontal gene transfer. Since the frequency of homologous recombination depends on the similarity of recombining segments, several studies examined whether this could lead to the emergence of subspecies. Most of them used simulations of fixed size Wright-Fisher populations, in which the genetic drift should be taken into account. Here, we use non-linear Markov chains to describe a bacterial population evolving under mutation and recombination processes. We consider a population as a space of genomes and a probability measure on it. Thus, …
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 population structure, the explicit exchange of migrants at specified rates has not hitherto been incorporated into the CSD in a principled framework. Recently, in the case of a single panmictic population, a sequentially Markov CSD has been developed as an accurate, efficient approximation to a principled CSD derived from the diffusion process dual to the coalesc…
We give a closed form of the discrete-time evolution of a recombination transformation in population genetics. This decomposition allows to define a Markov chain in a natural way. We describe the geometric decay rate to the limit distribution, and the quasi-stationary behavior when conditioned to the event that the chain does not hit the limit distribution.
We consider the discrete-time migration-recombination equation, a deterministic, nonlinear dynamical system that describes the evolution of the genetic type distribution of a population evolving under migration and recombination in a law of large numbers setting. We relate this dynamics (forward in time) to a Markov chain, namely a labelled partitioning process, backward in time. This way, we obtain a stochastic representation of the solution of the migration-recombination equation. As a consequence, one obtains an explicit solution of the nonlinear dynamics, simply in terms of powers of the t…
We introduce block Markov chains (BMCs) indexed by an infinite rooted tree. It turns out that BMCs define a new class of tree-indexed Markovian processes. We clarify the structure of BMCs in connection with Markov chains (MCs) and Markov random fields (MRFs). Mainly, show that probability measures which are BMCs for every root are indeed Markov chains (MCs) and yet they form a strict subclass of Markov random fields (MRFs) on the considered tree. Conversely, a class of MCs which are BMCs is characterized. Furthermore, we establish that in the one-dimensional case the class of BMCs coincides wi…
The goal of these lectures is to survey some of the recent progress on the description of large-scale structure of random trees. We use the framework of Markov-Branching sequences of trees and discuss several applications.
We study the discrete-time evolution of a transformation on a set of probability measures that is up-dated combining independently the marginals on the atoms of partitions. This model was recently introduced in Baake, Baake and Salamat (Discr. and contin. dynam. syst. 36, 2016) for continuous-time evolution and generalizes previous ones based upon dyadic partitions. We associate to the discrete-time evolution a natural Markov chain and describe its quasi-stationary behavior retrieving all the results we recently found for dyadic partitions.
Phylogenetic networks are an extension of phylogenetic trees which are used to represent evolutionary histories in which reticulation events (such as recombination and hybridization) have occurred. A central question for such networks is that of identifiability, which essentially asks under what circumstances can we reliably identify the phylogenetic network that gave rise to the observed data? Recently, identifiability results have appeared for networks relative to a model of sequence evolution that generalizes the standard Markov models used for phylogenetic trees. However, these results are…
We study the size properties of a general model of fractal sets that are based on a tree-indexed family of random compacts and a tree-indexed Markov chain. These fractals may be regarded as a generalization of those resulting from the Moran-like deterministic or random recursive constructions considered by various authors. Among other applications, we consider various extensions of Mandelbrot's fractal percolation process.
We construct the analogue of the local time -- at a fixed point $x$ -- for Markov processes indexed by Levy trees. We start by proving that Markov processes indexed by Levy trees satisfy a special Markov property which can be thought as a spatial version of the classical Markov property. Then, we construct the analogue of the local time by an approximation procedure and we characterize the support of its Lebesgue-Stieltjes measure. We also give an equivalent construction in terms of a special family of exit local times. Finally, combining these results, we show that the points at which the Mar…
We generalize recent results of Haas and Miermont to obtain scaling limits of Markov branching trees whose size is specified by the number of nodes whose out-degree lies in a given set. We then show that this implies that the scaling limit of finite variance Galton-Watson trees condition on the number of nodes whose out-degree lies in a given set is the Brownian continuum random tree. The key to this is a generalization of the classical Otter-Dwass formula.
We introduce a simple tree growth process that gives rise to a new two-parameter family of discrete fragmentation trees that extends Ford's alpha model to multifurcating trees and includes the trees obtained by uniform sampling from Duquesne and Le Gall's stable continuum random tree. We call these new trees the alpha-gamma trees. In this paper, we obtain their splitting rules, dislocation measures both in ranked order and in sized-biased order, and we study their limiting behaviour.
We present a new pruning procedure on discrete trees by adding marks on the nodes of trees. This procedure allows us to construct and study a tree-valued Markov process $\{{\cal G}(u)\}$ by pruning Galton-Watson trees and an analogous process $\{{\cal G}^*(u)\}$ by pruning a critical or subcritical Galton-Watson tree conditioned to be infinite. Under a mild condition on offspring distributions, we show that the process $\{{\cal G}(u)\}$ run until its ascension time has a representation in terms of $\{{\cal G}^*(u)\}$. A similar result was obtained by Aldous and Pitman (1998) in the special cas…
The standard coalescent is widely used in evolutionary biology and population genetics to model the ancestral history of a sample of molecular sequences as a rooted and ranked binary tree. In this paper, we present a representation of the space of ranked trees as a space of constrained ordered matched pairs. We use this representation to define ergodic Markov chains on labeled and unlabeled ranked tree shapes analogously to transposition chains on the space of permutations. We show that an adjacent-swap chain on labeled and unlabeled ranked tree shapes has mixing time at least of order $n^3$, …
A Markov tree is a random vector indexed by the nodes of a tree whose distribution is determined by the distributions of pairs of neighbouring variables and a list of conditional independence relations. Upon an assumption on the tails of the Markov kernels associated to these pairs, the conditional distribution of the self-normalized random vector when the variable at the root of the tree tends to infinity converges weakly to a random vector of coupled random walks called tail tree. If, in addition, the conditioning variable has a regularly varying tail, the Markov tree satisfies a form of one…
We consider a family of random trees satisfying a Markov branching property. Roughly, this property says that the subtrees above some given height are independent with a law that depends only on their total size, the latter being either the number of leaves or vertices. Such families are parameterized by sequences of distributions on partitions of the integers that determine how the size of a tree is distributed in its different subtrees. Under some natural assumption on these distributions, stipulating that "macroscopic" splitting events are rare, we show that Markov branching trees admit the…
We study the global and local regularity properties of random wavelet series whose coefficients exhibit correlations given by a tree-indexed Markov chain. We determine the law of the spectrum of singularities of these series, thereby performing their multifractal analysis. We also show that almost every sample path displays an oscillating singularity at almost every point and that the points at which a sample path has at most a given Holder exponent form a set with large intersection.
This paper concerns the Vertex Reinforced Jump Process (VRJP) and its representations as a Markov process in random environment. We show that all possible representations of the VRJP as a mixture of Markov processes can be expressed in a similar form, using a random potential and harmonic functions for an associated operator. This allows to show that the VRJP on $\mathbb{Z}^d$ (with certain initial conditions) has a unique representation, by proving that an associated Martin boundary is trivial. Moreover, on infinite trees, we construct a family of representations, that are all different when …
We provide deviation inequalities for properly normalized sums of bifurcating Markov chains on Galton-Watson tree. These processes are extension of bifurcating Markov chains (which was introduced by Guyon to detect cellular aging from cell lineage) in case the index set is a binary Galton-Watson process. As application, we derive deviation inequalities for the least-squares estimator of autoregressive parameters of bifurcating autoregressive processes with missing data. These processes allow, in case of cell division, to take into account the cell's death. The results are obtained under an uni…
We are interested in the local limits of families of random trees that satisfy the Markov branching property, which is fulfilled by a wide range of models. Loosely, this property entails that given the sizes of the sub-trees above the root, these sub-trees are independent and their distributions only depend upon their respective sizes. The laws of the elements of a Markov branching family are characterised by a sequence of probability distributions on the sets of integer partitions which describes how the sizes of the sub-trees above the root are distributed. We prove that under some natural a…
By studying an admissible family of branching mechanisms introduced in Li (2014), we obtain a pruning procedure on Lévy trees. Then we could construct a decreasing Lévy-CRT-valued process $\{{\mathcal T}_t\}$ by pruning Lévy trees and an analogous process $\{{\mathcal T}^*_t\}$ by pruning a critical Lévy tree conditioned to be infinite. Under a regular condition on the admissible family of branching mechanisms, we show that the law of $\{{\mathcal T}_t\}$ at the ascension time can be represented by $\{{\mathcal T}^*_t\}$. The results generalize those studied in Abraham and Delmas (2012).
The Horton and Tokunaga branching laws provide a convenient framework for studying self-similarity in random trees. The Horton self-similarity is a weaker property that addresses the principal branching in a tree; it is a counterpart of the power-law size distribution for elements of a branching system. The stronger Tokunaga self-similarity addresses so-called side branching. The Horton and Tokunaga self-similarity have been empirically established in numerous observed and modeled systems, and proven for two paradigmatic models: the critical Galton-Watson branching process with finite progeny …
By introducing a key combinatorial structure for words produced by a Variable Length Markov Chain (VLMC), the longest internal suffix, precise characterizations of existence and uniqueness of a stationary probability measure for a VLMC chain are given. These characterizations turn into necessary and sufficient conditions for VLMC associated to a subclass of probabilised context trees: the shift-stable context trees. As a by-product, we prove that a VLMC chain whose stabilized context tree is again a context tree has at most one stationary probability measure.
We consider the mean value properties for finite variation measures with respect to a Markov operator in a discrete environnement. We prove equivalent conditions for the weak mean value property in the case of general Markov operators and for the strong mean value property in the case of transient Markov operators adapted to a tree structure. In this last case, conditions for the equivalence between weak and strong mean value properties are given.
A Markov Additive Process is a bi-variate Markov process $(ξ,J)=\big((ξ_t,J_t),t\geq0\big)$ which should be thought of as a multi-type Lévy process: the second component $J$ is a Markov chain on a finite space $\{1,\ldots,K\}$, and the first component $ξ$ behaves locally as a Lévy process, with local dynamics depending on $J$. In the subordinator-like case where $ξ$ is nondecreasing, we establish several results concerning the moments of $ξ$ and of its exponential functional $I_ξ=\int_{0}^{\infty} e^{-ξ_t}\mathrm dt,$ extending the work of Carmona et al., and Bertoin and Yor. We then apply the…
We prove an apparently novel concentration of measure result for Markov tree processes. The bound we derive reduces to the known bounds for Markov processes when the tree is a chain, thus strictly generalizing the known Markov process concentration results. We employ several techniques of potential independent interest, especially for obtaining similar results for more general directed acyclic graphical models.
We introduce multi-type Markov Branching trees, which are simple random population tree models where individuals are characterized by their size and type and give rise to (size,type)-children in a Galton-Watson fashion, with the rule that the size of any individual is a least the sum of the sizes of its children. Assuming that macroscopic size-splittings are rare, we describe the scaling limits of multi-type Markov Branching trees in terms of multi-type self-similar fragmentation trees. We observe three different regimes according to whether the probability of type change of a size-biased chil…
We justify and discuss expressions for joint lower and upper expectations in imprecise probability trees, in terms of the sub- and supermartingales that can be associated with such trees. These imprecise probability trees can be seen as discrete-time stochastic processes with finite state sets and transition probabilities that are imprecise, in the sense that they are only known to belong to some convex closed set of probability measures. We derive various properties for their joint lower and upper expectations, and in particular a law of iterated expectations. We then focus on the special cas…
We consider a sequence of Markov chains $(\mathcal X^n)_{n=1,2,...}$ with $\mathcal X^n = (X^n_σ)_{σ\in\mathcal T}$, indexed by the full binary tree $\mathcal T = \mathcal T_0 \cup \mathcal T_1 \cup ...$, where $\mathcal T_k$ is the $k$th generation of $\mathcal T$. In addition, let $(Σ_k)_{k=0,1,2,...}$ be a random walk on $\mathcal T$ with $Σ_k \in \mathcal T_k$ and $\widetilde{\mathcal R}^n = (\widetilde R_t^n)_{t\geq 0}$ with $\widetilde R_t^n := X_{Σ_{[tn]}}$, arising by observing the Markov chain $\mathcal X^n$ along the random walk. We present a law of large numbers concerning the empir…
We consider a class of density-dependent branching processes which generalises exponential, logistic and Gompertz growth. A population begins with a single individual, grows exponentially initially, and then growth may slow down as the population size moves towards a carrying capacity. At a time while the population is still growing superlinearly, a fixed number of individuals are sampled and their coalescent tree is drawn. Taking the sampling time and carrying capacity simultaneously to infinity, we prove convergence of the coalescent tree to a limiting tree which is in a sense universal over…
Kirchhoff's matrix tree theorem is a well-known result that gives a formula for the number of spanning trees in a finite, connected graph in terms of the graph Laplacian matrix. A closely related result is Wilson's algorithm for putting the uniform distribution on the set of spanning trees. We will show that when one follows Greg Lawler's strategy for proving Wilson's algorithm, Kirchhoff's theorem follows almost immediately after one applies some elementary linear algebra. We also show that the same ideas can be applied to other computations related to general Markov chains and processes on a…
Given a finite typed rooted tree $T$ with $n$ vertices, the {\em empirical subtree measure} is the uniform measure on the $n$ typed subtrees of $T$ formed by taking all descendants of a single vertex. We prove a large deviation principle in $n$, with explicit rate function, for the empirical subtree measures of multitype Galton-Watson trees conditioned to have exactly $n$ vertices. In the process, we extend the notions of shift-invariance and specific relative entropy--as typically understood for Markov fields on deterministic graphs such as $\mathbb Z^d$--to Markov fields on random trees. We …
We develop a new Markov chain on graph partitions that makes relatively global moves yet is computationally feasible to be used as the proposal in the Metropolis-Hastings method. Our resulting algorithm can be made reversible and able to sample from a specified measure on partitions. Both of these properties are critical to some important applications and computational Bayesian statistics in general. Our proposal chain modifies the recently developed method called Recombination (ReCom), which draws spanning trees on joined partitions and then randomly cuts them to repartition. We improve the c…
We provide simplified proofs for the asymptotic distribution of the number of cuts required to cut down a Galton-Watson tree with critical, finite-variance offspring distribution, conditioned to have total progeny $n$. Our proof is based on a coupling which yields a precise, nonasymptotic distributional result for the case of uniformly random rooted labeled trees (or, equivalently, Poisson Galton-Watson trees conditioned on their size). Our approach also provides a new, random reversible transformation between Brownian excursion and Brownian bridge.
In an earlier paper we introduced a special kind of k-width junction tree, called k-th order t-cherry junction tree in order to approximate a joint probability distribution. The approximation is the best if the Kullback-Leibler divergence between the true joint probability distribution and the approximating one is minimal. Finding the best approximating k-width junction tree is NP-complete if k>2. In our earlier paper we also proved that the best approximating k-width junction tree can be embedded into a k-th order t-cherry junction tree. We introduce a greedy algorithm resulting very good app…
We give locally finite Markov trees in $L^p$-compact$,$ separable Hilbert$,$ supersymmetric process$:$ $[0,\infty)\!\times\!\mathbb{R}^{\lvert\mathcal{A}^{\otimes m}\rvert}/\mathcal{A}^{\otimes m}$ on quantum ${\rm U}(\lvert\mathcal{A}^{\otimes m}\rvert)$ semigroups$.$ In full automorphism group ${\rm Aut}({\rm\bf T})$ of modular subgroup$,$ asymptotic-ergodicity is entropy-worthy $\mathbb{R}$ shape for uniform partition$.$
We introduce an algorithm for generating a random sequence of fragmentation trees, which we call the ancestral branching algorithm. This algorithm builds on the recursive partitioning structure of a tree and gives rise to an associated family of Markovian transition kernels whose finite-dimensional transition probabilities can be written in closed-form as the product over partition-valued Markov kernels. The associated tree-valued Markov process is infinitely exchangeable provided its associated partition-valued kernel is infinitely exchangeable. We also identify a transition procedure on part…
In this paper, we aim to provide probabilistic and combinatorial insights into tree formulas for the Green function and hitting probabilities of Markov chains on a finite state space. These tree formulas are closely related to loop-erased random walks by Wilson's algorithm for random spanning trees, and to mixing times by the Markov chain tree theorem. Let $m_{ij}$ be the mean first passage time from $i$ to $j$ for an irreducible chain with finite state space $S$ and transition matrix $(p_{ij}; i, j \in S)$. It is well-known that $m_{jj} = 1/π_j = Σ^{(1)}/Σ_j$, where $π$ is the stationary dist…
