Related papers: On the variational distance of two trees
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…
Multivariate extreme value distributions are a common choice for modelling multivariate extremes. In high dimensions, however, the construction of flexible and parsimonious models is challenging. We propose to combine bivariate max-stable…
We present the simulation of the time evolution of the distance matrix. The result is the node-node distance distribution for various kinds of networks. For the exponential trees, analytical formulas are derived for the moments of the…
Given a graph, we can form a spanning forest by first sorting the edges in some order, and then only keep edges incident to a vertex which is not incident to any previous edge. The resulting forest is dependent on the ordering of the edges,…
Labelled Markov chains (LMCs) are widely used in probabilistic verification, speech recognition, computational biology, and many other fields. Checking two LMCs for equivalence is a classical problem subject to extensive studies, while the…
In this work we study the interleaving distance between merge trees from a combinatorial point of view. We use a particular type of matching between trees to obtain a novel formulation of the distance. With such formulation, we tackle the…
We consider the evolution of populations under the joint action of mutation and differential reproduction, or selection. The population is modelled as a finite-type Markov branching process in continuous time, and the associated…
For a vertex $v$ of a graph $G$, a spanning tree $T$ of $G$ is distance-preserving from $v$ if, for any vertex $w$, the distance from $v$ to $w$ on $T$ is the same as the distance from $v$ to $w$ on $G$. If two vertices $u$ and $v$ are…
We construct a family of trees on which a lazy simple random walk exhibits total variation cutoff. The main idea behind the construction is that hitting times of large sets should be concentrated around their means. For this sequence of…
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 log-det distance between two aligned DNA sequences was introduced as a tool for statistically consistent inference of a gene tree under simple non-mixture models of sequence evolution. Here we prove that the log-det distance, coupled…
In this paper we investigate the use of staged tree models for discrete longitudinal data. Staged trees are a type of probabilistic graphical model for finite sample space processes. They are a natural fit for longitudinal data because a…
Markov chains are convenient means of generating realizations of networks with a given (joint or otherwise) degree distribution, since they simply require a procedure for rewiring edges. The major challenge is to find the right number of…
Modelling the substitution of nucleotides along a phylogenetic tree is usually done by a hidden Markov process. This allows to define a distribution of characters at the leaves of the trees and one might be able to obtain polynomial…
Generating function equation has been derived for the probability distribution of the number of nodes with $k \ge 0$ outgoing lines in randomly evolving special trees. The stochastic properties of end-nodes (k=0) have been analyzed, and it…
We consider a conditioned Galton-Watson tree and prove an estimate of the number of pairs of vertices with a given distance, or, equivalently, the number of paths of a given length. We give two proofs of this result, one probabilistic and…
Rotation distance measures the difference in shape between binary trees of the same size by counting the minimum number of rotations needed to transform one tree to the other. We describe several types of rotation distance where…
The forest of mutations associated to a multitype branching forest is obtained by merging together all vertices of its clusters and by preserving connections between them. We first show that the forest of mutations of any mulitype branching…
Maximum parsimony distance is a measure used to quantify the dissimilarity of two unrooted phylogenetic trees. It is NP-hard to compute, and very few positive algorithmic results are known due to its complex combinatorial structure. Here we…
Distance-based approaches in phylogenetics such as Neighbor-Joining are a fast and popular approach for building trees. These methods take pairs of sequences from them construct a value that, in expectation, is additive under a stochastic…