Related papers: Exchangeable and Sampling Consistent Distributions…
A fringe subtree of a rooted tree is a subtree consisting of one of the nodes and all its descendants. In this paper, we are specifically interested in the number of non-isomorphic trees that appear in the collection of all fringe subtrees…
Phylogenetic networks are mathematical structures for modeling and visualization of reticulation processes in the study of evolution. Galled networks, reticulation visible networks, nearly-stable networks and stable-child networks are the…
We study the extreme local structure of plane binary trees through the distribution of leaves at maximum depth. We first address two basic questions: (i) the asymptotic probability that exactly two leaves occur at the deepest level, and…
This note defines a notion of multiplicity for nodes in a rooted tree and presents an asymptotic calculation of the maximum multiplicity over all leaves in a Bienaym\'e-Galton-Watson tree with critical offspring distribution $\xi$,…
The cellular tree classifier model addresses a fundamental problem in the design of classifiers for a parallel or distributed computing world: Given a data set, is it sufficient to apply a majority rule for classification, or shall one…
In a rooted tree, we call a vertex {\em balanced} if it is at equal distance from all its descendant leaves. We count balanced vertices in three different tree varieties. For decreasing binary trees, we can prove that the probability that a…
Deciding whether there is a single tree -a supertree- that summarizes the evolutionary information in a collection of unrooted trees is a fundamental problem in phylogenetics. We consider two versions of this question: agreement and…
In evolutionary biology, phylogenetic networks are graphs that provide a flexible framework for representing complex evolutionary histories that involve reticulate evolutionary events. Recently phylogenetic studies have started to focus on…
Phylogenetic Diversity (PD) is a prominent quantitative measure of the biodiversity of a collection of present-day species (taxa). This measure is based on the evolutionary distance among the species in the collection. Loosely speaking, if…
We study stability notions for networked many-to-many matching markets with individually insignificant agents in distributional form. Outcomes are formulated as joint distributions over characteristics of agents and contract choices.…
The ongoing explosion of genome sequence data is transforming how we reconstruct and understand the histories of biological systems. Across biological scales, from individual cells to populations and species, trees-based models provide a…
We introduce a correspondence between phylogenetic trees and Brauer diagrams, inspired by links between binary trees and matchings described by Diaconis and Holmes (1998). This correspondence gives rise to a range of semigroup structures on…
Phylogenetic networks are a generalization of evolutionary trees that are used by biologists to represent the evolution of organisms which have undergone reticulate evolution. Essentially, a phylogenetic network is a directed acyclic graph…
The Shapley value, a solution concept from cooperative game theory, has recently been considered for both unrooted and rooted phylogenetic trees. Here, we focus on the Shapley value of unrooted trees and first revisit the so-called split…
We observe $n$ sequences at each of $m$ sites, and assume that they have evolved from an ancestral sequence that forms the root of a binary tree of known topology and branch lengths, but the sequence states at internal nodes are unknown.…
Compatibility of unrooted phylogenetic trees is a well studied problem in phylogenetics. It asks to determine whether for a set of k input trees there exists a larger tree (called a supertree) that contains the topologies of all k input…
Given a collection $\tau$ of subsets of a finite set $X$, we say that $\tau$ is {\em phylogenetically flexible} if, for any collection $R$ of rooted phylogenetic trees whose leaf sets comprise the collection $\tau$, $R$ is compatible (i.e.…
A binary phylogenetic network on a taxon set $X$ is a rooted acyclic digraph in which the degree of each nonleaf node is three and its leaves (i.e.degree-one nodes) are uniquely labeled with the taxa of $X$. It is tree-child if each nonleaf…
In many applications involving binary variables, only pairwise dependence measures, such as correlations, are available. However, for multi-way tables involving more than two variables, these quantities do not uniquely determine the joint…
We study the Potts model on locally tree-like random graphs of arbitrary degree distribution. Using a population dynamics algorithm we numerically solve the problem exactly. We confirm our results with simulations. Comparisons with a…