相关论文: On joint subtree distributions under two evolution…

Tree shape statistics are important for investigating evolutionary mechanisms mediating phylogenetic trees. As a step towards bridging shape statistics between rooted and unrooted trees, we present a comparison study on two subtree…

Tree shape statistics provide valuable quantitative insights into evolutionary mechanisms underpinning phylogenetic trees, a commonly used graph representation of evolution systems ranging from viruses to species. By developing limit…

The Yule-Harding-Kingman (YHK) model and the proportional to distinguishable arrangements (PDA) model are two binary tree generating models that are widely used in evolutionary biology. Understanding the distributions of clade sizes under…

We study two fringe subtree counting statistics, the number of cherries and that of pitchforks for Ford's $\alpha$ model, a one-parameter family of random phylogenetic tree models that includes the uniform and the Yule models, two tree…

We consider exact enumerations and probabilistic properties of ranked trees when generated under the random coalescent process. Using a new approach, based on generating functions, we derive several statistics such as the exact probability…

The shapes of branching trees have been linked to disease transmission patterns. In this paper we use the general Crump-Mode-Jagers branching process to model an outbreak of an infectious disease under mild assumptions. Introducing a new…

A Yule tree is the result of a branching process with constant birth and death rates. Such a process serves as an instructive null model of many empirical systems, for instance, the evolution of species leading to a phylogenetic tree.…

We introduce the Pitman Yor Diffusion Tree (PYDT) for hierarchical clustering, a generalization of the Dirichlet Diffusion Tree (Neal, 2001) which removes the restriction to binary branching structure. The generative process is described…

For two decades, the Colless index has been the most frequently used statistic for assessing the balance of phylogenetic trees. In this article, this statistic is studied under the Yule and uniform model of phylogenetic trees. The main tool…

Efforts to reconstruct phylogenetic trees and understand evolutionary processes depend fundamentally on stochastic models of speciation and mutation. The simplest continuous-time model for speciation in phylogenetic trees is the Yule…

This work focuses on clustering populations with a hierarchical dependency structure that can be described by a tree. A particular example that is the focus of our work is the phylogenetic tree, with nodes often representing biological…

We introduce Joint Probability Trees (JPT), a novel approach that makes learning of and reasoning about joint probability distributions tractable for practical applications. JPTs support both symbolic and subsymbolic variables in a single…

In this article, we develop a new class of multivariate distributions adapted for count data, called Tree P\'olya Splitting. This class results from the combination of a univariate distribution and singular multivariate distributions along…

We provide a local probabilistic description of the limiting statistics of large preferential attachment trees in terms of the ordinary degree (number of neighbors) but augmented with information on leafdegree (number of neighbors that are…

We introduce two models for multi-type random trees motivated by studies of trait dependence in the evolution of species. Our discrete time model, the multi-type ERM tree, is a generalization of Markov propagation models on a random tree…

It has been suggested that a Random Tree Puzzle (RTP) process leads to a Yule-Harding (YH) distribution, when the number of taxa becomes large. In this study, we formalize this conjecture, and we prove that the two tree distributions…

Neutral macroevolutionary models, such as the Yule model, give rise to a probability distribution on the set of discrete rooted binary trees over a given leaf set. Such models can provide a signal as to the approximate location of the root…

Binary trees are fundamental objects in models of evolutionary biology and population genetics. Here, we discuss some of their combinatorial and structural properties as they depend on the tree class considered. Furthermore, the process by…

Given a gene-tree labeled topology $G$ and a species tree $S$, the "ancestral configurations" at an internal node $k$ of $S$ represent the combinatorially different sets of gene lineages that can be present at $k$ when all possible…

Following Poupard's study of strictly ordered binary trees with respect to two parameters, namely, "end of minimal chain" and "parent of maximum leaf" a true Tree Calculus is being developed to solve a partial difference equation system and…