相关论文: Tree Contractions and Evolutionary Trees

A chief problem in phylogenetics and database theory is the computation of a maximum consistent tree from a set of rooted or unrooted trees. A standard input are triplets, rooted binary trees on three leaves, or quartets, unrooted binary…

In evolutionary biology, phylogenetic trees are commonly inferred from a set of characters (partitions) of a collection of biological entities (e.g., species or individuals in a population). Such characters naturally arise from molecular…

Given a gene tree and a species tree, ancestral configurations represent the combinatorially distinct sets of gene lineages that can reach a given node of the species tree. They have been introduced as a data structure for use in the…

A fringe subtree of a rooted tree is a subtree induced by one of the vertices and all its descendants. We consider the problem of estimating the number of distinct fringe subtrees in two types of random trees: simply generated trees and…

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…

A subtree of a tree is any induced subgraph that is again a tree (i.e., connected). The mean subtree order of a tree is the average number of vertices of its subtrees. This invariant was first analyzed in the 1980s by Jamison. An intriguing…

Phylogenetic trees are leaf-labelled trees used to model the evolution of species. In practice it is not uncommon to obtain two topologically distinct trees for the same set of species, and this motivates the use of distance measures to…

A decision tree recursively splits a feature space $\mathbb{R}^{d}$ and then assigns class labels based on the resulting partition. Decision trees have been part of the basic machine-learning toolkit for decades. A large body of work treats…

A spanning tree of a graph $G$ is a connected acyclic spanning subgraph of $G$. We consider enumeration of spanning trees when $G$ is a $2$-tree, meaning that $G$ is obtained from one edge by iteratively adding a vertex whose neighborhood…

Routing tables in ad hoc and wireless routing protocols can be represented using rooted trees. The constant need for communication and storage of these trees in routing protocols demands an efficient rooted tree coding algorithm. This…

The problem of reconstructing evolutionary trees or phylogenies is of great interest in computational biology. A popular model for this problem assumes that we are given the set of leaves (current species) of an unknown binary tree and the…

Given an edge-weighted tree $T$ with $n$ leaves, sample the leaves uniformly at random without replacement and let $W_k$, $2 \le k \le n$, be the length of the subtree spanned by the first $k$ leaves. We consider the question, "Can $T$ be…

Trees without vertices of degree $2$ are sometimes named topological trees. In this work, we bring forward the study of the inducibility of (rooted) topological trees with a given number of leaves. The inducibility of a topological tree $S$…

Random forests and, more generally, (decision\nobreakdash-)tree ensembles are widely used methods for classification and regression. Recent algorithmic advances allow to compute decision trees that are optimal for various measures such as…

This paper introduces a new combinatorial framework for modeling the growth of binary trees through a discrete evolution process that incorporates a growing rule and an extinction rule. Building upon the theory of increasingly labeled…

Background: Tree reconciliation problems have long been studied in phylogenetics. A particular variant of the reconciliation problem for a gene tree T and a species tree S assumes that for each interior vertex x of T it is known whether x…

The structure of an evolving network contains information about its past. Extracting this information efficiently, however, is, in general, a difficult challenge. We formulate a fast and efficient method to estimate the most likely history…

Phylogenetic networks generalize phylogenetic trees by allowing the modelization of events of reticulate evolution. Among the different kinds of phylogenetic networks that have been proposed in the literature, the subclass of binary…

Survival analysis concerns the task of predicting the time until an event occurs. Often used in the medical field, survival analysis deals with incomplete (i.e., censored) data, for instance, from patients who did not experience the event…

For a model of molecular evolution to be useful for phylogenetic inference, the topology of evolutionary trees must be identifiable. That is, from a joint distribution the model predicts, it must be possible to recover the tree parameter.…