Related papers: Comparing and Aggregating Partially Resolved Trees
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…
Fitting distances to tree metrics and ultrametrics are two widely used methods in hierarchical clustering, primarily explored within the context of numerical taxonomy. Given a positive distance function…
In a recent paper on 'Estimating Species Trees from Unrooted Gene Trees' Liu and Yu observe that the distance matrix on the underlying taxon set, which is built up from expected internode distances on gene trees under the multispecies…
We propose a new topological invariant of unlabeled trees of N nodes. The invariant is a set of Nx2 matrices of integers, with sum_j k^{d_{i,j}} and v_i as the matrix elements, where d_{i,j} are the elements of the distance matrix and v_i…
Rotation distances measure the differences in structure between rooted ordered binary trees. The one-dimensional skeleta of associahedra are rotation graphs, where two vertices representing trees are connected by an edge if they differ by a…
Geometric graphs appear in many real-world data sets, such as road networks, sensor networks, and molecules. We investigate the notion of distance between embedded graphs and present a metric to measure the distance between two geometric…
An evolutionary tree (phylogenetic tree) is a binary, rooted, unordered tree that models the evolutionary history of currently living species in which leaves are labeled by species. In this paper, we investigate the problem of finding the…
Phylogenetic tree comparison metrics are an important tool in the study of evolution, and hence the definition of such metrics is an interesting problem in phylogenetics. In a paper in Taxon fifty years ago, Sokal and Rohlf proposed to…
Phylogenetic trees are leaf-labelled trees used to model the evolution of species. Here we explore the practical impact of kernelization (i.e. data reduction) on the NP-hard problem of computing the TBR distance between two unrooted binary…
It is well-known that the height profile of a critical conditioned Galton-Watson tree with finite offspring variance converges, after a suitable normalization, to the local time of a standard Brownian excursion. In this work, we study the…
Based on solid theoretical foundations, we present strong evidences that a number of real-life networks, taken from different domains like Internet measurements, biological data, web graphs, social and collaboration networks, exhibit…
A merge tree is a fundamental topological structure used to capture the sub-level set (and similarly, super-level set) topology in scalar data analysis. The interleaving distance is a theoretically sound, stable metric for comparing merge…
We present a new method to count unrooted maps on the sphere up to orientation-preserving homeomorphisms. The principle, called tree-decomposition, is to deform a map into an arborescent structure whose nodes are occupied by constrained…
In this paper we obtain the rates of convergence of the algorithms given in [13] and [14] for an automatic computation of the centered Hausdorff and packing measures of a totally disconnected self-similar set. We evaluate these rates…
By-tree information gathering is an essential task in precision agriculture achieved by ground mobile sensors, but it can be time- and labor-intensive. In this paper we present an algorithmic framework to perform real-time and on-the-go…
An ordered labeled tree is a tree in which the nodes are labeled and the left-to-right order among siblings is relevant. The edit distance between two ordered labeled trees is the minimum cost of changing one tree into the other through a…
In a population with haploid reproduction any individual has a single parent in the previous generation. If all genealogical distances among pairs of individuals (generations from the closest common ancestor) are known it is possible to…
Distance-based phylogenetic algorithms attempt to solve the NP-hard least squares phylogeny problem by mapping an arbitrary dissimilarity map representing biological data to a tree metric. The set of all dissimilarity maps is a Euclidean…
Computing the similarity between two data points plays a vital role in many machine learning algorithms. Metric learning has the aim of learning a good metric automatically from data. Most existing studies on metric learning for…
The matrices of spanning rooted forests are studied as a tool for analysing the structure of digraphs and measuring their characteristics. The problems of revealing the basis bicomponents, measuring vertex proximity, and ranking from…