Related papers: Tree Edit Distance with Variables. Measuring the S…
In this article we study the treewidth of the \emph{display graph}, an auxiliary graph structure obtained from the fusion of phylogenetic (i.e., evolutionary) trees at their leaves. Earlier work has shown that the treewidth of the display…
Tree comparison metrics have proven to be an invaluable aide in the reconstruction and analysis of phylogenetic (evolutionary) trees. The path-length distance between trees is a particularly attractive measure as it reflects differences in…
We introduce a scale-free method for testing the proportionality of branch lengths between two phylogenetic trees that have the same topology and contain the same set of taxa. This method scales both trees to a total length of 1 and sums up…
Given two strings of length $n$ over alphabet $\Sigma$, and an upper bound $k$ on their edit distance, the algorithm of Myers (Algorithmica'86) and Landau and Vishkin (JCSS'88) computes the unweighted string edit distance in…
Probabilistic graphical models offer a powerful framework to account for the dependence structure between variables, which is represented as a graph. However, the dependence between variables may render inference tasks intractable. In this…
The problem of approximate string matching is important in many different areas such as computational biology, text processing and pattern recognition. A great effort has been made to design efficient algorithms addressing several variants…
We study the number of distance queries needed to identify certain properties of a hidden tree $T$ on $n$ vertices. A distance query consists of two vertices $x,y$, and the answer is the distance of $x$ and $y$ in $T$. We determine the…
The \emph{distance-number} of a graph $G$ is the minimum number of distinct edge-lengths over all straight-line drawings of $G$ in the plane. This definition generalises many well-known concepts in combinatorial geometry. We consider the…
This paper revisits recent code similarity evaluation metrics, particularly focusing on the application of Abstract Syntax Tree (AST) editing distance in diverse programming languages. In particular, we explore the usefulness of these…
In the longest plane spanning tree problem, we are given a finite planar point set $\mathcal{P}$, and our task is to find a plane (i.e., noncrossing) spanning tree for $\mathcal{P}$ with maximum total Euclidean edge length. Despite more…
In a previous work, we gave a metric on the class of semibinary tree-sibling time consistent phylogenetic networks that is computable in polynomial time; in particular, the problem of deciding if two networks of this kind are isomorphic is…
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…
This paper presents enhancements to the projection pursuit tree classifier and visual diagnostic methods for assessing their impact in high dimensions. The original algorithm uses linear combinations of variables in a tree structure where…
Finding the graphs that are most similar to a query graph in a large database is a common task with various applications. A widely-used similarity measure is the graph edit distance, which provides an intuitive notion of similarity and…
The edit distance is a fundamental measure of sequence similarity, defined as the minimum number of character insertions, deletions, and substitutions needed to transform one string into the other. Given two strings of length at most $n$,…
We give algorithms to compute the Fr\'echet distance of trees and graphs with bounded tree width. Our algorithms run in $O(n^2)$ time for trees of bounded degree, and $O(n^2\sqrt{n \log n})$ time for trees of arbitrary degree. For graphs of…
The tree edit distance (TED) between two rooted ordered trees with $n$ nodes labeled from an alphabet $\Sigma$ is the minimum cost of transforming one tree into the other by a sequence of valid operations consisting of insertions, deletions…
The tree edit distance problem is a natural generalization of the classic string edit distance problem. Given two ordered, edge-labeled trees $T_1$ and $T_2$, the edit distance between $T_1$ and $T_2$ is defined as the minimum total cost of…
The problem of realizing finite metric spaces in terms of weighted graphs has many applications. For example, the mathematical and computational properties of metrics that can be realized by trees have been well-studied and such research…
Despite the common misconception of nearly static organisms, plants do interact continuously with the environment and with each other. It is fair to assume that during their evolution they developed particular features to overcome problems…