Related papers: Improved Methods for Computing Distances between U…
Merge trees are fundamental structures in topological data analysis. Interleaving distance is a widely accepted metric for comparing merge trees, with applications in visualization and scientific computing. While a greedy algorithm exists…
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…
Metric learning has the aim to improve classification accuracy by learning a distance measure which brings data points from the same class closer together and pushes data points from different classes further apart. Recent research has…
The graph edit distance is used for comparing graphs in various domains. Due to its high computational complexity it is primarily approximated. Widely-used heuristics search for an optimal assignment of vertices based on the distance…
We consider the numerical taxonomy problem of fitting a positive distance function ${D:{S\choose 2}\rightarrow \mathbb R_{>0}}$ by a tree metric. We want a tree $T$ with positive edge weights and including $S$ among the vertices so that…
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…
The three-in-a-tree problem is to determine if a simple undirected graph contains an induced subgraph which is a tree connecting three given vertices. Based on a beautiful characterization that is proved in more than twenty pages,…
Dual-tree algorithms are a widely used class of branch-and-bound algorithms. Unfortunately, developing dual-tree algorithms for use with different trees and problems is often complex and burdensome. We introduce a four-part logical split:…
In this paper, we propose new techniques for solving geometric optimization problems involving interpoint distances of a point set in the plane. Given a set $P$ of $n$ points in the plane and an integer $1 \leq k \leq \binom{n}{2}$, the…
We define, analyze, and give efficient algorithms for two kinds of distance measures for rooted and unrooted phylogenies. For rooted trees, our measures are based on the topologies the input trees induce on triplets; that is, on…
The subtree prune-and-regraft (SPR) distance metric is a fundamental way of comparing evolutionary trees. It has wide-ranging applications, such as to study lateral genetic transfer, viral recombination, and Markov chain Monte Carlo…
We present approximation algorithms for the following NP-hard optimization problems related to bottleneck spanning trees in metric spaces. 1. The disjoint bottleneck spanning tree problem: Given $n$ pairs of points in a metric space, find…
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…
Machine Learning has attracted considerable attention throughout the past decade due to its potential to solve far-reaching tasks, such as image classification, object recognition, anomaly detection, and data forecasting. A standard…
Edit distance is a fundamental measure of distance between strings and has been widely studied in computer science. While the problem of estimating edit distance has been studied extensively, the equally important question of actually…
String Edit Distance is a more-than-classical problem whose behavior in the dynamic setting, where the strings are updated over time, is well studied. A single-character substitution, insertion, or deletion can be processed in time…
Sorting is a foundational problem in computer science that is typically employed on sequences or total orders. More recently, a more general form of sorting on partially ordered sets (or posets), where some pairs of elements are…
In this work we define a novel edit distance for trees considered with some abstract weights on the edges. The metric is driven by the idea of considering trees as topological summaries in the context of persistence and topological data…
In the $k$-dispersion problem, we need to select $k$ nodes of a given graph so as to maximize the minimum distance between any two chosen nodes. This can be seen as a generalization of the independent set problem, where the goal is to…
The largest common embeddable subtree problem asks for the largest possible tree embeddable into two input trees and generalizes the classical maximum common subtree problem. Several variants of the problem in labeled and unlabeled rooted…