Related papers: Fitting Distances by Tree Metrics Minimizing the T…
Edit distance is a measure of similarity of two strings based on the minimum number of character insertions, deletions, and substitutions required to transform one string into the other. The edit distance can be computed exactly using a…
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 achieve a (randomized) polynomial-time approximation scheme (PTAS) for the Steiner Forest Problem in doubling metrics. Before our work, a PTAS is given only for the Euclidean plane in [FOCS 2008: Borradaile, Klein and Mathieu]. Our PTAS…
We describe a polynomial-time algorithm which, given a graph $G$ with treewidth $t$, approximates the pathwidth of $G$ to within a ratio of $O(t\sqrt{\log t})$. This is the first algorithm to achieve an $f(t)$-approximation for some…
Given a graph $G=(V,E)$ with non-negative real edge lengths and an integer parameter $k$, the Min-Max k-Tree Cover problem seeks to find a set of at most $k$ subtrees of $G$, such that the union of the trees is the vertex set $V$. The…
The best algorithm for approximating Steiner tree has performance ratio $\ln(4)+\epsilon \approx 1.386$ [J. Byrka et al., \textit{Proceedings of the 42th Annual ACM Symposium on Theory of Computing (STOC)}, 2010, pp. 583-592], whereas the…
We study the problem of maximizing a monotone submodular function with viability constraints. This problem originates from computational biology, where we are given a phylogenetic tree over a set of species and a directed graph, the…
Tree edit distance is a well-studied measure of dissimilarity between rooted trees with node labels. It can be computed in $O(n^3)$ time [Demaine, Mozes, Rossman, and Weimann, ICALP 2007], and fine-grained hardness results suggest that the…
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…
The search for similarity and dissimilarity measures on phylogenetic trees has been motivated by the computation of consensus trees, the search by similarity in phylogenetic databases, and the assessment of clustering results in…
We give an algorithm that, given an $n$-vertex graph $G$ and an integer $k$, in time $2^{O(k)} n$ either outputs a tree decomposition of $G$ of width at most $2k + 1$ or determines that the treewidth of $G$ is larger than $k$. This is the…
The (unweighted) tree edit distance problem for $n$ node trees asks to compute a measure of dissimilarity between two rooted trees with node labels. The current best algorithm from more than a decade ago runs in $O(n ^ 3)$ time [Demaine,…
The Hausdorff distance is a relatively new measure of similarity of graphs. The notion of the Hausdorff distance considers a special kind of a common subgraph of the compared graphs and depends on the structural properties outside of the…
Search trees on trees (STTs) generalize the fundamental binary search tree (BST) data structure: in STTs the underlying search space is an arbitrary tree, whereas in BSTs it is a path. An optimal BST of size $n$ can be computed for a given…
In the weighted flow-time problem on a single machine, we are given a set of n jobs, where each job has a processing requirement p_j, release date r_j and weight w_j. The goal is to find a preemptive schedule which minimizes the sum of…
In this paper we propose and study a new complexity model for approximation algorithms. The main motivation are practical problems over large data sets that need to be solved many times for different scenarios, e.g., many multicast trees…
Given two rooted, ordered, and labeled trees $P$ and $T$ the tree inclusion problem is to determine if $P$ can be obtained from $T$ by deleting nodes in $T$. This problem has recently been recognized as an important query primitive in XML…
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 phylogenetics, a central problem is to infer the evolutionary relationships between a set of species $X$; these relationships are often depicted via a phylogenetic tree -- a tree having its leaves univocally labeled by elements of $X$…
Consider a vertex-weighted graph $G$ with a source $s$ and a target $t$. Tracking Paths requires finding a minimum weight set of vertices (trackers) such that the sequence of trackers in each path from $s$ to $t$ is unique. In this work, we…