Related papers: A Simple 4-Approximation Algorithm for Maximum Agr…
The Steiner Forest problem is an important generalization of the Steiner Tree problem. We are given an undirected graph with nonnegative edge costs and a collection of pairs of vertices. The task is to compute a cheapest forest with the…
A \emph{binary tanglegram} is a drawing of a pair of rooted binary trees whose leaf sets are in one-to-one correspondence; matching leaves are connected by inter-tree edges. For applications, for example, in phylogenetics, it is essential…
Recently, considerable effort has been put into developing fast algorithms to reconstruct a rooted phylogenetic network that explains two rooted phylogenetic trees and has a minimum number of hybridization vertices. With the standard…
In this paper, we present a new simple degree-based estimator for the size of maximum matching in bounded arboricity graphs. When the arboricity of the graph is bounded by $\alpha$, the estimator gives a $\alpha+2$ factor approximation of…
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 describe a kernel of size 9k-8 for the NP-hard problem of computing the Tree Bisection and Reconnect (TBR) distance k between two unrooted binary phylogenetic trees. We achieve this by extending the existing portfolio of reduction rules…
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…
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…
In this paper we show how to find nearly optimal embeddings of large trees in several natural classes of graphs. The size of the tree T can be as large as a constant fraction of the size of the graph G, and the maximum degree of T can be…
The tree inclusion problem is, given two node-labeled trees $P$ and $T$ (the ``pattern tree'' and the ``target tree''), to locate every minimal subtree in $T$ (if any) that can be obtained by applying a sequence of node insertion operations…
We consider the tree consensus problem, an important problem in bioinformatics. Given a rooted tree $t$ and another tree $T$, one would like to incorporate compatible information from $T$ to $t$. This problem is a subproblem in the tree…
We propose an algorithm named best-scored random forest for binary classification problems. The terminology "best-scored" means to select the one with the best empirical performance out of a certain number of purely random tree candidates…
Finding a minimum spanning tree (MST) for $n$ points in an arbitrary metric space is a fundamental primitive for hierarchical clustering and many other ML tasks, but this takes $\Omega(n^2)$ time to even approximate. We introduce a…
Constrained forest problems form a class of graph problems where specific connectivity requirements for certain cuts within the graph must be satisfied by selecting the minimum-cost set of edges. The prize-collecting version of these…
In this experimental study we consider Steiner tree approximations that guarantee a constant approximation of ratio smaller than $2$. The considered greedy algorithms and approaches based on linear programming involve the incorporation of…
We study the following problem that is motivated by demand-aware network design: Given a tree~$G$, the task is to find a binary tree~$H$ on the same vertex set. The objective is to minimize the sum of distances in~$H$ between vertex pairs…
We define a search problem on trees that closely captures the backtracking behavior of all current practical graph isomorphism algorithms. Given two trees with colored leaves, the goal is to find two leaves of matching color, one in each of…
The basic goal of survivable network design is to build cheap networks that guarantee the connectivity of certain pairs of nodes despite the failure of a few edges or nodes. A celebrated result by Jain [Combinatorica'01] provides a…
Recent improvements in adder optimization could be achieved by optimizing the AND-trees occurring within the constructed circuits. The overlap of such trees and its potential for pure size optimization has not been taken into account…
This paper presents an efficient algorithm for retrieving from a database of trees, all trees that match a given query tree approximately, that is, within a certain error tolerance. It has natural language processing applications in…