Related papers: Chain Rotations: a New Look at Tree Distance
The Steiner Tree problem is a classical problem in combinatorial optimization: the goal is to connect a set $T$ of terminals in a graph $G$ by a tree of minimum size. Karpinski and Zelikovsky (1996) studied the $\delta$-dense version of…
We introduce top trees as a design of a new simpler interface for data structures maintaining information in a fully-dynamic forest. We demonstrate how easy and versatile they are to use on a host of different applications. For example, we…
The \emph{distance matrix} of a simple connected graph $G$ is $D(G)=(d_{ij})$, where $d_{ij}$ is the distance between the vertices $i$ and $j$ in $G$. We consider a weighted tree $T$ on $n$ vertices with edge weights are square matrix of…
An orientable sequence of order $n$ is a cyclic binary sequence such that each length-$n$ substring appears at most once \emph{in either direction}. Maximal length orientable sequences are known only for $n\leq 7$, and a trivial upper bound…
Let $X$ be a finite set, $\mathcal N$ be a reticulation-visible network on $X$, and $\mathcal T$ be a rooted binary phylogenetic tree. We show that there is a polynomial-time algorithm for deciding whether or not $\mathcal N$ displays…
A rectilinear Steiner tree for a set $P$ of points in $\mathbb{R}^2$ is a tree that connects the points in $P$ using horizontal and vertical line segments. The goal of Minimal Rectilinear Steiner Tree is to find a rectilinear Steiner tree…
Tree-width and path-width are well-known graph parameters. Many NP-hard graph problems allow polynomial-time solutions, when restricted to graphs of bounded tree-width or bounded path-width. In this work, we study the behavior of tree-width…
Understanding the evolution of a set of genes or species is a fundamental problem in evolutionary biology. The problem we study here takes as input a set of trees describing {possibly discordant} evolutionary scenarios for a given set of…
The problem of reconstructing evolutionary trees or phylogenies is of great interest in computational biology. A popular model for this problem assumes that we are given the set of leaves (current species) of an unknown binary tree and the…
In scientific visualization, scalar fields are often compared through edit distances between their merge trees. Typical tasks include ensemble analysis, feature tracking and symmetry or periodicity detection. Tree edit distances represent…
We present a linear programming based algorithm for computing a spanning tree $T$ of a set $P$ of $n$ points in $\Re^d$, such that its crossing number is $O(\min(t \log n, n^{1-1/d}))$, where $t$ the minimum crossing number of any spanning…
A proper vertex of a rooted tree with totally ordered vertices is a vertex that is less than all its proper descendants. We count several kinds of labeled rooted trees and forests by the number of proper vertices. Our results are all…
Binary search trees (BSTs) with rotations can adapt to various kinds of structure in search sequences, achieving amortized access times substantially better than the Theta(log n) worst-case guarantee. Classical examples of structural…
The treedepth of a graph $G$ is the least possible depth of an elimination forest of $G$: a rooted forest on the same vertex set where every pair of vertices adjacent in $G$ is bound by the ancestor/descendant relation. We propose an…
Let $G=(V,E)$ be a simple, unweighted, connected graph. Let $d(u,v)$ denote the distance between vertices $u,v$. A resolving set of $G$ is a subset $S$ of $V$ such that knowing the distance from a vertex $v$ to every vertex in $S$ uniquely…
The ternary betweenness relation of a tree, B(x,y,z) expresses that y is on the unique path between x and z. This notion can be extended to order-theoretic trees defined as partial orders such that the set of nodes larger than any node is…
Cyclic codes are an important class of linear codes. Bounding the minimum distance of cyclic codes is a long-standing research topic in coding theory, and several well-known and basic results have been developed on this topic. Recently,…
The subtrees and BC-subtrees (subtrees where any two leaves are at even distance apart) have been extensively studied in recent years. Such structures, under special constraints on degrees, have applications in many fields. Through an…
Optimal transport provides a metric which quantifies the dissimilarity between probability measures. For measures supported in discrete metric spaces, finding the optimal transport distance has cubic time complexity in the size of the…
It is known that any two trees on the same $n$ leaves can be displayed by a network with $n-2$ reticulations, and there are two trees that cannot be displayed by a network with fewer reticulations. But how many reticulations are needed to…