Related papers: Rotation Distance is Fixed-Parameter Tractable
This paper addresses the problem of finding a representation of a subtree distance, which is an extension of the tree metric. We show that a minimal representation is uniquely determined by a given subtree distance, and give a linear time…
We investigate exact crossing minimization for graphs that differ from trees by a small number of additional edges, for several variants of the crossing minimization problem. In particular, we provide fixed parameter tractable algorithms…
In the pattern formation problem, robots in a system must self-coordinate to form a given pattern, regardless of translation, rotation, uniform-scaling, and/or reflection. In other words, a valid final configuration of the system is a…
We present efficient algorithms for computing a maximum agreement forest (MAF) of a pair of multifurcating (nonbinary) rooted trees. Our algorithms match the running times of the currently best algorithms for the binary case. The size of an…
The associahedron $\mathcal{A}(G)$ of a graph $G$ has the property that its vertices can be thought of as the search trees on $G$ and its edges as the rotations between two search trees. If $G$ is a simple path, then $\mathcal{A}(G)$ is the…
We give a fixed-parameter tractable algorithm that, given a parameter $k$ and two graphs $G_1,G_2$, either concludes that one of these graphs has treewidth at least $k$, or determines whether $G_1$ and $G_2$ are isomorphic. The running time…
The tree edit distance is a natural dissimilarity measure between rooted ordered trees whose nodes are labeled over an alphabet $\Sigma$. It is defined as the minimum number of node edits (insertions, deletions, and relabelings) required to…
In order to conduct a statistical analysis on a given set of phylogenetic gene trees, we often use a distance measure between two trees. In a statistical distance-based method to analyze discordance between gene trees, it is a key to decide…
We consider three different schemes for signal routing on a tree. The vertices of the tree represent transceivers that can transmit and receive signals, and are equipped with i.i.d. weights representing the strength of the transceivers. The…
Despite widespread interest and practical use, the theoretical properties of random forests are still not well understood. In this paper we contribute to this understanding in two ways. We present a new theoretically tractable variant of…
A rotated odometer is an infinite interval exchange transformation (IET) obtained as a composition of the von Neumann-Kakutani map and a finite IET of intervals of equal length. In this paper, we consider rotated odometers for which the…
Dissimilarity measures for (possibly weighted) phylogenetic trees based on the comparison of their vectors of path lengths between pairs of taxa, have been present in the systematics literature since the early seventies. But, as far as…
Owing to their inherently interpretable structure, decision trees are commonly used in applications where interpretability is essential. Recent work has focused on improving various aspects of decision trees, including their predictive…
In this empirical study, I compare various tree distance measures -- originally developed in computational biology for the purpose of tree comparison -- for the purpose of parser evaluation. I will control for the parser setting by…
A transversal in a rooted tree is any set of nodes that meets every path from the root to a leaf. We let c(T,k) denote the number of transversals of size k in a rooted tree T. We define a partial order on the set of all rooted trees with n…
A merge tree is a fundamental topological structure used to capture the sub-level set (and similarly, super-level set) topology in scalar data analysis. The interleaving distance is a theoretically sound, stable metric for comparing merge…
In phylogenetics, distances are often used to measure the incongruence between a pair of phylogenetic trees that are reconstructed by different methods or using different regions of genome. Motivated by the maximum parsimony principle in…
Gromov-Hausdorff (GH) distance is a natural way to measure the distortion between two metric spaces. However, there has been only limited algorithmic development to compute or approximate this distance. We focus on computing the…
The Robinson-Foulds (RF) metric is arguably the most widely used measure of phylogenetic tree similarity, despite its well-known shortcomings: For example, moving a single taxon in a tree can result in a tree that has maximum distance to…
We address an open question of Francis and Steel about phylogenetic networks and trees. They give a polynomial time algorithm to decide if a phylogenetic network, N, is tree-based and pose the problem: given a fixed tree T and network N, is…