Related papers: Computing Geodesic Distances in Tree Space
We study the problem of finding a temporal hybridization network for a set of phylogenetic trees that minimizes the number of reticulations. First, we introduce an FPT algorithm for this problem on an arbitrary set of $m$ binary trees with…
We give an algorithm for determining the distance between two vertices of the complex of curves. While there already exist such algorithms, for example by Leasure, Shackleton, and Webb, our approach is new, simple, and more effective for…
A new class of distances for graph vertices is proposed. This class contains parametric families of distances which reduce to the shortest-path, weighted shortest-path, and the resistance distances at the limiting values of the family…
What is the shortest path between two data points lying in a high-dimensional space? While the answer is trivial in Euclidean geometry, it becomes significantly more complex when the data lies on a curved manifold -- requiring a Riemannian…
We study the problem of finding small trees. Classical network design problems are considered with the additional constraint that only a specified number $k$ of nodes are required to be connected in the solution. A prototypical example is…
Let $V$ be a separable Hilbert space, possibly infinite dimensional. Let $\St(p,V)$ be the Stiefel manifold of orthonormal frames of $p$ vectors in $V$, and let $\Gr(p,V)$ be the Grassmann manifold of $p$ dimensional subspaces of $V$. We…
We propose a statistical method to test whether two phylogenetic trees with given alignments are significantly incongruent. Our method compares the two distributions of phylogenetic trees given by the input alignments, instead of comparing…
We study parameterized versions of classical algorithms for computing shortest-path trees. This is most easily expressed in terms of tropical geometry. Applications include shortest paths in traffic networks with variable link travel times.
Given a set $P$ of $n$ points that are moving in the plane, we consider the problem of computing a spanning tree for these moving points that does not change its combinatorial structure during the point movement. The objective is to…
We give a greedy learning algorithm for reconstructing an evolutionary tree based on a certain harmonic average on triplets of terminal taxa. After the pairwise distances between terminal taxa are estimated from sequence data, the algorithm…
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…
We introduce a graph partitioning problem motivated by computational topology and propose two algorithms that produce approximate solutions. Specifically, given a weighted, undirected graph $G$ and a positive integer $k$, we desire to find…
We present two new and efficient algorithms for computing all-pairs shortest paths. The algorithms operate on directed graphs with real (possibly negative) weights. They make use of directed path consistency along a vertex ordering d. Both…
Given a point $s$ and a set of $h$ pairwise disjoint polygonal obstacles of totally $n$ vertices in the plane, we present a new algorithm for building an $L_1$ shortest path map of size O(n) in $O(T)$ time and O(n) space such that for any…
We study planar domains $G$ equipped with a hyperbolic type metric and approximate geodesics that join two points $x,y \in G$ and their lengths. We present an algorithm that enables one to approximate the shortest distance in polygonal…
Geodesic distance is the shortest path between two points in a Riemannian manifold. Manifold learning algorithms, such as Isomap, seek to learn a manifold that preserves geodesic distances. However, such methods operate on the ambient…
Given a set of pairwise disjoint polygonal obstacles in the plane, finding an obstacle-avoiding Euclidean shortest path between two points is a classical problem in computational geometry and has been studied extensively. Previously,…
The problem of comparing probability distributions is at the heart of many tasks in statistics and machine learning. Established comparison methods treat the standard setting that the distributions are supported in the same space. Recently,…
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…
We construct a minimum tree for some boundary symmetric tetrahedra R^3, which has two nodes (interior points) with equal weights (positive numbers) having the property that the common perpendicular of some two opposite edges passes through…