Related papers: Least Squares Methods for Equidistant Tree Reconst…
Extending some properties from the Euclidean plane to any normed plane, we show the validity of the Monma-Paterson-Suri-Yao algorithm for finding the maximum-weighted spanning tree of a set of $n$ points, where the weight of an edge is the…
Given a graph $G = (V, E)$, we wish to compute a spanning tree whose maximum vertex degree, i.e. tree degree, is as small as possible. Computing the exact optimal solution is known to be NP-hard, since it generalizes the Hamiltonian path…
The discussion of how to apply geometric algebra to euclidean $n$-space has been clouded by a number of conceptual misunderstandings which we first identify and resolve, based on a thorough review of crucial but largely forgotten themes…
Wasserstein distance, which measures the discrepancy between distributions, shows efficacy in various types of natural language processing (NLP) and computer vision (CV) applications. One of the challenges in estimating Wasserstein distance…
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…
The Euclidean distance geometry problem arises in a wide variety of applications, from determining molecular conformations in computational chemistry to localization in sensor networks. When the distance information is incomplete, the…
We consider the problem of minimizing the sum of two convex functions: one is differentiable and relatively smooth with respect to a reference convex function, and the other can be nondifferentiable but simple to optimize. We investigate a…
Nearest-neighbor search dominates the asymptotic complexity of sampling-based motion planning algorithms and is often addressed with k-d tree data structures. While it is generally believed that the expected complexity of nearest-neighbor…
Phylogenetic trees are leaf-labelled trees used to model the evolution of species. In practice it is not uncommon to obtain two topologically distinct trees for the same set of species, and this motivates the use of distance measures to…
We consider single-source shortest path algorithms that perform a sequence of relaxation steps whose ordering depends only on the input graph structure and not on its weights or the results of prior steps. Each step examines one edge of the…
This paper introduces constNJ, the first algorithm for phylogenetic reconstruction of sets of trees with constrained pairwise rooted subtree-prune regraft (rSPR) distance. We are motivated by the problem of constructing sets of trees which…
We develop optimal algorithms for learning undirected Gaussian trees and directed Gaussian polytrees from data. We consider both problems of distribution learning (i.e. in KL distance) and structure learning (i.e. exact recovery). The first…
The phylogenetic tree space introduced by Billera, Holmes, and Vogtmann (BHV tree space) is a CAT(0) continuous space that represents trees with edge weights with an intrinsic geodesic distance measure. The geodesic distance measure unique…
For a weighted graph $G = (V, E, w)$ and a designated source vertex $s \in V$, a spanning tree that simultaneously approximates a shortest-path tree w.r.t. source $s$ and a minimum spanning tree is called a shallow-light tree (SLT).…
Least squares estimation, a regression technique based on minimisation of residuals, has been invaluable in bringing the best fit solutions to parameters in science and engineering. However, in dynamic environments such as in Geomatics…
Ultrametric matrices are a class of covariance matrices that arise in latent tree models. As a parameter space in a statistical model, the set of ultrametric matrices is neither convex nor a smooth manifold. Focus in the literature has…
Applying a method to reconstruct a phylogenetic tree from random data provides a way to detect whether that method has an inherent bias towards certain tree `shapes'. For maximum parsimony, applied to a sequence of random 2-state data, each…
Given a set of points, we define a minimum Steiner point tree to be a tree interconnecting these points and possibly some additional points such that the length of every edge is at most 1 and the number of additional points is minimized. We…
The rooted subtree prune and regraft (rSPR) distance between two rooted binary phylogenetic trees is a well-studied measure of topological dissimilarity that is NP-hard to compute. Here we describe an improved linear kernel for the problem.…
Self-nested trees present a systematic form of redundancy in their subtrees and thus achieve optimal compression rates by DAG compression. A method for quantifying the degree of self-similarity of plants through self-nested trees has been…