相关论文: Computing Geodesic Distances in Tree Space

An important problem in geometric computing is defining and computing similarity between two geometric shapes, e.g. point sets, curves and surfaces, etc. Important geometric and topological information of many shapes can be captured by…

Phylogenetics is now fundamental in life sciences, providing insights into the earliest branches of life and the origins and spread of epidemics. However, finding suitable phylogenies from the vast space of possible trees remains…

By "geodesic" we mean any sequence of vertices $(v_1,v_2,...,v_k)$ of a graph $G$ that constitute a shortest path from $v_1$ to $v_k$. We propose a novel, natural algorithm to enumerate all geodesics of $G$, and pit it (using Mathematica)…

Phylogenetic inference-the derivation of a hypothesis for the common evolutionary history of a group of species- is an active area of research at the intersection of biology, computer science, mathematics, and statistics. One assumes the…

We study the geodesic complexity of the ordered and unordered configuration spaces of graphs in both the $\ell_1$ and $\ell_2$ metrics. We determine the geodesic complexity of the ordered two-point $\varepsilon$-configuration space of any…

We unveil an alluring alternative to parametric search that applies to both the non-geodesic and geodesic Fr\'echet optimization problems. This randomized approach is based on a variant of red-blue intersections and is appealing due to its…

We propose a novel method for the inference of phylogenetic trees that utilises point configurations on hyperbolic space as its optimisation landscape. Each taxon corresponds to a point of the point configuration, while the evolutionary…

We study augmenting a plane Euclidean network with a segment, called a shortcut, to minimize the largest distance between any two points along the edges of the resulting network. Problems of this type have received considerable attention…

Tree-width and path-width are widely successful concepts. Many NP-hard problems have efficient solutions when restricted to graphs of bounded tree-width. Many efficient algorithms are based on a tree decomposition. Sometimes the more…

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. The previous best…

We introduce the heat method for computing the shortest geodesic distance to a specified subset (e.g., point or curve) of a given domain. The heat method is robust, efficient, and simple to implement since it is based on solving a pair of…

Riemannian optimization uses local methods to solve optimization problems whose constraint set is a smooth manifold. A linear step along some descent direction usually leaves the constraints, and hence retraction maps are used 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…

An approximate Steiner tree is a Steiner tree on a given set of terminals in Euclidean space such that the angles at the Steiner points are within a specified error e from 120 degrees.This notion arises in numerical approximations of…

Ranked tree-child networks are a recently introduced class of rooted phylogenetic networks in which the evolutionary events represented by the network are ordered so as to respect the flow of time. This class includes the well-studied…

We give an accessible introduction and elaboration on the methods used in obtaining a geodesic, which is the curve of shortest length connecting two points lying on the surface of a function. This is found through computing what's known as…

Inferential summaries of tree estimates are useful in the setting of evolutionary biology, where phylogenetic trees have been built from DNA data since the 1960's. In bioinformatics, psychometrics and data mining, hierarchical clustering…

Geometry and topology have generated impacts far beyond their pure mathematical primitive, providing a solid foundation for many applicable tools. Typically, real-world data are represented as vectors, forming a linear subspace for a given…

Let $G$ be a unit disk graph in the plane defined by $n$ disks whose positions are known. For the case when $G$ is unweighted, we give a simple algorithm to compute a shortest path tree from a given source in $O(n\log n)$ time. For the case…

We give algorithms to compute the Fr\'echet distance of trees and graphs with bounded tree width. Our algorithms run in $O(n^2)$ time for trees of bounded degree, and $O(n^2\sqrt{n \log n})$ time for trees of arbitrary degree. For graphs of…