Related papers: Computing Geodesic Distances in Tree Space
We study the geometry of metrics and convexity structures on the space of phylogenetic trees, which is here realized as the tropical linear space of all \ ultrametrics. The ${\rm CAT}(0)$-metric of Billera-Holmes-Vogtman arises from the…
The metric space of phylogenetic trees defined by Billera, Holmes, and Vogtmann, which we refer to as BHV space, provides a natural geometric setting for describing collections of trees on the same set of taxa. However, it is sometimes…
In this work we study the interleaving distance between merge trees from a combinatorial point of view. We use a particular type of matching between trees to obtain a novel formulation of the distance. With such formulation, we tackle the…
Geodesic paths and distances are among the most popular intrinsic properties of 3D surfaces. Traditionally, geodesic paths on discrete polygon surfaces were computed using shortest path algorithms, such as Dijkstra. However, such algorithms…
We propose a new space of phylogenetic trees which we call wald space. The motivation is to develop a space suitable for statistical analysis of phylogenies, but with a geometry based on more biologically principled assumptions than…
The Gromov-Hausdorff (GH) distance is a natural way to measure distance between two metric spaces. We prove that it is $\mathrm{NP}$-hard to approximate the Gromov-Hausdorff distance better than a factor of $3$ for geodesic metrics on a…
This paper give a simple linear-time algorithm that, given a weighted digraph, finds a spanning tree that simultaneously approximates a shortest-path tree and a minimum spanning tree. The algorithm provides a continuous trade-off: given the…
In this paper we provide a method of finding possible numbers of shortest paths between two points in a space of compact sets in Euclidean space with Hausdorff distance. We also prove that there cannot be some of the numbers of shortest…
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…
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…
Graphs are interesting structures: extremely useful to depict real-life problems, extremely easy to understand given a sketch, extremely complicated to represent formally, extremely complicated to compare. Phylogeny is the study of the…
Phylogenetic trees summarize evolutionary relationships. The Billera-Holmes-Vogtmann (BHV) space for comparing phylogenetic trees has many elegant mathematical properties, but it does not encompass trees with differing leaf sets. To…
In this paper, we consider enumeration of geodesics on a polyhedron, where a geodesic means locally-shortest path between two points. Particularly, we consider the following preprocessing problem: given a point $s$ on a polyhedral surface…
The length of the geodesic between two data points along a Riemannian manifold, induced by a deep generative model, yields a principled measure of similarity. Current approaches are limited to low-dimensional latent spaces, due to the…
Let $P$ be a simple polygon with $n$ vertices. For any two points in $P$, the geodesic distance between them is the length of the shortest path that connects them among all paths contained in $P$. Given a set $S$ of $m$ sites being a subset…
Computing an array of all pairs of geodesic distances between the pixels of an image is time consuming. In the sequel, we introduce new methods exploiting the redundancy of geodesic propagations and compare them to an existing one. We show…
In this paper, we study the problem of computing Euclidean geodesic centers of a polygonal domain $\mathcal{P}$ with a total of $n$ vertices. We discover many interesting observations. We give a necessary condition for a point being a…
Rotation distances measure the differences in structure between rooted ordered binary trees. The one-dimensional skeleta of associahedra are rotation graphs, where two vertices representing trees are connected by an edge if they differ by a…
This paper provides a short and transparent solution for the covering cost of white-grey trees which play a crucial role in the algorithm of Bergeron {\it et al.}\ to compute the rearrangement distance between two multichromosomal genomes…
Geometric graphs appear in many real-world data sets, such as road networks, sensor networks, and molecules. We investigate the notion of distance between embedded graphs and present a metric to measure the distance between two geometric…