Related papers: The space of equidistant phylogenetic cactuses
A phylogenetic network is a graph-theoretical tool that is used by biologists to represent the evolutionary history of a collection of species. One potential way of constructing such networks is via a distance-based approach, where one is…
Learning faithful graph representations as sets of vertex embeddings has become a fundamental intermediary step in a wide range of machine learning applications. The quality of the embeddings is usually determined by how well the geometry…
In this work, we answer an open problem in the study of phylogenetic networks. Phylogenetic trees are rooted binary trees in which all edges are directed away from the root, whereas phylogenetic networks are rooted acyclic digraphs. For the…
A suffix tree is a data structure used mainly for pattern matching. It is known that the space complexity of simple suffix trees is quadratic in the length of the string. By a slight modification of the simple suffix trees one gets the…
An ultrametric Cantor set can be seen as the boundary of a rooted weighted tree called the Michon tree. The notion of Assouad dimension is re-interpreted as seen on the Michon tree. The Assouad dimension of an ultrametric Cantor set is…
In this paper, we provide an alternative description of the duality result for distributive lattices and coherent locales using ultraposet. In particular, we show that there are fully faithful embeddings from the opposite of the category of…
We introduce a notion of finite sampling consistency for phylogenetic trees and show that the set of finitely sampling consistent and exchangeable distributions on n leaf phylogenetic trees is a polytope. We use this polytope to show that…
We study asymptotic topological regularity of CAT(0) spaces. We prove that if a purely n-dimensional, proper, geodesically complete CAT(0) space has small volume growth, then it is homeomorphic to the n-dimensional Euclidean space. We also…
In this project we explore the geometry of general metric spaces, where we do not necessarily have the tools of differential geometry on our side. Some metric spaces $(X,d)$ allow us to define geodesics, permitting us to compare geodesic…
In phylogenetics, evolution is traditionally represented in a tree-like manner. However, phylogenetic networks can be more appropriate for representing evolutionary events such as hybridization, horizontal gene transfer, and others. In…
The center of distances of a metric space $(X,d)$ is the set $C(X)$ of all $t\in \mathbb R^+$ for which the equation $d(x,p)=t$ has a solution for each $p\in X$. We prove that the equalities $C(X)=\{0\}$ or $C(X)=\{0,\operatorname{diam}X\}…
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…
There is a well-known correspondence between infinite trees and ultrametric spaces which can be interpreted as an equivalence of categories and comes from considering the end space of the tree. In this equivalence, uniformly continuous maps…
Phrase structure trees have a hierarchical structure. In many subjects, most notably in Taxonomy such tree structures have been studied using ultrametrics. Here syntactical hierarchical phrase trees are subject to a similar analysis, which…
An equidistant set in the Euclidean space consists of points having equal distances to both members of a given pair of sets, called focal sets. Since there is no effective formula to compute the distance of a point and a set, it is hard to…
We study geodesically complete and locally compact Hadamard spaces X whose Tits boundary is a connected irreducible spherical building. We show that X is symmetric iff complete geodesics in X do not branch and a Euclidean building…
Phylogenetic networks generalize phylogenetic trees, and have been introduced in order to describe evolution in the case of transfer of genetic material between coexisting species. There are many classes of phylogenetic networks, which can…
We investigate the interrelations between labeled trees and ultrametric spaces generated by these trees. The labeled trees, which generate complete ultrametrics, totally bounded ultrametrics, and discrete ones, are characterized up to…
We describe Galois connections which arise between two kinds of combinatorial structures, both of which generalize trees with labelled leaves, and then apply those connections to a family of polytopes. The graphs we study can be imbued with…
Merge trees are a type of graph-based topological summary that tracks the evolution of connected components in the sublevel sets of scalar functions. They enjoy widespread applications in data analysis and scientific visualization. In this…