Related papers: The space of equidistant phylogenetic cactuses

In 1998, B\"{o}cker and Dress gave a 1-to-1 correspondence between symbolically dated rooted trees and symbolic ultrametrics. We consider the corresponding problem for unrooted trees. More precisely, given a tree $T$ with leaf set $X$ and a…

For every simplicial complex X, we construct a locally CAT(0) cubical complex T_X, a cellular isometric involution i on T_X and a map t_X from T_X to X with the following properties: t_Xi = t_X; t_X is a homology isomorphism; the induced…

Fitch graphs $G=(X,E)$ are digraphs that are explained by $\{\emptyset, 1\}$-edge-labeled rooted trees $T$ with leaf set $X$: there is an arc $(x,y) \in E$ if and only if the unique path in $T$ that connects the last common ancestor…

This paper demonstrates that every ultrametric space is homeomorphic to a clade space of a pruned tree, i.e., a subspace of a tree's canopy. Furthermore, it characterizes several topological properties of ultrametrizable spaces through the…

The tree metric theorem provides a combinatorial four point condition that characterizes dissimilarity maps derived from pairwise compatible split systems. A similar (but weaker) four point condition characterizes dissimilarity maps derived…

We investigate the interrelations between the metric properties, order properties and combinatorial properties of the set of balls in totally bounded ultrametric space. In particular, the Gurvich-Vyalyi representation of finite, ultrametric…

We introduce a new quasi-isometry invariant $\subcorank X$ of a metric space $X$ called {\it subexponential corank}. A metric space $X$ has subexponential corank $k$ if roughly speaking there exists a continuous map $g:X\to T$ such that for…

The asymmetric tropical distance is a distance measure on the tropical torus $\mathbb{R}^n/\mathbb{R}\mathbf{1}$ and in particular on the Bergman fan $B(K_N) \subseteq \mathbb{R}^{\binom{N}{2}}/\mathbb{R}\mathbf{1}$ of the complete…

We prove that if a metric space $X$ has Nagata dimension zero with constant $c$, then there exists a dense subset of $X$ that is $8c$-bilipschitz equivalent to a weighted tree. The factor $8$ is the best possible if $c=1$, that is, if $X$…

Cactus networks were introduced by Lam as a generalization of planar electrical networks. He defined a map from these networks to the Grassmannian Gr($n+1,2n$) and showed that the image of this map, $\mathcal X_n$ lies inside the totally…

We describe the conditions under which a set of continuous variables or characters can be described as an X-tree or a split network. A distance matrix corresponds exactly to a split network or a valued X-tree if, after ordering of the taxa,…

Suppose that there exists a discrete subset $X$ of a complete, connected, $n$-dimensional Riemannian manifold $M$ such that the Riemannian distances between points of $X$ correspond to the Euclidean distances of a net in $\mathbb{R}^{n}$.…

For a CAT(0) cube complex $\mathbf X$, we define a simplicial flag complex $\partial_\Delta\mathbf X$, called the \emph{simplicial boundary}, which is a natural setting for studying non-hyperbolic behavior of $\mathbf X$. We compare…

We extend decision tree and random forest algorithms to product space manifolds: Cartesian products of Euclidean, hyperspherical, and hyperbolic manifolds. Such spaces have extremely expressive geometries capable of representing many…

Geodesic distance, sometimes called shortest path length, has proven useful in a great variety of applications, such as information retrieval on networks including treelike networked models. Here, our goal is to analytically determine the…

Any symmetric affinity function $w: V\times V \to \mathbb{R}_+$ defined on a discrete set $V$ induces Euclidean space structure on $V$. In particular, an undirected graph specified by an affinity (or adjacency) matrix can be considered as a…

Three-way dissimilarities are a generalization of (two-way) dissimilarities which can be used to indicate the lack of homogeneity or resemblance between any three objects. Such maps have applications in cluster analysis, and have been used…

Let X be quasi-isometric to either the mapping class group equipped with the word metric, or to Teichmuller space equipped with either the Teichmuller metric or the Weil-Petersson metric. We introduce a unified approach to study the coarse…

Phylogenetic stochastic mapping is a method for reconstructing the history of trait changes on a phylogenetic tree relating species/organisms carrying the trait. State-of-the-art methods assume that the trait evolves according to a…

Phylogenetic networks are rooted, labelled directed acyclic graphs which are commonly used to represent reticulate evolution. There is a close relationship between phylogenetic networks and multi-labelled trees (MUL-trees). Indeed, any…