Related papers: Arboreal Ultrametrics
Phylogenetic trees and networks are leaf-labelled graphs used to model evolution. Display graphs are created by identifying common leaf labels in two or more phylogenetic trees or networks. The treewidth of such graphs is bounded as a…
Ultrametric matrices have a rich structure that is not apparent from their definition. Notably, the subclass of strictly ultrametric matrices are covariance matrices of certain weighted rooted binary trees. In applications, these matrices…
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…
Phylogenetic networks are a type of directed acyclic graph that represent how a set $X$ of present-day species are descended from a common ancestor by processes of speciation and reticulate evolution. In the absence of reticulate evolution,…
We study the conditions under which the isometry of spaces with metrics generated by weights given on the edges of finite trees is equivalent to the isomorphism of these trees. Similar questions are studied for ultrametric spaces generated…
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…
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…
A (pseudo-)metric $D$ on a finite set $X$ is said to be a `tree metric' if there is a finite tree with leaf set $X$ and non-negative edge weights so that, for all $x,y \in X$, $D(x,y)$ is the path distance in the tree between $x$ and $y$.…
It is known that PQ-symmetric maps on the boundary characterize the quasi-isometry type of visual hyperbolic spaces, in particular, of geodesically complete \br-trees. We define a map on pairs of PQ-symmetric ultrametric spaces which…
Metrics on rooted phylogenetic trees are integral to a number of areas of phylogenetic analysis. Cluster-similarity metrics have recently been introduced in order to limit skew in the distribution of distances, and to ensure that trees in…
Tree representations of (sets of) symmetric binary relations, or equivalently edge-colored undirected graphs, are of central interest, e.g.\ in phylogenomics. In this context symbolic ultrametrics play a crucial role. Symbolic ultrametrics…
Semidirected networks have received interest in evolutionary biology as the appropriate generalization of unrooted trees to networks, in which some but not all edges are directed. Yet these networks lack proper theoretical study. We define…
We study extremal properties of finite ultrametric spaces $X$ and related properties of representing trees $T_X$. The notion of weak similarity for such spaces is introduced and related morphisms of labeled rooted trees are found. It is…
Phylogenetic networks are a generalization of phylogenetic trees that allow for representation of reticulate evolution. Recently, a space of unrooted phylogenetic networks was introduced, where such a network is a connected graph in which…
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…
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…
We study the problem of how well a tree metric is able to preserve the sum of pairwise distances of an arbitrary metric. This problem is closely related to low-stretch metric embeddings and is interesting by its own flavor from the line of…
This paper addresses the basic question of how well can a tree approximate distances of a metric space or a graph. Given a graph, the problem of constructing a spanning tree in a graph which strongly preserves distances in the graph is a…
In Francis and Steel (2015), it was shown that there exists non-trivial networks on $4$ leaves upon which the distance metric affords a metric on a tree which is not the base tree of the network. In this paper we extend this result in two…
Let $L$ be a fixed branch -- that is, an irreducible germ of curve -- on a normal surface singularity $X$. If $A,B$ are two other branches, define $u_L(A,B) := \dfrac{(L \cdot A) \: (L \cdot B)}{A \cdot B}$, where $A \cdot B$ denotes the…