Related papers: Arboreal Ultrametrics
A large class of phylogenetic networks can be obtained from trees by the addition of horizontal edges between the tree edges. These networks are called tree based networks. Reticulation-visible networks and child-sibling networks are all…
Graphs drawn in the plane are ubiquitous, arising from data sets through a variety of methods ranging from GIS analysis to image classification to shape analysis. A fundamental problem in this type of data is comparison: given a set of such…
Rooted phylogenetic networks are used by biologists to infer and represent complex evolutionary relationships between species that cannot be accurately explained by a phylogenetic tree. Tree-child networks are a particular class of rooted…
Phylogenetic trees are the fundamental mathematical representation of evolutionary processes in biology. They are also objects of interest in pure mathematics, such as algebraic geometry and combinatorics, due to their discrete geometry.…
Let $\mathcal{T}$ be a rooted and weighted tree, where the weight of any node is equal to the sum of the weights of its children. The popular Treemap algorithm visualizes such a tree as a hierarchical partition of a square into rectangles,…
Tree sets are abstract structures that can be used to model various tree-shaped objects in combinatorics. Finite tree sets can be represented by finite graph-theoretical trees. We extend this representation theory to infinite tree sets.…
We will say that an infinite tree $T$ is almost a ray if $T$ is the union of a ray and a finite tree. Let $l$ be a non-degenerate labeling of the vertex set $V$ of almost a ray $T$ and let $d_l$ be the corresponding ultrametric on $V$. It…
Tree-based phylogenetic networks, which may be roughly defined as leaf-labeled networks built by adding arcs only between the original tree edges, have elegant properties for modeling evolutionary histories. We answer an open question of…
We describe the class of graphs for which all metric spaces with diametrical graphs belonging to this class are ultrametric. It is shown that a metric space $(X, d)$ is ultrametric iff the diametrical graph of the metric $d_{\varepsilon}(x,…
We begin with pervasive ultrametricity due to high dimensionality and/or spatial sparsity. How extent or degree of ultrametricity can be quantified leads us to the discussion of varied practical cases when ultrametricity can be partially or…
Bayesian phylogenetics is vital for understanding evolutionary dynamics, and requires accurate and efficient approximation of posterior distributions over trees. In this work, we develop a variational Bayesian approach for ultrametric…
We study infinite tree and ultrametric matrices, and their action on the boundary of the tree. For each tree matrix we show the existence of a symmetric random walk associated to it and we study its Green potential. We provide a…
It is shown that a minimum weight spanning tree of a finite ultrametric space can be always found in the form of path. As a canonical representing tree such path uniquely defines the whole space and, moreover, it has much more simple…
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…
Distance-based phylogenetic algorithms attempt to solve the NP-hard least squares phylogeny problem by mapping an arbitrary dissimilarity map representing biological data to a tree metric. The set of all dissimilarity maps is a Euclidean…
The graph edit distance is used for comparing graphs in various domains. Due to its high computational complexity it is primarily approximated. Widely-used heuristics search for an optimal assignment of vertices based on the distance…
When considering the number of subtrees of trees, the extremal structures which maximize this number among binary trees and trees with a given maximum degree lead to some interesting facts that correlate to other graphical indices in…
An important application of distance geometry to biochemistry studies the embeddings of the vertices of a weighted graph in the three-dimensional Euclidean space such that the edge weights are equal to the Euclidean distances between…
We introduce and investigate the space of \emph{equidistant} $X$-\emph{cactuses}. These are rooted, arc weighted, phylogenetic networks with leaf set $X$, where $X$ is a finite set of species, and all leaves have the same distance from the…
Metric embeddings are central to metric theory and its applications. Here we consider embeddings of a different sort: maps from a set to subsets of a metric space so that distances between points are approximated by minimal distances…