Related papers: A tropical interpretation of m-dissimilarity maps

Motivated by applications to low-rank matrix completion, we give a combinatorial characterization of the independent sets in the algebraic matroid associated to the collection of $m\times n$ rank-2 matrices and $n\times n$ skew-symmetric…

In this article, we propose tree edit distance with variables, which is an extension of the tree edit distance to handle trees with variables and has a potential application to measuring the similarity between mathematical formulas,…

An important problem in geometric computing is defining and computing similarity between two geometric shapes, e.g. point sets, curves and surfaces, etc. Important geometric and topological information of many shapes can be captured by…

We study distorted metrics on binary trees in the context of phylogenetic reconstruction. Given a binary tree $T$ on $n$ leaves with a path metric $d$, consider the pairwise distances $\{d(u,v)\}$ between leaves. It is well known that these…

There are several interrelated notions of discrete curvature on graphs. Many approaches utilize the optimal transportation metric on its probability simplex or the distance matrix of the graph. In this survey article, we compute formulas…

Given an edge-weighted tree $T$ with $n$ leaves, sample the leaves uniformly at random without replacement and let $W_k$, $2 \le k \le n$, be the length of the subtree spanned by the first $k$ leaves. We consider the question, "Can $T$ be…

We prove that, if $m$ is sufficiently large, every graph on $m+1$ vertices that has a universal vertex and minimum degree at least $\lfloor \frac{2m}{3} \rfloor$ contains each tree $T$ with $m$ edges as a subgraph. Our result confirms, for…

Let $k$, $d$ be a positive integer, $G$ be a connected graph of order $n$, $T$ be a tree. The leaf distance of a tree is defined as the minimum distance between any two leaves. For $v\in V(T)$, the leaf degree of $v$ in $T$ is the number of…

Kondo et al. (DS 2014) proposed methods for computing distances between unordered rooted trees by transforming an instance of the distance computing problem into an instance of the integer programming problem. They showed that the tree edit…

We study tropical commuting matrices from two viewpoints: linear algebra and algebraic geometry. In classical linear algebra, there exist various criteria to test whether two square matrices commute. We ask for similar criteria in the realm…

We establish a limit formula for the median of the distance between two leaves in a fully resolved unrooted phylogenetic tree with n leaves. More precisely, we prove that this median is equal, in the limit, to the square root of 4*ln(2)*n.

A tanglegram consists of two rooted binary trees with the same number of leaves and a perfect matching between the leaves of the trees. Given a size-$n$ tanglegram, i.e., a tanglegram for two trees with $n$ leaves, a multiset of induced…

We study the leaf-to-leaf distances on full and complete m-ary graphs using a recursive approach. In our formulation, leaves are ordered along a line. We find explicit analytical formulae for the sum of all paths for arbitrary leaf-to-leaf…

We propose a new graph metric and study its properties. In contrast to the standard distance in connected graphs, it takes into account all paths between vertices. Formally, it is defined as d(i,j)=q_{ii}+q_{jj}-q_{ij}-q_{ji}, where q_{ij}…

Given a rooted tree $T$ with vertices $u_1,u_2,\ldots,u_n$, the level matrix $L(T)$ of $T$ is the $n \times n$ matrix for which the $(i,j)$-th entry is the absolute difference of the distances from the root to $v_i$ and $v_j$. This matrix…

Let ${\cal G}=(G,w)$ be a weighted simple finite connected graph, that is, let $G$ be a simple finite connected graph endowed with a function $w$ from the set of the edges of $G$ to the set of real numbers. For any subgraph $G'$ of $G$, we…

Rotation distance between rooted binary trees is the minimum number of simple rotations needed to transform one tree into the other. Computing the rotation distance between a pair of rooted trees can be quickly reduced in cases where there…

Let $L(n,d)$ denote the minimum possible number of leaves in a tree of order $n$ and diameter $d.$ In 1975 Lesniak gave the lower bound $B(n,d)=\lceil 2(n-1)/d\rceil$ for $L(n,d).$ When $d$ is even, $B(n,d)=L(n,d).$ But when $d$ is odd,…

For a labelled tree on the vertex set $[n]:=\{1,2,..., n\}$, define the direction of each edge $ij$ to be $i\to j$ if $i<j$. The indegree sequence of $T$ can be considered as a partition $\lambda \vdash n-1$. The enumeration of trees with a…

Understanding the evolution of a set of genes or species is a fundamental problem in evolutionary biology. The problem we study here takes as input a set of trees describing {possibly discordant} evolutionary scenarios for a given set of…