Related papers: A matroid associated with a phylogenetic tree
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,…
Homogeneous matroids are characterized by the property that strength equals fractional arboricity, and arise in the study of base modulus [22]. For graphic matroids, Cunningham [9] provided efficient algorithms for calculating graph…
In the Inverse Matroid problem, we are given a matroid, a fixed basis $B$, and an initial weight function, and the goal is to minimally modify the weights -- measured by some function -- so that $B$ becomes a maximum-weight basis. The…
In this article, we investigate the multi-parametric matroid problem. The weights of the elements of the matroid's ground set depend linearly on an arbitrary but fixed number of parameters, each of which is taken from a real interval. The…
Minimum spanning trees and forests are powerful sparsification techniques that remove cycles from weighted graphs to minimize total edge weight while preserving node connectivity. They have applications in computer science, network science,…
The modular decomposition of a symmetric map $\delta\colon X\times X \to \Upsilon$ (or, equivalently, a set of symmetric binary relations, a 2-structure, or an edge-colored undirected graph) is a natural construction to capture key features…
We prove that every oriented tree on $n$ vertices with bounded maximum degree appears as a spanning subdigraph of every directed graph on $n$ vertices with minimum semidegree at least $n/2+o(n)$. This can be seen as a directed graph…
An independent edge set of graph $G$ is a matching, and is maximal if it is not a proper subset of any other matching of $G$. The number of all the maximal matchings of $G$ is denoted by $\Psi(G)$. In this paper, an algorithm to count…
A characterization of finite homogeneous ultrametric spaces and finite ultrametric spaces generated by unrooted labeled trees is found in terms of representing trees. A characterization of finite ultrametric spaces having perfect strictly…
The reliability of a phylogenetic inference method from genomic sequence data is ensured by its statistical consistency. Bayesian inference methods produce a sample of phylogenetic trees from the posterior distribution given sequence data.…
A \emph{matching} is a subset of edges in a graph $G$ that do not share an endpoint. A matching $M$ is a \emph{$\mathcal{P}$-matching} if the subgraph of $G$ induced by the endpoints of the edges of $M$ satisfies property $\mathcal{P}$. For…
Suppose N is a phylogenetic network indicating a complicated relationship among individuals and taxa. Often of interest is a much simpler network, for example, a species tree T, that summarizes the most fundamental relationships. The…
Comparing and computing distances between phylogenetic trees are important biological problems, especially for models where edge lengths play an important role. The geodesic distance measure between two phylogenetic trees with edge lengths…
Phylogenetic networks are a generalization of phylogenetic trees that allow for the representation of non-treelike evolutionary events, like recombination, hybridization, or lateral gene transfer. In a recent series of papers devoted to the…
We study questions inspired by Erd\H os' celebrated distance problems with dot products in lieu of distances, and for more than a single pair of points. In particular, we study point configurations present in large finite point sets in the…
We prove that if X is a complete geodesic metric space with uniformly generated first homology group and $f: X\to R$ is metrically proper on the connected components and bornologous, then X is quasi-isometric to a tree. Using this and…
A phylogenetic tree is a tree with a fixed set of leaves that has no vertices of degree two. In this paper, we axiomatically define four other discrete structures on the set of leaves. We prove that each of these structures is an equivalent…
Over a finite field $\mathbb{F}_{q^m}$, the evaluation of skew polynomials is intimately related to the evaluation of linearized polynomials. This connection allows one to relate the concept of polynomial independence defined for skew…
A communication network can be modeled as a directed connected graph with edge weights that characterize performance metrics such as loss and delay. Network tomography aims to infer these edge weights from their pathwise versions measured…
Metric embedding has become a common technique in the design of algorithms. Its applicability is often dependent on how high the embedding's distortion is. For example, embedding finite metric space into trees may require linear distortion…