Related papers: A matroid associated with a phylogenetic tree

The problem of reconstructing evolutionary trees or phylogenies is of great interest in computational biology. A popular model for this problem assumes that we are given the set of leaves (current species) of an unknown binary tree and the…

Ultrametric matrices are a class of covariance matrices that arise in latent tree models. As a parameter space in a statistical model, the set of ultrametric matrices is neither convex nor a smooth manifold. Focus in the literature has…

Phylogenetic trees are often constructed by using a metric on the set of taxa that label the leaves of the tree. While there are a number of methods for constructing a tree using a given metric, such trees will only display the metric if it…

We present a new class of metrics for unrooted phylogenetic $X$-trees derived from the Gromov-Hausdorff distance for (compact) metric spaces. These metrics can be efficiently computed by linear or quadratic programming. They are robust…

A treedepth decomposition of an undirected graph $G$ is a rooted forest $F$ on the vertex set of $G$ such that every edge $uv\in E(G)$ is in ancestor-descendant relationship in $F$. Given a weight function $w\colon V(G)\rightarrow…

In this article we study the treewidth of the \emph{display graph}, an auxiliary graph structure obtained from the fusion of phylogenetic (i.e., evolutionary) trees at their leaves. Earlier work has shown that the treewidth of the display…

Nonlinear metrics, such as the F1-score, Matthews correlation coefficient, and Fowlkes-Mallows index, are often used to evaluate the performance of machine learning models, in particular, when facing imbalanced datasets that contain more…

When does a graph admit a tree-decomposition in which every bag has small diameter? For finite graphs, this is a property of interest in algorithmic graph theory, where it is called having bounded ``tree-length''. We will show that this is…

Maximum parsimony distance is a measure used to quantify the dissimilarity of two unrooted phylogenetic trees. It is NP-hard to compute, and very few positive algorithmic results are known due to its complex combinatorial structure. Here we…

Merge trees are a type of graph-based topological summary that tracks the evolution of connected components in the sublevel sets of scalar functions. They enjoy widespread applications in data analysis and scientific visualization. In this…

A phylogenetic tree is a way to organize a finite set of species, individuals or other sources of related data. The species for which we have existing DNA data make up the set of leaves of the tree. The balanced minimal evolution method of…

Tree-cut width is a parameter that has been introduced as an attempt to obtain an analogue of treewidth for edge cuts. Unfortunately, in spite of its desirable structural properties, it turned out that tree-cut width falls short as an…

Let $G=(V,E)$ be a connected graph and $d_{G}(u,v)$ be the shortest distance between the vertices $u$ and $v$ in $G$. A set $S=\{s_{1},s_{2},\cdots,s_{n}\}\subset V(G)$ is said to be a {\em resolving set} if for all distinct vertices $u,v$…

We investigate isometric embeddings of finite metric trees into $(\mathbb{R}^n,d_{1})$ and $( \mathbb{R}^n, d_{\infty})$. We prove that a finite metric tree can be isometrically embedded into $(\mathbb{R}^n,d_{1})$ if and only if the number…

A matroid is a combinatorial structure that captures and generalizes the algebraic concept of linear independence under a broader and more abstract framework. Matroids are closely related with many other topics in discrete mathematics, such…

We investigate the complexity of counting trees, forests and bases of matroids from a parameterized point of view. It turns out that the problems of computing the number of trees and forests with $k$ edges are $\# W[1]$-hard when…

Fitting distances to tree metrics and ultrametrics are two widely used methods in hierarchical clustering, primarily explored within the context of numerical taxonomy. Given a positive distance function…

Let $G = (V,E)$ denote a simple graph with the vertex set $V$ and the edge set $E$. The profile of a vertex set $V'\subseteq V$ denotes the multiset of pairwise distances between the vertices of $V'$. Two disjoint subsets of $V$ are…

We prove that finding a rooted subtree with at least $k$ leaves in a digraph is a fixed parameter tractable problem. A similar result holds for finding rooted spanning trees with many leaves in digraphs from a wide family $\cal L$ that…

Trees with labelled leaves and with all other vertices of degree three play an important role in systematic biology and other areas of classification. A classical combinatorial result ensures that such trees can be uniquely reconstructed…