Related papers: A matroid associated with a phylogenetic tree
In phylogenetics, tree-based networks are used to model and visualize the evolutionary history of species where reticulate events such as horizontal gene transfer have occurred. Formally, a tree-based network $N$ consists of a phylogenetic…
We derive two formulas for the weighted sums of rooted spanning forests of particular sequence of graphs by using the matrix tree theorem. We consider cycle graphs with edges so called the pendant edges. One of our formula can be described…
In phylogenetic networks, it is desirable to estimate edge lengths in substitutions per site or calendar time. Yet, there is a lack of scalable methods that provide such estimates. Here we consider the problem of obtaining edge length…
We introduce the parametric matroid one-interdiction problem. Given a matroid, each element of its ground set is associated with a weight that depends linearly on a real parameter from a given parameter interval. The goal is to find, for…
The classic Maxwell formula calculates the length of a planar locally minimal binary tree in terms of coordinates of its boundary vertices and directions of incoming edges. However, if an extreme tree with a given topology and a boundary…
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…
In mathematics and computer science, connectivity is one of the basic concepts of matroid theory: it asks for the minimum number of elements which need to be removed to disconnect the remaining nodes from each other. It is closely related…
Given a non-negative $n \times n$ matrix viewed as a set of distances between $n$ points, we consider the property testing problem of deciding if it is a metric. We also consider the same problem for two special classes of metrics, tree…
We propose a family of graph structural indices related to the Matrix-forest theorem. The properties of the basic index that expresses the mutual connectivity of two vertices are studied in detail. The derivative indices that measure…
Phylogenetic tree shapes capture fundamental signatures of evolution. We consider ``ranked'' tree shapes, which are equipped with a total order on the internal nodes compatible with the tree graph. Recent work has established an elegant…
A hypertree is a connected hypergraph without cycles. Further a hypertree is called an $r$-tree if, additionally, it is $r$-uniform. Note that 2-trees are just ordinary trees. A classical result states that for any 2-tree $T$ with…
A simple binary matroid is called claw-free if none of its rank-3 flats are independent sets. These objects can be equivalently defined as the sets $E$ of points in $\mathrm{PG}(n-1,2)$ for which $|E \cap P|$ is not a basis of $P$ for any…
Assume that we embed the path $P_n$ as a subgraph of a $2$-dimensional grid, namely, $P_k \times P_l$. Given such an embedding, we consider the ordered set of subpaths $L_1, L_2, \ldots , L_m$ which are maximal straight segments in the…
An added edge to a graph is called an inset edge. Predicting k inset edges which minimize the average distance of a graph is known to be NP-Hard. However, when k = 1 the complexity of the problem is polynomial. In this paper, some tools for…
In phylogenetics it is of interest for rate matrix sets to satisfy closure under matrix multiplication as this makes finding the set of corresponding transition matrices possible without having to compute matrix exponentials. It is also…
A skew polynomial ring $R=K[x;\sigma,\delta]$ is a ring of polynomials with non-commutative multiplication. This creates a difference between left and right divisibility, and thus a concept of left and right evaluations and roots. A…
Phylogenetic Diversity (PD) is a prominent quantitative measure of the biodiversity of a collection of present-day species (taxa). This measure is based on the evolutionary distance among the species in the collection. Loosely speaking, if…
Let ${\cal G}=(G,w)$ be a weighted graph , that is, a graph $G$ endowed with a function $w$ from the edge set of $G$ to the set of real numbers; for any subset $S$ of the vertex set of $G$, we define $D_S({\cal G})$ to be the minimum of the…
A $d$-dimensional tensegrity framework $(T,p)$ is an edge-labeled geometric graph in ${\mathbb R}^d$, which consists of a graph $T=(V,B\cup C\cup S)$ and a map $p:V\to {\mathbb R}^d$. The labels determine whether an edge $uv$ of $T$…
We consider a class of infinite weighted metric trees obtained as perturbations of self-similar regular trees. Possible definitions of the boundary traces of functions in the Sobolev space on such a structure are discussed by using…