Related papers: A Short Note on Undirected Fitch Graphs
In this paper we further develop the theory of one sided shift spaces over infinite alphabets, characterizing one-step shifts as edge shifts of ultragraphs and partially answering a conjecture regarding shifts of finite type (we show that…
We classify the connected-homogeneous digraphs with more than one end. We further show that if their underlying undirected graph is not connected-homogeneous, they are highly-arc-transitive.
We consider, for complete bipartite graphs, the convex hulls of characteristic vectors of all matchings, extended by a binary entry indicating whether the matching contains two specific edges. These polytopes are associated to the quadratic…
We investigate subsets of the symmetric group with structure similar to that of a graph. The trees of these subsets correspond to minimal conjugate generating sets of the symmetric group. There are two main theorems in this paper. The first…
The complexity of the list homomorphism problem for signed graphs appears difficult to classify. Existing results focus on special classes of signed graphs, such as trees and reflexive signed graphs. Irreflexive signed graphs are in a…
A graph $G$ is called \emph{symmetric with respect to a functional $F_G(P)$} defined on the set of all the probability distributions on its vertex set if the distribution $P^*$ maximizing $F_G(P)$ is uniform on $V(G)$. Using the…
The concepts of orthology, paralogy, and xenology play a key role in molecular evolution. Orthology and paralogy distinguish whether a pair of genes originated by speciation or duplication. The corresponding binary relations on a set of…
Oriented graph complexes, in which graphs are not allowed to have oriented cycles, govern for example the quantization of Lie bialgebras and infinite dimensional deformation quantization. It is shown that the oriented graph complex GC^or_n…
In some applications of matching, the structural or hierarchical properties of the two graphs being aligned must be maintained. The hierarchical properties are induced by the direction of the edges in the two directed graphs. These…
\"Uberhomology is a recently defined homology theory for simplicial complexes, which yields subtle information on graphs. We prove that bold homology, a certain specialisation of \"uberhomology, is related to dominating sets in graphs. To…
We show that a smaller version of the Kontsevich graph complex spanned by triconnected graphs is quasi-isomorphic to the full Kontsevich graph complex.
The Divisibility Graph of a finite group $G$ has vertex set the set of conjugacy class lengths of non-central elements in $G$ and two vertices are connected by an edge if one divides the other. We determine the connected components of the…
We provide a characterization of two types of directed homology for fully-connected, feedforward neural network architectures. These exact characterizations of the directed homology structure of a neural network architecture are the first…
We introduce a new family of graphs, namely, hybrid graphs. There are infinitely many hybrid graphs associated to a single graph. We show that every hybrid graph associated to a given graph is Cohen Macaulay. Furthermore, we show that every…
The need for structures capable of accommodating complex evolutionary signals such as those found in, for example, wheat has fueled research into phylogenetic networks. Such structures generalize the standard phylogenetic tree model by also…
An orientation of a graph is semi-transitive if it contains no directed cycles and has no shortcuts. An undirected graph is semi-transitive if it can be oriented in a semi-transitive manner. The class of semi-transitive graphs includes…
We investigate the problem of when a chromatic quasisymmetric function (CQF) $X_G(x;q)$ of a graph $G$ is in fact symmetric. We first prove the remarkable fact that if a product of two quasisymmetric functions $f$ and $g$ in countably…
The present work is devoted to characterize the family of symmetric undirected Cayley graphs over finite Abelian groups for degrees 4 and 6.
Phylogenetic networks are rooted, labelled directed acyclic graphs which are commonly used to represent reticulate evolution. There is a close relationship between phylogenetic networks and multi-labelled trees (MUL-trees). Indeed, any…
Phylogenetics is the study of the evolutionary relationships between organisms. One of the main challenges in the field is to take biological data for a group of organisms and to infer an evolutionary tree, a graph that represents these…