Related papers: Generalized Fitch Graphs: Edge-labeled Graphs that…
Let $G$ be a graph each edge $e$ of which is given a length $\ell(e)$. This naturally induces a distance $d_\ell(x,y)$ between any two vertices $x,y$, and we let $\ell-TOP$ denote the completion of the corresponding metric space. It turns…
A graph is called pseudo-outerplanar if each block has an embedding on the plane in such a way that the vertices lie on a fixed circle and the edges lie inside the disk of this circle with each of them crossing at most one another. In this…
We define an equivalence relation on graphs with signed edges, such that the associated adjacency matrices of two equivalent graphs are congruent over $\mathbb{Z}$. We show that signed graphs whose eigenvalues are larger than $-2$ are…
In biology, a phylogenetic tree is a tool to represent the evolutionary relationship between species. Unfortunately, the classical Schr\"oder tree model is not adapted to take into account the chronology between the branching nodes. In…
Motivated by interpretability and reliability, we investigate whether large language models (LLMs) deploy universal geometric structures to encode discrete, graph-structured knowledge. To this end, we present two complementary experimental…
DNA rearrangement processes recombine gene segments that are organized on the chromosome in a variety of ways. The segments can overlap, interleave or one may be a subsegment of another. We use directed graphs to represent segment…
Phylogenetic trees are a central tool in understanding evolution. They are typically inferred from sequence data, and capture evolutionary relationships through time. It is essential to be able to compare trees from different data sources…
Phylogenetic networks are increasingly used in evolutionary biology to represent the history of species that have undergone reticulate events such as horizontal gene transfer, hybrid speciation and recombination. One of the most fundamental…
This paper considers generalised network, intended as networks where (a) the edges connecting the nodes are nonlinear, and (b) stochastic processes are continuously indexed over both vertices and edges. Such topological structures are…
Defining distances over finite fields formally by $||x-y||:=(x_1-y_1)^2+\cdots + (x_d-y_d)^2$ for $x,y\in \mathbb{F}_q^d$, distance problems naturally arise in analogy to those studied by Erd\H{o}s and Falconer in Euclidean space. Given a…
Discovering the underlying structures present in large real world graphs is a fundamental scientific problem. In this paper we show that a graph's clique tree can be used to extract a hyperedge replacement grammar. If we store an ordering…
A graph $G$ is said to be a `set graph' if it admits an acyclic orientation that is also `extensional', in the sense that the out-neighborhoods of its vertices are pairwise distinct. Equivalently, a set graph is the underlying graph of the…
Series-parallel (SP) graphs are binary edge-labeled graphs with a designated source and target vertex, built using serial and parallel composition. A set of graphs is recognizable if membership depends only on its image under a homomorphism…
Phylogenetic networks are a generalization of phylogenetic trees that allow for representation of reticulate evolution. Recently, a space of unrooted phylogenetic networks was introduced, where such a network is a connected graph in which…
A simple topological graph T = (V(T), E(T)) is a drawing of a graph in the plane where every two edges have at most one common point (an endpoint or a crossing) and no three edges pass through a single crossing. Topological graphs G and H…
In this work we consider the class of Cayley graphs known as generalized Paley graphs (GP-graphs for short) given by $\Gamma(k,q) = Cay(\mathbb{F}_q, \{x^k : x\in \mathbb{F}_q^* \})$, where $\mathbb{F}_q$ is a finite field with $q$…
Flip graphs are graphs on combinatorial objects in which the adjacency relation reflects a local change in the underlying objects. In this thesis we introduce Yoke graphs, a family of flip graphs that generalizes previously studied families…
Structural properties of finite digraphs $R$ and $S$ are studied which enforce $\# {\cal H}(G,R) \leq \# {\cal H}(G,S)$ for every finite digraph $G \in \mathfrak{ D }'$, where ${\cal H}(G,H)$ is the set of homomorphisms from $G$ to $H$, and…
Thin spanning trees lie at the intersection of graph theory, approximation algorithms, and combinatorial optimization. They are central to the long-standing \emph{thin tree conjecture}, which asks whether every $k$-edge-connected graph…
In this paper we introduce a generalization of the well known concept of a graceful labeling. Given a graph G with e=dm edges, we call d-graceful labeling of G an injective function from V(G) to the set {0,1,2,..., d(m+1)-1} such that…