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A rooted phylogenetic network is a directed acyclic graph with a single root, whose sinks correspond to a set of species. As such networks are useful for representing the evolution of species that have undergone reticulate evolution, there…
The independence polynomial $I(G, x)$ of a graph $G$ is the polynomial in variable $x$ in which the coefficient $a_n$ on $x^n$ gives the number of independent subsets $S \subseteq V(G)$ of vertices of $G$ such that $|S| = n$. $I(G, x)$ is…
Forbidden characterizations may sometimes be the most natural way to describe families of graphs, and yet these characterizations are usually very hard to exploit for enumerative purposes. By building on the work of Gioan and Paul (2012)…
The evolutionary relationships among organisms have traditionally been represented using rooted phylogenetic trees. However, due to reticulate processes such as hybridization or lateral gene transfer, evolution cannot always be adequately…
In the Telephone Broadcasting problem, the goal is to disseminate a message from a given source vertex of an input graph to all other vertices in the minimum number of rounds, where at each round, an informed vertex can send the message to…
Graph polynomials are graph parameters invariant under graph isomorphisms which take values in a polynomial ring with a fixed finite number of indeterminates. We study graph polynomials from a model theoretic point of view. In this paper we…
Motivation: The abundance of gene flow in the Tree of Life challenges the notion that evolution can be represented with a fully bifurcating process, as this process cannot capture important biological realities like hybridization,…
The Tutte polynomial of a graph is a 2-variable polynomial which is quite important in both combinatorics and statistical physics. It contains various numerical invariants and polynomial invariants, such as the number of spanning trees, the…
An important problem in evolutionary biology is to reconstruct the evolutionary history of a set $X$ of species. This history is often represented as a phylogenetic network, that is, a connected graph with leaves labelled by elements in $X$…
Rooted phylogenetic networks provide a more complete representation of the ancestral relationship between species than phylogenetic trees when reticulate evolutionary processes are at play. One way to reconstruct a phylogenetic network is…
Compatibility of unrooted phylogenetic trees is a well studied problem in phylogenetics. It asks to determine whether for a set of k input trees there exists a larger tree (called a supertree) that contains the topologies of all k input…
Recently, big data techniques such as machine learning and topological data analysis have made their way to theoretical mathematics. Motivated by the recent work with polynomial invariants for knots, we use manifold learning and topological…
Three new graph invariants are introduced which may be measured from a quantum graph state and form examples of a framework under which other graph invariants can be constructed. Each invariant is based on distinguishing a different number…
Tittmann, Averbouch and Makowsky [P. Tittmann, I. Averbouch, J.A. Makowsky, The enumeration of vertex induced subgraphs with respect to the number of components, European Journal of Combinatorics, 32 (2011) 954-974], introduced the subgraph…
The Tutte polynomial is a classical invariant, important in combinatorics and statistical mechanics. An essential feature of the Tutte polynomial is the duality for planar graphs G, $T_G(X,Y)\; =\; {T}_{G^*}(Y,X)$ where $G^*$ denotes the…
Symmetric edge polytopes of graphs and root polytopes of semi-balanced digraphs are two classes of lattice polytopes whose $h^*$-polynomials have interesting properties and generalize important graph polynomials. For both classes of…
Phylogenetic networks are a special type of graph which generalize phylogenetic trees and that are used to model non-treelike evolutionary processes such as recombination and hybridization. In this paper, we consider {\em unrooted}…
In this paper, we introduce the concept of the weighted (harmonic) chromatic polynomials of graphs and discuss some of its properties. We also present the notion of the weighted (harmonic) Tutte--Grothendieck polynomials of graphs and give…
We introduce the ``trivariate Tutte polynomial" of a signed graph as an invariant of signed graphs up to vertex switching that contains among its evaluations the number of proper colorings and the number of nowhere-zero flows. In this, it…
In this paper, we build on recent results by Chauve et al. (2014) and Bahrani and Lumbroso (2017), which combined the split-decomposition, as exposed by Gioan and Paul, with analytic combinatorics, to produce new enumerative results on…