Related papers: Polynomial invariants for cactuses
We introduce a notion of finite sampling consistency for phylogenetic trees and show that the set of finitely sampling consistent and exchangeable distributions on n leaf phylogenetic trees is a polytope. We use this polytope to show that…
The number of homomorphisms from a finite graph $F$ to the complete graph $K_n$ is the evaluation of the chromatic polynomial of $F$ at $n$. Suitably scaled, this is the Tutte polynomial evaluation $T(F;1-n,0)$ and an invariant of the cycle…
The topological framework of circuit topology has recently been introduced to complement knot theory and to help in understanding the physics of molecular folding. Naturally evolved linear molecular chains, such as proteins and nucleic…
This paper contributes to a programme initiated by the first author: `How much information about a graph is revealed in its Potts partition function?'. We show that the $W$-polynomial distinguishes non-isomorphic weighted trees of a…
In mathematical phylogenetics, evolutionary relationships are often represented by trees and networks. The latter are typically used whenever the relationships cannot be adequately described by a tree, which happens when so-called…
Univariate polynomial root-finding is a classical subject, still important for modern computing. Frequently one seeks just the real roots of a polynomial with real coefficients. They can be approximated at a low computational cost if the…
Algebraic techniques in phylogenetics have historically been successful at proving identifiability results and have also led to novel reconstruction algorithms. In this paper, we study the ideal of phylogenetic invariants of the…
In evolutionary biology, networks are becoming increasingly used to represent evolutionary histories for species that have undergone non-treelike or reticulate evolution. Such networks are essentially directed acyclic graphs with a leaf set…
Phylogenetic networks can model more complicated evolutionary phenomena that trees fail to capture such as horizontal gene transfer and hybridization. The same Markov models that are used to model evolution on trees can also be extended to…
Invariant theory is concerned with functions that do not change under the action of a given group. Here we communicate an approach based on tensor networks to represent polynomial local unitary invariants of quantum states. This graphical…
This paper revisits the notion of classical orthogonal polynomials from a broader functional-analytic point of view. It is intended neither as a survey of known results nor as a review of the literature, but rather as a conceptual…
The independence polynomial of a graph is the generating polynomial for the number of independent sets of each size, and its roots are called {\em independence roots}. We investigate the stability of such polynomials, that is, conditions…
This paper presents the novel `uniqueness tree' algorithm, as one possible method for determining whether two finite, undirected graphs are isomorphic. We prove that the algorithm has polynomial time complexity in the worst case, and that…
We consider polynomial maps described by so-called "(multivariate) linearized polynomials". These polynomials are defined using a fixed prime power, say q. Linearized polynomials have no mixed terms. Considering invertible polynomial maps…
We define an algorithm k which takes a connected graph G on a totally ordered vertex set and returns an increasing tree R (which is not necessarily a subtree of G). We characterize the set of graphs G such that k(G)=R. Because this set has…
We define a range of new coarse geometric invariants based on various graph-theoretic measures of complexity for finite graphs, including: treewidth, pathwidth, cutwidth and bandwidth. We prove that, for bounded degree graphs, these…
Given a graph G, an incidence matrix N(G) is defined for the set of distinct isomorphism types of induced subgraphs of G. If Ulam's conjecture is true, then every graph invariant must be reconstructible from this matrix, even when the…
We investigate the structure of the characteristic polynomial det(xI-T) of a transition matrix T that is associated to a train track representative of a pseudo-Anosov map [F] acting on a surface. As a result we obtain three new polynomial…
We introduce a new subclass of chordal graphs that generalizes split graphs, which we call well-partitioned chordal graphs. Split graphs are graphs that admit a partition of the vertex set into cliques that can be arranged in a star…
Given any unoriented link diagram, a group of new knot invariants are constructed. Each of them satisfies a generalized 4 term skein relation. The coefficients of each invariant is from a commutative ring. Homomorphisms and representations…