Related papers: Polynomial invariants for cactuses
The purpose of this article is to show how the isotropy subgroup of leaf permutations on binary trees can be used to systematically identify tree-informative invariants relevant to models of phylogenetic evolution. In the quartet case, we…
Building on prior work that established Matrix Quasi-tree Theorems for special embedded graphs, in this paper, we develop a comprehensive theory applicable to all embedded graphs. We introduce symbolic skew-adjacency matrices and reduction…
We consider the space $P$ of generic complex 5-degree polynomials. Critical values of such polynomial, i.e. four points in the complex plane, either are vertices of a convex quadrangle $Q$, or vertices of a triangle $T$ with one point…
In phylogenetics, evolution is traditionally represented in a tree-like manner. However, phylogenetic networks can be more appropriate for representing evolutionary events such as hybridization, horizontal gene transfer, and others. In…
Cyclically ordered graphs, or cogs, sit between abstract graphs and cellularly embedded graphs. They arise naturally in topological graph theory, knot theory, and mathematical biology. We develop a formal theory of cogs and establish a…
In this paper we introduce a novel polynomial-time algorithm to compute graph invariants based on the modified random walk idea on graphs. However not proved to be a full graph invariant by now, our method gives the right answer for the…
We introduce new methods for phylogenetic tree quartet construction by using machine learning to optimize the power of phylogenetic invariants. Phylogenetic invariants are polynomials in the joint probabilities which vanish under a model of…
Firstly, for a general graph, we find a recursion formula on the number of Hamiltonian cycles and one on cycles. By this result, we give some new polynomial invariants. Secondly, we give a condition to tell whether a polynomial defined by…
We introduce new polynomial isotopy invariants for closed braids. They are constructed as polynomial valued {\em Gauss diagram 1-cocycles} evaluated on the full rotation of the closed braid $\hat \beta$ around the core of the corresponding…
We present exact calculations of Potts model partition functions and the equivalent Tutte polynomials for polygon chain graphs with open and cyclic boundary conditions. Special cases of the results that yield flow and reliability…
An invariant for cospectral graphs is a property shared by all cospectral graphs. In this paper, we establish three novel arithmetic invariants for cospectral graphs, revealing deep connections between spectral properties and combinatorial…
To a singular knot K with n double points, one can associate a chord diagram with n chords. A chord diagram can also be understood as a 4-regular graph endowed with an oriented Euler circuit. L. Traldi introduced a polynomial invariant for…
Phylogenetic networks provide a means of describing the evolutionary history of sets of species believed to have undergone hybridization or gene flow during their evolution. The mutation process for a set of such species can be modeled as a…
Many polynomial invariants are defined on graphs for encoding the combinatorial information and researching them algebraically. In this paper, we introduce the cycle polynomial and the path polynomial of directed graphs for counting cycles…
In the Fully Leafed Induced Subtrees, one is given a graph $G$ and two integers $a$ and $b$ and the question is to find an induced subtree of $G$ with $a$ vertices and at least $b$ leaves. This problem is known to be NP-complete even when…
In this study, we present two results that relate Tutte polynomials. First, we provide new and complete polynomial invariants for graphs. We note that the number of variables of our polynomials is one. Second, let L_1 and L_2 be two…
The $M$-polynomial of a graph $G$ is defined as $\sum_{i\le j} m_{i,j}(G)x^iy^j$, where $m_{i,j}(G)$, $i,j\ge 1$, is the number of edges $uv$ of $G$ such that $\{d_v(G), d_u(G)\} = \{i,j\}$. Knowing the $M$-polynomial, formulas for bond…
We introduce and investigate the space of \emph{equidistant} $X$-\emph{cactuses}. These are rooted, arc weighted, phylogenetic networks with leaf set $X$, where $X$ is a finite set of species, and all leaves have the same distance from the…
We introduce a new one-variable polynomial invariant of graphs, which we call the skew characteristic polynomial. For an oriented simple graph, this is just the characteristic polynomial of its anti-symmetric adjacency matrix. For…
Unrooted phylogenetic networks are graphs used to represent evolutionary relationships. Accurately reconstructing such networks is of great relevance for evolutionary biology. It has recently been conjectured that all phylogenetic networks…