Combinatorial classes T that are recursively defined using combinations of the standard multiset, sequence, directed cycle and cycle constructions, and their restrictions, have generating series T(z) with a positive radius of convergence; for most of these a simple test can be used to quickly show that the form of the asymptotics is the same as that for the class of rooted trees: C ρ^{-n} n^{-3/2} where ρis the radius of convergence of T.
The number of tree-rooted maps, that is, rooted planar maps with a distinguished spanning tree, of size $n$ is C(n)C(n+1) where C(n)=binomial(2n,n)/(n+1) is the nth Catalan number. We present a (long awaited) simple bijection which explains this result. We prove that our bijection is isomorphic to a former recursive construction on shuffles of parenthesis systems due to Cori, Dulucq and Viennot.
General upper tail estimates are given for counting edges in a random induced subhypergraph of a fixed hypergraph H, with an easy proof by estimating the moments. As an application we consider the numbers of arithmetic progressions and Schur triples in random subsets of integers. In the second part of the paper we return to the subgraph counts in random graphs and provide upper tail estimates in the rooted case.
We prove that counting copies of any graph $F$ in another graph $G$ can be achieved using basic matrix operations on the adjacency matrix of $G$. Moreover, the resulting algorithm is competitive for medium-sized $F$: our algorithm recovers the best known complexity for rooted 6-clique counting and improves on the best known for 9-cycle counting. Underpinning our proofs is the new result that, for a general class of graph operators, matrix operations are homomorphisms for operations on rooted graphs.
We prove the conjecture by M. Yip stating that counting genus one partitions by the number of their elements and parts yields, up to a shift of indices, the same array of numbers as counting genus one rooted hypermonopoles. Our proof involves representing each genus one permutation by a four-colored noncrossing partition. This representation may be selected in a unique way for permutations containing no trivial cycles. The conclusion follows from a general generating function formula that holds for any class of permutations that is closed under the removal and reinsertion of trivial cycles. Ou…
The number of embeddings of a partially ordered set $S$ in a partially ordered set $T$ is the number of subposets of $T$ isomorphic to $S$. If both, $S$ and $T$, have only one unique maximal element, we define good embeddings as those in which the maximal elements of $S$ and $T$ overlap. We investigate the number of good and all embeddings of a rooted poset $S$ in the family of all binary trees on $n$ elements considering two cases: plane (when the order of descendants matters) and non-plane. Furthermore, we study the number of embeddings of a rooted poset $S$ in the family of all planted plan…
Phylogenetic networks generalize phylogenetic trees, and have been introduced in order to describe evolution in the case of transfer of genetic material between coexisting species. There are many classes of phylogenetic networks, which can all be modeled as families of graphs with labeled leaves. In this paper, we focus on rooted and unrooted level-k networks and provide enumeration formulas (exact and asymptotic) for rooted and unrooted level-1 and level-2 phylogenetic networks with a given number of leaves. We also prove that the distribution of some parameters of these networks (such as the…
Trees or rooted trees have been generously studied in the literature. A forest is a set of trees or rooted trees. Here we give recurrence relations between the number of some kind of rooted forest with $k$ roots and that with $k+1$ roots on $\{1,2,\ldots,n\}$. Classical formulas for counting various trees such as rooted trees, bipartite trees, tripartite trees, plane trees, $k$-ary plane trees, $k$-edge colored trees follow immediately from our recursive relations.
The simple connected graphs may be classified by their cycle composition (number and lengths of cycles). This work derives the counting series of the simple connected graphs that have cycles of unrestricted number and length, but no overlapping cycles. Cycle pairs of these graphs of interest must not have common nodes or edges. The recipe of counting these graphs is based on the counting series of the associated planted graphs, multisets of planted graphs, a recursive synthesis of enriched trees, and a generalized Otter's formula that maps the underlying rooted block graphs to the underlying b…
A universal framework for Hopf algebras in combinatorics
Research Center for Mathematics and Interdisciplinary Sciences, Shandong University（山东大学数学与交叉科学研究院）；Frontiers Science Center for Nonlinear Expectations, Ministry of Education（教育部非线性期望前沿科学中心）；Department of Mathematics, University of British Columbia（不列颠哥伦比亚大学数学系）
We present some exact expressions for the number of paths of a given length in a perfect $m$-ary tree. We first count the paths in perfect rooted $m$-ary trees and then use the results to determine the number of paths in perfect unrooted $m$-ary trees, extending a known result for binary trees.
Every binary De~Bruijn sequence of order n satisfies a recursion 0=x_n+x_0+g(x_{n-1}, ..., x_1). Given a function f on (n-1) bits, let N(f; r) be the number of functions generating a De Bruijn sequence of order n which are obtained by changing r locations in the truth table of f. We prove a formula for the generating function \sum_r N(\ell; r) y^r when \ell is a linear function. The proof uses a weighted Matrix Tree Theorem and a description of the in-trees (or rooted trees) in the n-bit De Bruijn graph as perturbations of the Hamiltonian paths in the same graph.
Given a collection of n rooted trees with depth h, we give a necessary and sufficient condition for this collection to be the collection of h-depth universal covering neighborhoods at each vertex.
Unanticipated connections between different fragments of lambda calculus and different families of embedded graphs (a.k.a. "maps") motivate the problem of enumerating $β$-normal linear lambda terms. In this brief note, it is shown (by appeal to a theorem of Arquès and Beraud) that the sequence counting isomorphism classes of $β$-normal linear lambda terms up to free exchange of adjacent lambda abstractions coincides with the sequence counting isomorphism classes of rooted maps on oriented surfaces (A000698).
The Hopf algebra and the Rota-Baxter algebra are the two algebraic structures underlying the algebraic approach of Connes and Kreimer to renormalization of perturbative quantum field theory. In particular the Hopf algebra of rooted trees serves as the "baby model" of Feynman graphs in their approach and can be characterized by certain universal properties involving a Hochschild 1-cocycle. Decorated rooted trees have also been applied to study Feynman graphs. We will continue the study of universal properties of various spaces of decorated rooted trees with such a 1-cocycle, leading to the conc…
For positive integers $n$ and $k$, the dendrimer $T_{n, k}$ is defined as the rooted tree of radius $n$ whose all vertices at distance less than $n$ from the root have degree $k$. The dendrimers are higly branched organic macromolecules having repeated iterations of branched units that surroundes the central core. Dendrimers are used in a variety of fields including chemistry, nanotechnology, biology. In this paper, for any positive integer $\ell$, we count the number of paths of length $\ell$ of $T_{n, k}$. As a consequence of our main results, we obtain the average distance of $T_{n, k}$ whi…
Given a lattice polytope $P$ (with underlying lattice $\lo$), the universal counting function $\uu_P(\lo')=|P\cap \lo'|$ is defined on all lattices $\lo'$ containing $\lo$. Motivated by questions concerning lattice polytopes and the Ehrhart polynomial, we study the equation $\uu_P=\uu_Q$.
Dartmouth College（达特茅斯学院）；Canisius University（卡尼西乌斯大学）；Iowa State University（爱荷华州立大学）；North Carolina School of Science and Mathematics（北卡罗来纳州科学与数学学校）；Institute of Discrete Mathematics, TU Graz（格拉茨工业大学离散数学研究所）；Department of Mathematics, Uppsala University（乌普萨拉大学数学系）
We present a surprisingly new connection between two well-studied combinatorial classes: rooted connected chord diagrams on one hand, and rooted bridgeless combinatorial maps on the other hand. We describe a bijection between these two classes, which naturally extends to indecomposable diagrams and general rooted maps. As an application, this bijection provides a simplifying framework for some technical quantum field theory work realized by some of the authors. Most notably, an important but technical parameter naturally translates to vertices at the level of maps. We also give a combinatorial…
In this paper, we redesign and simplify an algorithm due to Remy et al. for the generation of rooted planar trees that satisfies a given partition of degrees. This new version is now optimal in terms of random bit complexity, up to a multiplicative constant. We then apply a natural process "simulate-guess-and-proof" to analyze the height of a random Motzkin in function of its frequency of unary nodes. When the number of unary nodes dominates, we prove some unconventional height phenomenon (i.e. outside the universal square root behaviour.)
In this paper, we construct explicitly a noncommutative symmetric (${\mathcal N}$CS) system over the Grossman-Larson Hopf algebra of labeled rooted trees. By the universal property of the ${\mathcal N}$CS system formed by the generating functions of certain noncommutative symmetric functions, we obtain a specialization of noncommutative symmetric functions by labeled rooted trees. Taking the graded duals, we also get a graded Hopf algebra homomorphism from the Connes-Kreimer Hopf algebra of labeled rooted forests to the Hopf algebra of quasi-symmetric functions. A connection of the coefficient…
A tree-based network $\mathcal N$ on $X$ is universal if every rooted binary phylogenetic $X$-tree is a base tree for $\mathcal N$. Hayamizu and, independently, Zhang constructively showed that, for all positive integers $n$, there exists an universal tree-based network on $n$ leaves. For all $n$, Hayamizu's construction contains $Θ(n!)$ reticulations, while Zhang's construction contains $Θ(n^2)$ reticulations. A simple counting argument shows that an universal tree-based network has $Ω(n\log n)$ reticulations. With this in mind, Hayamizu as well as Steel posed the problem of determining wheth…
Random tensor models are generalizations of matrix models which also support a 1/N expansion. The dominant observables are in correspondence with some trees, namely rooted trees with vertices of degree at most $D$ and lines colored by a number $i$ from 1 to $D$ such that no two lines connecting a vertex to its descendants have the same color. In this Letter we study by independent methods a generating function for these observables. We prove that the number of such trees with exactly $p_i$ lines of color $i$ is $\frac{1}{\sum_{i=1}^D p_i +1} \binom{\sum_{i=1}^D p_i+1}{p_1} ... \binom{\sum_{i=1…
A tree-based network $N$ on $X$ is called universal if every phylogenetic tree on $X$ is a base tree for $N$. Recently, binary universal tree-based networks have attracted great attention in the literature and their existence has been analyzed in various studies. In this note, we extend the analysis to non-binary networks and show that there exist both a rooted and an unrooted non-binary universal tree-based network with $n$ leaves for all positive integers $n$.
Arborified zeta values are defined as iterated series and integrals using the universal properties of rooted trees. This approach allows to study their convergence domain and to relate them to multizeta values. Generalisations to rooted trees of the stuffle and shuffle products are defined and studied. It is further shown that arborifed zeta values are algebra morphisms for these new products on trees.
Given a set of species whose evolution is represented by a species tree, a gene family is a group of genes having evolved from a single ancestral gene. A gene family evolves along the branches of a species tree through various mechanisms, including - but not limited to - speciation, gene duplication, gene loss, horizontal gene transfer. The reconstruction of a gene tree representing the evolution of a gene family constrained by a species tree is an important problem in phylogenomics. However, unlike in the multispecies coalescent evolutionary model, very little is known about the search space …
Let $c_n$ denote the number of nodes at a distance $n$ from the root of a rooted tree. A criterion for proving the rationality and computing the rational generating function of the sequence $\{c_n\}$ is described. This criterion is applied to counting the number of conjugacy classes of commuting tuples in finite groups and the number of isomorphism classes of representations of polynomial algebras over finite fields. The method for computing the rational generating functions, when applied to the study of point configurations in finite sets, gives rise to some classical combinatorial results on…
A tree-based network on a set $X$ of $n$ leaves is said to be universal if any rooted binary phylogenetic tree on $X$ can be its base tree. Francis and Steel showed that there is a universal tree-based network on $X$ in the case of $n=3$, and asked whether such a network exists in general. We settle this problem by proving that there are infinitely many universal tree-based networks for any $n>1$.
The study of Reynolds algebras has its origin in the well-known work of O. Reynolds on fluid dynamics in 1895 and has since found broad applications. It also has close relationship with important linear operators such as algebra endomorphisms, derivations and Rota-Baxter operators. Many years ago G.~Birkhoff suggested an algebraic study of Reynolds operators, including the corresponding free algebras. We carry out such a study in this paper. We first provide examples and properties of Reynolds operators, including a multi-variant generalization of the Reynolds identity. We then construct the f…
We associate with a Bienayme-Galton-Watson branching process a family tree rooted at the ancestor. For a positive integer N, define a complete N-ary tree to be the family tree of a deterministic branching process with offspring generating function s^N. We study the random variables V(N,n) and V(N) counting the number of disjoint complete N-ary subtrees, rooted at the ancestor, and having height n and infinity, respectively. Dekking (1991) and Pakes and Dekking (1991) find recursive relations for Pr(V(N,n)>0) and Pr(V(N)>0) involving the offspring probability generation function (pgf) and its d…
Plane increasing trees are rooted labeled trees embedded into the plane such that the sequence of labels is increasing on any branch starting at the root. Relaxed binary trees are a subclass of unlabeled directed acyclic graphs. We construct a bijection between these two combinatorial objects and study the therefrom arising connections of certain parameters. Furthermore, we show central limit theorems for two statistics on leaves. We end the study by considering more than 20 subclasses and their bijective counterparts. Many of these subclasses are enumerated by known counting sequences, and th…
We study the supersymmetric ground states of the Kronecker model of quiver quantum mechanics. This is the simplest quiver with two gauge groups and bifundamental matter fields, and appears universally in four-dimensional N=2 systems. The ground state degeneracy may be written as a multi-dimensional contour integral, and the enumeration of poles can be simply phrased as counting bipartite trees. We solve this combinatorics problem, thereby obtaining exact formulas for the degeneracies of an infinite class of models. We also develop an algorithm to compute the angular momentum of the ground stat…
