Related papers: A note on naturally embedded ternary trees
Rooted phylogenetic networks allow biologists to represent evolutionary relationships between present-day species by revealing ancestral speciation and hybridization events. A convenient and well-studied class of such networks are…
Trees are partial orders in which every element has a linearly ordered set of predecessors. Here we initiate the exploration of the structural theory of trees with the study of different notions of \emph{branching in trees} and of…
Phylogenetic networks generalize phylogenetic trees by allowing the modelization of events of reticulate evolution. Among the different kinds of phylogenetic networks that have been proposed in the literature, the subclass of binary…
We introduce bijections between families of rooted maps with unfixed genus and families of so-called blossoming trees endowed with an arbitrary forward matching of their leaves. We first focus on Eulerian maps with controlled vertex…
We consider random binary trees that appear as the output of certain standard algorithms for sorting and searching if the input is random. We introduce the subtree size metric on search trees and show that the resulting metric spaces…
To any rooted tree, we associate a sequence of numbers that we call the logarithmic factorials of the tree. This provides a generalization of Bhargava's factorials to a natural combinatorial setting suitable for studying questions around…
Given a gene tree and a species tree, ancestral configurations represent the combinatorially distinct sets of gene lineages that can reach a given node of the species tree. They have been introduced as a data structure for use in the…
We prove a new formula for the generating function of multitype Cayley trees counted according to their degree distribution. Using this formula we recover and extend several enumerative results about trees. In particular, we extend some…
Connected acyclic graphs (trees) are data objects that hierarchically organize categories. Collections of trees arise in a diverse variety of fields, including evolutionary biology, public health, machine learning, social sciences and…
We study an abstract notion of tree structure which lies at the common core of various tree-like discrete structures commonly used in combinatorics: trees in graphs, order trees, nested subsets of a set, tree-decompositions of graphs and…
A chief problem in phylogenetics and database theory is the computation of a maximum consistent tree from a set of rooted or unrooted trees. A standard input are triplets, rooted binary trees on three leaves, or quartets, unrooted binary…
We study the bounded regions in a generic slice of the hyperplane arrangement in $\mathbb{R}^n$ consisting of the hyperplanes defined by $x_i$ and $x_i+x_j$. The bounded regions are in bijection with several classes of combinatorial…
When considering the number of subtrees of trees, the extremal structures which maximize this number among binary trees and trees with a given maximum degree lead to some interesting facts that correlate to other graphical indices in…
An increasing 1,2-tree is a labeled graph formed by starting with a vertex and then repeatedly attaching a leaf to a vertex or a triangle to an edge, the labeling of the vertices corresponding to the order in which the vertices are added.…
A numerical semigroup is said to be ordinary if it has all its gaps in a row. Indeed, it contains zero and all integers from a given positive one. One can define a simple operation on a non-ordinary semigroup, which we call here the…
The meander problem is a combinatorial problem which provides a toy model of the compact folding of polymer chains. In this paper we study various questions relating to the enumeration of meander diagrams, using diagrammatical methods. By…
We introduce an algorithmic approach based on generating tree method for enumerating the inversion sequences with various pattern-avoidance restrictions. For a given set of patterns, we propose an algorithm that outputs either an accurate…
Neural networks with tree-based sentence encoders have shown better results on many downstream tasks. Most of existing tree-based encoders adopt syntactic parsing trees as the explicit structure prior. To study the effectiveness of…
The Raney numbers $R_{p,r}(n)$ are a two-parameter generalization of the Catalan numbers that were introduced by Raney in his investigation of functional composition patterns \cite{Raney}. We give a new combinatorial interpretation for all…
Imitating a recently introduced invariant of trees, we initiate the study of the inducibility of $d$-ary trees (rooted trees whose vertex outdegrees are bounded from above by $d\geq 2$) with a given number of leaves. We determine the exact…