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The tree based representation described in this paper, hereditarily binary numbers, applies recursively a run-length compression mechanism that enables computations limited by the structural complexity of their operands rather than by their…
The perturbation expansion of the solution of a fixed point equation or of an ordinary differential equation may be expressed as a power series in the perturbation parameter. The terms in this series are indexed by rooted trees and depend…
A plane rooted tree is called a hipster tree if it has no nontrivial automorphisms. Equivalently, a tree is a hipster tree if no two siblings have isomorphic subtrees. We impose the hipster condition on various classes of rooted trees. By…
Recombining trinomial trees are a workhorse for modeling discrete-event systems in option pricing, logistics, and feedback control. Because each node stores a state-dependent quantity, a depth-$D$ tree naively yields $\mathcal{O}(3^{D})$…
We introduce a new model of random tree that grows like a random recursive tree, except at some exceptional "doubling events" when the tree is replaced by two copies of itself attached to a new root. We prove asymptotic results for the size…
We study the portraits of isometries of rooted trees - the labelling of the tree, at each vertex, by the permutation of its descendants - in terms of languages. We characterize regularly branched self-similar groups in terms of…
Combinatorial trees can be used to represent genealogies of asexual individuals. These individuals can be endowed with birth and death times, to obtain a so-called `chronological tree'. In this work, we are interested in the continuum…
An evolutionary tree (phylogenetic tree) is a binary, rooted, unordered tree that models the evolutionary history of currently living species in which leaves are labeled by species. In this paper, we investigate the problem of finding the…
We study the average number of distinct fringe subtrees in random trees generated by leaf-centric binary tree sources as introduced by Zhang, Yang and Kieffer. A leaf-centric binary tree source induces for every $n \geq 2$ a probability…
Treewidth is a well-known graph invariant with multiple interesting applications in combinatorics. On the practical side, many NP-complete problems are polynomial-time (sometimes even linear-time) solvable on graphs of bounded treewidth. On…
Phylogenetic networks provide a general framework for modeling reticulate evolutionary processes such as hybridization, recombination, and horizontal gene transfer. In this paper, we study the asymptotic counting of binary phylogenetic…
We give a counterexample to the conjecture of Martin and Thatte that two balanced rooted binary leaf-labelled trees on $n$ leaves have a maximum agreement subtree (MAST) of size at least $n^{\frac{1}{2}}$. In particular, we show that for…
We study the enumeration of spinal tree-child phylogenetic networks, a rigid family of tree-child networks in which all internal vertices lie on a single root--to--leaf path. We provide two complementary combinatorial frameworks. First, we…
Monadic second order logic can be used to express many classical notions of sets of vertices of a graph as for instance: dominating sets, induced matchings, perfect codes, independent sets or irredundant sets. Bounds on the number of sets…
Let $\T_{n}$ be the set of rooted labeled trees on $\set{0,...,n}$. A maximal decreasing subtree of a rooted labeled tree is defined by the maximal subtree from the root with all edges being decreasing. In this paper, we study a new…
A weighted recursive tree is an evolving tree in which vertices are assigned random vertex-weights and new vertices connect to a predecessor with a probability proportional to its weight. Here, we study the maximum degree and near-maximum…
We build on recent work of Yeats, Courtiel, and others involving connected chord diagrams. We first derive from a Hopf-algebraic foundation a class of tree-like functional equations and prove that they are solved by weighted generating…
We consider a general metric Steiner problem which is of finding a set $\mathcal{S}$ with minimal length such that $\mathcal{S} \cup A$ is connected, where $A$ is a given compact subset of a given complete metric space $X$; a solution is…
Phylogenetic networks are leaf-labelled directed acyclic graphs that are used to describe non-treelike evolutionary histories and are thus a generalization of phylogenetic trees. The hybridization number of a phylogenetic network is the sum…
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…