Related papers: On the enumeration of leaf-labelled increasing tre…
The in-order traversal provides a natural correspondence between binary trees with a decreasing vertex labeling and endofunctions on a finite set. By suitably restricting the vertex labeling we arrive at a class of trees that we call…
Whereas for strings, higher-order empirical entropy is the standard entropy measure, several different notions of empirical entropy for trees have been proposed in the past, notably label entropy, degree entropy, conditional versions of the…
Rooted phylogenetic networks are often constructed by combining trees, clusters, triplets or characters into a single network that in some well-defined sense simultaneously represents them all. We review these four models and investigate…
We consider so-called simple families of labelled trees, which contain, e.g., ordered, unordered, binary and cyclic labelled trees as special instances, and study the global and local behaviour of the number of inversions. In particular we…
Frequent tree mining asks us to enumerate tree patterns that occur frequently in a database of rooted trees. This problem is motivated by tree-structured data in bioinformatics, such as glycans and pseudoknot-free RNA secondary structures.…
Regular tree grammars and regular path expressions constitute core constructs widely used in programming languages and type systems. Nevertheless, there has been little research so far on frameworks for reasoning about path expressions…
This paper investigates some properties of the number of subtrees of a tree with given degree sequence. These results are used to characterize trees with the given degree sequence that have the largest number of subtrees, which generalizes…
In this paper, we propose a compositional nonparametric method in which a model is expressed as a labeled binary tree of $2k+1$ nodes, where each node is either a summation, a multiplication, or the application of one of the $q$ basis…
An evolutionary tree is a rooted tree where each internal vertex has at least two children and where the leaves are labeled with distinct symbols representing species. Evolutionary trees are useful for modeling the evolutionary history of…
We obtain bivariate asymptotics for the number of (unicellular) combinatorial maps (a model of discrete surfaces) as both the size and the genus grow. This work is related to two research topics that have been very active recently:…
Inspired by Stufler's recent probabilistic proof of Otter's asymptotic number of unlabeled trees, we revisit work of Palmer and Schwenk, and study unlabeled forests from a probabilistic point of view. We show that the number of trees in a…
Species trees represent the historical divergences of populations or species, while gene trees trace the ancestry of individual gene copies sampled within those populations. In cases involving rapid speciation, gene trees with topologies…
We prove that finding a rooted subtree with at least $k$ leaves in a digraph is a fixed parameter tractable problem. A similar result holds for finding rooted spanning trees with many leaves in digraphs from a wide family $\cal L$ that…
Galled trees are widely studied as a recombination model in population genetics. This class of phylogenetic networks is generalized into galled networks by relaxing a structural condition. In this work, a linear recurrence formula is given…
We study protected nodes in $m$-ary search trees, by putting them in context of generalised P\'olya urns. We show that the number of two-protected nodes (the nodes that are neither leaves nor parents of leaves) in a random ternary search…
We consider a model of random tree growth, where at each time unit a new vertex is added and attached to an already existing vertex chosen at random. The probability with which a vertex with degree $k$ is chosen is proportional to $w(k)$,…
Following Poupard's study of strictly ordered binary trees with respect to two parameters, namely, "end of minimal chain" and "parent of maximum leaf" a true Tree Calculus is being developed to solve a partial difference equation system and…
Phylogenetic trees canonically arise as embeddings of phylogenetic networks. We recently showed that the problem of deciding if two phylogenetic networks embed the same sets of phylogenetic trees is computationally hard, \blue{in…
We extend classical results on simple varieties of trees (asymptotic enumeration, average behavior of tree parameters) to trees counted by their number of leaves. Motivated by genome comparison of related species, we then apply these…
In 1989 Erd\H{o}s and Sz\'ekely showed that there is a bijection between (i) the set of rooted trees with $n+1$ vertices whose leaves are bijectively labeled with the elements of $[\ell]=\{1,2,\dots,\ell\}$ for some $\ell \leq n$, and (ii)…