Related papers: Tree hook length formulae, Feynman rules and B-ser…
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 define a notion of higher order renormalization group equation and investigate when a sequence of trees satisfies such an equation. In the strongest sense, the sequence of trees satisfies a $k$th order renormalization group equation when…
Tree-child networks are a recently-described class of directed acyclic graphs that have risen to prominence in phylogenetics (the study of evolutionary trees and networks). Although these networks have a number of attractive mathematical…
The structure of an evolving network contains information about its past. Extracting this information efficiently, however, is, in general, a difficult challenge. We formulate a fast and efficient method to estimate the most likely history…
We study a new class of polyominoes, called $p$-Fibonacci polyominoes, defined using $p$-Fibonacci words. We enumerate these polyominoes by applying generating functions to capture geometric parameters such as area, semi-perimeter, and the…
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.…
The reconstruction of a central tendency `species tree' from a large number of conflicting gene trees is a central problem in systematic biology. Moreover, it becomes particularly problematic when taxon coverage is patchy, so that not all…
We show that an algorithmic construction of sequences of recursive trees leads to a direct proof of the convergence of random recursive trees in an associated Doob-Martin compactification; it also gives a representation of the limit in…
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…
Pairwise ordered tree alignment are combinatorial objects that appear in RNA secondary structure comparison. However, the usual representation of tree alignments as supertrees is ambiguous, i.e. two distinct supertrees may induce identical…
Motivated by a formula of A. Postnikov relating binary trees, we define the hook length polynomials for m-ary trees and plane forests, and show that these polynomials have a simple binomial expression. An integer value of this expression is…
Stick-breaking (SB) processes are often adopted in Bayesian mixture models for generating mixing weights. When covariates influence the sizes of clusters, SB mixtures are particularly convenient as they can leverage their connection to…
We discuss a notion of convergence for binary trees that is based on subtree sizes. In analogy to recent developments in the theory of graphs, posets and permutations we investigate some general aspects of the topology, such as a…
A new tree model is introduced based on ordered trees, by distinguishing exactly one child of each node that \emph{has} children. The basic enumeration leads to a cubic equation of the generating function. The extraction of its coefficients…
We introduce a framework for constructing fractal trees via analytic generator fields, replacing discrete affine transformations and symbolic rewriting rules by the integration of smooth vector fields in an internal state space. In this…
We consider injective first-order interpretations that input and output trees of bounded height. The corresponding functions have polynomial output size, since a first-order interpretation can use a k-tuple of input nodes to represent a…
We generalize the concept of ascending and descending runs from permutations to rooted labelled trees and mappings, i.e., functions from the set $\{1, \dots, n\}$ into itself. A combinatorial decomposition of the corresponding functional…
In mathematical phylogenetics, the time-consistent galled trees provide a simple class of rooted binary network structures that can be used to represent a variety of different biological phenomena. We study the enumerative combinatorics of…
We present a link-by-link rule-based method for constructing all members of the ensemble of spanning trees for any recursively generated, finitely articulated graph, such as the DGM net. The recursions allow for many large-scale properties…
We introduce a class of quantum non-Markovian processes -- dubbed process trees -- that exhibit polynomially decaying temporal correlations and memory distributed across time scales. This class of processes is described by a tensor network…