Related papers: Yule-generated trees constrained by node imbalance
Given a rooted tree and a ranking of its leaves, what is the minimum number of inversions of the leaves that can be attained by ordering the tree? This variation of the problem of counting inversions in arrays originated in mathematical…
Evolutionary events such as incomplete lineage sorting and lateral gene transfer constitute major problems for inferring species trees from gene trees, as they can sometimes lead to gene trees which conflict with the underlying species…
We study the limiting behavior of a Bienayme-Galton-Watson tree conditioned to have a large number of vertices and either a fixed number of leaves or a fixed number of internal nodes. The first biconditioning gives a universal result with…
We investigate the number of permutations that occur in random labellings of trees. This is a generalisation of the number of subpermutations occurring in a random permutation. It also generalises some recent results on the number of…
In a phylogenetic tree, we often don't have information about the time a speciation event (inner node) occured. Under a neutral model for speciation, I develop fast algorithms for calculating the probability that an inner node i is the k-th…
In the paper we probe the possibilities of creating a Kurepa tree in a generic extension of a model of CH plus no Kurepa trees by an omega_1-preserving forcing notion of size at most omega_1. In the first section we show that in the Levy…
Genomes and genes diversify during evolution; however, it is unclear to what extent genes still retain the relationship among species. Model species for molecular phylogenetic studies include yeasts and viruses whose genomes were sequenced…
We study nongeneric planar trees and prove the existence of a Gibbs measure on infinite trees obtained as a weak limit of the finite volume measures. It is shown that in the infinite volume limit there arises exactly one vertex of infinite…
When using machine learning for imbalanced binary classification problems, it is common to subsample the majority class to create a (more) balanced training dataset. This biases the model's predictions because the model learns from data…
We present families of combinatorial classes described as trees with nodes that can carry one of two types of "flowers": integer partitions or integer compositions. Two parameters on the flowers of trees will be considered: the number of…
Understanding the evolution of a set of genes or species is a fundamental problem in evolutionary biology. The problem we study here takes as input a set of trees describing {possibly discordant} evolutionary scenarios for a given set of…
The alpha model, a parametrized family of probabilities on cladograms (rooted binary leaf labeled trees), is introduced. This model is Markovian self-similar, deletion-stable (sampling consistent), and passes through the Yule, Uniform and…
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…
We study a random tree, which was introduced by Ajazi et al. as part of a model of a neuronal network. Realising a scaling relation for the law of the tree, we can use elementary techniques to derive asymptotic results on the geometry as…
Unranked trees can be represented using their minimal dag (directed acyclic graph). For XML this achieves high compression ratios due to their repetitive mark up. Unranked trees are often represented through first child/next sibling (fcns)…
Shape is one of the important characteristics for the structures observed in living organisms. Whereas biologists have proposed models where the shape is controlled on a molecular level [1], physicists, following Turing [2] and d'Arcy…
We consider the set of random Bienaym\'e-Galton-Watson trees with a bounded number of offspring and bounded number of generations as a statistical mechanics model: a random tree is a rooted subtree of the maximal tree; the spin at a given…
By an omega_1 --tree we mean a tree of power omega_1 and height omega_1. We call an omega_1 --tree a Jech--Kunen tree if it has kappa --many branches for some kappa strictly between omega_1 and 2^{omega_1}. In this paper we construct the…
Motivation: Millions of genes in the modern species belong to only thousands of `gene families'. A gene family includes instances of the same gene in different species (orthologs) and duplicate genes in the same species (paralogs). Genes…
This paper is a contribution to the problem of counting geometric graphs on point sets. More concretely, we look at the maximum numbers of non-crossing spanning trees and forests. We show that the so-called double chain point configuration…