Related papers: A Beta-splitting model for evolutionary trees
A dynamical picture of phylogenetic evolution is given in terms of Markov models on a state space, comprising joint probability distributions for character types of taxonomic classes. Phylogenetic branching is a process which augments the…
We introduce some natural families of distributions on rooted binary ranked plane trees with a view toward unifying ideas from various fields, including macroevolution, epidemiology, computational group theory, search algorithms and other…
We introduce the Pitman Yor Diffusion Tree (PYDT) for hierarchical clustering, a generalization of the Dirichlet Diffusion Tree (Neal, 2001) which removes the restriction to binary branching structure. The generative process is described…
Forward-time models of diversification (i.e., speciation and extinction) produce phylogenetic trees that grow "vertically" as time goes by. Pruning the extinct lineages out of such trees leads to natural models for reconstructed trees…
We define and study a model of winding for non-colliding particles in finite trees. We prove that the asymptotic behavior of this statistic satisfies a central limiting theorem, analogous to similar results on winding of bounded particles…
Generating function equation has been derived for the probability distribution of the number of nodes with $k \ge 0$ outgoing lines in randomly evolving special trees. The stochastic properties of end-nodes (k=0) have been analyzed, and it…
Recent work has proven the existence of extreme inbreeding in a European ancestry sample taken from the contemporary UK population \cite{nature_01}. This result brings our attention again to a math problem related to inbreeding family trees…
The homogeneous reconstructed evolutionary process is a birth-death process without observed extinct lineages. Each species evolves independently with the same diversification rates (speciation rate $\lambda(t)$ and extinction rate…
Development combines three basic processes asymmetric --- cell division, signaling and gene regulation --- in a multitude of ways to create an overwhelming diversity of multicellular life-forms. Here, we attempt to chart this diversity…
Phylogenetic diversity is a measure for describing how much of an evolutionary tree is spanned by a subset of species. If one applies this to the (unknown) subset of current species that will still be present at some future time, then this…
We study a natural fragmentation process of the so-called stable tree introduced by Duquesne and Le Gall, which consists in removing the nodes of the tree according to a certain procedure that makes the fragmentation self-similar with…
A popular line of research in evolutionary biology is the use of time-calibrated phylogenies for the inference of diversification processes. This requires computing the likelihood of a given ultrametric tree as the reconstructed tree…
The basic object we consider is a certain model of continuum random tree, called the stable tree. We construct a fragmentation process $(F^-(t), t>=0)$ out of this tree by removing the vertices located under height $t$. Thanks to a…
The subject of pattern avoiding permutations has its roots in computer science, namely in the problem of sorting a permutation through a stack. A formula for the number of permutations of length n that can be sorted by passing it twice…
We study fragmentation of a random recursive tree into a forest by repeated removal of nodes. The initial tree consists of N nodes and it is generated by sequential addition of nodes with each new node attaching to a randomly-selected…
We introduce regenerative tree growth processes as consistent families of random trees with n labelled leaves, n>=1, with a regenerative property at branch points. This framework includes growth processes for exchangeably labelled Markov…
An evolutionary tree is a cascade of bifurcations starting from a single common root, generating a growing set of daughter species as time goes by. Species here is a general denomination for biological species, spoken languages or any other…
In this paper, we propose a new random forest algorithm that constructs the trees using a novel adaptive split-balancing method. Rather than relying on the widely-used random feature selection, we propose a permutation-based balanced…
Many processes and models --in biological, physical, social, and other contexts-- produce trees whose depth scales logarithmically with the number of leaves. Phylogenetic trees, describing the evolutionary relationships between biological…
Decision trees and randomized forests are widely used in computer vision and machine learning. Standard algorithms for decision tree induction optimize the split functions one node at a time according to some splitting criteria. This greedy…