Related papers: On the ideals of equivariant tree models
Tree-based ensemble methods such as random forests, gradient-boosted trees, and Bayesianadditive regression trees have been successfully used for regression problems in many applicationsand research studies. In this paper, we study ensemble…
A metric phylogenetic tree relating a collection of taxa induces weighted rooted triples and weighted quartets for all subsets of three and four taxa, respectively. New intertaxon distances are defined that can be calculated from these…
A new class of general exponential ranking models is introduced which we label angle-based models for ranking data. A consensus score vector is assumed, which assigns scores to a set of items, where the scores reflect a consensus view of…
This article is motivated by the following satisfiability question: pick uniformly at random an and/or Boolean expression of length n, built on a set of k_n Boolean variables. What is the probability that this expression is satisfiable?…
We introduce the package PhylogeneticTrees for Macaulay2 which allows users to compute phylogenetic invariants for group-based tree models. We provide some background information on phylogenetic algebraic geometry and show how the package…
We show that an infinite weighted tree admits a bi-Lipschitz embedding into Hilbert space if and only if it does not contain arbitrarily large complete binary trees with uniformly bounded distortion. We also introduce a new metric invariant…
For a graph G, we construct two algebras, whose dimensions are both equal to the number of spanning trees of G. One of these algebras is the quotient of the polynomial ring modulo certain monomial ideal, while the other is the quotient of…
Some tools and ideas are interchanged between random matrix theory and multivariate statistics. In the context of the random matrix theory, classes of spherical and generalised Wishart random matrix ensemble, containing as particular cases…
We studied how to obtain a distribution for the number of ancestors in species of sexual reproduction. Present models concentrate on the estimation of distributions repetitions of ancestors in genealogical trees. It has been shown that is…
In this paper, we introduce the notion of the quadratic graph, that is a graph whose eigenvalues are integral or quadratic algebraic integral, and determine nine infinite families of quadratic starlike trees, which are just all the…
This paper is devoted to understanding the defining ideal of a Nichols algebra from the decomposition of specific elements in the group algebra of braid groups. A family of primitive elements are found and algorithms are proposed. To prove…
We propose generalizations of a number of standard network models, including the classic random graph, the configuration model, and the stochastic block model, to the case of time-varying networks. We assume that the presence and absence of…
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…
We propose a method for the classification of objects that are structured as random trees. Our aim is to model a distribution over the node label assignments in settings where the tree data structure is associated with node attributes…
An ideal of polynomials is symmetric if it is closed under permutations of variables. We relate general symmetric ideals to the so called Specht ideals generated by all Specht polynomials of a given shape. We show a connection between the…
Random forests are decision tree ensembles that can be used to solve a variety of machine learning problems. However, as the number of trees and their individual size can be large, their decision making process is often incomprehensible. In…
Rooted bifurcating trees are mathematical objects used to model evolutionary relationships and arise naturally in both coalescent theory and phylogenetics. Recent numerical representations of tree topologies, known as F-matrices, allow for…
We introduce a new class of monomial ideals which we call symmetric shifted ideals. Symmetric shifted ideals are fixed by the natural action of the symmetric group and, within the class of monomial ideals fixed by this action, they can be…
Starting categorically, we give simple and precise models of equivariant classifying spaces. We need these models for work in progress in equivariant infinite loop space theory and equivariant algebraic K-theory, but the models are of…
Recent work has discussed the importance of multiplicative closure for the Markov models used in phylogenetics. For continuous-time Markov chains, a sufficient condition for multiplicative closure of a model class is ensured by demanding…