Related papers: Phylogenetic degrees for claw trees
Structural information of phylogenetic tree topologies plays an important role in phylogenetic inference. However, finding appropriate topological structures for specific phylogenetic inference tasks often requires significant design effort…
To an algebraic variety equipped with an involution, we associate a cycle class in the modulo two Chow group of its fixed locus. This association is functorial with respect to proper morphisms having a degree and preserving the involutions.…
We define the tropical Tevelev degrees, $\mathsf{Tev}_g^{trop}$, as the degree of a natural finite morphism between certain tropical moduli spaces, in analogy to the algebraic case. We develop an explicit combinatorial construction that…
Phylogenetic networks describe the evolution of a set of taxa for which reticulate events have occurred at some point in their evolutionary history. Of particular interest is when the evolutionary history between a set of just three taxa…
In this paper we study a class of dynamical systems generated by iterations of multivariate polynomials and estimate the degreegrowth of these iterations. We use these estimates to bound exponential sums along the orbits of these dynamical…
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…
A wide variety of stochastic models of cladogenesis (based on speciation and extinction) lead to an identical distribution on phylogenetic tree shapes once the edge lengths are ignored. By contrast, the distribution of the tree's edge…
Phylogenetic networks are an important way to represent evolutionary histories that involve reticulations such as hybridization or horizontal gene transfer, yet fundamental questions such as how many networks there are that satisfy certain…
The goal of these lectures is to review some mathematical aspects of random tree models used in evolutionary biology to model gene trees or species trees. We start with stochastic models of tree shapes (finite trees without edge lengths),…
In the past decade, Genome-Wide Association Studies (GWAS) have delivered an increasingly broad view of the genetic basis of human phenotypic variation. One of the major developments from GWAS is polygenic scores, a genetic predictor of an…
The conception of multi-alphabetical genetics is represented. Matrix forms of the representation of the multi-level system of molecular-genetic alphabets have revealed algebraic properties of this system. These properties are connected with…
We apply the theory of markov random fields on trees to derive a phase transition in the number of samples needed in order to reconstruct phylogenies. We consider the Cavender-Farris-Neyman model of evolution on trees, where all the inner…
Phylogenetic networks are increasingly used in evolutionary biology to represent the history of species that have undergone reticulate events such as horizontal gene transfer, hybrid speciation and recombination. One of the most fundamental…
Phylogenetic trees and networks are leaf-labelled graphs that are used to describe evolutionary histories of species. The Tree Containment problem asks whether a given phylogenetic tree is embedded in a given phylogenetic network. Given a…
We analyze the complexity of fitting a variety, coming from a class of varieties, to a configuration of points in $\Bbb C^n$. The complexity measure, called the algebraic complexity, computes the Euclidean Distance Degree (EDdegree) of a…
We revisit the representation theory in type $A$used previously to establish that the dissimilarity vectors of phylogenetic trees are points on the tropical Grassmannian variety. We use a different version of this construction to show that…
By applying interpretable machine learning methods such as decision trees, we study how simple models can classify the Galois groups of Galois extensions over $\mathbb{Q}$ of degrees 4, 6, 8, 9, and 10, using Dedekind zeta coefficients. Our…
The aim of this paper is to study the behavior of Hodge-theoretic (intersection homology) genera and their associated characteristic classes under proper morphisms of complex algebraic varieties. We obtain formulae that relate (parametrized…
In this paper, we study the parallel query complexity of reconstructing biological and digital phylogenetic trees from simple queries involving their nodes. This is motivated from computational biology, data protection, and computer…
We use the recently developed theory of forest algebras to find algebraic characterizations of the languages of unranked trees and forests definable in various logics. These include the temporal logics CTL and EF, and first-order logic over…