Related papers: Algebraic varieties representing group-based Marko…
We find presentations for subalgebras of invariants of the coordinate algebras of binary symmetric models of phylogenetic trees studied by Buczynska and Wisniewski in \cite{BW}. These algebras arise as toric degenerations of rings of global…
The purpose of this article is to show how the isotropy subgroup of leaf permutations on binary trees can be used to systematically identify tree-informative invariants relevant to models of phylogenetic evolution. In the quartet case, we…
For any $n\geq 1$, let $T_n$ be the complete binary rooted tree of height $n$, and $f(x)=(x+a)^2-a-1$ such that $a\neq \pm b^2$ for any $b\in \mathbb{Z}$. In \cite{Settled}, Jones and Boston empirically observed that iteratively applying a…
We describe the proalgebraic groups represented by three Hopf algebras on planar binary trees previously introduced by the author and Christian Brouder in relation with the renormalization of quantum electrodynamics. Using two monoidal…
This paper provides a unified approach to results on representations of affine Hecke algebras, cyclotomic Hecke algebras, affine BMW algebras, cyclotomic BMW algebras, Markov traces, Jacobi-Trudi type identities, dual pairs (Zelevinsky),…
To a tree of semi-simple algebras we associate a qurve (or formally smooth algebra) S. We introduce a Zariski- and etale quiver describing the finite dimensional representations of S. In particular, we show that all quotient varieties of…
Kirchhoff's matrix tree theorem is a well-known result that gives a formula for the number of spanning trees in a finite, connected graph in terms of the graph Laplacian matrix. A closely related result is Wilson's algorithm for putting the…
Representations of Spin groups and Clifford algebras derived from the structure of qubit trees are introduced in this work. For ternary trees the construction is more general and reduction to binary trees is formally defined by deletion of…
It is possible to represent each of a number of Markov chains as an evolving sequence of connected subsets of a directed acyclic graph that grow in the following way: initially, all vertices of the graph are unoccupied, particles are fed in…
In this paper we investigate properties of algebraic varieties representing group-based phylogenetic models. We propose a method of generating many phylogenetic invariants. We prove that we obtain all invariants for any tree for the binary…
We investigate topologies on groups which arise naturally from their algebraic structure, including the Frech\'et-Markov, Hausdorff-Markov, and various kinds of Zariski topologies. Answering a question by Dikranjan and Toller, we show that…
A polynomial transform is the multiplication of an input vector $x\in\C^n$ by a matrix $\PT_{b,\alpha}\in\C^{n\times n},$ whose $(k,\ell)$-th element is defined as $p_\ell(\alpha_k)$ for polynomials $p_\ell(x)\in\C[x]$ from a list…
We consider the problem of testing whether the points in a complex or real variety with non-zero coordinates form a multiplicative group or, more generally, a coset of a multiplicative group. For the coset case, we study the notion of…
Many of the stochastic models used in inference of phylogenetic trees from biological sequence data have polynomial parameterization maps. The image of such a map --- the collection of joint distributions for a model --- forms the model…
The mathematical modelling of genetic-metabolic networks is of out most importance in the field of systems biology. Different formalisms and a huge variety of classical mathematical tools have been used to describe and analyse such…
This paper presents a systematic methodology based on the algebraic theory of signal processing to classify and derive fast algorithms for linear transforms. Instead of manipulating the entries of transform matrices, our approach derives…
The framework of algebraically natural proofs was independently introduced in the works of Forbes, Shpilka and Volk (2018), and Grochow, Kumar, Saks and Saraf (2017), to study the efficacy of commonly used techniques for proving lower…
We consider the phylogenetic tree model in which every node of the tree is observed and binary and the transitions are given by the same matrix on each edge of the tree. We are able to compute the Grobner basis and Markov basis of the toric…
Elements of the tropical vertex group, introduced by Kontsevich and Soibelman, are formal families of symplectomorphisms of the 2-dimensional algebraic torus. We prove ordered product factorizations in the tropical vertex group are…
Algebraic datatypes, and among them lists and trees, have attracted a lot of interest in automated reasoning and Satisfiability Modulo Theories (SMT). Since its latest stable version, the SMT-LIB standard defines a theory of algebraic…