Related papers: Toric geometry of the 3-Kimura model for any tree

The Kimura 3-parameter model on a tree of n leaves is one of the most used in phylogenetics. The affine algebraic variety W associated to it is a toric variety. We study its geometry and we prove that it is isomorphic to a geometric…

Group-based models arise in algebraic statistics while studying evolution processes. They are represented by embedded toric algebraic varieties. Both from the theoretical and applied point of view one is interested in determining the ideals…

Motivated by phylogenetics, our aim is to obtain a system of equations that define a phylogenetic variety on an open set containing the biologically meaningful points. In this paper we consider phylogenetic varieties defined via group-based…

We address the problem of studying the toric ideals of phylogenetic invariants for a general group-based model on an arbitrary claw tree. We focus on the group $\mathbb Z_2$ and choose a natural recursive approach that extends to other…

Associated to any graph is a toric ideal whose generators record relations among the cuts of the graph. We study these ideals and the geometry of the corresponding toric varieties. Our theorems and conjectures relate the combinatorial…

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 study covers of the multiplicative group of an algebraically closed field as quasiminimal pregeometry structures and prove that they satisfy the axioms for Zariski-like structures presented in \cite{lisuriart}, section 4. These axioms…

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…

We generalize the notion of tight geodesics in the curve complex to tight trees. We then use tight trees to construct model geometries for certain surface bundles over graphs. This extends some aspects of the combinatorial model for doubly…

A new class of noncommutative $k$-algebras (for $k$ an algebraically closed field) is defined and shown to contain some important examples of quantum groups. To each such algebra, a first order theory is assigned describing models of a…

We propose a model-theoretic structure for Shimura varieties and give necessary and sufficient conditions to obtain categoricity. We show that these conditions are directly related to important conjectures in number theory coming from…

Let C be a complex smooth projective algebraic curve endowed with an action of a finite group G such that the quotient curve has genus at least 3. We prove that if the G-curve C is very general for these properties, then the natural map…

The purpose of this paper is to study reducibility properties in Sasakian geometry. First we give the Sasaki version of the de Rham Decomposition Theorem; however, we need a mild technical assumption on the Sasaki automorphism group which…

This is a foundation for algebraic geometry, developed internal to the Zariski topos, building on the work of Kock and Blechschmidt. The Zariski topos consists of sheaves on the site opposite to the category of finitely presented algebras…

We characterize the Zariski topologies over an algebraically closed field in terms of general dimension-theoretic properties. Some applications are given to complex manifold and to strongly minimal sets.

A family of fractal arrangements of circles is introduced for each imaginary quadratic field $K$. Collectively, these arrangements contain (up to an affine transformation) every set of circles in the extended complex plane with integral…

We study the critical points of monomial functions over an algebraic subset of the probability simplex. The number of critical points on the Zariski closure is a topological invariant of that embedded projective variety, known as its…

We provide descriptions of the Whitehead groups, and the algebraic $K$-theory groups, of the fundamental group of a connected, oriented, closed $3$-manifold in terms of Whitehead groups of their finite subgroups and certain Nil-groups. The…

We characterize the ``best'' model geometries for the class of virtually free groups, and we show that there is a countable infinity of distinct ``best'' model geometries in an appropriate sense--these are the maximally symmetric trees. The…

For any field k of characteristic at most 5 we exhibit an explicit smooth quartic surface in projective threespace over k with trivial automorphism group over the algebraic closure of k. We also show how this can be extended to higher…