Constructive degree bounds for group-based models

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 defining the varieties. Conjectural bounds on the degree in which these ideals are generated were given by Sturmfels and Sullivant. We prove that for the 3-Kimura model, corresponding to the group G=Z2xZ2, the projective scheme can be defined by an ideal generated in degree 4. In particular, it is enough to consider degree 4 phylogenetic invariants to test if a given point belongs to the variety. We also investigate G-models, a generalization of abelian group-based models. For any G-model, we prove that there exists a constant $d$, such that for any tree, the associated projective scheme can be defined by an ideal generated in degree at most d.Comment: Boundedness results for equations defining the projective scheme were extended to G-models (including 2-Kimura and all JC

Toric geometry of the 3-Kimura model for any tree

In this paper we present geometric features of group based models. We focus on the 3-Kimura model. We present a precise geometric description of the variety associated to any tree on a Zariski open set. In particular this set contains all biologically meaningful points. Our motivation is a conjecture of Sturmfels and Sullivant on the degree in which the ideal associated to 3-Kimura model is generated

Obstructions to combinatorial formulas for plethysm

Motivated by questions of Mulmuley and Stanley we investigate quasi-polynomials arising in formulas for plethysm. We demonstrate, on the examples of $S^3(S^k)$ and $S^k(S^3)$, that these need not be counting functions of inhomogeneous polytopes of dimension equal to the degree of the quasi-polynomial. It follows that these functions are not, in general, counting functions of lattice points in any scaled convex bodies, even when restricted to single rays. Our results also apply to special rectangular Kronecker coefficients.Comment: 7 pages; v2: Improved version with further reaching counterexamples; v3: final version as in Electronic Journal of Combinatoric

Derived category of toric varieties with Picard number three

We construct a full, strongly exceptional collection of line bundles on the variety X that is the blow up of the projectivization of the vector bundle O_{P^{n-1}}\oplus O_{P^{n-1}}(b) along a linear space of dimension n-2, where b is a non-negative integer

Secant cumulants and toric geometry

We study the secant line variety of the Segre product of projective spaces using special cumulant coordinates adapted for secant varieties. We show that the secant variety is covered by open normal toric varieties. We prove that in cumulant coordinates its ideal is generated by binomial quadrics. We present new results on the local structure of the secant variety. In particular, we show that it has rational singularities and we give a description of the singular locus. We also classify all secant varieties that are Gorenstein. Moreover, generalizing (Sturmfels and Zwiernik 2012), we obtain analogous results for the tangential variety.Comment: Some improvements to previous results, with other minor changes. Updated reference

Local equations for equivariant evolutionary models

Phylogenetic varieties related to equivariant substitution models have been studied largely in the last years. One of the main objectives has been finding a set of generators of the ideal of these varieties, but this has not yet been achieved in some cases (for example, for the general Markov model this involves the open “salmon conjecture”, see [2]) and it is not clear how to use all generators in practice. Motivated by applications in biology, we tackle the problem from another point of view. The elements of the ideal that could be useful for applications in phylogenetics only need to describe the variety around certain points of no evolution (see [13]). We produce a collection of explicit equations that describe the variety on a Zariski open neighborhood of these points (see Theorem 5.4). Namely, for any tree T on any number of leaves (and any degrees at the interior nodes) and for any equivariant model on any set of states ¿, we compute the codimension of the corresponding phylogenetic variety. We prove that this variety is smooth at general points of no evolution and, if a mild technical condition is satisfied (“d-claw tree hypothesis”), we provide an algorithm to produce a complete intersection that describes the variety around these points.Peer ReviewedPostprint (author's final draft

Polynomial systems admitting a simultaneous solution

We provide a complete description of the ideal that serves as the resultant ideal for n univariate polynomials of degree d. We in particular describe a set of generators of this resultant ideal arising as maximal minors of a set of cascading matrices formed from the coefficients of the polynomials, generalising the classical Sylvester resultant of two polynomials.Comment: 9 page