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Finiteness results for Abelian tree models

Jan Draisma, Rob H. Eggermont (2015)

Journal of the European Mathematical Society

Equivariant tree models are statistical models used in the reconstruction of phylogenetic trees from genetic data. Here equivariant§ refers to a symmetry group imposed on the root distribution and on the transition matrices in the model. We prove that if that symmetry group is Abelian, then the Zariski closures of these models are defined by polynomial equations of bounded degree, independent of the tree. Moreover, we show that there exists a polynomial-time membership test for that Zariski closure....

On the graph labellings arising from phylogenetics

Weronika Buczyńska, Jarosław Buczyński, Kaie Kubjas, Mateusz Michałek (2013)

Open Mathematics

We study semigroups of labellings associated to a graph. These generalise the Jukes-Cantor model and phylogenetic toric varieties defined in [Buczynska W., Phylogenetic toric varieties on graphs, J. Algebraic Combin., 2012, 35(3), 421–460]. Our main theorem bounds the degree of the generators of the semigroup by g + 1 when the graph has first Betti number g. Also, we provide a series of examples where the bound is sharp.

Representations of non-negative polynomials via KKT ideals

Dang Tuan Hiep (2011)

Annales Polonici Mathematici

This paper studies the representation of a non-negative polynomial f on a non-compact semi-algebraic set K modulo its KKT (Karush-Kuhn-Tucker) ideal. Under the assumption that f satisfies the boundary Hessian conditions (BHC) at each zero of f in K, we show that f can be represented as a sum of squares (SOS) of real polynomials modulo its KKT ideal if f ≥ 0 on K.

Sagbi bases of Cox–Nagata rings

Bernd Sturmfels, Zhiqiang Xu (2010)

Journal of the European Mathematical Society

We degenerate Cox–Nagata rings to toric algebras by means of sagbi bases induced by configurations over the rational function field. For del Pezzo surfaces, this degeneration implies the Batyrev–Popov conjecture that these rings are presented by ideals of quadrics. For the blow-up of projective n -space at n + 3 points, sagbi bases of Cox–Nagata rings establish a link between the Verlinde formula and phylogenetic algebraic geometry, and we use this to answer questions due to D’Cruz–Iarrobino and Buczyńska–Wiśniewski....

The F4-algorithm for Euclidean rings

Afshan Sadiq (2010)

Open Mathematics

In this short note, we extend Faugére’s F4-algorithm for computing Gröbner bases to polynomial rings with coefficients in an Euclidean ring. Instead of successively reducing single S-polynomials as in Buchberger’s algorithm, the F4-algorithm is based on the simultaneous reduction of several polynomials.

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