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....

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.

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.

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....

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.

Let $I$ be an ideal in a commutative Noetherian ring $R$. Then the ideal $I$ has the strong persistence property if and only if $\left(I^{k+1}{:}_{R}I\right)=I^k$ for all $k$, and $I$ has the symbolic strong persistence property if and only if $\left(I^{(k+1)}{:}_R{I}^{\left(1\right)}\right)=I^{\left(k\right)}$ for all $k$, where $I^{\left(k\right)}$ denotes the $k$th symbolic power of $I$. We study the strong persistence property for some classes of monomial ideals. In particular, we present a family of primary monomial ideals failing the strong persistence property. Finally, we show that every square-free monomial ideal has the...