Related papers: Toric ideals of homogeneous phylogenetic models
There is a natural infinite graph whose vertices are the monomial ideals in a polynomial ring. The definition involves Gr\"obner bases or the action of an algebraic torus. We present algorithms for computing the (affine schemes…
Associated to any vector configuration A is a toric ideal encoded by vectors in the kernel of A. Each toric ideal has two special generating sets: the universal Gr\"obner basis and the Graver basis. While the former is generally a proper…
This paper is concerned with the topological invariant of a graph given by the maximum degree of a Markov basis element for the corresponding graph model for binary contingency tables. We describe a degree four Markov basis for the model…
We introduce the theory of monoidal Groebner bases, a concept which generalizes the familiar notion in a polynomial ring and allows for a description of Groebner bases of ideals that are stable under the action of a monoid. The main…
We study existence and computability of finite bases for ideals of polynomials over infinitely many variables. In our setting, variables come from a countable logical structure A, and embeddings from A to A act on polynomials by renaming…
Null models of binary phylogenetic trees are useful for testing hypotheses on real world phylogenies. In this paper we consider phylogenies as binary trees without edge lengths together with a sampling measure and encode them as algebraic…
It is shown that up to dimension four, the toric ideal of a quiver polytope is generated in degree two, with the only exception of the four-dimensional Birkhoff polytope. As a consequence, B{\o}gvad's conjecture holds for quiver polytopes…
We show how tropical varieties of ideals I over a field K with non-trivial valuation can be traced back to tropical varieties of ideals in R[[t]][x] over some dense subring R in its ring of integers. Moreover, for homogeneous ideals, we…
We develop the theory of Gr\"obner bases for ideals in a polynomial ring with countably infinite variables over a field. As an application we reconstruct some of the one-one correspondences among various sets of partitions by using division…
We prove that the defining ideal of a sufficiently high Veronese subring of a toric algebra admits a quadratic Gr\"obner basis consisting of binomials. More generally, we prove that the defining ideal of a sufficiently high Veronese subring…
Phylogenetic networks generalise phylogenetic trees and allow for the accurate representation of the evolutionary history of a set of present-day species whose past includes reticulate events such as hybridisation and lateral gene transfer.…
Associated to any hypergraph is a toric ideal encoding the algebraic relations among its edges. We study these ideals and the combinatorics of their minimal generators, and derive general degree bounds for both uniform and non-uniform…
Relying on the combinatorial classification of toric ideals using their bouquet structure, we focus on toric ideals of hypergraphs and study how they relate to general toric ideals. We show that hypergraphs exhibit a surprisingly general…
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…
We resolve a conjecture about a class of binomial initial ideals of $I_{2,n}$, the ideal of the Grassmannian, Gr$(2,\mathbb{C}^n$), which are associated to phylogenetic trees. For a weight vector $\omega$ in the tropical Grassmannian,…
We investigate the computational complexity of problems on toric ideals such as normal forms, Gr\"obner bases, and Graver bases. We show that all these problems are strongly NP-hard in the general case. Nonetheless, we can derive efficient…
We compare the phylogenetic tensors for various trees and networks for two, three and four taxa. If the probability spaces between one tree or network and another are not identical then there will be phylogenetic tensors that could have…
We consider the three-state toric homogeneous Markov chain model (THMC) without loops and initial parameters. At time $T$, the size of the design matrix is $6 \times 3\cdot 2^{T-1}$ and the convex hull of its columns is the model polytope.…
We give a definition of Newton non degeneracy independent of the system of generators defining the variety. This definition extends the notion of Newton non degeneracy to varieties that are not necessarily complete intersection. As in the…
In this survey I summarize the constructions of toric degenerations obtained from valuations and Gr\"obner theory and describe in which sense they are equivalent. I show how adapted bases can be used to generalize the classical Newton…