Related papers: Toric ideals of homogeneous phylogenetic models

A cosmological polytope is defined for a given Feynman diagram, and its canonical form may be used to compute the contribution of the Feynman diagram to the wavefunction of certain cosmological models. Given a subdivision of a polytope, its…

We introduce two operads which own the set of planar forests as a basis. With its usual product and two other products defined by different types of graftings, the algebra of planar rooted trees H becomes an algebra over these operads. The…

We present a new family of zero-field Ising models over $N$ binary variables/spins obtained by consecutive "gluing" of planar and $O(1)$-sized components and subsets of at most three vertices into a tree. The polynomial-time algorithm of…

In this paper we complete the results of Sullivant and Sturmfels proving that many of the algebraic group-based models for Markov processes on trees are pseudo-toric. We also show in which cases these varieties are normal. This is done by…

Kazhdan-Lusztig ideals, a family of generalized determinantal ideals investigated in [Woo-Yong '08], provide an explicit choice of coordinates and equations encoding a neighbourhood of a torus-fixed point of a Schubert variety on a type A…

We describe a generating set for the initial ideal of simplicial toric ideals with respect to the graded reverse lexicographic order, using representations of elements of affine monoids as sums of irreducible elements. Although the…

Let I be the toric ideal defined by a 2 x n matrix of integers, A = ((1 1 ... 1)(a_1 a_2 ... a_n)) with a_1<a_2<...<a_n. We give a combinatorial proof that I is generated by elements of degree at most the sum of the two largest differences…

We apply the theory of markov random fields on trees to derive a phase transition in the number of samples needed in order to reconstruct phylogenies. We consider the Cavender-Farris-Neyman model of evolution on trees, where all the inner…

Algorithmic computation in polynomial rings is a classical topic in mathematics. However, little attention has been given to the case of rings with an infinite number of variables until recently when theoretical efforts have made possible…

Tree-based phylogenetic networks, which may be roughly defined as leaf-labeled networks built by adding arcs only between the original tree edges, have elegant properties for modeling evolutionary histories. We answer an open question of…

Bounds for the maximal degree of certain Gr\"obner bases of simplicial toric ideals are given. These bounds are close to the bound stated in Eisenbud-Goto's Conjecture on the Castelnuovo-Mumford regularity.

We describe the ideals, especially the prime ideals, of semirings of polynomials over layered domains, and in particular over supertropical domains. Since there are so many of them, special attention is paid to the ideals arising from…

Border bases arise as a canonical generalization of Gr\"obner bases. We provide a polyhedral characterization of all order ideals (and hence border bases) that are supported by a zero-dimensional ideal: order ideals that support a border…

We introduce balanced polyominoes and show that their ideal of inner minors is a prime ideal and has a quadratic Gr\"obner basis with respect to any monomial order, and we show that any row or column convex and any tree-like polyomino is…

A phylogenetic tree shows the evolutionary relationships among species. Internal nodes of the tree represent speciation events and leaf nodes correspond to species. A goal of phylogenetics is to combine such trees into larger trees, called…

In this paper we show that the agglomeration of rows or columns of a contingency table with a hierarchical clustering algorithm yields statistical models defined through toric ideals. In particular, starting from the classical independence…

We introduce the multigraded Hilbert scheme, which parametrizes all homogeneous ideals with fixed Hilbert function in a polynomial ring that is graded by any abelian group. Our construction is widely applicable, it provides explicit…

Given a finite, simple, vertex-weighted graph, we construct a graded associative (non-commutative) algebra, whose generators correspond to vertices and whose ideal of relations has generators that are graded commutators corresponding to…

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…

Computation of parallel lines (envelopes) to parabolas, ellipses, and hyperbolas is of importance in structure engineering and theory of mechanisms. Homogeneous polynomials that implicitly define parallel lines for the given offset to a…