An explicit lattice point realization is provided for the primary components of an arbitrary binomial ideal in characteristic zero. This decomposition is derived from a characteristic-free combinatorial description of certain primary components of binomial ideals in affine semigroup rings, namely those that are associated to faces of the semigroup. These results are intimately connected to hypergeometric differential equations in several variables.
Primary decomposition of commutative monoid congruences is insensitive to certain features of primary decomposition in commutative rings. These features are captured by the more refined theory of mesoprimary decomposition of congruences, introduced here complete with witnesses and associated prime objects. The combinatorial theory of mesoprimary decomposition lifts to arbitrary binomial ideals in monoid algebras. The resulting binomial mesoprimary decomposition is a new type of intersection decomposition for binomial ideals that enjoys computational efficiency and independence from ground fiel…
Parity binomial edge ideals of simple undirected graphs are introduced. Unlike binomial edge ideals, they do not have square-free Gröbner bases and are radical if only if the graph is bipartite or the characteristic of the ground field is not two. The minimal primes are determined and shown to encode combinatorics of even and odd walks in the graph. A mesoprimary decomposition is determined and shown to be a primary decomposition in characteristic two.
We classify all binomial edge ideals that are complete intersection and Cohen-Macaulay almost complete intersection. We also describe an algorithm and provide an implementation to compute primary decomposition of binomial edge ideals.
In this paper we introduce a binomial ideal derived from a binary linear code. We present some applications of a Gröbner basis of this ideal with respect to a total degree ordering. In the first application we give a decoding method for the code. By associating the code with the set of cycles in a graph, we can solve the problem of finding all codewords of minimal length (minimal cycles in a graph), and show how to find a minimal cycle basis. Finally we discuss some results on the computation of the Gröbner basis.
Recent results of Kahle and Miller give a method of constructing primary decompositions of binomial ideals by first constructing "mesoprimary decompositions" determined by their underlying monoid congruences. These mesoprimary decompositions are highly combinatorial in nature, and are designed to parallel standard primary decomposition over Noetherean rings. In this paper, we generalize mesoprimary decomposition from binomial ideals to "binomial submodules" of certain graded modules over the corresponding monoid algebra, analogous to the way primary decomposition of ideals over a Noetherean ri…
This survey of methods surrounding lattice point methods for binomial ideals begins with a leisurely treatment of the geometric combinatorics of binomial primary decomposition. It then proceeds to three independent applications whose motivations come from outside of commutative algebra: hypergeometric systems, combinatorial game theory, and chemical dynamics. The exposition is aimed at students and researchers in algebra; it includes many examples, open problems, and elementary introductions to the motivations and background from outside of algebra.
The second Veronese ideal $I_n$ contains a natural complete intersection $J_n$ generated by the principal $2$-minors of a symmetric $(n\times n)$-matrix. We determine subintersections of the primary decomposition of $J_n$ where one intersectand is omitted. If $I_n$ is omitted, the result is the other end of a complete intersection link as in liaison theory. These subintersections also yield interesting insights into binomial ideals and multigraded algebra. For example, if $n$ is even, $I_n$ is a Gorenstein ideal and the intersection of the remaining primary components of $J_n$ equals $J_n+\lan…
We investigate the structure of ideals generated by binomials (polynomials with at most two terms) and the schemes and varieties associated to them. The class of binomial ideals contains many classical examples from algebraic geometry, and it has numerous applications within and beyond pure mathematics. The ideals defining toric varieties are precisely the binomial prime ideals. Our main results concern primary decomposition: If $I$ is a binomial ideal then the radical, associated primes, and isolated primary components of $I$ are again binomial, and $I$ admits primary decompositions in terms …
We study the combinatorics of Gröbner degenerations of Grassmannians and the Schubert varieties inside them. We provide a family of binomial ideals whose combinatorics is governed by tableaux induced by matching fields in the sense of Sturmfels and Zelevinsky. We prove that these ideals are all quadratically generated and they yield a SAGBI basis of the Plücker algebra. This leads to a new family of toric degenerations of Grassmannians. Moreover, we apply our results to construct a family of Gröbner degenerations of Schubert varieties inside Grassmannians. We provide a complete characterizatio…
A natural candidate for a generating set of the (necessarily prime) defining ideal of an $n$-dimensional monomial curve, when the ideal is an almost complete intersection, is a full set of $n$ critical binomials. In a somewhat modified and more tractable context, we prove that, when the exponents are all positive, critical binomial ideals in our sense are not even unmixed for $n\geq 4$, whereas for $n\leq 3$ they are unmixed. We further give a complete description of their isolated primary components as the defining ideals of monomial curves with coefficients. This answers an open question on …
The package Binomials contains implementations of specialized algorithms for binomial ideals, including primary decomposition into binomial ideals. The current implementation works in characteristic zero. Primary decomposition is restricted to binomial ideals with trivial coefficients to avoid computations over the algebraic numbers. The basic ideas of the algorithms go back to Eisenbud and Sturmfels' seminal paper on the subject. Two recent improvements of the algorithms are discussed and examples are presented.
We present Binomials, a package for the computer algebra system Macaulay2, which specializes well known algorithms to binomial ideals. These come up frequently in algebraic statistics and commutative algebra, and it is shown that significant speedup of computations like primary decomposition is possible. While central parts of the implemented algorithms go back to Eisenbud and Sturmfels (1996), we also discuss a new algorithm for computing the minimal primes of a binomial ideal. All decompositions make significant use of combinatorial structure found in binomial ideals, and to demonstrate the …
The cut sets of a graph are special sets of vertices whose removal disconnects the graph. They are fundamental in the study of binomial edge ideals, since they encode their minimal primary decomposition. We introduce the class of accessible graphs as the graphs with unmixed binomial edge ideal and whose cut sets form an accessible set system. We prove that the graphs whose binomial edge ideal is Cohen-Macaulay are accessible and we conjecture that the converse holds. We settle the conjecture for large classes of graphs, including chordal and traceable graphs, providing a purely combinatorial d…
In this paper, we prove that every binomial ideal in a polynomial ring over an algebraically closed field of characteristic zero admits a canonical primary decomposition into binomial ideals. Moreover, we prove that this special decomposition is obtained from a cellular decomposition which is also defined in a canonical way and does not depend on the field.
Without any restrictions on the base field, we compute the hull and prove a conjecture of Eisenbud and Sturmfels giving an unmixed decomposition of a cellular binomial ideal. Over an algebraically closed field, we further obtain an explicit (but not necessarily minimal) primary decomposition of such an ideal.
We study quotients of the Weyl algebra by left ideals whose generators consist of an arbitrary Z^d-graded binomial ideal I along with Euler operators defined by the grading and a parameter in C^d. We determine the parameters for which these D-modules (i) are holonomic (equivalently, regular holonomic, when I is standard-graded); (ii) decompose as direct sums indexed by the primary components of I; and (iii) have holonomic rank greater than the generic rank. In each of these three cases, the parameters in question are precisely those outside of a certain explicitly described affine subspace arr…
Let $G$ be a graph on $[n]$ and $J_G$ be the binomial edge ideal of $G$ in the polynomial ring $S=\mathbb{K}[x_1,\ldots,x_n,y_1,\ldots,y_n]$. In this paper we investigate some topological properties of a poset associated to the minimal primary decomposition of $J_G$. We show that this poset admits some specific subposets which are contractible. This in turn, provides some interesting algebraic consequences. In particular, we characterize all graphs $G$ for which $\mathrm{depth}\hspace{1.2mm} S/J_G=4$.
This paper studies a class of binomial ideals associated to graphs with finite vertex sets. They generalize the binomial edge ideals, and they arise in the study of conditional independence ideals. A Gröbner basis can be computed by studying paths in the graph. Since these Gröbner bases are square-free, generalized binomial edge ideals are radical. To find the primary decomposition a combinatorial problem involving the connected components of subgraphs has to be solved. The irreducible components of the solution variety are all rational.
In this paper, we consider the set of all domino tilings of a cubiculated region. The primary question we explore is: How can we move from one tiling to another? Tiling spaces can be viewed as spaces of subgraphs of a fixed graph with a fixed degree sequence. Moves to connect such spaces have been explored in algebraic statistics. Thus, we approach this question from an applied algebra viewpoint, making new connections between domino tilings, algebraic statistics, and toric algebra. Using results from toric ideals of graphs, we are able to describe moves that connect the tiling space of a give…
Recent results of Kahle and Miller give a method of constructing primary decompositions of binomial ideals by first constructing "mesoprimary decompositions" determined by their underlying monoid congruences. Monoid congruences (and therefore, binomial ideals) can present many subtle behaviors that must be carefully accounted for in order to produce general results, and this makes the theory complicated. In this paper, we examine their results in the presence of a positive $A$-grading, where certain pathologies are avoided and the theory becomes more accessible. Our approach is algebraic: whil…
We introduce binomial edge ideals attached to a simple graph $G$ and study their algebraic properties. We characterize those graphs for which the quadratic generators form a Gröbner basis in a lexicographic order induced by a vertex labeling. Such graphs are chordal and claw-free. We give a reduced squarefree Gröbner basis for general $G$. It follows that all binomial edge ideals are radical ideals. Their minimal primes can be characterized by particular subsets of the vertices of $G$. We provide sufficient conditions for Cohen--Macaulayness for closed and nonclosed graphs. Binomial edge ideal…
We study the degree of non-homogeneous lattice ideals over arbitrary fields, and give formulae to compute the degree in terms of the torsion of certain factor groups of Z^s and in terms of relative volumes of lattice polytopes. We also study primary decompositions of lattice ideals over an arbitrary field using the Eisenbud-Sturmfels theory of binomial ideals over algebraically closed fields. We then use these results to study certain families of integer matrices (PCB, GPCB, CB, GCB matrices) and the algebra of their corresponding matrix ideals. In particular, the family of generalized positiv…
We use methods from combinatorics and algebraic statistics to study analogues of birth-and-death processes that have as their state space a finite subset of the $m$-dimensional lattice and for which the $m$ matrices that record the transition probabilities in each of the lattice directions commute pairwise. One reason such processes are of interest is that the transition matrix is straightforward to diagonalize, and hence it is easy to compute $n$ step transition probabilities. The set of commuting birth-and-death processes decomposes as a union of toric varieties, with the main component bein…
