A contemporary and exciting application of Groebner bases is their use in computational biology, particularly in the reverse engineering of gene regulatory networks from experimental data. In this setting, the data are typically limited to tens of points, while the number of genes or variables is potentially in the thousands. As such data sets vastly underdetermine the biological network, many models may fit the same data and reverse engineering programs often require the use of methods for choosing parsimonious models. Grobner bases have recently been employed as a selection tool for polynomial dynamical systems that are characterized by maps in a vector space over a finite field.
While there are numerous existing algorithms to compute Groebner bases, to date none has been specifically designed to cope with large numbers of variables and few distinct data points. In this paper, we present an algorithm for computing Grobner bases of zero-dimensional ideals that is optimized for the case when the number m of points is much smaller than the number n of indeterminates. The algorithm identifies those variables that are essential, that is, in the support of the standard monomials associated to a polynomial ideal, and computes the relations in the Groebner bases in terms of these variables. When n is much larger than m, the complexity is dominated by nm^3. The algorithm has been implemented and tested in the computer algebra system Macaulay 2. We provide a comparison of its performance to the Buchberger-Moeller algorithm, as built into the system.
We determine a Groebner basis for the secant ideal of the toric ideal associated to the second hypersimplex, with respect to any circular term order. The Groebner basis of the secant ideal requires polynomials of odd degree up to n. This shows that the circular term order is 2-delightful, resolving a conjecture of Drton, Sturmfels, and the author. The proof uses Groebner degenerations for secant ideals, combinatorial characterizations of the secant ideals of monomial ideals, and the relations between secant ideals and prolongations.
In this article we produce Groebner bases for the defining ideal of a monomial curve that corresponds to an almost arithmetic sequence of positive integers, correcting previous work of Sengupta,(2003).
We give an introduction to the theory of determinantal ideals and rings, their Groebner bases, initial ideals and algebras, respectively. The approach is based on the straightening law and the Knuth-Robinson-Schensted correspondence. The article contains a section treating the basic results about the passage to initial ideals and algebras.
We describe the universal Groebner basis of the ideal of maximal minors and the ideal of $2$-minors of a multigraded matrix of linear forms. Our results imply that the ideals are radical and provide bounds on the regularity. In particular, the ideals of maximal minors have linear resolutions. Our main theoretical contribution consists of introducing two new classes of ideals named after Cartwright and Sturmfels, and proving that they are closed under multigraded hyperplane sections. The gins of the ideals that we study enjoy special properties.
In this article we present two new algorithms to compute the Groebner basis of an ideal that is invariant under certain permutations of the ring variables and which are both implemented in SINGULAR (cf. [DGPS12]). The first and major algorithm is most performant over finite fields whereas the second algorithm is a probabilistic modification of the modular computation of Groebner bases based on the articles by Arnold (cf. [A03]), Idrees, Pfister, Steidel (cf. [IPS11]) and Noro, Yokoyama (cf. [NY12], [Y12]). In fact, the first algorithm that mainly uses the given symmetry, improves the necessary…
In this paper we consider Hibi rings and Rees rings attached to a poset. We classify the ideal lattices of posets whose Hibi relations are indispensable and the ideal lattices of posets whose Hibi relations form a quadratic Groebner basis with respect to the rank lexicographic order. Similar classifications are obtained for Rees rings of Hibi ideals.
We present an algorithm for computing Groebner bases of vanishing ideals of points that is optimized for the case when the number of points in the associated variety is less than the number of indeterminates. The algorithm first identifies a set of essential variables, which reduces the time complexity with respect to the number of indeterminates, and then uses PLU decompositions to reduce the time complexity with respect to the number of points. This gives a theoretical upper bound for its time complexity that is an order of magnitude lower than the known one for the standard Buchberger-Moell…
We outline a generalization of the Groebner fan of a homogeneous ideal with maximal cells parametrizing truncated Groebner bases. This "truncated" Groebner fan is usually much smaller than the full Groebner fan and offers the natural framework for conversion between truncated Groebner bases. The generic Groebner walk generalizes naturally to this setting by using the Buchberger algorithm with truncation on facets. We specialize to the setting of lattice ideals. Here facets along the generic walk are given by unique (facet) binomials. This along with the representation of binomials as integer v…
Previous work by Mora and Sala provides the reduced Groebner basis of the ideal formed by the elementary symmetric polynomials in $n$ variables of degrees $k=1,\dots,n$, $\langle e_{1,n}(x), \dots, e_{n,n}(x) \rangle$. Haglund, Rhoades, and Shimonozo expand upon this, finding the reduced Groebner basis of the ideal of elementary symmetric polynomials in $n$ variables of degree $d$ for $d=n-k+1,\dots,n$ for $k\leq n$. In this paper, we further generalize their findings by using symbolic computation and experimentation to construct the reduced Groebner basis for the ideal generated by the elemen…
In this paper we introduce a new and large family of configurations whose toric ideals possess quadratic Groebner bases. As an application, a generalization of algebras of Segre-Veronese type will be studied.
The paper has two goals: the study the associated graded ring of contracted homogeneous ideals in $K[x,y]$ and the study of the Groebner fan of the ideal $P$ of the rational normal curve in ${\bf P}^d$. These two problems are, quite surprisingly, very tightly related. We completely classify the contracted ideals with a Cohen-Macaulay associated graded rings in terms of the numerical invariants arising from Zariski's factorization. We determine explicitly all the initial ideals (monomial or not) of $P$ that are Cohen-Macaulay.
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 motivation for developing this theory is to prove finiteness theorems in commutative algebra and its applications. A major result of this type is that ideals in infinitely many indeterminates stable under the action of the symmetric group are finitely generated up to symmetry. We use this machinery to give new proofs of some classical finiteness theorems in algebra…
In this paper we study homological properties of the Rees ring R of the graded maximal ideal of a standard graded k-algebra A. In particular we are interested the comparison of the depth and regularity of A and R.
We develop the theory of Gröbner 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 algorithm.
Let $I\subseteq S=K[x_1,\ldots,x_n]$ be a homogeneous ideal equipped with a monomial order $<$. We show that if $\operatorname{in}_<(I)$ is a square-free monomial ideal, then $S/I$ and $S/\operatorname{in}_<(I)$ have the same connectedness dimension. We also show that graphs related to connectedness of these quotient rings have the same number of components. We also provide consequences regarding Lyubeznik numbers. We obtain these results by furthering the study of connectedness modulo a parameter in a local ring.
We construct an explicit minimal strong Groebner basis of the ideal of vanishing polynomials in the polynomial ring over Z/m for m>=2. The proof is done in a purely combinatorial way. It is a remarkable fact that the constructed Groebner basis is independent of the monomial order and that the set of leading terms of the constructed Groebner basis is unique, up to multiplication by units. We also present a fast algorithm to compute reduced normal forms, and furthermore, we give a recursive algorithm for building a Groebner basis in Z/m[x_1,x_2,...,x_n] along the prime factorization of m. The ob…
Classically, Groebner bases are computed by first prescribing a set monomial order. Moss Sweedler suggested an alternative and developed a framework to perform such computations by using valuation rings in place of monomial orders. We build on these ideas by providing a class of valuations on rational function fields of two variables that are suitable for this framework. For these valuations, we explicitly compute the image of an underlying polynomial ring and use this to perform computations concerning ideals in the polynomial ring. Interestingly, for these valuations, some ideals have a fini…
Hara, Takemura and Yoshida discuss toric ideals arising from two way subtable sum problems and shows that these toric ideals are generated by quadratic binomials if and only if the subtables are either diagonal or triangular. In the present paper, we show that if the subtables are either diagonal or triangular, then their toric ideals possess quadratic Groebner bases.
This paper presents algorithms for computing the Groebner fan of an arbitrary polynomial ideal. The computation involves enumeration of all reduced Groebner bases of the ideal. Our algorithms are based on a uniform definition of the Groebner fan that applies to both homogeneous and non-homogeneous ideals and a proof that this object is a polyhedral complex. We show that the cells of a Groebner fan can easily be oriented acyclically and with a unique sink, allowing their enumeration by the memory-less reverse search procedure. The significance of this follows from the fact that Groebner fans ar…
The Groebner fan of an ideal $I\subset k[x_1,...,x_n]$, defined by Mora and Robbiano, is a complex of polyhedral cones in $R^n$. The maximal cones of the fan are in bijection with the distinct monomial initial ideals of $I$ as the term order varies. If $I$ is homogeneous the Groebner fan is complete and is the normal fan of the state polytope of $I$. In general the Groebner fan is not complete and therefore not the normal fan of a polytope. We may ask if the restricted Groebner fan, a subdivision of $R_{>=0}^n$, is regular i.e. the normal fan of a polyhedron. The main result of this paper is a…
Let K be a field with a valuation and let S be the polynomial ring S:= K[x_1,..., x_n]. We discuss the extension of Groebner theory to ideals in S, taking the valuations of coefficients into account, and describe the Buchberger algorithm in this context. In addition we discuss some implementation and complexity issues. The main motivation comes from tropical geometry, as tropical varieties can be defined using these Groebner bases, but we also give examples showing that the resulting Groebner bases can be substantially smaller than traditional Groebner bases. In the case K = Q with the p-adic …
The toric ideals of $3\times 3$ transportation polytopes $T$ are quadratically generated. The only exception is the Birkhoff polytope $B_3$. If $T$ is not a multiple of $B_3$, these ideals even have squarefree quadratic initial ideals. This class contains all smooth $3 \times 3$ transportation polytopes.
Hilbert schemes of zero-dimensional ideals in a polynomial ring can be covered with suitable affine open subschemes whose construction is achieved using border bases. Moreover, border bases have proved to be an excellent tool for describing zero-dimensional ideals when the coefficients are inexact. And in this situation they show a clear advantage with respect to Groebner bases which, nevertheless, can also be used in the study of Hilbert schemes, since they provide tools for constructing suitable stratifications. In this paper we compare Groebner basis schemes with border basis schemes. It is…
In this paper, we give a sufficient condition for a set $\mathal G$ of polynomials to be a Gröbner basis with respect to a given term-order for the ideal $I$ that it generates. Our criterion depends on the linkage pattern of the ideal $I$ and of the ideal generated by the initial terms of the elements of $\mathcal G$. We then apply this criterion to ideals generated by minors and pfaffians. More precisely, we consider large families of ideals generated by minors or pfaffians in a matrix or a ladder, where the size of the minors or pfaffians is allowed to vary in different regions of the matrix…
In 1992, V. Weispfenning proved the existence of Comprehensive Groebner Bases (CGB) and gave an algorithm to compute one. That algorithm was not very efficient and not canonical. Using his suggestions, A. Montes obtained in 2002 a more efficient algorithm (DISPGB) for Discussing Parametric Groebner Bases. Inspired in its philosophy, V. Weispfenning defined, in 2002, how to obtain a Canonical Comprehensive Groebner Basis (CCGB) for parametric polynomial ideals, and provided a constructive method. In this paper we use Weispfenning's CCGB ideas to make substantial improvements on Montes DISPGB al…
This is the continuation of Montes' paper "On the canonical discussion of polynomial systems with parameters". In this paper we define the Minimal Canonical Comprehensive Groebner System (MCCGS) of a parametric ideal and fix under which hypothesis it exists and is computable. An algorithm to obtain a canonical description of the segments of the MCCGS is given, completing so the whole MCCGS algorithm (implemented in Maple). We show its high utility for applications, like automatic theorem proving and discovering, and compare it with other existing methods. A way to detect a counterexample is ou…
In the first part of this article, we consider a Groebner basis of the differential ideal {x_1^2} with respect to "the" weighted lexicographical monomial order and show that its computation is related with an identity involving the partitions that appear in the first Rogers-Ramanujan identity. We then prove that a Grobener basis of this ideal is not differentially finite in contrary with the case of "the" weighted reverse lexicographical order. In the second part, we give a simple and direct proof of a theorem of Nguyen Duc Tam about the Groaner basis of the differential ideal {x_1y_1}; we the…
Let I be a homogeneous ideal of a polynomial ring S. We prove that if the initial ideal J of I, w.r.t. a term order on S, is square-free, then the extremal Betti numbers of S/I and of S/J coincide. In particular, depth(S/I)=depth(S/J) and reg(S/I)=reg(S/J).
Given a finite set $\mathbf{X}$ of distinct points, Marinari-Mora's 'Axis of Evil Theorem' states that a combinatorial algorithm and interpolation enable to find a 'linear' factorization for a lexicographical minimal Groebner basis $\mathcal{G}(I(\mathbf{X}))$ of the zerodimensional radical ideal $I(\mathbf{X})$. In this work we provide such algorithm, showing that it ends in a finite number of steps and that it actually provides the correct result. The 'Axis of Evil' algorithm takes as input the monomial basis of the initial ideal $T(I(\mathbf{X}))$ but its starting point is the (finite) Groe…
We introduce the notion of monomial group action and study some of its consequences for Groebner basis theory. As an application we prove a conjecture of V. Batyrev and O. Popov describing the Cox rings of Del Pezzo surfaces (of degree at least 3) as quotients of a polynomial ring by an ideal generated by quadrics.
This paper is an outcome of the author's master thesis written under the supervision of Aldo Conca. We prove some results relating connectedness properties with (local) cohomological dimension. As an interesting corollary we have that every initial complex of a Cohen-Macaulay ideal is strongly connected.
The aim of this note is to discuss the following quite queer Problem: \noindent GIVEN \noindent i) the free non-commutative polynomial ring, ${\Cal P} := {\Bbb F}\langle X_1,\ldots,X_n\rangle$ {\em (public)}, \noindent ii) a bilateral ideal ${\sf I}\subset {\Bbb F}\langle X_1,\ldots,X_n\rangle$ {\em (private)}, \noindent iii) a finite set $G := \{g_1,\ldots,g_l\}\subset{\sf I}$ of elements of the ideal ${\sf I}$ {\em (public)}, \noindent a noetherian semigroup term-ordering $\prec,$ {\rm (private)}, on the word semigroup ${\Cal T} := < X_1,\ldots,X_n>$, \noindent COMPUTE \noindent --a finite s…
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.
A set of polynomials G in a polynomial ring S over a field is said to be a universal Groebner basis, if G is a Groebner basis with respect to every term order on S. Twenty years ago Bernstein, Sturmfels, and Zelevinsky proved that the set of the maximal minors of a matrix X of variables is a universal Groebner basis. Boocher recently proved that any initial ideal of the ideal of maximal minors of X has a linear resolution. In this paper we give a quick proof of the results mentioned above. Our proof is based on a specialization argument. Then we show that similar statements hold in a more g…
The purpose of this paper is twofold. In the first part we concentrate on hyperplane sections of algebraic schemes, and present results for determining when Gröbner bases pass to the quotient and when they can be lifted. The main difficulty to overcome is the fact that we deal with non-homogeneous ideals. As a by-product we hint at a promising technique for computing implicitization efficiently. In the second part of the paper we deal with families of algebraic schemes and the Hough transforms, in particular we compute their dimension, and show that in some interesting cases it is zero. Then w…
The interpolation step of Guruswami and Sudan's list decoding of Reed-Solomon codes poses the problem of finding the minimal polynomial of an ideal with respect to a certain monomial order. An efficient algorithm that solves the problem is presented based on the theory of Groebner bases of modules. In a special case, this algorithm reduces to a simple Berlekamp-Massey-like decoding algorithm.
In 1990 Cerlienco and Mureddu gave a combinatorial iterative algorithm which, given an ordered set of points, returns the lexicographical Groebner escalier of the ideal of these points. There are many alternatives to this algorithm and in particular, the most efficient is the Lex Game, which is not iterative on the points, but its performances are definitely better. In this paper, we develop an iterative alternative to Lex Game algorithm, whose performances are very near to those of the original Lex Game, by means of the Bar Code, a diagram which allows to keep track of information on the poin…
This paper describes a Buchberger-style algorithm to compute a Groebner basis of a polynomial ideal, allowing for a selection strategy based on "signatures". We explain how three recent algorithms can be viewed as different strategies for the new algorithm, and how other selection strategies can be formulated. We describe a fourth as an example. We analyze the strategies both theoretically and empirically, leading to some surprising results.
In this paper we describe an efficient involutive algorithm for constructing Groebner bases of polynomial ideals. The algorithm is based on the concept of involutive monomial division which restricts the conventional division in a certain way. In the presented algorithm a reduced Groebner basis is the internally fixed subset of an involutive basis, and having computed the later, the former can be output without any extra computational costs. We also discuss some accounts of experimental superiority of the involutive algorithm over Buchberger's algorithm.
Let $I$ be an ideal of the polynomial ring $A[x]=A[x_1,...,x_n]$ over the commutative, noetherian ring $A$. Geometrically $I$ defines a family of affine schemes over $\Spec(A)$: For $\p\in\Spec(A)$, the fibre over $\p$ is the closed subscheme of affine space over the residue field $k(\p)$, which is determined by the extension of $I$ under the canonical map $σ_\p:A[x]\to k(\p)[x]$. If $I$ is homogeneous there is an analogous projective setting, but again the ideal defining the fibre is $\sigI$. For a chosen term order this ideal has a unique reduced Gröbner basis which is known to contain consi…
A topological space TO(S) of total orderings on any given set S is introduced and it is shown that TO(S) is compact if S is countable. The set NO(N) of all normal orderings of the nth Weyl algebra W is a closed subspace of TO(N), where N is the set of all normal monomials of W. Hence NO(N) is compact and, as a consequence of this fact and by a division theorem valid in W, we give a proof that each left ideal of W admits a universal Groebner basis.
The Groebner walk is an algorithm for conversion between Groebner bases for different term orders. It is based on the polyhedral geometry of the Groebner fan and involves tracking a line between cones representing the initial and target term order. An important parameter is explicit numerical perturbation of this line. This usually involves both time and space demanding arithmetic of integers much larger than the input numbers. In this paper we show how the explicit line may be replaced by a formal line using Robbiano's characterization of group orders on Q^n. This gives rise to the generic Gr…
We present here an overview of the hypermatrix spectral decomposition deduced from the Bhattacharya-Mesner hypermatrix algebra. We describe necessary and sufficient conditions for the existence of a spectral decomposition. We further extend to hypermatrices the notion of resolution of identity and use them to derive hypermatrix analog of matrix spectral bounds. Finally we describe an algorithm for computing generators of the spectral elimination ideals which considerably improves on Groebner basis computation suggested in.
Two fundamental questions in the theory of Groebner bases are decision ("Is a basis G of a polynomial ideal a Groebner basis?") and transformation ("If it is not, how do we transform it into a Groebner basis?") This paper considers the first question. It is well-known that G is a Groebner basis if and only if a certain set of polynomials (the S-polynomials) satisfy a certain property. In general there are m(m-1)/2 of these, where m is the number of polynomials in G, but criteria due to Buchberger and others often allow one to consider a smaller number. This paper presents two original results.…
In this paper we describe how an idea centered on the concept of self-saturation allows several improvements in the computation of Groebner bases via Buchberger's Algorithm.
We consider the Rosenfeld-Groebner algorithm for computing a regular decomposition of a radical differential ideal generated by a set of ordinary differential polynomials in n indeterminates. For a set of ordinary differential polynomials F, let M(F) be the sum of maximal orders of differential indeterminates occurring in F. We propose a modification of the Rosenfeld-Groebner algorithm, in which for every intermediate polynomial system F, the bound M(F) is less than or equal to (n-1)!M(G), where G is the initial set of generators of the radical ideal. In particular, the resulting regular syste…
The aim of this note is to present an easy proof of Hilbert's Nullstellensatz using Groebner basis. I believe, that the proof has some methodical advantage in a course on Groebner bases. Key words: Hilbert's Nullstellensatz, Groebner bases.
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 present algorithms on how the latter can be computed in finite time, provided that generators are polynomial in t. While doing so, we also comment on the computation of the Groebner polytope structure and p-adic Groebner bases using our framework. All algorithms solely rely on existing standard basis techniques.
This paper presents an algorithm for computing Groebner bases based upon labeled polynomials and ideas from the algorithm F5. The main highlights of this algorithm compared with analogues are simplicity both of the algorithm and of the its correctness proof achieved without loss of the efficiency. This leads to simple implementation which performance is in par with more complex analogues
In this paper we present an improved version of HF-hash, viz., GB-hash : Hash Functions Using Groebner Basis. In case of HF-hash, the compression function consists of 32 polynomials with 64 variables which were taken from the first 32 polynomials of hidden field equations challenge-1 by forcing last 16 variables as 0. In GB-hash we have designed the compression function in such way that these 32 polynomials with 64 variables form a minimal Groebner basis of the ideal generated by them with respect to graded lexicographical (grlex) ordering as well as with respect to graded reverse lexicographi…
In this paper we describe a combination of ideas to improve incremental signature-based Groebner basis algorithms having a big impact on their performance. Besides explaining how to combine already known optimizations to achieve more efficient algorithms, we compare the quite different effects on the two best-known algorithms in this area, F5 and G2V, both from a theoretical and a practical point of view.
Let T(x) in k[x] be a monic non-constant polynomial and write R=k[x] / (T) the quotient ring. Consider two bivariate polynomials a(x, y), b(x, y) in R[y]. In a first part, T = p^e is assumed to be the power of an irreducible polynomial p. A new algorithm that computes a minimal lexicographic Groebner basis of the ideal ( a, b, p^e), is introduced. A second part extends this algorithm when T is general through the "local/global" principle realized by a generalization of "dynamic evaluation", restricted so far to a polynomial T that is squarefree. The algorithm produces splittings according to t…
In this paper, we consider parametric ideals and introduce a notion of comprehensive involutive system. This notion plays the same role in theory of involutive bases as the notion of comprehensive Groebner system in theory of Groebner bases. Given a parametric ideal, the space of parameters is decomposed into a finite set of cells. Each cell yields the corresponding involutive basis of the ideal for the values of parameters in that cell. Using the Gerdt-Blinkov algorithm for computing involutive bases and also the Montes algorithm for computing comprehensive Groebner systems, we present an alg…
The first sections contain a survey of the application of the Knuth-Robinson-Schensted corerspondence to the computation of Groebner bases of determinantal ideals. We also set up a conceptual framework for this application in terms of so-called "KRS invariants". Then we show that the initial ideal of a determinantal ideal "defined by shape" is given by its KRS image. We furthermore characterize those among these ideals that even have a Groebner basis of products of minors, and show that they can be characterized in terms of Greene's KRS invariants. Furthermore it is shown that for the ideal ge…
We present foundational work on standard bases over rings and on Boolean Groebner bases in the framework of Boolean functions. The research was motivated by our collaboration with electrical engineers and computer scientists on problems arising from formal verification of digital circuits. In fact, algebraic modelling of formal verification problems is developed on the word-level as well as on the bit-level. The word-level model leads to Groebner basis in the polynomial ring over Z/2n while the bit-level model leads to Boolean Groebner bases. In addition to the theoretical foundations of both …
