Efficiently computing Groebner bases of ideals of points

ACM Communications in Computer Algebra, 2006

A contemporary and exciting application of Gröbner 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. Gröbner 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 Gröbner 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 Gröbner bases of zero-dimensional ideals that is optimized for the ca...

Arxiv preprint arXiv:1101.3589, 2011

This paper describes a Buchberger-style algorithm to compute a Gröbner 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.

SIAM Journal on Discrete Mathematics, 2016

Chordal structure and bounded treewidth allow for efficient computation in numerical linear algebra, graphical models, constraint satisfaction, and many other areas. In this paper, we begin the study of how to exploit chordal structure in computational algebraic geometry-in particular, for solving polynomial systems. The structure of a system of polynomial equations can be described in terms of a graph. By carefully exploiting the properties of this graph (in particular, its chordal completions), more efficient algorithms can be developed. To this end, we develop a new technique, which we refer to as chordal elimination, that relies on elimination theory and Gröbner bases. By maintaining graph structure throughout the process, chordal elimination can outperform standard Gröbner bases algorithms in many cases. The reason is because all computations are done on "smaller" rings of size equal to the treewidth of the graph (instead of the total number of variables). In particular, for a restricted class of ideals, the computational complexity is linear in the number of variables. Chordal structure arises in many relevant applications. We demonstrate the suitability of our methods in examples from graph colorings, cryptography, sensor localization, and differential equations.

Proceedings of the 1993 international symposium on Symbolic and algebraic computation - ISSAC '93, 1993

2007

In the computation of Groebner bases using Buchberger's Algorithm, a key issue for improving the efficiency is to create techniques to help us avoid as many unnecessary pairs of polynomials from the non-computed set of pairs as possible. A good solution would be to avoid those pairs that can be easily ignored without computing their S-polynomials, and hence to process only on the set of pairs of generators of the module generated by syzygies. This paper details an improvment of Buchberger's Algorithm for computing Groebner bases by defining the module of solutions of a homogeneous linear equation with polynomial coefficients (called the syzygy module). As a consequence, we use these syzygy modules to give another equivalent condition for a set to be a Groebner basis for an ideal. As a result we demonastrate that this new condition can significantly improve the Buchberger's Algorithm to compute Groebner bases.

HAL (Le Centre pour la Communication Scientifique Directe), 2022

Journal of Symbolic Computation, 2011

We construct an explicit minimal strong Gröbner 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 Gröbner basis is independent of the monomial order and that the set of leading terms of the constructed Gröbner 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 Gröbner basis in Z/m[x1, x2, . . . , xn] along the prime factorization of m. The obtained results are not only of mathematical interest but have immediate applications in formal verification of data paths for microelectronic systems-on-chip.

1993

Almost every Computer Algebra System contains some implementation of the Gr obner bases algorithm. The present implementation has the following speci c features:

Advances in Applied Mathematics, 2003

We provide a polynomial time algorithm for computing the universal Gröbner basis of any polynomial ideal having a finite set of common zeros in fixed number of variables. One ingredient of our algorithm is an effective construction of the state polyhedron of any member of the Hilbert scheme Hilb d n of n-long d-variate ideals, enabled by introducing the Hilbert zonotope H d n and showing that it simultaneously refines all state polyhedra of ideals on Hilb d n .

2007

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 obtained results are not only of mathematical interest but have immediate applications in formal verification of data paths for microelectronic systems-on-chip.