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Register a new userEfficiently computing Groebner bases of ideals of points
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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-Moeller algorithm if the number of indeterminates is much larger than the number of points. Comparison of implementations of our algorithm and the standard Buchberger-Moeller algorithm in Macaulay 2 confirm the theoretically predicted speedup. This work is motivated by recent applications of Groebner bases to the problem of network reconstruction in molecular biology.
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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.
In this paper we consider the problem of computing all possible order ideals and also sets connected to 1, and the corresponding border bases, for the vanishing ideal of a given finite set of points. In this context two different approaches are discussed: based on the Buchberger-Moller Algorithm, we first propose a new algorithm to compute all possible order ideals and the corresponding border bases for an ideal of points. The second approach involves adapting the Farr-Gao Algorithm for finding all sets connected to 1, as well as the corresponding border bases, for an ideal of points. It should be noted that our algorithms are term ordering free. Therefore they can compute successfully all border bases for an ideal of points. Both proposed algorithms have been implemented and their efficiency is discussed via a set of benchmarks.
In the context of modeling biological systems, it is of interest to generate ideals of points with a unique reduced Groebner basis, and the first main goal of this paper is to identify classes of ideals in polynomial rings which share this property. Moreover, we provide methodologies for constructing such ideals. We then relax the condition of uniqueness. The second and most relevant topic discussed here is to consider and identify pairs of ideals with the same number of reduced Groebner bases, that is, with the same cardinality of their associated Groebner fan.
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.
Let $X$ be a set of points whose coordinates are known with limited accuracy; our aim is to give a characterization of the vanishing ideal $I(X)$ independent of the data uncertainty. We present a method to compute a polynomial basis $B$ of $I(X)$ which exhibits structural stability, that is, if $widetilde X$ is any set of points differing only slightly from $X$, there exists a polynomial set $widetilde B$ structurally similar to $B$, which is a basis of the perturbed ideal $ I(widetilde X)$.
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