Gr\"obner Bases of Neural Ideals

TL;DR

This paper explores the relationship between canonical forms and Gr"obner bases of neural ideals, revealing conditions under which the canonical form is a universal Gr"obner basis and its implications for understanding neural receptive fields.

Contribution

It establishes a connection between canonical forms and Gr"obner bases of neural ideals, providing criteria for when the canonical form is a universal Gr"obner basis and exploring its biological significance.

Findings

Canonical form equals the universal Gr"obner basis when it consists solely of pseudo-monomials.

The universal Gr"obner basis contains only pseudo-monomials precisely when the canonical form is a Gr"obner basis.

Partial answers are provided for when the canonical form is a Gr"obner basis and the implications of non-pseudo-monomial elements.

Abstract

The brain processes information about the environment via neural codes. The neural ideal was introduced recently as an algebraic object that can be used to better understand the combinatorial structure of neural codes. Every neural ideal has a particular generating set, called the canonical form, that directly encodes a minimal description of the receptive field structure intrinsic to the neural code. On the other hand, for a given monomial order, any polynomial ideal is also generated by its unique (reduced) Gr\"obner basis with respect to that monomial order. How are these two types of generating sets -- canonical forms and Gr\"obner bases -- related? Our main result states that if the canonical form of a neural ideal is a Gr\"obner basis, then it is the universal Gr\"obner basis (that is, the union of all reduced Gr\"obner bases). Furthermore, we prove that this situation -- when the canonical form is a Gr\"obner basis -- occurs precisely when the universal Gr\"obner basis contains only pseudo-monomials (certain generalizations of monomials). Our results motivate two questions: (1)~When is the canonical form a Gr\"obner basis? (2)~When the universal Gr\"obner basis of a neural ideal is {\em not} a canonical form, what can the non-pseudo-monomial elements in the basis tell us about the receptive fields of the code? We give partial answers to both questions. Along the way, we develop a representation of pseudo-monomials as hypercubes in a Boolean lattice.