Gröbner bases of neural ideals

DOI10.1142/S0218196718500261zbMATH Open1395.92013arXiv1612.05660OpenAlexW2963289040MaRDI QIDQ4576004FDOQ4576004

Ethan Petersen, R. E. Garcia, Jessica Liu, Kaitlyn Phillipson, Luis David Garcia Puente, Ryan Kruse, Anne Shiu, Dane Miyata

Publication date: 12 July 2018

Published in: International Journal of Algebra and Computation (Search for Journal in Brave)

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.

Full work available at URL: https://arxiv.org/abs/1612.05660

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zbMATH Keywords

receptive fieldcanonical formBoolean latticeneural codeGröbner basis

Mathematics Subject Classification ID

Symbolic computation and algebraic computation (68W30) Applications of commutative algebra (e.g., to statistics, control theory, optimization, etc.) (13P25) Mathematical biology in general (92B99)

Cites Work

• Polybori: A framework for Gröbner-basis computations with Boolean polynomials
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Cited In (12)

• Gröbner Bases of Convex Neural Code Ideals (Research)
• Geometric characterization of data sets with unique reduced Gröbner bases
• Small Gröbner fans of ideals of points
• Open, closed, and non-degenerate embedding dimensions of neural codes
• Hyperplane Neural Codes and the Polar Complex
• Polarization of neural rings
• Homomorphisms preserving neural ideals
• Nondegenerate Neural Codes and Obstructions to Closed-Convexity
• Neural Codes, Decidability, and a New Local Obstruction to Convexity
• Embedding dimension phenomena in intersection complete codes
• Neural codes and the factor complex
• The case for algebraic biology: from research to education

Uses Software

• PolyBoRi
• SageMath
• neural ideal

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