Neural ideals in SageMath

DOI10.1007/978-3-319-96418-8_22zbMATH Open1395.68351arXiv1609.09602OpenAlexW2963052859MaRDI QIDQ1662229FDOQ1662229

Dane Miyata, Luis David Garcia Puente, Ethan Petersen, Ryan Kruse, Nora Youngs, R. E. Garcia

Publication date: 17 August 2018

Abstract: A major area in neuroscience research is the study of how the brain processes spatial information. Neurons in the brain represent external stimuli via neural codes. These codes often arise from stereotyped stimulus-response maps, associating to each neuron a convex receptive field. An important problem consists in determining what stimulus space features can be extracted directly from a neural code. The neural ideal is an algebraic object that encodes the full combinatorial data of a neural code. This ideal can be expressed in a canonical form that directly translates to a minimal description of the receptive field structure intrinsic to the code. In here, we describe a SageMath package that contains several algorithms related to the canonical form of a neural ideal.

Full work available at URL: https://arxiv.org/abs/1609.09602

zbMATH Keywords

canonical formneural codesneural ringneural ideal

Mathematics Subject Classification ID

Symbolic computation and algebraic computation (68W30) Neural biology (92C20) Applications of commutative algebra (e.g., to statistics, control theory, optimization, etc.) (13P25)

Cited In (17)

• Gröbner Bases of Convex Neural Code Ideals (Research)
• Canonical forms of neural ideals
• On the $8$ case of the Sylvester conjecture
• Homomorphisms preserving neural ideals
• Nondegenerate Neural Codes and Obstructions to Closed-Convexity
• An efficient lattice reduction using reuse technique blockwisely on NTRU
• Periodic neural codes and sound localization in barn owls
• neural ideal
• Diameter of io-decomposable Riordan graphs of the Bell type
• A Note On a Prey-Predator Model with Constant-Effort Harvesting
• Triameter of graphs
• Neural codes and the factor complex
• Harmonic index designs in binary Hamming schemes
• Algebraic signatures of convex and non-convex codes
• Gröbner bases of neural ideals
• The case for algebraic biology: from research to education
• On spherical designs of some harmonic indices

Uses Software

• SageMath

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