A sparse reformulation of the Green's function formalism allows efficient simulations of morphological neuron models

DOI10.1162/NECO_A_00788zbMATH Open1414.92129arXiv1504.03746WikidataQ50208103 ScholiaQ50208103MaRDI QIDQ5380356FDOQ5380356

Authors: Willem A. M. Wybo, Daniele Boccalini, Benjamin Torben-Nielsen, Marc-Oliver Gewaltig 

Publication date: 4 June 2019

Published in: Neural Computation (Search for Journal in Brave)

Abstract: We prove that when a class of partial differential equations, generalized from the cable equation, is defined on tree graphs, and when the inputs are restricted to a spatially discrete, well chosen set of points, the Green's function (GF) formalism can be rewritten to scale as $O(n)$ with the number $n$ of input locations, contrary to the previously reported $O(n^2)$ scaling. We show that the linear scaling can be combined with an expansion of the remaining kernels as sums of exponentials, to allow efficient simulations of equations from the aforementioned class. We furthermore validate this simulation paradigm on models of nerve cells and explore its relation with more traditional finite difference approaches. Situations in which a gain in computational performance is expected, are discussed.

Full work available at URL: https://arxiv.org/abs/1504.03746

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zbMATH Keywords

Green's function reformulationmorphological neuron models

Mathematics Subject Classification ID

Neural biology (92C20)

Cites Work

• Introduction to Theoretical Neurobiology
• The path integral for dendritic trees
• Computational convergence of the path integral for real dendritic morphologies
• Branching dendrites with resonant membrane: a ``sum-over-trips approach
• Fast Convolution for Nonreflecting Boundary Conditions
• Title not available (Why is that?)
• Exact digital simulation of time-invariant linear systems with applications to neuronal modeling
• The Green's function formalism as a bridge between single- and multi-compartmental modeling

Cited In (2)

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• Computational convergence of the path integral for real dendritic morphologies

Uses Software

• NEURON

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