A Novel Multiple Objective Optimization Framework for Constraining Conductance-Based Neuron Models by Experimental Data

We present a novel framework for automatically constraining parameters of compartmental models of neurons, given a large set of experimentally measured responses of these neurons. In experiments, intrinsic noise gives rise to a large variability (e.g., in firing pattern) in the voltage responses to repetitions of the exact same input. Thus, the common approach of fitting models by attempting to perfectly replicate, point by point, a single chosen trace out of the spectrum of variable responses does not seem to do justice to the data. In addition, finding a single error function that faithfully characterizes the distance between two spiking traces is not a trivial pursuit. To address these issues, one can adopt a multiple objective optimization approach that allows the use of several error functions jointly. When more than one error function is available, the comparison between experimental voltage traces and model response can be performed on the basis of individual features of interest (e.g., spike rate, spike width). Each feature can be compared between model and experimental mean, in units of its experimental variability, thereby incorporating into the fitting this variability. We demonstrate the success of this approach, when used in conjunction with genetic algorithm optimization, in generating an excellent fit between model behavior and the firing pattern of two distinct electrical classes of cortical interneurons, accommodating and fast-spiking. We argue that the multiple, diverse models generated by this method could serve as the building blocks for the realistic simulation of large neuronal networks.

[1]  Kalyanmoy Deb,et al.  Multi-objective optimization using evolutionary algorithms , 2001, Wiley-Interscience series in systems and optimization.

[2]  J. Bower,et al.  An active membrane model of the cerebellar Purkinje cell. I. Simulation of current clamps in slice. , 1994, Journal of neurophysiology.

[3]  J M Bekkers,et al.  Properties of voltage‐gated potassium currents in nucleated patches from large layer 5 cortical pyramidal neurons of the rat , 2000, The Journal of physiology.

[4]  Kalyanmoy Deb,et al.  A fast and elitist multiobjective genetic algorithm: NSGA-II , 2002, IEEE Trans. Evol. Comput..

[5]  Eve Marder,et al.  Structure and visualization of high-dimensional conductance spaces. , 2006, Journal of neurophysiology.

[6]  Kalyanmoy Deb,et al.  Simulated Binary Crossover for Continuous Search Space , 1995, Complex Syst..

[7]  J. Victor,et al.  Nature and precision of temporal coding in visual cortex: a metric-space analysis. , 1996, Journal of neurophysiology.

[8]  Maria V. Sanchez-Vives,et al.  Influence of low and high frequency inputs on spike timing in visual cortical neurons. , 1997, Cerebral cortex.

[9]  E. Marder,et al.  Similar network activity from disparate circuit parameters , 2004, Nature Neuroscience.

[10]  F. A. Seiler,et al.  Numerical Recipes in C: The Art of Scientific Computing , 1989 .

[11]  Shigeru Shinomoto,et al.  Differences in Spiking Patterns Among Cortical Neurons , 2003, Neural Computation.

[12]  A. Alonso,et al.  Biophysical Properties and Slow Voltage-Dependent Inactivation of a Sustained Sodium Current in Entorhinal Cortex Layer-II Principal Neurons , 1999, The Journal of general physiology.

[13]  Fiona E. N. LeBeau,et al.  Single-column thalamocortical network model exhibiting gamma oscillations, sleep spindles, and epileptogenic bursts. , 2005, Journal of neurophysiology.

[14]  G. Stuart,et al.  Single Ih Channels in Pyramidal Neuron Dendrites: Properties, Distribution, and Impact on Action Potential Output , 2006, The Journal of Neuroscience.

[15]  Eve Marder,et al.  The dynamic clamp comes of age , 2004, Trends in Neurosciences.

[16]  Roger D. Traub,et al.  Self-Organized Synaptic Plasticity Contributes to the Shaping of γ and β Oscillations In Vitro , 2001, The Journal of Neuroscience.

[17]  R. Traub,et al.  Self-organized synaptic plasticity contributes to the shaping of gamma and beta oscillations in vitro. , 2001, The Journal of neuroscience : the official journal of the Society for Neuroscience.

[18]  Jean-Marc Goaillard,et al.  Quantitative expression profiling of identified neurons reveals cell-specific constraints on highly variable levels of gene expression , 2007, Proceedings of the National Academy of Sciences.

[19]  E. Marder,et al.  Failure of averaging in the construction of a conductance-based neuron model. , 2002, Journal of neurophysiology.

[20]  J M Bekkers,et al.  Distribution and activation of voltage‐gated potassium channels in cell‐attached and outside‐out patches from large layer 5 cortical pyramidal neurons of the rat , 2000, The Journal of physiology.

[21]  Tim Gollisch,et al.  Modeling Single-Neuron Dynamics and Computations: A Balance of Detail and Abstraction , 2006, Science.

[22]  H. Markram,et al.  Correlation maps allow neuronal electrical properties to be predicted from single-cell gene expression profiles in rat neocortex. , 2004, Cerebral cortex.

[23]  Noam Peled,et al.  Constraining compartmental models using multiple voltage recordings and genetic algorithms. , 2005, Journal of neurophysiology.

[24]  C. Hwang Multiple Objective Decision Making - Methods and Applications: A State-of-the-Art Survey , 1979 .

[25]  Bruce R. Johnson,et al.  Activity-Independent Homeostasis in Rhythmically Active Neurons , 2003, Neuron.

[26]  J. Ruppersberg Ion Channels in Excitable Membranes , 1996 .

[27]  T. Sejnowski,et al.  A model of spike initiation in neocortical pyramidal neurons , 1995, Neuron.

[28]  H. Markram,et al.  Interneurons of the neocortical inhibitory system , 2004, Nature Reviews Neuroscience.

[29]  E. Marder,et al.  Variability, compensation and homeostasis in neuron and network function , 2006, Nature Reviews Neuroscience.

[30]  James M. Bower,et al.  A Comparative Survey of Automated Parameter-Search Methods for Compartmental Neural Models , 1999, Journal of Computational Neuroscience.

[31]  E. Marder,et al.  Global Structure, Robustness, and Modulation of Neuronal Models , 2001, The Journal of Neuroscience.

[32]  Idan Segev,et al.  Ion Channel Stochasticity May Be Critical in Determining the Reliability and Precision of Spike Timing , 1998, Neural Computation.

[33]  M. London,et al.  Dendritic computation. , 2005, Annual review of neuroscience.

[34]  Zbigniew Michalewicz,et al.  Genetic Algorithms + Data Structures = Evolution Programs , 1996, Springer Berlin Heidelberg.

[35]  David F. Heidel,et al.  An Overview of the BlueGene/L Supercomputer , 2002, ACM/IEEE SC 2002 Conference (SC'02).

[36]  C. Koch,et al.  Methods in Neuronal Modeling: From Ions to Networks , 1998 .

[37]  Idan Segev,et al.  Modeling back propagating action potential in weakly excitable dendrites of neocortical pyramidal cells. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[38]  E. Marder,et al.  Variable channel expression in identified single and electrically coupled neurons in different animals , 2006, Nature Neuroscience.

[39]  D. Prince,et al.  Patch-clamp studies of voltage-gated currents in identified neurons of the rat cerebral cortex. , 1991, Cerebral cortex.

[40]  Melanie Mitchell,et al.  An introduction to genetic algorithms , 1996 .

[41]  N. Marrion,et al.  Small-Conductance, Calcium-Activated Potassium Channels from Mammalian Brain , 1996, Science.

[42]  Jared L. Cohon,et al.  6 – Multicriteria programming: brief review and application , 1985 .

[43]  Erik De Schutter,et al.  Complex Parameter Landscape for a Complex Neuron Model , 2006, PLoS Comput. Biol..

[44]  Nicholas T. Carnevale,et al.  Simulation of networks of spiking neurons: A review of tools and strategies , 2006, Journal of Computational Neuroscience.

[45]  Gongyu Y. Shen,et al.  Computational analysis of action potential initiation in mitral cell soma and dendrites based on dual patch recordings. , 1999, Journal of neurophysiology.

[46]  Michael L. Hines,et al.  The NEURON Book , 2006 .

[47]  Eve Marder,et al.  Alternative to hand-tuning conductance-based models: construction and analysis of databases of model neurons. , 2003, Journal of neurophysiology.

[48]  R. Maex,et al.  Introduction to Equation Solving and Parameter Fitting , 2000 .

[49]  B. Sakmann,et al.  Voltage‐gated K+ channels in layer 5 neocortical pyramidal neurones from young rats: subtypes and gradients , 2000, The Journal of physiology.

[50]  Bernardo Rudy,et al.  Kv3 channels: voltage-gated K+ channels designed for high-frequency repetitive firing , 2001, Trends in Neurosciences.

[51]  T. Sejnowski,et al.  Reliability of spike timing in neocortical neurons. , 1995, Science.

[52]  A. Friedman,et al.  Stepwise repolarization from Ca2+ plateaus in neocortical pyramidal cells: evidence for nonhomogeneous distribution of HVA Ca2+ channels in dendrites , 1993, The Journal of neuroscience : the official journal of the Society for Neuroscience.

[53]  C. D. Gelatt,et al.  Optimization by Simulated Annealing , 1983, Science.

[54]  David E. Goldberg,et al.  Genetic Algorithms with Sharing for Multimodalfunction Optimization , 1987, ICGA.