FNS: an event-driven spiking neural network simulator based on the LIFL neuron model

Limitations in processing capabilities and memory of today's computers make spiking neuron-based (human) whole-brain simulations inevitably characterized by a compromise between bio-plausibility and computational cost. It translates into brain models composed of a reduced number of neurons and a simplified neuron's mathematical model, leading to the search for new simulation strategies. Taking advantage of the sparse character of brain-like computation, the event-driven technique could represent a way to carry out efficient simulation of large-scale Spiking Neural Networks (SNN). The recent Leaky Integrate-and-Fire with Latency (LIFL) spiking neuron model is event-driven compatible and exhibits some realistic neuronal features, opening new avenues for brain modelling. In this paper we introduce FNS, the first LIFL-based spiking neural network framework, which combines spiking/synaptic neural modelling with the event-driven approach, allowing us to define heterogeneous neuron modules and multi-scale connectivity with delayed connections and plastic synapses. In order to allow multi-thread implementations a novel parallelization strategy is also introduced. This paper presents mathematical models, software implementation and simulation routines on which FNS is based. Finally, a brain subnetwork is modeled on the basis of real brain structural data, and the resulting simulated activity is compared with associated brain functional (source-space MEG) data, demonstrating a good matching between the activity of the model and that of the experimetal data. This work aims to lay the groundwork for future event-driven based personalised brain models.

[1]  Damien Coyle,et al.  Compensating for thalamocortical synaptic loss in Alzheimer's disease , 2014, Front. Comput. Neurosci..

[2]  G. Edelman,et al.  Spike-timing dynamics of neuronal groups. , 2004, Cerebral cortex.

[3]  Morten L. Kringelbach,et al.  Single or multiple frequency generators in on-going brain activity: A mechanistic whole-brain model of empirical MEG data , 2017, NeuroImage.

[4]  Simon J Thorpe,et al.  SpikeNET: an event-driven simulation package for modelling large networks of spiking neurons , 2003, Network.

[5]  Michele Giugliano,et al.  Event-Driven Simulation of Spiking Neurons with Stochastic Dynamics , 2003, Neural Computation.

[6]  Alain Destexhe,et al.  Analytical Integrate-and-Fire Neuron Models with Conductance-Based Dynamics and Realistic Postsynaptic Potential Time Course for Event-Driven Simulation Strategies , 2012, Neural Computation.

[7]  Wulfram Gerstner,et al.  Spike-timing dependent plasticity , 2010, Scholarpedia.

[8]  Z Kourtzi,et al.  How structure sculpts function: Unveiling the contribution of anatomical connectivity to the brain's spontaneous correlation structure. , 2016, Chaos.

[9]  Joachim K. Anlauf,et al.  Distributed, Event Driven Simulation of Spiking Neural Networks , 1998, NC.

[10]  G L Shulman,et al.  INAUGURAL ARTICLE by a Recently Elected Academy Member:A default mode of brain function , 2001 .

[11]  Michiel D'Haene A Framework for Parallel Event Driven Simulation of Large Spiking Neural Networks , 2006 .

[12]  Edward T. Bullmore,et al.  Fundamentals of Brain Network Analysis , 2016 .

[13]  Gian Carlo Cardarilli,et al.  Spiking neural networks based on LIF with latency: Simulation and synchronization effects , 2013, 2013 Asilomar Conference on Signals, Systems and Computers.

[14]  Duncan J. Watts,et al.  Collective dynamics of ‘small-world’ networks , 1998, Nature.

[15]  Hengtong Wang,et al.  First-spike latency in Hodgkin's three classes of neurons. , 2013, Journal of theoretical biology.

[16]  Thomas H. Cormen,et al.  Introduction to algorithms [2nd ed.] , 2001 .

[17]  Moritz Helias,et al.  A General and Efficient Method for Incorporating Precise Spike Times in Globally Time-Driven Simulations , 2010, Front. Neuroinform..

[18]  C. Koch,et al.  The origin of extracellular fields and currents — EEG, ECoG, LFP and spikes , 2012, Nature Reviews Neuroscience.

[19]  Maxim Bazhenov,et al.  Pathological Effect of Homeostatic Synaptic Scaling on Network Dynamics in Diseases of the Cortex , 2008, The Journal of Neuroscience.

[20]  Romain Brette,et al.  Adaptive Exponential Integrate-and-Fire Model as an Effective Description of Neuronal Activity , 2005 .

[21]  Gianluca Susi,et al.  Bio-Inspired Temporal-Decoding Network Topologies for the Accurate Recognition of Spike Patterns , 2015 .

[22]  Shawn D. Burton,et al.  NeuroElectro: a window to the world's neuron electrophysiology data , 2014, Front. Neuroinform..

[23]  Fernando Maestú,et al.  The Default Mode Network is functionally and structurally disrupted in amnestic mild cognitive impairment — A bimodal MEG–DTI study , 2014, NeuroImage: Clinical.

[24]  Eduardo Ros,et al.  Event- and Time-Driven Techniques Using Parallel CPU-GPU Co-processing for Spiking Neural Networks , 2017, Front. Neuroinform..

[25]  Eduardo Ros,et al.  Event-Driven Simulation Scheme for Spiking Neural Networks Using Lookup Tables to Characterize Neuronal Dynamics , 2006, Neural Computation.

[26]  L. Abbott,et al.  Synaptic plasticity: taming the beast , 2000, Nature Neuroscience.

[27]  Eugene M. Izhikevich,et al.  Which model to use for cortical spiking neurons? , 2004, IEEE Transactions on Neural Networks.

[28]  M. Corbetta,et al.  Temporal dynamics of spontaneous MEG activity in brain networks , 2010, Proceedings of the National Academy of Sciences.

[29]  J. Thivierge Neural diversity creates a rich repertoire of brain activity , 2008, Communicative & integrative biology.

[30]  Benjamin Schrauwen,et al.  Toward Unified Hybrid Simulation Techniques for Spiking Neural Networks , 2014, Neural Computation.

[31]  Richard M. Fujimoto,et al.  Parallel event-driven neural network simulations using the Hodgkin-Huxley neuron model , 2005, Workshop on Principles of Advanced and Distributed Simulation (PADS'05).

[32]  Tim Gollisch,et al.  Rapid Neural Coding in the Retina with Relative Spike Latencies , 2008, Science.

[33]  Alessandro Cristini,et al.  Accurate Latency Characterization for Very Large Asynchronous Spiking Neural Networks , 2011, BIOINFORMATICS.

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

[35]  Hamid Reza Mohseni,et al.  How delays matter in an oscillatory whole-brain spiking-neuron network model for MEG alpha-rhythms at rest , 2014, NeuroImage.

[36]  Wulfram Gerstner,et al.  Neuronal Dynamics: From Single Neurons To Networks And Models Of Cognition , 2014 .

[37]  Mark C. W. van Rossum,et al.  Soft-bound Synaptic Plasticity Increases Storage Capacity , 2012, PLoS Comput. Biol..

[38]  O. Sporns,et al.  Mapping the Structural Core of Human Cerebral Cortex , 2008, PLoS biology.

[39]  G. Deco,et al.  Ongoing Cortical Activity at Rest: Criticality, Multistability, and Ghost Attractors , 2012, The Journal of Neuroscience.

[40]  R. FitzHugh Mathematical models of threshold phenomena in the nerve membrane , 1955 .

[41]  Alessandro Cristini,et al.  A Continuous-Time Spiking Neural Network Paradigm , 2015, Advances in Neural Networks.

[42]  Xiao-Jing Wang,et al.  What determines the frequency of fast network oscillations with irregular neural discharges? I. Synaptic dynamics and excitation-inhibition balance. , 2003, Journal of neurophysiology.

[43]  Paolo Del Giudice,et al.  Efficient Event-Driven Simulation of Large Networks of Spiking Neurons and Dynamical Synapses , 2000, Neural Computation.

[44]  David Cai,et al.  Dynamics of the exponential integrate-and-fire model with slow currents and adaptation , 2014, Journal of Computational Neuroscience.

[45]  Olaf Sporns,et al.  The Human Connectome: A Structural Description of the Human Brain , 2005, PLoS Comput. Biol..

[46]  Kenneth J. Smith Conduction properties of central demyelinated and remyelinated axons, and their relation to symptom production in demyelinating disorders , 1994, Eye.

[47]  Örjan Ekeberg,et al.  Massively parallel simulation of brain-scale neuronal network models , 2005 .

[48]  D. Hansel,et al.  How Spike Generation Mechanisms Determine the Neuronal Response to Fluctuating Inputs , 2003, The Journal of Neuroscience.

[49]  G. Bi,et al.  Synaptic Modifications in Cultured Hippocampal Neurons: Dependence on Spike Timing, Synaptic Strength, and Postsynaptic Cell Type , 1998, The Journal of Neuroscience.

[50]  Viktor K. Jirsa,et al.  The Virtual Brain: a simulator of primate brain network dynamics , 2013, Front. Neuroinform..

[51]  Hamid Reza Mohseni,et al.  Exploring mechanisms of spontaneous functional connectivity in MEG: How delayed network interactions lead to structured amplitude envelopes of band-pass filtered oscillations , 2014, NeuroImage.

[52]  Karl J. Friston,et al.  The Dynamic Brain: From Spiking Neurons to Neural Masses and Cortical Fields , 2008, PLoS Comput. Biol..

[53]  David Kappel,et al.  NEVESIM: event-driven neural simulation framework with a Python interface , 2014, Front. Neuroinform..

[54]  Gustavo Deco,et al.  Role of local network oscillations in resting-state functional connectivity , 2011, NeuroImage.

[55]  Bruno D. Zumbo,et al.  Bias in Estimation and Hypothesis Testing of Correlation , 2003 .

[56]  Boris D. Lubachevsky,et al.  Efficient distributed event-driven simulations of multiple-loop networks , 1988, CACM.

[57]  A. Hodgkin,et al.  A quantitative description of membrane current and its application to conduction and excitation in nerve , 1952, The Journal of physiology.

[58]  Anders M. Dale,et al.  An automated labeling system for subdividing the human cerebral cortex on MRI scans into gyral based regions of interest , 2006, NeuroImage.

[59]  Julien Ponge Fork and Join: Java Can Excel at Painless Parallel Programming Too! , 2011 .

[60]  Gustavo Deco,et al.  Structure-Function Discrepancy: Inhomogeneity and Delays in Synchronized Neural Networks , 2014, PLoS Comput. Biol..

[61]  Nicolas Brunel,et al.  Fast Global Oscillations in Networks of Integrate-and-Fire Neurons with Low Firing Rates , 1999, Neural Computation.

[62]  Y. Dan,et al.  Spike timing-dependent plasticity: a Hebbian learning rule. , 2008, Annual review of neuroscience.

[63]  Olaf Sporns,et al.  Mechanisms of Zero-Lag Synchronization in Cortical Motifs , 2013, PLoS Comput. Biol..

[64]  Jeremy D. Schmahmann,et al.  A Proposal for a Coordinated Effort for the Determination of Brainwide Neuroanatomical Connectivity in Model Organisms at a Mesoscopic Scale , 2009, PLoS Comput. Biol..

[65]  Srikantan S Nagarajan,et al.  The relationship between magnetic and electrophysiological responses to complex tactile stimuli , 2009, BMC Neuroscience.

[66]  S. Solla,et al.  Multiple attractors, long chaotic transients, and failure in small-world networks of excitable neurons. , 2007, Chaos.

[67]  Rodolphe Sepulchre,et al.  First spike latency sensitivity of spiking neuron models , 2013, BMC Neuroscience.

[68]  Francisco del Pozo,et al.  HERMES: Towards an Integrated Toolbox to Characterize Functional and Effective Brain Connectivity , 2013, Neuroinformatics.

[69]  Gianluca Susi,et al.  A Neuro-Inspired System for Online Learning and Recognition of Parallel Spike Trains, Based on Spike Latency, and Heterosynaptic STDP , 2018, Front. Neurosci..

[70]  Leonardo L. Gollo,et al.  Dynamical relaying can yield zero time lag neuronal synchrony despite long conduction delays , 2008, Proceedings of the National Academy of Sciences.

[71]  Markus Diesmann,et al.  Exact Subthreshold Integration with Continuous Spike Times in Discrete-Time Neural Network Simulations , 2007, Neural Computation.

[72]  Leonardo L. Gollo,et al.  Dynamic control for synchronization of separated cortical areas through thalamic relay , 2010, NeuroImage.

[73]  Leonardo L. Gollo,et al.  Diversity improves performance in excitable networks , 2015, PeerJ.

[74]  Eugene M. Izhikevich,et al.  Simple model of spiking neurons , 2003, IEEE Trans. Neural Networks.

[75]  Gian Carlo Cardarilli,et al.  Hardware design of LIF with Latency neuron model with memristive STDP synapses , 2017, Integr..

[76]  Oleg V Maslennikov,et al.  Modular networks with delayed coupling: synchronization and frequency control. , 2014, Physical review. E, Statistical, nonlinear, and soft matter physics.

[77]  Alessandro Barardi,et al.  Phase-Coherence Transitions and Communication in the Gamma Range between Delay-Coupled Neuronal Populations , 2014, PLoS Comput. Biol..

[78]  Alessandro Cristini,et al.  Path multimodality in a feedforward SNN module, using LIF with latency model , 2016 .