Neural Codes: Firing Rates and Beyond
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Neural Coding and the Statistical Modeling of Neuronal Responses By
Neural coding and the statistical modeling of neuronal responses by Jonathan Pillow A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy Center for Neural Science New York University Jan 2005 Eero P. Simoncelli TABLE OF CONTENTS LIST OF FIGURES v INTRODUCTION 1 1 Characterization of macaque retinal ganglion cell responses using spike-triggered covariance 5 1.1NeuralCharacterization.................... 9 1.2One-DimensionalModelsandtheSTA............ 12 1.3Multi-DimensionalModelsandSTCAnalysis........ 16 1.4 Separability and Subspace STC ................ 21 1.5 Subunit model . ....................... 23 1.6ModelValidation........................ 25 1.7Methods............................. 28 2 Estimation of a Deterministic IF model 37 2.1Leakyintegrate-and-firemodel................. 40 2.2Simulationresultsandcomparison............... 41 ii 2.3Recoveringthelinearkernel.................. 42 2.4Recoveringakernelfromneuraldata............. 44 2.5Discussion............................ 46 3 Estimation of a Stochastic, Recurrent IF model 48 3.1TheModel............................ 52 3.2TheEstimationProblem.................... 54 3.3ComputationalMethodsandNumericalResults....... 57 3.4TimeRescaling......................... 60 3.5Extensions............................ 61 3.5.1 Interneuronalinteractions............... 62 3.5.2 Nonlinear input ..................... 63 3.6Discussion............................ 64 AppendixA:ProofofLog-ConcavityofModelLikelihood..... 65 AppendixB:ComputingtheLikelihoodGradient........ -
Neural Oscillations As a Signature of Efficient Coding in the Presence of Synaptic Delays Matthew Chalk1*, Boris Gutkin2,3, Sophie Dene` Ve2
RESEARCH ARTICLE Neural oscillations as a signature of efficient coding in the presence of synaptic delays Matthew Chalk1*, Boris Gutkin2,3, Sophie Dene` ve2 1Institute of Science and Technology Austria, Klosterneuburg, Austria; 2E´ cole Normale Supe´rieure, Paris, France; 3Center for Cognition and Decision Making, National Research University Higher School of Economics, Moscow, Russia Abstract Cortical networks exhibit ’global oscillations’, in which neural spike times are entrained to an underlying oscillatory rhythm, but where individual neurons fire irregularly, on only a fraction of cycles. While the network dynamics underlying global oscillations have been well characterised, their function is debated. Here, we show that such global oscillations are a direct consequence of optimal efficient coding in spiking networks with synaptic delays and noise. To avoid firing unnecessary spikes, neurons need to share information about the network state. Ideally, membrane potentials should be strongly correlated and reflect a ’prediction error’ while the spikes themselves are uncorrelated and occur rarely. We show that the most efficient representation is when: (i) spike times are entrained to a global Gamma rhythm (implying a consistent representation of the error); but (ii) few neurons fire on each cycle (implying high efficiency), while (iii) excitation and inhibition are tightly balanced. This suggests that cortical networks exhibiting such dynamics are tuned to achieve a maximally efficient population code. DOI: 10.7554/eLife.13824.001 *For correspondence: Introduction [email protected] Oscillations are a prominent feature of cortical activity. In sensory areas, one typically observes Competing interests: The ’global oscillations’ in the gamma-band range (30–80 Hz), alongside single neuron responses that authors declare that no are irregular and sparse (Buzsa´ki and Wang, 2012; Yu and Ferster, 2010). -
The Human Brain Project
HBP The Human Brain Project Madrid, June 20th 2013 HBP The Human Brain Project HBP FULL-SCALE HBP Ramp-up HBP Report mid 2013-end 2015 April, 2012 HBP-PS (CSA) (FP7-ICT-2013-FET-F, CP-CSA, Jul-Oct, 2012 May, 2011 HBP-PS Proposal (FP7-ICT-2011-FET-F) December, 2010 Proposal Preparation August, 2010 HBP PROJECT FICHE: PROJECT TITLE: HUMAN BRAIN PROJECT COORDINATOR: EPFL (Switzerland) COUNTRIES: 23 (EU MS, Switzerland, US, Japan, China); 22 in Ramp Up Phase. RESEARCH LABORATORIES: 256 in Whole Flagship; 110 in Ramp Up Phase RESEARCH INSTITUTIONS (Partners): • 150 in Whole Flagship • 82 in Ramp Up Phase & New partners through Competitive Call Scheme (15,5% of budget) • 200 partners expected by Y5 (Project participants & New partners through Competitive Call Scheme) DIVISIONS:11 SUBPROJECTS: 13 TOTAL COSTS: 1.000* M€; 72,7 M€ in Ramp Up Phase * 1160 M€ Project Total Costs (October, 2012) HBP Main Scheme of The Human Brain Project: HBP Phases 2013 2015 2016 2020 2023 RAMP UP (A) FULLY OPERATIONAL (B) SUSTAINED OPERATIONS (C) Y1 Y2 Y3a Y3b Y4 Y5 Y6 Y7 Y8 Y9 Y10 2014 2020 HBP Structure HBP: 11 DIVISIONS; 13 SUBPROJECTS (10 SCIENTIFIC & APPLICATIONS & ETHICS & MGT) DIVISION SPN1 SUBPROJECTS AREA OF ACTIVITY MOLECULAR & CELLULAR NEUROSCIENCE SP1 STRATEGIC MOUSE BRAIN DATA SP2 STRATEGIC HUMAN BRAIN DATA DATA COGNITIVE NEUROSCIENCE SP3 BRAIN FUNCTION THEORETICAL NEUROSCIENCE SP4 THEORETICAL NEUROSCIENCE THEORY NEUROINFORMATICS SP5 THE NEUROINFORMATICS PLATFORM BRAIN SIMULATION SP6 BRAIN SIMULATION PLATFORM HIGH PERFORMANCE COMPUTING (HPC) SP7 HPC -
An Optogenetic Approach to Understanding the Neural Circuits of Fear Joshua P
Controlling the Elements: An Optogenetic Approach to Understanding the Neural Circuits of Fear Joshua P. Johansen, Steffen B.E. Wolff, Andreas Lüthi, and Joseph E. LeDoux Neural circuits underlie our ability to interact in the world and to learn adaptively from experience. Understanding neural circuits and how circuit structure gives rise to neural firing patterns or computations is fundamental to our understanding of human experience and behavior. Fear conditioning is a powerful model system in which to study neural circuits and information processing and relate them to learning and behavior. Until recently, technological limitations have made it difficult to study the causal role of specific circuit elements during fear conditioning. However, newly developed optogenetic tools allow researchers to manipulate individual circuit components such as anatom- ically or molecularly defined cell populations, with high temporal precision. Applying these tools to the study of fear conditioning to control specific neural subpopulations in the fear circuit will facilitate a causal analysis of the role of these circuit elements in fear learning and memory. By combining this approach with in vivo electrophysiological recordings in awake, behaving animals, it will also be possible to determine the functional contribution of specific cell populations to neural processing in the fear circuit. As a result, the application of optogenetics to fear conditioning could shed light on how specific circuit elements contribute to neural coding and to fear learning and memory. Furthermore, this approach may reveal general rules for how circuit structure and neural coding within circuits gives rise to sensory experience and behavior. Key Words: Electrophysiology, fear conditioning, learning and circuits and the identification of sites of neural plasticity in these memory, neural circuits, neural plasticity, optogenetics circuits. -
6 Optogenetic Actuation, Inhibition, Modulation and Readout for Neuronal Networks Generating Behavior in the Nematode Caenorhabditis Elegans
Mario de Bono, William R. Schafer, Alexander Gottschalk 6 Optogenetic actuation, inhibition, modulation and readout for neuronal networks generating behavior in the nematode Caenorhabditis elegans 6.1 Introduction – the nematode as a genetic model in systems neurosciencesystems neuroscience Elucidating the mechanisms by which nervous systems process information and gen- erate behavior is among the fundamental problems of biology. The complexity of our brain and plasticity of our behaviors make it challenging to understand even simple human actions in terms of molecular mechanisms and neural activity. However the molecular machines and operational features of our neural circuits are often found in invertebrates, so that studying flies and worms provides an effective way to gain insights into our nervous system. Caenorhabditis elegans offers special opportunities to study behavior. Each of the 302 neurons in its nervous system can be identified and imaged in live animals [1, 2], and manipulated transgenically using specific promoters or promoter combinations [3, 4, 5, 6]. The chemical synapses and gap junctions made by every neuron are known from electron micrograph reconstruction [1]. Importantly, forward genetics can be used to identify molecules that modulate C. elegans’ behavior. Forward genetic dis- section of behavior is powerful because it requires no prior knowledge. It allows mol- ecules to be identified regardless of in vivo concentration, and focuses attention on genes that are functionally important. The identity and expression patterns of these molecules then provide entry points to study the molecular mechanisms and neural circuits controlling the behavior. Genetics does not provide the temporal resolution required to study neural circuit function directly. -
Exploring the Function of Neural Oscillations in Early Sensory Systems
FOCUSED REVIEW published: 15 May 2010 doi: 10.3389/neuro.01.010.2010 Exploring the function of neural oscillations in early sensory systems Kilian Koepsell1*, Xin Wang 2, Judith A. Hirsch 2 and Friedrich T. Sommer1* 1 Redwood Center for Theoretical Neuroscience, University of California, Berkeley, CA, USA 2 Neuroscience Graduate Program, University of Southern California, Los Angeles, CA, USA Neuronal oscillations appear throughout the nervous system, in structures as diverse as the cerebral cortex, hippocampus, subcortical nuclei and sense organs. Whether neural rhythms contribute to normal function, are merely epiphenomena, or even interfere with physiological processing are topics of vigorous debate. Sensory pathways are ideal for investigation of oscillatory activity because their inputs can be defined. Thus, we will focus on sensory systems Edited by: S. Murray Sherman, as we ask how neural oscillations arise and how they might encode information about the University of Chicago, USA stimulus. We will highlight recent work in the early visual pathway that shows how oscillations Reviewed by: can multiplex different types of signals to increase the amount of information that spike trains Michael J. Friedlander, Baylor College of Medicine, USA encode and transmit. Last, we will describe oscillation-based models of visual processing and Jose-Manuel Alonso, Sociedad Espanola explore how they might guide further research. de Neurociencia, Spain; University of Connecticut, USA; State University Keywords: LGN, retina, visual coding, oscillations, multiplexing of New York, USA Naoum P. Issa, University of Chicago, USA NEURAL OSCILLATIONS IN EARLY However, the autocorrelograms are subject to *Correspondence: SENSORY SYSTEMS confounds caused by the refractory period and Oscillatory neural activity has been observed spectral peaks often fail to reveal weak rhythms. -
Neuronal Dynamics
Week 7 – part 7: Helping Humans 7.1 What is a good neuron model? - Models and data 7.2 AdEx model Neuronal Dynamics: - Firing patterns and analysis Computational Neuroscience 7.3 Spike Response Model (SRM) of Single Neurons - Integral formulation 7.4 Generalized Linear Model (GLM) Week 7 – Optimizing Neuron Models - Adding noise to the SRM For Coding and Decoding 7.5 Parameter Estimation - Quadratic and convex optimization Wulfram Gerstner 7.6. Modeling in vitro data EPFL, Lausanne, Switzerland - how long lasts the effect of a spike? 7.7. Helping Humans Week 7 – part 7: Helping Humans 7.1 What is a good neuron model? - Models and data 7.2 AdEx model - Firing patterns and analysis 7.3 Spike Response Model (SRM) - Integral formulation 7.4 Generalized Linear Model (GLM) - Adding noise to the SRM 7.5 Parameter Estimation - Quadratic and convex optimization 7.6. Modeling in vitro data - how long lasts the effect of a spike? 7.7. Helping Humans Neuronal Dynamics – Review: Models and Data -Predict spike times -Predict subthreshold voltage -Easy to interpret (not a ‘black box’) -Variety of phenomena -Systematic: ‘optimize’ parameters BUT so far limited to in vitro Neuronal Dynamics – 7.7 Systems neuroscience, in vivo Now: extracellular recordings visual cortex A) Predict spike times, given stimulus B) Predict subthreshold voltage C) Easy to interpret (not a ‘black box’) Model of ‘Encoding’ D) Flexible enough to account for a variety of phenomena E) Systematic procedure to ‘optimize’ parameters Neuronal Dynamics – 7.7 Estimation of receptive fields Estimation of spatial (and temporal) receptive fields ut() k I u LNP =+∑ kKk− rest firing intensity ρϑ()tfutt= ( ()− ()) Neuronal Dynamics – 7.7 Estimation of Receptive Fields visual LNP = stimulus Linear-Nonlinear-Poisson Special case of GLM= Generalized Linear Model GLM for prediction of retinal ganglion ON cell activity Pillow et al. -
A Barrel of Spikes Reach out and Touch
HIGHLIGHTS NEUROANATOMY Reach out and touch Dendritic spines are a popular sub- boutons (where synapses are formed ject these days. One theory is that on the shaft of the axon) would occur they exist, at least in part, to allow when dendritic spines were able to axons to synapse with dendrites bridge the gap between dendrite and without deviating from a nice axon. They carried out a detailed straight path through the brain. But, morphological study of spiny neuron as Anderson and Martin point out in axons in cat cortex to test this Nature Neuroscience, axons can also hypothesis. form spine-like structures, known as Perhaps surprisingly, they found terminaux boutons. Might these also that the two types of synaptic bouton be used to maintain economic, did not differentiate between den- straight axonal trajectories? dritic spines and shafts. Axons were Anderson and Martin proposed just as likely to use terminaux boutons that, if this were the case, the two to contact dendritic spines as they types of axonal connection — were to use en passant boutons, even terminaux boutons and en passant in cases where it would seem that the boutons — would each make path of the axon would allow it to use synapses preferentially with different an en passant bouton. So, why do types of dendritic site. Terminaux axons bother to construct these deli- boutons would be used to ‘reach out’ cate structures, if not simply to con- to dendritic shafts, whereas en passant nect to out-of-the-way dendrites? NEURAL CODING exploring an environment, a rat will use its whiskers to collect information by sweeping them backwards and forwards, and it could use a copy of the motor command to predict A barrel of spikes when the stimulus was likely to have occurred. -
Hebbian Learning and Spiking Neurons
PHYSICAL REVIEW E VOLUME 59, NUMBER 4 APRIL 1999 Hebbian learning and spiking neurons Richard Kempter* Physik Department, Technische Universita¨tMu¨nchen, D-85747 Garching bei Mu¨nchen, Germany Wulfram Gerstner† Swiss Federal Institute of Technology, Center of Neuromimetic Systems, EPFL-DI, CH-1015 Lausanne, Switzerland J. Leo van Hemmen‡ Physik Department, Technische Universita¨tMu¨nchen, D-85747 Garching bei Mu¨nchen, Germany ~Received 6 August 1998; revised manuscript received 23 November 1998! A correlation-based ~‘‘Hebbian’’! learning rule at a spike level with millisecond resolution is formulated, mathematically analyzed, and compared with learning in a firing-rate description. The relative timing of presynaptic and postsynaptic spikes influences synaptic weights via an asymmetric ‘‘learning window.’’ A differential equation for the learning dynamics is derived under the assumption that the time scales of learning and neuronal spike dynamics can be separated. The differential equation is solved for a Poissonian neuron model with stochastic spike arrival. It is shown that correlations between input and output spikes tend to stabilize structure formation. With an appropriate choice of parameters, learning leads to an intrinsic normal- ization of the average weight and the output firing rate. Noise generates diffusion-like spreading of synaptic weights. @S1063-651X~99!02804-4# PACS number~s!: 87.19.La, 87.19.La, 05.65.1b, 87.18.Sn I. INTRODUCTION In contrast to the standard rate models of Hebbian learn- ing, we introduce and analyze a learning rule where synaptic Correlation-based or ‘‘Hebbian’’ learning @1# is thought modifications are driven by the temporal correlations be- to be an important mechanism for the tuning of neuronal tween presynaptic and postsynaptic spikes. -
Neural Coding Computation and Dynamics
Neural Coding Computation and Dynamics September 15–18, 2007 Sporting Casino Hossegor 119, avenue Maurice Martin Hossegor, France Programme Summary Saturday, September 15 18:30 – 20:00 Reception 20:00 – 22:00 Dinner Sunday, September 16 10:00 – 11:15 Talks: Ganguli, Ratcliff . 7, 11 11:15 – 11:45 Break 11:45 – 13:00 Talks: Beck, Averbeck . 6, 5 13:15 – 14:30 Lunch 15:30 – 17:30 Posters 17:30 – 18:15 Talks: Kass ..................................... 8 18:15 – 18:45 Break 18:45 – 19:45 Talks: Staude, Roxin . 15, 11 20:00 – 22:00 Dinner Monday, September 17 10:00 – 11:15 Talks: Smith, H¨ausler . 13, 8 11:15 – 11:45 Break 11:45 – 13:00 Talks: Thiele, Tolias . 16, 16 13:15 – 14:30 Lunch 15:30 – 17:30 Posters 17:30 – 18:15 Talks: Nirenberg . 10 18:15 – 18:45 Break 18:45 – 19:45 Talks: Shlens, Kretzberg . 13, 9 20:00 – 22:00 Dinner Tuesday, September 18 10:00 – 11:15 Talks: Shenoy, Solla . 12, 14 11:15 – 11:45 Break 11:45 – 13:00 Talks: Harris, Machens . 7, 9 13:15 – 14:30 Lunch 14:30 – 15:15 Talks: O’Keefe . 10 15:15 – 15:45 Break 15:45 – 16:45 Talks: Siapas, Frank . 13, 6 ii NCCD 07 Programme Saturday – Sunday Programme Saturday, September 15 Evening 18:30 – 20:00 Reception 20:00 – 22:00 Dinner Sunday, September 16 Morning 10:00 – 10:45 Spikes, synapses, learning and memory in simple networks Surya Ganguli, University of California, San Francisco . 7 10:45 – 11:15 Modeling behavioural reaction time (RT) data and neural firing rates Roger Ratcliff, Ohio State University . -
Connectivity Reflects Coding: a Model of Voltage-‐Based Spike-‐ Timing-‐Dependent-‐P
Connectivity reflects Coding: A Model of Voltage-based Spike- Timing-Dependent-Plasticity with Homeostasis Claudia Clopath, Lars Büsing*, Eleni Vasilaki, Wulfram Gerstner Laboratory of Computational Neuroscience Brain-Mind Institute and School of Computer and Communication Sciences Ecole Polytechnique Fédérale de Lausanne 1015 Lausanne EPFL, Switzerland * permanent address: Institut für Grundlagen der Informationsverarbeitung, TU Graz, Austria Abstract Electrophysiological connectivity patterns in cortex often show a few strong connections, sometimes bidirectional, in a sea of weak connections. In order to explain these connectivity patterns, we use a model of Spike-Timing-Dependent Plasticity where synaptic changes depend on presynaptic spike arrival and the postsynaptic membrane potential, filtered with two different time constants. The model describes several nonlinear effects in STDP experiments, as well as the voltage dependence of plasticity. We show that in a simulated recurrent network of spiking neurons our plasticity rule leads not only to development of localized receptive fields, but also to connectivity patterns that reflect the neural code: for temporal coding paradigms with spatio-temporal input correlations, strong connections are predominantly unidirectional, whereas they are bidirectional under rate coded input with spatial correlations only. Thus variable connectivity patterns in the brain could reflect different coding principles across brain areas; moreover simulations suggest that plasticity is surprisingly fast. Keywords: Synaptic plasticity, STDP, LTP, LTD, Voltage, Spike Introduction Experience-dependent changes in receptive fields1-2 or in learned behavior relate to changes in synaptic strength. Electrophysiological measurements of functional connectivity patterns in slices of neural tissue3-4 or anatomical connectivity measures5 can only present a snapshot of the momentary connectivity -- which may change over time6. -
© CIC Edizioni Internazionali
4-EDITORIALE_FN 3 2013 08/10/13 12:22 Pagina 143 editorial The XXIV Ottorino Rossi Award Who was Ottorino Rossi? Ottorino Rossi was born on 17th January, 1877, in Solbiate Comasco, a tiny Italian village near Como. In 1895 he enrolled at the medical fac- ulty of the University of Pavia as a student of the Ghislieri College and during his undergraduate years he was an intern pupil of the Institute of General Pathology and Histology, which was headed by Camillo Golgi. In 1901 Rossi obtained his medical doctor degree with the high- est grades and a distinction. In October 1902 he went on to the Clinica Neuropatologica (Hospital for Nervous and Mental Diseases) directed by Casimiro Mondino to learn clinical neurology. In his spare time Rossi continued to frequent the Golgi Institute which was the leading Italian centre for biological research. Having completed his clinical prepara- tion in Florence with Eugenio Tanzi, and in Munich at the Institute directed by Emil Kraepelin, he taught at the Universities of Siena, Sassari and Pavia. In Pavia he was made Rector of the University and was instrumental in getting the buildings of the new San Matteo Polyclinic completed. Internazionali Ottorino Rossi made important contributions to many fields of clinical neurology, neurophysiopathology and neuroanatomy. These include: the identification of glucose as the reducing agent of cerebrospinal fluid, the demonstration that fibres from the spinal ganglia pass into the dorsal branch of the spinal roots, and the description of the cerebellar symp- tom which he termed “the primary asymmetries of positions”. Moreover, he conducted important studies on the immunopathology of the nervous system, the serodiagnosis of neurosyphilis and the regeneration of the nervous system.