Computational neuroscience

Computational neuroscience
Computational neuroscience is the study of brain function in terms of the information processing properties of the
structures that make up the nervous system.[1] It is an interdisciplinary science that links the diverse fields of
neuroscience, cognitive science and psychology with electrical engineering, computer science, mathematics and
physics.
Computational neuroscience is somewhat distinct from psychological connectionism and theories of learning from
disciplines such as machine learning, neural networks and computational learning theory in that it emphasizes
descriptions of functional and biologically realistic neurons (and neural systems) and their physiology and dynamics.
These models capture the essential features of the biological system at multiple spatial-temporal scales, from
membrane currents, protein and chemical coupling to network oscillations, columnar and topographic architecture
and learning and memory. These computational models are used to frame hypotheses that can be directly tested by
current or future biological and/or psychological experiments.

History
The term "computational neuroscience" was introduced by Eric L. Schwartz, who organized a conference, held in
1985 in Carmel, California at the request of the Systems Development Foundation, to provide a summary of the
current status of a field which until that point was referred to by a variety of names, such as neural modeling, brain
theory and neural networks. The proceedings of this definitional meeting were later published as the book
"Computational Neuroscience" (1990).[2]
The early historical roots of the field can be traced to the work of people such as Louis Lapicque, Hodgkin &
Huxley, Hubel & Wiesel, and David Marr, to name but a few. Lapicque introduced the integrate and fire model of
the neuron in a seminal article published in 1907;[3] this model is still one of the most popular models in
computational neuroscience for both cellular and neural networks studies, as well as in mathematical neuroscience
because of its simplicity (see the recent review article [4] published recently for the centenary of the original
Lapicque's 1907 paper - this review also contains an English translation of the original paper). About 40 years later,
Hodgkin & Huxley developed the voltage clamp and created the first biophysical model of the action potential.
Hubel & Wiesel discovered that neurons in the primary visual cortex, the first cortical area to process information
coming from the retina, have oriented receptive fields and are organized in columns.[5] David Marr's work focused
on the interactions between neurons, suggesting computational approaches to the study of how functional groups of
neurons within the hippocampus and neocortex interact, store, process, and transmit information. Computational
modeling of biophysically realistic neurons and dendrites began with the work of Wilfrid Rall, with the first
multicompartmental model using cable theory.

Major topics
Research in computational neuroscience can be roughly categorized into several lines of inquiry. Most computational
neuroscientists collaborate closely with experimentalists in analyzing novel data and synthesizing new models of
biological phenomena.

Single-neuron modeling
Even single neurons have complex biophysical characteristics. Hodgkin and Huxley's original model only employed
two voltage-sensitive currents, the fast-acting sodium and the inward-rectifying potassium. Though successful in
predicting the timing and qualitative features of the action potential, it nevertheless failed to predict a number of
important features such as adaptation and shunting. Scientists now believe that there are a wide variety of
voltage-sensitive currents, and the implications of the differing dynamics, modulations and sensitivity of these

Computational neuroscience
currents is an important topic of computational neuroscience.[6]
The computational functions of complex dendrites are also under intense investigation. There is a large body of
literature regarding how different currents interact with geometric properties of neurons.[7]
Some models are also tracking biochemical pathways at very small scales such as spines or synaptic clefts.
There are many software packages, such as GENESIS and NEURON, that allow rapid and systematic in silico
modeling of realistic neurons. Blue Brain, a project founded by Henry Markram from the cole Polytechnique
Fdrale de Lausanne, aims to construct a biophysically detailed simulation of a cortical column on the Blue Gene
supercomputer.

Development, axonal patterning and guidance

How do axons and dendrites form during development? How do axons know where to target and how to reach these
targets? How do neurons migrate to the proper position in the central and peripheral systems? How do synapses
form? We know from molecular biology that distinct parts of the nervous system release distinct chemical cues, from
growth factors to hormones that modulate and influence the growth and development of functional connections
between neurons.
Theoretical investigations into the formation and patterning of synaptic connection and morphology are still nascent.
One hypothesis that has recently garnered some attention is the minimal wiring hypothesis, which postulates that the
formation of axons and dendrites effectively minimizes resource allocation while maintaining maximal information
storage.[8]

Sensory processing
Early models of sensory processing understood within a theoretical framework is credited to Horace Barlow.
Somewhat similar to the minimal wiring hypothesis described in the preceding section, Barlow understood the
processing of the early sensory systems to be a form of efficient coding, where the neurons encoded information
which minimized the number of spikes. Experimental and computational work have since supported this hypothesis
in one form or another.
Current research in sensory processing is divided among biophysical modelling of different subsystems and more
theoretical modelling of perception. Current models of perception have suggested that the brain performs some form
of Bayesian inference and integration of different sensory information in generating our perception of the physical
world.

Memory and synaptic plasticity

Earlier models of memory are primarily based on the postulates of Hebbian learning. Biologically relevant models
such as Hopfield net have been developed to address the properties of associative, rather than content-addressable
style of memory that occur in biological systems. These attempts are primarily focusing on the formation of
medium-term and long-term memory, localizing in the hippocampus. Models of working memory, relying on
theories of network oscillations and persistent activity, have been built to capture some features of the prefrontal
cortex in context-related memory.[9]
One of the major problems in neurophysiological memory is how it is maintained and changed through multiple time
scales. Unstable synapses are easy to train but also prone to stochastic disruption. Stable synapses forget less easily,
but they are also harder to consolidate. One recent computational hypothesis involves cascades of plasticity[10] that
allow synapses to function at multiple time scales. Stereochemically detailed models of the acetylcholine
receptor-based synapse with Monte Carlo method, working at the time scale of microseconds, have been built.[11] It
is likely that computational tools will contribute greatly to our understanding of how synapses function and change
in relation to external stimulus in the coming decades.

Computational neuroscience

Behaviors of networks
Biological neurons are connected to each other in a complex, recurrent fashion. These connections are, unlike most
artificial neural networks, sparse and most likely, specific. It is not known how information is transmitted through
such sparsely connected networks. It is also unknown what the computational functions, if any, of these specific
connectivity patterns are.
The interactions of neurons in a small network can be often reduced to simple models such as the Ising model. The
statistical mechanics of such simple systems are well-characterized theoretically. There has been some recent
evidence that suggests that dynamics of arbitrary neuronal networks can be reduced to pairwise
interactions.(Schneidman et al., 2006; Shlens et al., 2006.)[12] It's unknown, however, whether such descriptive
dynamics impart any important computational function. With the emergence of two-photon microscopy and calcium
imaging, we now have powerful experimental methods with which to test the new theories regarding neuronal
networks.
In some cases the complex interactions between inhibitory and excitatory neurons can be simplified using mean field
theory that gives rise to population model of neural networks. While many neuro-theorists prefer such models with
reduced complexity, others argue that uncovering structure function relations depends on including as much neuronal
and network structure as possible. Models of this type are typically built in large simulations platforms like
GENESIS or Neuron. There have been some attempts to provide unified methods that bridge and integrate these
levels of complexity.[13]

Cognition, discrimination and learning

Computational modeling of higher cognitive functions has only recently begun. Experimental data comes primarily
from single-unit recording in primates. The frontal lobe and parietal lobe function as integrators of information from
multiple sensory modalities. There are some tentative ideas regarding how simple mutually inhibitory functional
circuits in these areas may carry out biologically relevant computation.[14]
The brain seems to be able to discriminate and adapt particularly well in certain contexts. For instance, human beings
seem to have an enormous capacity for memorizing and recognizing faces. One of the key goals of computational
neuroscience is to dissect how biological systems carry out these complex computations efficiently and potentially
replicate these processes in building intelligent machines.
The brain's large-scale organizational principles are illuminated by many fields, including biology, psychology, and
clinical practice. Integrative neuroscience attempts to consolidate these observations through unified descriptive
models and databases of behavioral measures and recordings. These are the basis for some quantitative modeling of
large-scale brain activity.[15]

Consciousness
One of the ultimate goals of psychology/neuroscience is to be able to explain the everyday experience of conscious
life. Francis Crick and Christof Koch made some attempts in formulating a consistent framework for future work in
neural correlates of consciousness (NCC), though much of the work in this field remains speculative.[16]

References
Notes
[1] What is computational neuroscience? Patricia S. Churchland, Christof Koch, Terrence J. Sejnowski. in Computational Neuroscience
pp.46-55. Edited by Eric L. Schwartz. 1993. MIT Press (http:/ / mitpress. mit. edu/ catalog/ item/ default. asp?ttype=2& tid=7195)
[2] Schwartz, Eric (1990). Computational neuroscience. Cambridge, Mass: MIT Press. ISBN0-262-19291-8.
[3] Lapicque L (1907). "Recherches quantitatives sur l'excitation lectrique des nerfs traite comme une polarisation". J. Physiol. Pathol. Gen. 9:
620635.

Computational neuroscience
[4] Brunel N, Van Rossum MC (2007). "Lapicque's 1907 paper: from frogs to integrate-and-fire". Biol. Cybern. 97 (5-6): 337339.
doi:10.1007/s00422-007-0190-0. PMID17968583.
[5] Hubel DH, Wiesel TN (1962). "Receptive fields, binocular interaction and functional architecture in the cat's visual cortex" (http:/ / www.
jphysiol. org/ cgi/ pmidlookup?view=long& pmid=14449617). J. Physiol. (Lond.) 160: 10654. PMC1359523. PMID14449617. .
[6] Wu, Samuel Miao-sin; Johnston, Daniel (1995). Foundations of cellular neurophysiology. Cambridge, Mass: MIT Press.
ISBN0-262-10053-3.
[7] Koch, Christof (1999). Biophysics of computation: information processing in single neurons. Oxford [Oxfordshire]: Oxford University Press.
ISBN0-19-510491-9.
[8] Chklovskii DB, Mel BW, Svoboda K (October 2004). "Cortical rewiring and information storage". Nature 431 (7010): 7828.
Bibcode2004Natur.431..782C. doi:10.1038/nature03012. PMID15483599.
Review article
[9] Durstewitz D, Seamans JK, Sejnowski TJ (2000). "Neurocomputational models of working memory". Nat Neurosci. 3 (Suppl): 118491.
doi:10.1038/81460. PMID11127836.
[10] Fusi S, Drew PJ, Abbott LF (2005). "Cascade models of synaptically stored memories". Neuron 45 (4): 599611.
doi:10.1016/j.neuron.2005.02.001. PMID15721245.
[11] Coggan JS, Bartol TM, Esquenazi E, et al. (2005). "Evidence for ectopic neurotransmission at a neuronal synapse". Science 309 (5733):
44651. Bibcode2005Sci...309..446C. doi:10.1126/science.1108239. PMC2915764. PMID16020730.
[12] Schneidman E, Berry MJ, Segev R, Bialek W (2006). "Weak pairwise correlations imply strongly correlated network states in a neural
population". Nature 440 (7087): 100712. arXiv:q-bio/0512013. Bibcode2006Natur.440.1007S. doi:10.1038/nature04701. PMC1785327.
PMID16625187.
[13] Anderson, Charles H.; Eliasmith, Chris (2004). Neural Engineering: Computation, Representation, and Dynamics in Neurobiological
Systems (Computational Neuroscience). Cambridge, Mass: The MIT Press. ISBN0-262-55060-1.
[14] Machens CK, Romo R, Brody CD (2005). "Flexible control of mutual inhibition: a neural model of two-interval discrimination". Science
307 (5712): 11214. Bibcode2005Sci...307.1121M. doi:10.1126/science.1104171. PMID15718474.
[15] Robinson PA, Rennie CJ, Rowe DL, O'Connor SC, Gordon E (2005). "Multiscale brain modelling". Philosophical Transactions of the Royal
Society B 360 (1457): 10431050. doi:10.1098/rstb.2005.1638. PMC1854922. PMID16087447.
[16] Crick F, Koch C (2003). "A framework for consciousness". Nat Neurosci. 6 (2): 11926. doi:10.1038/nn0203-119. PMID12555104.

General references
Chklovskii DB (2004). "Synaptic connectivity and neuronal morphology: two sides of the same coin". Neuron 43
(5): 60917. doi:10.1016/j.neuron.2004.08.012. PMID15339643.
Sejnowski, Terrence J.; Churchland, Patricia Smith (1992). The computational brain. Cambridge, Mass: MIT
Press. ISBN0-262-03188-4.
Abbott, L. F.; Dayan, Peter (2001). Theoretical neuroscience: computational and mathematical modeling of
neural systems. Cambridge, Mass: MIT Press. ISBN0-262-04199-5.
Eliasmith, Chris; Anderson, Charles H. (2003). Neural engineering: Representation, computation, and dynamcs
in neurobiological systems. Cambridge, Mass: MIT Press. ISBN0-262-05071-4.
Hodgkin AL, Huxley AF (28 August 1952). "A quantitative description of membrane current and its application
to conduction and excitation in nerve" (http://www.jphysiol.org/cgi/pmidlookup?view=long&
pmid=12991237). J Physiol. (Lond.) 117 (4): 50044. PMC1392413. PMID12991237.
William Bialek; Rieke, Fred; David Warland; Rob de Ruyter van Steveninck (1999). Spikes: exploring the neural
code. Cambridge, Mass: MIT. ISBN0-262-68108-0.
Schutter, Erik de (2001). Computational neuroscience: realistic modeling for experimentalists. Boca Raton: CRC.
ISBN0-8493-2068-2.
Sejnowski, Terrence J.; Hemmen, J. L. van (2006). 23 problems in systems neuroscience. Oxford [Oxfordshire]:
Oxford University Press. ISBN0-19-514822-3.
Michael A. Arbib, Shun-ichi Amari, Prudence H. Arbib (2002). The Handbook of Brain Theory and Neural
Networks. Cambridge, Massachusetts: The MIT Press. ISBN0-262-01197-2.

Computational neuroscience

External links
Journals

Network: Computation in Neural Systems (http://www.informaworld.com/network)

Biological Cybernetics (http://www.springerlink.com/openurl.asp?genre=journal&issn=0340-1200)
Journal of Computational Neuroscience (http://www.springer.com/10827)
Neural Computation (http://www.mitpressjournals.org/loi/neco)
Neural Networks (http://www.sciencedirect.com/science/journal/08936080)
Neurocomputing (http://www.elsevier.com/locate/neucom)
Cognitive Neurodynamics (http://www.springerlink.com/content/1871-4099/)
Frontiers in Computational Neuroscience (http://frontiersin.org/neuroscience/computationalneuroscience/)
PLoS Computational Biology (http://www.ploscompbiol.org/home.action)
Frontiers in Neuroinformatics (http://www.frontiersin.org/Journal/specialty.aspx?s=752&
name=neuroinformatics&x=y)

Software
Emergent, neural simulation software.
Genesis (http://genesis-sim.org/), a general neural simulation system.
ModelDB (http://senselab.med.yale.edu/modeldb), a large open-access database of program codes of
published computational neuroscience models.
NEST (http://www.nest-initiative.org), a simulation tool for large neuronal systems.
Neuroconstruct (http://www.neuroconstruct.org), software for developing biologically realistic 3D neural
networks.
NEURON (http://www.neuron.yale.edu/), a neuron simulator also useful to simulate neural networks.
SNNAP (http://snnap.uth.tmc.edu/), a single neuron and neural network simulator tool.
ReMoto (http://remoto.leb.usp.br/remoto/index.html), a web-based simulator of the spinal cord and
innervated muscles of the human leg.

Conferences
Computational and Systems Neuroscience (COSYNE) (http://www.cosyne.org) a computational neuroscience
meeting with a systems neuroscience focus.
Annual Computational Neuroscience Meeting (CNS) (http://www.cnsorg.org) a yearly computational
neuroscience meeting.
Neural Information Processing Systems (NIPS) (http://www.nips.cc) a leading annual conference covering
other machine learning topics as well.
Computational Cognitive Neuroscience Conference (CCNC) (http://www.ccnconference.org) a yearly
conference.
International Conference on Cognitive Neurodynamics (ICCN) (http://www.iccn2007.org/) a yearly
conference.
UK Mathematical Neurosciences Meeting (http://www.icms.org.uk/workshops/mathneuro) a new yearly
conference, focused on mathematical aspects.
The NeuroComp Conference (http://www.neurocomp.fr/index.php?page=welcome) a yearly computational
neuroscience conference (France).
Bernstein Conference on Computational Neuroscience (BCCN) (http://www.nncn.de/Aktuelles-en/
bernsteinsymposium/Symposium/view?set_language=en) a yearly conference in Germany, organized by the
Bernstein Network for Computational Neuroscience (http://www.nncn.de/willkommen-en/

Computational neuroscience
view?set_language=en).
AREADNE Conferences (http://www.areadne.org/index.html) a biennial meeting that includes theoretical
and experimental results, held in even years in Santorini, Greece.

Social Networks
Maciej Lazarewicz's Computational Neuroscience Linkedin group (http://www.linkedin.com/groups/
Computational-Neuroscience-1376707)

Websites
Perlewitz's computational neuroscience on the web (http://home.earthlink.net/~perlewitz/)
Encyclopedia of Computational Neuroscience (http://www.scholarpedia.org/article/
Encyclopedia_of_Computational_Neuroscience), part of Scholarpedia, an online expert curated encyclopedia on
computational neuroscience, dynamical systems and machine intelligence

Article Sources and Contributors

Article Sources and Contributors

Computational neuroscience Source: http://en.wikipedia.org/w/index.php?oldid=464818094 Contributors: A314268, APH, ASmartKid, Aaron Schulz, Alex.tan, Alterego, Alv, Andorin,
Ariangiovanni, Arne Heise, Ashleyisachild, BUCompNeuro, Bayle Shanks, Benhocking, BertSeghers, Bkroeger, Brainboychik, Cardoso44, Cardosodeoliveira, CasperEACClemence, CesarB,
Ceyockey, Chardar, Chealer, Chzz, Cleanwiki, Clicketyclack, CortexSurfer, Cuaxdon, Cyberfay, Database, Davidcofer73, Deodar, Destexhe, Dicklyon, DividedByNegativeZero, Djhbrown,
Docu, Dontaskme, DrPhoenix, Duagloth, Ebegoli, Eerosim, Epugachev, ErikDS59, Flynner, Gaelle Desbordes, Gal chechik, Ha-reed, Hiturik, Hu, James-davis, Jean-Francois Gariepy, Joeyo,
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Mattisse, Meduz, Memming, Michael Hardy, Mosquitopsu, N d s f, Necrotranson, Nectarflowed, Neurocompute, Neuromusic, NeuronExMachina, Neuropsychology, Ngoddard, Niarb, Novum,
Obankston, Occhanikov, Orvilleduck, Pascal.Tesson, Pgr94, Pillai ajay, Pointer2948, Polarwind13, Psyklic, RDBrown, Rbrette, Rich Farmbrough, Rjanag, Rjwilmsi, Rnwatanabe, Robclewley,
Ryly, SamuelRiv, Sardanaphalus, Scott Illini, Sjs2008, Sluox, SparkOfCreation, Specdude, Srikanth rswamy, SunCreator, Talanvalash, Teemu08, TjeerdB, Toddphen, Torcini, Transient cns,
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