Springer handbook of bio- neuroinformatics

1239 Pages·2014·23.122 MB·English

by  Kasabov, Nikola (ed.)

Springer

Handbook
oƒ
Bio-/Neuro-
Informatics
Kasabov
Editor
123
Springer Handbook
of Bio-/Neuroinformatics
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Springer
Handbook
of Bio-/Neuroinformatics
Nikola Kasabov (Ed.)
With490Figuresand92Tables
123
Editor
NikolaKasabov
AucklandUniversityofTechnology
KEDRI–KnowledgeEngineeringandDiscoveryResearchInstitute
120MayoralDrive
Auckland,NewZealand
ISBN:978-3-642-30573-3 e-ISBN:978-3-642-30574-0
DOI10.1007/978-3-642-30574-0
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V
FormymotherKapkaNikolovaMankova-Kassabova(1920–2012)
whowroteinBulgarian,amongmanyothers,thelittlepoems:
Iwillrunoutoftime
(cid:0)(cid:2)(cid:3)(cid:2)(cid:4)(cid:5)(cid:6)(cid:7)(cid:5)(cid:8)(cid:9)(cid:10)(cid:7)(cid:11)(cid:9)(cid:5)(cid:7)(cid:2)
Tounlockallthesecrets,
(cid:12)(cid:10)(cid:13)(cid:10)(cid:14)(cid:8)(cid:10)(cid:11)(cid:10)(cid:15)(cid:7)(cid:10)(cid:16)(cid:9)(cid:5)(cid:7)(cid:2)(cid:9)(cid:10)(cid:17)(cid:5)(cid:7)(cid:5)(cid:2)(cid:7)(cid:18)
Tohealallthewounds,
(cid:12)(cid:10)(cid:5)(cid:14)(cid:19)(cid:2)(cid:20)(cid:21)(cid:22)(cid:10)(cid:4)(cid:23)(cid:18)(cid:22)(cid:2)(cid:24)(cid:20)(cid:5)(cid:7)(cid:2)(cid:13)(cid:10)(cid:9)(cid:5)
Toexpressallmylove.
(cid:25)(cid:11)(cid:10)(cid:5)(cid:14)(cid:20)(cid:10)(cid:26)(cid:10)(cid:19)(cid:27)(cid:17)(cid:18)(cid:22)(cid:7)(cid:10)(cid:6)(cid:5)
FromtheeditorofthisSpringerHandbook,NikolaKasabov
VII
Foreword
Life is a striking state of material that emerged 3.6billion years ago on our earth.
It has the ability of self-reproduction, by keeping information about itself in itself.
The marriage of information and matter makes it possible to implement the evolu-
tionalmechanism.Thus,lifehasdevelopedtoachieveavarietyofamazingstructures
and functions. In particular, we humans have appeared, with the characteristics of
intelligenceandconsciousness,constructingsocietiesandculture.
Now the time is ripe to understand the mechanisms of living systems, where in-
formationiskeptandprocessedefficientlyandrobustly.Thesemechanismsarehighly
complex and exquisite; their structures range from the molecular level to the higher
level of the brain function. Advanced information science/technology is required to
deciphertheinformationmechanismsoflife.Thisresearchfieldiscomposedofbioin-
formaticsandneuroinformatics,whicharecloselyrelated.Theyincludeawiderange
of hierarchical levels of molecules, cells, systems, and individuals. We need a good
Shun-ichiAmari
perspectiveoftheseextremelywidefieldsinasystematicandunderstandableway.
ThepresentHandbookisintendedtoprovidenotonlyanoverviewofthestateof
theartinbioinformaticsandneuroinformaticsandtherelatedresearchproblems,but
also detailed informatics methods and techniques to address them. In this Handbook
onecaneasilyfindimportanttheoreticalinformaticstoolsnecessaryforbioinformatics
andneuroinformaticsresearch,includingthenecessarydetails.
Iamhighlypleasedtoseethatsuchahandbook,coveringallaspectsofbioinfor-
maticsandneuroinformaticstogetherwiththeirtoolsandmethods,isbeingpublished.
BrainScienceInstitute
RIKEN,Saitama Shun-ichiAmari
Professor Shun-ichi Amari is IEEE Life Fellow, foreign member of the Polish
Academy of Science and Professor-Emeritus at the University of Tokyo. He is past-
Director of he RIKEN Brain Science Institute and is now a senior advisor. He has
publishedmorethan300papers,includinginitiationofinformationgeometryandpi-
oneering works on neural networks. He is the past President of International Neural
NetworksSociety(INNS),theInstituteofElectronic,InformationandCommunication
Engineers, Japan (IEICE) and founding President of Asian-Pacific Neural Networks
Assembly(APNNA).Heisafoundingco-editor-in-chiefofNeuralNetworks.Here-
ceived the Emanuel A. Piore Award and Neural Networks Pioneer Award from the
IEEE,theJapanAcademyAward,theJapaneseOrderofCulturalMerit,andtheINNS
GaborAward,amongmanyothers.
IX
Foreword
FromDatatoSynthesis:TheHumanBrainProject anaccelerateddevelopmentofbrain
inspired computing technologies.
Brain research is entering its maturing stage. Enor- Those technologies will be based
mous amounts of data, information, and knowledge on the knowledge generated from
havebeenaccumulatedandarebeingaccumulatedev- the new insights of brain struc-
ery day. The challenge now is to put all these into ture and function obtained in the
integrated models and systems and to facilitate a bet- HBP. Specifically, the HBP will
terunderstandingofthebrain.ThisSpringerHandbook develop a high performance, visu-
ofBio-/Neuroinformaticsisverytimelyinthisrespect. allyinteractiveexa-scalecomputing
The European Commission has recently approved infrastructure,novellowpower,ro-
the Human Brain Project (HBP) as a flagship in bust, self-adapting computing, and
the Future Emerging Technologies (FET) program communication devices and with
(www.humanbrainproject.eu). The HBP commenced this lay the groundwork for a new Foto:F.Hentschel
a30monthsramp-upphasein2013andisexpectedto fundamentallydifferentparadigmof KarlheinzMeier
continueforatotalof10years.Theoverallgoalofthe computing. UniversitätHeidelberg
projectistobuildanewEuropeanresearchinfrastruc- In order to achieve these goals, Kirchhoff-Institut
tureforbrainrelatedresearchwithastrongemphasison the HBP has started to build six fürPhysik
Co-Directorofthe
state-of-the-art information and communication tech- technology platforms, which will
HumanBrainProject
nologies (ICT). Through the development of methods serve the scientific community in
and tools, the integration of data, and the construction Europe and beyond in addressing the goals described
of technology platforms the HBP will follow the suc- above. The six platforms will be hosted by partner
cessfulmodeloflarge-scaleresearchinfrastructuresin groups of the HBP and dedicate their work to the fol-
other scientific fields to tackle one of the most funda- lowingtasks:
mentalchallengesofbasicresearch,linkingtheresults
directlytomedicalandcomputingapplications. 1. Neuroinformaticsplatform:Thetaskistoaggregate
TheHBPaddressesthreemajorresearchareas:neu- neurosciencedataandtodeliverbrainatlases.
roscience, neuromedicine, and future computing. In 2. Medical informatics platform: the task is to ag-
neuroscience the project aims at an accelerated under- gregate clinical records and to classify brain dis-
standingofthehumanbrainbybuildingandsimulating eases.
unifyingbrainmodels.Progressinthischallengingarea 3. Brain simulation platform: the task is to develop
of basic research is expected by increasing the value software tools and to run closed loop brain simu-
ofpastandfutureexperimentsthroughintegrationinto lations.
publiclyavailablebrainatlases;fillingopenknowledge 4. High performance computing platform: the task is
gaps using predictive software tools and strategically todevelopandoperateHPCsystemsoptimizedfor
selectedexperiments,whichwillbeprioritizedandop- brainsimulations.
timized for the use in simulations. In neuromedicine 5. Neuromorphic computing platform: the task is to
thegoalistoacceleratetheunderstandingofbraindis- developandoperatenovelbrainderivedcomputing
easesbyincreasingthevalueofexistingclinicalrecords hardware.
anddatawithmoderndatastorageandmachinelearn- 6. Neurorobotics platform: the task is to develop
ing technologies. By systematically understanding the virtualroboticsystemsforclosedloopcognitiveex-
similarities and differences of brain diseases the HBP periments.
expects to provide tools for pharmaceutical and nutri-
tion companies to prevent, diagnose, and treat brain The platforms will be complemented by a new
diseases. The future computing research area aims at European Institute for Theoretical Neuroscience to in-
X
tegratebasicresearchoninformationprocessinginthe goingresearchandtotheenableapermanentdiscourse
brainandtousetheHBPplatformstoinspirenewthe- withthepublic.
oreticalapproachestothestudyofthebrain.Also,the
project will have a strong ethics group to monitor on- Heidelberg,July2013 KarlheinzMeier
CurriculumVitae
•
since2011:Co-DirectoroftheEUHumanBrainProject,ETFlagshipProject
•
since2011:InvitedprofessoratEPFL(Lausanne,Switzerland)
•
since2010:CoordinatoroftheEUBrainScaleSConsortium
•
since2009:CoordinatoroftheMarie-CurieNetworkFACETS-ITN
•
2005–2010:CoordinatoroftheEUFACETSConsortium
•
1999:FoundingDirectoroftheKirchhoffInstitutfürPhysik
•
1994–2012:ProjectleaderoftheLHC-ATLASTriggerPreProcessor
•
since1992:ChairExperimentalPhysics,Ruprecht-Karls-UniversitätHeidelberg
•
1990–1992:ScientificStaff(tenure)atDESY(Hamburg)
•
1988–1990:ScientificStaffatCERN(Geneva,Switzerland)
•
1984–1988:ResearchFellowatCERN(Geneva,Switzerland)
•
1984:PhDinPhysicsfromHamburgUniversity
•
1981:DiplomainPhysicsfromHamburgUniversity
FieldsofInterest
Experimentalparticlephysics,microelectronicsinstrumentation,physicsfoundationsofinformationprocessing,
brain-inspiredcomputing
XI
Preface
Oneofthegreatestscientificachievementsofthetwen- tions in a computer system. This will enable a better
tiethcenturywasthedecipheringofthehumangenome understanding of many cognitive processes and brain
and the genomes of many other species. The Hu- diseases,suchasAlzheimer’sdisease,stroke,epilepsy,
man Genome Project revealed the “mystery” of the Parkinson’sdisease,mentalretardation,andaging.The
human genome and provided us with an enormous BRAINproject,foundedintheUSAalsoin2013,aims
quantity of data and information that still needs to at the development of a broad set of activities for the
be properly processed in order to obtain new knowl- studyofthehumanbrainincluding:keyinvestmentsto
edge about the human race and its living environment jumpstarttheeffort,strongacademicleadership,public-
on this planet, their biological co-evolution, their cur- private partnerships, and maintaining highest ethical
rent state of development, and possibly, their future. standards.
These scientific and technological advancements led The active research in bio- and neuroinformatics
to the firm establishment of the science discipline and the vast amount of data and information, much of
bioinformatics. New biological data, information, and it overlapping and strongly related, requires a unified
knowledge have been produced in many institutes approachtotheanalysisofthisdataforthesakeofnew
from all over the world, for example: the Euro- knowledgediscovery.Thisistobeprovidedbyinforma-
pean Bioinformatics Institute, the National Centre for tionscienceasdemonstratedinthisSpringerHandbook
Biotechnology Information, and the RIKEN Bioinfor- ofBio-/Neuroinformatics.
maticsInstitute. TheSpringerHandbookwasachallengingproject,
Itisagreedthatthetwenty-firstcenturywillbede- as for the first time it puts together both the founda-
voted to the deciphering of the human brain. Several tions and the state-of-the art of three major science
projectsandinstituteshavealreadyaddressedthischal- disciplinesintheirinteractionandmutualrelationship,
lenge. The Blue Brain Project aimed at the computer namely: information science (IS), bioinformatics (BI),
simulation of brain functions at a low level of brain andneuroinformatics(NI).
informationprocessing.TheAllenBrainScienceInsti-
tute has already mapped tens of thousands of human
genestothebrainstructuresandfunctionsofmiceand
humans, providing an enormous amount of data (see
Chap.62). The goals of the RIKEN Brain Science In-
Bioinformatics Neuroinformatics
stituteforthetwenty-firstcenturyaretounderstand,to
create, and to protect the brain (see the Foreword by
Prof.Amari).Thereisaninternationalcoordinationof Information
neuroinformaticsactivitiesintheInternationalNeuroin- Science
formatics Coordinating Facilities, in which Japan has
taken a leading role (see Part J). All these activities
haveledtothefirmestablishmentofanotherscientific
discipline–neuroinformatics.
Recently, several new large-scale world projects The text contains 62 peer reviewed chapters orga-
have started to generate by the hour new, large-scale nized in 12 parts, 6 of them covering topics from IS
dataandinformationaboutthehumanbrain,including andBI,and6topicsfromISandNI.Eachchaptercon-
data related to biology, physiology, psychology, cog- sistsofthreemainsections:introductiontothesubject
nitive studies, and brain diseases. The Human Brain area,presentationofmethods,andadvancedandfuture
Project was founded in 2013 by the European Union. developments.
It includes more than 80 participants from Europe. It Some of the IS methods are presented separately,
aims at collecting data at each level of brain function- someareusedtoaddressproblemsinBIor/andNI,but
ing–molecular,genetic,proteomic,synaptic,neuronal there are also specific methods designed for BI or NI
ensembles, and cognitive, and to simulate brain func- only. The BI and NI areas also share IS methods, as