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Neuronformatics and Emerging Technologies February 19, 2007

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Title: Neuronformatics and Emerging Technologies February 19, 2007


1
Neuronformatics and Emerging TechnologiesFebruary
19, 2007
  • Team 3 - Tensa Zangetsu
  • Chiranjeev Bordoloi
  • Koch Geevarghese
  • Romerl Elizes
  • Yonesy Nunez

2
Agenda
  • Introduction
  • Definitions
  • Background
  • Current Work and Experiments
  • Current Support
  • Links
  • References

3
Introduction
  • Understanding the human nervous system is one of
    the greatest challenges of 21st century science
  • The topic we will focus on is neuroinformatics
  • The goal for this presentation is a general
    overview of neuroinformatics
  • Brain informatics is a subset of
    neuroinformatics, but most of the literature in
    neuroinformatics focuses on the brain

4
Definitions
  • Neuroscience
  • Field devoted to the scientific study of the
    nervous system
  • Disciplines include structure, function,
    development, genetics, biochemistry,
    pharmacology, and pathology.
  • Focuses on the investigation of the brain and
    mind.

5
Definitions
  • Neuroinformatics
  • intersection of neuroscience and information
    science.
  • many points of contact between the
    neuroscience-related life-sciences and the
    information sciences and related disciplines
  • Life sciences neuroscience, neurology,
    psychology, linguistics, biology, chemistry,
    physics, etc.
  • Information sciences computer science,
    mathematics, statistics, physics, electrical
    engineering, robotics, etc.
  • Goals of neuroinformatics
  • developing and applying computational methods to
    the study of brain and behavior
  • applying advanced IT methods to deal with the
    huge quantity and great complexity of
    neuroscientific data
  • exploiting our insights into the principles
    underlying brain function to develop new IT
    technologies.

6
Background
  • Neuroscience
  • In Egyptian times, the heart, not the brain, was
    classified as the seat of intelligence.
  • Hippocrates was the first to indicate that the
    brain was the seat of intelligence.
  • Roman physician, Galen, further backed this by
    providing evidence that Roman gladiators lost
    their mental faculties when they sustained severe
    damage to their brains.
  • Further studies of the brain was stagnant until
    the invention of the microscope. The work at
    first focused on the individual neurons.

7
Background
  • Neuroscience
  • Camillo Golgi in the 1890s silver chromate salt
    to reveal intricate structures of single neurons
  • Santiago Ramon y Cajal used Golgis information
    to develop the neuron doctrine. The hypothesis is
    that the functional unit of the brain is the
    neuron.
  • Santiago Ramon y Cajal and Camillo Golgi received
    the Nobel Prize in 1906 for Physiology for their
    work on the structure of the nervous system

8
Background
  • Neuroinformatics
  • Neuroinformatics is formally established by the
    National Institute of Mental Health in 1993 under
    the Human Brain Project.
  • In the Bioinformatics realm, the Institute for
    Genomic Research was established in 1992 in
    Rockville, Maryland.
  • The exponential growth of information
    technologies especially the Internet in the
    1990s has prompted the growth of
    neuroinformatics.

9
Background
  • Neuroinformatics
  • By 2000, 40 web-based projects with digital
    databases were steered by the Human Brain Project
  • This work impacts molecular biology and cellular
    physiology
  • Society of Neuroscience is formally established
    in 2003 to prompt the development and
    popularization of neuroscience to the world
    community.
  • In 2004, Program in International
    Neuroinformatics was established by 16 countries
    and the EU commission to promote international
    collaboration, dialogue, and support mechanisms
    for neuroscience application research.

10
Current Work and Experiments
  • This section will focus on
  • Posit Science
  • Brain-Gene Ontology Project
  • Human Brain Mapping
  • Brain Computer Interface
  • Snapshot of published papers in Neuroinformatics

11
Current Work and Experiments
  • Posit Science
  • Dr. Michael Merzenich and Dr. Henry Mahncke with
    other scientists developed a hypothesis designed
    to rejuvenate the brains plasticity.
  • Posit Science Inc. was founded in 2003 in San
    Francisco to develop a software program that
    could test and validate these neuroscientists
    hypothesis.

12
Current Work and Experiments
  • Posit Science
  • The connections in the brain are plastic, meaning
    that when we learn something, the properties of
    our synapses and other neural circuits change,
    thus improving their processing speed and the
    fidelity of the information encoded.
  • As we age, this natural learning process starts
    to deteriorate. This slowing is at the root of
    some age-related memory loss.
  • Recent research has shown that reading the
    newspaper or doing crosswords can help keep older
    people mentally fit.

13
Current Work and Experiments
  • Posit Science
  • Dr. Merzenich research study involves the
    subjects being asked questions from recorded
    narratives.
  • The narratives are played slowly at first and
    progressively become faster.
  • The narratives are easy at first and
    progressively become difficult.
  • The narratives are delivered via a computer-based
    training module with minimal interaction with
    researchers.
  • The level of challenge is crucial component in
    triggering brain plasticity.
  • The study was conducted with 95 older people aged
    63-94.
  • The exercises were speed of processing, spatial
    syllable match memory, forward word recognition
    span, working memory, and narrative memory.
  • The goal was for the subjects to train one hour a
    day for eight weeks.

14
Current Work and Experiments
  • Posit Science
  • Results
  • People who trained the full eight weeks
    significantly improved their scores on memory
    tests.
  • People who progressed to the most difficult
    levels of the narratives showed the greatest
    improvements.
  • Majority of participants gained ten
    neurocognitive years.
  • Exercise results
  • Speed of Processing 93 of participants
    improved by 41
  • Spatial syllable match memory 77 of
    participants improved by 10
  • Forward word recognition span 91 of
    participants improved by 18
  • Working memory 80 of participants improved by
    13
  • Narrative memory 91 of participants improved
    by 18

15
Current Work and Experiments
  • Posit Science
  • Other disciplines affected gerontology.
  • Papers derived from this work
  • Brain plasticity and functional losses in the
    aged scientific bases for a novel intervention
  • Memory enhancement in healthy older adults using
    a brain plasticity-based training program A
    randomized, controlled study

16
Current Work and Experiments
  • Brain-Gene Ontology
  • Nikola Kasabov, Vishal Jain, and other authors
    from Auckland University of Technology in New
    Zealand undertook the Brain-Gene Ontology (BGO)
    Project mapping the relationship between the
    brain and the genes.
  • The goals of the BGO project, through a software
    application, are to find if these relationships
    can be used for further investigations in
    neuroinformatics and bioinformatics.
  • A side goal of the BGO project is that it can be
    used as a training tool for researchers and
    students.
  • The project was presented in the Sixth Annual
    Conference of Hybrid Intelligent Systems in
    December 2006 under the title Brain-Gene
    Ontology Integrating Bioinformatics and
    Neuroinformatics Data, Information and Knowledge
    to Enable Discoveries.

17
Current Work and Experiments
  • Brain-Gene Ontology
  • BGO application consists of three parts
  • Brain organization and function contains
    information about neurons, synapses and
    electroencephalogram (EEG) data for normal and
    epileptic brain states.
  • Gene regulatory network contains sections on
    neuro-genetic processing, gene expression
    regulation, protein synthesis, and abstract GRN.
  • Simulation modeling contains sections on
    computational neurogenetic modeling (CNGM),
    evolutionary computation, evolving connectionist
    systems, spiking neural network, simulation
    tools, and CNGM results

18
Snapshot of the BGO neuro-genetic simulation tool
19
(No Transcript)
20
Snapshot of the BGO detail showing relations
between genes, proteins, neuronal functions and
diseases
21
Neurons entering the brain simulated activity
22
Snapshot signal propagation in neurons of the
brain
23
Current Work and Experiments
  • Mitre Corporation Human Brain Mapping
  • Human brain mapping data (MRI, fMRI, Cryosection,
    EEG, etc.) is rapidly accumulating worldwide
    (many terabytes)
  • but it is not widely shared
  • potential value of its scale is not being
    realized
  • Significant need for an appropriate information
    infrastructure.
  • Our goal
  • The goal of this proposal is to enable the
    world-wide exploration, analysis, and
    dissemination of the growing corpus of human
    brain mapping information.
  • Three basic architecture components
  • digital library, associated repository, warehouse
  • Five basic workflows
  • submission, retrieval, migration, definition,
    exploration

24
Overview Of Proposed System 5 Processes
5
4
Warehouse
Atlas Generation
Exploration - brain attributes - visualization -
spatial reasoning - content-based retrieval
Features
Probabilistic Atlases
Volume 3.2
3
Migration
Digital Library
Metadata Repository
Retrieval
Data Archive
partitions
2
gender race test score ....
Submission
1
25
Process 1 Submission To Library
Metadata Repository
Data Archive (structural MRI partition)
core images
non-core
race gender age
test scores genetic info scan conditions etc....
tissue-labeled, scalped, normalized
noise (motion) corrected

reconstructed
T1
PD
T2
(256 x 256 x 170 voxel matrix)
Data Validation Tests
Mapping Data
survey test (1) test (2) etc.
Associated Metadata
26
Process 2 Retrieval From Library
Query
Selected Data
Apply Access Policy
Data Archive (structural MRI partition)
core images
non-core
Repository
LRR
tissue-labeled, scalped, normalized
race gender age
test scores genetic info etc....
noise (motion) corrected

reconstructed
T1
T2
PD
(Library Retrieval Request)
27
Process 3 Migration Into Warehouse
Individual Brain Object
Data Warehouse


Feature Attributes
Labeled Brain Volume
Deformation Field
Structural Brain Hierarchy
(One instance per core scanned brain)
Extract Features And Annotate Structure Hierarchy
Replicate Associated Metadata
Voxel-Label Anatomic Regions
Warp To A Standard Space, (Generate Deformation
Field)
core images
T1 / tissue labeled brain volume
Digital Library
Repository
28
Process 4 Exploration Of Warehouse
Describe Query
Visualization
Spatial Reasoning
Content-based Retrieval
Standard Attribute/Value
Extended Feature
Query Interface
Data Warehouse
Queries
Answers
Optimization
Optional LRR
Individual Brain Objects


Feature Attributes
Labeled Brain Volume
Deformation Field
Structural Brain Hierarchy
29
Process 5 Atlas Definition Within Warehouse
genotype
gender male
25 lt age lt 30
Describe Subpopulation Characteristics
fact table
disease state
etc (extensible)
feature (e.g. hippocampal volume size)
Atlas Definition
Data Warehouse
Composite Brain Objects


Feature Attributes
Deformation Field Of Population Center To
Standard Space
Labeled Probabilistic Brain Volume
Structural Brain Hierarchy
30
Process 4 (revisited) Exploration (Atlases)
Describe Query
Visualization
Spatial Reasoning
Population Comparison
Standard Attribute/Value
Query Interface
Queries
Answers
Optimization
Data Warehouse
Atlas Data Model


Feature Attributes
Labeled Probabilistic Brain Volume
Deformation Field Of Population Center To
Standard Space
Structural Brain Hierarchy
31
Current Work and Experiment
  • Brain Computer Interface
  • Nick Chisolm is a man who became paralyzed in a
    rugby accident at age 23 in 1998.
  • He suffers from locked-in syndrome which is a
    condition where you have lost almost all physical
    motion in the body but not the brain. The brain
    is still working at 100 efficiency.
  • Nick only had physical movement with his eyes.
    When he needed to compose a sentence or word, he
    had to use his eyes to indicate the validity of a
    letter of a word.
  • This rehabilitation process is time consuming and
    extremely frustrating for the victim.
  • His suffering prompted the work on BCI for
    paralyzed people.

32
Introduction
  • Brain-Computer Interface (BCI) is a device which
    allows the human to control electronic devices
    just by thinking.
  • Current BCIs are based on Electroencephalogram
    (EEG) .
  • Peirre Glorr and Hans Berger discovered EEG in
    1969.
  • First BCI was built by Vidal in 1973
  • For more than 2 decades no real development was
    done in BCIs, mostly waiting for the technology
    to catch up.

33
BCI- How does it Works?
  • Amplify the EEG signals.
  • Digitize the signals.
  • Elimination of unwanted signals
  • Other necessary manipulation.
  • Translate the signals to computer commands.

34
BCI- Goes Wireless
  • Wearable or Wireless BCI is developed because of
    the advanced communication devices.
  • Wireless BCI interact with a PDA equipped with is
    the best visualization.
  • - Bluetooth for portability
  • GPS -- to be aware of the environment
  • WLAN 802.11b For access to the processing power
    in Office/Home.

35
BCI- Wireless Visualization
36
BCI- Current Issues
  • BCI is interested only in EEG wavelets from the
    Cerebrum (Thinking Center) .Eliminating other
    wavelets like Electrooculogram (EOG) ,
    Electromaygram (EMG), etc. is one issue.
  • Other Problems are
  • Slow user response times
  • Excessive error rates
  • High cost
  • Actual appearance
  • Long initial training periods

37
Current Work and Experiments
  • Brain Computer Interface
  • Paper from K. Navarro Wearable, Wireless Brain
    Computer Interfaces In Augmented Reality
    Environments
  • Current BCI does not currently follow design
    principles of the Human Computer Interaction
    (HCI) discipline. BCI should use this knowledge
    and follow this pattern language.
  • Author proposes the use of Augmented Reality
    Environments (AR) for the BCI wearer. Augmented
    Reality systems enhance the real world by
    superimposing information onto it. Ex pair of
    glasses with information overlaid on the screen.
  • Problem with making it reality Developing a BCI
    for an AR environment addresses a specific
    problem. The goal of the BCI is to work in a
    highly changing environment.

38
Current Work and Experiments
  • Brain Computer Interface
  • Dr. Jonathan Wolpow, Chief of Laboratory of
    Nervous Systems Disorders in NYS Department of
    Health Wadsworth Center spearheads an
    extraordinary BCI initiative.
  • Dr. Scott Mackler is one of his success stories.
    Dr. Mackler suffers from progressive
    neurodegenerative disease. He lost all movement
    in 1999.
  • With the help of Wolpows innovative approaches
    to BCI implementation, Dr. Mackler still goes to
    work.

39
Current Work and Experiments
  • Published papers from the Institute of
    Neuroinformatics for 2007
  • Fast sensory motor control based on event-based
    neuromorphic-procedural systems
  • The role of first and second order stimulus
    features of human overt attention
  • Modulation of synchrony without changes in firing
    rates
  • Sleep-related spike bursts in HVC are driven by
    the nucleus interface of the nidopallium
  • Time and space are complementary in encoding
    dimensions in the moth antennal lobe.
  • Gamma range cortico-muscular coherence during
    dynamic force output
  • Implementing homeostatic plasticity in VLSI
    networks of spiking neurons

40
Current Support
  • Human Brain Project
  • Sponsored by the National Institute of Mental
    Health of the National Institutes of Health
  • Established in 1993 to support the research
    efforts in neuroinformatics.
  • Find new ways in spearheading neuroinformatics
    research
  • Develop informatics tools and resources for
    neuroscience.

41
Current Support
  • Human Brain Project - Agenda of Annual Meeting
    April 24, 2006
  • Current Initiatives
  • Improving Image Analysis Tools
  • Create physiological data and exploit using
    simulation
  • Creation of ASTYNAX A pilot exploration of web
    technology
  • Problems with Data gathering
  • Data
  • Data heterogeneity
  • Lack of data standards
  • Cultural gap requires paradigm shift
  • Practice
  • Few repositories available for willing
    stakeholders
  • Information sparseness
  • Lack of Incentive

42
Current Support
  • Insititute of Neuroinformatics
  • Established in 1995 by the University of Zurich
  • States that 1 trillion dollars is spent on
    neuroinformatics mosty on communications,
    processing, and information management. Creating
    autonomous intelligent systems is slow.
  • Projects pursued within the institute are
  • Behavior and Learning in Intelligent Autonomous
    Systems
  • Representation and Sensory Motor Integration
  • Neuronal Architectures and Computation
  • Neuromorphic Chips and Systems
  • Neurotechnologies

43
Current Support
  • Computational Neuroscience/Neuroinformatics
  • Aims to unravel the complex structure-function
    relationships of the brain at all levels from
    molecular to behavioral in an integrative effort
    with many scientific disciplines.
  • Based in Europe, the organization is one of the
    primary sponsors in conferences geared toward
    computational informatics. Some of these
    conferences are in United States and Canada as
    well.
  • Sixteenth Annual Computational Neuroscience
    Meeting CNS, Toronto, Canada July 2007
  • MBX Special Topic Courses Neuroinformatics,
    Wood Holes, MA August 2006
  • Tenth Annual Conference on Cognitive and Neural
    Systems, Boston MA May 2006

44
Current Support
  • NYS Department of Health Wadsworth Center
  • Under Dr. Jonathan Wolpows supervision, are
    working on bring the BCI technology into home
    use.
  • Streamlined version of the Wadsworth BCI consists
    of
  • laptop computer
  • portable amplifier
  • breathable cap which contains just 8 electrodes,
    down from the original 64
  • currently about 4,000, but will price will drop
    as technology improves
  • Dr. Wolpow estimates that 70-80 with severe
    disabilities could use the Wadsworth BCI System.
  • Heavy funding from NIH for the next few years.

45
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46
(No Transcript)
47
Links
  • Brain-Computer Interfaces Come Home. National
    Institutes of Health National Institute of
    Biomedical Imaging and Bioengineering. November
    28, 2006. http//www.nibib.nih.gov/HealthEdu/Pubs
    Features/eAdvances/28Nov06
  • The Brain Computer Interface with Natasha
    Mitchell. AllInTheMind, ABC National Radio,
    Austraila. December 2, 2006. http//abc.net.au/rn/
    allinthemind/stories/2006/1799619.htm
  • Computational Neuroscience/Neuroinformatics.
    http//www.hirnforschung.net/cneuro/
  • The Human Brain Project. National Institutes of
    Health National Institute of Mental Health.
    http//www.nimh.nih.gov/neuroinformatics/
  • Institute of Neuroinformatics. University of
    Zurich. http//www.ini.unizh.ch/public/
  • Mitre Corporation Neuroinformatics website.
    http//neuroinformatics.mitre.org/index.html
  • Neuroinformatics. Wiki site. http//en.wikipedia.o
    rg/wiki/Neuroinformatics
  • Neuroscience. Wiki site. http//en.wikipedia.org/w
    iki/Neuroscience
  • Wadsworth Center New York State Department of
    Health. Home page. http//www.wadsworth.org/index.
    html

48
References
  • N. Kasabov, V. Jain, P. Gottgtroy, L. Benuskova,
    F. Joseph. Brain-Gene Ontology Integrating
    Bioinformatics and Neuroinformatics Data,
    Information and Knowledge to Enable Discoveries.
    Proceedings of the Sixth International Conference
    on Hybrid Intelligent Systems (HIS'06), pp. 13.
    December 2006.
  • H. Mahnke, A Bronstone, MM Merzenich. Brain
    plasticity and functional losses in the aged
    scientific bases for a novel intervention.
    Journal of Progress in Brain Research. Volume
    157. p. 81-109. 2006
  • H. Mahnke, B. Connor, J. Appelman, O. Ahsanuddin,
    J. Hardy, R. Wood, N. Joyce, T. Boniske, S.
    Atkins, M. Merzenich. Memory enhancement in
    healthy older adults using a brain
    plasticity-based training program A randomized,
    controlled study. Procceedings of the National
    Academy of Sciences. August 23, 2006.
  • K. Navarro. Wearable, wireless brain computer
    interfaces in augmented reality environments.
    Proceedings of the International Conference on
    Information Technology Coding and Computing
    (ITCC'04) Volume 2, p. 643. April 2004
  • E. Singer. Exercising the Brain Innovative
    training software could turn back the clock on
    aging brains. Technology Review, Massachusetts
    Institute of Technology, Cambridge, MA. November
    21, 2005
  • Wearable, Wireless Brain Computer Interfaces In
    Augmented Reality Environments. By Karla Felix
    Navarro, University of Technology, Sydney IEEE
    2004
  • P300 Detection for Brain-Computer Interface from
    Electroencephalogram Contaminated by
    Electrooculogram. By Motoki Sakai, Hiroyuki
    Ishita, Yuuki Ohshiba, Wenxi Chen, and Daining
    Wei Graduate School of Computer Science and
    Engineering, The University of Aizu, Ikki-machi,
    Aizu- Wakamatsu City, Fukushima 965-8580, Japan
    IEEE 2006
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