Transcript Epilepsy Sonification (Vicinanza et al) - Indico

Grid Computing and Data Sonification tools as
SaaS for supporting neuroscientists in analysing
EEGs of patients affected by drug-resistant
epilepsy
Roberto BARBERA
University of Catania & INFN CT, Italy
Francesca FALCETTA
The Mario Negri Institute for Pharmacological Research, Milan, Italy
Massimo RIZZI
The Mario Negri Institute for Pharmacological Research & ARCEM, Milan, Italy
Giuseppe LA ROCCA
INFN CT & IGI, Italy
Mariapaola SORRENTINO
ASTRA Project
Domenico VICINANZA
DANTE, Cambridge, UK
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Outline
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The Data Sonification process in a nutshell
How does the sonification process work ?
 The Mario Negri Institute
The Epilepsy disease
– EEGs
– Intracranial vs. conventional EEGs recording
The mission
 The role of advanced R&E networking and Computing Infrastructures
The Catania Science Gateway components
The Sonification process running on a Science Gateway
First preliminary results
 Summary & Conclusions
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 The Data Sonification process in a nutshell
 How does the sonification process work ?
 Benefits of the sonification techniques
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Data sonification
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Representation of data sets and information through sounds and
melodies
 Same as creating a graph
 using notes and tones instead of lines and points
Credits: D. Vicinanza et al. LHC Open Symphony
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How does sonification work?
Associating a musical note to each value
Two conditions:
Uniqueness:
– Same value  same note
– Ex: 25  middle C
Covariance:
– Melody varies as quickly as the data.
– Ex: 25  C, 26  D, 27  E …
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Advantages of sonification
Sonic representations are particularly useful when dealing
with
complex, high-dimensional data,
data monitoring tasks
pattern detection
Transitions between random states and periodic/regular
ones
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The Mario Negri Institute
What is Epilepsy ?
Epilepsy in numbers
EEGs
Intracranial EEGs recording
The mission
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The Mario Negri Institute for
Pharmacological Research
Not-for-profit biomedical research organisation (est 1961)
From the molecular level to the whole human being
Developing new drugs and
Making existing ones more effective
Main research headings:
Cancer research
Nervous and mental illnesses
Cardiovascular and kidney diseases
Rare diseases
Toxic effects of environmental contaminants
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What is Epilepsy ?

Epilepsy is a brain disorder that causes people
to have recurring seizures
 The seizures happen when clusters of nerve
cells, or neurons, in the brain send out the
wrong signals
 People may have strange sensations and
emotions or behave strangely.
 Violent muscle spasms, auras, convulsions or
lose consciousness
 Epilepsy has many possible causes, including illness, brain injury and
abnormal brain development. In many cases, the cause is unknown
 Epilepsy is an illness as old as human kind. It was mentioned in ancient
Babylon more than 3,000 years ago
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Epilepsy in numbers
Still an unresolved problem
Still one of the most common neurological disorder
~ 1% of the world-wide population affected
50 million people
– 90% in developing countries
More likely to occur in young children or over 65
~ 25% of patients refractory to the conventional anti-epileptic
drugs
Famous people affected by epileptic seizures:
Vincent van Gogh
Julius Caesar
Alexander the Great
Lord Byron
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…
EEGs
 Diagnose: Brain scans, EEGs…
 An electroencephalogram (EEG) is a test used to
 record the brain’s electrical activity
 From EEGs physicians can look for abnormal patterns:
 seizures
 encephalopathies
Red-colored area highlights the abnormal
EEG activity peculiar of a seizure
Usually, the onset of a seizure is
associated to a rapid build up of 4 to under
8 Hz rhythmic activity of EEG.
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Intracranial EEGs recording

Usually recorded from scalp,
 also from electrodes within the brain - intracranial EEGs recording
 less affected by spurious signals
Electrode strip
Source: Freiburg’s EEG database
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The mission
“inter-ictal” EEGs
– EEGs recorded sufficiently far from seizures
Analysed for the first time using a sonification technique
– to identify a baseline condition (hopefully, a marker)
This may help to:
 highlight and characterize patterns
 provide a powerful tool for seizure prevention
 by listening to how musical patterns change
 forecast an impeding seizure in advance.
 promote the investigation for new therapeutic
interventions
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The role of advanced R&E networking and Computing Infrastructures
 The Sonification process running on a Science Gateway
 The Catania Science Gateway components
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The role of advanced R&E Networking
and Computing Infrastructures
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Sonification and subsequent data analysis requires enormous amounts of
networking and processing power to produce results
– EEG sequences needs to be analysed using different parameters and
different mapping options
– High quality audio files (displaying the evolution of the melody) need to
be generated for each EEG data sequence
• For this analysis we used the MidiToolbox software
• Other tools are under investigation (i.e. WaveLab)
– To analyse just a few MB of data using, for example, 100 different
configurations would require a few hours on a standard laptop (2.4
GHz Intel Core 2 Duo, 2 GB RAM) and just a few minutes on the grid
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The GÉANT Network
http://www.geant.net
25 European
POPs
12,000km of dark
fibre on 18 routes
50,000km network
infrastructure on
44 routes
Diversified footprint
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Serves 40 million users
8,000 institutions
Across 40 European
countries
• GÉANT is co-funded by Europe’s NRENs and the European
Commission (EC) under the Seventh Framework Programme (FP7)
• Project Partners are 32 European NRENs, TERENA and DANTE
• 150 FTEs’ annual effort (> 350 individuals) working in GÉANT
across Europe
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Courtesy of T. Fryer
GÉANT: Global Reach
http://global.geant.net/
GÉANT connects to 62 countries
outside Europe
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The Science Gateway
Primary requirements:
Based on standards
Modular
Easy to use
Re-usabile
The architecture:
JSR 286 standard and Liferay as portlet container
Identity Federations based on the SAML 2.0/Shibboleth
Computing resources access: (J)SAGA
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Grid transactions
Grid transactions:
Robot X.509 certificates
JAX-RS and PKCS#11 standards
Compliant with:
EGI VO Portal Policy
EGI Grid Security Traceability and Logging Policy
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The Catania Science Gateway
Components
Science
Gateway
Standard-based (SAGA)
middleware-independent Grid Engine
Administrator
Power User
Basic User
Users from
different
organizations
having different
roles and
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privileges
Access the data
Sonification process
running on http://gw.ct.infn.it
It provides
instructions for
users and
configuration
settings
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Select the computing resource
running on
http://gw.ct.infn.it
It shows the
computing
resources where
the SW has been
successfully
deployed
It is possible to
select & rank the
generic computing
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resource
Select the data set
running on
http://gw.ct.infn.it
Select the
type of
algorithm to
be used
Upload the data
set as ASCII file or
using the
text-area
Job description
Enable the
analysis of
MIDI file
with Matlab
Enable e-mail
notification
Configure some
advanced settings
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Check the status of the
simulations
Shows the
status of the
simulations
Asks for support
Automatic jobs
output
downloading
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
First preliminary results
 EEG analysis: tonal map
 EEG analysis: melodic event series
 EEG analysis: melodic contour
 EEG analysis: interval distribution
 Summary & Conclusions
 Links & Contacts
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EEGs analysis:
Tonal Map
The idea: correlate
tonal distribution with
the disease stages to
find a marker
Frame extracted from a tonal map animation showing the evolution of the
melody around a tonal centre.
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EEGs analysis:
Melodic Event series
The idea: find clustering and changes in the distribution and
correlate them with phases or stages in the disease
The series of music events (notes) as a function of time.
The ultimate goal is to contribute to the determination of an actual music
marker
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EEGs analysis:
Melodic Contour
The idea: find clustering and
changes in the distribution
The series of music events (note pitches), connected by line segments, as a
function of time.
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EEGs analysis:
Interval Distribution
The ideafind the proper
mapping so to correlate
that distribution with the
disease stages to find a
marker
The distribution of music intervals in the analysed EEGs
Here as well, the hope is to
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Summary and Conclusions
 Advanced R&E networking and e-Infrastructures have been used to
identify “markers” for denoting some specific epileptic EEG states
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Sonification techniques are the most appropriate tools for extrapolating
temporal-correlated properties in time series as musical patterns
 Visual approaches don’t take temporal information into account
 Our research is at early stage.
 Only few EEGs have been analysed.
 More research is needed to corroborate preliminary results!
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Download the Sonification White paper (PDF)
EEG Sonification For Epilepsy Surgery: A Clinical Work-In Progress [link]
Midi Toolbox [link]
Contacts:
Roberto Barbera ([email protected])
Francesca Falcetta ([email protected])
Giuseppe La Rocca ([email protected])
Massimo Rizzi ([email protected])
Mariapaola Sorrentino ([email protected])
Domenico Vicinanza ([email protected])
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