Transcript sma2-lifescience

Introduction to the
Knowledge Discovery Department
Institute for Infocomm Research
Limsoon Wong
Deputy Executive Director (Research)
I2R: Imagination to reality
I2R Knowledge Discovery Dept:
INTRODUCTION
I2R
•
BMRC
SERC
•
IMRE
IME
DSI
IHPC
ICES
SIMTECH
•
Advance Infocomm
Technology to benefit
humanity and create
prosperity for S’pore
core values: Dedication to
excellence, passion for
innovation, integrity &
respect
size: 350 RSEs
mission:
Organization
I 2R
Services & Applications
Infocomm
Security
• Cryptography
• Network security
• Information
security
Communications & Devices
Knowledge
Discovery
E-Service
Infrastructure
• Knowledge
Extraction
• Decision Systems
• Discovery
Systems
• Service
Composition
• Service creation
• Data-in-Network
• Connected Home
• Secure Filesystem/
DBMS
Embedded
Systems
Radio Systems
• Terminal
• Software Defined
Radio
• Transceiver system
• Antenna
• Radio Over Fiber
• UWB
Media
Media
Processing
• Mutimedia Signal
Processing
• Noise Reduction
Networking
• Next Gen IP
• End-to-end QoS
• Mobile Middleware
• Mobile Adhoc Networks
• Mobile Sensor Networks
Media
Semantics
Human Computer
Interaction
• Media Adaptation
• Mixed Media Mining
• Natural Language
Synergy
• Pervasive Media
Digital Wireless
• Modem Technology
• Multiple Access
• Smart Antenna Array
Systems
• Perceptual Human
Media
• Speech & Dialogue
• Biometrics
Lightwave
• Network Design
• WDM Systems
• Fibre Technology
History
8 years of
bioinformatics
R&D in
Singapore
Integration
Technology
(Kleisli)
MHC-Peptide Protein Interactions
Extraction (PIES)
Binding
(PREDICT)
Gene Expression
Molecular
Cleansing &
Connections & Medical Record
Warehousing
Datamining (PCL)
(FIMM)
Gene Feature
Recognition (Dragon)
Venom
Informatics
GeneticXchange
1994
ISS
1996
1998
KRDL
2000
Biobase
2002
LIT/I2R
Direction & Plan
• Objectives
– Translate inspiration from
biological systems into
advancement of life and
computing sciences
– Advance data mining
technologies in decision
systems for complex
problems
• To work on practical
systems for
– data mining
– data cleansing
– knowledge extraction
• Applied to
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–
–
–
gene regulation
protein interaction
clinical data analysis
ligand-receptor
interaction
in addition to non-bio areas
I2R Knowledge Discovery Dept:
RECENT ACCOMPLISHMENTS
Predict Epitopes,
Find Vaccine Targets
• Vaccines are often the only
solution for viral diseases
• Finding & developing
effective vaccine targets
(epitopes) is slow and
expensive process
• Develop systems to recognize
protein peptides that bind
MHC molecules
• Develop systems to recognize
hot spots in viral antigens
Recognize Functional Sites,
Help Scientists
• Effective recognition of
initiation, control, and
termination of biological
processes is crucial to
speeding up and focusing
scientific experiments
• Data mining of bio seqs to
find rules for recognizing &
understanding functional
sites
Dragon’s 10x
reduction of
TSS recognition
false positives
Diagnose Leukaemia,
Benefit Children
• Childhood leukaemia is a
heterogeneous disease
• Treatment is based on subtype
• 3 different tests and 4 different
experts are needed for diagnosis
 Curable in USA,
 fatal in Indonesia
Cancer Cell, 1:133-143, 2002
• A single platform diagnosis
based on gene expression
• Data mining to discover
rules that are easy for
doctors to understand
Understand Proteins,
Fight Diseases
• Understanding function and role of
protein needs organised info on
interaction pathways
• Such info are often reported in
scientific paper but are seldom
found in structured databases
• Knowledge extraction
system to process free text
• extract protein names
• extract interactions
Recent Collaborations/Partners
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Molecular Connections, India
FANTOM2 Consortium
RIKEN, Japan
Nature 420, 563-573, 2002
St Jude, USA
BioBase, Germany
Canberra Hosp., Australia
GIS, Singapore
I2R Knowledge Discovery Dept:
PEOPLE
Who will you be working with...
Heads
of labs
Jinyan Li
Other PIs
Vladimir Bajic
• 18 full-time staff comprising
9 PhD, 6MSc, and 3BSc
• Our faculty holds adjunct
professorial positions in
SANBI, Univ. of Canberra,
NUS, and NTU
Limsoon Wong
See-Kiong Ng
Vladimir Brusic
Track Record
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3 chief editorial
roles, and 9 editorial
board memberships
International Conferences (last 5 years): 4
conference chairs, and
more than 40 program
committee roles, 10
keynote lectures, and
dozens of plenary talks
Journals:
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More than
100 in last 5 years,
mostly in reputable
journals (e.g. Nature,
PNAS, Cancer Cell,
JACM) and top
conferences.
Patents (last 5 years): 1 granted and
6 pending
Commercialization (last 5 years): 2
international start-ups
and one software
licensed
Publications (last 5 years):