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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 – – – – 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 • • • • • • 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 • • 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: • • • 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):