The FDK Unit Scientific Advisory Board Meeting

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The FDK UnitScientific Advisory Board Meeting

• Thursday Nov 28 2002
• Department of Computer Science
• University of Helsinki

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Who are we?

• Host institutions
• University of Helsinki, Department of Computer
  Science
• Helsinki University of Technology, Labortory of
  Computer and Information Science
• about 50 people altogether
• seniors Esko Ukkonen (director), Heikki
  Mannila, Tapio Elomaa, Helena Ahonen-Myka, Jaakko
  Hollmen, Hannu Toivonen
• postdocs Kimmo Fredriksson, Juha Kärkkäinen,
  Kjell Lemström, Greger Linden, Juho Rousu, Marko
  Salmenkivi

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What do we do?

• The FDK unit develops methods for forming useful
  knowledge from large masses of data. The unit
  operates in multidisciplinary fashion,
  integrating in its research groups excellence in
  computational methods, statistical techniques,
  and application sciences.
• data gt computational methods gt knowledge

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Core competence

• Combinatorial Pattern Matching searching and
  matching of strings and more complicated
  (discrete) patterns, derive their combinatorial
  properties, and exploit these to achieve superior
  performance for the corresponding computational
  problems
• Data Mining finding interesting and useful
  patterns from masses of data
• gt Combinatorial algorithms probabilistic models

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The 6 step FDK model
1. Find an interesting computational problem on
an application area 2. Find a conceptual basis
and formalize the problem 3. Develop a solution
algorithm 4. Analyse the algorithm 5. Implement
the algorithm as a prototype software 6.
Experiment with the method and tune it using real
data
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Themes

• Theme I Data mining and machine learning
• Theme II Computational methods in medical
  genetics and expression data analysis
  (bioinformatics)
• Theme III Combinatorial pattern matching and
  information retrieval
• Theme IV Computational structural biology

Coherence and interaction!
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Teams

• Team Mannila data mining, computational biology,
  ...
• Team Elomaa algorithmic machine learning
• Team Toivonen data mining, computational
  biology,...
• Team Ahonen-Myka IR, language technology
• Team Hollmén data analysis
• Teams Ukkonen/Lemström/Rousu pattern matching,
  computational biology, music IR

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Contacts

• Finland
• - HIIT Basic Research Unit
• - VTT Biotech/Hans Söderlund Biology/Dennis
  Bamford, Medical Genetics/Leena Palotie, Juha
  Kere, Linguistics/Kimmo Koskenniemi,
  Paleoecology/Atte Korhola,... of UH Nevanlinna
  Institute
• - Nokia, Sonera, other companies
• Graduate schools ComBi, HeCSE, ComMIT, LangTech

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Contacts

• International EU, European Bioinformatics
  Institute, Max-Planck-Institute
  Saarbruecken/Berlin, Bielefeld, Freiburg, UC
  Irvine, Microsoft Research, Padova, Bergen,
  Stanford...

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Activities

• research work in teams
• study seminars, teaching
• ECML02 and PKDD02 conferences in August 2002
• Masters program in bioinformatics (will start
  2003)
• PhD education (grad schools etc)
• visitors coming and going
• contact seminars Biocentrum Viikki, Biomedicum

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Personnel

• A. Finnish Male Female Total
• Professors 5 1 6
• Other senior researchers 1 1
• Postdocs 6 1 7
• Grad school students (Min of Education) 14 5 19
• Other postgrad students 1 3 4
• Other academic 10 10
• Auxiliary personnel
• B. Foreign
• Professors
• Other senior researchers
• Postdocs
• Grad school students (Min of Education)
• Other postgrad students 2 1 3
• Other academic 3 3
• Auxiliary personnel
• TOTAL 42 11 53

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Funding in 2002 (KEuros)

• Domestic
• Own basic funding (home inst) 286
• Academy of Finland 60
• National Technology Agency 110
• Other domestic
• - Academy of Finland 537
• - Univ Helsinki 75
• - Univ Helsinki (project) 35
• - Min of Education (grad schools) 140
• - Helsinki Univ Technology (home inst) 90
• - enterprises 230
• - VTT 10
• B. Foreign
• - Max-Planck-Institut 40
• - EU
• TOTAL 1616

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FDK Future Goals

• more postdocs, more visitors
• EU projects, TEKES, Systems biology
  programme/Academy
• Focus combinatorial algorithms probabilistic
  models
• - foundations of combinatorial pattern matching
• - foundations of data mining
• - genome structure
• - regulatory networks in comp biology
• - human language applications

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Plans for 2003
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FDK Future Goals

• more postdocs, more visitors
• EU projects, TEKES, Systems biology
  programme/Academy
• Focus combinatorial algorithms probabilistic
  models
• - foundations of combinatorial pattern matching
• - foundations of data mining
• - genome structure
• - regulatory networks in comp biology
• - human language applications