Ei dian otsikkoa

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Department of Computer ScienceIntroduction

• Jukka Paakki
• Head of Department

Faculty of Science Department of Computer Science
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General

• Faculty of Science
• Department of Astronomy
• Department of Chemistry
• Department of Computer Science
• Department of Geography
• Department of Geology
• Department of Mathematics and Statistics
• Department of Physical Sciences
• Department founded in 1967
• Since 2004, located at Kumpula campus

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Research strategy

• Research Teaching
• Five specialization areas of core computer
  science algorithms, information systems,
  intelligent systems, software engineering,
  distributed systems and data communications
• One applied specialization area bioinformatics
  and computational biology
• Research units Research groups
• Theory Applications Co-operation
• Basic research Applied research
• Core computer science Modern areas

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Staff 2004 (person-years)

• Professors 13
• Other senior staff 10
• Postdoctoral staff 18
• Doctoral students 59
• Other teaching staff 41
• Support and administrative staff 18
• Research active staff overall 115 (in 1998 68)
• Staff altogether 174 (in 1998 110)

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Publications
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Funding (Millions of Euros)
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Funding structure in 2004
Total funding
External (research) funding
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Studies
1999 2000 2001 2002 2003 2004
New Students MSc Students MSc Degrees PhD
Degrees Credit units (29 of the Faculty)
300 328 304 346 231 252
1982 2110 2230 2351 2364 2462
55 64 61 72 60 68
3 4 4 3 7 9
21345 20554 22004 20512 19841 17244
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Strengths

• Research connected to teaching and students
• Several internationally strong research groups
• Two large research units
• From Data to Knowledge - FDK
• Helsinki Institute for Information Technology -
  HIIT (Basic Research Unit - BRU)
• Research infrastructure
• Computing facilities
• Administration and IT support
• Kumpula science library
• Good success in the competition of research
  funding

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Opportunities

• Still stronger networking with international
  scientific community
• Joint European projects
• International recruiting
• Still stronger co-operation within Kumpula campus
• Other departments of the Faculty
• Finnish Meteorological Institute
• Finnish Institute of Marine Research
• Still stronger co-operation with other sciences
• Bioinformatics
• Geoinformatics
• Still stronger interaction with society
• Industrial innovations
• Linux and open-source software development

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Research presentations

• From Data to Knowledge - FDK
• Algorithms and Bioinformatics
  Professor Esko Ukkonen
• Information Systems Professor Hannu Toivonen
• Intelligent Systems Professor Petri Myllymäki
• Software Engineering Professor Inkeri Verkamo
• Distributed Systems and Data Communications
  Professor Kimmo Raatikainen

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The From Data to Knowledge (FDK) Research Unit
Algorithms and bioinformatics

• Esko Ukkonen

Faculty of Science Department of Computer Science
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Structure of the FDK

• national Center-of-Excellence status (Academy of
  Finland) for 2002-2007 basic funding 267 k /
  year
• host institutions
• University of Helsinki, Dept of Computer Science
• Helsinki University of Technology, Laboratory of
  Computer and Information Science
• about 60 members
• professors
• Esko Ukkonen (director, academy professor -2004)
  
• Heikki Mannila (academy professor 2004 -)
• Hannu Toivonen
• Helena Ahonen-Myka
• Juho Rousu (2005 -)
• Tapio Elomaa -gt Tampere Univ of Technology
• (Jaakko Hollmen (TKK))

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Mission and goals

• The FDK unit develops methods for forming useful
  knowledge from large masses of data. The unit
  operates in multi-disciplinary fashion,
  integrating in its research groups excellence in
  computational methods, statistical techniques,
  and application sciences.
• data gt computational methods gt knowledge
• problem gt concepts and formalization gt
  algorithm gt algorithm analysis gt
  implementation gt evaluation in practice

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Core competence

• Combinatorial Pattern Matching searching,
  matching and finding patterns in strings and in
  more complicated (discrete) structures, deriving
  their combinatorial properties, and exploiting
  these to achieve superior performance for the
  corresponding computational problems (Esko
  Ukkonen 1980 - )
• Data Mining finding interesting and useful
  patterns from masses of data (Heikki Mannila 1992
  - )
• gt Combinatorial algorithms probabilistic
  models
• Strong international reputation Mannila
  Toivonen Ukkonen on the top-ten list of most
  cited Finnish computer scientists

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People and groups

• Group Mannila
• H Mannila/SA
• G Linden/SA
• P Tsaparas/HIIT
• A Hinneburg/HIIT
• J Muilu/HIIT
• S Hyvönen/HIIT
• M Salmenkivi/HY
• A Patrikainen/ComBi
• J Seppänen/ComBi
• J Heino/HeCSE
• T Kujala/HY
• A Leino/HY
• N Tatti/TKK
• T Mielikäinen/HECSE FDK
• K Korpiaho/TKK SA
• J Juhala/TKK SA
• E Bingham/TKK

• Group Ahonen-Myka
• - H Ahonen-Myka/HY
• R Yangarber/FDK
• L Aunimo/KIT
• J Makkonen/FDK
• A Doucet/FDK
• M Lehtonen/HeCSE
• R Kuuskoski/Tekes
• O Heinonen/HY

• Group Ukkonen
• E Ukkonen/HY
• S Inenaga/FDK
• V Mäkinen/Bielefeld
• M Kääriäinen/Tekes FDK
• K Palin/ComBi EU
• P Rastas/FDK
• T Ojamies/HY
• M Lukk/FDK
• M Michael/ComBi
• J Lindgren/HecSE
• J Borras/HY

• Group Hollmen
• J Hollmen/TKK
• S Ruosaari/ComBi
• H Hiisilä/TKK
• M Korpela/TKKSA
• J Toivola/Tekes
• A Rasinen/TKKSA
• A Savolainen/TKK

• Group Rousu
• J Rousu/EU
• A Rantanen/SA
• E Pitkänen/Tekes SA
• P Parikka/Tekes
• A Åkerlund/Tekes

• Subgroup Lemström
• - K Lemström/HY FDK
• A Pienimäki/HY
• N Mikkilä/FDK

• Subgroup Gionis
• A Gionis/SA
• F Afrati/FDK
• N Haiminen/FDK

• Group Toivonen
• H Toivonen/HY
• P Sevon/Tekes FDK
• R Petit/SA
• P Hintsanen/Tekes
• L Eronen/HIIT
• K Laasonen/HeSCE
• M Raento/SA

• Subgroup Kärkkäinen
• J Kärkkäinen/HY FDK
• J Toivonen/FDK
• S Burkhard/FDK

• Subgroup Koivisto
• M Koivisto/FDK
• J Kollin/SA

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Internal collaborations

• Group Mannila
• H Mannila/SA
• G Linden/SA
• P Tsaparas/HIIT
• A Hinneburg/HIIT
• J Muilu/HIIT
• S Hyvönen/HIIT
• M Salmenkivi/HY
• A Patrikainen/ComBi
• J Seppänen/ComBi
• J Heino/HeCSE
• T Kujala/HY
• A Leino/HY
• N Tatti/TKK
• T Mielikäinen/HECSE FDK
• K Korpiaho
• J Juhala
• E Bingham/TKK

• Group Ahonen-Myka
• - H Ahonen-Myka/HY
• R Yangarber/FDK
• L Aunimo/KIT
• J Makkonen/FDK
• A Doucet/FDK
• M Lehtonen/HeCSE
• R Kuuskoski/Tekes
• O Heinonen/HY

• Group Ukkonen
• E Ukkonen/HY
• S Inenaga/FDK
• V Mäkinen/Bielefeld
• M Kääriäinen/Tekes FDK
• K Palin/ComBi
• P Rastas/FDK
• T Ojamies/HY
• M Lukk/FDK
• M Michael/ComBi
• J Lindgren/HecSE
• J Borras/HY

• Group Hollmen
• J Hollmen/TKK
• S Ruosaari/ComBi
• H Hiisilä/TKK
• M Korpela/TKKSA
• J Toivola/Tekes
• A Rasinen/TKKSA
• A Savolainen/TKK

• Group Rousu
• J Rousu/EU
• A Rantanen/SA
• E Pitkänen/Tekes SA
• P Parikka/Tekes
• A Åkerlund/Tekes

• Subgroup Lemström
• - K Lemström/HY FDK
• A Pienimäki/HY
• N Mikkilä/FDK

• Subgroup Gionis
• A Gionis/SA
• F Afrati/FDK
• N Haiminen/FDK

• Group Toivonen
• H Toivonen/HY
• P Sevon/Tekes FDK
• R Petit/SA
• P Hintsanen/Tekes
• L Eronen/HIIT
• K Laasonen/HeSCE
• M Raento/SA

• Subgroup Koivisto
• M Koivisto/FDK
• J Kollin/SA

• Subgroup Kärkkäinen
• J Kärkkäinen/HY FDK
• J Toivonen/FDK
• S Burhard/FDK

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External collaborations

• Finland
• Univ Helsinki Biology, Medical Genetics, Genome
  certer, Cancer biology, Institute of
  Biotechnology, Linguistics, Geography, Rolf
  Nevanlinna Institute, Atmospheric sciences,
• VTT Biotech, VTT Processes, Natl Public Health
  Inst,
• Nokia, TietoEnator, Orion, Fujitsu-Invia, other
  companies
• Graduate schools ComBi (director H. Mannila),
  HeCSE, ComMIT, LangTech
• International EU, European Bioinformatics
  Institute, Max-Planck-Institute
  Saarbruecken/Berlin, Bielefeld, Freiburg, UC
  Irvine, UC Berkeley, New York U, London,
  Southampton, Padova, Lyon, Haifa, Fukuoka, Seoul,
  

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EU projects

• Pascal (NoE on machine learning)
• Biosapiens European Network for Integrated
  Genome Annotation
• Regulatory Genomics (STREP)
• APRIL (STREP on combining logical and
  probabilistic framework for biological data)
• Inductive Queries for Mining Patterns and Models
  (STREP)

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Highlights 18 PhD dissertations from FDK in
1999-2004

• Mannila group
• Mika Klemettinen Knowledge discovery for
  telecommunication alarms.
• Nokia Research
• Pirjo Moen Similarity notions for data mining.
• lecturer at CS/UH
• Barbara Heikkinen Document structures and
  document assembly.
• Nokia Research.
• Vesa Ollikainen Simulation techniques for
  disease gene localization.
• Center for Scientific Computing.
• Marko Salmenkivi Computational methods for
  intensity models.
• postdoc at CS/UH.
• Mikko Koivisto Algorithms for the analysis of
  genetic risks.
• Academy postdoc at HIIT/BRU
• HMM techniques for genome analysis

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Highlights 18 PhD dissertations (cont)

• Toivonen group
• Kari Vasko Computational methods for
  paleoecology.
• Center for Scientific computing
• private company Ekahau
• Petteri Sevon Association-based gene mapping.
• Karolinska Institutet
• project manager at HIIT/BRU

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Highlights 18 PhD dissertations (cont)

• Elomaa group
• Juho Rousu Range partitioning in classification
  learning.
• VTT Biotech,
• London/Southampton (Marie Curie),
• now professor of bioinformatics at CS/UH
• dataflow techniques for metabolic modeling
• machine learning for structured data
• Matti Kääriäinen Learning small trees and graphs
  that generalize.
• postdoc at International Computer Science
  Institute (ICSI) of UC Berkeley (Richard Karps
  group)

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Highlights 18 PhD dissertations (cont)

• Ukkonen group
• Juha Kärkkäinen Text indexing algorithms.
• Postdoc at MPI Saarbruecken,
• EU project manager at CS/UH
• string algorithms library
• strong new algorithms for suffix arrays
• Kimmo Fredriksson Rotation invariant matching.
• Academy postdoc at Univ Joensuu, Finland
• Jaak Vilo Pattern discovery from biosequences.
• European Bioinformatics Institute (UK)
• Egeen Univ Tartu, Estonia
• Kjell Lemström String matching for music
  retrieval.
• City Univ London
• Academy Research Fellow at CS/UH
• query-by-humming systems
• geometric algorithms for music retrieval

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Highlights 18 PhD dissertations (cont)

• Ukkonen group (cont)
• Veli Mäkinen Parametrized approximate string
  matching.
• Postdoc in Bielefeld
• lecturer and Academy postdoc at CS/UH
• transposition invariant string matching
• Janne Ravantti Reconstruction of macromolecular
  complexes from electron microscopy images.
• postdoc at Structural biology CoE at Dept Biology
  of UH
• Teemu Kivioja Computational tools for a
  transcriptional profiling method.
• researcher at VTT Biotech
• Hellis Tamm Minimality of multitape finite
  automata.
• postdoc in Tallinn, Estonia

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FDK presentations in the site visit program

• Esko Ukkonen
• Hannu Toivonen
• Heikki Mannila (HIIT session)

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Algorithmic machine learning

• Group Jyrki Kivinen
• Computational learning theory on-line learning
• Motivation large multi-dimensional data sets
• Method comparative worst-case analysis
• Example on-line linear regression including
  kernel methods (a la SVM)
• President of Association for Computational
  Learning
• Group Tapio Elomaa (now with Tampere Technical
  University)
• decision trees and other classification methods
• two PhDs

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Algorithmics (E Ukkonen co)

• Publications (examples)
• Algorithmica, JCSS, SIAM J. Comput., J.
  Algorithms, J. Struct. Biol., Genome Research,
  Bioinformatics, Theoretical Computer Science,
  Information Systems, CPM, STACS, ISMB, WABI, PSB,
  
• Examples of algorithmic research
• fast suffix array direct construction of a
  suffix array in linear time
• immediately included in teaching materials
  internationally
• J. Kärkkäinen, P. Sanders, S. Burkhardt Linear
  work suffix array construction, J. ACM (in press)
• transposition invariant variants of string
  matching algorithms (Veli Mäkinen, Kjell
  Lemström, Gonzalo Navarro)

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Example applications
Hidden Markov Models for genome analysis ( H
Mannila M Koivisto)
Music retrieval ( K Lemström)
Uncovering gene enhancer elements
Metabolic networks and systems biology ( J Rousu
VTT Biotech)
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Uncovering gene enhancer elements ( J Taipale,
Biomedicum)
enhancer module
gene1
gene2
gene3
gene4
DNA
transcription
transcription factors
RNA
translation
Proteins
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Model of cell type specific regulation of target
gene expression
Common targets (e.g. Patched)
GLI
GLI
Ubiquitously expressed TF
transcription
Cell type specific targets (e.g. N-myc)
GLI
X
Y (tissue specific TFs)
transcription
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Binding affinity matrices

• Transcription factor binding sites represented
  by affinity matrices
• Discovered
• Computationally
• Traditional wet lab
• Microarrays

9 11 49 51 0 1 1 4 19 3 0 0
0 45 25 16 5 1 2 0 17 0 4 21
18 36 0 0 34 5 21 10
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Finding preserved motifs of binding sites

• looking at one (human) genome gives too many
  positives
• comparative approach take the 200 kB regions
  surrounding the same genes (paralogs and
  orthologs) of different mammals (human, mouse,
  chicken, ), find preserved clusters (motifs) of
  binding sites
• Smith-Waterman type dynamic programing algorithm
  with a novel scoring function

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Wet-lab verification

• Selected predicted cis-modules for wet-lab
  verification
• Fused 1kb DNA segment containing the predicted
  enhancer to a marker gene with a minimal promoter
  and generated transgenic embryos.

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Enhancer prediction for N-myc
200 kb Mouse N-Myc genomic region
200 kb Human N-Myc genomic region
Conserved GLI binding sites in two predicted
enhancer elements, CM5 and CM7
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Future plan, profile

• concentrate on sequences inversion problems on
  sequences
• internal patterns and structures of sequences
• sequence generating models
• sequence distances
• generalised sequences music, 2D, 3D, event
  sequences, time series,
• combine combinatorial and probabilistic framework

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Personnel

• group Esko Ukkonen
• V Mäkinen (postdoc)
• M Kääriäinen (Berkeley)
• K Palin
• P Rastas
• M Lukk
• M Michael
• I Autio
• P Parikka
• A Åkerlund
• Markus Heinonen
• J Borras/HY
• C Pizzi (postdoc/Padova)

• group Juho Rousu
• Ari Rantanen
• Esa Pitkänen
• subgroup Kjell Lemström
• A Pienimäki
• N Mikkilä
• subgroup Juha Kärkkäinen
• J Toivonen
• Former members visitors
• T Elomaa
• A Brazma
• G Navarro
• S Inenaga
• S Burkhardt
• J Vilo
• K Fredriksson
• T Kivioja
• H Tamm

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From Data to Knowledge Research Unit -
Information systems

• Hannu Toivonen

Faculty of Science Department of Computer Science
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Mission and goals

• Mission provide methods for analysing and
  querying masses of data for useful inferred
  knowledge.
• Research on data mining
• Computational methods for data analysis
• Theory of data mining, algorithms
• Implementations and applications
• Data mining in bioinformatics and language
  technology
• Interaction of applications and theory

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Structure

• Volumes in 1999-2004
• Personnel (current)
• 3 professors 2 postdocs 3 lecturers
• 14 PhD students
• 27 refereed journal articles, 48 refereed
  conference articles
• 8 PhDs
• External research funding 1.3 M
• 400 k Academy, 500 k Tekes, 400 k industry
• (127 MSc theses)
• Research done within FDK and HIIT BRU
• Networking across units, disciplines and industry

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Researchers and groups

• Prof. Hannu ToivonenData mining, bioinformatics
• Petteri Sevon, postdoc
• PhD students
• Lauri Eronen
• Petteri Hintsanen
• Kari Laasonen
• Renaud Petit
• Mika Raento
• Former members
• Floris Geerts, postdoc
• Päivi Onkamo, postdoc
• Kari Vasko, PhD 2004

• Prof. Helena Ahonen-MykaDoremi group data
  mining, language technology
• Roman Yangarber, postdoc
• PhD students
• Lili Aunimo
• Antoine Doucet
• Oskari Heinonen
• Reeta Kuuskoski
• Miro Lehtonen
• Juha Makkonen
• Jussi Piitulainen
• Former members
• Greger Linden, postdoc
• Mika Klemettinen, postdoc
• Barbara Heikkinen, PhD 2000

• Seppo Sippu, Prof.
• Harri Laine, Univ. Lect.
• Pirjo Moen, Univ. Lect.
• Greger Linden, Univ. Lect. (also BRU ACS)
• PhD students
• Satu Eloranta, Assistant
• Antti Leino, Assistant (also BRU data mining)
• Former members
• Heikki Mannila, Prof.
• Hannu Erkiö, Prof., Lect.
• Pekka Kilpeläinen, Prof.
• Juha Puustjärvi, Lect.
• Marko Salmenkivi, postdoc

(BRU data mining)
(BRU ACS)
(BRU data mining)
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Research topics

• Non-redundant association rules
• Frequent Datalog patterns
• Fast pattern enumeration and evaluation
  algorithms
• Discovery of functional dependencies
• Text pattern induction by alignment
• Discovery of maximal frequent sequences in text
• Unsupervised methods for knowledge acquisition in
  text
• Methods for text segmentation and its evaluation
• Time series segmentation
• (Efficient algorithms for) variable length Markov
  models
• Bayesian model fitting using MCMC
• Nested permutation tests

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Research projects (grouped by applications)

• Focus on selected application topics
• in bioinformatics and language technology
• where we can have a significant impact
• where we can team up with excellent application
  partners
• Gene mapping (Profs. Leena Peltonen, Juha Kere)
• discover genetic patterns in case-control data
• Haplotyping (Profs. Leena Peltonen, Juha Kere)
• find the highest probability strings (haplotypes)
  explaining sequences of pairs (genotypes)
• Information extraction from epidemiological
  reports (ProMED-mail/Harvard Medical School)
• extract facts (disease, location, time,) from
  plain text

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Research projects (grouped by applications)

• Question answering systems (Cross-language
  evaluation forum)
• find an answer to a users question in a document
  collection
• How many divorces were there in Bulgaria in
  2000?
• Ubiquitous computing (MIT, Berkeley, Oslo, UIAH)
• learn typical contexts by on-line clustering of
  stream data
• Reconstruction of past climate (Prof. Atte
  Korhola)
• regression predict past temperatures based on
  microfossils
• Metapopulation analysis and modeling (Prof. Ilkka
  Hanski)
• predict if a network of populations will survive
  or not
• Contributions to three strategic areas of the
  departmentdata mining, bioinformatics, language
  technology

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Highlights

• Discovery of a new asthma gene (Science 9.4.04)
• Evolution telecom alarm analysis ? concepts for
  frequent patterns ? levelwise search methods ?
  novel gene mapping algorithms (HPM, TreeDT) ?
  fielded application ? discovery of a new gene (?
  design of new medication)
• The first question-answering system for the
  Finnish language ( English and French)
• Based on language-independent pattern discovery
  methods for semantic annotation, question
  analysis and answer extraction

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Gene genealogy and TreeDT gene mapping
disease gene location
True genealogy
X
founder
5th generation
X
X
15th generation
X
X
X
X

• Mapping between biological concepts (genealogy)
  and computational concepts (trie)
• Tree disequilibrium tests if the estimated
  genealogy explains the disease
• Efficient algorithms, nested permutation tests

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Trend selected activities since 2002

• Publications
• with universities of Oxford, Antwerpen, Munich,
  Freiburg, Wales, NJIT, RPI, UC Riverside, Tufts
• in ACM Tr. on Database Systems, Information
  Retrieval, IEEE Pervasive Computing,
  Bioinformatics, Annals of Human Genetics,
  Ecology, Quaternary Science Reviews,
• publications since 2002 cited 150 times (Google
  scholar)
• Editorial activities
• Editor of Data Mining and Knowledge Discovery,
  Board member of Int. J. of Data Mining and
  Bioinformatics
• PC (vice) chairs in ECML, PKDD, ICDM, ICML,
  BIOKDD
• PC members in ACM SIGKDD, SIAM DM, ICDM, PKDD,
  PAKDD ICML, ECML, DS ACM SIGIR ICDE, SSDBM
  AAAI, ECAI,
• Edited book Data mining in bioinformatics
  (Springer)

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Relevance and interaction with society

• Fielded applications in industry and public
  sector
• Software for human genetics (HaploRec, HPM,
  TreeDT), epidemiological fact base (ProMED-PLUS),
  technical documentation, context analysis
  (ContextPhone)
• Licensed to Finland, USA, GB, Iceland, Belgium,
  Canada
• 2 granted patents, several pending applications
• Research funding from 10 companies
• Fujitsu, Nokia, Lingsoft, Wärtsilä, Citec,
  Jurilab, GeneOS, Biocomputing Platforms,
  Cyberell, Licentia,
• 400.000 of industrial funding during the
  evaluation period

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Future vision

• Continue work on important data analysis problems
  in bioinformatics and language technology
• Applications, including fielded and
  commercialized ones
• Theory and method development
• Collaboration across units, disciplines, industry
• Future emphasis on
• Mining rich public biological databases
• Discovery of patterns in complex irregular
  structures, discovery of similarities and
  analogies
• Methods for semantic analysis of large text
  collections
• language and domain-independence, efficiency

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Intelligent Systems

• Petri Myllymäki

Faculty of Science Department of Computer Science
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Mission and goals

• Main objective to develop computationally
  efficient, general-purpose intelligent methods
  for solving large-scale real-world problems
• Basic research areas
• information-theoretic modeling
• Minimum Description Length (MDL)
• Normalized Compression Distance (NCD)
• probabilistic graphical models
• Bayesian networks, Causal networks, Discrete
  PCA,...
• Application-oriented research areas
• next generation information retrieval methods
• semantic web
• technologies for networked collaborative working
  environments

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Structure and themes

• Complex Systems Computation Research Group
  (CoSCo)
• Head of the group Professor Henry Tirri (on
  industrial leave as Nokia Research Fellow since
  2004), Professor Petri Myllymäki (2004?)
• Senior researchers Jorma Rissanen, Wray Buntine,
  Jaakko Kurhila
• Externally funded full-time researchers (2004)
  20 man years
• Funding Tekes, Academy of Finland, EU, Industry
• Semantic Computing Research Group (SeCo)
• Head of the group Professor Eero Hyvönen
• Externally funded full-time researchers (2004)
  10 man years
• Funding Tekes, Industry

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Current Researchers in Intelligent Systems

• Cosco
• Director Petri Myllymäki (Henry Tirri)
• Senior researchers
• Jorma Rissanen, Wray Buntine, Jaakko Kurhila
• Researchers
• Raul Hakli
• Petri Kontkanen
• Jussi Lahtinen
• Jaakko Löfström
• Tuomas Lepola
• Miikka Miettinen
• Tommi Mononen
• Jukka Perkiö
• Sami Perttu
• Vladimir Poroshin
• Teemu Roos
• Tomi Silander
• Antti Tuominen

• SeCo
• Director Eero Hyvönen
• Researchers
• Mikko Apiola
• Markus Holi
• Miikka Junnila
• Petri Lindgren
• Tomi Kauppinen
• Suvi Kettula
• Ville-Pekka Komulainen
• Eetu Mäkelä
• Samppa Saarela
• Mirva Salminen
• Satu Savia
• Katri Seppälä
• Teemu Sidoroff

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Highlights (International co-operation)

• Established formal co-operation projects and
  long-term visiting researcher exchange activities
  with
• UC Berkeley (Prof. Michael Jordan)
• Tsinghua University (Prof. Lizhu Zhou)
• CWI Amsterdam (Dr. Peter Grünwald, Prof. Paul
  Vitanyi)
• CERN/HiP (Dr. Miika Tuisku)
• Coordinator of the EU Strep Superpeer Semantic
  Search Engine (Alvis) with 11 European and 1
  Chinese partner
• Tirri/Myllymäki a core site manager and member of
  the steering committee of the Pascal EU Network
  of Excellence
• Myllymäki founded the MDL Special Interest Group
  within Pascal

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Highlights (National co-operation)

• Joint research projects with several Finnish
  universities and public organizations
• University of Tampere (Unit for Computer-Human
  Interaction, Dept. of Information Studies),
  University of Kuopio, Helsinki School of
  Economics, Helsinki University of Technology
  (Lab. of Computational Engineering, Dept. of
  Computational Linguistics), Helsinki Institute of
  Physics, National Board of Antiquities, Kiasma
  Museum, Finnish Museum of Photography, Finnish
  Centre for Technical Terminology, The Finnish
  National Gallery, Finnish Agriculture Museum, The
  National Library of Finland, Antikvaria-group,
  Espoo City Museum, Helsinki University Museum,
  National Research and Development Centre for
  Welfare and Health (Stakes), Ministry of Finance.
• Professor Eero Hyvönen key figure in initiating
  semantic web research in Finland
• Semantic Web Kick-off in Finland, 2001, Helsinki
• Towards Semantic Web and Web Services, XML
  Finland 2002, Helsinki, 2002
• National Semantic Web Ontology Project (FinnONTO)

58
Highlights (Research)

• All in all, over 100 international publications,
  some examples below.
• P.Kontkanen, P.Myllymäki, W.Buntine, J.Rissanen,
  H.Tirri, An MDL Framework for Data Clustering. In
  Advances in Minimum Description Length Theory
  and Applications, edited by P. Grünwald, I.J.
  Myung and M. Pitt.
• Research area based on Jorma Rissanens seminal
  work on information-theoretic modelling
• www.mdl-research.org
• W. Buntine, J. Löfström, J. Perkiö, S. Perttu,
  V. Poroshin, T. Silander, H. Tirri, A. Tuominen,
  V. Tuulos, A Scalable Topic-Based Open Source
  Search Engine. Web Intelligence 2004.
• New research area initiated by Wray Buntine
• Aino a Finnish search engine

59
Highlights (Research)

• T.Roos, P.Myllymäki, H.Tirri, P.Misikangas,
  J.Sievänen, A Probabilistic Approach to WLAN User
  Location Estimation. International Journal of
  Wireless Information Networks.
• Spin-off Ekahau Inc.
• P.Kontkanen, J.Lahtinen, P.Myllymäki, T.Silander,
  and H.Tirri, Supervised Model-Based Visualization
  of High-Dimensional Data. Intelligent Data
  Analysis.
• Spin-off BayesIT Inc.
• P.Myllymäki, T.Silander, H.Tirri, P.Uronen,
  B-Course A Web-Based Tool for Bayesian and
  Causal Data Analysis. International Journal on
  Artificial Intelligence Tools.
• B-Course a publicly available data-analysis
  server
• Eero Hyvönen, Eetu Mäkelä, Mirva Salminen, Arttu
  Valo, Kim Viljanen, Samppa Saarela, Miikka
  Junnila, and Suvi Kettula, MuseumFinland
  Finnish Museums on the Semantic Web. Journal of
  Web Semantics.
• MuseumFinland a public portal to Finnish museums

60
Highlights (Research)

• M.Miettinen, P.Nokelainen, J.Kurhila, T.Silander,
  H.Tirri, Adaptive Profiling Tool for Teacher
  Education. SITE 2002.
• Receiver of the Outstanding Paper Award.
• T. Kauppinen, E. Hyvönen Modeling Coverage
  Between Geospatial Resources. ESWC 2005.
• Receiver of the Best Poster Award
• T. Silander 2001 KDD Cup Competition.
• 2nd prize (among the 114 participants).
• P. Kontkanen CoIL Challenge 2000 Competition.
• 2nd prize (among the 147 participants).

61
Highlights (Industrial impact)

• Industrial partners in Tekes projects or with
  direct contracts
• AlmaMedia, Nokia, TietoEnator, AAC Global,
  Connexor, Leiki, M-Brain, Finnish Yellow Pages,
  Fonecta, TeliaSonera, Kibron, Kone, ABB, Finnish
  Broadcasting Company YLE, Space Systems Finland
  (European Space Agency).
• Spin-off companies
• Ekahau probabilistic methods for locating
  devices in wireless networks
• European Union The European Information Society
  Technology Prize 2002
• Technology Marketing Corporation (TMC) Best
  product of the year 2002
• Planet PDA, the Global Summit on Enterprise
  Custom Volume Handheld Computing Best of show
• Software Industry Summit Best commercialized
  innovation in Finland in 2002
• SearchNetworking.com Bronze medal, best product
  of the year 2003
• Wi-Fi Planet 2004 Best of Show.
• BayesIT probabilistic methods for visualization
  of high-dimensional data
• Koptimi software for constrained bin-packing, in
  fielded use at StoraEnso since year 2000

62
Highlights (Interaction with the society)

• MuseumFinland a semantic portal to Finnish
  museums
• Semantic Web Challenge Award 2004
• Finnish Prime Ministers honourable mention for
  most innovative web application in the Quality
  on the web competition 2004.
• b-course.cs.helsinki.fi a publicly available
  data-analysis server with over 13 000 users
  world-wide
• Ourweb software for collaborative E-learning,
  used at several Finnish universities
• Election candidate selection machine a public
  service hosted by Helsingin Sanomat, the largest
  newspaper in Finland
• Aino a Finnish search engine

63
Future vision

• Probabilistic modelling
• model complexity regularization
• theoretical elegance vs. computational efficiency
  
• MDL vs. Bayes
• Information retrieval
• hierarchical models
• more sophisticated language models
• Related research issues
• data pre-processing, data visualization, grid
  computing, intelligent web crawling
• Rising focus areas
• large-scale sensor network data analysis
• causal inference

64
Software Engineering

• Inkeri Verkamo

Faculty of Science Department of Computer Science
65
Mission and goals

• Research problems of both scientific and
  industrial relevance
• Emphasis on the early phases of software
  development
• object-oriented software architectures
• frameworks, building blocks, product families
• methods for measurement and prediction of
  software quality
• Utilization of the connections to
• teaching
• student software projects (part of BSc studies)
• industry
• industry professorship 1999-2003
• research projects with industrial partners

66
Structure and themes

• Several research projects within the same area
  (synergy)
• Fred JavaFrames framework and pattern based
  development environment
• Vilpert framework for implementing visual
  languages
• Maisa design quality measurement and system
  quality prediction
• CAFÉ Families testing of product families
• Volume during 1999-2004
• 2 professors, 7 researchers (mostly part time)
• 2 PhLic Theses, 2 PhD Theses ( 1 in process)
• 90 MSc Theses (volume increasing)
• 20 journal or conference articles technical
  reports

67
Highlights

• typical example Fred JavaFrames
• two joint research projects with University of
  Tampere, Tampere University of Technology
• funded by Tekes (National Technology Agency) and
  a large number of software companies
• architecture-oriented software development
  environment
• Fred (1997-2000) methodology and first version
  of tool
• JavaFrames (2001-2004) enhancement of theory,
  redesign to serve practical needs, further tool
  development
• long-term research to produce a stable industry
  quality tool
• industry contacts necessary for evaluation of
  tools
• two full time researchers at UH (? PhD)

68
Future vision

• connection between research and education
• take advantage of increasing number of Masters
  theses
• industry initiated theses containing case studies
  (40)
• empirical software engineering
• student projects as an experimental platform
• comparison and experimentation on tools and
  methods
• joint student projects with University of
  Petrozavodsk
• cross-cultural, distributed software development
• first experience in spring 2004 with good results
• software performance engineering
• in cooperation with industry (Nokia Research
  Center)

69
Researchers

• Jukka Paakki, professor
• Inkeri Verkamo, professor
• Juha Taina, university lecturer
• Sari A. Laakso, university lecturer
• Jukka Viljamaa, PhD
• Juha Gustafsson, PhD student
• Raine Kauppinen, PhD student
• Former members
• Antti-Pekka Tuovinen, PhD
• Antti Viljamaa, PhLic (?PhD)
• Lilli Nenonen, MSc
• Antti Tevanlinna, MSc

70
Research in Distributed Systems and Data
Communications

• Kimmo Raatikainen

Faculty of Science Department of Computer Science
71
NODES Group

• Research challenge
• Composing systems of autonomous units
• How the units interact and behave as a system
• Four informal research teams
• Wireless Internet
• Collaborative and Interoperable Computing
• Formal Methods
• Computing Architectures and Platforms
• People
• 2 professors and 9 other senior/post doc persons
• c. 20 researchers (M.Sc./Ph.D. students) in
  projects
• c. 10 Ph.D. students in industry
• Funding EC, Tekes, industry (c. 0.7M/year)

72
NODES Research Impact
Scientific Publications
Education
Research
Open Source Software
International Standards
73
NODES Achievements 1999-2004

• 93 refereed journal articles and conference
  papers
• Strong impact on standards 7 co-authored
  Internet RFCs
• 6 edited proceedings of international conferences
• 9 Ph.D. theses
• 96 M.Sc. theses of which 23 in research projects
• International co-operation
• European networks ANWIRE, MiNEMA, InterOp
• Kings College, Aachen, Fokus, TU Madrid, TU
  Lisbon, Paris 6, EPF Lausanne, Trinity,
  Lancaster, Chalmers, Aarhus, ...
• Participation in 8 European research projects
• 4 joint Ph.D. Workshops with UC Berkeley (Randy
  Katz)
• Active participation in international
  standardization
• IETF, OMG, W3C, WWRF, ISO/ITU

74
Result Highlights

• TCP enhancements Internet community and Linux
  kernel
• IP Quality-of-Service in access networks
• Standardized Mobile Middleware
• Wireless CORBA (OMG)
• Wireless JAVA Remote Method Invocation (on-going
  in JCP)
• Efficient Agent communication (FIPA)
• Efficient XML Interchange (on-going in W3C)
• Contributions to Wireless World Research Forum
• visions of wireless future
• Open Distributed Processing (ODP) standards
• trading, type repository, interface references
  and binding
• Middleware for distributed management of virtual
  enterprise lifecycle and interoperability

75
NODES Books
76
Vision of the Future

• User expectations
• Future applications and platforms will be
  context-sensitive, adaptive, and personalized.
• They need to be run, in a reasonable and secure
  manner, on variety of execution environments
  anywhere, anyhow, anytime, by anyone.
• Required system properties
• self-aware, distributable, reconfigurable,
  proactive, collaborative, secure, trusted,
  privacy providing, mobile, diversely accessible,
  extendable, incrementally deployable, resource
  aware,

77
NODES Research Challenge Space
Tools and Methods Formal Methods Performance
Analysis Programming Models
Software Artifacts Operating Systems Internet
Protocols Middleware
Research Themes Context Sensitivity Security
Trust Privacy Mobile Always-On
Connectivity Interoperability
78
NODES Research Topics 2005-

• Wireless Internet
• Efficient and secure always-on connectivity in
  mobile world
• Proximity networking
• Mobility middleware
• Collaborative and Interoperable Computing
• Interoperability middleware for inter-enterprise
  collaboration
• Trust management
• Formal Specification and Verification
• Methods for protocol verification
• Computing Architectures and Platforms
• Resource awareness and run-time reconfiguration
• Linux enhancements timeliness,
  high-availability, small size
• Note One of the two professorships to be filled
  in 2006

79
Current NODES Researchers

• Staff
• Alanko Timo
• Häkkinen, Auvo
• Karvi, Timo
• Kerola, Teemu
• Kojo Markku
• Kutvonen, Lea
• Kuuppelomäki, Päivi
• Manner, Jukka
• Marttinen, Liisa
• Niklander, Tiina
• Raatikainen, Kimmo
• Project researchers (Ph.D. students)
• Daniel, Laila
• Kangasharju, Jaakko
• Leggio, Simone
• Metso, Janne
• Riva, Oriana

• Externals (Postdocs Ph.D. students)
• Astuti, Davide (Nokia)
• Bogoiavlenskaia, Olga (Petrozavodsk)
• Campadello, Stefano (Nokia)
• Chande, Suresh (Nokia)
• di Flora, Cristiano (Nokia)
• Gourtov, Andrei (HIIT)
• Korhonen, Jouni (TeliaSonera)
• Koskimies, Oskari (Nokia)
• Laukkanen, Mikko (TeliaSonera)
• Miettinen, Markus (Nokia)
• Pöyhönen Petteri (Nokia)
• Sarolahti, Pasi (Nokia)
• Strandell, Toni (Nokia)
• Past personnel
• Laukkanen, Aki
• Lindström, Jan
• Luukkainen, Matti