Helsinki Institute for Information Technology HIIT

tealackingAI and Robotics

Nov 8, 2013 (3 years and 8 months ago)

544 views

Computer Science in Finland 2000
-
2006

Evaluation Form


1

Evaluation of Computer Science in Finland (2000
-
2006)

Helsinki Institute for Information Technology HIIT


GENERAL INFORMATION

................................
................................
................................
................................
..........

2

G.1.

P
ERCENTAGE THAT COMPU
TER SCIENCE REPRESEN
TS IN THE RESEARCH C
ARRIED OUT IN THE UN
IT

.......................

3

G.2.

T
HE UNIT

S RESEARCH PROFILE W
ITHIN COMPUTER SCIEN
CE

................................
................................
..................

4

G.3.

O
THER RELEVANT FIELDS

CONNECTED TO THE UNI
T
'
S RESEARCH PROFILE
................................
..............................

5

1. RESOURCES

................................
................................
................................
................................
................................

6

1.1.

S
TAFF IN
2000
-
2006

(
PE
RSON
-
MONTHS
)

................................
................................
................................
..................

6

1.2.

S
ENIOR AND POSTDOCTOR
AL RESEARCHERS

................................
................................
................................
............

6

2. RESEARCH OUTPUT

................................
................................
................................
................................
................

8

2.1.

D
ESCRIBE THE
U
NIT

S RESEARCH
(
MAX
.

4

PAGES
)

................................
................................
................................
...

8

2.2.

N
UMBER OF SCIENTIFIC
PUBLICATIONS AND OTH
ER OUTPUTS
2000
-
2006

................................
..............................

14

2.3.

L
ISTS OF MOST IMPORTA
NT PUBLICATIONS BY R
ESEARCHERS WITH DOCT
ORAL DEGREE
(
MAX
7

PUBLICATIONS
/
PERSON
)

................................
................................
................................
................................
................

14

2.4.

C
OPIES OF THE
U
NIT

S BEST PUBLICATIONS

................................
................................
................................
...........

40

3. DOCTORAL TRAINING

................................
................................
................................
................................
..........

43

3.1.

N
UMBER OF STUDENTS WH
O IN
2000
-
2006

................................
................................
................................
............

43

3.2.

L
IST OF DOCTORAL DI
SSERTATIONS IN
2000
-
2006

AND PRESENT EMPLOYME
NT

................................
....................

43

4. NATIONAL AND INTE
RNATIONAL COLLABORAT
ION

................................
................................
...............

45

4.1.

N
ATIONAL COLLABORATIO
N

................................
................................
................................
................................
..

45

4.2.

V
ISITS ABROAD
(
MINIMUM DURATION OF
VISIT
:

ONE MONTH
)

................................
................................
...............

52

4.3.

V
ISITS TO THE
U
NIT
(
MINIMUM DURATION OF
VISIT
:

ONE MONTH
)

................................
................................
.........

55

4.4.

S
HORT BUT PARTICULARL
Y IMPORTANT VISITS

................................
................................
................................
......

57

4.5.

M
OST IMPORTANT FOREIG
N COLLABORATORS

................................
................................
................................
.......

59

4.6.

D
ESCRIBE THE MOST IMP
ORTANT OUTCOMES OF T
HE VISITS AND COLLAB
ORATION CONTACTS
(
MAX
.

1

PAGE
)

.....

71

4.7.

N
ON
-
ACADEMIC COLLABORATI
ON

................................
................................
................................
.........................

73

5. OTHER SCIENTIFIC
AND SOCIETAL ACTIVIT
IES

................................
................................
........................

75

5.1.

I
NVITED PRESENTATIONS

IN SCIENTIFIC CONFER
ENCES

................................
................................
..........................

75

5.2.

M
EMBERSHIPS IN EDITOR
IAL BOARDS OF SCIENT
IFIC JOURNALS

................................
................................
............

80

5.3.

P
RIZES AWARDED TO RES
EARCHERS
,

HONOURS AND SCIENTIF
IC POSITIONS OF TRUS
T

................................
...........

81

5.4.

M
EMBERSHIPS IN COMMIT
TEES AND IN SCIENTIF
IC ADVISORY BOARDS O
F BUSINESS COMPANIES

OR OTHER SIMILAR
TASKS OF NO PRIMARIL
Y ACADEMIC NATURE

................................
................................
................................
...............

86

6. THE UNIT’S SELF
-
A
SSESSMENT

................................
................................
................................
.........................

88

6.1

SWOT



EVALUATION OF THE
U
NIT

S SCIENTIFIC STRENGT
HS
,

WEAKNESSES
,

OPPORTUNITIES AND TH
REATS
(
EXPERTISE
,

FUNDING
,

FACILITIES
,

ORGANISATION
;

MAX
.

2

PAGES
).

................................
................................
............

88

6.2.

E
VALUATE THE
U
NIT IN RELATION TO I
TS LEADING SCIENTIFI
C COMPETITORS
(
MAX
1

PAGE
).

..............................

89

6.3.

T
HE
U
NIT

S RESEARCH STRATEGY
2008

2010

(
RELATION TO

THE PARENT ORGANISAT
ION

S STRATEGY
,

PRIORITY
AREAS IN RESEARCH
,

DEVELOPMENT MEASURES
;

MAX
2

PAGES
)

................................
................................
..................

90

6.4.

T
HE SOCIETAL IMPACT O
F THE
U
NIT

S ACTIVITIES
(
MAX
.

1

PAGE
)

................................
................................
.........

91

6.5.

A
SSESS THE ACADEMIC A
ND SOCIETAL NEED FOR

DOCTORAL TRAINING WI
THIN THE
U
NIT

S RESEARCH FIELDS AN
D
THE
U
NIT

S ROLE IN DOCTORAL T
RAINING
(
MAX
.

1

PAGE
).

................................
................................
...........................

92

6.6.

A
SSESS THE RESEARCH I
NFRASTRUCTURE AVAILA
BLE
(
MAX
1

PAGE
)

................................
................................
....

92

7. FUNDING

................................
................................
................................
................................
................................
....

94

7.1.

T
HE
U
NIT

S CORE AND EXTERNAL
FUNDIN
G RECEIVED FROM THE
PARENT ORGANISATION
.

................................
..

94

7.2.

E
VALUATE THE ROLE OF
THE FUNDING BY
A
CADEMY OF
F
INLAND IN PROMOTING
THE SCIENTIFIC AND S
OCIETAL
IMPACT OF RESEARCH
(
MAX
.

1

PAGE
)

................................
................................
................................
...........................

95

7.3.

E
VALUATE THE ROLE OF
FUNDING AWARDED BY D
IFFERENT FUNDING ORG
ANISATIONS IN PROMOT
ING THE
SCIENTIFIC AND SOCIE
TAL IMPACTS OF RESEA
RCH
,

EXCLUDING FUNDING FR
OM THE
A
CADEMY OF
F
INLAND
(
MAX
.

1

PAGE
)

................................
................................
................................
................................
................................
............

95

Computer Science in Finland 2000
-
2006

Evaluation Form


2


GENERAL INFORMATION


Organisation

Helsinki University of Technology &

University of Helsinki

Department or equivalent

Helsinki Institute for Information
Technology HIIT

Address


P.O. Box 9800 (Metsäneidonkuja 4,
Espoo)

FI
-
02015 TKK

Finland


P.O. Box 5400 (Konemiehentie 2,
Espoo)

FI
-
02015 TKK

Finland


P.O. Box 68 (Gustaf Hällströmin katu
2b, Helsinki),

FI
-
00014 UNIVERSITY OF
HELSINKI, Finland

Phone

+358
-
9
-
6949768

+358
-
9
-
4513277

+358
-
9
-
1911

Internet home page

http://www.hi
it.fi



Head of the Department

Professor Martti Mäntylä

Phone

+358
-
9
-
4518138

Email

Martti.Mantyla@hiit.fi

Contact person for the Evaluation

Päivi Saarinen

Phone

+358
-
9
-
4518139

Email

Paivi.Saarinen@hiit.fi

Head of the Department

Professor Esko Ukkon
en

Phone

+358
-
9
-
19151280

Email

Esko.Ukkonen@cs.helsinki.fi

Contact person for the Evaluation

Greger Lindén

Phone

+358
-
9
-
19151233

Email

Greger.Linden@cs.helsinki.fi






Computer Science in Finland 2000
-
2006

Evaluation Form


3



G.1. Percentage that computer science represents in the research
carried out in

the unit
1


95




1

Please see the instructions at th
e end of this document

Computer Science in Finland 2000
-
2006

Evaluation Form


4


G.2. The unit’s research profile within computer science

(give estimate of the percentage)


Research field

(%)

Theory of computation


Algorithms and data structures

5

Programming languages


Software engineering


Parallel and distribu
ted systems

5

Databases, data mining

25

Communications

25

Computer architecture


Human
-
computer interaction

10

Artificial intelligence, machine learning, computer
vision

20

Computer graphics


Other: Digital media

10



Computer Science in Finland 2000
-
2006

Evaluation Form


5

G.3. Other relevant fields co
nnected to the unit's research profile

(Mark with x the columns 1, 2 or 3, where 1=collaboration, 2=joint projects, 3=integrated in the
group. More than one column can be marked in the same row.)


Research field

1

2

3

Mathematics

x



Physics

x

x


Chemis
try




Process technology




Automation technology




Signal processing

x



Electrical engineering




Information systems science




Bioinformatics

x

x

x

Biomedical engineering




Psychology

x

x

x

Modelling and simulation, computational science

x

x

x

Biology

x

x


Medicine

x

x

x

Nanoscience




Other (what)




Industrial art and design

x

x

x

Linguistics and language technology

x

x

x

Neuroscience

x

x

x

Law and social sciences

x


x

Statistics

x


x

Forestry

x



Economics

x



Paper and print
ing technology

x

x


Architecture


x


Drama


x


Media art


x



Computer Science in Finland 2000
-
2006

Evaluation Form


6





1. RESOURCES

1.1. Staff in 2000
-
2006 (person
-
months)

See fill
-
in instructions at the end of the report.




2000

2001

2002

2003

2004

2005

2006

Total

Professors


12

13

57

60

52

60

63

3
15

Other senior researchers

0

0

20

69

75

87

102

354

Postdoctoral researchers

0

0

22

42

101

138

165

467

Postgraduate students


25

120

374

541

587

604

601

2850

Other academic staff

5

127

139

182

213

215

268

1149

Visiting researchers and
visiting resear
ch students

1

5

21

53

93

120

170

423

Total active research staff

43

264

633

948

1120

1211

1367

5585

Administrative personnel
1)

12

28

53

48

50

52

70

313

Technical personnel
2)

0

2

11

18

32

34

30

126

Other (e.g., teachers)
3)

0

0

0

0

0

0

0

0

Total staff a
t the unit

55

293

696

1014

1202

1296

1467

6024



1)

Includes all administrative personnel at the unit

2)

Includes all technical personnel at the unit

3)

Includes all personnel not included in the other categories in the table.



1.2. Senior and postdoctor
al researchers

In case person's duties have changed during the period under review (e.g. from technical personnel
to active research staff), indicate the person's both tasks and period according to the format.



Name

Title

Period

Senior staff



Buntine,
Wray

Senior Research Scientist

1/2003
-

Floréen, Patrik

Research Coordinator

8/2002
-

Gurtov, Andrei

Senior Research Scientist

8/2004
-

Gionis, Ari
s
tides

University Lecturer, Senior
R
e
searcher, Postdoc Research
Fellow

8/2003
-
11/2006

Himanen, Jari Pekka

Senior Research Scientist

Principal Scientist

2/2003
-
7/2005

8/2005
-
7/2010

Hollmén, Jaakko

Chief Research Scientist

1/2002
-

Hyvärinen, Aapo

Senior Research Scientist,
Academy Research Fe
l
low

5/2003
-

Karila, Arto

Principal Scientist

10/2006
-

Lindén, Gr
e
g
er

University Lecturer, Senior
3/2002
-

Computer Science in Finland 2000
-
2006

Evaluation Form


7

Researcher,

Lindström, Jan

Senior Research Scientist

8/2003
-
9/2004

Mannila, Heikki

Research Director, Academy
Professor

12/2001

Mäntylä, Martti

Research Director, Professor

1/2000
-

Myllymäki, Petri

Professor

0
8/2003


Academy Research Fellow

1/2000
-
7/2003

Nikander, Pekka

Ericsson Affiliate Senior
Research Scientist


Raatikainen, Ki
m
mo

Professor

1/2000
-

Rimey, Kenneth

Senior Research Scientist

5/2002
-

Rissanen, Jorma

HIIT Research Fellow

7/2002
-
11/2002

Sa
ari Timo

Senior Research Scientist

8/2003
-

Stenborg, Markku Ilmari

Senior Research Scientist

4
-
8/2004

Tirri, Henry

Professor, Senior Researcher

1/2000
-
7/2003

Toivonen, Hannu

Professor

11/2006
-

Turpeinen, Marko

Senior Research Scientist

12/2002
-

9/200
5


Principal Scientist

10/2005
-


Ukkonen, Esko

Academy Profe
s
sor, Profe
s
sor,
Research Director

9/2004
-

Postdoctoral staff



Bingham, Ella

University Researcher

8/2005
-

Geerts, Fl
o
ris

Resea
r
cher

9/2002
-
4/2004

Goethals, Bart

Resea
r
cher

1/2003
-
9/2
004

Hoyer, Pa
t
rik

Researcher, Postdoc Research
Fe
l
low

1/2004
-

Hurri, Ja
r
mo

Doctoral Assistant, Researcher

1/2004
-

Hyvönen, Saara

Researcher

1/2004
-


Researcher

9/2003
-
10/2003


Researcher

8/2002
-
10/2002

Ilmonen, Tommi

Researcher

1/2006
-
12/2006


Research Scientist

1/2007
-

Inki, Mika

University Researcher

7/2006
-

Jacucci, Giulio

Researcher

8/2004
-
12/2004


Research Scientist

1/2005
-

Kääriäinen, Matti

Postdoc Researcher

11/2004
-

Kankainen Anu

Researcher

1
-
12/2003

Kaski, Petteri

University R
esearcher

1/2006
-

Koivisto, Mikko

Postdoc Research Fellow,
Researcher

4/2004
-


Researcher

1/2002
-
3/2004

Korzun, Dmitry

Research Scientist

1/2005
-

Mielikäinen, Taneli

Researcher

7/2005
-
2/2007


PhD student

1/2003
-
6/2005


Researcher

9/2002
-
12/2002

O
llikainen, Vesa

Researcher

6/2002
-
12/2002


Researcher

1/2002
-
5/2002

Onkamo, Päivi

Researcher

11/2002
-
12/2004

Oulasvirta, Antti

Researcher

8/2002
-
11/2006

Computer Science in Finland 2000
-
2006

Evaluation Form


8


Research Scientist

12/2006
-

Pitkänen, Olli

Researcher

6/2000
-
12/2001


Research coordinator

1/2002
-
3/2006


Research Scientist

4/2006
-

Puolamäki, Kai


2005
-

Salmenkivi, Marko

University Lecturer, Postdoc
Research Fe
l
low, Doctoral
Assistant

8/2002
-

Sarvas, Risto

Researcher

1/2002
-
12/2006


Research Scientist

1/2007
-

Seppänen, Jouni

Researcher

1/2005
-

Sevon, Pe
t
teri

Researcher

10/2004
-


PhD student

10/2002
-
9/2004

Tarkoma, Sasu

Researcher

2/2002
-
4/2006


Research Scientist

5/2006
-

Tsaparas, P
a
nayiotis

Researcher, Postdoc R
e
search
Fellow

2/2004
-
6/2006

Virtanen, Veli Perttu

Researcher

6/20
01
-
2/2005


Research Scientist

3
-
7/2005



2. RESEARCH OUTPUT


2.1. Describe the Unit’s research (max. 4 pages)

This question surveys how the research carried out in the Unit has impacted research in its own
field(s). Describe the orientation of scientifi
c publishing, most important research results and the
role of multidisciplinarity or interdisciplinarity etc. Also, describe the role of basic and applied
research. In case the research carried out in the Unit is clearly specialised in the different fields

of
computer science, describe each field separately (see also question 6.3).


The Helsinki Institute for Information Technology HIIT is a joint research institute of the two
leading research universities in Finland, the University of Helsinki (UH) and the

Helsinki
University of Technology (TKK). It was founded in 1999. At present, HIIT has some 135
researchers and staff. It operates in close collaboration with the Computer Science Departments of
the parent universities at three locations: Ruoholahti, Otani
emi (TKK campus) and Kumpula (UH
campus).
Administratively, HIIT presently consists of two units: the Advanced Research Unit
(ARU) founded in 1999 and the Basic Research Unit (BRU) founded in late 2001. The ARU is
located in TKK and the BRU in UH.


HIIT co
nducts internationally high
-
level strategic research in information technology and related
multi
-
disciplinary topics, especially in areas where Finnish IT industry has a significant role. It
works in close co
-
operation with Finnish universities, research i
nstitutes, and industry, aiming at
significant scientific impact that also benefits the industry and the progress of the Finnish
information society. HIIT has a strong network of international partnerships with leading foreign
research universities and ins
titutions.


HIIT's work is organised in long
-
term research programmes, each consisting of several co
-
operating
groups with a total of 25
-
40 researchers and led by a senior professor
-
level researcher. Each
programme has an Advisory Board consisting of repre
sentatives from industry and academia. An
Computer Science in Finland 2000
-
2006

Evaluation Form


9

internal Management Board consisting of the senior researchers participating in the programme
coordinates the research of each programme. Programmes operate through various instruments,
such as externally funded pr
ojects (TEKES, Academy of Finland, EU, companies), research
positions (internal and Academy of Finland funding) and graduate school positions.


Programmes combine basic and strategic research with activities aimed at innovations. Through
this, they aim at

scientific impact

through publications and influence on the scientific community,
industrial impact

through research prototypes and demonstrations, standardization activities, and
close linkage with leading companies, and
societal impact

through participa
tion in information
society research, innovation
-
oriented activities, direct links with decision
-
makers, and active
participation in public debate. For scientific impact, HIIT publishes its results in high
-
quality
scientific journals and leading conference
s, and also in open
-
source software. It also maintains close
links with leading researchers in its fields through research visits and personal communication.


The present research programmes of HIIT (since 1.1.2006) are as follows:


Algorithmic Data Analys
is (ADA). Director: Academy Professor Heikki Mannila

The development in measurement and data collection technologies have made it possible to
gather and store large amount of information in many areas of science and industry. The ability
to analyze these m
asses of raw data has increased at a much slower speed, however. The
research programme on data analysis develops data mining and computational statistics methods
for various application tasks.


Future Internet (FI). Director: Prof. Kimmo Raatikainen

Enhan
cing Internet infrastructure to enable efficient, secure and trusted always
-
on connectivity
and services.


Network Society (NS). Director: Prof. Marko Turpeinen

Human
-
centric multidisciplinary anticipation and development of ubiquitous information and
comm
unication technology, which is based on deep understanding of needs and practices of our
everyday life and our social relations in a network society.


Probabilistic Adaptive Systems (PAS). Director: Prof. Petri Myllymäki

Study and further development of th
e theory of sophisticated probabilistic models and exploring
their applications for solving problems appearing in complex real
-
world stochastic systems.


The following paragraphs give selected highlights of HIIT’s research results. They have been
chosen to

display different research approaches and forms of impact as well as multi
-
disciplinary
research lines covering bioinformatics, behavioural sciences, political science, and law.


Host Identity Protocol and related Internet infrastructure


The Host Ident
ity Protocol is an approach to solving the present architectural deficiencies of the
Internet protocol stack, especially support for mobility and multihoming, by introducing a new
protocol layer at the “waist” of the stack. The layer introduces a new name
space of Host Identities
(HI) in the stack, effectively replacing IP numbers from the higher levels of the protocols. This
separates the presently bundled functions of IP numbers as both locators and identities.

Computer Science in Finland 2000
-
2006

Evaluation Form


10


HIIT has been involved in the (initially sm
all) HIP research community since 2002. We have
developed our own HIP implementation, HIP for Linux (HIPL), and also various network
infrastructure components related to rendezvous service, HI
-
IP mapping, and support of various
kinds of middleboxes. Jointl
y with UC Berkeley, HIIT also developed the Hi3 overlay
infrastructure for managing HIP sessions, and has performed extensive testing of it on the
PlanetLab network.


HIIT is presently a central node in the increasing network of HIP
-
inspired researchers. I
n particular,
HIIT’s Dr. Andrei Gurtov co
-
leads the IRTF working group related to HIP, and HIIT has
contributed significantly to the Internet Drafts related to HIP infrastructure. As another direct result
of our work, HIP support was in late 2006 integrate
d with the standard Linux kernel, with the
results that all Linuxes now are HIP
-
compatible.


Fuego Core middleware platform


The Fuego Core middleware platform is the result of a series of related projects focusing on
middleware for future mobile Internet.

It covers various themes considered of fundamental
significance: XML processing and messaging, mobile distributed event system, XML
synchronization and data access, and software configuration management. With this, the work has
contributed to internationa
l standardization, particularly to IETF (SIMPLE WG) and W3C (Mobile
Web Initiative and Device Independence Activity). The platform has also been adopted by industry
for its own research and development.


ContextPhone



In the area of context
-
awareness and

smart phones, there has been significant success in recognizing
context by analysing user situation data. The results include a prototyping platform ContextPhone
for context
-
aware applications running on Smartphones, specifically on Nokia’s S60 platform.
ContextPhone consists of about 30 distinct components that implement data gathering, generalized
event services, data logging, user interfaces, network protocols and debugging facilities. The
platform has been published in both the sense of academic public
ations and as freely downloadable
software, licensed both under GPL version 2 and MIT free software licenses.


Applications built on top of ContextPhone have been used in several research institutes. The data
logging application ContextLogger was used to
gather a unique dataset from one hundred
participants over nine months by Nathan Eagle at the MIT Media Lab, and has been the basis for
data analysis method development at HIIT.


ContextMedia, a contextual mobile media gathering tool, has been used togeth
er with the
University of Art and Design Helsinki in several artist
-
led workshops around the world as well as
by the Garage Cinema Research Group at UCB, with an end
-
user version released for public
consumption under the name Merkitys

Meaning. A special
-
pu
rpose sensor network version of
ContextPhone is used in a artist
-
led cross
-
disciplinary project (Evans in press). Datasets from these
experiments have been released publicly and have been used amongst others by research at the
University of Helsinki and Un
iversity of Jyväskylä (Mazhelis
et al.
, HICSS, 2006).


Computer Science in Finland 2000
-
2006

Evaluation Form


11

Future Internet search


Future Internet search technologies have been a focus area of the PAS programme since 2002. The
work uses probabilistic and information
-
theoretic methods to model information r
etrieval, also
following the principles of open source software development. The underlying hypothesis of the
work is that distributed, semantic
-
based and multilingual methods will have a central role in the
future of information retrieval. The work has be
en carried out in several parallel projects funded by
the Academy of Finland, TEKES, and EU’s 6
th

framework programme.


Highlights of this work include algorithms and freely available software for learning latent variable
models for text analysis, develope
d by W. Buntine and others, which have made it possible to create
radically novel, semantic (content
-
based) search engines. In another line of work, new results in the
Minimum Description Length (MDL) theory by J. Rissanen, P. Myllymäki and others, have be
en
successfully applied in clustering, density estimation and image denoising.


Methods and tools for gene mapping, haplotyping, diagnostic markers and gene regulation


This line of research is based on a fruitful long
-
term collaboration of HIIT researche
rs with medical
geneticists. We started with the problem of how to find loci in the genome that predispose to certain
diseases. The first important results included tools for association analysis of haplotype data using
techniques from data mining (Toivone
n
et al.
, American Journal of Human Genetics, 2000). This
algorithm was then successfully used by geneticists in the Karolinska Institutet, Stockholm, to
locate the asthma gene, a highly significant finding that was published in
Science
.


Later, we develo
ped a novel model for genomes of a population which led to a new efficient
algorithm for haplotyping genome data, using hidden Markov techniques (Ukkonen, WABI 2003;
Koivisto
et al.
, WABI 2005). The resulting haplotyping software has accuracy and speed tha
t is
among the very best available at the moment. A similar founder approach has recently been applied
by at least two leading groups elsewhere.


With gene copy number analyses, one patent application has been filed covering the diagnostic use
of the chro
mosomal copy number change regions.



Most recently, we have developed in collaboration with Professor Jussi Taipale (Biomedicum,
Helsinki) a new model for so
-
called gene enhancer elements in mammalian genomes. Such
elements have important role in the regu
lation of gene activity. We carried out a genomewide
comparative analysis and predicted several new enhancer elements that were successfully verified
in vivo (Hallikas
et al.
, Cell 2006; Palin
et al.
, Nature Protocols 2006).


Finding orders from data


In c
ertain data analysis applications there is a natural ordering for the rows or columns of the data.
For example, in paleontological presence/absence data the rows represent sites and the columns
represent species: the task is to find an ordering for the sit
es so that for each species its occurrences
are in consecutive observations. In the error
-
free case this seriation problem reduces to consecutive
ones problem, but it is NP
-
hard for realistic data. We have in the last years developed novel
algorithms for t
his seriation task (Gionis
et al.
, Paleobiology 2006; Puolamäki
et al.
, PLoS
Computational Biology 2006); their performance is excellent compared to previous approaches.
Recent results (Gionis
et al.
, KDD 2006) show also that finding partial orders can be
done
efficiently.

Computer Science in Finland 2000
-
2006

Evaluation Form


12


Techniques and tools for learning linear latent variable models


A common data
-
analysis framework for continuous data is to describe the data as a linear mixture
of some underlying hidden variables. This family of methods includes Indep
endent Component
Analysis (ICA) and Non
-
negative Matrix Factorization (NMF), which both have received
considerable attention in the machine learning community. We have contributed significantly to the
problem formulation, solution algorithms, and software
for these methods. In particular, we have
published a book which is now the standard reference on ICA (Hyvärinen
et al.
, Independent
Component Analysis, Wiley, 2001). We have also developed and improved the FastICA MATLAB
package (
www.cis.hut.fi/projects/ica/fastica/
), implementing the world
-
wide most widely
-
used ICA
algorithm, which we developed in the 1990’s.


Furthermore, we have focused on the important problem of estimating the reliability o
f ICA
components (Himberg
et al.
, NeuroImage, 2004). We have extended the standard NMF method to
include sparseness constraints. The resulting method (Hoyer, JMLR, 2004) has become a main
reference for modern approaches to NMF, and our corresponding MATLAB

package is widely
-
used.


Social media, especially mobile photography and mobile spectator media


In this line of work, mobile media services, especially for social photography and large
-
scale
events, have been conceptualized, developed and extensively tes
ted. This work has resulted in
service design principles for mobile group media, as well as explorative implementations in
commercial products (Kuvaboxi, Jaiku, Comeks), service prototypes (Comedia), and open mobile
application platforms (MUPE). The work h
as been performed in close co
-
operation with UC
Berkeley (prof. Marc Davis and prof. Nancy van House).


Mobility and cognition


The long
-
term objective of this line of research is to understand qualitatively and quantitatively the
impact of mobile computin
g and communication to the interactive behaviour of users and user
groups. To this end, the research has focused on three major lines: 1) the investigation of cognitive
regulation of action in mobile human
-
computer interaction; 2) the description of the fu
ndamental
limitations in interacting with mobile devices when mobile; and 3) the charting of possible user
interface solutions.


During the research, several innovative research methods and instruments have been developed to
facilitate experimental resear
ch in naturalistic real
-
world settings. For instance, HIIT has developed
a state
-
of
-
the art wearable video recording system that makes it possible to collect rich data for
mobile human
-
computer interaction studies.


Availability of such data has enabled u
s to study phenomena that would not appear in a laboratory
setting. As an example, we built a predictive model of a mobile user’s attention, basing on Bayesian
networks and data collected from 28 users of mobile web browsers. The results are promising, wit
h
accuracy in binary classification reaching 72% (22% above default), even with realistic sensors.


Computer Science in Finland 2000
-
2006

Evaluation Form


13

Creative Commons licenses for media sharing


After introducing the Creative Commons (CC) licenses in Finland in 2003, HIIT researchers have
focused on pros

and cons of applying CC
-
licenses to community
-
created content and peer
-
to
-
peer
media creation and delivery. We have also aimed to understand the new media business models and
large
-
scale societal implications of Creative Commons approach. We are also buil
ding concrete
experiments especially related to media archive sharing (the P2P Fusion EU project) and
educational material distribution (the EduGrid initiative). The work has had a significant societal
impact through facilitating the adoption and use of CC

licenses in Finland and elsewhere.


Global network society research


The aim of this research line is to analyse at macroscopic societal level the logic and global
challenges of the network society. The baseline of the work is given by the studies of Prof
. Pekka
Himanen with Prof. Manual Castells, who have analysed comparatively the Finnish/European, the
Silicon Valley/USA, and Singapore/Chinese network society models. An interim goal of the work is
to develop an integrated set of indicators, the
Global Fu
ture Index
, for describing the relations of
network society development to innovation systems and social context. Outcomes of the work
include a draft version of the index that has been presented to the World Economic Forum.

Computer Science in Finland 2000
-
2006

Evaluation Form


14


2.2. Number of scientific pu
blications and other outputs 2000
-
2006

In the summary table, calculate the number of each type of outcome in the list during the period
under review.


Type of output

2000

2001

2002

2003

2004

2005

2006

1. Articles in refereed scientific
journals


2

17

23

20

30

41

2. Articles in refereed scientific
edited volumes and conference
proceedings


3

60

77

103

115

108

3. Monographs published
1)


1


15

5

5

1

8

4. Other scientific
publications
2)



22

14

19

13

14

5. Text books and other
research
-
related publication
s
3)








6. Patents



1

2

5

3


7. Computer programs and
algorithms
3)


ca 5

ca 5

ca 10

ca 10

ca 10

ca 10

8. Visiting lectures

numerous

numerous

numerous

numerous

numerous

numerous

numerous

9. Articles, radio and television
programmes and journals
pop
ularising science

numerous

numerous

numerous

numerous

numerous

numerous

numerous

10. Other output









1)

Includes PhD theses and monographs in university series

2)
Includes edited proceedings, collections and special issues of scientific journals, an
d unrefereed
scientific articles

3)

Approximates the number of programs and algorithms that have been in use outside the unit.



2.3. Lists of most important publications by researchers with doctoral
degree (max 7 publications/person)

Each senior researche
r will list seven of his/her key publications during the period under review,
indicated in the order of quality. Unlike other information, the list may also include manuscripts
published in 2007 or manuscripts approved for publication but still unpublished
. References to
books should give the names of any editors, place of publication, editor, and year.


Only publications of researchers that have obtained their doctoral degree or who have defended
their thesis
before 31 December 2006

are listed.



Ella Bin
gham


Bingham Ella & Gionis, Aristides & Haiminen, Niina & Hiisilä, Heli & Mannila, Heikki & Terzi,
Evimaria: Segmentation and dimensionality reduction. Proc. 2006 SIAM Conference on Data
Mining, April 20
-
22, 2006, Bethesda, Maryland, USA, 372
-
383.

Computer Science in Finland 2000
-
2006

Evaluation Form


15


Kaban,

Ata & Bingham, Ella: ICA
-
based Binary Feature Construction". Independent Component
Analysis and Blind Signal Separation. Proc. 6th International Conference, ICA 2006, Charleston,
SC, USA, March 5
-
8, 2006, edited by Justinian Rosca, Deniz Erdogmus, Jose C.

Principe, Simon
Haykin, 140
-

148.


Hiisilä, Heli & Bingham, Ella: Dependencies between transcription factor binding sites: comparison
between ICA, NMF, PLSA and frequent sets. Proceedings of the 4th IEEE International Conference
on Data Mining, November
1
-
4, 2004, Brighton, UK, 114
-
121.


Kaban, Ata & Bingham, Ella & Hirsimäki, Teemu: Learning to read between the lines: The aspect
Bernoulli model. Proceedings of the 4th SIAM International Conference on Data Mining, April 22
-
24, 2004, Lake Buena Vista, Flor
ida, USA, 462
-
466.


Seppänen, Jouni K. & Bingham, Ella & Mannila, Heikki: A simple algorithm for topic
identification in 0
-
1 data. Proc. 7th European Conference on Principles and Practice of Knowledge
Discovery in Databases (PKDD 2003), Cavtat
-
Dubrovnik, C
roatia, September 2003, Number 2838
in Lecture Notes in Artificial Intelligence, Springer, 423
-
434.


Bingham, Ella & Kaban, Ata & Girolami, Mark: Topic identification in dynamical text by
complexity pursuit. Neural Processing Letters 17, 1 (2003), 69
-
83.


Hyvärinen, Aapo & Bingham, Ella: Connection between multi
-
layer perceptrons and regression
using independent component analysis, Neurocomputing 50C (January 2003), 211
-
222.



Wray Buntine


Buntine, Wray L. & Jakulin, Aleks: Discrete Component Analysis. In

C. Saunders, M. Grobelnik,
S. Gunn, and J. Shawe
-
Taylor, editors, Subspace, Latent Structure and Feature Selection
Techniques. Springer
-
Verlag, 2006.


Buntine, Wray L.: Open source search: A data mining platform. SIGIR Forum, 39, 2005.


Gray, A. G. & Fisc
her, B. & Schumann, J. & Buntine, Wray L.: Automatic derivation of statistical
algorithms: The EM family and beyond. In S. Becker, S. Thrun, and K. Obermayer, editors,
Advances in Neural Information Processing Systems 15, pages 673
-
680. MIT Press, 2003.


B
untine, Wray L. & Jakulin, Aleks: Applying discrete PCA in data analysis. In UAI
-
2004, Banff,
Canada, 2004


Kontkanen, Petri & Myllymäki, Petri & Buntine, Wray & Rissanen, Jorma & Tirri, Henry: An
MDL Framework for Data Clustering. In P. Grünwald, I.J. Myu
ng and M. Pitt, editors, Advances in
Minimum Description Length: Theory and Applications, The MIT Press, 2005.


Perkiö, Jukka & Buntine, Wray L. & Tirri, Henry: A temporally adaptive content
-
based relevance
ranking algorithm. In SIGIR '05: Proceedings of t
he 28th annual international ACM SIGIR
conference on Research and development in information retrieval. ACM Press, 2005.



Computer Science in Finland 2000
-
2006

Evaluation Form


16

Patrik Floréen


Floréen, Patrik & Kaski, Petteri & Kohonen, Jukka & Orponen, Pekka: Exact and approximate
balanced data gathering in

energy
-
constrained sensor networks. Theoretical Computer Science 344
(2005), 30
-
46.


Floréen, Patrik & Kaski, Petteri & Kohonen, Jukka & Orponen, Pekka: Lifetime maximization for
multicasting in energy
-
constrained wireless networks. IEEE Journal on Select
ed Areas in
Communications 23 (2005), 117
-
126.


Floréen, Patrik & Kaski, Petteri & Suomela, Jukka: A distributed approximation scheme for sleep
scheduling in sensor networks. To appear in Proceedings of the 4th Annual IEEE Communications
Society Conference

on Sensor, Mesh and Ad Hoc Communications and Networks (SECON, San
Diego, California USA June 2007).


Nurmi, Petteri & Przybilski, Michael & Lindén, Greger & Floréen, Patrik: An architecture for
distributed agent
-
based data preprocessing. Proceedings of t
he Workshop on Autonomous
Intelligent Systems: Agents and Data Mining (AIS
-
ADM 2005, St. Petersburg, Russia, 6
-
8 June
2005). Eds. V. Gorodetsky, J. Liu and V. A. Skormin, Lecture Notes in Computer Science 3505,
Springer
-
Verlag, Berlin, 2005, 123
-
133.


Falc
k, Emil & Floréen, Patrik & Kaski, Petteri & Kohonen, Jukka & Orponen, Pekka: Balanced
data gathering in energy
-
constrained sensor networks. Proceedings of the 1st International
Workshop on Algorithmic Aspects of Wireless Sensor Networks (Algosensors 2004,

Turku, July
16, 2004). Lecture Notes in Computer Science 3121, Springer
-
Verlag, Berlin, 2004, 59
-
70.


Floréen, Patrik & Kaski, Petteri & Kohonen, Jukka & Orponen, Pekka: Multicast time
maximization in energy constrained wireless networks. Proceedings of t
he DIALM
-
POMC Joint
Workshop on Foundations of Mobile Computing (DIALM
-
POMC 2003 at MobiCom 2003, San
Diego, Sept. 19, 2003), ACM, 2003, 50
-
58.


Nokelainen, Petri & Miettinen, Miikka & Kurhila, Jaakko & Floréen, Patrik & Tirri, Henry: A
shared document
-
bas
ed annotation tool to support learner
-
centered collaborative learning. British
Journal of Educational Technology 36 (2005) 5, 757
-
770.



Floris Geerts


Geerts, Floris & Goethals, Bart & Mielikäinen, Taneli: Tiling Databases. The 7th International
Conferen
ce on Discovery Science (DS'04), 2004. LNAI 3245, 278
-
289.


Geerts, Floris & Mannila, Heikki & Terzi, Evimaria: Relational Link
-
Based Ranking. The 30th
International Conference on Very Large Data Bases (VLDB'04) , 2004, 552
-
563.


Eronen, Lauri & Geerts, Fl
oris & Toivonen, Hannu: A Markov Chain Approach to Reconstruction
of Long Haplotypes. The 9th Pacific Symposium on Biocomputing (PSB'04), 2004, 104
-
115


Geerts, Floris & Goethals, Bart & Mielikäinen, Taneli: What You Store Is What You Get. The 2nd
Internat
ional Workshop on Knowledge Discovery in Inductive Databases (KDID'03), 2003, 60
-
69.


Computer Science in Finland 2000
-
2006

Evaluation Form


17

Aristides Gionis


Gionis, Aristides & Mannila, Heikki & Tsaparas, Panayoitis: Clustering aggregation. 21st
International Conference on Data Engineering (ICDE) 2005.


Afra
ti, Foto & Gionis, Aristides & Mannila, Heikki: Approximating a collection of frequent sets.
10th International Conference on Knowledge Discovery and Data Mining (KDD) 2004.


Bawa, Mayank & Garcia
-
Molina, Hector & Gionis, Aristides & Motwani, Rajeev: The p
rice of
validity in dynamic networks. 23rd International Conference on Management of Data (SIGMOD)
2004.


Gionis, Aristides & Kujala, Teija & Mannila, Heikki: Fragments of orders. 9th International
Conference on Knowledge Discovery and Data Mining (KDD) 20
03, pp. 129
-
136.


Gionis, Aristides & Mannila, Heikki: Finding recurrent sources in sequences. 7th International
Conference on Research in Computational Molecular Biology (RECOMB) 2003, pp. 123
-
130.


Datar, Mayur & Gionis, Aristides & Indyk, Piotr & Motwan
i, Rajeev: Maintaining Stream Statistics
over Sliding Windows. SIAM Journal on Computing, 31(6).


Haveliwala, Taher & Gionis, Aristides & Klein, Dan & Indyk, Piotr: Similarity Search on the Web:
Evaluation and Scalability Considerations. 11th International

World Wide Web Conference 2002.



Bart Goethals


Geerts, Floris & Goethals, Bart & Van den Bussche, Jan: Tight upper bounds on the number of
candidate patterns. ACM Trans. on Database Systems, 30, 2 (2005), 333

363.


Calders, Toon & Goethals, Bart: Minima
l k
-
Free Representations of Frequent Sets. Proceedings of
the International Conference on Principles of Data Mining and Knowledge Discovery (PKDD),
2003, 71

82.



Geerts, Floris & Goethals, Bart & Mielikäinen, Taneli: What You Store is What You Get.
Procee
dings of the Second International Workshop on Inductive Databases, 2003, 60
-
69.



Goethals, Bart & Zaki, Mohammed Javeed: Advances in Frequent Itemset Mining Implementations.
ACM SIGKDD Explorations 6, 1 (2004), 109

117.



Goethals, Bart: Memory issues in
frequent itemset mining. Proceedings of the 2004 ACM
Symposium on Applied Computing (SAC) 2004, 530

534.


Goethals, Bart & Laur, Sven & Lipmaa, Helger & Mielikäinen, Taneli: On private scalar product
computation for privacy
-
preserving data mining. In Choon
sik Park and Seongtaek Chee (Eds.):
Proceedings of the 7th International Conference on Information Security and Cryptology


ICISC
2004, Seoul, Korea, December 2

3, 2004, Volume 3506 of Lecture Notes in Computer Science,
pages 104

120. Springer, 2005.


Computer Science in Finland 2000
-
2006

Evaluation Form


18

Gee
rts, Floris & Goethals, Bart & Mielikäinen, Taneli: Tiling Databases. The 7th International
Conference on Discovery Science (DS'04), 2004. LNAI 3245, 278
-
289.



Andrei Gurtov


Dmitry Korzun and Andrei Gurtov, On Scalability Properties of the Hi3 Control Pl
anes, Elsevier
Computer Communications, 29(17):3591
-
3601, November 2006.


Tuomas Aura, Aarthi Nagarajan, Andrei Gurtov, Analysis of the HIP Base Exchange Protocol, in
Proc. of ACISP'05, July 2005.


Teemu Koponen, Andrei Gurtov and Pekka Nikander, Applicati
on Mobility with HIP, in Proc. of
ICT'05, May 2005.


H. Tschofenig, A. Gurtov, J. Ylitalo, A. Nagarajan, M. Shanmugam,

Traversing Middleboxes with the Host Identity Protocol, in Proc. of the 10th Australasian
Conference

on Information Security and Privacy
(ACISP), July 2005.


Miika Komu, Sasu Tarkoma, Jaakko Kangasharju and Andrei Gurtov, Applying a Cryptographic
Namespace to Applications, Proceedings of the 1st ACM workshop on Dynamic interconnection of
networks, 2005


D. Korzun, A. Gurtov, On Applying Lin
ear Diophantine Equations to Route Modeling in Self
-
Organizing Networks, Elektrosvyaz, 6:34
-
38, June 2006. ISSN 0013
-
5771.


A.
Gurtov
, A. D. Joseph, Friends or Rivals: Insights from Integrating HIP and i3, Workshop on HIP
and Related Architectures, Novembe
r 2004



Pekka Himanen


“The Hacker Ethic as the Culture of the Informational Economy” in Castells, Manuel (ed.), The
Network Society: A Global Perspective. Edward Elgar, 2004.


“Comparison of Silicon Valley and Finnish Models of the Information Society” (
with Manuel
Castells) in Castells, Manuel (ed.), The Network Society: A Global Perspective. Edward Elgar,
2004.


“The Nordic Model of Information Society: The Case of Finland” in Palme, Joakim and Kangas,
Olli (eds.) Social Policy in Late Industrializers:
The Nordic Countries. United Nations Research
Institute for Social Development, 2004.


“Managing the Culture of Innovation” (with Matti Alahuhta) in Harvard Business Review
(forthcoming).


“The E
-
Welfare State: The Public Culture of Innovation” (with Antti

Hautamäki). Berkeley Center
for Information Society Working Papers, 2004.


Computer Science in Finland 2000
-
2006

Evaluation Form


19

“The Social Web” (with Jerome Feldman and Steve Weber). Berkeley Center for Information
Society Working Papers, 2003.


The Challenges of Finland: The Global Information Society Dev
elopment and Finland (Suomen
haasteet: Globaali tietoyhteiskuntakehitys ja Suomi). Helsinki: The National Technology Agency,
2004.



Jaakko Hollmén


Wikman, Harriet & Kettunen, Eeva & Seppänen, Jouni K. & Karjalainen, Antti & Hollmén, Jaakko
& Anttila, Sis
ko & Knuutila, Sakari: Identification of differentially expressed genes in pulmonary
adenocarcinoma by using a cDNA array. Oncogene, 21(37):5804
-
5813, 2002. Nature Publishing
Group.


Kettunen, Eeva & Anttila, Sisko & Seppänen, Jouni K. & Karjalainen, Antti

& Edgren, Henrik &
Lindström, Irmeli & Salovaara, Reijo & Nissén, Anna
-
Maria & Salo, Jarmo & Mattson, Karin &
Hollmén, Jaakko & Knuutila, Sakari & Wikman, Harriet: Differentially expressed genes in
nonsmall cell lung cancer: expression profiling of cancer
-
related genes in squamous cell lung
cancer. Cancer Genetics and Cytogenetics, 149(2):98
-
106, 2004.


Luyssaert, Sebastiaan & Sulkava, Mika & Raitio, Hannu & Hollmén, Jaakko: Evaluation of forest
nutrition based on large
-
scale foliar surveys: are nutrition
profiles the way of the future? Journal of
Environmental Monitoring, 6(2):160
-
167, 2004.


Wikman, Harriet & Seppänen, Jouni K. & Sarhadi, Virinder K. & Kettunen, Eeva & Salmenkivi,
Kaisa & Kuosma, Eeva & Vainio
-
Siukola, Katri & Nagy, Balint & Karjalainen,
Antti & Sioris,
Thanos & Salo, Jarmo & Hollmén, Jaakko & Knuutila, Sakari & Anttila, Sisko: Caveolins as tumor
markers in lung cancer detected by combined use of cDNA and tissue microarrays. Journal of
Pathology, 203:584
-
593, 2004.


Gopalacharyulu, Peddint
i V. & Lindfors, Erno & Bounsaythip, Catherine & Kivioja, Teemu &
Yetukuri, Laxman & Hollmén, Jaakko & Oresic, Matej; Data integration and visualization system
for enabling conceptual biology. Bioinformatics, 21(Suppl.1):i177
-
i185, 2005.


Luyssaert, Sebast
iaan & Sulkava, Mika & Raitio, Hannu & Hollmén, Jaakko: Are N and S
deposition altering the chemical composition of Norway spruce and Scots pine needles in Finland?
Environmental Pollution, 138(1):5
-
17, 2005.


Sulkava, Mika & Tikka, Jarkko & Hollmén, Jaakk
o: Sparse regression for analyzing the
development of foliar nutrient concentrations in coniferous trees. Ecological Modeling, 191(1):118
-
130, 2006.



Patrik Hoyer


Shimizu, Shohei & Hoyer, Patrik, O. & Hyvärinen, Aapo & Kerminen, Antti, J.: A linear non
-
g
aussian acyclic model for causal discovery. Journal of Machine Learning Research 7:2003
-
2030,
2006.


Computer Science in Finland 2000
-
2006

Evaluation Form


20

Hoyer, Patrik, O.: Non
-
negative Matrix Factorization with sparseness constraints. Journal of
Machine Learning Research, 5, pp. 1457
-
1469, 2004.


Vicente, A
sun & Hoyer, Patrik, O. & Hyvärinen, Aapo: Equivalence of some common linear
feature extraction techniques for appearance
-
based object recognition tasks. IEEE Transactions on
Pattern Analysis and Machine Intelligence, in press.


Hoyer, Patrik, O. & Shimizu
, Shohei & Kerminen, Antti, J.: Estimation of linear, non
-
gaussian
causal models in the presence of confounding latent variables. In Proc. Third European Workshop
on Probabilistic Graphical Models (PGM'06), pp. 155
-
162, Prague, Czech Republic, 2006.


Shimi
zu, Shohei & Hyvärinen, Aapo, P.O. & Hoyer Kano, Yutaka: Finding a causal ordering via
independent component analysis. Computational Statistics & Data Analysis 50 (11): 3278
-
3293,
2006.


Hyvärinen, Aapo & Gutmann, Michael &Hoyer, Patrik. O.: Statistical mo
del of natural stimuli
predicts edge
-
like pooling of spatial frequency channels in V2. BMC Neuroscience, 6 (12), 2005.


Shimizu, Shohei & Hyvärinen, Aapo & Kano, Yutaka & Hoyer, Patrik, O.: Discovery of non
-
gaussian linear causal models using ICA. In Proce
edings of the 21st Conference on Uncertainty in
Artificial Intelligence (UAI
-
2005), pp. 526
-
533, 2005.



Jarmo Hurri


Hurri, Jarmo: Learning Cue
-
Invariant Visual Responses. Advances in Neural Information
Processing Systems, volume 18, edited by Y. Weiss, B
. Schölkopf and J. Platt. The MIT Press,
2006.


Bas, Patrick & Hurri, Jarmo: Vulnerability of DM watermarking of non
-
iid host signals to attacks
utilising the statistics of independent components. IEE Proceedings
-

Information Security 153, 3

(2006), 127
-
1
39.


Lindgren, Jussi & Hurri, Jarmo & Hyvärinen, Aapo. The statistical properties of local log
-
contrast
in natural images. Proceedings of the 15th Scandinavian Conference on Image Analysis, accepted,
2007.


Bas, Patrick & Hurri Jarmo. Security of DM quanti
zation watermarking schemes: A practical study
for digital images. Proceedings of the International Workshop on Digital Watermarking, edited by
M. Barni, I. Cox, T. Kalker and H. J. Kim. Springer, 2005.


Hyvärinen, Aapo & Hoyer, Patrik & Hurri, Jarmo & Mic
hael Gutmann: Statistical models of
images and early vision. Proceedings of the International and Interdisciplinary Conference on
Adaptive Knowledge Representation and Reasoning, edited by T. Honkela, V. Könönen, M. Pöllä
and O. Simula, Olli. Helsinki Univ
ersity of Technology, 2005.



Computer Science in Finland 2000
-
2006

Evaluation Form


21

Aapo Hyvärinen


Hyvärinen, Aapo: Estimation of non
-
normalized statistical models using score matching. Journal of
Machine Learning Research, 6, pp. 695
-
709, 2005.


Shimizu, Shohei & Hoyer, Patrik. O. & Hyvärinen, Aapo & Kermin
en, Antti. A linear nongaussian
acyclic model for causal discovery. J. of Machine Learning Research 7:2003
-
2030, 2006.


Himberg, Johan & Hyvärinen, Aapo & Esposito, Fabrizio: Validating the independent components
of neuroimaging time
-
series via clustering
and visualization. NeuroImage, 22 (3), pp. 1214
-
1222,
2004.


Hyvärinen, Aapo & Hurri, Jarmo. Blind separation of sources that have spatiotemporal variance
dependencies. Signal Processing, 84(2):247?254, 2004.


Hyvärinen, Aapo & Gutmann, Michael & Hoyer, Pa
trik, O.. Statistical model of natural stimuli
predicts edge
-
like pooling of spatial frequency channels in V2. BMC Neuroscience, 6(12), 2005.


Hyvärinen, Aapo. A unifying model for blind separation of independent sources. Signal Processing,

85(7):1419?1427
, 2005.


Esposito, Fabrizio & Scarabino, Tommaso & Hyvärinen, Aapo & Himberg, Johan & Formisano,
Elia & Comani, Silvia & Tedeschi, Giaocchino & Goebel, Rainer & Seifritz, Erich & Di Salle,
Francesco: Independent component analysis of fMRI group studies by
self
-
organizing clustering.
NeuroImage, 25(1):193?205, 2005.



Saara Hyvönen


Hyvönen, Saara & Junninen, Heikki & Laakso, Lauri & Dal Maso, Miikka & Grönholm, Tiia &
Bonn, Boris & Keronen, Petri & Aalto, Pasi & Hiltunen, Veijo & Pohja, Petri & Launiainen,
Samuli & Hari, Pertti & Mannila, Heikki & Kulmala, Markku: A look at aerosol formation using
data mining techniques. Atmospheric Chemistry and Physics, Vol. 5, pp 3345
-
3356, 14
-
12
-
2005.


Hyvönen, Saara, & Leino, Antti & Salmenkivi, Marko: Multivariate Anal
ysis of Finnish Dialect
Data
-

an overview of lexical variation. To appear in Literary and Linguistic Computing.


Leino, Antti & Hyvönen, Saara & Salmenkivi, Marko: Mitä murteita Suomessa onkaan?
Murresanaston levikin kvantitatiivista analyysiä. Virittäjä
1/2006, 26
-
45.


Toivonen, Hannu & Hyvönen, Saara & Sevon, Petteri: Combining phenotypic and genotypic data to
discover multiple disease genes. Symposium on Knowledge Representation in Bioinformatics
(KRBIO'05), 7
-
14, Espoo, Finland, June 2005.


Hyvönen, Sa
ara & Junninen, Heikki & Laakso, Lauri & Dal Maso, Miikka & Grönholm, Tiia &
Bonn, Boris & Keronen, Petri & Aalto, Pasi & Hiltunen, Veijo & Pohja, Petri & Launiainen,
Samuli & Tunved, Peter & Hanssen, HC & Hari, Pertti & Mannila, Heikki & Kulmala, Markku:
Data mining approaches to explaining aerosol formation. In: Voinov, A., Jakeman, A., Rizzoli, A.
(eds). Proceedings of the iEMSs Third Biennial Meeting: "Summit on Environmental Modelling
Computer Science in Finland 2000
-
2006

Evaluation Form


22

and Software". International Environmental Modelling and Software So
ciety, Burlington, USA,
July 2006. CD ROM. Internet: http://www.iemss.org/iemss2006/sessions/all.html


Salmenkivi, Marko & Hyvönen, Saara & Leino, Antti & Tuominen, Heikki: Computational survey
of clustering in Finnish place name elements. In: Proceedings
of the twenty
-
second International
Congress of Onomastic Sciences (ICOS XXII), Pisa, Italy, August
-
September 2005. To appear.


Grönholm, Tiia & Hiltunen, Veijo & Laakso, Lauri & Aalto, Pasi P.& Rinne, Janne & Hyvönen,
Saara & Rannik, Ullar & Kulmala, Markk
u: Measurements of aerosol particle dry deposition
velocities using relaxed eddy accumulation technique. To appear in Tellus.



Tommi Ilmonen


Ilmonen, Tommi, Tools and Experiments on Multimodal Interaction, Doctoral Thesis, Espoo,
Finland, 2006.


Ilmonen
, Tommi & Lokki, Tapio. Extreme Filters


Cache
-
Efficient Implementation of High
Order IIR and FIR Filters. In IEEE Signal Processing Letters 13(7), Editor

in
-
Chief: Gershman, B.
2006.


Jacucci, Giulio & Oulasvirta, Antti & Ilmonen, Tommi & Evans, John &
Salovaara, Antti.
CoMedia: Mobile Group Media for Active Spectatorship. Accepted to CHI2007, 28 April
-

3 May,
2007 San Jose, USA, ACM Press, 2007.


Ilmonen, Tommi & Takala, Tapio & Laitinen, Juha. Collision Avoidance and Surface Flow for
Particle Systems
Using Distance/Normal Grid. In Full Papers Proceedings of the Winter School on
Computer Graphics, Editors: Joaquim Jorge and Vaclav Skala, Plzen, Czech Republic, 2006.


Ilmonen, Tommi & Takala, Tapio & Laitinen, Juha. Soft Edges and Burning Things


Enhanc
ed
Real
-
Time Rendering of Particle Systems. In Full Papers Proceedings of the Winter School on
Computer Graphics, Editors: Joaquim Jorge and Vaclav Skala, Plzen, Czech Republic, 2006.



Mika Inki


Inki, Mika: Least mean square covariance transformations an
d generalized orthogonalization.
Submitted manuscript.



Giulio Jacucci


Macaulay, C., G. Jacucci, S. O'Neill, T. Kankaineen and M. Simpson. The emerging roles of
performance within HCI and interaction design. In Interacting with Computers, 6 (2006), Elsev
ier,
pp.942
-
955.


Jacucci, G.; Oulasvirta, A.; Salovaara, A.: Active construction of experience through multimedia: a
field study with implications for recording and sharing. Personal and Ubiquitous Computing, 2006.
http://dx.doi.org/10.1007/s00779
-
006
-
008
4
-
5


Computer Science in Finland 2000
-
2006

Evaluation Form


23

Jacucci, G., Oulasvirta, A., Ilmonen, T., Evans, J., Salovaara, A., (2007) CoMedia: Mobile Group
Media for Active Spectatorship. Accepted to CHI2007, 28 April
-

3 May, 2007 San Jose, USA,
ACM Press.


Salovaara, A., Jacucci, G., Oulasvirta, A., Kanerva
, P., Kurvinen, E., Tiitta, S., (2006) Collective
creation and sense
-
making of mobile media, Proceedings of the SIGCHI conference on Human
Factors in Computing Systems, Montréal, Québec, Canada. ACM Press, Pp: 1211


1220.


Jacucci, G., Wagner, I. (2005) P
erformative Uses of Space in Mixed Media Environments. In:
Davenport, E., Turner P., Spaces, Spatiality and Technologies, Springer, London, 2005.


Jacucci, G., Linde, P., Wagner, I., (2005) Exploring relationships between learning, artifacts,
physical spac
e, and computing. In Digital Creativity Journal, 2005, Vol. 16, No. 1, pp. 19

30.


Jacucci Giulio, Oulasvirta, A., Salovaara, A., Psik, T., Wagner, I., (2005) Augmented Reality
Painting and Collage: Evaluating Tangible Interaction in a Field Study. Tenth I
FIP TC13
International Conference on Human
-
Computer Interaction, Rome, September 2005.



Matti Kääriäinen


Kääriäinen, Matti: Generalization error bounds using unlabeled data. In Learning Theory: 18th
Annual Conference on Learning Theory, COLT '05 (pp. 127
-
142). Springer, 2005.


Kääriäinen, Matti: Active Learning in the Non
-
realizable Case. In Algorithmic Learning Theory,
ALT 2006 (pp. 63
-
77). LNCS 4264. Springer, 2006.


Kääriäinen, Matti & Langford, John: A comparison of tight generalization error bounds.
In The
22nd International Conference on Machine Learning (ICML 2005).


Kääriäinen, Matti & Malinen, Tuomo & Elomaa, Tapio: Selective Rademacher penalization and
reduced error pruning of decision trees. Journal of Machine Learning Research, volume 5: 1107
-
1
126, 2004.


Nock, Richard & Elomaa, Tapio & Kääriäinen, Matti: Reduced Error Pruning of Branching
Programs Cannot Be Approximated to within a Logarithmic Factor. Information Processing Letters
87, 2 (2003) 73
-
78.


Elomaa, Tapio & Kääriäinen, Matti: Progres
sive Rademacher sampling. Proc. 18th National
Conference on Artificial Intelligence, AAAI
-
2002 (pp. 140
-
145). AAAI Press & MIT Press, 2002.


Elomaa, Tapio & Kääriäinen, Matti: An analysis of reduced error pruning. Journal of Artificial
Intelligence Researc
h 15 (Sept. 2001) 163
-
187.



Petteri Kaski


Björklund, Andreas & Husfeldt, Thore & Kaski, Petteri & Koivisto: Mikko: Fourier meets Möbius:
fast subset convolution, Proceedings of the 39th ACM Symposium on Theory of Computing (San
Diego, CA, June 11
-
13, 200
7), to appear.

Computer Science in Finland 2000
-
2006

Evaluation Form


24


Kaski, Petteri & Östergård, Patrik, R. J.: Classification Algorithms for Codes and Designs,
Springer
-
Verlag, Berlin Heidelberg, 2006.


Greig, Malcolm &. Haanpää, Harri & Kaski, Petteri: On the coexistence of conference matrices and
near res
olvable 2
-
(2k+1,k,k
-
1) designs, Journal of Combinatorial Theory, Series A 113 (2006), 703
-
711.


Kaski, Petteri & Östergård, Patrik &. J. & Pottonen, Olli: The Steiner quadruple systems of order
16, Journal of Combinatorial Theory, Series A 113 (2006), 1764
-
1770.


Kaski, Petteri & Östergård, Patrik, R. J.: There are exactly five biplanes with k=11, Journal of
Combinatorial Designs, to appear.


T. Junttila & Kaski, Petteri: Engineering an efficient canonical labeling tool for large and sparse
graphs, Proceedi
ngs of ALENEX07 Workshop on Algorithm Engineering and Experiments (New
Orleans, January 6, 2007), to appear.


Floréen, Patrik & Kaski, Petteri & Suomela, Jukka: A distributed approximation scheme for sleep
scheduling in sensor networks, Proceedings of the
4th Annual IEEE Communications Society
Conference on Sensor, Mesh, and Ad Hoc Communications and Networks (San Diego, CA, June
18
-
21, 2007), to appear.



Jukka Kemppinen


Kemppinen, Jukka Digitaaliongelma
-

Kirjoitus oikeudesta ja ympäristöstä. Lappeenrant
a 2006,
Lappeenranta University of Technology. 502 pp.


Martikainen, Petri (editor); Karila, Arto; Kemppinen, Jukka; Kontiainen, Mikko; Kurvinen, Esko;
Mäntylä, Martti; Oulasvirta, Antti; Pitkänen, Olli; Raento, Mika; Salovaara, Antti; Sarkio, Katri;
Sarva
s, Risto; Turpeinen, Marko; Virtanen, Perttu Towards Ubiquitous Network Society. Helsinki:
Tietotekniikan tutkimuslaitos HIIT, 2006. 96 pp. (HIIT Report Series 2006
-
3).


Pitkänen, Olli; Mäntylä, Martti; Välimäki, Mikko; Kemppinen, Jukka Assessing Legal Cha
llenges
on the Mobile Internet. International Journal of Electronic Commerce, 2003. Vol. 8, No. 1, 101
-
120.


Pitkänen, Olli; Välimäki, Mikko; Kemppinen, Jukka; Mäntylä, Martti Assessing Legal Challenges
on the Mobile Web. First International Conference of

Mobile Business, Athens, Greece, July 2002.



Mikko Koivisto


Koivisto, Mikko. An O(2^n) algorithm for graph coloring and other partitioning problems via
inclusion
-
exclusion. Proceedings of the 47th Annual IEEE Symposium on Foundations of
Computer Science

(FOCS 2006), pp. 583
-
590, IEEE Computer Society, 2006.


Björklund, Andreas & Husfeldt, Thore & Kaski, Petteri & Mikko Koivisto. Fourier meets Möbius:
fast subset convolution. 39th ACM Symposium on Theory of Computing (STOC 2007), to appear.


Computer Science in Finland 2000
-
2006

Evaluation Form


25

Koivisto, Mik
ko & Sood, Kismat: Exact Bayesian structure discovery in Bayesian networks.
Journal of Machine Learning Research, 5 (2004), 549
-
573.


Koivisto, Mikko & Perola, Markus & Varilo, Teppo & Hennah, William & Ekelund, Jesper &
Lukk, Margus & Peltonen, Leena & Uk
konen, Esko & Mannila, Heikki. An MDL method for
finding haplotype blocks and for estimating the strength of haplotype block boundaries. Pacific
Symposium on Biocomputing 2003 (PSB 2003), edited by R.B. Altman, A.K. Dukner, L. Hunter,
T.A. Jung and T.E. Kl
ein, pp. 502
-
513. World Scientific, 2002.


Koivisto, Mikko & Mannila, Heikki: Offspring risk and sibling risk for multilocus traits. Human
Heredity, 51 (2001), 209
-
216.


Rastas, Pasi & Koivisto, Mikko & Mannila, Heikki & Ukkonen, Esko. A hidden Markov tech
nique
for haplotype reconstruction. Algorithms in Bioinformatics: 5th International Workshop (WABI
2005), edited by R. Casadio and G. Myers. LNCS 3692, pp. 140
-
151, Springer, 2005.


Koivisto, Mikko. Parent assignment is hard for the MDL, AIC, and NML costs
. The 19th Annual
Conference on Learning Theory (COLT 2006), edited by G. Lugosi and H.U. Simon. LNAI 4005,
pp. 289
-
303, Springer, 2006.



Greger Lindén


Nurmi, Petteri & Przybilski, Michael & Lindén, Greger & Floréen, Patrik: An architecture for
distribut
ed agent
-
based data preprocessing. In proceedings of the Autonomous Intelligent Systems:
Agents and Data Mining Workshop (AIS
-
ADM 2005), No. 3505 in Series Lecture Notes in
Artificial Intelligence, V. Gorodetsky, J. Liu and V.A. Skormin (eds.), 123
-

133,
Springer
-
Verlag,
2005.


Nurmi, Petteri & Floréen, Patrik & Przybilski, Michael & Lindén, Greger: A Framework for
Distributed Activity Recognition in Ubiquitous Systems Proceedings of the International
Conference on Artificial Intelligence, Las Vegas, 27
-

30 June, 2005.


Lehtonen, Miro & Petit, Renaud & Heinonen, Oskari & Lindén, Greger: A Dynamic User Interface
for Document Assembly. In Proceedings of the ACM Symposium on Document Engineering
(DocEng'02), 134
-
141. ACM Press, 2002.



Heikki Mannila


Hand, D
avid, J. & Mannila, Heikki & Smyth, Padhraic: Principles of Data Mining. MIT Press 2001
Chinese translation, China Machine Press, ISBN 7
-
111
-
11577
-
5, 2003. Polish translation
"Eksploracja danych", Wydawnictwa Naukowo
-
Techniczne, ISBN 83
-
204
-
3053
-
4, 2005.


Gunopulos, Dimitrios & Khardon, Roni & Mannila, Heikki & Saluja, Sanjeev & Toivonen, Hannu
& Sharma, Ram Shewak: Discovering all most specific sentences. ACM Transactions on Database
Systems 28 (2): 140
-

174, June 2003.


Fortelius, Mikael & Gionis, Aristi
des & Jernvall, Jukka & Mannila, Heikki: Spectral Ordering and
Biochronology of European Fossil Mammals, Paleobiology 32, 2, 206
-
214, 2006.

Computer Science in Finland 2000
-
2006

Evaluation Form


26


Gionis, Aristides & Mannila, Heikki & Mielikäinen, Taneli & Tsaparas, Panayoitis: Assessing Data
Mining Results via

Swap Randomization, 12th International Conference on Knowledge Discovery
and Data Mining (KDD) 2006, 167
-
176.


Han, Jiawei & Altman, Russ B. & Kumar, Vipin & Mannila, Heikki, Pregibon, Daryl: Emerging
Scientific Applications in Data Mining. Communications

of the ACM 45, 8 (August 2002), 54
-
58.


Gionis, Aristides & Mannila, Heikki & Tsaparas, Panayoitis: Clustering aggregation, In 21st
International Conference on Data Engineering (ICDE) 2005, 341
-
352; journal version to appear in
ACM Transactions on Knowled
ge discovery from Data (TKDD).


Geerts, Floris & , Mannila, Heikki & Terzi, Evimaria: Relational link
-
based ranking . The 30th
International Conference on Very Large Data Bases (VLDB'04), 2004, 552
-
563.



Martti Mäntylä


Olli Pitkänen, Martti Mäntylä, Mikk
o Välimäki, and Jukka Kemppinen: Assessing Legal
Challenges on the Mobile Internet. International Journal of Electronic Commerce, Vol. 8, nr 1, 101
-
120, Fall 2003.


Matti Rantanen, Antti Oulasvirta, Jan Blom, Sauli Tiitta, and Martti Mäntylä, M. InfoRadar:

Group
and public messaging in mobile context. Proc. NordiCHI’04, November 2004, Tampere, Finland.


Sari Kujala and Martti Mäntylä. Is User Involvement Harmful or Useful in the Early Stages of
Product Development? Proc. CHI'2000 Conference, The Hague, The
Netherlands, 1
-
6 April. U.S.A.
2000, ACM Press, pp. 285
-
286.


Pekka Isto, Juha Tuominen, and Martti Mäntylä: Adaptive Strategies for Probabilistic Roadmap
Construction. 2003 International Conference on Advanced Robotics. 682
-
687, 2003.


Sari Kujala and Mar
tti Mäntylä. How Effective Are User Studies? HCI'2000, Sunderland, UK, 6
-
8
September, 2000. GB 2000, Springer, pp. 61
-
71.


Katri Sarkio and Martti Mäntylä, Is Your Neighbor a Traitor? Distributed Reputation Management
in Member
-
Initiated Virtual Communitie
s. HIIT Technical Report 2006
-
1, March 2006.


Alex G. Büchner, Mervi Ranta, John G. Hughes, and Martti Mäntylä. Semantic information
mediation among multiple product ontologies. Presented at the Fifth World Conference on
Integrated Design and Process Techn
ology, Dallas, Texas, June 4

8, 2000.



Taneli Mielikäinen


Gionis, Aristides & Mannila, Heikki & Mielikäinen, Taneli & Tsaparas, Panayiotis: Assessing data
mining results via swap randomization. In Mark Craven and Dimitrios Gunopulos (Eds.):
Proceedings o
f the Twelfth Annual SIGKDD International Conference on Knowledge Discovery
and Data Mining (KDD 2006), Philadelphia, USA, August 20

23, 2006. ACM, 2006.


Computer Science in Finland 2000
-
2006

Evaluation Form


27

Goethals, Bart & Laur, Sven & Lipmaa, Helger & Mielikäinen, Taneli: On private scalar product
computa
tion for privacy
-
preserving data mining. In Choonsik Park and Seongtaek Chee (Eds.):
Proceedings of the 7th International Conference on Information Security and Cryptology


ICISC
2004, Seoul, Korea, December 2

3, 2004, Volume 3506 of Lecture

Notes in Com
puter Science, pages 104

120. Springer, 2005.


Mielikäinen, Taneli: Frequency
-
based views to pattern collections. Discrete Applied Mathematics
154(7), pages 1113

1139. Elsevier, 2006.


Mielikäinen, Taneli & Ravantti, Janne & Ukkonen, Esko: The computationa
l complexity of
orientation search in cryo
-
electron microscopy. In Marian Bubak, G. Dick van Albada, Peter M. A.
Sloot, and Jack J. Dongarra (Eds.): Computational Science


ICCS 2004: 4th International
Conference, Krakow, Poland, June 6

9, 2004, Proceeding
s, Part I. Volume 3036 of Lecture Notes
in Computer Science, pages 231

238. Springer, 2004.


Mielikäinen, Taneli & Terzi, Evimaria & Tsaparas, Panayiotis: Aggregating Time Partitions. In
Mark Craven and Dimitrios Gunopulos (Eds.): Proceedings of the Twelft
h Annual SIGKDD
International Conference on Knowledge Discovery and Data Mining (KDD 2006), Philadelphia,
USA, August 20

23, 2006. ACM, 2006.


Mielikäinen, Taneli & Ukkonen, Esko: The complexity of maximum matroid
-
greedoid intersection
and weighted greedoi
d maximization. Discrete Applied Mathematics 154(4), pages 684

691.
Elsevier, 2006.


Rantanen, Ari & Mielikäinen, Taneli & Rousu, Juho & Maaheimo, Hannu & Ukkonen, Esko:
Planning optimal measurements of isotopomer distributions for estimation of metabolic
fluxes.
Bioinformatics 22(10):1198

1206. Oxford University Press, 2006.



Petri Myllymäki


Kontkanen, Petri & P. Myllymäki: MDL Histogram Density Estimation. In Proceedings of the
Eleventh International Conference on Artificial Intelligence and Statistics,

Puerto Rico, March
2007.


Kontkanen, Petri & Myllymäki, Petri & Buntine, Wray & Rissanen, Jorma & Tirri, Henry: 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. The MIT Press, 2005.


Roos, Teemu & Wettig, Hannes & Grünwald, Peter & Myllymäki, Petri & Tirri, Henry: On
Discriminative Bayesian Network Classifiers and Logistic Regression. Machine Learning 59
(2005):3, pp. 267
-
296.


Roos, Teemu & Grünwald, Pe
ter & Myllymäki, Petri & Tirri, Henry: Generalization to Unseen
Cases. In Proceedings of the 19th Annual Conference on Neural Information Processing Systems
(NIPS 2005). MIT Press, 2006.


Kontkanen, Petri & Myllymäki, Petri & Roos, Teemu & Tirri, Henry & V
altonen, Kimmo &
Wettig, Hannes: Probabilistic Methods for Location Estimation in Wireless Networks. Chapter 11
Computer Science in Finland 2000
-
2006

Evaluation Form


28

in Emerging Location Aware Broadband Wireless Adhoc Networks, edited by R.Ganesh, S.Kota,
K.Pahlavan and R.Agusti. Kluwer Academic Publishers, 2
004


Silander, Tomi & Myllymäki, Petri: A Simple Approach for Finding the Globally Optimal Bayesian
Network Structure. Pp. 445
-
452 in Proceedings of the 22nd Conference on Uncertainty in Artificial
Intelligence (UAI
-
2006), edited by R. Dechter and T. Richa
rdson. AUAI Press, 2006.


Myllymäki, Petri & Silander, Tomi & Tirri, Henry & Uronen, Pekka: B
-
Course: A Web
-
Based Tool
for Bayesian and Causal Data Analysis. International Journal on Artificial Intelligence Tools, Vol.
11 (2002), No. 3, 369
-
387.



Pekka Ni
kander


Tuomas Aura, Pekka Nikander, and Jussipekka Leiwo,
"DOS
-
resistant Authentication with Client
Puzzles,"

in Christianson, Malcolm, Crispo, and Roe (Eds.)
Security Protocols, 8th International
Workshop, Cambridge, UK, April 3
-
5, 2000; revised papers
,
LNCS 2133, pp. 170
-
177, Springer
2001.


Robert Moskowitz and Pekka Nikander, “Host Identity Protocol (HIP) Architecture”, RFC 4423,
Internet Engineering Task Force, May 2006.


Pekka Nikander, Jukka Ylitalo, and Jorma Wall,
"Integrating Security, Mobility, and Multi
-
Homing
in a HIP Way,"

in
Proceedings of Network and Distributed Systems Security Symposium (NDSS'03),

February 6
-
7, 2003, San Diego, CA, pp. 87
-
99, Internet Society,

February, 2003.


Tuomas Aura, Pekka Nikander, and Gonzalo Camarillo,
"Effects of Mobility and Multihoming on
Transport
-
Layer Security,"

in
Proceedings of IEEE Symposi
um on Security and Privacy,

Berkeley/Oakland, California, May 9