Where academic tradition
meets the exciting future

TUCS Newsletter 28.4.2015

Content of the newsletter

TUCS activities

New courses


Latest publications at TUCS

TUCS activities

TUCS Research Programme activities

Title: DNA Rendering of Polyhedral Meshes at the Nanoscale

Abstract: The presentation will concentrate over the newly introduced algorithmic design scheme for DNA-based 3D polyhedral nanostructures. The technique introduces a way of tracing a long DNA scaffold strand through these structures, using a "one helix per edge" principle, thus enabling the design of structures that could not previously be realized before. The fully automated design process takes arbitrary polygonal mesh designs and converts them to molecular designs suitable for DNA nanostructure folding. A routing algorithm, based on Eulerian paths, and a relaxation simulation, are used to traverse the scaffold across the edges of the triangulated meshes. Both the fundamental design methods as well as concrete examples and their experimental implementations will be presented.

"Perspectives of feature selection in bioinformatics: from relevance to causal inference"

Abstarct: A major goal of the scientific activity is to model real phenomena by studying the dependency between entities, objects or more in general variables. Sometimes the goal of the modeling activity is simply predicting future behaviors. Sometimes the goal is to understand the causes of a phenomenon (e.g. a disease). Finding causes from data is particular challenging in bioinformatics where often the number of features (e.g. number of SNPs or microarray probes) is huge with respect to the number of samples. In this context, even when experimental interventions are possible, performing thousands of experiments to discover causal relationships between thousands of variables is not practical. Dimensionality reduction techniques have been largely discussed and used in bioinformatics to deal with the curse of dimensionality. However, most of the time these techniques focus on improving prediction accuracy, neglecting causal aspects. This talk will discuss a major open issue : may feature selection techniques be useful also for causal feature selection? Is prediction accuracy compatible with causal discovery? Some results based on an information theory approach will be used to illustrate the issue.

TUCS Distinguished Lecture Series

         Title: “Standing on the Shoulders of a Giant: One Person’s Experience of Turing’s Impact”

         Host: Ion Petre, Åbo Akademi and Turku Centre for Computer Science

Abstract: The talk will briefly describe three of Turing’s major achievements, in three different fields: computability, biological modeling and artificial intelligence.  Interspersed with this, I will explain how each of them directly motivated and inspired me to work on a number of topics over a period of 30 years, the results of which can all be viewed humbly as extensions and generalizations of Turing’s pioneering and ingenious insights.


Bio: Prof. David Harel has been a faculty member at the Weizmann Institute of Science in Israel since 1980. He was Head of the Department of Applied Mathematics and Computer Science from 1989 to 1995, and was Dean of the Faculty of Mathematics and Computer Science between 1998 and 2004. He is also co-founder of I-Logix, Inc. He received his PhD from the Massachusetts Institute of Technology in 1978 in record time of 20 months. He spent two years of postdoctoral work at IBM's Yorktown Heights research center, and sabbatical years at Carnegie-Mellon University, Cornell University and the University of Edinburgh. In the past he worked in several areas of theoretical computer science, including computability theory, logics of programs, database theory, and automata theory.  Over the years his activity in these areas diminished, and he became involved in several other areas, including software and systems engineering, visual languages, layout of diagrams, modeling and analysis of biological systems, and the synthesis and communication of smell. He is the inventor of the language of Statecharts and co-inventor of Live Sequence Charts (LSCs), and was part of the team that designed the tools Statemate, Rhapsody, the Play-Engine and PlayGo. He devotes part of his time to expository work: He has delivered a lecture series on Israeli radio and has hosted a series of programs on Israeli television. Some of his writing is intended for a general audience (see, for example, Computers Ltd.: What They Really Can't Do (2000, 2012), and Algorithmics: The Spirit of Computing (1987, 1992, 2003, 2012), which was the Spring 1988 Main Selection of the Macmillan Library of Science. He has received a number of awards, including the ACM Karlstrom Outstanding Educator Award (1992), the Israel Prize (2004), the ACM Software System Award (2007), the Emet Prize (2010), and five honorary degrees. He is a Fellow of the ACM (1994), the IEEE (1995) and the AAAS (2007), and a member of the Academia Europaea (2006) and the Israel Academy of Sciences (2010), and a foreign member of the US National Ac ademy of Engineering (2014), and the American Academy of Arts and Sciences (2014).


Title: “Design and Implementation of Adaptive Stream Mining Systems using Lightweight Dataflow Graphs”

Host: Prof. Johan Lilius, Åbo Akademi University


Abstract: With the increasing need for accurate mining and classification from multimedia data content, and the growth of such multimedia applications in mobile and distributed architectures, stream mining systems require increasing amounts of flexibility, extensibility, and adaptivity for effective deployment. In this talk, I will present a novel approach to address this challenge. This approach rigorously integrates foundations of dataflow modeling for high-–level signal processing system design, and adaptive stream mining based on dynamic topologies of classifiers. In particular, I will introduce a new design environment, called the lightweight dataflow for dynamic data driven adaptive systems (LiD4E) environment. LiD4E provides formal semantics, rooted in dataflow principles, for design and implementation of a broad class of multimedia stream mining topologies. I will demonstrate the utility of these new design methods on an energy–constrained, multi–mode stream mining system for face detection.

This work is joint with Kishan Sudusinghe, Inkeun Cho, and Mihaela van der Schaar.


Bio: Shuvra S. Bhattacharyya is a Professor in the Department of Electrical and Computer Engineering at the University of Maryland, College Park. He holds a joint appointment in the University of Maryland Institute for Advanced Computer Studies (UMIACS). He is also a part time visiting professor in the Department of Pervasive Computing at the Tampere University of Technology, Finland, as part of the Finland Distinguished Professor Programme (FiDiPro). He is an author of six books, and over 240 papers in the areas of signal processing, embedded systems, electronic design automation, wireless communication, and wireless sensor networks. He received the B.S. degree from the University of Wisconsin at Madison, and the Ph.D. degree from the University of California at Berkeley. He has previously held industrial positions as a Researcher at the Hitachi America Semiconductor Research Laboratory (San Jose, California), and Compiler Developer at Kuck & Associates (Champaign, Illinois). He has held a visiting research position at the US Air Force Research Laboratory (Rome, New York). He is a Fellow of the IEEE.

Title: "Looking for Computers in the Biological Cell. After Twenty Years"

Host: Ion Petre, Åbo Akademi and Turku Centre for Computer Science

Abstract: A glimpse on natural computing is carried out, with an autobiographical eye, hence with some details about DNA computing and membrane computing. Besides (types of) problems and results (applications included), some research directions are mentioned which need further efforts. Then the question is raised whether or not "we dream too much" in this area, of bio-inspired computing. Some "impossibility theorems" as those of R. Gandhy and M. Conrad are mentioned.

CV: Gheorghe Paun is a researcher in the Institute of Mathematics of the Romanian Academy, Bucharest. Interested in formal language theory, automata theory, mathematical linguistics, DNA computing, and membrane computing. Long research stages in Germany, Finland, The Netherlands, Canada, Spain, Japan, many visits in universities from other countries (over 100 collaborators from all these countries). Several of his books, written alone or in collaboration, became standard references, e.g., in regulated rewriting, Marcus contextual grammars, grammar systems, DNA computing, membrane computing. This last research area was initiated by him, in 1998, see TUCS Technical Report No. 208, November 1998, www.tucs.fi) and it was soon considered by ISI as a "fast emerging research area of computer science". A comprehensive coverage of the domain is "The Oxford Handbook of Membrane Computing", 2010, edited by Gh. Paun, G. Rozenberg, A. Salomaa.

Gh. Paun is a member of the Romanian Academy and of Academia Europaea.

New courses

TUCS short course: Introduction to the security of WEB applications

Lecturer: Dr. Serghei Verlan, University Paris 12, France, http://lacl.univ-paris12.fr/verlan/index.html

May 19 at 9-12 (Gamma) and May 21 at 9-12 (Algol)

Abstract: The course gives an introduction to the security risks for WEB applications. The presentation will be based on the Top Ten Open Web Application Security Project (OWASP) list. A particular attention will be given to SQL injection and Cross-Site Scripting (XSS) vulnerabilities. The lab will introduce "ZAP Proxy" - an open tool for penetration testing and will familiarize students with common vulnerabilities using WebGoat and DVWA projects.

In order to follow the lab it is required to have a laptop with latest version of Java installed. It is also necessary to preliminary download the following tools:



WebGoat 6.0.1:


OWASP BWA virtual machine:


VMware Player or VirtualBox.

New course: Logic for High School Mathematics

Special course in Computer Science

Special course in Mathematics

Lectures: Wednesdays 14 - 16.

Excercises: Wednesdays 13 - 14.

Course duration: April 1 - May 27

Place: ICT House, room B3040  (Cobol)

Lecturer: Ralph-Johan Back

The course starts on April 1, at 14, in Cobol . More information about the course is given on the course web page: http://users.abo.fi/backrj/HighSchoolLogic/


The course is intended for M.Sc and Ph.D. students in Mathematics, Computer Science and Computer Engineering. Lectures are in English,  but assignments can be done in Finnish, Swedish or English.

Course description: Mathematics is based on logic. But logic is not really used in practice in high school mathematics.  A course on logic may be offered in the curriculum, but it is usually taught as a separate course, focusing on the foundations of mathematics, rather than seeing logic as a  tool  that can be used in all mathematics throughout high school. Our aim in this course is to show how logic can be used as a highly practical tool for solving mathematical problems in high school and first year university courses. We base our approach on structured derivations,  a new format for presenting mathematical calculations, proofs and general derivations. We show how  the use of logic in combination with structured derivations allows us to present clear and easily understandable solutions to rather complicated mathematical problems. We will present the basics of  propositional calculus and predicate calculus in this course, and show how these reasoning tools can be used in typical high school problem solving.  Our aim is also to present a simple general reasoning framework that we hope will clear up much of the conceptual mess that many students experience when trying to understand the underlying logic behind informal mathematical argumentations.  The last part of the course treats some more advanced topics, like induction proofs and the epsilon-delta method.

New INFORTE course

SW Technologies and Development for Multi-Device

June 16th – 17th



Professor Cesare Pautasso (University of Lugano, Switzerland)

Professor Juan Manuel Murillo Rodríguez (Universidad de Extremadura, Spain)

Professor Sasu Tarkoma (University of Helsinki, Finland)


Professor Kari Systä (Tampere University of Technology, Finland)

Registration closing date: June 7th

Registration and more information: http://inforte.jyu.fi/events/multi-device_environments


Please, see all detailed programs in INFORTE.fi


Cyber Defence

September 21st – 22nd




Adjunct professor Martti Lehto (University of Jyväskylä, Finland)

Professor  Rauno Kuusisto (Finnish Defence Research Agency, Finland)

Associate Professor Rain Ottis (Tallinn University of Technology, Estonia)

Dr. Saara Jantunen (Finnish Defence Research Agency, Finland)


Adjunct professor Martti Lehto (University of Jyväskylä, Finland)


Registration is open: June 1st – September 11th

Registration and more information: http://inforte.jyu.fi/events/cyber-defence


Please, see all detailed programs in INFORTE.fi


Organising of INFORTE.fi courses

Inforte.fi program started operating originally in 2001.During this wholeperiod, the Inforte.fi program has however maintained its standing as a stat- wide program for ICT professionals. It is designed to offer networking and education events to PhD students and professionals working in Finnish companies, polytechnics and public administration. Invited speakers are some of the top international researchers or industry representatives in their field. Inforte.fi’s member university departments will annually organize about 12 workshops and seminars on diverse areas of ICT. The main areas of focus are:

These intensive events can be used as tools for professional education, or as parts of doctoral education. Inforte.fi program delivers certificates of participation, and participants negotiate how these achievements can be included in their studies with their home universities. Inforte.fi events are a way to connect you with other ICT professionals and academics in your field, and build important social networks. Inforte.fi events allow you to update your knowledge and keep on track with the latest scientific and practical knowledge in the ICT field.


Anyone within the member departments can suggest an event. We hope that the event is in line with our main areas of focus. If you have something in mind, contact the Inforte.fi staff and let’s start planning the event!

Inforte.fi’s member university departments are:


The organizer’s payment for organizing an one-day event is 250 € and for a two-day event 500 €. The organizer has to send the Inforte.fi staff his or hers separate tax card or otherwise the Finnish tax authorities will take off 60 % taxes from the payment. Inforte.fi staff will send the organizer a travelling expenses claim form and a bank and personal information form. The travelling expenses claim form needs to be filled only if needed, but the bank and personal information form needs to be filled always. The Inforte.fi office will organize morning coffee with something small to bite to the events, but lunch and afternoon coffee can be bought at participant’s own expense. The organizer can however buy his/her and the speaker’s lunch and afternoon coffee and reimburse those expenses from the Inforte.fi office with the travelling expense claim. Also one feasible dinner with the speaker is allowed to reimburse with the travelling expense claim. However when using the travelling expenses claim, the organizer needs to send all of the original documents and receipts to Inforte.fi office (the address is at the bottom of this document).

The speaker’s payment Inforte.fi pays 120 € / lecturing hour and 60 € / group work hour at most. Lecturing fee is considered salary by Finnish tax office. Because the work is done in Finland, the Finnish tax authorities will automatically take off approximately 35 % taxes. In addition, it is mandatory to take off around 4 % other social security and pension contribution payments from the fee. This will happen automatically - no fee can be paid without these deductions.In addition to travel expenses and accommodation Inforte.fi will pay the speaker daily allowance. Daily allowance is 39 euros or 18 euros per travelling day. Inforte.fi will calculate the daily allowances. Inforte.fi does not cover meal expenses according to receipts. The fee and travel expenses will be paid separately and it may take approximately a month until the payment is on the speaker’s bank account.

The speaker’s travelling and accommodation

Inforte.fi pays for the speakers travelling and accommodation expenses and helps with the arrangements regarding these. If the Inforte.fi event will be merged with other activities in Finland (e.g. seminars) or during the trip, Inforte.fi will pay only a part of the expenses. If the speaker decides to book the trip independently, he/she needs to be in contact with the Inforte.fi staff because only travelling in Economy class will be accepted as expenses. Inforte.fi will book the hotel for the speaker.

Date and other important information about the event

The date of the event has to be agreed on in good time and the Inforte.fi staff has to be informed about it immediately after that. In addition to this the Inforte.fi staff will need the following information as soon as possible:

Remote access

The organizer has to agree with the speaker if participants can be included in the event with remote access. If both sides agree that it can be handled, the organizer has to find out that with what kind of system the speaker is used to and whether the remote access is possible to organize at the event location.

Inforte.fi staff’s contact information:

Annemari Soranto

Project Researcher

Email: office@inforte.fi

Phone: +358 400 247700

Nina Jakonen

Programme planner


Phone: +358 400 247700

Courses on transferable skills at University of Turku



Computer Science Days, June 4-5

The Annual Finnish Computer Science Days 2015 (in Jyväskylä June 4-5, 2015): Call for Papers


Topic: "ICT for teaching and the research of current issues."

The Organizing Committee invites ICT researchers to submit abstracts (max 3 pages) and to make a presentation, as well as to network with other researchers in the field. Both beginners and more advanced researchers are welcome. Topics include programming, teaching, teaching tools, learning environments (including online and blended learning), K-12 education in information technology, project teaching as well as research methods. The presentations are encouraged to include research proposals for cooperation in networking context.

Abstracts should be delivered to the committee by e-mail tktpaivat-edu.group@korppi.jyu.fi.  Abstracts written in Finnish or English in PDF format should be sent no later than 04/15/2015. The selections will be made by 04/25/2015.

Further info: https://www.jyu.fi/it/konferenssit/tkt_paivat_2015/call_for_papers.

TUCS will have a small number of travel grants to support participation to the conference, especially for PhD students; the deadline for applying for such a grant is May 15.”

Finnish Bank of Science Terminology

Bank of Finnish computer science terminology


Information about the term bank can be found at:



The whole community’s help to build the terminology for “computer science (in a broad sense)” is of great importance, so read and contribute!

Call for nominations: the best PhD thesis in CS in Finland and the Cor Baayen award

The call for nominations for the award for the best PhD thesis in Computer Science in Finland in 2014 and for Finland’s nomination for the European competition on the Cor Baayen award. The Cor Baayen Award is awarded each year by the European Research Consortium for Informatics and Mathematics (ERCIM) to a promising young researcher in computer science and applied mathematics.

Read more here: http://www.ercim.eu/activity/cor-baayen-award

The nominations should be sent to the Finnish Society for Computer Science (markku.tukiainen@uef.fi and jaakko.hakulinen@sis.uta.fi). The deadline for both calls is April 1. The committee for both competitions consists of Mikko Koivisto (University of Helsinki), Tapio Pahikkala (chair, TUCS, TY) and Ion Petre (TUCS, ÅA).

Nobel seminar on Friday, May 8th, Medisiina

Nobel seminar and student meeting with Nobel Prize Laureate Stefan W. Hell on Friday, May 8th


9.30 - 11.30: Break the limits with Stefan Hell


Opportunity for graduate and undergraduate students to break the limits with an outstanding scientist through an out of the box chit-chat!


Register to the event via: http://www.bioimaging.fi/stefan-hell (there will be place for 20-30 students). Registration by 1st of May. Some of the participants will be invited to a lunch with Nobel Prize Laureate.


13.00: Nobel Seminar ”Optical Nanoscopy with Focused Light” - Stefan Hell. Chair prof. Pekka Hänninen. Osmo Järvi lecture hall, Medisiina

EIT ICT Labs: New course on business modelling

“BUSINESS MODELLING" innovation and entrepreneurship (I&E) course for PhD students


EIT ICT Labs organizes an unique opportunity for doctoral students to learn how to develop a modern business plan for a new start-up or a new business inside an industrial corporation.

The Business Modelling module organized Helsinki Doctoral Training Centre is aimed at all the doctoral students of the Doctoral School of EIT ICT Labs. Also all the doctoral students of Aalto University can participate.

The module gives hands-on training on the main elements of any business model and resulting plan:

* Market analysis

* Offering definition

* Go-to-market plan

* Financing and other resourcing

* Selling and other execution

* Monetizing intellectual property

* Teamwork

* Pitching to investors and other decision makers

The module consists of three parts

1. a seven week course with lectures once a week April 16-May 28; and three assignments. It is possible to participate this module mainly remotely;

2. one week intensive course in the first week of September 2015 in Helsinki node of EIT ICT Labs with one assignment;

3. one and half day closing session in late September (the exact timing and and place to be agreed together with the participants of the module).

By completing the whole module and all the assignments, the student can get a maximum of 11 ECTS.

The first part of the course is organized together with Aalto Venture Program as their following course


The lectures are once a week Thursday afternoons (13-16) in Computer Science and Engineering building (Konemiehentie 2, Espoo). The lectures will take place April 16th, to May 28th.

REGISTRATION via the link at the course website:

As a doctoral student, you should not use the WebOodi registration referred on the noppa.aalto.fi, but the registration link on the course website.

More information: Jussi.i.autere@aalto.fi

EATCS Bulletin Issue 115 available online

The 114th issue of the EATCS Bulletin, is

now available online at


You can download a pdf with the printed version of the bulletin from


As an EATCS member, you have access to

the members area which contains news and related articles. Young researchers

can find announcements of open positions, news and related articles.

To find out the latest information on EATCS news, activities, conferences,

and much more, find us via social media:

facebook page: https://www.facebook.com/eatcs

google+ : https://plus.google.com/112559236052381533540/posts

youtube channel: http://www.youtube.com/channel/UChc3QOHDEbDdPRErx1uSl6A

twitter: http://twitter.com/eatcs_secretary

Linkedin EATCS group: http://www.linkedin.com/groups?gid=3412855 

EATCS - Young researchers Linkedin group:


Future & Emerging Technologies (FET) Newsletter — Issue Apr 2015


TUCS GP travel reports

TUCS GP Student Jose Teixeira's Travel Report from EASE

Full name of the event:18th International Conference on Evaluation and Assessment in Software Engineering

Place and date: London, UK, May 13th – 14th, 2014

Type of event: conference

My article:

Title: Understanding Collaboration in the Open-Source Arena

Authors: Jose Teixeira

The scientific profile of the event:The International Conference on Evaluation and Assessment in Software Engineering (EASE) has been a forum for knowledge sharing about issues related to empirical software engineering and their application in software development practice. In a workshop-like atmosphere, researchers present and discuss the latest results of empirical and evaluation studies covering a wide range of topics in software engineering.

Opinion on the best paper and its topic: Katia Felizardo, Elisa Nakagawa, Stephen MacDonell and José Carlos Maldonado. A Visual Analysis Approach to Update Systematic Reviews

Number of participants: 50

Social events: One evening dinner

Touristic impressions: Brunel is a suburb of London, very close to London heathrow airport. Expensive hotel airports around and no time to check the city.

Open jobs at University of Turku and Åbo Akademi University

Latest publications at TUCS

Edited books (1):

Edited special issues of journals (1):

Articles in journals (3):

Articles in proceedings (18):

Ph.D. thesis (1):

Technical reports (2):