ICS Recreation Day 19 September 2011
September 22nd, 2011
ICS Summer Excursion 2009
August 31st, 2009Below are some photos from this year’s summer excursion to Soukka Boating Club that took place on the 16th of June.
[Photos: Mikko Korpela and Kimmo Järvinen]
ISMB/ECCB in Stockholm 27.6.-2.4.2009
August 13th, 2009The 17th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) and 8th European Conference on Computational Biology was held in Stockholm, Sweden at the end of June. Due to the short (and supposedly cheap) travelling to Stockholm there were as many as seven participants from the Statistical Machine Learning and Bioinformatics group (Leo, José, Ali, Ilkka, Hasan, Jarkko and Juuso, that is, me), accompanied with a semi- group member Antti H. and former member Merja.
The week was extremely hot with temperature close to 30 degrees, but luckily the conference venue in the Stockholmsmässan (Stockholm International Fairs) had proper air conditioning (the same didn’t apply to our hotel rooms, though..). The overall number of people was, well, a lot. I don’t know the exact number, but I heard someone saying 1400, which is probably close to correct.
The conference started already on Saturday, 27th, with a Student Council and continued with tutorials on Sunday. Some of us were present from the beginning, I myseld arrived only on Monday morning, when the main program started. It consisted of two Proceedings tracks, two Highlights tracks, two Technology tracks and then some special session. These were all held in parallel, causing some really tough choices to be made. The fact that the distance between the furthest presentation rooms was several hundreds of meters didn’t help much… Good exercise, anyway. Interestingly, the program involved more Highlight presentations (interesting work published in good journals during the last year) than actual Proceedings stuff, and I found myself listening to the Highlights more often than Proceedings presentations.
José presenting an outstanding visualization of the model.
The highlight for our group was José Caldas’ presentation with the topic “Probabilistic retrieval and visualization of biologically relevant experiments”. In addition to the good presentation the work raised interest in the poster session, held partly by the co-authors Ali Faisal and Nils Gehlenborg. The poster got the Best Poster award at the 5th ISCB Student Council Symposium. Gongrats! Most of the other people from our group presented a poster. There were about a thousand posters in total, and finding and going through all the relevant and interesting ones was really a burden.
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Ali presenting the award-winning poster.
Unfortunately, I had to travel to Leuven, Belgium, to participate in the Mining and Learning with Graphs (MLG) workshop before the conference closing dinner. Anyway, the program says that ” the dinner will be held at the Vasa Museum, Scandinacia’s most visited museum. The Vasa is the world’s only surviving 17th-century ship and one of the foremost tourist sights in the world.” Well, the swedes sure know how to advertise things, remembering that the Vasa ship did sink in its maiden trip right after exiting the harbour – a detail that they apparently didn’t find worth mentioning =)
Leo having fun during the poster session.
Text and photos by Juuso Parkkinen
Tommi Syrjänen’s defence, Mar 20, 2009
May 11th, 2009
Tommi giving his lectio
Lic.Tech.(Sc.) Tommi Syrjänen defended his dissertation “Logic Programs and Cardinality Constraints: Theory and Practice” on Friday, the 20th of March, 2009. In his thesis Tommi has developed a rule based language for answer set programming (ASP) which extends logic program type rules with cardinality constraints. ASP is a novel approach to constraint programming in which solutions to a problem are described declaratively using a rule-based language. Tommi has developed a key component of an ASP system, a grounder, that transforms programs with variables to ground programs which is then taken has input by another key component, ASP solver, capable of finding models (answer sets) for the ground program. The thesis provides the theory behind grounding and a grounder software tool called lparse which is very widely used in dozens of research groups all over the world and combined with a number of ASP solvers.
The official opponent was Prof. Vladimir Lifschitz from University of Texas at Austin, one of father of stable model semantics providing the formal foundations for ASP and the custos was Prof. Ilkka Niemelä.
Congratulations, Tommi!
Tommi with Mr. and Mrs. Lifschitz in Villa Elfvik
“… and the steering group starts at half past two”
April 23rd, 2009Head of ICS department, Pekka Orponen, turned fifty.
Our suprise was sniffed and Pekka carried a bunch of cakes for all congratulators. Ilkka Niemelä raised the glass and thanked Pekka for all work done for the department. Steering the department is like conducting the orchestra in the opera. Pekka thanked the audience in turned and reminded that the steering group starts – a quarter later than usual.
[ Text and photos by Jukka Parviainen ]
“Vastakkainasettelun aika on ohi”
February 3rd, 2009Our ICS department has a bulletin board at 3rd floor in the main lobby. For ten years it was used as a place for course advertisements and final results. Now, Noppa edu portal has replaced it. However, the board is in a good location as students walk by to the upstairs entrance of T1 hall. Last autumn we set up our “proffagalleria” with photos, in the left board Pekka, Kaisa, Keijo and Ilkka (major “tietojenkäsittelyteoria”) and right Erkki, Olli, Heikki, Juha and Sami (major “informaatiotekniikka”).
Some weeks ago it had appeared a yellow Post-It at the border of the boards, between the professors: “Vastakkainasettelun aika ei ole ohi! ?”
While we are now one and only one department – as stated top of the bulletin board – the gallery was today re-organised. No borders any more! May I quote Harri Haanpää:
“Nyt uskoisin, että mielessämme alkaa olla selkiytynyt, että ilmoitustaulu on nimenomaan laitoksen ilmoitustaulu eikä esimerkiksi pääaineiden ilmoitustaulu, vaikka tietysti pääaineet ovat ikään kuin se tuote, mitä opiskelijoille tarjotaan, ja tuollaisen mainostaulun pääasiallinen kohderyhmä varmaankin on juuri opiskelijat.
Vaikka vastakkainasettelun aika olisikin ohi, olisi ehkä syytä silti miettiä, miten tiivis yhteisö laitoksen tulisi olla. Onko laitos sateenvarjo-organisaatio, jonka alla tutkimusryhmät työskentelevät tiiviisti kukin erillään, vai tiivis tutkimusyhteisö, jossa ryhmät toki toimivat kukin keskenään, mutta myös kommunikoivat aktiivisesti toisilleen?”
[ Text and photos by Jukka Parviainen ]
Matti Järvisalo’s doctoral defence
December 23rd, 2008Lic.Sc.(Tech.) Matti Järvisalo defended his dissertation “Structure-Based Satisfiability Checking: Analyzing and Harnessing the Potential” on November 29, 2008. The official opponent was Prof. Bart Selman, Cornell University, USA and the custos Prof. Ilkka Niemelä.
The thesis studies search-based techniques for solving large structured propositional satisfiability (SAT) problems originating from real-world application areas. It analyzes mathematically and experimentally the fundamental properties of a key component of such techniques, the branching heuristics; develops a novel type of local search which is very competitive against previous local search techniques for structured SAT problems and devices methods for generating computationally exceptionally hard satisfiable SAT problem instances.
In his lectio precursoria Matti illustrated, for example, the size of the search space of typical real-world problems which exceeds easily the number of particles in the known universe.
The official opponent, Prof. Bart Selman, scrutinized Matti’s claims thoroughly.
Here Matti is explaining how the novel local search method works on Boolean circuits.
After hard work it’s time for some coffee and cake. From left to right: Dr. Tommi Junttila (instructor), Prof. Bart Selman (opponent), Matti Järvisalo, Prof. Ilkka Niemelä (custos).
Congratulations, Matti, on the excellent thesis and the successful defence!
[Photos by Tommi Junttila and Emilia Oikarinen, Posted by Ilkka Niemelä]
Barton Fan Club at Utrecht
November 28th, 2008ACM has arranged the International Collegiate Programming Contest for student teams annually since 1970. The competition has grown rapidly, and in 2007 more than 6700 teams from 1821 universities participated.
In the competition, three-student teams have five hours to solve approximately ten programming assignments. Each team only has one computer, and the solutions must be coded in C, C++ or Java. The only reference material allowed is a 25-page Team Contest Reference prepared by the team itself.
As the competition is so large, there are qualification rounds. To go to the world finals, a TKK team would first have to beat other TKK teams at the Nordic Collegiate Programming Contest and then place among the top two or three at the Northwestern European Regional Contest. The world finals are four-day events organized at the finest venues; last April they were at the Fairmont Banff Springs hotel.
The competition is relatively unknown in Finland, but quite popular in our neighboring countries. There were 64 Swedish student teams participating in this years Nordic Contest on October 4, and 41 teams from Norway. By far the strongest country in ICPC is Russia, with hundreds of teams, many of which extremely good. The competition seems to be catching on in Finland too, though: last year only one Finnish team – Barton Fan Club from TKK – participated in the Nordic Contest, but this October there were already six teams from TKK and two from the University of Helsinki. In the Nordic contest, Barton Fan Club – who had obtained a very respectable shared 23rd place in last season’s world finals – again did very well and reached 2nd place among the 120 student teams. Another team worth watching will be Team-uh from the University of Helsinki: this freshman team placed 6th. After doing so well at the Nordic Collegiate Programming Contest, Barton Fan Club and Team-uh advanced to the Northwestern European Regional Contest, which took place in Utrecht, Netherlands, on Sunday 23rd November. Barton Fan Club – Markus Ojala, Veli Peltola and Ville Pettersson – and their coach Harri Haanpää arrived on Saturday morning. Saturday’s programme included some guest talks, technical testing of the competition system, and a short guided tour of the historical centre of the beautiful city of Utrecht. Unfortunately the weather was not favourable, as it was windy and snowing, which is rather unusual for Utrecht in November.
Barton Fan Club in action (photo by Fredrik Niemelä)
The competition started on Sunday at 10 o’clock. During the competition the coaches decided that next year’s competition would take place in Nuremburg, Germany, and the Nordic coaches decided that next year’s NCPC would take place on October 3rd. In the competition the Oxford team Marta, Irene and Sirup, who had won NWERC in 2007 and reached a shared 23rd place in the World Finals, outclassed the others by solving a total of 9 problems in the allotted time. The following eight teams solved six problems and had to be ordered by using a tie-break formula that depends on the time when the solutions are submitted and the number of incorrect submissions. These teams were from Cambridge, Leiden, Aarhus, Delft, Eindhoven, Jacobs University and Chalmers.
Unfortunately Sunday was not the best day for Barton Fan Club. In the end they solved five problems and placed tenth. Margins are often small in these competitions, and so this time too: our team had completely misread one of the easiest problems, problem I, and were unable to debug their code for problem B before time ran out. The code turned out to contain a bug in determining the strongly connected components in a directed graph. With these two additional problems solved they would have placed second and would most likely have advanced to the World Finals, which will take place in April in Stockholm.
Next year two members of the team will no longer be eligible to compete as students, so there will be room for up-and-coming talent at TKK to show their skills. The Nordic Collegiate Programming Contest will be arranged on October 3rd in several Nordic universities at the same time. See you there!
FIMM seminar @Biomedicum
November 25th, 2008Institute for Molecular Medicine Finland (FIMM) was established in 2006 “to advance new fundamental understanding of the molecular, cellular and etiological basis of human diseases”. It is therefore a highly interesting collaboration partner for our bioinformatics research branch. To promote research collaboration FIMM organized a seminar on Thursday 20.11.08 in Biomedicum (where the institute is located), giving an overview of the FIMM concept and research infrastructure plans. In addition a few talks were given by new staff.
The seminar was opened with an introduction by Director, Prof. Olli Kallioniemi. He covered all the basics of the FIMM concept, including important stakeholders and scientific goals. Current focus is on three themes; human genomics, medical systems biology and translational research. According to Prof. Kallioniemi the aim is to merge strategic resources and research in the field. Vice Rector Matti Tikkanen from University of Helsinki said a few words as well, pointing out that FIMM is a strategic target of the University.
Director Professor Olli Kallioniemi presenting other directors in FIMM
The actual content of the seminar were three talks by newly recruited foreign staff: FiDiPro Professor Joseph D. Terwilliger (Columbia University, USA and University of Helsinki) and FIMM International Group Leaders Dr Emmy Verschuren and Dr Sergey Kuznetsov.
Prof. Terwilliger gave an exciting talk about gene mapping, which he has been studying before. His current (very strong) view was that gene mapping has generally failed miserably. Numerous studies have shown how genome wide association and common disease – common variance -thinking have failed to produce any remarkable results and should therefore be forgotten.
After Terwilliger’s crushing talk Dr. Verschuren was a bit afraid of talking about her cancer related studies, but she managed to convince her audience of her cause. She concentrated on cell cycle and role of p53 and EMI 1 (named after her favorite record-company) in cancer development. The other group leader, Dr. Kuznetsov, is involved in translational research. He’s as well focusing in cancer research, mainly breast cancer and the famous breast cancer genes BRCA1 and BRCA2.
All in all the talks were interesting, although they didn’t touch my personal research interests directly. But anyone searching for biology-related research collaboration should definitely keep FIMM in mind.
Text: Juuso Parkkinen, Photo: Antti Honkela
Zhirong Yang’s doctoral defense
November 25th, 2008On Friday 14th of November 2008, Zhirong Yang defended his thesis titled Discriminative learning with application to interactive facial image retrieval. The defense was held in auditorium TU2 in front of an intrigued audience. The opponent Prof. Irwin King had arrived from the Chinese University of Hong Kong. Professor Erkki Oja acted as the Custodian in the defense.
Opponent Prof. Irwin King and Zhirong Yang
Zhirong had to take his hands into use in explaining the finest points of multiplicative updates of non-negative projections. The Opponent was satisfied with the answer.
Opponent Prof. Irwin King and Zhirong Yang
“There might be something wrong in the fundamental assumptions of the natural gradient principle,” said Zhirong. “Now this starts to get interesting,” thought the Opponent. The audience held their breath. After the discussion the Opponent promised to ask Amari San’s opinion when they’ll meet during the next week.
Interested audience moving for coffee and cake
After the defense, Zhirong received well-deserved congratulations from the audience. Even the Opponent could then relax and smile while chatting with Erkki.
Opponent Prof. Irwin King, Custodian Prof. Erkki Oja and Zhirong Yang
Coffee and cake were served downstairs in a small seminar room. Zhirong received a customized copy of the famous “Guess who?” game as a surprise present from his co-workers at the department.
Congratulations again Zhirong for your excellent thesis and its successful defense!
[Photos by Yanyi Wang, Text by Jorma Laaksonen and Markus Koskela]