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Parsimonious Modelling

The research group Parsimonious Modelling develops computational methods for data analysis and applies these methods on two particular application fields: cancer genomics and environmental informatics. Both of these application fields exhibit problems of high dimensional data and complex, unknown interactions between measurements.

Parsimonious modeling aims at achieving maximally simple or compact models as a result of the data analysis process. In practical problems, parsimony makes results more understandable and interpretable. For instance, feature variable selection aims at parsimony in terms of the number of variables in the model. The computational methods are based on regularization or penalization of the cost function in the original process of learning from data and may be also combined with heuristic search procedures.

Group members:

• Jaakko Hollmén, D.Sc.(Tech.) (group leader)
• Mika Sulkava, D.Sc.(Tech.)
• Mikko Korpela,, M.Sc.(Tech.)
• Janne Toivola, M.Sc.(Tech.)
• Prem Raj Adhikari, M.Sc.(Tech.)
• Olli-Pekka Rinta-Koski, M.Sc.(Tech.)

Former personnel and visitors:

• Salla Ruosaari, Ph.D.
• Jarkko Tikka, D.Sc.(Tech.)
• Miguel Angel Prada, Ph.D.
• Ana González Marcos, Ph.D.
• Serafin Alonso Castro
• Antonio Morán
• Andrés Sanz Garcia
• Luis Gabriel De Alba Rivera, M.Sc.(Tech.)
• Klaus Venesmaa, M.Sc.(Tech.)
• Igor Antovski
• Bratislav Antanasijevic
• Paul Grouchy

Selected publications:

1. Anu Usvasalo, Riikka Raty, Arja Harila-Saari, Pirjo Koistinen, Eeva-Riitta Savolainen, Sakari Knuutila, Erkki Elonen, Ulla M. Saarinen-Pihkala, Jaakko Hollmén. Prognostic classification of patients with acute lymphoblastic leukemia by using gene copy number profiles identified from array-based comparative genomic hybridization data. Leukemia Research, 34(11):1476–1482, November, 2010.
2. Prem Raj Adhikari and Jaakko Hollmén. Patterns from Multi-Resolution 0-1 Data. In Bart Goethals, Nikolaj Tatti, and Jilles Vreeken, editors, In Proceedings of the ACM SIGKDD Workshop on Useful Patterns (UP'10), pages 8—12. July 25, 2010. Washington, DC, USA.
3. Mikko Korpela, Harri Mäkinen, Pekka Nöjd, Jaakko Hollmén, and Mika Sulkava. Automatic detection of onset and cessation of tree stem radius increase using dendrometer data. Neurocomputing, 73(10–12):2039–2046, June, 2010.
4. Janne Toivola, Miguel A. Prada and Jaakko Hollmén. Novelty detection in projected spaces for structural health monitoring. In Paul R. Cohen, Niall M. Adams, and Michael R. Berthold, editors, Advances in Intelligent Data Analysis IX, volume 6065 of LNCS, pages 208–219. Springer-Verlag. May 2010. Tucson, Arizona, USA.
5. S. Luyssaert, P. Ciais, S. L. Piao, E.-D. Schulze, M. Jung, S. Zaehle, M. J. Schelhaas, M. Reichstein, G. Churkina, D. Papale, G. Abril, C. Beer, J. Grace, D. Loustau, G. Matteucci, F. Magnani, G. J. Nabuurs, H. Verbeeck, M. Sulkava, G. R. van der Werf, and I. A. Janssens. The european carbon balance. part 3: forests. Global Change Biology, 16(5):1429–1450, May 2010.
6. Laxman Yetukuri, Jarkko Tikka, Jaakko Hollmén, and Matej Orešič. Functional prediction of unidentified lipids using supervised classifiers. Metabolomics, 6(1):18–26, March, 2010.
7. Michaela Wrage, Salla Ruosaari, Paul P. Eijk, Jussuf T. Kaifi, Jaakko Hollmén, Emre F. Yekebas, Jacob R. Izbicki, Ruud H. Brakenhoff, Thomas Streichert, Sabine Riethdorf, Bauke Ylstra, Klaus Pantel, and Harriet Wikman. Genomic profiles associated with early micrometastatis in lung cancer: Relevance of 4q deletion. Clinical Cancer Research, 15(5):1566–1574, 2009.
8. Janne Toivola and Jaakko Hollmén. Feature extraction and selection from vibration measurements for structural health monitoring. In Niall M. Adams, Céline Robardet, Arno Siebes, Jean-François Boulicaut, editors, In Proceedings of the 8th International Symposium on Intelligent Data Analysis (IDA 2009), volume 5772 of Lecture Notes in Computer Science, pages 213–224. Springer-Verlag, 2009.
9. Jarkko Tikka. Input variable selection methods for construction of interpretable regression models. Doctoral dissertation, Helsinki University of Technology, December, 2008.
10. Salla Ruosaari. Microarrays in Lung Cancer Research: From Comparative Analyses to Verified Findings. Doctoral dissertation, University of Helsinki, June, 2008.
11. Samuel Myllykangas, Jarkko Tikka, Tom Böhling, Sakari Knuutila and Jaakko Hollmén. Classification of human cancers based on DNA copy number amplification modeling. BMC Medical Genomics,1(15), May 2008.
12. Mika Sulkava. Learning from environmental data: methods for analysis of forest nutrition time series. Doctoral dissertation, Helsinki University of Technology, January 2008.
13. Jarkko Tikka, Jaakko Hollmén. Sequential Input Selection Algorithm for Long-term Prediction of Time Series. Neurocomputing, 71(13–15): 2604–2615, August 2008.
14. S. Luyssaert, I.A. Janssens, M. Sulkava, D. Papale, A.J. Dolman, M. Reichstein, J. Hollmén J.G. Martin, T. Suni, T. Vesala, D. Lousteau, B.E. Law, and E.J. Moors. Photosynthesis drives anomalies in net carbon-exchange of pine forests at different latitudes. Global Change Biology, 13(10):2110–2127, October 2007.
15. Timo Similä and Jarkko Tikka. Input selection and shrinkage in multiresponse linear regression. Computational Statistics & Data Analysis, 52(1):406–422, September, 2007.
16. Jaakko Hollmén and Jarkko Tikka. Compact and Understandable Descriptions of Mixtures of Bernoulli Distributions. In Proceedings of the 7th International Symposium on Intelligent Data Analysis (IDA 2007), volume 4723 of Lecture Notes in Computer Science, pages 1–12. Springer-Verlag, September 2007. Ljubljana, Slovenia.
17. H. Wikman, S.Ruosaari, P. Nymark, V.K. Sarhadi, J. Saharinen, E. Vanhala, A. Karjalainen, J. Hollmén S. Knuutila, S. Anttila, S. Knuutila. Gene expression and copy number profiling suggests the importance of allelic imbalance in 19p in asbestos-associated lung cancer. Oncogene, 26(32):4730–4737, July 2007.
18. Mika Sulkava, Sebastiaan Luyssaert, Pasi Rautio, Ivan A. Janssens, Jaakko Hollmén. Modeling the effects of varying data quality on trend detection in environmental monitoring. Ecological Informatics, 2(1):167–176, June 2007.
19. Penny Nymark, Pamela M. Lindholm, Mikko V. Korpela, Leo Lahti, Salla Ruosaari, Samuel Kaski, Jaakko Hollmén Sisko Anttila, Vuokko L. Kinnula and Sakari Knuutila. Gene Expression Profiles in Asbestos-exposed Epithelial and Mesothelial Lung Cell Lines. BMC Genomics, 8(62), March 2007.
20. S. Myllykangas, J. Himberg, T. Böhling, B. Nagy, J. Hollmén, and S. Knuutila. DNA copy number amplification profiling of human neoplasms. Oncogene, 25(55):7324–7332, November 2006.
21. Penny Nymark, Harriet Wikman, Salla Ruosaari, Jaakko Hollmén, Esa Vanhala, Antti Karjalainen, Sisko Anttila, and Sakari Knuutila. Identification of specific gene copy number changes in asbestos-related lung cancer. Cancer Research, 66(11):5737–5743, June 2006.
22. Mika Sulkava, Jarkko Tikka, and Jaakko Hollmén. Sparse regression for analyzing the development of foliar nutrient concentrations in coniferous trees. Ecological Modeling, 191(1):118–130, January 2006.