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Department: Any ÅAU / Department of Information Technologies UTU / Department of Information Technology UTU / Department of Mathematics and Statistics UTU / Turku School of Economics, Institute of Information Systems Sciences

Research Unit: Any Algorithmics and Computational Intelligence Group (ACI) Biomathematics Research Unit (BIOMATH) Communication Systems (ComSys) Computational Biomodeling Laboratory (Combio Lab) Data Mining and Knowledge Management Laboratory Distributed Systems Laboratory (DS Lab) Embedded Computer and Electronic Systems (ECES) Embedded Systems Laboratory (ESLAB) FUNDIM, Fundamentals of Computing and Discrete Mathematics Institute for Advanced Management Systems Research (IAMSR) Learning and Reasoning Lab Software Construction Laboratorium Software Development Laboratory (SwDev) Software Engineering Laboratory (SE Lab) Turku BioNLP Group Turku Optimization Group (TOpGroup) UTU Information Systems Science (ISS)

Publication type: Any Monographs Edited books Edited special issues of journals Edited proceedings Articles in journals Articles in proceedings Chapters in edited books Ph.D. thesis Lic. thesis Technical reports

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Articles in journals (13):

• Tapio Pahikkala, Hanna Suominen, Jorma Boberg, Efficient Cross-Validation for Kernelized Least-Squares Regression with Sparse Basis Expansions. Machine Learning 87(3), 381–407, 2012.
• Tapio Pahikkala, Sampo Pyysalo, Jorma Boberg, Jouni Järvinen, Tapio Salakoski, Matrix Representations, Linear Transformations, and Kernels for Disambiguation in Natural Language. Machine Learning 74(2), 133–158, 2009.
• Tapio Pahikkala, Evgeni Tsivtsivadze, Antti Airola, Jouni Järvinen, Jorma Boberg, An efficient algorithm for learning to rank from preference graphs . Machine Learning 75(1), 129–165, 2009.
• Evgeni Tsivtsivadze, Tapio Pahikkala, Jorma Boberg, Tapio Salakoski, Locality Kernels for Sequential Data and Their Applications to Parse Ranking. Applied Intelligence , 2008.
• Sampo Pyysalo, Filip Ginter, Juho Heimonen, Jari Björne, Jorma Boberg, Jouni Järvinen, Tapio Salakoski, BioInfer: A Corpus for Information Extraction in the Biomedical Domain. BMC Bioinformatics 8(50), 2007.
• Sampo Pyysalo, Filip Ginter, Tapio Pahikkala, Jorma Boberg, Jouni Järvinen, Tapio Salakoski, Evaluation of Two Dependency Parsers on Biomedical Corpus Targeted at Protein–Protein Interactions. International Journal of Medical Informatics, special issue on Recent Advances in Natural Language Processing for Biomedical Applications 75(6), 430-442, 2006.
• Tapio Pahikkala, Filip Ginter, Jorma Boberg, Jouni Järvinen, Tapio Salakoski, Contextual Weighting for Support Vector Machines in Literature Mining: An Application to Gene Versus Protein Name Disambiguation. BMC Bioinformatics 6(157), 2005.
• Filip Ginter, Jorma Boberg, Jouni Järvinen, Tapio Salakoski, New Techniques for Disambiguation in Natural Language and Their Application to Biological Text. Journal of Machine Learning Research 5, 605–621, 2004.
• Pentti Riikonen, Jorma Boberg, Tapio Salakoski, Mauno Vihinen, Mobile Access to Biological Databases on the Internet. IEEE TRANSACTIONS ON BIOMEDICAL ENGINEERING 49(12), 1477–1479, 2002.
• Jorma Boberg, Pentti Riikonen, Tapio Salakoski, Mauno Vihinen, BioWAP: Mobile Internet service for bioinformatics. Bioinformatics (9), 855–856, 2001.
• Jorma Boberg, Tapio Salakoski, Representative noise-free complete-link classification with application to protein structures. Pattern Recognition (3), 467–482, 1997.
• Jorma Boberg, Tapio Salakoski, M. Vihinen, Representative Selection of Proteins Based on Nuclear Families. Protein Engineering , 1995.
• Jorma Boberg, Tapio Salakoski, M. Vihinen, Accurate Prediction of Protein Secondary Structural Class with Fuzzy Structural Vectors. Protein Engineering , 1995.

Articles in proceedings (24):

• Antti Airola, Tapio Pahikkala, Jorma Boberg, Tapio Salakoski, Applying Permutation Tests for Assessing the Statistical Significance of Wrapper Based Feature Selection. In: Sorin Khoshgoftaar Taghi M. Palade Vasile Pedrycz Witold Wani M. Arif Zhu Xinquan (Hill) Draghici (Ed.), Proceedings of the Ninth International Conference on Machine Learning and Applications (ICMLA 2010), 989-994, IEEE Computer Society, 2010.
• Antolin Janssen, Evgeni Tsivtsivadze, Jorma Boberg, Tjeerd M.H. Dijkstra, Tom Heskes, Efficient Remote Homology Detection. In: Supplementary Proceedings of Pattern Recognition in Bioinformatics, 5th IAPR International Conference, PRIB 2010 Nijmegen, The Netherlands, September 22-24, 2010, 2010.
• Tapio Pahikkala, Hanna Suominen, Jorma Boberg, Tapio Salakoski, Efficient Hold-Out for Subset of Regressors. In: Mikko Kolehmainen, Pekka Toivanen, Bartlomiej Beliczynski (Eds.), Proceedings of the 9th International Conference on Adaptive and Natural Computing Algorithms (ICANNGA'09), 5495, 350-359, Springer, 2009.
• Tapio Pahikkala, Antti Airola, Jorma Boberg, Tapio Salakoski, Exact and Efficient Leave-Pair-Out Cross-Validation for Ranking RLS. In: Timo Honkela, Matti Pöllä, Mari-Sanna Paukkeri, Olli Simula (Eds.), Proceedings of the 2nd International and Interdisciplinary Conference on Adaptive Knowledge Representation and Reasoning (AKRR08), 1-8, Helsinki University of Technology, 2008.
• Tapio Pahikkala, Antti Airola, Hanna Suominen, Jorma Boberg, Tapio Salakoski, Efficient AUC Maximization with Regularized Least-Squares. In: Per Kreuger Anders Holst, Peter Funk (Eds.), Proceedings of the Tenth Scandinavian Conference on Artificial Intelligence, Frontiers in Artificial Intelligence and Applications 173, 12–19, IOS Press, 2008.
• Evgeni Tsivtsivadze, Fabian Gieseke, Tapio Pahikkala, Jorma Boberg, Tapio Salakoski, Learning Preferences with Co-Regularized Least-Squares. In: Proceedings of the ECML/PKDD Workshop on Preference Learning (PL-08), 2008.
• Evgeni Tsivtsivadze, Tapio Pahikkala, Antti Airola, Jorma Boberg, Tapio Salakoski, A Sparse Regularized Least-Squares Preference Learning Algorithm. In: Anders Holst, Per Kreuger, Peter Funk (Eds.), Proceedings of the Tenth Scandinavian Conference on Artificial Intelligence (SCAI 2008), Frontiers in Artificial Intelligence and Applications 173, 76–83, IOS Press, 2008.
• Tapio Pahikkala, Hanna Suominen, Jorma Boberg, Tapio Salakoski, Transductive Ranking via Pairwise Regularized Least-Squares. In: Paolo Frasconi, Kristian Kersting, Koji Tsuda (Eds.), Workshop on Mining and Learning with Graphs (MLG'07), 175-178, 2007.
• Tapio Pahikkala, Evgeni Tsivtsivadze, Antti Airola, Jorma Boberg, Tapio Salakoski, Learning to Rank with Pairwise Regularized Least-Squares. In: Thorsten Joachims, Hang Li, Tie-Yan Liu, ChengXiang Zhai (Eds.), SIGIR 2007 Workshop on Learning to Rank for Information Retrieval, 27-33, 2007.
• Evgeni Tsivtsivadze, Jorma Boberg, Tapio Salakoski, Locality Kernels for Protein Classification. In: Sridhar Hannenhalli Raffaele Giancarlo (Ed.), Algorithms in Bioinformatics, 7th International Workshop, Lecture Notes in Computer Science 4645, 2–11, Springer, 2007.
• Filip Ginter, Sampo Pyysalo, Jorma Boberg, Tapio Salakoski, Regular Approximation of Link Grammar. In: Advances in Natural Language Processing, 5th International Conference, FinTAL 2006 Turku, Finland, August 23-25, 2006 Proceedings, Lecture Notes in Computer Science 4139, 564–575, Springer Berlin / Heidelberg, 2006.
• Tapio Pahikkala, Jorma Boberg, Aleksandr Mylläri, Tapio Salakoski, Incorporating External Information in Bayesian Classifiers Via Linear Feature Transformations. In: Tapio Salakoski, Filip Ginter, Sampo Pyysalo, Tapio Pahikkala (Eds.), Advances in Natural Language Processing, 5th International Conference on NLP, FinTAL 2006 Turku, Finland, August 23-25, 2006 Proceedings , Lecture Notes in Computer Science 4139/2006, 399–410, Springer Berlin / Heidelberg, 2006.
• Tapio Pahikkala, Jorma Boberg, Tapio Salakoski, Fast n-Fold Cross-Validation for Regularized Least-Squares. In: Timo Honkela, Tapani Raiko, Jukka Kortela, Harri Valpola (Eds.), Proceedings of the Ninth Scandinavian Conference on Artificial Intelligence (SCAI 2006), 83-90, Otamedia Oy, 2006.
• Tapio Pahikkala, Evgeni Tsivtsivadze, Jorma Boberg, Tapio Salakoski, Graph Kernels versus Graph Representations: a Case Study in Parse Ranking. In: Thomas Gärtner, Gemma C. Garriga, Thorsten Meinl (Eds.), Proceedings of the ECML/PKDD'06 workshop on Mining and Learning with Graphs (MLG'06), 181-188, 2006.
• Evgeni Tsivtsivadze, Tapio Pahikkala, Jorma Boberg, Tapio Salakoski, Locality-Convolution Kernel and Its Application to Dependency Parse Ranking. In: Advances in Applied Artificial Intelligence, 19th International Conference on Industrial, Engineering and Other Applications of Applied Intelligent Systems, IEA/AIE 2006, Annecy, France, June 27-30, 2006. Proceedings, Lecture Notes in Computer Science 4031, 610–618, Springer, 2006.
• Filip Ginter, Tapio Pahikkala, Sampo Pyysalo, Evgeni Tsivtsivadze, Jorma Boberg, Jouni Järvinen, Aleksandr Mylläri, Tapio Salakoski, Information Extraction from Biomedical Text: The BioText Project. In: Margit Langemets, Priit Penjam (Eds.), Proceedings of the Second Baltic Conference on Human Language Technologies (HLT 2005), 131-136, Institute of Cybernetics, Tallinn University of Technology and Institute of the Estonian Language, 2005.
• Tapio Pahikkala, Sampo Pyysalo, Jorma Boberg, Aleksandr Mylläri, Tapio Salakoski, Improving the Performance of Bayesian and Support Vector Classifiers in Word Sense Disambiguation using Positional Information. In: Ville Könönen Matti Pöllä Olli Simula Timo Honkela (Ed.), Proceedings of the International and Interdisciplinary Conference on Adaptive Knowledge Representation and Reasoning (AKRR'05), 90-97, Helsinki University of Technology, 2005.
• Tapio Pahikkala, Sampo Pyysalo, Filip Ginter, Jorma Boberg, Jouni Järvinen, Tapio Salakoski, Kernels Incorporating Word Positional Information in Natural Language Disambiguation Tasks. In: Ingrid Russell, Zdravko Markov (Eds.), Proceedings of the Eighteenth International Florida Artificial Intelligence Research Society Conference, 442-448, AAAI Press, 2005.
• Evgeni Tsivtsivadze, Tapio Pahikkala, Sampo Pyysalo, Jorma Boberg, Aleksandr Mylläri, Tapio Salakoski, Regularized Least-Squares for Parse Ranking. In: In proceedings of the 6th International Symposiumon Intelligent Data Analysis, Lecture Notes in Computer Science, 464–474, Springer-Verlag Berlin Heidelberg 2005, 2005.
• Filip Ginter, Tapio Pahikkala, Sampo Pyysalo, Jorma Boberg, Jouni Järvinen, Tapio Salakoski, Extracting Protein-Protein Interaction Sentences by Applying Rough Set Data Analysis. In: Roman Slowinski Jan Komorowski et al. Shusaku Tsumoto (Ed.), Proceedings of the Fourth International Conference on Rough Sets and Current Trends in Computing (RSCTC 2004), Lecture Notes in Artificial Intelligence , Vol. 3066, 780-785, 2004.
• Filip Ginter, Sampo Pyysalo, Jorma Boberg, Jouni Järvinen, Tapio Salakoski, Ontology-Based Feature Transformations: A Data-Driven Approach. In: Martínez-Barco P. Muñoz R. Noeda M. S. Vicedo J. L. (Ed.), Advances in Natural Language Processing. Proceedings of the 4th International Conference EsTAL 2004., LNCS, Lecture Notes in Artificial Intelligence 3230, 279-290, Springer, Heidelberg, 2004.
• Sampo Pyysalo, Filip Ginter, Tapio Pahikkala, Jeppe Koivula, Jorma Boberg, Jouni Järvinen, Tapio Salakoski, Analysis of Link Grammar on Biomedical Dependency Corpus Targeted at Protein-Protein Interactions. In: Patrick Ruch Adeline Nazarenko Nigel Collier (Ed.), Proceedings of the International Workshop on Natural Language Processing in Biomedicine and its Applications (JNLPBA), 15-21, 2004.
• Tapio Salakoski, Jorma Boberg, Approaches to Representative Classification of Biological Structures and Mathematical Formalization of Homologous Classes. In: Abstracts for PMMB V Conference: Statistics and Inference in Molecular Biology, Santa Fe, NM, USA, 1997.
• Tapio Salakoski, Jorma Boberg, M. Vihinen, Prerequisites for Accurate Prediction of Protein Folding Type: A Comparative Evaluation of the Predictive Power of Composition and Sequence. In: Abstracts for PMMB IV Conference: From DNA Sequence to Protein Structure and Function, Santa Fe, NM, USA, 1995.

Chapters in edited books (2):

• Evgeni Tsivtsivadze, Tapio Pahikkala, Jorma Boberg, Tapio Salakoski, Tom Heskes, Co-Regularized Least-Squares for Label Ranking. In: Johannes Fürnkranz, Eyke Hüllermeier (Eds.), Preference Learning, 107–123, Springer, 2010.
• Evgeni Tsivtsivadze, Tapio Pahikkala, Jorma Boberg, Tapio Salakoski, Kernels for Text Analysis. In: Aixin Sun Han Tong Loh Wen Feng Lu Ee-Peng Lim Ying Liu (Ed.), Advances of Computational Intelligence in Industrial Systems, Studies in Computational Intelligence Volume 116/2008, 81–97, Springer Berlin / Heidelberg, 2008.

Ph.D. thesis (1):

• Jorma Boberg, Cluster Analysis. A Mathematical Approach with Applications to Protein Structures. TUCS Dissertations 20. Turku Centre for Computer Science, 1999.

Technical reports (1):

• Tapio Pahikkala, Sampo Pyysalo, Jorma Boberg, Jouni Järvinen, Tapio Salakoski, Matrix Representations, Linear Transformations, and Kernels for Disambiguation in Natural Language. TUCS Technical Reports 890, Turku Centre for Computer Science, 2008.