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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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Edited proceedings (1):

• Tapio Salakoski, Filip Ginter, Sampo Pyysalo, Tapio Pahikkala (Eds.), Advances in Natural Language Processing, 5th International Conference, FinTAL 2006 Turku, Finland, August 23-25, 2006 Proceedings, Lecture Notes in Computer Science 4139, Springer Berlin / Heidelberg, 2006.

Articles in journals (48):

• Elina Kontio, Antti Airola, Tapio Pahikkala, Heljä Lundgren-Laine, Kristiina Junttila, Heikki Korvenranta, Tapio Salakoski, Sanna Salanterä, Predicting Patient Acuity from Electronic Patient Records. Journal of Biomedical Informatics 51, 35–40, 2014.
• Pekka Naula, Antti Airola, Tapio Salakoski, Tapio Pahikkala, Multi-Label Learning Under Feature Extraction Budgets. Pattern Recognition Letters 40, 56–65, 2014.
• Sebastian Okser, Tapio Pahikkala, Antti Airola, Tapio Salakoski, Samuli Ripatti, Tero Aittokallio, Regularized Machine Learning in the Genetic Prediction of Complex Traits. Plos Genetics 10(11), e1004754, 2014.
• Katri Haverinen, Jenna Nyblom, Timo Viljanen, Veronika Laippala, Samuel Kohonen, Anna Missilä, Stina Ojala, Tapio Salakoski, Filip Ginter, Building the Essential Resources for Finnish: The Turku Dependency Treebank. Language Resources and Evaluation , 2013.
• Predrag Radivojac, Wyatt T. Clark, Tal Ronnen Oron, Alexandra M. Schnoes, Tobias Wittkop Wittkop, Artem Sokolov, Kiley Graim, Christopher Funk, Karin Verspoor, Asa Ben-Hur, Gaurav Pandey, Jeffrey M. Yunes, Ameet S. Talwalkar, Susanna Repo, Michael L. Souza, Damiano Piovesan, Rita Casadio, Zheng Wang, Jianlin Cheng, Hai Fang, Julian Gough, Patrik Koskinen, Petri Törönen, Jussi Nokso-Koivisto, Liisa Holm, Domenico Cozzetto, Daniel W. A. Buchan, Kevin Bryson, David T. Jones, Bhakt Limave, Harshal Inamdar, Avik Datta, Sunitha K. Manjari, Rajendra Joshi, Meghana Chitale, Daisuke Kihara, Andreas M. Lisewski, Serkan Erdin, Eric Venner, Olivier Lichtarge, Robert Rentzsch, Haixuan Yang, Alfonso E. Romero, Prajwal Bhat, Alberto Paccanaro, Tobias Hamp, Rebecca Kaßner, Stefan Seemayer, Esmeralda Vicedo, Christian Schaefer, Dominik Achten, Florian Auer, Ariane Boehm, Tatjana Braun, Maximilian Hecht, Mark Heron, Peter Hönigschmid, Thomas A. Hopf, Stefanie Kaufmann, Michael Kiening, Denis Krompass, Cedric Landerer, Yannick Mahlich, Manfred Roos, Jari Björne, Tapio Salakoski, Andrew Wong, Hagit Shatkay, Fanny Gatzmann, Ingolf Sommer, Mark N. Wass, Michael J. E. Sternberg, Nives Škunca, Fran Supek, Matko Bošnjak, Panče Panov, Sašo Džeroski, Tomislav Šmuc, Yiannis A. I. Kourmpetis, Aalt D. J. van Dijk, Cajo J. F. ter Braak, Yuanpeng Zhou, Qingtian Gong, Xinran Dong, Weidong Tian, Marco Falda, Paolo Fontana, Enrico Lavezzo, Barbara Di Camillo, Stefano Toppo, Liang Lan, Nemanja Djuric, Yuhong Guo, Slobodan Vucetic Vucetic, Amos Bairoch, Michal Linial, Patricia C. Babbitt, Steven E. Brenner, Christine Orengo, Burkhard Rost, Sean D. Mooney, Iddo Friedberg, A Large-Scale Evaluation of Computational Protein Function Prediction. Nature methods 10, 221–227, 2013.
• Olli Sjöblom, Laura-Maria Murtola, Juho Heimonen, Lotta Kauhanen, Veronika Laippala, Heljä Lundgren-Laine, Tapio Salakoski, Sanna Salanterä, Using Cluster Analysis to Identify Weak Signals of Lethal Trends in Aviation and Healthcare Documentation. International Journal of Networking and Virtual Organisations 13, 66–80, 2013.
• Tapio Pahikkala, Antti Airola, Thomas Canhao Xu, Pasi Liljeberg, Hannu Tenhunen, Tapio Salakoski, Parallelized Online Regularized Least-Squares for Adaptive Embedded Systems. International Journal of Embedded and Real-Time Communication Systems 3(2), 73–91, 2012.
• Tapio Pahikkala, Sebastian Okser, Antti Airola, Tapio Salakoski, Tero Aittokallio, Wrapper-based selection of genetic features in genome-wide association studies through fast matrix operations. Algorithms for Molecular Biology 7, 1–11, 2012.
• Sofie Van Landeghem, Jari Björne, Thomas Abeel, Bernard De Baets, Tapio Salakoski, Yves Van de Peer, Semantically linking molecular entities in literature through entity relationships. BMC bioinformatics 13, S6, 2012.
• Willem Waegeman, Tapio Pahikkala, Antti Airola, Tapio Salakoski, Michiel Stock, Bernard De Baets, A Kernel-based Framework for Learning Graded Relations from Data. IEEE TRANSACTIONS ON FUZZY SYSTEMS 20(6), 1090–1101, 2012.
• Antti Airola, Tapio Pahikkala, Tapio Salakoski, On Learning and Cross-Validation with Decomposed Nyström Approximation of Kernel Matrix. Neural Processing Letters 33(1), 17–30, 2011.
• Antti Airola, Tapio Pahikkala, Tapio Salakoski, Training Linear Ranking SVMs in Linearithmic Time Using Red–Black Trees. Pattern Recognition Letters 32(9), 1328–1336 , 2011.
• Antti Airola, Tapio Pahikkala, Willem Waegeman, Bernard De Baets, Tapio Salakoski, An Experimental Comparison of Cross-Validation Techniques for Estimating the Area Under the ROC Curve. Computational Statistics and Data Analysis 55(4), 1828–1844, 2011.
• Jari Björne, Juho Heimonen, Filip Ginter, Antti Airola, Tapio Pahikkala, Tapio Salakoski, Extracting Contextualized Complex Biological Events with Rich Graph-Based Feature Sets. Computational Intelligence 27, 541–557, 2011.
• Yoshinobu Kano, Jari Björne, Filip Ginter, Tapio Salakoski, Ekaterina Buyko, Udo Hahn, Kevin Cohen, Katrin Verspoor, Christophe Roeder, Lawrence Hunter, Halil Kilicoglu, Sabine Bergler, Sofie Van Landeghem, U-Compare Bio-Event Meta-Service: Compatible BioNLP Event Extraction Services. BMC Bioinformatics 12(1), 481, 2011.
• Jari Björne, Finter Ginter, Sampo Pyysalo, Jun'ichi Tsujii, Tapio Salakoski, Complex Event Extraction at PubMed Scale . Bioinformatics (ISMB'2010 proceedings volume) 26, 382-390, 2010.
• Satu Jääskeläinen, Pentti Riikonen, Tapio Salakoski, Mauno Vihinen, Accuracy of Protein Hydropathy Predictions. Int. J. Data Mining and Bioinformatics, 4(6), 733-752, 2010.
• Erkki Kaila, Teemu Rajala, Mikko-Jussi Laakso, Tapio Salakoski, Effects of Course-Long Use of a Program Visualization Tool. Conferences in Research and Practice in Information Technology 103, 97–106, 2010.
• Tapio Pahikkala, Willem Waegeman, Evgeni Tsivtsivadze, Tapio Salakoski, Bernard De Baets, Learning Intransitive Reciprocal Relations with Kernel Methods. European Journal of Operational Research 206(3), 676–685, 2010.
• Hanna Suominen, Tapio Salakoski, Supporting Communication and Decision Making in Finnish Intensive Care with Language Technology. Journal of Healthcare Engineering 1(4), 595-614, 2010.
• Filip Ginter, Hanna Suominen, Sampo Pyysalo, Tapio Salakoski, Combining Hidden Markov Models and Latent Semantic Analysis for Topic Segmentation and Labeling: Method and Clinical Application. International Journal of Medical Informatics, Special Issue on Mining of Clinical and Biomedical Text and Data 78(12), e1-e6, 2009.
• Erkki Kaila, Teemu Rajala, Mikko-Jussi Laakso, Tapio Salakoski, Effects, Experiences and Feedback from Studies of a Program Visualization Tool. Informatics in Education 8(1), 17–34, 2009.
• Veronika Laippala, Filip Ginter, Sampo Pyysalo, Tapio Salakoski, Towards Automated Processing of Clinical Finnish: Sublanguage Analysis and a Rule-Based Parser. International Journal of Medical Informatics 78(12), e7–e12, 2009.
• 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.
• Antti Airola, Sampo Pyysalo, Jari Björne, Tapio Pahikkala, Filip Ginter, Tapio Salakoski, All-paths Graph Kernel for Protein-Protein Interaction Extraction With Evaluation of Cross-Corpus Learning. BMC Bioinformatics 9 (Suppl 11), 2008.
• Chang Sik Kim, Pentti Riikonen, Tapio Salakoski, Detecting Biological Associations Between Genes Based on the Theory of Phase Synchronization . Biosystems 92(2), 99–113 , 2008.
• Mikko-Jussi Laakso, Lauri Malmi, Ari Korhonen, Teemu Rajala, Erkki Kaila, Tapio Salakoski, Using Roles of Variables to Enhance Novices Debugging Work. Journal of Information Technology Education: Innovations in Practice 5, 281–296, 2008.
• Sampo Pyysalo, Antti Airola, Juho Heimonen, Jari Björne, Filip Ginter, Tapio Salakoski, Comparative analysis of five protein-protein interaction corpora. BMC Bioinformatics 9 (supplement 3)(6), 2008.
• Teemu Rajala, Mikko-Jussi Laakso, Erkki Kaila, Tapio Salakoski, Effectiveness of Program Visualization: A Case Study with the ViLLE Tool. Journal of Information Technology Education: Innovations in Practice 7, IIP 15–32, 2008.
• Evgeni Tsivtsivadze, Tapio Pahikkala, Jorma Boberg, Tapio Salakoski, Locality Kernels for Sequential Data and Their Applications to Parse Ranking. Applied Intelligence , 2008.
• Kristiina A. Vuori, Eija Nordlund, Jenny Kallio, Tapio Salakoski, Mikko Nikinmaa, Tissue-Specific Expression of Aryl Hydrocarbon Receptor and Putative Developmental Regulatory Modules in Baltic Salmon Yolk-Sac Fry. Aquatic Toxicology 87(1), 19–27, 2008.
• Marketta Hiissa, Tapio Pahikkala, Hanna Suominen, Tuija Lehtikunnas, Barbro Back, Helena Karsten, Sanna Salanterä, Tapio Salakoski, Towards Automated Classification of Intensive Care Nursing Narratives. International Journal of Medical Informatics 76S3, S362–S368, 2007.
• 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.
• Teemu Rajala, Mikko-Jussi Laakso, Erkki Kaila, Tapio Salakoski, VILLE – A Language-Independent Program Visualization Tool. Conferences in Research and Practice in Information Technology 88, 151–159, 2007.
• Hanna Suominen, Tuija Lehtikunnas, Barbro Back, Helena Karsten, Tapio Salakoski, Sanna Salanterä, Applying Language Technology to Nursing Documents: Pros and Cons with a Focus on Ethics. International Journal of Medical Informatics 76S2, S293–S301, 2007.
• Linda Mannila, Mia Peltomäki, Tapio Salakoski, What About a Simple Language? Analyzing the Difficulties in Learning to Program. Computer Science Education 16(3), 211–228, 2006.
• 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.
• Sampo Pyysalo, Tapio Salakoski, Sophie Aubin, Adeline Nazarenko, Lexical Adaptation of Link Grammar to the Biomedical Sublanguage: A Comparative Evaluation of Three Approaches. BMC Bioinformatics 7(Suppl 3), 2006.
• Mikko-Jussi Laakso, Tapio Salakoski, Linda Grandell, Xuemei Qiu, Ari Korhonen, Lauri Malmi, Multi-Perspective Study of Novice Learners Adopting the Visual Algorithm Simulation Exercise System TRAKLA2. Informatics in Education 4(1), 49–68, 2005.
• Aleksandr Mylläri, Tapio Salakoski, Alexey Pasechnik, On the Visualization of the DNA Sequence and its Nucleotide Content. ACM SIGSAM Bulletin 39(4), 131 - 135, 2005.
• 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.
• Veronika Laippala, Timo Viljanen, Antti Airola, Jenna Kanerva, Sanna Salanterä, Tapio Salakoski, Filip Ginter, Statistical Parsing of Varieties of Clinical Finnish. Artificial Intelligence in Medicine 61(3), 131–136, 0000.

Articles in proceedings (142):

• Erkki Kaila, Teemu Rajala, Mikko-Jussi Laakso, Rolf Lindén, Einari Kurvinen, Tapio Salakoski, Comparing Student Performance Between Traditional and Technologically Enhanced Programming Course. In: Unknown Unknown (Ed.), In proceedings of the Seventeenth Australasian Computing Education Conference (ACE2015), Australasian Computing Education Conference 160, 147–154, ACM, 2015.