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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 (3):

• Sasu Tarkoma, Joni-Kristian Kämäräinen, Tapio Pahikkala (Eds.), The Federated Computer Science Event, Unigrafia Oy, 2012.
• Tapio Pahikkala, Jaakko Väyrynen, Jukka Kortela, Antti Airola (Eds.), Proceedings of the 14th Finnish Artificial Intelligence Conference, STeP 2010, Aalto-Print, 2010.
• 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 (55):

• Lotta Hamari, Tiina Kullberg, Jukka Ruohonen, Olli J. Heinonen, Natalia Díaz Rodríguez, Johan Lilius, Anni Pakarinen, Annukka Myllymäki, Ville Leppänen, Sanna Salanterä, Physical Activity Among Children – Objective Measurements Using Fitbit One® and ActiGraph. BMC Research Notes 10, 1–6, 2017.
• Suwisa Kaewphan, Sofie Van Landeghem, Tomoko Ohta, Yves Van de Peer, Filip Ginter, Sampo Pyysalo, Cell Line Name Recognition in Support of the Identification of Synthetic Lethality in Cancer from Text. Bioinformatics , 1–7, 2015.
• Hanna Pirinen, Lotta Kauhanen, Riitta Danielsson-Ojala, Johan Lilius, Ilona Tuominen, Natalia Díaz Rodríguez, Sanna Salanterä, Registered Nurses’ Experiences with the Medication Administration Process. Advances in Nursing 2015, 1–10, 2015.
• Janne Savela, Osmo Eerola, Olli Aaltonen, Weighted Prototypes in Finnish and German. Journal of the Acoustical Society of America 135, 1530–1540, 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.
• Jyrki Tuomainen, Janne Savela, Jonas Obleser, Olli Aaltonen, Attention Modulates the Use of Spectral Attributes in Vowel Discrimination: Behavioral and Event-Related Potential Evidence. Brain Research 1940, 170–183, 2013.
• Björne Jari, Ginter Filip, Salakoski Tapio, University of Turku in the BioNLP'11 Shared Task. BMC Bioinformatics 13, S4, 2012.
• Osmo Eerola, Janne Savela, Production of Short and Long Finnish ­Vowels with and without Noise Masking . Linguistica Uralica 48, 200–208, 2012.
• Osmo Eerola, Janne Savela, Juha-Pertti Laaksonen, Olli Aaltonen, The Effect of Duration on Vowel Categorization and Perceptual Prototypes in a Quantity Language. Journal of Phonetics 40 (2), 315–328, 2012.
• Fabian Gieseke, Oliver Kramer, Antti Airola, Tapio Pahikkala, Efficient Recurrent Local Search Strategies for Semi- and Unsupervised Regularized Least-Squares Classification. Evolutionary Intelligence 5(3), 189–205, 2012.
• 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.
• 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.
• 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.
• R. Karthikeyan, Tapio Pahikkala, Seppo Virtanen, Jouni Isoaho, K. Manickavasagam, KVV. Murthy, Fuzzy Logic Based Control for Parallel Cascade Control . International Journal on Automatic Control and System Engineering 10(2), 39-48, 2010.
• Sebastian Okser, Terho Lehtimäki, Laura L. Elo, Nina Mononen, Nina Peltonen, Mika Kähönen, Markus Juonala, Yue-Mei Fan, Jussi A. Hernesniemi, Tomi Laitinen, Leo-Pekka Lyytikäinen, Riikka Rontu, Carit Eklund, Genetic Variants and Their Interactions in the Prediction of Increased Pre-Clinical Carotid Atherosclerosis: The Cardiovascular Risk in Young Finns Study. PLoS Genetics , 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.
• Helena Karsten, Hanna Suominen, Mining of Clinical and Biomedical Text and Data: Editorial of the Special Issue. International Journal of Medical Informatics 78(12), 786–787, 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.
• Heljä Lundgrén-Laine, Hanna Suominen, Mistä näitä tietoja oikein tulee? Kieliteknologialla tehohoidon tiedot hallintaan. [Where do all these data come from? Solving problems in knowledge management of intensive care data via human language technology]. . Tehohoito [Journal of the Finnish Society of Intensive Care, FSIC] 27(2), 102-104, 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.
• 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.
• Olli Aaltonen, Åke Hellström, Maija Peltola, Janne Savela, Henna Tamminen, Brain Responses Reveal Hardwired Detection of Native-Language Rule Violations. Neuroscience Letters 444, 56–59, 2008.
• 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.
• 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.
• Pentti Riikonen, Mauno Vihinen, National Research Contributions: A Case Study on Finnish Biomedical Research . Scientometrics 77(2), 207–222, 2008.
• Hanna Suominen, Kieliteknologiasta ratkaisu potilasdokumentaation hyödynnettävyyteen. Tietojenkäsittelytiede 28, 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.
• 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.
• 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.