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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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Monographs (3):

• Jouni Smed, Harri Hakonen, コンピュータゲームのアルゴリズム&ネットワーキング. Born Digital, 2007.
• Jouni Smed, Harri Hakonen, Timo Raita, Sopimuspohjainen olio-ohjelmointi Java-kielellä. 2007.
• Jouni Smed, Harri Hakonen, Algorithms and Networking for Computer Games. John Wiley & Sons, 2006.

Edited books (2):

• John Impagliazzo, Timo Järvi, Petri Paju (Eds.), History of Nordic Computing 2. Second IFIP WG 9.7 Conference, HiNC 2, Turku, Finland, August 21-23, 2007, Revised Selected Papers, AICT 303, Springer, 2009.
• Risto Lahdelma, Kaisa Miettinen, Pekka Salminen, Ahti Salo (Eds.), Proceedings of the 67th meeting of the European Working Group "Multiple Criteria Decision Aiding", Reports of the Department of Mathematical Information Technology, Series A. Collections., University of Jyväskylä, 2008.

Edited proceedings (2):

• Sasu Tarkoma, Joni-Kristian Kämäräinen, Tapio Pahikkala (Eds.), The Federated Computer Science Event, Unigrafia Oy, 2012.
• Hannu Tenhunen, T. Ming Jiang, Xiaoqing Liu, Ville Leppänen (Eds.), Proceedings of 32nd Annual IEEE International Computer Software and Applications Conference, COMPSAC'08, IEEE Computer Society, 2008.

Articles in journals (176):

• Sari Pihlasalo, Ileana M. Perez, Niklas Hollo, Elina Hokkanen, Tapio Pahikkala, Harri Härmä, Luminometric Label Array for Quantification and Identification of Metal Ions. Analytical chemistry 88(10), 5271–5280, 2016.
• Mika Murtojärvi, Olli Nevalainen, Ville Leppänen, Performance Tuning and Sparse Traversal Technique for a Cell-Based Fetch Length Algorithm on a GPU. Concurrency and Computation: Practice and Experience 27(17), 5114–5133, 2015.
• Fabian Gieseke, Antti Airola, Tapio Pahikkala, Oliver Kramer, Fast and Simple Gradient-Based Optimization for Semi-Supervised Support Vector Machines. Neurocomputing 123, 23–32, 2014.
• 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.
• Anne-Maarit Majanoja, Linnéa Linko, Ville Leppänen, A Globally Integrated Supply Chain Delivery Quality Strategy: Transformation Insights at the Nokia Devices Unit. American Journal of Industrial and Business Management 4, 413–431, 2014.
• Anne-Maarit Majanoja, Linnéa Linko, Ville Leppänen, The Challenge of Global Selective Outsourcing Environment: Implementing Customer-Centric IT Service Operations and ITIL Processes. Journal of Service Science and Management, 7, 396–410, 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.
• Olli Kannaste, Tomi Suomi, Jussi Salmi, Esa Uusipaikka, Olli Nevalainen, Garry L. Corthals, Cross-Correlation of Spectral Count Ranking to Validate Quantitative Proteome Measurements. Journal of Proteome Research 13(4), 1957–1968, 2014.
• Tapio Pahikkala, Antti Airola, Fabian Gieseke, Oliver Kramer, On Unsupervised Training of Multi-Class Regularized Least-Squares Classifiers. Journal of Computer Science and Technology 29(1), 90–104, 2014.
• Michiel Stock, Thomas Fober, Eyke Hüllermeier, Serghei Glinca, Gerhard Klebe, Tapio Pahikkala, Antti Airola, Bernard De Baets, Willem Waegeman, Identification of Functionally Related Enzymes by Learning-to-Rank Methods. IEEE-ACM Transactions on Computational Biology and Bioinformatics 11(6), 1157–1169, 2014.
• Jussi Toivonen, Harri Merisaari, Marko Pesola, Pekka Taimen, Peter J. Boström, Tapio Pahikkala, Hannu J. Aronen, Ivan Jambor, Mathematical Models for Diffusion-Weighted Imaging of Prostate Cancer Using B Values Up to 2000 S/mm2: Correlation with Gleason Score and Repeatability of Region of Interest Analysis. Magnetic Resonance in Medicine , 1–9, 2014.
• Frans Vainio, Tapio Pahikkala, Mika Johnsson, Olli S. Nevalainen, Timo Knuutila, Estimating the production time of a PCB assembly job without solving the optimised machine control. International Journal of Computer Integrated Manufacturing 27 (2014)(4/2014), 1 –13, 2014.
• Heta Mattila, Pertti Valli, Tapio Pahikkala, Jukka Teuhola, Olli S. Nevalainen, Esa Tyystjärvi, Comparison of Chlorophyll Fluorescence Curves and Texture Analysis for Automatic Plant Identification. Precision Agriculture 14(6), 621–636, 2013.
• Sebastian Okser, Tapio Pahikkala, Tero Aittokallio, Genetic Variants and Their Interactions in Disease Risk Prediction - Machine Learning and Network Perspectives. Biodata Mining 6, 1–15, 2013.
• Tapio Pahikkala, Antti Airola, Michiel Stock, Bernard De Baets, Willem Waegeman, Efficient Regularized Least-Squares Algorithms for Conditional Ranking on Relational Data. Machine Learning 93(2-3), 321–356, 2013.
• 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.
• Kai Kallio, Mika Johnsson, Olli S. Nevalainen, Estimating the Operation Time of Flexible Surface Mount Placement Machines. Production Engineering, Research and Development , 1–10, 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.
• Robert D. Scott, Jukka Heikkonen, Estimating Age at First Maturity in Fish from Change-Points in Growth Rate. Marine Ecology-Progress Series 450, 147–157, 2012.
• Maaria Tringham, Johanna Kurko, Laura Tanner, Johannes Tuikkala, Olli S. Nevalainen, Harri Niinikoski, Kirsti Näntö-Salonen, Marja Hietala, Olli Simell, Juha Mykkänen, Exploring the Transcriptomic Variation Caused by the Finnish Founder Mutation of Lysinuric Intolerance (LPI). Molecular genetics and metabolism (IF3.539) 105, 408-415, 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, 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.
• Jean-Noel Druon, Jean-Marc Fromentin, Florian Aulanier, Heikkonen Jukka, Potential Feeding and Spawning Habitats of Atlantic Bluefin Tuna in the Mediterranean Sea. MARINE ECOLOGY PROGRESS SERIES 439, 223–240, 2011.
• Martti Forsell, Ville Leppänen, A Moving Threads Processor Architecture MTPA. Journal of Supercomputing 57(1), 5–19, 2011.
• Vibhor Kumar, Sarah J Butcher, Katariina Öörni, Peter Engelhardt, Jukka Heikkonen, Kimmo Kaski, Mika Ala-Korpela, Petri T Kovanen, Three-Dimensional cryoEM Reconstruction of Native LDL Particles to 16A° Resolution at Physiological Body Temperature . PloS ONE 6(5), 1–11, 2011.
• Mika Murtojärvi, Tapio Suominen, Esa Uusipaikka, Olli S. Nevalainen, Optimising an Observational Water Monitoring Network for Archipelago Sea, South West Finland. Computers & Geosciences 37(7), 844-854, 2011.
• Juan Cicuendez Perez, Alvarez Marlene Alvarez, Jukka Heikkonen, Marte Indregard, Identification of Bluefin Tuna Cages in Mediterranean Sea Fishing Grounds from SAR Images. International Journal of Remote Sensing 32(16), 4461–4474, 2011.
• Csaba Ráduly-Baka, Timo Knuutila, Mika Johnsson, OlliS. Nevalainen, Organizing the Operation of Radial Machine Sequencers for Multiple PCB Types. Computers & Industrial Engineering 61, 1003–1010, 2011.
• Aiying Rong, Attila Toth, Olli S. Nevalainen, Timo Knuutila, Risto Lahdelma, Modeling the machine configuration and line-balancing problem of a PCB assembly line with modular placement machines. International Journal of Advanced Manufacturing Technology 54, 349–360, 2011.
• Jukka Teuhola, Nonblock Coding of Binary Sources by Probabilistic Enumeration. IEEE Transactions on Information Theory 57(9), 6170–6179, 2011.
• Jukka Teuhola, Interpolative Coding of Integer Sequences Supporting Log-Time Random Access. Information Processing and Management 47(5), 742–761, 2011.
• Heidi Vähämaa, Ville R. Koskinen, Waltteri Hosia, Robert Moulder, Olli S. Nevalainen, Riitta Lahesmaa, Tero Aittokallio, Jussi Salmi, PolyAlign: A Versatile LC-MS Data Alignment Tool for Landmark-Selected and -Automated Use. International Journal of Proteomics Vol. 2011 , 9, 2011.
• Marius C. Codrea, Marja Hakala-Yatkin, Anna Kårlund-Marttila, Ladislav Nedbal, Tero Aittokallio, Olli S. Nevalainen, Esa Tyystjärvi, Mahalanobis Distance Screening of Arabidopsis Mutans with Chlorophyll Fluorescence. Photosynthesis Research 105, 273–283, 2010.
• Stefan Emet, Timo Knuutila, Esa Alhoniemi, Michael Maier, Mika Johnsson, Olli S. Nevalainen, Workload Balancing in Printed Circuit Board Assembly. International Journal of Advanced Manufacturing Technology , 2010.
• Anssi Kautonen, Ville Leppänen, Martti Penttonen, Thinning Protocols for Routing h-Relations Over Shared Media. Journal of Parallel and Distributed Computing 70(8), 783–789, 2010.
• Niina Lietzén, Lari Natri, Olli Nevalainen, Jussi Salmi, Tuula Nyman, Compid – A New Software Tool to Integrate and Compare MS/MS Based Protein Identification Results from Mascot and Paragon. Journal of Proteome Research , 2010.
• Mirva Piippo, Niina Lietzen, Olli S. Nevalainen, Jussi Salmi, Tuula A. Nyman, 233. Pripper: Prediction of Caspase Cleavage Sites from Whole Proteomes. BMC Bioinformatics DOI: 10.1186/1471-2105-11-320, 1–7, 2010.
• Csaba Raduly-Baka, Timo Knuutila, Mika Johnsson, Olli S. Nevalainen, Construction of Component Tapes for Radial Placement Machines. Computers & Operations Research Vol. 37, , 1488-1499, 2010.
• K. Talvinen, J. Tuikkala, M. Nykänen, A. Nieminen, J. Anttinen, O.S. Nevalainen, S. Hurme, T. Kuopio, P. Kronqvist, 232. Altered Expression of p120catenin Predicts Poor Outcome in Invasive Breast Cancer. Journal of Cancer Research and Clinical Oncology 136, 1377–1387, 2010.
• Jukka Teuhola, Interpolative Coding of Integer Sequences Supporting Log-Time Random Access. Information Processing and Management , 2010.