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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 (37):

• Harri Merisaari, Parisa Mohavedi, Ileana M. Perez, Jussi Toivonen, Marko Pesola, Pekka Taime, Peter J. Boström, Tapio Pahikkala, Aida Kiviniemi, Hannu J. Aronen, Ivan Jambor, Fitting Methods for Intravoxel Incoherent Motion Imaging of Prostate Cancer on Region of Interest Level: Repeatability and Gleason Score Prediction. 77, 2017.
• Fahimeh Farahnakian, Tapio Pahikkala, Pasi Liljeberg, Juha Plosila, Hieu Nguyen Trung, Hannu Tenhunen, Energy-Aware VM Consolidation in Cloud Data Centers Using Utilization Prediction Model. IEEE TRANSACTION ON CLOUD COMPUTING , 1–13, 2016.
• 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.
• Fahimeh Farahnakian, Adnan Ashraf, Tapio Pahikkala, Pasi Liljeberg, Juha Plosila, Ivan Porres, Hannu Tenhunen, Using Ant Colony System to Consolidate VMs for Green Cloud Computing. IEEE Transactions on Services Computing PP(99), 13, 2015.
• Tapio Pahikkala, Antti Airola, Sami Pietilä, Sushil Shakyawar, Agnieszka Szwajda, Jing Tang, Tero Aittokallio, Toward More Realistic Drug-Target Interaction Predictions. Briefings in Bioinformatics 16(2), 325–37, 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.
• 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.
• 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.
• 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.
• 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.
• 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.
• 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.
• 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.
• 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.
• Evgeni Tsivtsivadze, Tapio Pahikkala, Jorma Boberg, Tapio Salakoski, Locality Kernels for Sequential Data and Their Applications to Parse Ranking. Applied Intelligence , 2008.
• Tero Aittokallio, Jani S. Malminen, Tapio Pahikkala, Olli Polo, Olli S. Nevalainen, Inspiratory Flow Shape Clustering: An Automated Method to Monitor Upper Airway Performance During Sleep. Computer Methods and Programs in Biomedicine 85(1), 8–18, 2007.
• 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.
• Heidi Vähämaa, Pekka Ojala, Tapio Pahikkala, Olli S. Nevalainen, Riitta Lahesmaa, Tero Aittokallio, Computer-Assisted Identification of Multi-Trace Electrophoretic Patterns in Differential Display Experiments. Electrophoresis 28(6), 879–893, 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.
• Tero Aittokallio, Tapio Pahikkala, Pekka Ojala, Timo J. Nevalainen, Olli Nevalainen, Electrophoretic Signal Comparison Applied to mRNA Differential Display Analysis. BioTechniques 34(1), 116–122, 2003.

Articles in proceedings (68):

• Fahimeh Farahnakian, Rami Bahsoon, Pasi Liljeberg, Tapio Pahikkala, Self-Adaptive Resource Management System in IaaS Clouds. In: Carl Kesselman (Ed.), IEEE CLOUD, 381–388, IEEE Computer Society Conference Publishing Services, 2016.
• Fahimeh Farahnakin, Rami Bahsoon, Pasi Liljeberg, Tapio Pahikkala, Self-Adaptive Resource Management System in IaaS Clouds. In: Rami Bahsoon, Pasi Liljeberg, Tapio Pahikkala (Eds.), 9th International Conference on Cloud Computing (IEEE CLOUD), 553–560, IEEE, 2016.
• Fahimeh Farahnakian, Tapio Pahikkala, Pasi Liljeberg, Juha Plosila, Hannu Tenhunen, Utilization Prediction Aware VM Consolidation Approach for Green Cloud Computing. In: da Silva Dilma (Ed.), IEEE, 1–1, IEEE, 2015.
• Mohammad Fattah, Antti Airola, Rachata Ausavarungnirun, Nima Mirzaei, Pasi Liljeberg, Juha Plosila, Siamak Mohammadi, Tapio Pahikkala, Onur Mutlu, Hannu Tenhunen, A Low-Overhead, Fully-Distributed, Guaranteed-Delivery Routing Algorithm for Faulty Network-on-Chips. In: Andre Ivanov, Diana Marculescu (Eds.), 2015 9th ACM/IEEE International Symposium on Networks-on-Chip, 1–8, ACM/IEEE, 2015.
• Shima Soroushnia, Masoud Daneshtalab, Tapio Pahikkala, Juha Plosila, Parallel Implementation of Fuzzified Pattern Matching Algorithm on GPU. In: 2015 23rd Euromicro International Conference on Parallel, Distributed, and Network-Based Processing, 2015.
• Thomas Xu, Jonne Pohjankukka, Paavo Nevalainen, Ville Leppänen, Tapio Pahikkala, Parallel Applications and On-chip Traffic Distributions: Observation, Implication and Modelling. In: Pascal Lorenz, Leszek Maciaszek (Eds.), Proceedings of the 10th International Conference on Software Engineering and Applications, 443–449, SciTePress, 2015.
• Fahimeh Farahnakian, Adnan Ashraf, Pasi Liljeberg, Tapio Pahikkala, Juha Plosila, Ivan Porres, Hannu Tenhunen, Energy-Aware Dynamic VM Consolidation in Cloud Data Centers Using Ant Colony System. In: Carl Kesselman (Ed.), 7th IEEE International Conference on Cloud Computing, 104–111, IEEE, 2014.
• Fahimeh Farahnakian, Tapio Pahikkala, Juha Plosila, Tenhunen Hannu, Hierarchical Agent-Based Architecture for Resource Management in Cloud Data Centers. In: WU Qishi (Ed.), 7th IEEE International Conference on Cloud Computing (IEEE CLOUD), 928 – 929, IEEE, 2014.
• Fahimeh Farahnakin, Tapio Pahikkala, Pasi Liljeberg, Juha Plosila, Hannu Tenhunen, Multi-Agent Based Architecture for Dynamic VM Consolidation in Cloud Data Centers. In: 40th Euromicro Conference on Software Engineering and Advanced Applications (SEAA), 111 – 118, IEEE, 2014.
• Juho Heimonen, Tapio Salakoski, Tapio Pahikkala, Properties of Object-Level Cross-Validation Schemes for Symmetric Pair-Input Data. In: Pasi Fränti, Gavin Brown, Marco Loog, Francisco Escolano, Marcello Pelillo (Eds.), Structural, Syntactic, and Statistical Pattern Recognition, Lecture Notes in Computer Science 8621, 384–393, Springer Berlin Heidelberg, 2014.