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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 Pahikkala, Jaakko Väyrynen, Jukka Kortela, Antti Airola (Eds.), Proceedings of the 14th Finnish Artificial Intelligence Conference, STeP 2010, Aalto-Print, 2010.

Articles in journals (20):

• 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.
• 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.
• 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.
• 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.
• 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.
• 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 (36):

• 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.
• Hans Moen, Juho Heimonen, Laura-Maria Murtola, Antti Airola, Tapio Pahikkala, Virpi Terävä, Riitta Danielsson-Ojala, Tapio Salakoski, Sanna Salanterä, On Evaluation of Automatically Generated Clinical Discharge Summaries. In: Ellen A. A. Jaatun, Elizabeth Brooks, Kirsti Berntsen, Heidi Gilstad, Martin Gilje Jaatun (Eds.), Proceedings of the 2nd European Workshop on Practical Aspects of Health Informatics (PAHI 2014), Ceur Workshop Proceedings 1251, 101–114, WISU Verlag Aachen, 2014.
• Tapio Pahikkala, Michiel Stock, Antti Airola, Tero Aittokallio, Bernard De Baets, Willem Waegeman, A Two-Step Learning Approach for Solving Full and Almost Full Cold Start Problems in Dyadic Prediction. In: Toon Calders, Floriana Esposito, Eyke Hüllermeier, Rosa Meo (Eds.), Machine Learning and Knowledge Discovery in Databases (ECML PKDD 2014), Lecture Notes in Computer Science 8725, 517–532 , Springer, 2014.
• Antti Airola, Tapio Pahikkala, Heljä Lundgrén-Laine, Anne Santalahti, Päivi Rautava, Sanna Salanterä, Tapio Salakoski, A Machine Learning Approach Towards Early Detection of Frequent Health Care Users. In: Hanna Suominen (Ed.), Proceedings of the 4th International Louhi Workshop on Health Document Text Mining and Information Analysis, National ICT Australia, 2013.
• Veronika Laippala, Timo Viljanen, Antti Airola, Jenna Nyblom, Sanna Salanterä, Tapio Salakoski, Filip Ginter, Statistical Parsing of Varieties of Clinical Finnish. In: Hanna Suominen (Ed.), Proceedings of the 4th International Louhi Workshop on Health Document Text Mining and Information Analysis, 1–6, National ICT Australia, 2013.
• Sebastian Okser, Antti Airola, Tapio Salakoski, Tero Aittokallio, Tapio Pahikkala, Parallel Feature Selection for Regularized Least-Squares. In: Pekka Manninen, Per Öster (Eds.), Applied Parallel and Scientific Computing, Lecture Notes in Computer Science 7782, 280–294, Springer, 2013.
• Antti Airola, Machine Learning and Performance Estimation Methods for Ranking Problems. In: Sasu Tarkoma, Joni-Kristian Kämäräinen, Tapio Pahikkala (Eds.), Proceedings of the Federated Computer Science Event 2012, 8–14, University of Helsinki, 2012.
• Fabian Gieseke, Antti Airola, Tapio Pahikkala, Oliver Kramer, Sparse Quasi-Newton Optimization for Semi-Supervised Support Vector Machines. In: Pedro Latorre Carmona, J. Salvador Sánchez, Ana L. N. Fred (Eds.), Proceedings of the 1st International Conference on Pattern Recognition Applications and Methods (ICPRAM), 45–54, SciTePress, 2012.
• Tapio Pahikkala, Antti Airola, Fabian Gieseke, Oliver Kramer, Unsupervised Multi-Class Regularized Least-Squares Classification. In: Mohammed J. Zaki, Arno Siebes, Jeffrey Xu Yu, Bart Goethals, Geoff Webb, Xindong Wu (Eds.), The 12th IEEE International Conference on Data Mining (ICDM 2012), 585–594, IEEE Computer Society, 2012.
• Michiel Stock, Tapio Pahikkala, Antti Airola, Tapio Salakoski, Bernard De Baets, Willem Waegeman, Learning Monadic and Dyadic Relations: Three Case Studies in Systems Biology. In: Oliver Ray, Katsumi Inoue (Eds.), Proceedings of the ECML/PKDD 2012 Workshop on Learning and Discovery in Symbolic Systems Biology, 74–84, ECML/PKDD 2012 Workshop on Learning and Discovery in Symbolic Systems Biology, 2012.
• Willem Waegeman, Tapio Pahikkala, Antti Airola, Tapio Salakoski, Bernard De Baets, Learning Valued Relations from Data. In: Pedro Melo-Pinto, Pedro Couto, Carlos Serôdio, János Fodor, Bernard De Baets (Eds.), Eurofuse 2011, Advances in Soft Computing 107, 257–268, Springer, 2012.
• Willem Waegeman, Michiel Stock, Bernard De Baets, Tapio Pahikkala, Antti Airola, Tapio Salakoski, Conditional Ranking Algorithms for Efficient Object Retrieval and Object Querying on Relational Data. In: Thomas Demeester, Johannes Deleu, Laurent Mertens, Dieter Plaetinck, An De Moor, Thong Hoang, Tim Wauters, Chris Develder, Brecht Vermeulen, Piet Demeester (Eds.), Proceedings of the 12th Dutch-Belgian Information Retrieval Workshop (DIR 2012), 59–60, Ghent University, 2012.
• Thomas Canhao Xu, Tapio Pahikkala, Antti Airola, Pasi Liljeberg, Juha Plosila, Tapio Salakoski, Hannu Tenhunen, Implementation and Analysis of Block Dense Matrix Decomposition on Network-on-Chips. In: Geyong Min, Jia Hu, Lei (Chris) Liu, Laurence Tianruo Yang, Seetharami Seelam, Laurent Lefevre (Eds.), Proceedings of the 14th IEEE International Conference on High Performance Computing and Communications (HPCC), 516–523, IEEE, 2012.
• Antti Airola, Tapio Pahikkala, Tapio Salakoski, An Improved Training Algorithm for the Linear Ranking Support Vector Machine. In: Timo Honkela, Wlodzislaw Duch, Mark Girolami, Samuel Kaski (Eds.), Proceedings of the 21st International Conference on Artificial Neural Networks (ICANN 2011), 6791, 134–141, Springer, 2011.
• Jari Björne, Antti Airola, Tapio Pahikkala, Tapio Salakoski, Drug-Drug Interaction Extraction with RLS and SVM Classifiers. In: Isabel Segura-Bedmar, Paloma Martinez, Daniel Sanchez-Cisneros (Eds.), Proceedings of the First Challenge task on Drug- Drug Interaction Extraction (DDIExtraction 2011), Ceur Workshop Proceedings, 35–42, CEUR Workshop Proceedings, 2011.
• Fabian Gieseke, Oliver Kramer, Antti Airola, Tapio Pahikkala, Speedy Local Search for Semi-Supervised Regularized Least-Squares. In: Joscha Bach, Stefan Edelkamp (Eds.), KI 2011: Advances in Artificial Intelligence, Lecture Notes in Computer Science 7006, 87–98, Springer, 2011.
• Pekka Naula, Tapio Pahikkala, Antti Airola, Tapio Salakoski, Learning Multi-Label Predictors under Sparsity Budget. In: Anders Kofod-petersen, Fredrik Heintz, Helge Langseth (Eds.), Proceedings of the Eleventh Scandinavian Conference on Artificial Intelligence (SCAI 2011), Frontiers in Artificial Intelligence and Applications 227, 30–39, IOS Press, 2011.
• Pekka Naula, Tapio Pahikkala, Antti Airola, Tapio Salakoski, Greedy Regularized Least-Squares for Multi-Task Learning. In: Myra Spiliopoulou, Haixun Wang, Diane Cook, Jian Pei, Wei Wang, Osmar Zaïane, Xindong Wu (Eds.), 11th IEEE International Conference on Data Mining Workshops (ICDMW'11), 527-533, IEEE Computer Society, 2011.
• Sebastian Okser, Tapio Pahikkala, Antti Airola, Tero Aittokallio, Tapio Salakoski, Fast and Parallelized Greedy Forward Selection of Genetic Variants in Genome-Wide Association Studies. In: Yidong Chen, Yufei Huang, Edward Dougherty (Eds.), IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS'11), 214-217, IEEE Signal Processing Society, 2011.
• Tapio Pahikkala, Antti Airola, Thomas Canhao Xu, Pasi Liljeberg, Hannu Tenhunen, Tapio Salakoski, A parallel online regularized least-squares machine learning algorithm for future multi-core processors. In: César Benavente-peces, Joaquim Filipe (Eds.), Proceedings of the 1st International Conference on Pervasive and Embedded Computing and Communication Systems (PECCS 2011), 590-599, SciTePress, 2011.
• 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.
• Antti Airola, Tapio Pahikkala, Tapio Salakoski, Large Scale Training Methods for Linear RankRLS. In: Eyke Fürnkranz Johannes Hüllermeier (Ed.), ECML/PKDD-10 Workshop on Preference Learning, 2010.
• Antti Airola, Tapio Pahikkala, Willem Waegeman, Bernard De Baets, Tapio Salakoski, A Comparison of AUC Estimators in Small-Sample Studies . In: Sašo Geurts Pierre Rousu Juho Džeroski (Ed.), Machine Learning in Systems Biology, JMLR Workshop and Conference Proceedings 8, 3–13, MIT Press, 2010.
• Tapio Pahikkala, Antti Airola, Pekka Naula, Tapio Salakoski, Greedy RankRLS: a Linear Time Algorithm for Learning Sparse Ranking Models. In: Evgeniy Gabrilovich, Alexander J. Smola, Naftali Tishby (Eds.), SIGIR 2010 Workshop on Feature Generation and Selection for Information Retrieval, 11-18, ACM, 2010.
• Tapio Pahikkala, Antti Airola, Tapio Salakoski, Speeding up Greedy Forward Selection for Regularized Least-Squares. In: Sorin Khoshgoftaar Taghi M. Palade Vasile Pedrycz Witold Wani M. Arif Zhu Xingquan Draghici (Ed.), Proceedings of The Ninth International Conference on Machine Learning and Applications (ICMLA'10), 325-330, IEEE Computer Society, 2010.
• Tapio Pahikkala, Antti Airola, Tapio Salakoski, Feature Selection for Regularized Least-Squares: New Computational Short-Cuts and Fast Algorithmic Implementations. In: Samuel Kaski, David J. Miller, Erkki Oja, Antti Honkela (Eds.), Proceedings of the IEEE International Workshop on Machine Learning for Signal Processing (MLSP 2010), 295–300, IEEE, 2010.
• Tapio Pahikkala, Willem Waegeman, Antti Airola, Tapio Salakoski, Bernard De Baets, Conditional Ranking on Relational Data. In: José L. Balcázar, Francesco Bonchi, Aristides Gionis, Michèle Sebag (Eds.), Machine Learning and Knowledge Discovery in Databases European Conference, ECML PKDD 2010, Barcelona, Spain, September 20-24, 2010, Proceedings, Part II, 6322, 499–514, Springer, 2010.
• Antti Airola, Tapio Pahikkala, Willem Waegeman, Bernard De Baets, Tapio Salakoski, A Comparison of AUC Estimators in Small-Sample Studies. In: Saso Geurts Pierre Rousu Juho Dzeroski (Ed.), Proceedings of the Third International Workshop on Machine Learning in Systems Biology (MLSB'09), 15-23, 2009.
• Jari Björne, Juho Heimonen, Filip Ginter, Antti Airola, Tapio Pahikkala, Tapio Salakoski, Extracting Complex Biological Events with Rich Graph-Based Feature Sets. In: Jun'ichi Tsujii (Ed.), Proceedings of the BioNLP 2009 Workshop Companion Volume for Shared Task, 10–18, Association for Computational Linguistics (ACL), 2009.