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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 (10):

• 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.
• 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.
• 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.
• 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.
• 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.
• 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.
• 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.

Articles in proceedings (23):

• Veronika Laippala, Jenna Kanerva, Sampo Pyysalo, Anna Missilä, Tapio Salakoski, Filip Ginter, Towards the Classification of the Finnish Internet Parsebank: Detecting Translations and Informality. In: 20th Nordic Conference of Computational Linguistics (Nodalida 2015), NEALT Proceedings Series 23, 2015.
• Jari Björne, Sofie van Landeghem, Sampo Pyysalo, Tomoko Ohta, Filip Ginter, Yves van de Peer, Sophia Ananiadou, Tapio Salakoski, PubMed-Scale Event Extraction for Post-Translational Modifications, Epigenetics and Protein Structural Relations. In: Kevin Bretonnel Cohen, Dina Demner-Fushman, Sophia Ananiadou, John Pestian (Eds.), Proceedings of the 2012 Workshop on Biomedical Natural Language Processing (BioNLP 2012), 82–90, Association for Computational Linguistics, 2012.
• Jari Björne, Filip Ginter, Sampo Pyysalo, Jun'ichi Tsujii, Tapio Salakoski, Scaling up Biomedical Event Extraction to the Entire PubMed. In: Proceedings of the 2010 Workshop on Biomedical Natural Language Processing, pp. 28-36, 2010.
• Jari Björne, Filip Ginter, Juho Heimonen, Sampo Pyysalo, Tapio Salakoski, Learning to Extract Biological Event and Relation Graphs. In: Proceedings of the 17th Nordic Conference of Computational Linguistics NODALIDA 2009, NEALT Proceedings Series Vol. 4 (2009), 18-25, Northern European Association for Language Technology (NEALT), 2009.
• Antti Airola, Sampo Pyysalo, Jari Björne, Tapio Pahikkala, Filip Ginter, Tapio Salakoski, A Graph Kernel for Protein-Protein Interaction Extraction. In: Sophia Ananiadou K. Bretonnel Cohen John Pestian Jun'ichi Tsujii Dina Demner-Fushman, Bonnie Webber (Eds.), Proceedings of ACL-08: HLT BioNLP 2008 Workshop: Current Trends in Biomedical Natural Language Processing, 1–9, The Association for Computational Linguistics, 2008.
• Jari Björne, Sampo Pyysalo, Filip Ginter, Tapio Salakoski, How Complex are Complex Protein-protein Interactions?. In: Proceedings of SMBM 2008, 2008.
• 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 . In: Dietrich Rebholz-Schuhmann Sampo Pyysalo Tapio Salakoski (Ed.), Proceedings of the Third International Symposium on Semantic Mining in Biomedicine (SMBM 2008), TUCS General Publication, 37-44, Turku Centre for Computer Science, Turku, Finland, 2008.
• Katri Haverinen, Filip Ginter, Sampo Pyysalo, Tapio Salakoski, Accurate Conversion of Dependency Parses: Targeting the Stanford Scheme. In: Tapio Salakoski, Rebholz-Schuhmann Dietrich, Sampo Pyysalo (Eds.), Proceedings of SMBM'08, 133-136, 2008.
• Juho Heimonen, Sampo Pyysalo, Filip Ginter, Tapio Salakoski, Complex-to-Pairwise Mapping of Biological Relationships Using a Semantic Network Representation. In: Tapio Salakoski, Dietrich Rebholz-Schuhmann, Sampo Pyysalo (Eds.), Proceedings of the Third International Symposium on Semantic Mining in Biomedicine (SMBM 2008), 45–52, Turku Centre for Computer Science (TUCS), 2008.
• Veronika Laippala, Filip Ginter, Sampo Pyysalo, Tapio Salakoski, Towards Resource-Efficient Construction of a Full Parser for Finnish Nursing Narratives. In: H. Back B. Salakoski T. Salanterä S. & Suominen H. Karsten (Ed.), Proceedings of Louhi '08 The First Conference on Text and Data Mining of Clinical Documents, TUCS General Publication , 34-53, Painosalama, 2008.
• Sampo Pyysalo, Rune Sætre, Jun'ichi Tsujii, Tapio Salakoski, Why Biomedical Relation Extraction Results are Incomparable and What to do about it. In: Dietrich Rebholz-Schuhmann Sampo Pyysalo Tapio Salakoski (Ed.), Proceedings of the Third International Symposium on Semantic Mining in Biomedicine (SMBM'08), TUCS General Publication, 149-152, Turku Centre for Computer Science, Turku, Finland, 2008.
• Hanna Suominen, Filip Ginter, Sampo Pyysalo, Antti Airola, Tapio Pahikkala, Sanna Salanterä, Tapio Salakoski, Machine Learning to Automate the Assignment of Diagnosis Codes to Free-text Radiology Reports: a Method Description. In: Dale Schuurmans Csaba Szepesvari Milos Hauskrecht (Ed.), Proceedings of the ICML/UAI/COLT 2008 Workshop on Machine Learning for Health-Care Applications; 2008 July 9: Helsinki, Finland, 2008.
• Hanna Suominen, Sampo Pyysalo, Filip Ginter, Tapio Salakoski, Automated Text Segmentation and Topic Labeling of Clinical Narratives. In: Barbro Back Tapio Salakoski Sanna Salanterä Hanna Suominen Helena Karsten (Ed.), Proceedings of the First Conference on Text and Data Mining of Clinical Documents (Louhi'08), TUCS General Publication, 99-103, 2008.
• Sampo Pyysalo, Filip Ginter, Veronika Laippala, Katri Haverinen, Juho Heimonen, Tapio Salakoski, On the Unification of Syntactic Annotations under the Stanford Dependency Scheme: A Case Study on BioInfer and GENIA. In: Proceedings of BioNLP 2007: Biological, Translational, and Clinical Language Processing, 25-32, ACL, 2007.
• Filip Ginter, Sampo Pyysalo, Jorma Boberg, Tapio Salakoski, Regular Approximation of Link Grammar. In: Advances in Natural Language Processing, 5th International Conference, FinTAL 2006 Turku, Finland, August 23-25, 2006 Proceedings, Lecture Notes in Computer Science 4139, 564–575, Springer Berlin / Heidelberg, 2006.
• Filip Ginter, Tapio Pahikkala, Sampo Pyysalo, Evgeni Tsivtsivadze, Jorma Boberg, Jouni Järvinen, Aleksandr Mylläri, Tapio Salakoski, Information Extraction from Biomedical Text: The BioText Project. In: Margit Langemets, Priit Penjam (Eds.), Proceedings of the Second Baltic Conference on Human Language Technologies (HLT 2005), 131-136, Institute of Cybernetics, Tallinn University of Technology and Institute of the Estonian Language, 2005.
• Filip Ginter, Sampo Pyysalo, Tapio Salakoski, Document Classification Using Semantic Networks with An Adaptive Similarity Measure. In: Galia Angelova, Kalina Bontcheva, Ruslan Mitkov, Nicolas Nicolov, Nikolai Nikolov (Eds.), Proceedings of the International Conference on Recent Advances in Natural Language Processing RANLP 05, Borovets, Bulgaria, 204-211, Incoma, Bulgaria, 2005.
• Tapio Pahikkala, Sampo Pyysalo, Jorma Boberg, Aleksandr Mylläri, Tapio Salakoski, Improving the Performance of Bayesian and Support Vector Classifiers in Word Sense Disambiguation using Positional Information. In: Ville Könönen Matti Pöllä Olli Simula Timo Honkela (Ed.), Proceedings of the International and Interdisciplinary Conference on Adaptive Knowledge Representation and Reasoning (AKRR'05), 90-97, Helsinki University of Technology, 2005.
• Tapio Pahikkala, Sampo Pyysalo, Filip Ginter, Jorma Boberg, Jouni Järvinen, Tapio Salakoski, Kernels Incorporating Word Positional Information in Natural Language Disambiguation Tasks. In: Ingrid Russell, Zdravko Markov (Eds.), Proceedings of the Eighteenth International Florida Artificial Intelligence Research Society Conference, 442-448, AAAI Press, 2005.
• Evgeni Tsivtsivadze, Tapio Pahikkala, Sampo Pyysalo, Jorma Boberg, Aleksandr Mylläri, Tapio Salakoski, Regularized Least-Squares for Parse Ranking. In: In proceedings of the 6th International Symposiumon Intelligent Data Analysis, Lecture Notes in Computer Science, 464–474, Springer-Verlag Berlin Heidelberg 2005, 2005.
• Filip Ginter, Tapio Pahikkala, Sampo Pyysalo, Jorma Boberg, Jouni Järvinen, Tapio Salakoski, Extracting Protein-Protein Interaction Sentences by Applying Rough Set Data Analysis. In: Roman Slowinski Jan Komorowski et al. Shusaku Tsumoto (Ed.), Proceedings of the Fourth International Conference on Rough Sets and Current Trends in Computing (RSCTC 2004), Lecture Notes in Artificial Intelligence , Vol. 3066, 780-785, 2004.
• Filip Ginter, Sampo Pyysalo, Jorma Boberg, Jouni Järvinen, Tapio Salakoski, Ontology-Based Feature Transformations: A Data-Driven Approach. In: Martínez-Barco P. Muñoz R. Noeda M. S. Vicedo J. L. (Ed.), Advances in Natural Language Processing. Proceedings of the 4th International Conference EsTAL 2004., LNCS, Lecture Notes in Artificial Intelligence 3230, 279-290, Springer, Heidelberg, 2004.
• Sampo Pyysalo, Filip Ginter, Tapio Pahikkala, Jeppe Koivula, Jorma Boberg, Jouni Järvinen, Tapio Salakoski, Analysis of Link Grammar on Biomedical Dependency Corpus Targeted at Protein-Protein Interactions. In: Patrick Ruch Adeline Nazarenko Nigel Collier (Ed.), Proceedings of the International Workshop on Natural Language Processing in Biomedicine and its Applications (JNLPBA), 15-21, 2004.

Chapters in edited books (2):

• Hanna Suominen, Sampo Pyysalo, Marketta Hiissa, Filip Ginter, Shuhua Liu, Dorina Marghescu, Tapio Pahikkala, Barbro Back, Helena Karsten, Tapio Salakoski, Performance Evaluation Measures for Text Mining. In: Min Song, Yi-Fang Wu (Eds.), Handbook of Research on Text and Web Mining Technologies, 2, 724–747, IGI Global, 2008.
• Filip Ginter, Sampo Pyysalo, Tapio Salakoski, Document Classification Using Semantic Networks with an Adaptive Similarity Measure. In: Kalina Bontcheva Galia Angelova Nicolas Nicolov, Ruslan Mitkov (Eds.), Recent Advances in Natural Language Processing IV: Selected papers from RANLP 2005, Current Issues in Linguistic Theory 292, 137–146, John Benjamins, The Netherlands, 2007.

TUCS General Series (1):

• Tapio Salakoski, Dietrich Rebholz-Schuhmann, Sampo Pyysalo (Eds.), Proceedings of the Third International Symposium on Semantic Mining in Biomedicine (SMBM 2008), TUCS General Publication, Turku Centre for Computer Science, 2008.

Ph.D. thesis (1):

• Sampo Pyysalo, A Dependency Parsing Approach to Biomedical Text Mining. TUCS Dissertations 105. Turku Centre for Computer Science, 2008.

Technical reports (2):

• Tapio Pahikkala, Sampo Pyysalo, Jorma Boberg, Jouni Järvinen, Tapio Salakoski, Matrix Representations, Linear Transformations, and Kernels for Disambiguation in Natural Language. TUCS Technical Reports 890, Turku Centre for Computer Science, 2008.
• Filip Ginter, Sampo Pyysalo, Jari Björne, Juho Heimonen, Tapio Salakoski, BioInfer Relationship Annotation Manual. TUCS Technical Reports 806, Turku Centre for Computer Science, 2007.