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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 (13):

• 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.
• 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.
• 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.
• 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.
• 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.
• 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.
• Filip Ginter, Jorma Boberg, Jouni Järvinen, Tapio Salakoski, New Techniques for Disambiguation in Natural Language and Their Application to Biological Text. Journal of Machine Learning Research 5, 605–621, 2004.
• 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 (39):

• 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.
• Suwisa Kaewphan, Kai Hakala, Filip Ginter, UTU: Disease Mention Recognition and Normalization with CRFs and Vector Space Representations. In: Preslav Nakov, Torsten Zesch (Eds.), Proceedings of the 8th International Workshop on Semantic Evaluation (SemEval 2014) ,, 807–811, Association for Computational Linguistics, 2014.
• Jenna Kanerva, Filip Ginter, Post-hoc Manipulations of Vector Space Models with Application to Semantic Role Labeling . In: Alexandre Allauzen, Raffaella Bernardi, Edward Grefenstette, Hugo Larochelle, Christopher Manning, Scott Wen-tau Yih (Eds.), Proceedings of the 2nd Workshop on Continuous Vector Space Models and their Compositionality (CVSC) , 1–10, Association for Computational Linguistics, 2014.
• Jenna Kanerva, Juhani Luotolahti, Filip Ginter, Turku: Broad-Coverage Semantic Parsing with Rich Features . In: Preslav Nakov, Torsten Zesch (Eds.), Proceedings of the 8th International Workshop on Semantic Evaluation (SemEval 2014), 678–682, Association for Computational Linguistics and Dublin City University, 2014.
• Jenna Kanerva, Juhani Luotolahti, Veronika Laippala, Filip Ginter, Syntactic N-gram Collection from a Large-Scale Corpus of Internet Finnish. In: Andrius Utka, Gintarė Grigonytė, Jurgita Kapočiūtė-Dzikienė, Jurgita Vaičenonienė (Eds.), Proceedings of the Sixth International Conference Baltic HLT 2014, 184–191, IOS Press, 2014.
• Farrokh Mehryary, Suwisa Kaewphan, Kai Hakala, Filip Ginter, Eliminating Incorrect Events from Large‐Scale Event Networks by Trigger Word Clustering and Pruning. In: Olivier Bodenreider, Fabio Rinaldi, José Luis Oliveira (Eds.), Proceedings of the 6th International Symposium on Semantic Mining in Biomedicine (SMBM 2014), 75–79, University of Aveiro, 2014.
• Kai Hakala, Farrokh Mehryary, Suwisa Kaewphan, Filip Ginter, Hypothesis Generation in Large-Scale Event Networks. In: Fabio Rinaldi, Kim Jin-Dong (Eds.), Proceedings of the 5th International Symposium on Language in Biology and Medicine (LBM 2013), 19–27, Database Center for Life Science, 2013.
• Katri Haverinen, Veronika Laippala, Samuel Kohonen, Anna Missilä, Jenna Nyblom, Stina Ojala, Timo Viljanen, Tapio Salakoski, Filip Ginter, Towards a Dependency-based PropBank of General Finnish. In: Stephan Oepen, Kristin Hagen, Janne Bondi Johannesse (Eds.), Proceedings of the 19th Nordic Conference of Computational Linguistics (NODALIDA 2013), NEALT Proceedings Series 16, 41–57, Linköping University Electronic Press, 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.
• Sofie van Landeghem, Suwisa Kaewphan, Filip Ginter, Yves van de Peer, Evaluating Large-Scale Text Mining Applications Beyond the Traditional Numeric Performance Measures. In: Claire Nédellec, Robert Bossy, Jin-Dong Kim, Jung-jae Kim, Tomoko Ohta, Sampo Pyysalo, Pierre Zweigenbaum (Eds.), Proceedings of the 2013 Workshop on Biomedical Natural Language Processing (BioNLP'13), 63–71, Association for Computational Linguistics (ACL), 2013.
• 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.
• Kai Hakala, Sofie van Landeghem, Suwisa Kaewphan, Tapio Salakoski, Yves van de Peer, Filip Ginter, CyEVEX: Literature-Scale Network Integration and Visualization Through Cytoscape. In: Sophia Ananiadou, Sampo Pyysalo, Dietrich Rebholz-Schuhmann, Fabio Rinaldi, Tapio Salakoski (Eds.), Proceedings of the 5th International Symposium on Semantic Mining in Biomedicine, 91–96, ACM Press, 2012.
• Suwisa Kaewphan, Sanna Kreula, Sofie Van Landeghem, Yves Van de Peer, Patrik R. Jones, Filip Ginter, Integrating Large-Scale Text Mining and Co-Expression Networks: Targeting NADP(H) Metabolism in E. coli with Event Extraction. In: Sophia Ananiadou, Kevin Cohen, Dina Demner-Fushman, Paul Thompson (Eds.), Third Workshop on Building and Evaluating Resources for Biomedical Text Mining, 8–15, European Language Resources Association (ELRA), 2012.
• Katri Haverinen, Filip Ginter, Veronika Laippala, Samuel Kohonen, Timo Viljanen, Jenna Nyblom, Tapio Salakoski, A Dependency-Based Analysis of Treebank Annotation Errors. In: Kim Gerdes, Eva Hajicova, Leo Wanner (Eds.), Proceedings of International Conference on Dependency Linguistics, 115-124, N/A, 2011.
• Sofie Van Landeghem, Filip Ginter, Yves Van de Peer, Tapio Salakoski, EVEX: A PubMed-Scale Resource for Homology-Based Generalization of Text Mining Predictions. In: Proceedings of BioNLP'11 Workshop, 28-37, ACL, 2011.
• 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.
• Katri Haverinen, Filip Ginter, Timo Viljanen, Veronika Laippala, Tapio Salakoski, Dependency-Based PropBanking of Clinical Finnish. In: Proceedings of the Fourth Linguistic Annotation Workshop, 137-141, ACL, 2010.
• Katri Haverinen, Timo Viljanen, Veronika Laippala, Samuel Kohonen, Filip Ginter, Tapio Salakoski, Treebanking Finnish. In: Markus Dickinson, Kaili Müürisep, Marco Passarotti (Eds.), Proceedings of the Ninth International Workshop on Treebanks and Linguistic Theories, 79-90, Northern European Association fo Language Technology (NEALT), 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.
• 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.
• Katri Haverinen, Filip Ginter, Veronika Laippala, Tapio Salakoski, Parsing Clinical Finnish: Experiments with Rule-Based and Statistical Dependency Parsers. In: Proceedings of NODALIDA 2009, 65-72, NEALT, 2009.
• Katri Haverinen, Filip Ginter, Veronika Laippala, Timo Viljanen, Tapio Salakoski, Dependency Annotation of Wikipedia: First Steps Towards a Finnish Treebank. In: Marco Passarotti, Adam Przepiórkowski, Sabina Raynaud, Frank van Eynde (Eds.), Proceedings of the eighth international workshop on Treebanks and Linguistic Theories, 95-105, EduCatt, 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.
• 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, Aleksandr Mylläri, Tapio Salakoski, A Probabilistic Search for the Best Solution Among Partially Completed Candidates. In: Proceedings of the Workshop on Computationally Hard Problems and Joint Inference in Speech and Language Processing (HLT/NAACL'06), New York City, New York, USA, 33-40, Association for Computational Linguistics (ACL), 2006.
• 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, 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.