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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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Articles in journals (4):

• Olli Sjöblom, Laura-Maria Murtola, Juho Heimonen, Lotta Kauhanen, Veronika Laippala, Heljä Lundgren-Laine, Tapio Salakoski, Sanna Salanterä, Using Cluster Analysis to Identify Weak Signals of Lethal Trends in Aviation and Healthcare Documentation. International Journal of Networking and Virtual Organisations 13, 66–80, 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.
• 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.

Articles in proceedings (11):

• Kristiina Heikkilä, Juho Heimonen, Tapio Salakoski, Sanna Salanterä, Sydänleikattujen potilaiden kivun kirjaaminen. In: Mira Palonen, Marja Kaunonen, Päivi Åstedt-Kurki (Eds.), Perhe, yhteiskunta ja hoitotiede, 45–54, Hoitotieteiden tutkimusseura HTTS ry, 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.
• Lotta Kauhanen, Laura-Maria Murtola, Juho Heimonen, Tuija Leskinen, Kari Kalliokoski, Elina Raivo, Tapio Salakoski, Sanna Salanterä, Documentation of the Clinical Phase of the Cardiac Rehabilitation Process in a Finnish University Hospital District. In: Kaija Saranto, Maaret Castrén, Tiina Kuusela, Sami Hyrynsalmi, Stina Ojala (Eds.), Safe and Secure Cities, Communications in Computer and Information Science 450, 57–67, Springer International Publishing, 2014.
• 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.
• Juho Heimonen, Tapio Salakoski, Sanna Salanterä, An Ontology to Improve Accessibility and Quality of Patient Instructions. In: Pamela Forner, Jussi Karlgren, Christa Womser-Hacker (Eds.), Proceedings of CLEF 2012 Evaluation Labs and Workshop, 137, Fondazione Bruno Kessler Press, 2012.
• Olli Sjöblom, Juho Heimonen, Lotta Kauhanen, Veronika Laippala, Heljä Lundgrén-Laine, Laura-Maria Murtola, Tapio Salakoski, Sanna Salanterä, Avoiding Hazards - What Can Health Care Learn from Aviation?. In: Kristina Eriksson-Backa, Annika Luoma, Erica Krook (Eds.), Exploring the Abyss of Inequalities - Proceedings of the 4th International Conference on Well-Being in the Information Society, Communications in Computer and Information Science 313, 119–127, Springer, 2012.
• Juho Heimonen, Jari Björne, Tapio Salakoski, Reconstruction of Semantic Relationships from Their Projections in Biomolecular Domain. In: Proceedings of the 2010 Workshop on Biomedical Natural Language Processing, 108--116, Association for Computational Linguistics, 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.
• 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.
• 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.

Ph.D. thesis (1):

• Juho Heimonen, Knowledge Representation and Text Mining in Biomedical, Healthcare, and Political Domains. TUCS Dissertations 246. 2019.

Technical reports (1):

• Filip Ginter, Sampo Pyysalo, Jari Björne, Juho Heimonen, Tapio Salakoski, BioInfer Relationship Annotation Manual. TUCS Technical Reports 806, Turku Centre for Computer Science, 2007.