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Sampo Pyysalo
2010 – today
- 2013
[j22]Makoto Miwa, Tomoko Ohta, Rafal Rak, Andrew Rowley, Douglas B. Kell, Sampo Pyysalo, Sophia Ananiadou: A method for integrating and ranking the evidence for biochemical pathways by mining reactions from text. Bioinformatics 29(13): 44-52 (2013)- [j21]Claudiu Mihaila, Tomoko Ohta, Sampo Pyysalo, Sophia Ananiadou: BioCause: Annotating and analysing causality in the biomedical domain. BMC Bioinformatics 14: 2 (2013)
- [j20]Makoto Miwa, Sampo Pyysalo, Tomoko Ohta, Sophia Ananiadou: Wide coverage biomedical event extraction using multiple partially overlapping corpora. BMC Bioinformatics 14: 175 (2013)
- 2012
- [j19]Sampo Pyysalo, Tomoko Ohta, Makoto Miwa, Han-Cheol Cho, Junichi Tsujii, Sophia Ananiadou: Event extraction across multiple levels of biological organization. Bioinformatics 28(18): 575-581 (2012)
- [j18]Sampo Pyysalo, Tomoko Ohta, Rafal Rak, Dan Sullivan, Chunhong Mao, Chunxia Wang, Bruno W. S. Sobral, Jun'ichi Tsujii, Sophia Ananiadou: Overview of the ID, EPI and REL tasks of BioNLP Shared Task 2011. BMC Bioinformatics 13(S-11): S2 (2012)
- [c10]Pontus Stenetorp, Sampo Pyysalo, Goran Topic, Tomoko Ohta, Sophia Ananiadou, Jun'ichi Tsujii: brat: a Web-based Tool for NLP-Assisted Text Annotation. EACL 2012: 102-107
- 2011
- [j17]Yoshinobu Kano, Jari Björne, Filip Ginter, Tapio Salakoski, Ekaterina Buyko, Udo Hahn, K. Bretonnel Cohen, Karin Verspoor, Christophe Roeder, Lawrence E. Hunter, Halil Kilicoglu, Sabine Bergler, Sofie Van Landeghem, Thomas Van Parys, Yves Van de Peer, Makoto Miwa, Sophia Ananiadou, Mariana L. Neves, Alberto D. Pascual-Montano, Arzucan Özgür, Dragomir R. Radev, Sebastian Riedel, Rune Sætre, Hong-Woo Chun, Jin-Dong Kim, Sampo Pyysalo, Tomoko Ohta, Jun'ichi Tsujii: U-Compare bio-event meta-service: compatible BioNLP event extraction services. BMC Bioinformatics 12: 481 (2011)
- [j16]Jin-Dong Kim, Tomoko Ohta, Sampo Pyysalo, Yoshinobu Kano, Jun'ichi Tsujii: Extracting Bio-molecular Events from literature - the BioNLP'09 Shared Task. Computational Intelligence 27(4): 513-540 (2011)
- 2010
- [j15]Jari Björne, Filip Ginter, Sampo Pyysalo, Jun'ichi Tsujii, Tapio Salakoski: Complex event extraction at PubMed scale. Bioinformatics [ISMB] 26(12): 382-390 (2010)
- [j14]Filip Ginter, Jari Björne, Sampo Pyysalo: Event extraction on PubMed scale. BMC Bioinformatics 11(S-5): O2 (2010)
- [j13]Sampo Pyysalo: Entities, relations, events: representing biomolecular semantics. BMC Bioinformatics 11(S-5): O6 (2010)
- [j12]Tomoko Ohta, Takuya Matsuzaki, Naoaki Okazaki, Makoto Miwa, Rune Sætre, Sampo Pyysalo, Jun'ichi Tsujii: Medie and Info-pubmed: 2010 update. BMC Bioinformatics 11(S-5): P7 (2010)
- [j11]Yue Wang, Jin-Dong Kim, Rune Sætre, Sampo Pyysalo, Tomoko Ohta, Jun'ichi Tsujii: Improving the Inter-Corpora Compatibility for protein Annotations. J. Bioinformatics and Computational Biology 8(5): 901-916 (2010)
- [j10]Tomoko Ohta, Sampo Pyysalo, Jin-Dong Kim, Jun'ichi Tsujii: A Re-Evaluation of Biomedical Named Entity-Term Relations. J. Bioinformatics and Computational Biology 8(5): 917-928 (2010)
- [c9]Makoto Miwa, Sampo Pyysalo, Tadayoshi Hara, Jun'ichi Tsujii: Evaluating Dependency Representations for Event Extraction. COLING 2010: 779-787
- [c8]Robert Hoehndorf, Axel-Cyrille Ngonga Ngomo, Sampo Pyysalo, Tomoko Ohta, Anika Oellrich, Dietrich Rebholz-Schuhmann: Applying ontology design patterns to the implementation of relations in GENIA. Semantic Mining in Biomedicine 2010
- [c7]Tomoko Ohta, Sampo Pyysalo, Makoto Miwa, Jun'ichi Tsujii: Event extraction for DNA methylation. Semantic Mining in Biomedicine 2010
- [c6]Sampo Pyysalo, Tomoko Ohta, Jun'ichi Tsujii: An Analysis of gene/protein associations at PubMed scale. Semantic Mining in Biomedicine 2010
- [e2]Nigel Collier, Udo Hahn, Dietrich Rebholz-Schuhmann, Fabio Rinaldi, Sampo Pyysalo (Eds.): Proceedings of the Fourth International Symposium for Semantic Mining in Biomedicine, Cambridge, United Kingdom, October, 2010. CEUR Workshop Proceedings 714, CEUR-WS.org 2010
2000 – 2009
- 2009
- [j9]Yue Wang, Jin-Dong Kim, Rune Sætre, Sampo Pyysalo, Jun'ichi Tsujii: Investigating heterogeneous protein annotations toward cross-corpora utilization. BMC Bioinformatics 10: 403 (2009)
- [j8]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. I. J. Medical Informatics 78(12): 1-6 (2009)
- [j7]Veronika Laippala, Filip Ginter, Sampo Pyysalo, Tapio Salakoski: Towards automated processing of clinical Finnish: Sublanguage analysis and a rule-based parser. I. J. Medical Informatics 78(12): 7-12 (2009)
- [j6]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)
- 2008
- [j5]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(S-11) (2008)
- [j4]Sampo Pyysalo, Antti Airola, Juho Heimonen, Jari Björne, Filip Ginter, Tapio Salakoski: Comparative analysis of five protein-protein interaction corpora. BMC Bioinformatics 9(S-3) (2008)
- 2007
- [j3]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 (2007)
- 2006
- [j2]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(S-3) (2006)
- [j1]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. I. J. Medical Informatics 75(6): 430-442 (2006)
- [c5]Filip Ginter, Sampo Pyysalo, Jorma Boberg, Tapio Salakoski: Regular Approximation of Link Grammar. FinTAL 2006: 564-575
- [e1]Tapio Salakoski, Filip Ginter, Sampo Pyysalo, Tapio Pahikkala (Eds.): Advances in Natural Language Processing, 5th International Conference on NLP, FinTAL 2006, Turku, Finland, August 23-25, 2006, Proceedings. Lecture Notes in Computer Science 4139, Springer 2006, ISBN 3-540-37334-9
- [i1]Sampo Pyysalo, Tapio Salakoski, Sophie Aubin, Adeline Nazarenko: Lexical Adaptation of Link Grammar to the Biomedical Sublanguage: a Comparative Evaluation of Three Approaches. CoRR abs/cs/0606119 (2006)
- 2005
- [c4]Tapio Pahikkala, Sampo Pyysalo, Filip Ginter, Jorma Boberg, Jouni Järvinen, Tapio Salakoski: Kernels Incorporating Word Positional Information in Natural Language Disambiguation Tasks. FLAIRS Conference 2005: 442-448
- [c3]Evgeni Tsivtsivadze, Tapio Pahikkala, Sampo Pyysalo, Jorma Boberg, Aleksandr Mylläri, Tapio Salakoski: Regularized Least-Squares for Parse Ranking. IDA 2005: 464-474
- 2004
- [c2]Filip Ginter, Tapio Pahikkala, Sampo Pyysalo, Jorma Boberg, Jouni Järvinen, Tapio Salakoski: Extracting Protein-Protein Interaction Sentences by Applying Rough Set Data Analysis. Rough Sets and Current Trends in Computing 2004: 780-785
- [c1]Filip Ginter, Sampo Pyysalo, Jorma Boberg, Jouni Järvinen, Tapio Salakoski: Ontology-Based Feature Transformations: A Data-Driven Approach. EsTAL 2004: 280-291
Coauthor Index
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last updated on 2013-10-02 11:13 CEST by the dblp team