Pyysalo, S. - NaCTeM Publications - Aigaion 2.0

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First name(s):	S.
Last name(s):	Pyysalo

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Pyysalo, S., Ohta, T., Rak, R., Rowley, A., Chun, H.-W., Jung, S. -J., Choi, S. -P., Tsujii, J. and Ananiadou, S., Overview of the Cancer Genetics and Pathway Curation tasks of BioNLP Shared Task 2013 (2015), in: BMC BioInformatics, 16(Suppl 10):Suppl 10(S2)

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Stenetorp, P., Pyysalo, S., Ananiadou, S. and Tsujii, J., Generalising semantic category disambiguation with large lexical resources for fun and profit (2014), in: Journal of Biomedical Semantics, 5(26)

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Pyysalo, S., Ginter, F., Moen, H., Salakoski, T. and Ananiadou, S., Distributional Semantics Resources for Biomedical Text Processing, in: Proceedings of LBM 2013, pages 39-44, 2013

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Pyysalo, S. and Ananiadou, S., Anatomical Entity Mention Recognition at Literature Scale (2014), in: Bioinformatics, 30:6(868-875)

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NÃ©dellec, C., Bossy, R., Kim, J.-D., Kim, J-J., Ohta, T., Pyysalo, S. and Zweigenbaum, P., Overview of BioNLP Shared Task 2013, in: Proceedings of the BioNLP Shared Task 2013 Workshop, pages 1--7, Association for Computational Linguistics, 2013

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Ohta, T., Pyysalo, S., Rak, R., Rowley, A., Chun, H.-W., Jung, S. -J., Choi, S. -P. and Ananiadou, S., Overview of the Pathway Curation (PC) task of BioNLP Shared Task 2013, in: Proceedings of the BioNLP Shared Task 2013 Workshop, Sofia, Bulgaria, pages 67-75, Association for Computational Linguistics, 2013

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Pyysalo, S., Ohta, T. and Ananiadou, S., Overview of the Cancer Genetics (CG) task of BioNLP Shared Task 2013, in: Proceedings of the BioNLP Shared Task 2013 Workshop, Sofia, Bulgaria, pages 58-66, Association for Computational Linguistics, 2013

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Miwa, M., Ohta, T., Rak, R., Rowley, A., Kell, D. B., Pyysalo, S. and Ananiadou, S., A method for integrating and ranking the evidence for biochemical pathways by mining reactions from text (2013), in: Bioinformatics, 29:13(i44-i52)

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Miwa, M., Pyysalo, S., Ohta, T. and Ananiadou, S., Wide coverage biomedical event extraction using multiple partially overlapping corpora (2013), in: BMC Bioinformatics, 14:175

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Van Landeghem, S., BjÃ¶rne, J., Wei, C-. H, Hakala, K., Pyysalo, S., Ananiadou, S., Kao, H. -Y., Lu, Z., Salakoski, T., Van de Peer, Y. and Ginter, F., Large-scale event extraction from literature with multi-level gene normalization (2013), in: PLOS ONE, 8:4(e55814)

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MihÄƒilÄƒ, C., Ohta, T., Pyysalo, S. and Ananiadou, S., BioCause: Annotating and Analysing Causality in the Biomedical Domain (2013), in: BMC Bioinformatics, 14:1(2)

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Pyysalo, S., Ohta, T., Miwa, M., Cho, H. -C., Tsujii, J. and Ananiadou, S., Event extraction across multiple levels of biological organization (2012), in: Bioinformatics, 28:18(i575-i581)

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Selected articles from the BioNLP Shared Task 2011, 2012

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Stenetorp, P., Pyysalo, S., Ohta, T., Ananiadou, S. and Tsujii, J., Bridging the Gap Between Scope-based and Event-based Negation/Speculation Annotations: A Bridge Not Too Far, in: Proceedings of ExProM 2012, pages 47-56, 2012

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Ohta, T., Pyysalo, S., Tsujii, J. and Ananiadou, S., Open-domain Anatomical Entity Mention Detection, in: Proceedings of the ACL Workshop on Detecting Stucture in Scholarly Discourse (DSSD), pages 27-36, 2012

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Pyysalo, S., Stenetorp, P., Ohta, T., Kim, J.-D. and Ananiadou, S., New Resources and Perspectives for Biomedical Event Extraction, in: Proceedings of BioNLP 2012, pages 100-108, 2012

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BjÃ¶rne, J., Van Landeghem, S., Pyysalo, S., Ohta, T., Ginter, F., Van de Peer, Y., Ananiadou, S. and Salakoski, T., PubMed-Scale Event Extraction for Post-Translational Modifications, Epigenetics and Protein Structural Relations, in: Proceedings of BioNLP 2012, pages 82-90, 2012

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Pyysalo, S., Ohta, T., Rak, R., Sullivan, D., Mao, C., Wang, C., Sobral, B., Tsujii, J. and Ananiadou, S., Overview of the ID, EPI and REL tasks of BioNLP Shared Task 2011 (2012), in: BMC Bioinformatics, 13:Suppl. 11(S2)

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Stenetorp, P., Pyysalo, S., TopiÄ‡, G., Ohta, T., Ananiadou, S. and Tsujii, J., brat: a Web-based Tool for NLP-Assisted Text Annotation, in: Proceedings of the Demonstrations at the 13th Conference of the European Chapter of the Association for Computational Linguistics, Avignon, France, pages 102-107, Association for Computational Linguistics, 2012

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Kano, Y., BjÃ¶rne, J., Ginter, F., Salakoski, T., Buyko, E., Hahn, U., Cohen, K. B., Verspoor, K., Roeder, C., Hunter, L., Kilicoglu, H., Bergler, S., Van Landeghem, S., Van Parys, T., Van de Peer, Y., Miwa, M., Ananiadou, S., Neves, M., Pascual-Montano, A., Ozgur, A., Radev, D. R., Riedel, S., SÃ¦tre, R., Chun, H.-W., Kim, J.-D., Pyysalo, S., Ohta, T. and Tsujii, J., U-Compare bio-event meta-service: compatible BioNLP event extraction services (2011), in: BMC Bioinformatics, 12(481)

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Kim, J.-D., Ohta, T., Pyysalo, S., Kano, Y. and Tsujii, J., Extracting Bio-Molecular Events From Literatureâ€”The BioNLPâ€™09 Shared Task (2011), in: Computational Intelligence, 27:4(513-540)

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Stenetorp, P., Pyysalo, S., Ananiadou, S. and Tsujii, J., Almost Total Recall: Semantic Category Disambiguation Using Large Lexical Resources and Approximate String Matching (2011), in: Proceedings of the Fourth International Symposium on Languages in Biology and Medicine (LBM 2011)

Ohta, T., Pyysalo, S., Ananiadou, S. and Tsujii, J., Pathway Curation Support as an Information Extraction Task, in: Proceedings of the Fourth International Symposium on Languages in Biology and Medicine (LBM 2011), 2011

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Pyysalo, S., Ohta, T. and Ananiadou, S., Anatomical Entity Recognition with Open Biomedical Ontologies, in: Proceedings of the Fourth International Symposium on Languages in Biology and Medicine (LBM 2011), 2011

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Pyysalo, S., SÃ¦tre, R., Tsujii, J. and Salakoski, T., Why Biomedical Relation Extraction Results are Incomparable and What to do about it, in: Proceedings of the Third International Symposium on Semantic Mining in Biomedicine (SMBM 2008), pages 149--152, 2008

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