Sampo Pyysalo

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Filip GinterUniversity of TurkuVerified email at utu.fi
Junichi TsujiiArtificial Intelligence Research Center, AISTVerified email at aist.go.jp
Tomoko OHTAtextimiVerified email at textimi.com
Tapio SalakoskiProfessor of Computer Science, University of TurkuVerified email at utu.fi
Sophia AnaniadouProfessor, Computer Science, Manchester University, National Centre for Text MiningVerified email at manchester.ac.uk
Jin-Dong KimAssociate Professor of Database Center for Life ScienceVerified email at dbcls.rois.ac.jp
Jari BjörnePost-doctoral researcher, University of Turku, FinlandVerified email at utu.fi
Anna KorhonenProfessor, Computer Science and Linguistics, University of CambridgeVerified email at cam.ac.uk
Tapio PahikkalaAssociate Professor, University of turku, FinlandVerified email at utu.fi
Jouni JärvinenAdjunct professor, Department of Mathematics and Statistics, University of Turku, FinlandVerified email at utu.fi
Jenna KanervaDepartment of Computing, University of TurkuVerified email at utu.fi
Makoto MiwaAssociate Professor, Toyota Technological InstituteVerified email at toyota-ti.ac.jp
Billy ChiuPhD student at University of CambridgeVerified email at cam.ac.uk
Gamal CrichtonUniversity of CambridgeVerified email at cam.ac.uk
Yoshinobu KanoFaculty of Informatics, Shizuoka UniversityVerified email at inf.shizuoka.ac.jp
Antti AirolaAssistant Professor, University of TurkuVerified email at utu.fi
Jan HajicProfessor of Computational Linguistics, Charles University, Prague, Czech RepublicVerified email at ufal.mff.cuni.cz
Joakim NivreProfessor of Computational Linguistics, Uppsala University; Senior Researcher, RISEVerified email at lingfil.uu.se
Marie-Catherine de MarneffeAssociate Professor, Linguistics, The Ohio State UniversityVerified email at ling.ohio-state.edu
Daniel ZemanInstitute of Formal and Applied Linguistics, Faculty of Mathematics and Physics, Charles UniversityVerified email at ufal.mff.cuni.cz

Sampo Pyysalo

University of Turku

Verified email at utu.fi


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Universal dependencies v1: A multilingual treebank collection J Nivre, MC De Marneffe, F Ginter, Y Goldberg, J Hajic, CD Manning, ... Proceedings of the Tenth International Conference on Language Resources and …, 2016	1226	2016
BRAT: a web-based tool for NLP-assisted text annotation P Stenetorp, S Pyysalo, G Topić, T Ohta, S Ananiadou, J Tsujii Proceedings of the Demonstrations at the 13th Conference of the European …, 2012	1141	2012
Overview of BioNLP’09 shared task on event extraction JD Kim, T Ohta, S Pyysalo, Y Kano, J Tsujii Proceedings of the BioNLP 2009 workshop companion volume for shared task, 1-9, 2009	749	2009
The STRING database in 2021: customizable protein–protein networks, and functional characterization of user-uploaded gene/measurement sets D Szklarczyk, AL Gable, KC Nastou, D Lyon, R Kirsch, S Pyysalo, ... Nucleic acids research 49 (D1), D605-D612, 2021	682	2021
BioInfer: a corpus for information extraction in the biomedical domain S Pyysalo, F Ginter, J Heimonen, J Björne, J Boberg, J Järvinen, ... BMC bioinformatics 8 (1), 1-24, 2007	510	2007
Distributional semantics resources for biomedical text processing S Pyysalo, F Ginter, H Moen, T Salakoski, S Ananiadou Languages in Biology and Medicine, 2013	501*	2013
CoNLL 2017 shared task: Multilingual parsing from raw text to universal dependencies D Zeman, M Popel, M Straka, J Hajic, J Nivre, F Ginter, J Luotolahti, ... CoNLL 2017 Shared Task: Multilingual Parsing from Raw Text to Universal …, 2017	468	2017
All-paths graph kernel for protein-protein interaction extraction with evaluation of cross-corpus learning A Airola, S Pyysalo, J Björne, T Pahikkala, F Ginter, T Salakoski BMC bioinformatics 9 (11), 1-12, 2008	349	2008
How to train good word embeddings for biomedical NLP B Chiu, G Crichton, A Korhonen, S Pyysalo Proceedings of the 15th workshop on biomedical natural language processing …, 2016	331	2016
Comparative analysis of five protein-protein interaction corpora S Pyysalo, A Airola, J Heimonen, J Björne, F Ginter, T Salakoski BMC bioinformatics 9 (3), 1-11, 2008	279	2008
Event extraction for systems biology by text mining the literature S Ananiadou, S Pyysalo, J Tsujii, DB Kell Trends in biotechnology 28 (7), 381-390, 2010	252	2010
Overview of BioNLP shared task 2013 C Nédellec, R Bossy, JD Kim, JJ Kim, T Ohta, S Pyysalo, P Zweigenbaum Proceedings of the BioNLP shared task 2013 workshop, 1-7, 2013	225	2013
Universal Dependencies 1.2 J Nivre, Ž Agić, MJ Aranzabe, M Asahara, A Atutxa, M Ballesteros, J Bauer, ... Universal Dependencies Consortium, 2015	221	2015
Universal Dependencies v2: An evergrowing multilingual treebank collection J Nivre, MC de Marneffe, F Ginter, J Hajič, CD Manning, S Pyysalo, ... arXiv preprint arXiv:2004.10643, 2020	202	2020
Attending to characters in neural sequence labeling models M Rei, GKO Crichton, S Pyysalo arXiv preprint arXiv:1611.04361, 2016	187	2016
A neural network multi-task learning approach to biomedical named entity recognition G Crichton, S Pyysalo, B Chiu, A Korhonen BMC bioinformatics 18 (1), 1-14, 2017	158	2017
Complex event extraction at PubMed scale J Björne, F Ginter, S Pyysalo, J Tsujii, T Salakoski Bioinformatics 26 (12), i382-i390, 2010	144	2010
Multilingual is not enough: BERT for Finnish A Virtanen, J Kanerva, R Ilo, J Luoma, J Luotolahti, T Salakoski, F Ginter, ... arXiv preprint arXiv:1912.07076, 2019	140	2019
Event extraction across multiple levels of biological organization S Pyysalo, T Ohta, M Miwa, HC Cho, J Tsujii, S Ananiadou Bioinformatics 28 (18), i575-i581, 2012	129	2012
Large-scale event extraction from literature with multi-level gene normalization S Van Landeghem, J Björne, CH Wei, K Hakala, S Pyysalo, S Ananiadou, ... PloS one 8 (4), e55814, 2013	122	2013

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