Sampo Pyysalo

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Filip GinterUniversity of TurkuVerified email at utu.fi
Tomoko OHTAtextimiVerified email at textimi.com
Junichi TsujiiArtificial Intelligence Research Center, AISTVerified email at aist.go.jp
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 PahikkalaProfessor, University of turku, FinlandVerified email at utu.fi
Lars Juhl JensenUniversity of CopenhagenVerified email at cpr.ku.dk
Katerina NastouPostdoctoral MSCA Fellow, Novo Nordisk Foundation Center of Protein Research, University ofVerified email at biol.uoa.gr
Jenna KanervaDepartment of Computing, University of TurkuVerified email at utu.fi
Jouni JärvinenUniversity lecturer, LUT UniversityVerified email at lut.fi
Makoto MiwaAssociate Professor, Toyota Technological InstituteVerified email at toyota-ti.ac.jp
Damian SzklarczykSIB Swiss Institute of Bioinformatics / University of ZurichVerified email at isb-sib.ch
Peer BorkDirector of EMBL HeidelbergVerified email at embl.de
Christian von MeringProfessor of Computational Biology, University of Zurich and Swiss Institute of BioinformaticsVerified email at imls.uzh.ch
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

Sampo Pyysalo

University of Turku

Verified email at utu.fi


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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	2644	2021
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	1397	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	1340	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	776	2009
Distributional semantics resources for biomedical text processing S Pyysalo, F Ginter, H Moen, T Salakoski, S Ananiadou Languages in Biology and Medicine, 2013	554*	2013
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, 1-24, 2007	532	2007
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	374	2016
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, 1-12, 2008	354	2008
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	332	2020
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	289	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	258	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	245	2013
Universal Dependencies 2.2 J Nivre, M Abrams, Ž Agić, L Ahrenberg, L Antonsen, MJ Aranzabe, ...	234	2018
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	220	2019
Attending to characters in neural sequence labeling models M Rei, GKO Crichton, S Pyysalo arXiv preprint arXiv:1611.04361, 2016	214	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	191	2017
Complex event extraction at PubMed scale J Björne, F Ginter, S Pyysalo, J Tsujii, T Salakoski Bioinformatics 26 (12), i382-i390, 2010	147	2010
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	145	2012
Intrinsic evaluation of word vectors fails to predict extrinsic performance B Chiu, A Korhonen, S Pyysalo Proceedings of the 1st workshop on evaluating vector-space representations …, 2016	130	2016
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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