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Sampo Pyysalo
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
59872021
The STRING database in 2023: protein–protein association networks and functional enrichment analyses for any sequenced genome of interest
D Szklarczyk, R Kirsch, M Koutrouli, K Nastou, F Mehryary, R Hachilif, ...
Nucleic acids research 51 (D1), D638-D646, 2023
21552023
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
16762016
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
16242012
Bloom: A 176b-parameter open-access multilingual language model
T Le Scao, A Fan, C Akiki, E Pavlick, S Ilić, D Hesslow, R Castagné, ...
14822023
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
8242009
Distributional semantics resources for biomedical text processing
S Pyysalo, F Ginter, H Moen, T Salakoski, S Ananiadou
Languages in Biology and Medicine, 2013
613*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
5862007
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
5602020
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
4322016
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
3852008
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
3332019
Comparative analysis of five protein-protein interaction corpora
S Pyysalo, A Airola, J Heimonen, J Björne, F Ginter, T Salakoski
BMC bioinformatics 9, 1-11, 2008
3072008
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
2892013
A neural network multi-task learning approach to biomedical named entity recognition
G Crichton, S Pyysalo, B Chiu, A Korhonen
BMC bioinformatics 18, 1-14, 2017
2672017
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
2662010
Attending to characters in neural sequence labeling models
M Rei, GKO Crichton, S Pyysalo
arXiv preprint arXiv:1611.04361, 2016
2602016
Universal Dependencies 1.2
J Nivre, Ž Agić, MJ Aranzabe, M Asahara, A Atutxa, M Ballesteros, J Bauer, ...
Universal Dependencies Consortium, 2015
2502015
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
1802012
Complex event extraction at PubMed scale
J Björne, F Ginter, S Pyysalo, J Tsujii, T Salakoski
Bioinformatics 26 (12), i382-i390, 2010
1592010
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Articles 1–20