Jari Björne
Jari Björne
Post-doctoral researcher, University of Turku, Finland
Verified email at utu.fi
Title
Cited by
Cited by
Year
A large-scale evaluation of computational protein function prediction
P Radivojac, WT Clark, TR Oron, AM Schnoes, T Wittkop, A Sokolov, ...
Nature methods 10 (3), 221-227, 2013
7792013
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
4782007
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
3372008
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
2612008
Extracting complex biological events with rich graph-based feature sets
J Björne, J Heimonen, F Ginter, A Airola, T Pahikkala, T Salakoski
Proceedings of the BioNLP 2009 Workshop Companion Volume for Shared Task, 10-18, 2009
2392009
Complex event extraction at PubMed scale
J Björne, F Ginter, S Pyysalo, J Tsujii, T Salakoski
Bioinformatics 26 (12), i382-i390, 2010
1402010
Generalizing biomedical event extraction
J Björne, T Salakoski
Proceedings of BioNLP Shared Task 2011 Workshop, 183-191, 2011
1322011
TEES 2.1: Automated annotation scheme learning in the BioNLP 2013 Shared Task
J Björne, T Salakoski
Proceedings of the BioNLP Shared Task 2013 Workshop, 16-25, 2013
1172013
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
1162013
A graph kernel for protein-protein interaction extraction
A Airola, S Pyysalo, J Björne, T Pahikkala, F Ginter, T Salakoski
Proceedings of the workshop on current trends in biomedical natural language …, 2008
1112008
The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens
N Zhou, Y Jiang, TR Bergquist, AJ Lee, BZ Kacsoh, AW Crocker, ...
Genome biology 20 (1), 1-23, 2019
932019
UTurku: Drug Named Entity Recognition and Drug-Drug Interaction Extraction Using SVM Classification and Domain Knowledge
J Björne, S Kaewphan, T Salakoski
Second Joint Conference on Lexical and Computational Semantics (*SEM …, 2013
882013
University of Turku in the BioNLP'11 shared task
J Björne, F Ginter, T Salakoski
BMC bioinformatics 13 (11), 1-13, 2012
712012
Extracting contextualized complex biological events with rich graph-based feature sets
J Björne, J Heimonen, F Ginter, A Airola, T Pahikkala, T Salakoski
Computational Intelligence 27 (4), 541-557, 2011
522011
Deep learning with minimal training data: TurkuNLP entry in the BioNLP shared task 2016
F Mehryary, J Björne, S Pyysalo, T Salakoski, F Ginter
Proceedings of the 4th BioNLP shared task workshop, 73-81, 2016
372016
Drug-Drug Interaction Extraction from Biomedical Texts with SVM and RLS Classifiers
J Björne, A Airola, T Pahikkala, T Salakoski
Proceedings of the 1st Challenge Task on Drug-Drug Interaction Extraction …, 2011
372011
Scaling up biomedical event extraction to the entire PubMed
J Björne, F Ginter, S Pyysalo, J Tsujii, T Salakoski
Proceedings of the 2010 workshop on biomedical natural language processing …, 2010
372010
Biomedical event extraction using convolutional neural networks and dependency parsing
J Björne, T Salakoski
Proceedings of the BioNLP 2018 workshop, 98-108, 2018
332018
Biomedical Event Extraction with Machine Learning
J Björne
TUCS Dissertations, 2014
272014
TEES 2.2: biomedical event extraction for diverse corpora
J Björne, T Salakoski
BMC bioinformatics 16 (16), 1-20, 2015
262015
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Articles 1–20