Publications

Jari Björne edited this page May 16, 2013 · 8 revisions

This page lists the scientific publications describing the development and use of TEES. If you have made an article that uses TEES, feel free to add it here. The primary articles describing how TEES works are marked with a (!) sign.

2013

  • Sofie Van Landeghem, Jari Björne, Chih-Hsuan Wei, Kai Hakala, Sampo Pyysalo, Sophia Ananiadou, Hung-Yu Kao, Zhiyong Lu, Tapio Salakoski, Yves Van de Peer and Filip Ginter. Large-scale event extraction from literature with multi-level gene normalization. PloS one, volume 8, issue 4, 2013. HTML

2012

  • Jari Björne, Sofie Van Landeghem, Sampo Pyysalo, Tomoko Ohta, Filip Ginter, Yves Van de Peer, Sofia Ananiadou and Tapio Salakoski, PubMed-Scale Event Extraction for Post-Translational Modifications, Epigenetics and Protein Structural Relations. Proceedings of BioNLP 2012, pages 82-90, 2012. PDF
  • Jari Björne, Filip Ginter and Tapio Salakoski, University of Turku in the BioNLP'11 Shared Task. BMC Bioinformatics 2012, 13(Suppl 11):S4 PDF

2011

  • Jari Björne, Juho Heimonen, Filip Ginter, Antti Airola, Tapio Pahikkala, Tapio Salakoski, Extracting Contextualized Complex Biological Events with Rich Graph-Based Feature Sets. Computational Intelligence 27, 541--557, 2011. Accepted in 2009. PDF (!)
  • Jari Björne, Antti Airola, Tapio Pahikkala, Tapio Salakoski, Drug-Drug Interaction Extraction from Biomedical Texts with RLS and SVM Classifiers. In: Isabel Segura-Bedmar, Paloma Martinez, Daniel Sanchez-Cisneros (Eds.), Proceedings of the First Challenge task on Drug-Drug Interaction Extraction (DDIExtraction 2011), 35-42, CEUR Workshop Proceedings, 2011. PDF (!)
  • Jari Björne, Tapio Salakoski, Generalizing Biomedical Event Extraction. In: Proceedings of the BioNLP Shared Task 2011 Workshop, 183--191, Association for Computational Linguistics, 2011. PDF (!)

2010

  • Jari Björne, Finter Ginter, Sampo Pyysalo, Jun'ichi Tsujii, Tapio Salakoski, Complex Event Extraction at PubMed Scale . Bioinformatics (ISMB'2010 proceedings volume) 26, 382-390, 2010. PDF
  • Jari Björne, Filip Ginter, Sampo Pyysalo, Jun'ichi Tsujii, Tapio Salakoski, Scaling up Biomedical Event Extraction to the Entire PubMed. In: Proceedings of the 2010 Workshop on Biomedical Natural Language Processing, pp. 28-36, 2010. PDF
  • Juho Heimonen, Jari Björne, Tapio Salakoski, Reconstruction of Semantic Relationships from Their Projections in Biomolecular Domain. In: Proceedings of the 2010 Workshop on Biomedical Natural Language Processing, 108--116, Association for Computational Linguistics, 2010. PDF

2009

  • Jari Björne, Filip Ginter, Juho Heimonen, Sampo Pyysalo, Tapio Salakoski, Learning to Extract Biological Event and Relation Graphs. In: Proceedings of the 17th Nordic Conference of Computational Linguistics NODALIDA 2009, NEALT Proceedings Series Vol. 4 (2009), 18-25, Northern European Association for Language Technology (NEALT), 2009. PDF
  • Jari Björne, Juho Heimonen, Filip Ginter, Antti Airola, Tapio Pahikkala, Tapio Salakoski, Extracting Complex Biological Events with Rich Graph-Based Feature Sets. In: Proceedings of the BioNLP 2009 Workshop Companion Volume for Shared Task, 10-18, Association for Computational Linguistics (ACL), 2009. PDF

2008

  • Jari Björne, Sampo Pyysalo, Filip Ginter, Tapio Salakoski, How Complex are Complex Protein-protein Interactions?. In: Proceedings of SMBM 2008, 2008. PDF
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