Jari Björne
PhD
jakrbj@utu.fi Vesilinnantie 5 Turku ORCID identifier: https://orcid.org/0000-0003-1722-6404(external) |
Areas of expertise
Machine Learning, Big Data, BioNLP
Machine Learning, Big Data, BioNLP
Research community or research topic
Artificial Intelligence, Bioinformatics, Text Mining
Artificial Intelligence, Bioinformatics, Text Mining
Biography
I am a docent of biomedical data science. I graduated as a doctor of computer science in 2014, and as a master of biotechnology in 2008. After my PhD I worked for three years as an Academy of Finland post-doctoral researcher.
Research
My primary research focus is text mining from scientific literature using machine learning, with the intent to provide novel methods and applications to aid in bioscientific research. In these areas I have contributed the TEES (Turku Event Extraction System) machine learning software which was also the focus of my PhD thesis. Central additional research tasks include the CAFA (automated protein function prediction) task and organizing the EPE (extrinsic parser evaluation) shared task.
Teaching
I have been working in the AI academy project since 2020 and I'm currently a lecturer in this project. Due to my cross-disciplinary background I'm particularly interested in approaches to illustrate and elucidate computer science concepts also for people coming from non-CS backgrounds.
Publications 
2 of 3
- A Large-Scale Evaluation of Computational Protein Function PredictionReconstruction of Semantic Relationships from Their Projections in Biomolecular Domain (2013)
- Nature Methods
(A1 Refereed original research article in a scientific journal) - Analyzing the Japanese Toxicogenomics Project Dataset with SVM and RLS ClassifiersUTurku: Drug Named Entity Recognition and Drug-Drug Interaction Extraction Using SVM Classification and Domain Knowledge (2013) 13th Annual International Conference on Critical Assessment of Massive Data Analysis (CAMDA 2013) Björne J, Airola A, Pahikkala T, Salakoski T
(Other publication) - Large-scale event extraction from literature with multi-level gene normalizationA Graph Kernel for Protein-Protein Interaction Extraction (2013)
- PLoS ONE
(A1 Refereed original research article in a scientific journal) - TEES 2.1: Automated annotation scheme learning in the BioNLP 2013 Shared TaskUniversity of Turku in the BioNLP'11 Shared TaskAll-paths graph kernel for protein-protein interaction extraction with evaluation of cross-corpus learning (2013) Proceedings of the BioNLP Shared Task 2013 Workshop Jari Björne, Tapio Salakoski
(A4 Refereed article in a conference publication ) - A Machine Learning Model and Evaluation of Text Mining for Protein Function PredictionComparative analysis of five protein-protein interaction corpora (2013) Second Joint Conference on Lexical and Computational Semantics (*SEM), Volume 2: Proceedings of the Seventh International Workshop on Semantic Evaluation (SemEval 2013) Jari Björne, Suwisa Kaewphan, Tapio Salakoski
(A4 Refereed article in a conference publication ) - PubMed-Scale Event Extraction for Post-Translational Modifications, Epigenetics and Protein Structural RelationsDrug-Drug Interaction Extraction with RLS and SVM Classifiers (2012) BioNLP: Proceedings of the 2012 Workshop on Biomedical Natural Language Processing Björne J, Van Landeghem S, Pyysalo S, Ohta T, Ginter F, Van de Peer Y, Ananiadou S, Salakoski T
(A4 Refereed article in a conference publication ) - Semantically linking molecular entities in literature through entity relationships (2012)
- BMC Bioinformatics
(A1 Refereed original research article in a scientific journal) - 2012
- BMC Bioinformatics
- U-Compare bio-event meta-service: compatible BioNLP event extraction services (2011) Björne Jari, Salakoski Tapio
(A4 Refereed article in a conference publication ) - Complex Event Extraction at {PubMed} Scale (2011)
- CEUR Workshop Proceedings
(A4 Refereed article in a conference publication ) - EXTRACTING CONTEXTUALIZED COMPLEX BIOLOGICAL EVENTS WITH RICH GRAPH-BASED FEATURE SETS (2011)
- Computational Intelligence
(A1 Refereed original research article in a scientific journal) - Generalizing Biomedical Event Extraction (2011) Björne Jari, Salakoski Tapio
(A4 Refereed article in a conference publication ) - (2011)
- BMC Bioinformatics
(A1 Refereed original research article in a scientific journal) - Extracting Complex Biological Events with Rich Graph-Based Feature Sets2010
- Bioinformatics
(A1 Refereed original research article in a scientific journal) - 2010Proceedings of the 2010 Workshop on Biomedical Natural Language Processing Heimonen J, Björne J, Salakoski T
(A4 Refereed article in a conference publication ) - Scaling up Biomedical Event Extraction to the Entire {PubMed} (2010) Proceedings of the 2010 Workshop on Biomedical Natural Language Processing (BioNLP'10) Björne J, Ginter F, Pyysalo S, Tsujii J, Salakoski T
(A4 Refereed article in a conference publication ) - (2009) Proceedings of the BioNLP 2009 Workshop Companion Volume for Shared Task Björne J, Heimonen J, Ginter F, Airola A, Pahikkala T, Salakoski T
(A4 Refereed article in a conference publication ) - (2008) Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing (BioNLP 2008) Airola A, Pyysalo S, Björne J, Pahikkala T, Ginter F, Salakoski T
(A4 Refereed article in a conference publication ) - (2008)
- BMC Bioinformatics
(A1 Refereed original research article in a scientific journal) - (2008)
- BMC Bioinformatics
(A1 Refereed original research article in a scientific journal)
UTU Research Portal