Jari Björne
PhD
jakrbj@utu.fi Vesilinnantie 5 Turku ORCID identifier: https://orcid.org/0000-0003-1722-6404 |
Machine Learning, Big Data, BioNLP
Artificial Intelligence, Bioinformatics, Text Mining
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.
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.
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.
- 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 ) - U-Compare bio-event meta-service: compatible BioNLP event extraction services (2011)
- BMC Bioinformatics
(A1 Refereed original research article in a scientific journal) - Complex Event Extraction at {PubMed} Scale (2010)
- Bioinformatics
(A1 Refereed original research article in a scientific journal) - Reconstruction of Semantic Relationships from Their Projections in Biomolecular Domain (2010) Proceedings 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 ) - Extracting Complex Biological Events with Rich Graph-Based Feature Sets (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 ) - A Graph Kernel for Protein-Protein Interaction Extraction (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 ) - All-paths graph kernel for protein-protein interaction extraction with evaluation of cross-corpus learning (2008)
- BMC Bioinformatics
(A1 Refereed original research article in a scientific journal) - Comparative analysis of five protein-protein interaction corpora (2008)
- BMC Bioinformatics
(A1 Refereed original research article in a scientific journal)
