Jari Björne
PhD
jakrbj@utu.fi Vesilinnantie 5 Turku |
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.
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- AI-Assisted Learning with ChatGPT and Large Language Models: Implications for Higher Education (2023)
- IEEE International Conference on Advanced Learning Technologies
- Neural Network and Random Forest Models in Protein Function Prediction (2022)
- IEEE/ACM Transactions on Computational Biology and Bioinformatics
- Striving for platform independence in the e-learning landscape: a study on a flexible exercise creation system (2022)
- IEEE International Conference on Advanced Learning Technologies
- Towards Automated Screening of Literature on Artificial Intelligence in Nursing (2022)
- World congress on medical and health informatics
- BioVerbNet: a large semantic-syntactic classification of verbs in biomedicine (2021)
- Journal of Biomedical Semantics
- Convolutional neural network architectures for CAFA4 (2020)
- F1000Research
- Propagating AI Knowledge Across University Disciplines- The Design of A Multidisciplinary AI Study Module (2020)
- Conference proceedings : Frontiers in Education Conference
- The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens (2019)
- Genome Biology
- Biomedical Event Extraction Using Convolutional Neural Networks and Dependency Parsing (2018) Proceedings of the BioNLP 2018 workshop, Melbourne, Australia, July 19, 2018 Björne J, Salakoski T
- Combining support vector machines and LSTM networks for chemical-protein relation extraction (2018) Proceedings of the BioCreative VI Workshop Farrokh Mehryary, Jari Björne, Tapio Salakoski, Filip Ginter
- Potent pairing: ensemble of long short-term memory networks and support vector machine for chemical-protein relation extraction (2018)
- Database: The Journal of Biological Databases and Curation
- The 2018 Shared Task on Extrinsic Parser Evaluation: On the Downstream Utility of English Universal Dependency Parsers (2018) Proceedings of the CoNLL 2018 Shared Task: Multilingual Parsing from Raw Text to Universal Dependencies Fares M, Oepen S, Øvrelid L, Björne J, Johansson R
- End-to-End System for Bacteria Habitat Extraction (2017) SIGBioMed Workshop on Biomedical Natural Language: Proceedings of the 16th BioNLP Workshop Farrokh Mehryary, Kai Hakala, Suwisa Kaewphan, Jari Björne, Tapio Salakoski, Filip Ginter
- EPE 2017: The Biomedical Event Extraction Downstream Application (2017) Proceedings of the 2017 Shared Task on Extrinsic Parser Evaluation (EPE 2017) at the Fourth International Conference on Dependency Linguistics (Depling 2017) and the 15th International Conference on Parsing Technologies (IWTP 2017) Björne J, Ginter F, Salakoski T
- The 2017 Shared Task on Extrinsic Parser Evaluation. Towards a Reusable Community Infrastructure (2017) Proceedings of the 2017 Shared Task on Extrinsic Parser Evaluation (EPE 2017) at the Fourth International Conference on Dependency Linguistics (Depling 2017) and the 15th International Conference on Parsing Technologies (IWTP 2017) Oepen S, Øvrelid L, Björne J, Johansson R, Lapponi E, Ginter F, Velldal E
- Deep Learning With Minimal Training Data: TurkuNLP Entry in the BioNLP Shared Task 2016 (2016) Proceedings of the 4th BioNLP Shared Task Workshop Farrokh Mehryary, Jari Bjorne, Sampo Pyysalo, Tapio Salakoski, Filip Ginter
- UTU at SemEval-2016 Task 10: Binary Classification for Expression Detection (BCED) (2016) Proceedings of the 10th International Workshop on Semantic Evaluation (SemEval-2016) Björne J, Salakoski T
- Cancer Progression Classification for Mutation Analysis (2015) The 14th Annual International Conference On Critical Assessment of Massive Data Analysis (CAMDA) Björne J, Salakoski T
- TEES 2.2: Biomedical Event Extraction for Diverse Corpora (2015)
- BMC Bioinformatics
- Biomedical Event Extraction with Machine Learning (2014) Björne Jari
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