Jari Björne
 PhD


jakrbj@utu.fi

Vesilinnantie 5

Turku


ORCID identifierhttps://orcid.org/0000-0003-1722-6404





Areas of expertise
Machine Learning, Big Data, BioNLP

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
  
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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
    2023 IEEE International Conference on Advanced Learning Technologies, ICALT 2023 Laato Samuli, Morschheuser Benedikt, Hamari Juho, Björne Jari
    (
    Refereed article in conference proceedings (A4))


  • Neural Network and Random Forest Models in Protein Function Prediction  (2022)  
    • IEEE/ACM Transactions on Computational Biology and Bioinformatics
     Hakala Kai, Kaewphan Suwisa, Björne Jari, Mehryary Farrokh, Moen Hans, Tolvanen Martti, Salakoski Tapio, Ginter Filip
    (
    Refereed journal article or data article (A1))


  • 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
    2022 International Conference on Advanced Learning Technologies (ICALT) Laato Samuli, Murtojärvi Mika, Airola Antti, Björne Jari
    (
    Refereed article in conference proceedings (A4))


  • Towards Automated Screening of Literature on Artificial Intelligence in Nursing  (2022)  
    • World congress on medical and health informatics
    MEDINFO 2021: One World, One Health – Global Partnership for Digital Innovation Moen Hans, Alhuwail Dari, Björne Jari, Block Lori, Celin Sven, Jeon Eunjoo, Kreiner Karl, Mitchell James, Ožegović Gabriela, Ronquillo Charlene Esteban, Sequeira Lydia, Tayaben Jude, Topaz Maxim, Veeranki Sai Pavan Kumar, Peltonen Laura-Maria
    (
    Refereed article in conference proceedings (A4))


  • BioVerbNet: a large semantic-syntactic classification of verbs in biomedicine  (2021)  
    • Journal of Biomedical Semantics
     Majewska Olga, Collins Charlotte, Baker Simon, Björne Jari, Brown Susan Windisch, Korhonen Anna, Palmer Martha
    (
    Refereed journal article or data article (A1))


  • Convolutional neural network architectures for CAFA4  (2020)  
    • F1000Research
     Björne Jari
    (
    Other (O2))


  • Propagating AI Knowledge Across University Disciplines- The Design of A Multidisciplinary AI Study Module  (2020)  
    • Conference proceedings : Frontiers in Education Conference
    2020 IEEE Frontiers in Education Conference (FIE) Samuli Laato, Henna Vilppu, Juho Heimonen, Antti Hakkala, Jari Björne, Ali Farooq, Tapio Salakoski, Antti Airola
    (
    Refereed article in conference proceedings (A4))


  • The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens  (2019)  
    • Genome Biology
     Naihui Zhou, Yuxiang Jiang, Timothy R. Bergquist, Alexandra J. Lee, Balint Z. Kacsoh, Alex W. Crocker, Kimberley A. Lewis, George Georghiou, Huy N. Nguyen, Md Nafiz Hamid, Larry Davis, Tunca Dogan, Volkan Atalay, Ahmet S. Rifaioglu, Alperen Dalkıran, Rengul Cetin Atalay, Chengxin Zhang, Rebecca L. Hurto, Peter L. Freddolino, Yang Zhang, Prajwal Bhat, Fran Supek, José M. Fernández, Branislava Gemovic, Vladimir R. Perovic, Radoslav S. Davidović, Neven Sumonja, Nevena Veljkovic, Ehsaneddin Asgari, Mohammad R.K. Mofrad, Giuseppe Profiti, Castrense Savojardo, Pier Luigi Martelli, Rita Casadio, Florian Boecker, Heiko Schoof, Indika Kahanda, Natalie Thurlby, Alice C. McHardy, Alexandre Renaux, Rabie Saidi, Julian Gough, Alex A. Freitas, Magdalena Antczak, Fabio Fabris, Mark N. Wass, Jie Hou, Jianlin Cheng, Zheng Wang, Alfonso E. Romero, Alberto Paccanaro, Haixuan Yang, Tatyana Goldberg, Chenguang Zhao, Liisa Holm, Petri Törönen, Alan J. Medlar, Elaine Zosa, Itamar Borukhov, Ilya Novikov, Angela Wilkins, Olivier Lichtarge, Po-Han Chi, Wei-Cheng Tseng, Michal Linial, Peter W. Rose, Christophe Dessimoz, Vedrana Vidulin, Saso Dzeroski, Ian Sillitoe, Sayoni Das, Jonathan Gill Lees, David T. Jones, Cen Wan, Domenico Cozzetto, Rui Fa, Mateo Torres, Alex Warwick Vesztrocy, Jose Manuel Rodriguez, Michael L. Tress, Marco Frasca, Marco Notaro, Giuliano Grossi, Alessandro Petrini, Matteo Re, Giorgio Valentini, Marco Mesiti, Daniel B. Roche, Jonas Reeb, David W. Ritchie, Sabeur Aridhi, Seyed Ziaeddin Alborzi, Marie-Dominique Devignes, Da Chen Emily Koo, Richard Bonneau, Vladimir Gligorijević, Meet Barot, Hai Fang, Stefano Toppo, Enrico Lavezzo, Marco Falda, Michele Berselli, Silvio C.E. Tosatto, Marco Carraro, Damiano Piovesan, Hafeez Ur Rehman, Qizhong Mao, Shanshan Zhang, Slobodan Vucetic, Gage S. Black, Dane Jo, Erica Suh, Jonathan B. Dayton, Dallas J. Larsen, Ashton R. Omdahl, Liam J. McGuffin, Danielle A. Brackenridge, Patricia C. Babbitt, Jeffrey M. Yunes, Paolo Fontana, Feng Zhang, Shanfeng Zhu, Ronghui You, Zihan Zhang, Suyang Dai, Shuwei Yao, Weidong Tian, Renzhi Cao, Caleb Chandler, Miguel Amezola, Devon Johnson, Jia-Ming Chang, Wen-Hung Liao, Yi-Wei Liu, Stefano Pascarelli, Yotam Frank, Robert Hoehndorf, Maxat Kulmanov, Imane Boudellioua, Gianfranco Politano, Stefano Di Carlo, Alfredo Benso, Kai Hakala, Filip Ginter, Farrokh Mehryary, Suwisa Kaewphan, Jari Björne, Hans Moen, Martti E.E. Tolvanen, Tapio Salakoski, Daisuke Kihara, Aashish Jain, Tomislav Šmuc, Adrian Altenhoff, Asa Ben-Hur, Burkhard Rost, Steven E. Brenner, Christine A. Orengo, Constance J. Jeffery, Giovanni Bosco, Deborah A. Hogan, Maria J. Martin, Claire O’Donovan, Sean D. Mooney, Casey S. Greene, Predrag Radivojac, Iddo Friedberg
    (
    Refereed journal article or data article (A1))


  • 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
    (
    Refereed article in conference proceedings (A4))


  • 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​
    (
    Refereed article in conference proceedings (A4))


  • 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
     Farrokh Mehryary, Jari Björne, Tapio Salakoski, Filip Ginter
    (
    Refereed journal article or data article (A1))


  • 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
    (
    Refereed article in conference proceedings (A4))


  • 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
    (
    Refereed article in conference proceedings (A4))


  • 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
    (
    Refereed article in conference proceedings (A4))


  • 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
    (
    Refereed article in conference proceedings (A4))


  • 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
    (
    Refereed article in conference proceedings (A4))


  • 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
    (
    Refereed article in conference proceedings (A4))


  • Cancer Progression Classification for Mutation Analysis  (2015)  The 14th Annual International Conference On Critical Assessment of Massive Data Analysis (CAMDA) Björne J, Salakoski T
    (
    Other (O2))


  • TEES 2.2: Biomedical Event Extraction for Diverse Corpora  (2015)  
    • BMC Bioinformatics
     Björne J, Salakoski T
    (
    Refereed journal article or data article (A1))


  • Biomedical Event Extraction with Machine Learning  (2014)   Björne Jari
    (
    Doctoral dissertation (article) (G5))



Last updated on 2023-12-07 at 12:00