PhD Jari Björne - UTU Research Portal

Jari Björne
PhD

- University Lecturer,
- Docent
Department of Computing (Faculty of Technology)

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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A Large-Scale Evaluation of Computational Protein Function Prediction (2013)
- Nature Methods
Radivojac P, Clark WT, Oron TR, Schnoes AM, Wittkop TW, Sokolov A, Graim K, Funk C, Verspoor K, Ben-Hur A, Pandey G, Yunes JM, Talwalkar AS, Repo S, Souza ML, Piovesan D, Casadio R, Wang Z, Cheng J, Fang H, Gough J, Koskinen P, Törönen P, Nokso-Koivisto J, Holm L, Cozzetto D, Buchan DWA, Bryson K, Jones DT, Limave B, Inamdar H, Datta A, Manjari SK, Joshi R, Chitale M, Kihara D, Lisewski AM, Erdin S, Venner E, Lichtarge O, Rentzsch R, Yang H, Romero AE, Bhat P, Paccanaro A, Hamp T, Kaßner R, Seemayer S, Vicedo E, Schaefer C, Achten D, Auer F, Boehm A, Braun T, Hecht M, Heron M, Hönigschmid P, Hopf TA, Kaufmann S, Kiening M, Krompass D, Landerer C, Mahlich Y, Roos M, Björne J, Salakoski T, Wong A, Shatkay H, Gatzmann F, Sommer I, Wass MN, Sternberg MJE, Škunca N, Supek F, Bošnjak M, Panov P, Džeroski S, Šmuc T, Kourmpetis YAI, Dijk ADJv, Braak CJFt, Zhou Y, Gong Q, Dong X, Tian W, Falda M, Fontana P, Lavezzo E, Camillo BD, Toppo S, Lan L, Djuric N, Guo Y, Vucetic SV, Bairoch A, Linial M, Babbitt PC, Brenner SE, Orengo C, Rost B, Mooney SD, Friedberg I
Analyzing the Japanese Toxicogenomics Project Dataset with SVM and RLS Classifiers (2013) 13th Annual International Conference on Critical Assessment of Massive Data Analysis (CAMDA 2013) Björne J, Airola A, Pahikkala T, Salakoski T
Large-scale event extraction from literature with multi-level gene normalization (2013)
- PLoS ONE
Van Landeghem Sofie, Björne Jari, Wei Chih-Hsuan, Hakala Kai, Pyysalo Sampo, Ananiadou Sophia, Kao Hung-Yu, Lu Zhiyong, Salakoski Tapio, Van de Peer Yves, Ginter Filip
TEES 2.1: Automated annotation scheme learning in the BioNLP 2013 Shared Task (2013) Proceedings of the BioNLP Shared Task 2013 Workshop Jari Björne, Tapio Salakoski
UTurku: Drug Named Entity Recognition and Drug-Drug Interaction Extraction Using SVM Classification and Domain Knowledge (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
PubMed-Scale Event Extraction for Post-Translational Modifications, Epigenetics and Protein Structural Relations (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
Semantically linking molecular entities in literature through entity relationships (2012)
- BMC Bioinformatics
Van Landeghem S, Björne J, Abeel T, De Baets B, Salakoski T, Peer Y
University of Turku in the BioNLP'11 Shared Task (2012)
- BMC Bioinformatics
Björne J, Ginter F, Salakoski T
A Machine Learning Model and Evaluation of Text Mining for Protein Function Prediction (2011) Björne Jari, Salakoski Tapio
Drug-Drug Interaction Extraction with RLS and SVM Classifiers (2011)
- CEUR Workshop Proceedings
Jari Björne, Antti Airola, Tapio Pahikkala, Tapio Salakoski
EXTRACTING CONTEXTUALIZED COMPLEX BIOLOGICAL EVENTS WITH RICH GRAPH-BASED FEATURE SETS (2011)
- Computational Intelligence
Bjorne J, Heimonen J, Ginter F, Airola A, Pahikkala T, Salakoski T
Generalizing Biomedical Event Extraction (2011) Björne Jari, Salakoski Tapio
U-Compare bio-event meta-service: compatible BioNLP event extraction services (2011)
- BMC Bioinformatics
Kano Y, Björne J, Ginter F, Salakoski T, Buyko E, Hahn U, Cohen K, Verspoor K, Roeder C, Hunter L, Kilicoglu H, Bergler S, Landeghem S, Parys T, {Van de Peer} Y, Miwa M, Ananiadou S, Neves M, Pascual-Montano A, Ozgur A, Radev D, Riedel S, Saetre R, Chun H, Kim J, Pyysalo S, Ohta T, Tsujii J
Complex Event Extraction at {PubMed} Scale (2010)
- Bioinformatics
Björne J, Ginter F, Pyysalo S, Tsujii J, Salakoski T
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
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
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
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
All-paths graph kernel for protein-protein interaction extraction with evaluation of cross-corpus learning (2008)
- BMC Bioinformatics
Airola A, Pyysalo S, Bjorne J, Pahikkala T, Ginter F, Salakoski T
Comparative analysis of five protein-protein interaction corpora (2008)
- BMC Bioinformatics
Pyysalo S, Airola A, Heimonen J, Bjorne J, Ginter F, Salakoski T