PhD Jari Björne - UTU Research Portal

Jari Björne
PhD

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

jakrbj@utu.fi

Vesilinnantie 5

Turku

ORCID identifier: https://orcid.org/0000-0003-1722-6404(external)

Areas of expertise

Machine Learning, Big Data, BioNLP

Research community or research topic

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 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 IA1 Refereed original research article in a scientific journal
Analyzing the Japanese Toxicogenomics Project Dataset with SVM and RLS ClassifiersU-Compare bio-event meta-service: compatible BioNLP event extraction services (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 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
(A1 Refereed original research article in a scientific journal)
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
(A4 Refereed article in a conference publication )
(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 )
(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 )
(2012)
- BMC Bioinformatics
Van Landeghem S, Björne J, Abeel T, De Baets B, Salakoski T, Peer Y
(A1 Refereed original research article in a scientific journal)
University of Turku in the BioNLP'11 Shared Task2012
- BMC BioinformaticsBMC Bioinformatics
Björne J, Ginter F, Salakoski T
(A1 Refereed original research article in a scientific journal)
A Machine Learning Model and Evaluation of Text Mining for Protein Function Prediction (2011) Björne Jari, Salakoski Tapio
(A4 Refereed article in a conference publication )
Drug-Drug Interaction Extraction with RLS and SVM Classifiers (2011)
- CEUR Workshop Proceedings
Jari Björne, Antti Airola, Tapio Pahikkala, Tapio Salakoski
(A4 Refereed article in a conference publication )
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
(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
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
(A1 Refereed original research article in a scientific journal)
Complex Event Extraction at {PubMed} Scale (2010)
- Bioinformatics
Björne J, Ginter F, Pyysalo S, Tsujii J, Salakoski T
(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)
Airola A, Pyysalo S, Bjorne J, Pahikkala T, Ginter F, Salakoski T
(A1 Refereed original research article in a scientific journal)
Comparative analysis of five protein-protein interaction corpora (2008)
- BMC Bioinformatics
Pyysalo S, Airola A, Heimonen J, Bjorne J, Ginter F, Salakoski T
(A1 Refereed original research article in a scientific journal)