Jari Björne profile picture
Jari
Björne
Docent, ​Department of Computing
University Lecturer, ​Department of Computing
PhD
Artificial Intelligence, Bioinformatics, Text Mining

Contact

Vesilinnantie 5
20500
Turku

Links

ORCID

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.

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.

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.

Publications

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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
(Vertaisarvioitu alkuperäisartikkeli tai data-artikkeli tieteellisessä aikakauslehdessä (A1))

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
(Vertaisarvioitu alkuperäisartikkeli tai data-artikkeli tieteellisessä aikakauslehdessä (A1))
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