Jari Björne


Postdoctoral Researcher, Language and Speech Technology (Department of Future Technologies)

jakrbj@utu.fi
+358 2 333 8681
Vesilinnantie 5
Turku





Publications
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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
(
A4 Article in conference proceedings)

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​
(
A4 Article in conference proceedings)

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
(
A1 Journal article – refereed)

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
(
A4 Article in conference proceedings)

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
(
A4 Article in conference proceedings)

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
(
A4 Article in conference proceedings)

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
(
A4 Article in conference proceedings)

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
(
A4 Article in conference proceedings)

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
(
A4 Article in conference proceedings)

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

TEES 2.2: Biomedical Event Extraction for Diverse Corpora (2015)
BMC Bioinformatics
Björne J, Salakoski T
(
A1 Journal article – refereed)

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

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
(
A1 Journal article – refereed)

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
(
O2 Other)

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 Journal article – refereed)

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 Article in conference proceedings)

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
(
A4 Article in conference proceedings)

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
(
A4 Article in conference proceedings)

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
(
A1 Journal article – refereed)

University of Turku in the BioNLP'11 Shared Task (2012)
BMC Bioinformatics
Björne J, Ginter F, Salakoski T
(
A1 Journal article – refereed)


Last updated on 2019-20-07 at 02:24

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