Kai Hakala
TitleCited byYear
An expanded evaluation of protein function prediction methods shows an improvement in accuracy
Y Jiang, TR Oron, WT Clark, AR Bankapur, D D’Andrea, R Lepore, ...
Genome biology 17 (1), 184, 2016
1992016
Large-scale event extraction from literature with multi-level gene normalization
S Van Landeghem, J Björne, CH Wei, K Hakala, S Pyysalo, S Ananiadou, ...
PloS one 8 (4), e55814, 2013
992013
Exploring biomolecular literature with EVEX: connecting genes through events, homology, and indirect associations
S Van Landeghem, K Hakala, S Rönnqvist, T Salakoski, Y Van de Peer, ...
Advances in bioinformatics 2012, 2012
402012
EVEX in ST’13: Application of a large-scale text mining resource to event extraction and network construction
K Hakala, S Van Landeghem, T Salakoski, Y Van de Peer, F Ginter
Proceedings of the BioNLP Shared Task 2013 Workshop, 26-34, 2013
372013
UTU: disease mention recognition and normalization with CRFs and vector space representations
S Kaewphan, K Hakala, F Ginter
Proceedings of the 8th international workshop on semantic evaluation …, 2014
162014
Syntactic analyses and named entity recognition for PubMed and PubMed Central—up-to-the-minute
K Hakala, S Kaewphan, T Salakoski, F Ginter
Proceedings of the 15th Workshop on Biomedical Natural Language Processing …, 2016
152016
Data and systems for medication-related text classification and concept normalization from Twitter: insights from the Social Media Mining for Health (SMM4H)-2017 shared task
A Sarker, M Belousov, J Friedrichs, K Hakala, S Kiritchenko, F Mehryary, ...
Journal of the American Medical Informatics Association 25 (10), 1274-1283, 2018
132018
End-to-end system for bacteria habitat extraction
F Mehryary, K Hakala, S Kaewphan, J Björne, T Salakoski, F Ginter
BioNLP 2017, 80-90, 2017
102017
Sharing annotations better: RESTful open annotation
S Pyysalo, J Campos, JM Cejuela, F Ginter, K Hakala, C Li, P Stenetorp, ...
Proceedings of ACL-IJCNLP 2015 System Demonstrations, 91-96, 2015
82015
Application of the EVEX resource to event extraction and network construction: Shared Task entry and result analysis
K Hakala, S Van Landeghem, T Salakoski, Y Van de Peer, F Ginter
BMC bioinformatics 16 (16), S3, 2015
42015
The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens
N Zhou, Y Jiang, TR Bergquist, AJ Lee, BZ Kacsoh, AW Crocker, ...
bioRxiv, 653105, 2019
32019
TurkuNLP entry for interactive Bio-ID assignment
S Kaewphan, F Mehryary, K Hakala, T Salakoski, F Ginter
Proceedings of the BioCreative VI Workshop. Bethesda, MD, 32-35, 2017
32017
Hypothesis generation in large-scale event networks
K Hakala, F Mehryary, S Kaewphan, F Ginter
Proceedings of the 5th International Symposium on Languages in Biology and …, 2013
22013
CyEVEX: Literature-scale network integration and visualization through Cytoscape
K Hakala, S Van Landeghem, S Kaewphan, T Salakoski, Y Van de Peer, ...
Proceedings of SMBM 12, 91-96, 2012
22012
Evaluation of a prototype system that automatically assigns subject headings to nursing narratives using recurrent neural network
H Moen, K Hakala, LM Peltonen, H Suhonen, P Loukasmäki, T Salakoski, ...
Proceedings of the Ninth International Workshop on Health Text Mining and …, 2018
12018
Ensemble of Convolutional Neural Networks for Medicine Intake Recognition in Twitter
K Hakala, F Mehryary, H Moen, S Kaewphan, T Salakoski, F Ginter
Proceedings of the 2nd Social Media Mining for Health Research and …, 2017
12017
UTU: adapting biomedical event extraction system to disorder attribute detection
K Hakala
Proceedings of the 9th International Workshop on Semantic Evaluation …, 2015
12015
Eliminating Incorrect Events from Large-Scale Event Networks by Trigger Word Clustering and Pruning
F Mehryary, S Kaewphan, K Hakala, F Ginter
The University of Turku Graduate School (UTUGS), University of Turku, Finland, 2013
12013
Biomedical Named Entity Recognition with Multilingual BERT
K Hakala, S Pyysalo
Proceedings of The 5th Workshop on BioNLP Open Shared Tasks, 56-61, 2019
2019
Supporting the use of standardized nursing terminologies with automatic subject heading prediction: a comparison of sentence-level text classification methods
H Moen, K Hakala, LM Peltonen, H Suhonen, F Ginter, T Salakoski, ...
Journal of the American Medical Informatics Association, 2019
2019
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Articles 1–20