| 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 | 197 | 2016 |
| 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 | 99 | 2013 |
| 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 | 39 | 2012 |
| 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 | 37 | 2013 |
| 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 | 16 | 2014 |
| 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 | 14 | 2016 |
| 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 | 13 | 2018 |
| 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 | 10 | 2017 |
| 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 | 8 | 2015 |
| 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 | 4 | 2015 |
| 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 | 3 | 2019 |
| 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 | 3 | 2017 |
| 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 | 2 | 2013 |
| 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 | 2 | 2012 |
| 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 | 1 | 2018 |
| 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 | 1 | 2017 |
| UTU: adapting biomedical event extraction system to disorder attribute detection K Hakala Proceedings of the 9th International Workshop on Semantic Evaluation …, 2015 | 1 | 2015 |
| 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 | 1 | 2013 |
| 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 |
