| 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), 1-19, 2016 | 301 | 2016 |
| 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, ... Genome biology 20 (1), 1-23, 2019 | 140 | 2019 |
| 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 | 119 | 2013 |
| 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 | 54 | 2018 |
| 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 | 51 | 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 | 46 | 2012 |
| 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 | 30 | 2016 |
| Biomedical named entity recognition with multilingual BERT K Hakala, S Pyysalo Proceedings of The 5th Workshop on BioNLP Open Shared Tasks, 56-61, 2019 | 28 | 2019 |
| UTU: Disease mention recognition and normalization with CRFs and vector space representations S Kaewphan, K Hakaka, F Ginter | 17 | 2014 |
| 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 | 14 | 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 | 9 | 2015 |
| Wide-scope biomedical named entity recognition and normalization with CRFs, fuzzy matching and character level modeling S Kaewphan, K Hakala, N Miekka, T Salakoski, F Ginter Database 2018, 2018 | 8 | 2018 |
| TurkuNLP entry for interactive Bio-ID assignment S Kaewphan, F Mehryary, K Hakala, T Salakoski, F Ginter Proceedings of the BioCreative VI Workshop, 32-35, 2017 | 6 | 2017 |
| 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), 1-12, 2015 | 6 | 2015 |
| 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 27 (1), 81-88, 2020 | 5 | 2020 |
| Leveraging Text Repetitions and Denoising Autoencoders in OCR Post-correction K Hakala, A Vesanto, N Miekka, T Salakoski, F Ginter arXiv preprint arXiv:1906.10907, 2019 | 5 | 2019 |
| Neural network and random forest models in protein function prediction K Hakala, S Kaewphan, J Björne, F Mehryary, H Moen, M Tolvanen, ... BioRxiv, 690271, 2019 | 5 | 2019 |
| Assisting nurses in care documentation: from automated sentence classification to coherent document structures with subject headings H Moen, K Hakala, LM Peltonen, HM Matinolli, H Suhonen, K Terho, ... Journal of Biomedical Semantics 11 (1), 1-12, 2020 | 3 | 2020 |
| 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 | 3 | 2018 |
| Cyevex: literature-scale network integration and visualization through cytoscape K Hakala, S Van Landeghem, S Kaewphan, T Salakoski, Y Van de Peer, ... Proc. SMBM 12, 91-96, 2012 | 3 | 2012 |
