Exploring Biomolecular Literature with EVEX: Connecting Genes through Events, Homology, and Indirect Associations. - Sofie Van Landeghem; Kai Hakala; Samuel Rönnqvist; Tapio Salakoski; Yves Van de Peer; Filip Ginter (Adv. Bioinformatics, 2012)

EVEX in ST'13: Application of a large-scale text mining resource to event extraction and network construction. - Kai Hakala; Sofie Van Landeghem; Tapio Salakoski; Yves Van de Peer; Filip Ginter (BioNLP@ACL (Shared Task), 2013)

UTU: Disease Mention Recognition and Normalization with CRFs and Vector Space Representations. - Suwisa Kaewphan; Kai Hakala; Filip Ginter (SemEval@COLING, 2014)

Sharing annotations better: RESTful Open Annotation. - Sampo Pyysalo; Jorge Campos; Juan Miguel Cejuela; Filip Ginter; Kai Hakala; Chen Li; Pontus Stenetorp; Lars Juhl Jensen (ACL (System Demonstrations), 2015)

UTU: Adapting Biomedical Event Extraction System to Disorder Attribute Detection. - Kai Hakala (SemEval@NAACL-HLT, 2015)

Application of the EVEX resource to event extraction and network construction: Shared Task entry and result analysis. - Kai Hakala; Sofie Van Landeghem; Tapio Salakoski; Yves Van de Peer; Filip Ginter (BMC Bioinform., 2015)

Syntactic analyses and named entity recognition for PubMed and PubMed Central - up-to-the-minute. - Kai Hakala; Suwisa Kaewphan; Tapio Salakoski; Filip Ginter (BioNLP@ACL, 2016)

Filtering large-scale event collections using a combination of supervised and unsupervised learning for event trigger classification. - Farrokh Mehryary; Suwisa Kaewphan; Kai Hakala; Filip Ginter (J. Biomed. Semant., 2016)

Ensemble of Convolutional Neural Networks for Medicine Intake Recognition in Twitter. - Kai Hakala; Farrokh Mehryary; Hans Moen; Suwisa Kaewphan; Tapio Salakoski; Filip Ginter (SMM4H@AMIA, 2017)

End-to-End System for Bacteria Habitat Extraction. - Farrokh Mehryary; Kai Hakala; Suwisa Kaewphan; Jari Björne; Tapio Salakoski; Filip Ginter (BioNLP, 2017)

Detecting mentions of pain and acute confusion in Finnish clinical text. - Hans Moen; Kai Hakala; Farrokh Mehryary; Laura-Maria Peltonen; Tapio Salakoski; Filip Ginter; Sanna Salanterä (BioNLP, 2017)

Evaluation of a Prototype System that Automatically Assigns Subject Headings to Nursing Narratives Using Recurrent Neural Network. - Hans Moen; Kai Hakala; Laura-Maria Peltonen; Henry Suhonen; Petri Loukasmäki; Tapio Salakoski; Filip Ginter; Sanna Salanterä (Louhi@EMNLP, 2018)

Wide-scope biomedical named entity recognition and normalization with CRFs, fuzzy matching and character level modeling. - Suwisa Kaewphan; Kai Hakala; Niko Miekka; Tapio Salakoski; Filip Ginter (Database J. Biol. Databases Curation, 2018)

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. - Abeed Sarker; Maksim Belousov; Jasper Friedrichs; Kai Hakala; Svetlana Kiritchenko; Farrokh Mehryary; Sifei Han; Tung Tran 001; Anthony Rios; Ramakanth Kavuluru; Berry de Bruijn; Filip Ginter; et al. (J. Am. Medical Informatics Assoc., 2018)

Biomedical Named Entity Recognition with Multilingual BERT. - Kai Hakala; Sampo Pyysalo (BioNLP-OST@EMNLP-IJNCLP, 2019)

Leveraging Text Repetitions and Denoising Autoencoders in OCR Post-correction. - Kai Hakala; Aleksi Vesanto; Niko Miekka; Tapio Salakoski; Filip Ginter (CoRR, 2019)

Assisting nurses in care documentation: from automated sentence classification to coherent document structures with subject headings. - Hans Moen; Kai Hakala; Laura-Maria Peltonen; Hanna-Maria Matinolli; Henry Suhonen; Kirsi Terho; Riitta Danielsson-Ojala; Maija Valta; Filip Ginter; Tapio Salakoski; Sanna Salanterä (J. Biomed. Semant., 2020)

Supporting the use of standardized nursing terminologies with automatic subject heading prediction: a comparison of sentence-level text classification methods. - Hans Moen; Kai Hakala; Laura-Maria Peltonen; Henry Suhonen; Filip Ginter; Tapio Salakoski; Sanna Salanterä (J. Am. Medical Informatics Assoc., 2020)

Combining supervised and unsupervised named entity recognition to detect psychosocial risk factors in occupational health checks. - Leena Uronen; Sanna Salanterä; Kai Hakala; Jaakko Hartiala; Hans Moen (Int. J. Medical Informatics, 2022)

Neural Network and Random Forest Models in Protein Function Prediction. - Kai Hakala; Suwisa Kaewphan; Jari Björne; Farrokh Mehryary; Hans Moen; Martti Tolvanen; Tapio Salakoski; Filip Ginter (IEEE ACM Trans. Comput. Biol. Bioinform., 2022)