Deep Learning with Minimal Training Data: TurkuNLP Entry in the BioNLP Shared Task 2016. - Farrokh Mehryary; Jari Björne; Sampo Pyysalo; Tapio Salakoski; Filip Ginter (BioNLP (Shared Task), 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)

Potent pairing: ensemble of long short-term memory networks and support vector machine for chemical-protein relation extraction. - Farrokh Mehryary; Jari Björne; 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)

Entity-Pair Embeddings for Improving Relation Extraction in the Biomedical Domain. - Farrokh Mehryary; Hans Moen; Tapio Salakoski; Filip Ginter (ESANN, 2020)

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)

Overview of DrugProt task at BioCreative VII: data and methods for large-scale text mining and knowledge graph generation of heterogenous chemical-protein relations. - Antonio Miranda-Escalada; Farrokh Mehryary; Jouni Luoma; Darryl Estrada-Zavala; Luis Gascó; Sampo Pyysalo; Alfonso Valencia; Martin Krallinger (Database J. Biol. Databases Curation, 2023)

The STRING database in 2023: protein-protein association networks and functional enrichment analyses for any sequenced genome of interest. - Damian Szklarczyk; Rebecca Kirsch; Mikaela Koutrouli; Katerina C. Nastou; Farrokh Mehryary; Radja Hachilif; Annika L. Gable; Tao Fang; Nadezhda T. Doncheva; Sampo Pyysalo; Peer Bork; Lars Juhl Jensen; et al. (Nucleic Acids Res., 2023)

RegulaTome: a corpus of typed, directed, and signed relations between biomedical entities in the scientific literature. - Katerina C. Nastou; Farrokh Mehryary; Tomoko Ohta; Jouni Luoma; Sampo Pyysalo; Lars Juhl Jensen (Database J. Biol. Databases Curation, 2024)

An Expanded Massive Multilingual Dataset for High-Performance Language Technologies (HPLT). - Laurie Burchell; Ona De Gibert Bonet; Nikolay Arefyev; Mikko Aulamo; Marta Bañón; Pinzhen Chen; Mariia Fedorova; Liane Guillou; Barry Haddow; Jan Hajic; Jindrich Helcl; Erik Henriksson; et al. (ACL (1), 2025)

An Expanded Massive Multilingual Dataset for High-Performance Language Technologies. - Laurie Burchell; Ona de Gibert; Nikolay Arefyev; Mikko Aulamo; Marta Bañón; Pinzhen Chen; Mariia Fedorova; Liane Guillou; Barry Haddow; Jan Hajic; Jindrich Helcl; Erik Henriksson; et al. (CoRR, 2025)