Farrokh Mehryary profile picture
Farrokh
Mehryary
Senior Researcher, Data analytics
PhD in Computer Science
Biomedical Natural Language Processing (BioNLP) and text mining

Contact

Links

Google Scholar
Github
Mehryary_CV.pdf
ORCID

Areas of expertise

Natural language processing (NLP)
text mining
Information Extraction (IE)
Bioinformatics
protein function prediction
deep learning
machine learning

Biography

Farrokh is a senior researcher at the Department of Computing, University of Turku, Finland and for the last 11 years, he has been part of the TurkuNLP group, developing different NLP and text mining pipelines for the biomedical domain, as well as taking part in various bioinformatics projects such as protein function prediction.

Farrokh has a doctoral degree certificate in Computer Science (University of Turku) and two master’s degree certificates, one in Computer Science (Master’s Degree Programme in Bioinformatics, University of Turku), and one in Computer Software Engineering (Iran University of Science and Technology). 

Teaching


I have been the responsible teacher for the course Algorithms in Bioinformatics, University of Turku, 2015-2020. I have also helped in teaching other NLP courses including Text mining and Deep Learning in Language Technology ​​​​​​​ at the Department of Computing, University of Turku. 


Research

With a strong track record in publication, achieving high ranks in several international text mining and machine learning competitions, and achieving the state-of-the-art results on several important datasets, Farrokh has been specializing in deep learning-based methods for Biomedical Natural Language Processing (BioNLP) and text mining. His research has focused on low-resource setups, where minimal training data is available.  

During 2021, Farrokh has worked as an AI scientist for Silo AI, developing text mining systems for clients, and as a researcher for AI academy, helping in the development of Massive Open Online Courses (MOOC). In 2022, Farrokh received his PhD degree certificate in Computer Science from University of Turku, with his thesis on ‘Optimizing Text Mining Methods for Biomedical Natural Language Processing’. Currently, Farrokh has a senior researcher position in TurkuNLP group, working on biomedical natural language processing and text mining. 

Publications

Sort by:

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 (2018)

Journal of the American Medical Informatics Association
Abeed Sarker, Maksim Belousov, Jasper Friedrichs, Kai Hakala, Svetlana Kiritchenko, Farrokh Mehryary, Sifei Han, Tung Tran, Anthony Rios, Ramakanth Kavuluru, Berry de Bruijn, Filip Ginter, Debanjan Mahata, Saif M. Mohammad, Goran Nenadic, Graciela Gonzalez-Hernandez
(Vertaisarvioitu alkuperäisartikkeli tai data-artikkeli tieteellisessä aikakauslehdessä (A1))

End-to-End System for Bacteria Habitat Extraction (2017)

Workshop on Biomedical Natural Language Processing
Farrokh Mehryary, Kai Hakala, Suwisa Kaewphan, Jari Björne, Tapio Salakoski, Filip Ginter
(Vertaisarvioitu artikkeli konferenssijulkaisussa (A4))

An expanded evaluation of protein function prediction methods shows an improvement in accuracy (2016)

Genome Biology
Jiang YX, Oron TR, Clark WT, Bankapur AR, D'Andrea D, Lepore R, Funk CS, Kahanda I, Verspoor KM, Ben-Hur A, Koo DCE, Penfold-Brown D, Shasha D, Youngs N, Bonneau R, Lin A, Sahraeian SME, Martelli PL, Profiti G, Casadio R, Cao RZ, Zhong Z, Cheng JL, Altenhoff A, Skunca N, Dessimoz C, Dogan T, Hakala K, Kaewphan S, Mehryary F, Salakoski T, Ginter F, Fang H, Smithers B, Oates M, Gough J, Toronen P, Koskinen P, Holm L, Chen CT, Hsu WL, Bryson K, Cozzetto D, Minneci F, Jones DT, Chapman S, Dukka BKC, Khan IK, Kihara D, Ofer D, Rappoport N, Stern A, Cibrian-Uhalte E, Denny P, Foulger RE, Hieta R, Legge D, Lovering RC, Magrane M, Melidoni AN, Mutowo-Meullenet P, Pichler K, Shypitsyna A, Li B, Zakeri P, ElShal S, Tranchevent LC, Das S, Dawson NL, Lee D, Lees JG, Sillitoe I, Bhat P, Nepusz T, Romero AE, Sasidharan R, Yang HX, Paccanaro A, Gillis J, Sedeno-Cortes AE, Pavlidis P, Feng S, Cejuela JM, Goldberg T, Hamp T, Richter L, Salamov A, Gabaldon T, Marcet-Houben M, Supek F, Gong QT, Ning W, Zhou YP, Tian WD, Falda M, Fontana P, Lavezzo E, Toppo S, Ferrari C, Giollo M, Piovesan D, Tosatto SCE, del Pozo A, Fernandez JM, Maietta P, Valencia A, Tress ML, Benso A, Di Carlo S, Politano G, Savino A, Rehman HU, Re M, Mesiti M, Valentini G, Bargsten JW, van Dijk ADJ, Gemovic B, Glisic S, Perovic V, Veljkovic V, Veljkovic N, Almeida-e-Silva DC, Vencio RZN, Sharan M, Vogel J, Kansakar L, Zhang S, Vucetic S, Wang Z, Sternberg MJE, Wass MN, Huntley RP, Martin MJ, O'Donovan C, Robinson PN, Moreau Y, Tramontano A, Babbitt PC, Brenner SE, Linial M, Orengo CA, Rost B, Greene CS, Mooney SD, Friedberg I, Radivojac P
(Vertaisarvioitu alkuperäisartikkeli tai data-artikkeli tieteellisessä aikakauslehdessä (A1))
People search