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

Contact

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

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Neural Network and Random Forest Models in Protein Function Prediction (2020)

IEEE/ACM Transactions on Computational Biology and Bioinformatics
Hakala Kai, Kaewphan Suwisa, Björne Jari, Mehryary Farrokh, Moen Hans, Tolvanen Martti, Salakoski Tapio, Ginter Filip
(Vertaisarvioitu alkuperäisartikkeli tai data-artikkeli tieteellisessä aikakauslehdessä (A1))

The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens (2019)

Genome Biology
Naihui Zhou, Yuxiang Jiang, Timothy R. Bergquist, Alexandra J. Lee, Balint Z. Kacsoh, Alex W. Crocker, Kimberley A. Lewis, George Georghiou, Huy N. Nguyen, Md Nafiz Hamid, Larry Davis, Tunca Dogan, Volkan Atalay, Ahmet S. Rifaioglu, Alperen Dalkıran, Rengul Cetin Atalay, Chengxin Zhang, Rebecca L. Hurto, Peter L. Freddolino, Yang Zhang, Prajwal Bhat, Fran Supek, José M. Fernández, Branislava Gemovic, Vladimir R. Perovic, Radoslav S. Davidović, Neven Sumonja, Nevena Veljkovic, Ehsaneddin Asgari, Mohammad R.K. Mofrad, Giuseppe Profiti, Castrense Savojardo, Pier Luigi Martelli, Rita Casadio, Florian Boecker, Heiko Schoof, Indika Kahanda, Natalie Thurlby, Alice C. McHardy, Alexandre Renaux, Rabie Saidi, Julian Gough, Alex A. Freitas, Magdalena Antczak, Fabio Fabris, Mark N. Wass, Jie Hou, Jianlin Cheng, Zheng Wang, Alfonso E. Romero, Alberto Paccanaro, Haixuan Yang, Tatyana Goldberg, Chenguang Zhao, Liisa Holm, Petri Törönen, Alan J. Medlar, Elaine Zosa, Itamar Borukhov, Ilya Novikov, Angela Wilkins, Olivier Lichtarge, Po-Han Chi, Wei-Cheng Tseng, Michal Linial, Peter W. Rose, Christophe Dessimoz, Vedrana Vidulin, Saso Dzeroski, Ian Sillitoe, Sayoni Das, Jonathan Gill Lees, David T. Jones, Cen Wan, Domenico Cozzetto, Rui Fa, Mateo Torres, Alex Warwick Vesztrocy, Jose Manuel Rodriguez, Michael L. Tress, Marco Frasca, Marco Notaro, Giuliano Grossi, Alessandro Petrini, Matteo Re, Giorgio Valentini, Marco Mesiti, Daniel B. Roche, Jonas Reeb, David W. Ritchie, Sabeur Aridhi, Seyed Ziaeddin Alborzi, Marie-Dominique Devignes, Da Chen Emily Koo, Richard Bonneau, Vladimir Gligorijević, Meet Barot, Hai Fang, Stefano Toppo, Enrico Lavezzo, Marco Falda, Michele Berselli, Silvio C.E. Tosatto, Marco Carraro, Damiano Piovesan, Hafeez Ur Rehman, Qizhong Mao, Shanshan Zhang, Slobodan Vucetic, Gage S. Black, Dane Jo, Erica Suh, Jonathan B. Dayton, Dallas J. Larsen, Ashton R. Omdahl, Liam J. McGuffin, Danielle A. Brackenridge, Patricia C. Babbitt, Jeffrey M. Yunes, Paolo Fontana, Feng Zhang, Shanfeng Zhu, Ronghui You, Zihan Zhang, Suyang Dai, Shuwei Yao, Weidong Tian, Renzhi Cao, Caleb Chandler, Miguel Amezola, Devon Johnson, Jia-Ming Chang, Wen-Hung Liao, Yi-Wei Liu, Stefano Pascarelli, Yotam Frank, Robert Hoehndorf, Maxat Kulmanov, Imane Boudellioua, Gianfranco Politano, Stefano Di Carlo, Alfredo Benso, Kai Hakala, Filip Ginter, Farrokh Mehryary, Suwisa Kaewphan, Jari Björne, Hans Moen, Martti E.E. Tolvanen, Tapio Salakoski, Daisuke Kihara, Aashish Jain, Tomislav Šmuc, Adrian Altenhoff, Asa Ben-Hur, Burkhard Rost, Steven E. Brenner, Christine A. Orengo, Constance J. Jeffery, Giovanni Bosco, Deborah A. Hogan, Maria J. Martin, Claire O’Donovan, Sean D. Mooney, Casey S. Greene, Predrag Radivojac, Iddo Friedberg
(A1 Vertaisarvioitu alkuperäisartikkeli tieteellisessä lehdessä )