Benjamin Gyori
Associate Professor

Education
- PhD in Computational Biology, National University of Singapore
- BSc in Computer Engineering, Budapest University of Technology and Economics — Hungary
Biography
Benjamin M. Gyori is an associate professor in the Khoury College of Computer Sciences and the College of Engineering at Northeastern University, based in Boston.
Gyori’s research combines computational modeling, machine learning, natural language processing, and human–machine interaction to improve our understanding of complex human biology, opening doors to advances in healthcare. His interest in the interdisciplinary field of computational systems biology stems from his fascination with mathematical and computational models of natural systems.
During his tenure as director of machine-assisted modeling and analysis at Harvard Medical School’s Laboratory of Systems Pharmacology, Gyori was the principal investigator on multiple DARPA-funded research grants; he also led a research team focused on AI-based approaches to modeling and managing biological processes and other complex systems. Throughout, Gyori has sought to create computational frameworks that combine high-throughput data with the biological mechanisms that govern health. In doing so, he has earned DARPA’s Young Faculty, Director’s Fellowship, and Riser Awards, and has published in Molecular Systems Biology, Cell Systems, and Scientific Data, among other journals.
Since joining Khoury College in 2023, Gyori has taught data science courses and led several research projects focused on AI approaches to complex systems modeling, biomedical data integration, and accelerating vaccine development with funding from DARPA, DTRA, and the Chan-Zuckerberg Initiative. He is an advocate for open science and open-source scientific software, and has mentored a team of scientific software developers and researchers.
Recent publications
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A simple standard for ontological mappings 2023: updates on data model, collaborations and tooling
Citation: Nicolas Matentzoglu, Ian Braun, Anita R. Caron, Damien Goutte-Gattat, Benjamin M. Gyori, Nomi L. Harris, Emily Hartley, Harshad B. Hegde, Sven Hertling, Charles Tapley Hoyt, Hyeongsik Kim , Huanyu Li , James A. McLaughlin, Cássia Trojahn, Nicole A. Vasilevsky, Christopher J. Mungall. (2023). A simple standard for ontological mappings 2023: updates on data model, collaborations and tooling OM@ISWC, 73-78. https://ceur-ws.org/Vol-3591/om2023_STpaper3.pdf -
Prediction and curation of missing biomedical identifier mappings with Biomappings
Citation: Charles Tapley Hoyt, Amelia L. Hoyt, Benjamin M. Gyori. (2023). Prediction and curation of missing biomedical identifier mappings with Biomappings Bioinform., 39. https://doi.org/10.1093/bioinformatics/btad130 -
NDEx IQuery: a multi-method network gene set analysis leveraging the Network Data Exchange
Citation: Rudolf T. Pillich, Jing Chen, Christopher Churas, Dylan Fong, Benjamin M. Gyori, Trey Ideker, Klas Karis, Sophie N. Liu, Keiichiro Ono, Alexander R. Pico, Dexter Pratt. (2023). NDEx IQuery: a multi-method network gene set analysis leveraging the Network Data Exchange Bioinform., 39. https://doi.org/10.1093/bioinformatics/btad118 -
ChemicalX: A Deep Learning Library for Drug Pair Scoring
Citation: Benedek Rozemberczki, Charles Tapley Hoyt, Anna Gogleva, Piotr Grabowski, Klas Karis, Andrej Lamov, Andriy Nikolov, Sebastian Nilsson, Michaël Ughetto, Yu Wang , Tyler Derr, Benjamin M. Gyori. (2022). ChemicalX: A Deep Learning Library for Drug Pair Scoring KDD, 3819-3828. https://doi.org/10.1145/3534678.3539023