Automated scientific knowledge assembly and modeling for rapid pandemic response
Visiting speaker
Benjamin M. Gyori
Associate Professor, Khoury College of Computer Sciences and Department of Bioengineering, College of Engineering, Northeastern University
Past Talk
Hybrid talk
Friday
Jan 12, 2024
Watch video
11:00 am
EST
Virtual
177 Huntington Ave.
11th floor
11th floor
Devon House
58 St Katharine's Way
London E1W 1LP, UK
58 St Katharine's Way
London E1W 1LP, UK
Effective response to emerging crises such as the COVID-19 pandemic requires rapid decision making informed by scientific knowledge. However, scientific knowledge is fragmented across unstructured text in publications, partially overlapping knowledge bases, and software code corresponding to model implementations. In addition, new findings appear at a pace intractable for any human scientist, with around four thousand new publications a day in biomedicine alone. To address these challenges, we present a framework for biomedical knowledge assembly and modeling at scale, illustrated through three applications relevant to pandemic response: (1) automated generation of mechanistic hypotheses for antiviral drug response using self-updating molecular biology models, (2) extraction and assembly of vaccine and pathogen knowledge from literature and databases to assess vaccine platform-pathogen compatibility, and (3) rapid prototyping and reuse of epidemiology models using machine-assisted modeling.
About the speaker
About the speaker
Benjamin M. Gyori is an associate professor in the Khoury College of Computer Sciences at Northeastern University, based in Boston. He is jointly appointed with the Department of Bioengineering in the College of Engineering.
Gyori’s research combines computational modeling, machine learning, natural language processing, and human–machine interaction to improve our understanding of complex human biology, thereby opening doors to advances in health care. His interest in the interdisciplinary field of computational systems biology stems from his fascination for 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 has been leading several research projects focused on artificial intelligence 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.
Benjamin M. Gyori is an associate professor in the Khoury College of Computer Sciences at Northeastern University, based in Boston. He is jointly appointed with the Department of Bioengineering in the College of Engineering.
Gyori’s research combines computational modeling, machine learning, natural language processing, and human–machine interaction to improve our understanding of complex human biology, thereby opening doors to advances in health care. His interest in the interdisciplinary field of computational systems biology stems from his fascination for 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 has been leading several research projects focused on artificial intelligence 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.
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