Benjamin M. Gyori, Ph.D.

Ben leads the Machine-assisted Modeling & Analysis team at the Laboratory of Systems Pharmacology, Harvard Medical School. He is the recipient of a DARPA Young Faculty Award for 2020-2022 and the DARPA Director's Fellowship Award for 2022-2023.

Ben's research is at the intersection of systems biology, bioinformatics and artificial intelligence, and aims to understand how biological cells work and react to drugs and environmental signals using computational approaches. Ben developed INDRA, a software tool which automatically assembles biochemical mechanisms extracted from the scientific literature into explanatory models. He is also working on a human-machine communication system which allows scientists to interact with a computer partner to construct and test hypotheses about molecular systems. Ben obtained his Ph.D. in computational systems biology from the National University of Singapore. 

• In August 2022, I started the MIRA project as part of the DARPA ASKEM program whose aim is to accelerate scientific modeling
• In June 2022 I received the DARPA Director's Fellowship Award to continue my team's work started as part of my DARPA Young Faculty Award.
• I presented at the Knowledge Graph Conference on automated knowledge graph assembly and human-machine interaction for biomedicine: https://healthcare-life-sciences.github.io/benjamin.html
• I was invited to the 1st Workshop on Nobel Turing Challenge where I presented on "Large-scale Knowledge Assembly for Hypothesis Generation and Human-machine Interaction"
• I was an invited participant and speaker at the NSF Workshop on the Future of Protein Functional Annotation in Orlando where we discussed an action plan for integrating and making accessible all available knowledge about proteins and their families.
• I was invited to give the first ISCBAcademy semniar for SysMod COSI, the recording is available here: https://www.youtube.com/watch?v=v_XC_JUADOQ
• I was awarded the DARPA Young Faculty Award (https://www.darpa.mil/work-with-us/for-universities/young-faculty-award) for 2020-2022
  (https://hms.harvard.edu/news/awards-recognitions-august-2020)
• An interview  in Harvard Medicine News about my YFA award and ongoing projects is available at https://hms.harvard.edu/news/ais-next-wave.
• The COVID-19 Disease Map to which the INDRA, EMMAA, CLARE and Bob systems have contributed in various ways is now published in Molecular Systems Biology.
• Our preprint on the Gilda grounding system is now available on bioRxiv: https://www.biorxiv.org/content/10.1101/2021.09.10.459803v1
• I was invited to attend the Future Scientifics Methodologies meeting organized by DOE (https://www.orau.gov/2020doe-coi/participants.htm) to create a vision for how future computational fabrics may shape, and be shaped by, scientific advances over the next 10-30 years. 
• Our paper on the INDRA Interactive Pathway Map is now out, visit http://pathwaymap.indra.bio to try it out and check out the Twitter tutorial with videos.
• I recently gave a talk in the Stanford Center for Cancer Systems Biology seminar series: http://ccsb.stanford.edu/events/seminars/2019-seminars.html
• My recent invited talk at the Network Science Institute at Northeastern University is available at: https://www.youtube.com/watch?v=LjRSCE3towM
• I am on the conference committee of the Modeling the World's Systems 2019 conference, accepting submissions until February 1, 2019
• I'm co-PI on our project to build an Ecosystem of Machine-maintained Models with Automated Analysis (EMMAA) which was awarded in November 2018 under the DARPA Automating Scientific Knowledge Extraction program, the first of DARPA's Artificial Intelligence Exploration programs. See http://emmaa.indra.bio.
• In October 2018 I gave a keynote talk at the Integrative Pathway Modelling in Systems Biology and Systems Medicine conference in Germany: http://www.integrative-pathway-models.de/meetings/income2018-conference-...
• I was selected as a DARPA Riser to participate in DARPA's 60th anniversary Symposium (DARPA60) in Sept 2018, National Harbor, MD. I presented "Model-building machines that monitor, understand, and explain complex systems at scale".
• In May 2018 I was an invited speaker at the Modeling the World's Systems conference in Pittsburgh and gave a tutorial on automated model assembly with INDRA
• An intro video for our paper "From word models to executable models of signaling networks using automated assembly" is now available at: https://vimeo.com/265004298