James Fairbanks, PhD

Education | Work Experience | Achievements | Teaching | Mentoring | Selected Technical Skills

Education

Georgia Institute of Technology

Ph.D Computational Science and Engineering, 2012 -- 2016 (Atlanta, GA)

  • Research Assistant 2012, NDSEG Fellow 2013-16, Teaching Assistant 2016
  • Adviser: Professor David A. Bader
  • Dissertation: Graph Analysis Combining Numerical Statistical and Streaming Techniques
  • Qualifier: Computational Data Analysis (ML) and High Performance Computing (HPC)
  • Committee: Rich Vuduc, Haesun Park, Polo Chau, Dana Randall, G. Sanders (LLNL)

University of Florida

B.S. Mathematics, 2009 -- 2012 (Gainesville, FL)

  • Summa cum laude
  • Thesis: A Ramsey Theorem for Indecomposable Matchings

Work Experience

  • University of Florida (Gainesville, FL)

    Assistant Professor, Jan 2021 - Present

    • Leading the Generalized Algebraic Techniques Advancing Science (GATAS) Lab
    • Research focus: advancing computational science and engineering with the techniques of applied category theory
    • Teaching focus: scientific computing

  • Georgia Tech Research Institute (GTRI) (Atlanta, GA)

    Research Engineer, May 2016 - Dec 2020

    • Conduct research into high performance data analysis algorithms and applications
    • Win and manage federally funded research contracts
    • Deliver applied research projects to sponsors such as source code, web applications, technical reports
    • Mentor and advise students in connection to research projects

  • Ionic Security (Atlanta, GA)

    Data Scientist, 2015

    • Developed data analytics software
    • Designed a service oriented architecture for near real time analysis written in Go and Julia
    • Leveraged time series and network database technologies including Heka, InfluxDB, RabbitMQ, and ElasticSearch

  • DOE -- Lawrence Livermore National Laboratory (Livermore, CA)

    Institute for Scientific Computing Research Intern, 2014

    • Studied relationship between numerical accuracy of eigensolvers and solution quality of mincut graph partitioning
    • Developed very fast approximate eigensolvers for large graphs
    • Applied probabilistic reasoning to describe numerical computations
    • Presented results at LLNL poster session

  • IDA -- Center for Computing Sciences (Bowie, MD)

    Adjunct Faculty, 2013

    • Conducted research into Malware structure and similarities by studying execution patterns of malicious programs
    • Developed clustering and methods for understanding the structure of malicious programs with graph analytics
    • Built a high performance distributed system for conducting these analyses with ZeroMQ communication

Funding

DatesRoleSponsorTitleAgreementAmount
2022 -- 2026 Principal Investigator DARPA ASKEM: Generalized Algebraic Techniques Advancing Scientific Discovery HR00112220038 5.8M
2022 -- 2023 Principal Investigator DARPA Director's Fellowship: Model Aware Scientific Computing ~W911NF2110323 250K
2022 -- 2025 Co-PI DARPA Perceptual Task Guidance: ENKIx HR00112220004 4.8M
2020 -- 2022 Principal Investigator DARPA Young Faculty Award: Model Aware Scientific Computing Agreement No.~W911NF2010292 500K
2020 -- 2021 Principal Investigator DARPA AIE: Automating Scientific Knowledge Extraction Extended Agreement No.~HR00111990008 700K
2019 -- 2021 Principal Investigator DARPA Directly Computable Models: Generalized Algebraic Theories Enhancing Multiphysics Agreement No.~HR00112090067 1M
2018 -- 2020 Principal Investigator DARPA Artificial Intelligence Exporation: Automating Scientific Knowledge Extraction Agreement No.~HR00111990008 1M
2019 -- 2023 Principal Investigator DARPA Artificial Social Intelligence for Successful Teams (ASIST) Agreement No.~HR001119C0135-001 400K
2016 -- 2018 Principal Investigator NIJ Developing Novel Means of Evidence Collection Grant Number 2016-MU-MU-K004 400K
2019 -- 2022 Co-PI ONR Extracting, Explaining, and Estimating Information in Sonar Data (E3ISD) Contract No. N00014-19-C-2069 695K
2019 -- 2021 Co-PI ONR Mine Counter-measures Situational Awareness 375K
2016 -- 2019 Key Personnel ONR Performance Estimation of Underwater Mine Counter-measures Operations Contract No. N00014-16-C-3041 990K
2016 -- 2019 Key Personnel GTRI SI Multi-source Anticipatory Intelligence 900K

Achievements

Honors, Awards, and Fellowships

May 2022 American Mathematical Society: Mathematical Research Community on Applied Category Theory
2018 Office of the Director of National Intelligence -- XAMINE Challenge
2013-16 National Defense Science and Engineering Fellowship
2012-16 Presidential Fellowship for Graduate Study at Georgia Tech
2011-12 University Scholar at the University of Florida
2012 Kermit Sigmon Scholarship for service to the mathematical community
2015 Tau Beta Pi, Engineering Honor Society, Georgia Tech Chapter
2012 Phi Beta Kappa, University of Florida Chapter

Leadership and Service

2022 Proposal Referee: Army Research Office, Topic: Network Science, ARO, Proposal Referee in Network Science
2022 Journal Referee: Compositionality, Editor: Pawel Sobocinski
2023 Applied Category Theory Conference General Chair and Program Committee Member
2022 Applied Category Theory Conference Organizer and Program Committee Member
Aug 2022 DARPA AI Strategy meeting for UF, S. Jaishankar, G. Michailidis, F. Masters, A. Zare, J. P. Fairbanks, Lewis and Burke Associates
Spring 2021 Upper Division Cirriculum Committee, Chair: Jeremiah Blanchard, UF CISE
  • Developed Syllabi for new courses in CISE, including COP 4533 Algorithms Abstraction and Design
Spring 2021 Programming Language Task Force, Chair: Parisa Rashidi, UF HWCOE
Feb 2021 PhD Student Recruitment Panel, UF CISE
2019 JuliaCon Organizing Program Committee
2018 JuliaCon Organizing Committee Vice Program Chair
  • Organized the technical program of a 3 day international conference on the Julia programming language
  • Ran Program Committee meetings to decide on accepted abstracts and presentations
  • Led poster session preparations
2017 Tau Beta Pi Atlanta Alumni Chapter President
  • Organized professional networking events for local Atlanta Area Engineers
2015 Georgia Tech College of Computing Graduate Student Association VP for the School of CSE
  • Represented department students to university administration committees on curriculum and funding
  • Organized social and professional networking events for graduate students
  • Chaired the organizing committee of HotCSE graduate research seminar providing early career presentation opportunities to graduate students
2011 Univ. Florida Pi Mu Epsilon Chapter President
  • Organized a series of talks for the mathematics students at UF on diverse mathematical topics and skills incl. LaTeX, programming and technical communication in the field.
2009 Eagle Scout

Teaching

University of Florida

Spring 2021 COT 4501 - Numerical Analysis a Computational Approach
Fall 2021 CIS 4930 - Abstraction Composition Computation
Fall 2021 CIS 6930 - Abstraction Composition Computation

Professional Education

Aug 2022 CANMOD Mathematical and Computational Modeling of Epidemics Workshop, Organizer and Instructor 1 week training for mathematical epidemiologists to learn applied category theoretic tools, Nathaniel Osgood, Simon Frasier University, Vancouver, Canada (virtual due to Covid-19)
Spring 2021 ACT Adjoint School Instructor, Organizers: S. Libkind, D. J. Myers, Coteacher: E. Patterson, TA: O. Lynch, Applied Category Theory Conference
Spring 2019 Data Analytics Methodology with J. Poovey
Fall 2018 Programming for Data Science with Beverly Wright
Spring 2017 Data Analytics Methodology with J. Poovey, D. Ediger, and M. Rost.
Fall 2016 Big Data Analytics with J. Poovey, D. Ediger, and M. Rost.

Teaching Assistant at Georgia Tech

Spring 2016 CSE 6643 Numerical Linear Algebra with Prof. Haesun Park
Spring 2014 CSE 6220 High Performance Computing with Prof. Srinivas Aluru

Mentoring

DatesNameDegreeGraduationEmployment
2022-2023 University Multicultural Mentoring Program BS 2022 UMMP Mentor
2022-Present Adam Gregory PhD 2022 Thesis Committee
2022-Present Hong Yu PhD 2022 Thesis Committee
2022-Present Daniel A. Delgado PhD 2022 Thesis Committee
2021-Present Luke Morris PhD 2021 Thesis Advisor
2021-Present Tyler Hanks PhD Student, NSF GRFP Fellow 2021 Thesis Advisor
2021-22 Kris Brown Post-Doctoral Researcher 2022 UF
2021 UF HWCOE Mentoring Academy Participant 2021
2021 ACT Adjoint School 2021 A. Knoerr, G. Generaux, A. Searle
2021-2022 Kris Brown Chemical Engineering, Stanford University 2021
2020-Present Sophie Libkind Mathematics, Stanford University 2021
2020-Present Owen Lynch Statistics University of Utrecht 2021
2021-22 Julian Perez BS BME GT 2021
2021 Stephen Wellburg BS DAS UF 2021
2018-19 Sreenath Reparti BS ISYE Georgia Tech 2019 KPMG
2019 Kun Cao MS CS Georgia Tech 2019 GT
2019 Abhinav Mehndiratta 2019 Google Summer of Code
2016-18 Rohit Varkey MS CS Georgia Tech 2018 Google
2016-19 Micah Halter BS CS Georgia Tech 2019 GTRI
2016 Nate Knauf BS CS Georgia Tech 2019 GT
2015 Pushkar Godbole MS CSE Georgia Tech 2016 Yelp

Selected Technical Skills

  • Programming languages (most familiar to least) Julia, Golang, SQL, Python, C, Bash
  • Computational Data Analysis (pandas, sklearn, Jupyter)
  • Web development with Golang and Python (flask)
  • Database Applications primarily with PostgreSQL and MongoDB
  • Practical computing skills such as \texttt{LINUX, git, make,} \LaTeX
  • Continuous Integration/Deployment

Research

Peer Reviewed Journal Articles

Aug 2022 An Algebraic Framework for Rapid Epidemic Modeling, S. Libkind, A. Baas, M. Halter, E. Patterson, and J. P. Fairbanks, Proc. of the Royal Society Phil. Trans.
Aug 2022 The application of applied category theory to quantify mission success, R. Garrett, J. Fairbanks, M. Loper, J. Moreland, Simulation
May 2022 A Diagrammatic View of Differential Equations in Physics, E. Patterson, A. Baas, T. Hosgood, J. P. Fairbanks, Mathematics in Engineering
Feb 2022 Categorical Data Structures for Technical Computing, E. J. Patterson, O. Lynch, J. P. Fairbanks, Compositionality
Jan 2021 Category-theoretic formulation of the model-based systems architecting cognitive-computational Cycle, Y. Mordecai, J. P. Fairbanks, E.F. Crawley, MDPI Applied Sciences
2017 Spectral Partitioning with Blends of Eigenvectors, J. P. Fairbanks, D. A. Bader, G. D. Sanders, Journal of Complex Networks
2015 Behavioral Clusters in Dynamic Graphs, J. P. Fairbanks, R. Kannan, H. Park, D. A. Bader, Parallel Computing Special Issue of Scientific Graph Analysis
Dec 2011 A Ramsey Theorem for Indecomposable Matchings, J. P. Fairbanks, Electronic Journal of Combinatorics, Vol 18(1)

Peer Reviewed Conference Publications

Jul 2022 Compositional Exploration of Combinatorial Scientific Models, K. Brown, T. Hanks, J. P. Fairbanks, Applied Category Theory
Jul 2022 Computational Category-Theoretic Rewriting, K. Brown, E. Patterson, T. Hanks, J. P. Fairbanks, International Conference on Graph Transformation
Jul 2021 Operadic Modeling of Dynamical Systems: Mathematics and Computation, S. Libkind, A. Baas, E. J. Patterson, J. P. Fairbanks, Applied category Theory
Jul 2020 SemanticModels.jl: A Julia Package for Scientific Model Augmentation, M. Halter, S. Raparti, K. Cao, C. Herlihy, J. P. Fairbanks, Proceedings of the JuliaCon Conferences
Aug 2019 Constructing Knowledge Graphs from Scientific Texts, K. Cao, J. P. Fairbanks, KDD workshop on Machine Learning in Graphs
July 2019 A Compositional Framework for Scientific Model Augmentation, M. Halter, C. Herlihy, J. P. Fairbanks, Applied Category Theory
May 2019 Semantic Program Analysis for Scientific Model Augmentation, J. P. Fairbanks, C. Herlihy, K. Cao, S. Reparthi, Modeling the Worlds Systems
Oct 2018 Digital Witness: Remote Methods for Volunteering Digital Evidence on Mobile Devices, N. Campbell, T. Goodyear, W. Messer, E. Stuart, J. P. Fairbanks, IEEE Technologies for Homeland Security
Sep 2018 Performance Effects of Backing Data Stores in Community Detection Algorithms, R. Varkey Thankachan, B. P. Swenson, J. P. Fairbanks, IEEE High Performance Extreme Computing
Feb 2018 Credibility Assessment in the News: Do we need to read?, N. Fitch, N. Knauf, J. P. Fairbanks, E. Briscoe, ACM WSDM MIS2
Sep 2017 Integrating Productivity-Oriented Programming Languages with High-Performance Data Structures, R. Varkey Thankachan, E. Hein, B. P. Swenson, J. P. Fairbanks, IEEE High Performance Extreme Computing
2017 Deriving Streaming Graph Algorithms from Static Definitions, J. P. Fairbanks, D. M. Ediger, IEEE International Parallel and Distributed Processing Graph Algorithms Building Blocks
Jan 2017 Graph Partitioning with Spectral Blends, J. P. Fairbanks, D. A. Bader, and G. D. Sanders, Oxford Journal of Complex Networks
2017 Ranking in Dynamic Graphs Using Exponential Centrality, E. Nathan, J. P. Fairbanks, D. A. Bader, International Conference on Complex Networks and their Applications
2017 Graph Ranking Guarantees for Numerical Approximations to Katz Centrality, E. Nathan, G. Sanders, J. P. Fairbanks, V. Henson and D. Bader, International Conference On Computational Science
2017 Deriving Streaming Graph Algorithms from Static Definitions., D. M. Ediger and J. P. Fairbanks, IEEE Parallel and Distributed Processing - Graph Algorithm Building Blocks
A local measure of community change in dynamic graphs., A. Zakrzewska, E. Nathan, J. P. Fairbanks, D. A. Bader, IEEE/ACM ASONAM
Jul 2016 Novel Stopping Criteria for Spectral Partitioning, J. P. Fairbanks, A. Zakrzewska, D.A. Bader, SIAM Network Science
Aug 2013 A Statistical Framework for Analyzing Streaming Graphs, J. P. Fairbanks, D. Ediger, R. McColl, D.A. Bader, E. Gilbert, IEEE/ACM ASONAM

Panels

May 2022 HWCOE Early Career Researcher Award Panel, UF ECR Development Workshop
  • Host: Forrest Masters (UF)
May 2019 Abstract Representations of Scientific Models, Paul Cohen (Pitt), Eric Davis (Galois Inc), Alec Nielson (Azimov.io), DARPA ASKE Principal Investigator Meeting
  • Host: Josh Elliot (DARPA), Moderator: J. P. Fairbanks
May 2019 Toward the Modeling Stack Panel, Joshua Elliot (DARPA), John Bachman (Harvard Medical School), Eric Davis (Galois), Clayton Morrison (Arizona), J. P. Fairbanks (GTRI), Modeling the World's Systems 2019
  • Host: Paul Cohen (Pitt), Moderator: Bruce Childers (Pitt)

Conference Presentations

Jul 2022 Diagrammatic differential equations: Formal categorical framework and applications to multiphysics simulation,, E. Patterson, T. Hosgood (speaker), A. Baas, J. Fairbanks, Applied Category Theory 2022
Jul 2022 Typed and stratified models with slice categories, S. Libkind (speaker), E. Patterson, A. Baas, M. Halter, J. Fairbanks, Applied Category Theory 2022
Jul 2022 Individual.jl: Rewriting individual-based models for epidemiology using graph rewriting, S. Wu (speaker), K. Browm, and J. Fairbanks, Applied Category Theory 2022
Jul 2021 AlgebraicDynamics: Compositional dynamical systems, S. Libkind, J. P. Fairbanks, JuliaCon, Online
Jul 2021 Shaped Data with Acsets, O. Lynch, E. J. Patterson, J. P. Fairbanks, JuliaCon, Online
Jul 2019 SemanticModels.jl: Not Just Another Modeling Framework, J. P. Fairbanks and C. R. Herlihy, JuliaCon, Baltimore, MD
Apr 2019 Complex Systems Analysis of Hybrid Warfare, M. Nadolski and J. P. Fairbanks, Conference on Systems Engineering Research
2018 Graph Interfaces: Bespoke Graphs for Every Occasion, M. Besan\c{c}on, J. P. Fairbanks, JuliaCon, London, UK
2018 The JuliaGraphs Ecosystem: Move Fast and Don't Break Things, J. P. Fairbanks, JuliaCon, London, UK
2017 Assessing Credibility in Global Media Networks, J. P. Fairbanks, Human Language Technologies
2017 Using Big Data to Predict and Analyze Cooperation and Conflict, T. Frederick, C. Herlihy, J. P. Fairbanks, The Conflict Conference at UT-Austin
2017 LightGraphs: Our Network, Our Story, S. Bromberger, J. P. Fairbanks, JuliaCon, Berkeley, CA

Invited Talks

Oct 2022 Computational Physics with Categories, J. P. Fairbanks, Institute of Theoretical Physics Friedrich-Alexander-Universität Erlangen-Nürnberg
Sept 2022 Using Category Theory to Design Computational Mathematics Software, J. P. Fairbanks, UF -- Numerical Analysis and SIAM seminar
Jun 2022 Model Aware Scientific Computing with Categories, J. P. Fairbanks, Air Force Research Lab -- Information Directorate, Rome, NY
May 2022 Diagrammatic Equations in Numerical Multiphysics, J. P. Fairbanks, Simula Research Laboratory Numerical Analysis Research Seminar (Oslo, NO)
May 2022 Introduction to Applied Category Theory, J. P. Fairbanks, Simula Research Laboratory Coffee and Theorems (Oslo, NO)
Mar 2022 Scientific Modeling with AlgebraicJulia, J. P. Fairbanks, Rel.ai Research Seminar
Spring 2022 Automated Model Space Exploration, K. Brown and J. P. Fairbanks, Topos Institute and UW-IHME Compositional Epidemiology Modeling Working Group
Fall 2022 Compositional Modeling of Disease Dynamics, S. Libkind and J. P. Fairbanks, Topos Institute and UW-IHME Compositional Epidemiology Modeling Working Group
Jan 2022 Computational Modeling with Category Theory, J. P. Fairbanks, UF College of Medicine -- Laboratory for Systems Medicine
Jul 2021 Compositional Modeling with AlgebraicJulia, E. J. Patterson and J. P. Fairbanks, NIH IMAG MSM Viral Pandemic Meetings
Jun 2021 The Algebraic Julia Ecosystem, a categorical approach to technical computing, J. P. Fairbanks, Topos Institute Berkeley Seminar
May 2021 Computational Categorical Algebra with Catlab, J. P. Fairbanks, Greta: Graph Transformation, Theory, and Applications Seminar
Feb 2021 Introduction to the AlgebraicJulia Software Ecosystem, J. P. Fairbanks, UF CISE and LLNL Advisory Board Annual Meeting
Feb 2021 Rethinking Set Theory and Applications, J. P. Fairbanks, UF University Math Society
Feb 2021 Model Aware Scientific Computing with Categories, J. P. Fairbanks, DARPA Young Faculty Award Principal Investigators Meeting Poster Session
Feb 2020 Automating Model Fusion with Decorated Cospan Categories, J. P. Fairbanks, MIT Category Theory Seminar
Jun 2019 Model IR Working Group: Initial Progress, J. P. Fairbanks, E. Davis, C. Morrison, DARPA ASKE Program Meeting
April 2019 Semantic Program Analysis for Scientific Model Augmentation, J. P. Fairbanks, Lawrence Livermore National Lab
March 2019 Program Analysis for Scientific Model Augmentation, J. P. Fairbanks, University of Florida Informatics Institute Spring Symposium
Nov 2018 Data Science and Graph Analytics with Julia, J. P. Fairbanks, University of Florida Informatics Institute
2018 Solving Applied Graph Theory Problems in the JuliaGraphs ecosystem, J. P. Fairbanks, MIT CSAIL Seminar

Posters

Oct 2021 Parameter Estimation by Minimizing the Loss with Respect to a Finite Difference Approximation on the Vector Field, J. L. Perez, A. Baas, M. C. Ferrall-Fairbanks, M. O. Platt, J. P. Fairbanks, Biomedical Engineering Society Annial Meeting
June 2021 Graphical Semantic Modeling with Semagrams.jl, O. Lynch, J. P. Fairbanks, E. J. Patterson, Applied Category Theory 2021
May 2019 Semantic Model Understanding for Scientific Model Augmentation, J. P. Fairbanks, Systems Biology of Human Disease, (Berlin, GER)
2017 QueryGarden: growing healthy applications in well prepared SQL, J. P. Fairbanks, OHDSI Symposium
2017 Implementing Real-Time Patient Level Predictions Using PLP Models, C. S. Brown, J. D. Duke, , J. P. Fairbanks, C. Herlihy, K. Mukadam, J. Poovey, M. Rost, OHDSI Symposium
Mar 2015 Discovering Block Structure with Approximate Eigenvectors, SIAM Computational Science and Engineering
2012 Ramsey Theorem for Indecomposable Matchings, Graph Theory at Georgia Tech (GT@GT)

Technical Reports

Dec 2018 Remote Methods for Volunteering Digital Evidence on Mobile Devices, E. Stuart, J. P. Fairbanks, National Institutes of Justice