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 201316, 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/Users/fairbanksj/DropboxUFL/Dropbox (UFL)/FARs/20222023 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
Dates  Role  Sponsor  Title  Agreement  Amount 

2023  2026  Principal Investigator  ONR  Domain Transfer for Continuity of Performance Across Synthetic Aperture Sonar  N0001423SB001  500K 
2022  2023  CoInvestigator  ARO  Machine Learningbased Sensor Fusion for Electrooptical and Infrared Target Detection  FA807518D0002DO015Gators  175K 
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  CoPI  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.~HR001119C0135001  400K 
2016  2018  Principal Investigator  NIJ  Developing Novel Means of Evidence Collection  Grant Number 2016MUMUK004  400K 
2019  2022  CoPI  ONR  Extracting, Explaining, and Estimating Information in Sonar Data (E3ISD)  Contract No. N0001419C2069  695K 
2019  2021  CoPI  ONR  Mine Countermeasures Situational Awareness  375K  
2016  2019  Key Personnel  ONR  Performance Estimation of Underwater Mine Countermeasures Operations  Contract No. N0001416C3041  990K 
2016  2019  Key Personnel  GTRI SI  Multisource 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 
201316  National Defense Science and Engineering Fellowship 
201216  Presidential Fellowship for Graduate Study at Georgia Tech 
201112  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

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

2017  Tau Beta Pi Atlanta Alumni Chapter President

2015  Georgia Tech College of Computing Graduate Student Association VP for the School of CSE

2011  Univ. Florida Pi Mu Epsilon Chapter President

2009  Eagle Scout 
Teaching
University of Florida
Spring 2024  COT 4501  Numerical Analysis a Computational Approach 
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 Covid19) 
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
Dates  Name  Degree  Graduation  Employment  

2024Present  Richard Samuelson  2024  Thesis Advisor  
20222023  University Multicultural Mentoring Program  2022  UMMP Mentor  
2022Present  Adam Gregory  2022  Thesis Committee  
2022Present  Hong Yu  2022  Thesis Committee  
2022Present  Daniel A. Delgado  2022  Thesis Committee  
2021Present  Luke Morris  2021  Thesis Advisor  
2021Present  Tyler Hanks  2021  Thesis Advisor  
202122  Kris Brown  2022  UF  
2021  UF HWCOE Mentoring Academy Participant  2021  
2021  ACT Adjoint School  2021  A. Knoerr, G. Generaux, A. Searle  
20212022  Kris Brown  2021  
2020Present  Sophie Libkind  2021  
2020Present  Owen Lynch  2021  
202122  Julian Perez  2021  
2021  Stephen Wellburg  2021  
201819  Sreenath Reparti  2019  KPMG  
2019  Kun Cao  2019  GT  
2019  Abhinav Mehndiratta  2019  Google Summer of Code  
201618  Rohit Varkey  2018  
201619  Micah Halter  2019  GTRI  
2016  Nate Knauf  2019  GT  
2015  Pushkar Godbole  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
Jan 2024  The Diagrammatic Presentation of Equations in Categories, Arxiv preprint 
Aug 2023  Computational CategoryTheoretic Rewriting, J. Logical and Algebraic Methods in Programming 
submitted  A compositional account of motifs, mechanisms, and dynamics in biochemical regulatory networks, arXiv preprint arXiv:2301.01445 
2023  The application of applied category theory to quantify mission success, SIMULATION 99 (2) 201220 
Under Review. 2023  Decapodes: A Diagrammatic Tool for Representing, Composing, and Computing Spatialized Partial Differential Equations, Journal of Computational Science 
Compositional Algorithms on Compositional Data: Deciding Sheaves on Presheaves, arxiv  
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. 
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  Categorytheoretic formulation of the modelbased systems architecting cognitivecomputational Cycle, Y. Mordecai, J. P. Fairbanks, E.F. Crawley, MDPI Applied Sciences 11 (4), 1945 
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
2023  A Compositional Framework for Convex Model Predictive Control, Submitted to IEEE CDC 
2023  Characterizing Compositionality of LQR from the Categorical Perspective, Submitted to IEEE CDC 
2022  Compositional Exploration of Combinatorial Scientific Models, Applied Category Theory 
Jul 2022  Compositional Exploration of Combinatorial Scientific Models, K. Brown, T. Hanks, J. P. Fairbanks, Applied Category Theory 
Jul 2022  Computational CategoryTheoretic Rewriting, K. Brown, E. Patterson, T. Hanks, J. P. Fairbanks, International Conference on Graph Transformation (Best Paper Award) 
Jul 2021  Operadic Modeling of Dynamical Systems: Mathematics and Computation, S. Libkind, A. Baas, E. J. Patterson, J. P. Fairbanks, Applied category Theory (Proceedings) 
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 ProductivityOriented Programming Languages with HighPerformance 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

May 2019  Abstract Representations of Scientific Models, Paul Cohen (Pitt), Eric Davis (Galois Inc), Alec Nielson (Azimov.io), DARPA ASKE Principal Investigator Meeting

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

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 individualbased 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 
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 UTAustin 
2017  LightGraphs: Our Network, Our Story, S. Bromberger, J. P. Fairbanks, JuliaCon, Berkeley, CA 
Invited Talks
2023  Abstraction and Composition in Modeling and Simulation, Luke Morris, Andrew Baas, Jesus Arias, Maia Gaitlin, James Fairbanks, SIAM Conference on Computational Science and Engineering 
Aug 2022  Applied Category Theory for the Mathematics of Disease, James Fairbanks, Canadian Network for Modeling Infections Disease 
Jan 2023  Computational Category Theory in Applied Mathematics, JP Fairbanks and O Lynch, Joint Mathematics Meetings 
Jan 2023  A Categorical Framework for (Gene) Regulatory Networks, R Aduddell, PS Ocal, JP Fairbanks, E Patterson, B Shapiro, and A Kumar, Joint Mathematics Meetings 
Nov 2022  Scientific and Engineering Modeling with Applied Category Theory, James Fairbanks, DARPA Young Faculty Colloquium 
Jun 2022  Diagrammatic Equations in Physics: Directly Computable Models, James Fairbanks, Lawrence Livermore National Laboratory Center for Applied Scientific Computing 
Feb 2023  Chopping things up to decide stuff fast, Ben Bumpus, James Fairbanks, 54th Southeastern International Conference on Combinatorics Graph Theory and Computing, Boca Raton, Florida, USA 
Abstraction and Composition in Modeling and Simulation, Luke Morris, Andrew Baas, Jesus Arias, Maia Gaitlin, James Fairbanks, University of Florida Graduate Mathematics Association (GMA)  
Sep 2022  Abstraction and Composition in Modeling and Simulation Seminar, James Fairbanks, Mechanical and Aerospace Engineering Department Affiliate Seminar 
Aug 2022  Scientific and Engineering Modeling with Applied Category Theory, James Fairbanks, MAE Control Theory Working Group 
June 2022  Diagrammatic Equations for Complex Machine Learning Formulations, James Fairbanks and Alina Zare, ECE Department ONR Site Visit 
Mar 2023  Decapodes.jl: A Framework for Multiphysics Simulation, James Fairbanks, MAE Department AFOSR Visit 
October 2022  Enkix Task Reasoning, James Fairbanks and Evan Patterson, DARPA Site Visit 
Nov 2022  Enkix Task Reasoning, James Fairbanks and Evan Patterson, DARPA Program Review 
May 2022  Computational Modeling with Category Theory, Systems Medicine Laboratory Seminar at UF College of Medicine 
Oct 2022  Computational Physics with Categories, J. P. Fairbanks, Institute of Theoretical Physics FriedrichAlexanderUniversität ErlangenNürnberg 
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 UWIHME Compositional Epidemiology Modeling Working Group 
Fall 2022  Compositional Modeling of Disease Dynamics, S. Libkind and J. P. Fairbanks, Topos Institute and UWIHME 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. FerrallFairbanks, 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 RealTime 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 