CV

Contact Information

Name Joshua C. Macdonald
Professional Title Computational Scientist
Email jmacdo16@jh.edu
Website https://jcmacdonald.dev

Research Profile

Computational scientist whose work determines what actions to take, what experiments to run, and what measurements are worth collecting in systems where interventions are costly and uncertainty is unavoidable. I develop methods, scientific AI/ML, and research software for partially observed systems across earth, environmental, and health sciences — integrating generative modeling (mechanistic, statistical, and hybrid), Bayesian inference, uncertainty quantification, and scientific computing to build defensible decision support. Current application areas include infectious disease forecasting and intervention timing, surveillance design, marine and terrestrial ecology, and cultural transmission dynamics.

Education

  • 2017 - 2022

    Lafayette, Louisiana, USA

    PhD
    University of Louisiana at Lafayette
    Mathematics
    • Advisor: Hayriye Gulbudak
    • Dissertation: Population Dynamics Under Disturbance in Ecology and Epidemiology
  • 2017 - 2020

    Lafayette, Louisiana, USA

    MS
    University of Louisiana at Lafayette
    Mathematics
  • 2014 - 2016

    Asheville, North Carolina, USA

    BA
    University of North Carolina Asheville
    Mathematics
  • 2008 - 2013

    Greensboro, North Carolina, USA

    BA
    University of North Carolina Greensboro
    Archaeology

Appointments

  • 2024 - present

    Baltimore, Maryland, USA

    Postdoctoral Scholar
    Johns Hopkins Bloomberg School of Public Health
    International Vaccine Access Center, Department of International Health. Mentor: Shaun Truelove. Research focus: infectious disease modeling and inference, scientific computing, decision support systems, and research software engineering.
  • 2022 - 2024

    Tel Aviv, Israel

    Zuckerman STEM Leadership Postdoctoral Fellow
    Tel Aviv University
    School of Zoology. Mentor: Yoav Ram. Research drew directly on archaeological training in the study of material culture diversity and cultural transmission, applying Bayesian dimensionality reduction and multivariate data analysis to cultural datasets.

Computational Expertise

Modeling: Generative models (ODE/PDE/stochastic/hybrid); compartmental and agent-based models; scientific AI/ML (physics-embedded surrogates, lawful learning); multivariate data analysis and dimensionality reduction; stability, bifurcation, and sensitivity analysis; parameter identifiability and inverse problems
Inference: Bayesian hierarchical models; variational and simulation-based inference; data assimilation; uncertainty quantification; model calibration and validation; proper scoring rules and forecast evaluation
Computing: Python, Julia, C++, Stan, R, MATLAB. Scientific computing; high-performance numerical solvers; operator splitting; data pipelines and exploratory analysis; reproducible workflows (Git, CI/CD, containerization)

Published Papers

Papers Under Review

  • 2026
    An immuno-epidemiological model of foot-and-mouth disease in African buffalo with carrier transmission

    S. AtkinsH. GulbudakS. WelkerH. Smith***J.C. Macdonald***B.R. BeechlerA.E. Jolles

    Under review, Bulletin of Mathematical Biology

Preprints

Manuscripts in Preparation

  • 2026
    Convergence characterization of coordinate-ascent variational inference for Bayesian PCA

    ***J.C. Macdonald***Y. Ram

    In preparation

  • 2026
    Posterior predictive eigenvalue testing for spectral dimensionality selection

    ***J.C. Macdonald***S. NaimY. Ram

    In preparation for Bioinformatics or PLOS Computational Biology

  • 2026
    Lawful Learning: Embedding Physical Laws into Surrogate Representations for Robust Extrapolation

    ***J.C. Macdonald***

    In preparation for Proceedings of the Royal Society A

  • 2026
    Structured observables: recovering dynamical structure from parameter-indexed generators

    ***J.C. Macdonald***

    In preparation for SIAM Journal on Applied Dynamical Systems

  • 2026
    Shapelet analysis of infectious disease forecasts reveals heterogeneity across epidemic phases

    K. RoosaL.A. WhiteT.M. Leon***J.C. Macdonald***A. SrivastavaS. Truelove

    In preparation for Epidemics

Research Support

  • In review
    National One Health Mission India ($1M / 3 years) — Pending

    Development of an Integrated One Health Disease Modelling and Digital Health Program in Human, Livestock, and Wildlife. Co-Investigator. Research role: mathematical model parameterization and data analysis; mechanistic modeling for HPAI and anthrax in India; stakeholder training in modeling; and supervision of postdoctoral and doctoral trainees.

  • USDA-NIFA AFRI US--UK Collaboration (Award #1032897)

    Quiescence to emergence: Does nairovirus diversity loss increase disease transmission, severity and the risk of emergence? US PIs: Brianna Beechler, Anna Jolles, Cameron Browne, and Hayriye Gulbudak; linked UKRI award BB/Z516934/1 with Emma Thomson, Teresa Lambe, Roman Biek, and Georgina Limon-Vega. Collaborator (40% FTE). Research role: mathematical model parameterization, data analysis, and advising on mathematical and statistical methods.

  • USDA-ARS Cooperative Agreement (3022-32000-021-018-S)

    Investigating the Epidemiology of CCHFV in an Endemic Setting: Uganda. PIs: Bree Beechler and Anna Jolles (Oregon State University). Collaborator. Research role: mathematical modeling of cross-species CCHFV transmission dynamics, surveillance design optimization, and advising on mathematical and statistical methods for decision support.

  • CDC-RFA-FT-23-0069 (NU38FT000012)

    Atlantic Coast Center for Infectious Disease Dynamics and Analytics (ACCIDDA). Directors: Justin Lessler, Kimberly Powers, and Shaun Truelove. Postdoctoral Scholar (60% FTE). Insight Net center for infectious disease forecasting and outbreak analytics. Research role: operational modeling, forecasting pipeline development, and computational infrastructure.

Research Software -- Lead Developer

  • OP System (Operator-Partitioned System)

    ACCIDDA. Declarative specification language and compiler for structured dynamical systems. Researchers define models via explicit equations or transition diagrams with multi-axis stratification; specifications compile to validated, safe bytecode closures with structured metadata passed to downstream solvers. Specification layer of the operator-partitioned simulation stack.

  • pp-eigentest

    Posterior predictive eigenvalue testing for determining signal rank in high-dimensional datasets. Three-layer consensus architecture combining dimensionality heuristics, adaptive thresholding, and multiple testing correction (FWER, FDR). NumPy and JAX backends; designed to consume VBPCApy posterior outputs.

  • Trade Study (Python + Julia)

    Design and evaluation framework for scientific simulation studies. Simulators with known latent state provide controlled environments to score competing configurations — model formulations, solver choices, measurement strategies, or any design decision — against ground truth using proper scoring rules and multi-objective Pareto optimization. Hierarchical phases, Bayesian model stacking, and global sensitivity analysis. Available in Python and Julia.

  • OP Engine (Operator-Partitioned Engine)

    ACCIDDA. Operator-partitioned ODE/PDE solver core. Splits the right-hand side into explicit and implicit parts, advancing them jointly via nine methods (explicit, IMEX, fully implicit) with adaptive step-size control. Cached implicit solves with dense/sparse autodispatch; zero per-step allocation. Consumes OP System specifications.

  • vbpca-py

    Variational Bayesian PCA for incomplete data with native per-entry missingness handling, full posterior uncertainty quantification, automatic component pruning, and built-in model selection. Missing-aware preprocessing pipeline and C++-accelerated kernels; scikit-learn-compatible API. Applied to genetic, cultural, and ecological datasets.

Research Software -- Collaborative Infrastructure

  • FlepiMoP2 (Flexible Epidemic Modeling Pipeline 2)

    ACCIDDA. Contributor to the configuration-driven orchestration engine for CDC-supported infectious disease forecasting and scenario analysis. Plugin architecture decouples model specification, numerical integration, and output persistence.

  • TabularEpi

    UNC / ACCIDDA. Tabular epidemic simulator supporting mixed deterministic-stochastic models. Conducted systematic performance benchmarking that identified bottlenecks, informing the design of the next-generation pipeline.

  • FlepiMoP (Flexible Epidemic Modeling Pipeline)

    Hopkins IDD / ACCIDDA. Developed simulation and statistical inference components for operational influenza modeling; conducted benchmarking that identified 5–20x performance improvements, informing the next-generation pipeline architecture.

Research Software -- Operational Deployments

  • Hib Vaccination Modeling (Navajo Nation)

    ACCIDDA. Technical supervisor managing PhD students in implementation of an age- and immune-status-structured Hib model for the Navajo Nation to evaluate the impact of long-running vaccination programs.

  • Flu Scenario Modeling Hub

    ACCIDDA. Lead Model Developer across the 2024/25, 2025/26, and 2026/27 seasons. Set up the ACCIDDA flu model and operational pipeline (2024/25). Extensive work with external modeling packages drove contributions that led to FlepiMoP2 (2025/26). Supervising an undergraduate student in a scientific overhaul of the flu model for the 2026/27 round.

Invited Talks and Seminars

  • 2026
    FlepiMoP2 and the Operator-Partitioned Simulation Stack

    Tools Workshop, Insight Net Third Annual Meeting, Friday Center, Chapel Hill, North Carolina

  • 2026
    Cross-Scale Feedback Motifs: Structure-Preserving Models and Computational Tools for Complex Systems

    Biological Oceanography Seminar, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts

  • 2026
    Decision-Support Modeling for One Health Pathogens

    Differential Equations Seminar, University of Maryland Baltimore County, Baltimore, Maryland

  • 2025
    Modeling long-term viral infections

    Mathematics Seminar, Shippensburg University, Shippensburg, Pennsylvania

  • 2025
    Scenario and forecast modeling for respiratory viruses

    Navajo Nation Epidemiology Center Data Summit, Window Rock, Arizona

  • 2024
    Impacts of host behavior and viral life history on infectious disease transmission

    Department of Mathematics, Virginia Tech; Infectious Disease Dynamics Group, Johns Hopkins University

  • 2024
    Within-host viral life histories predict FMDV transmission dynamics for African buffalo

    Hawlena Lab, Ben-Gurion University, Midreshet Ben Gurion, Israel

  • Modeling process-based effects of harmful algal blooms

    University of Essex (2024); Tel Aviv University (2023); Israel Oceanographic and Limnological Research, Haifa (2023); Inter-University Institute for Marine Sciences, Eilat (2023)

  • 2023
    Patterns of cultural variation in the Austronesian expansion

    Fortunato Lab, University of Oxford (virtual)

  • 2022
    Consilience in FMDV ecology

    Gresham Lab, New York University; Obolski Lab, Tel Aviv University

Selected Conference Presentations

  • 2026
    Decision-Support Modeling for One Health Pathogens: Using Mechanistic Models for Surveillance and Forecast Design

    Society for Mathematical Biology Annual Meeting, Graz, Austria; mini-symposium talk

  • 2025
    Recovering Ecological Geometry: A Trait- and Depth-Structured IPDE Model of Plankton Dynamics

    Society for Mathematical Biology Annual Meeting, Edmonton, Alberta, Canada; mini-symposium talk

  • 2025
    Biologically Grounded Surrogate-Driven Parameter Inference for Sparsely Observed Dynamical Systems

    Symposium on Biomathematics and Ecology Education and Research (BEER), Fairfax, Virginia; contributed talk

  • 2023
    Forward hysteresis and Hopf bifurcation in an NPZD model with application to harmful algal blooms

    Society for Mathematical Biology Annual Meeting, Columbus, Ohio; mini-symposium talk

  • Within-host viral growth and immune response rates predict FMDV transmission dynamics for African buffalo

    SIAM TXLA, Lafayette, Louisiana (2023); SMB Epidemiology-Immunology Midyear Meeting (2022, virtual)

  • Dengue immunodynamics: antibody-dependent enhancement, cross-reactive immunity, and model--data confrontation

    SIAM TXLA (2023); Mathematical Perspectives on Immuno-Biology, Bulgaria (2023); Center for Combatting Pandemics, Tel Aviv (2023); European Conference on Theoretical and Mathematical Biology, Heidelberg (2022)

  • 2021
    Disease dynamics necessarily operate across scales

    SIAM TXLA, South Padre Island, Texas; mini-symposium talk

  • 2021
    Modeling COVID-19 outbreaks in the United States with distinct testing, lockdown speed, and fatigue rates

    Society for Mathematical Biology Annual Meeting (virtual); contributed talk

Workshop Facilitation

  • -

    Chapel Hill, North Carolina, USA

    Tools Workshop Presenter
    Insight Net Third Annual Meeting
    Presenting FlepiMoP2 and the op_system/op_engine simulation stack at the Insight Net Third Annual Meeting tools workshop, Friday Center, University of North Carolina at Chapel Hill.
  • -

    Chapel Hill, North Carolina, USA

    Technical Support
    Insight Net Second Tech Transfer Workshop
    ACCIDDA. Technical support for the Insight Net Second Tech Transfer Workshop at UNC Chapel Hill. Assisted participants with Python package installation and environment setup for Epydemics tools.
  • -

    Baltimore, Maryland, USA

    Workshop Facilitator
    ACCIDDA
    Facilitator for the Applied Modeling in Public Health (AMPH) Workshop, October 15–17, 2025, Johns Hopkins Bloomberg School of Public Health.
  • -

    Baltimore, Maryland, USA

    Workshop Facilitator
    ACCIDDA
    Facilitator for the Applied Modeling in Public Health (AMPH) Workshop, August 12–15, 2024, Johns Hopkins Bloomberg School of Public Health.

Teaching

  • 2025 - 2025

    Baltimore, Maryland, USA

    Teaching Assistant
    Johns Hopkins University
    Teaching assistant for Topics in Infectious Disease Epidemiology with Shaun Truelove and Sara Loo.
  • 2017 - 2020

    Lafayette, Louisiana, USA

    Teaching Assistant and Instructor of Record
    University of Louisiana at Lafayette
    Instructor of record for elementary statistics (3 sections), survey of calculus (2 sections), precalculus (2 sections), and college algebra (2 sections). Teaching assistant for calculus, linear algebra, differential equations, and basic statistics.
  • 2016 - 2017

    Teaching and Tutoring
    McDowell County Schools / Memorial University / UNC Asheville
    Instructor of record for North Carolina Math III / Algebra II (2017). Mathematics and statistics tutoring at Memorial University of Newfoundland (2016–2017) and University of North Carolina Asheville (2016).

Mentoring

  • Mentoring students and postdoctoral researchers
    • Jolles and Beechler Labs, Oregon State University (2025–present)
    • Society for Mathematical Biology (2022–present)
    • Association for Women in Mathematics (2023–2025)
    • Ram Lab, Tel Aviv University (2022–2024)
    • MIDAS Network (2021–2022)
    • Gulbudak Group, University of Louisiana at Lafayette (2021–2022)
  • 2024
    Undergraduate Research Supervision: Shany Naim

    Tel Aviv University. Supervised undergraduate research project: initial translation of the VBPCApy variational Bayesian PCA codebase from MATLAB to Python.

Community Outreach

  • Science communication and research dissemination
    • University of Louisiana R1 Showcase: selected to present COVID-19 modeling research at the university-wide showcase (2022)
    • Ocean View United Methodist Church, Oak Island, NC: community discussion on vaccines and COVID-19, with on-site pharmacist for vaccination (2021)

Professional Service

  • SMB Diversity, Equity, and Inclusion Committee

    Member

  • Session Chair / Leader
    • SMB Early Career Workshop: Applying for postdoctoral funding (2023)
    • SMB Epidemiology-Immunology Midyear Meeting: Contributed talks (2022)
    • SMB Annual Meeting: CT04-MEPI contributed talks in mathematical epidemiology (2021)
  • Mini-symposium Co-organizer
    • SIAM TXLA: Data-driven mathematical and statistical modeling approaches to population biology (2023)
    • SMB Annual Meeting: Disease Dynamics Across Scales (2023)
    • SMB/ESTMB Joint Meeting: Multi-scale and data-driven modeling approaches in ecology, immunology, and epidemiology (2022)
    • SIAM TXLA: Reproducibility, reliability, and robustness: confronting models from across mathematical biology with data (2021)
    • SIAM TXLA: Population Dynamics in Ecology and Epidemiology (2019)
  • Secretary, University of Louisiana AMS Graduate Student Chapter

Journal Reviewing

2022–present: PLOS ONE, Journal of Biological Systems, Journal of Biological Dynamics, Frontiers in Public Health, Frontiers in Veterinary Science, Computational and Applied Mathematics, Mathematical Biosciences, Scientific Reports, PLOS Computational Biology, and BMC Infectious Diseases.

Honors and Awards

  •

    SIAM, Society for Mathematical Biology, and University of Louisiana Graduate Research Association

  • 2021

Professional Affiliations

Society for Mathematical Biology; Society for Industrial and Applied Mathematics; International Society for Bayesian Analysis; United States Research Software Engineer Association; MIDAS Network; Association for Women in Mathematics; Institute of Industrial and Systems Engineers; Society for Health Systems (SHS/IISE); and Healthcare Information and Management Systems Society (HIMSS).