CV

Contact Information

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

Research Profile

Computational scientist developing methods, scientific AI/ML, and research software for partially observed systems across earth, environmental, and health sciences. My work integrates generative modeling (mechanistic, statistical, and hybrid), Bayesian inference, uncertainty quantification, and scientific computing to build defensible inference under structural incompleteness — where the full system state is never directly observed and prediction alone is not enough. Current application areas include infectious disease dynamics and forecasting, host–pathogen and comparative health systems, marine and terrestrial ecology, environmental hazards, and computational tools for decision support.

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.

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
    Lawful learning: a scientific machine learning approach to dynamical systems inference

    ***J.C. Macdonald***

    In preparation for SIAM Journal on Scientific Computing

  • 2026
    Structured observables: a physics-based approach to dynamical systems inference

    ***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

  • National One Health Mission India ($1M / 3 years)

    Development of an Integrated One Health Disease Modelling and Digital Health Program in Human, Livestock, and Wildlife. Co-Investigator (pending). 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: nairovirus diversity loss and disease transmission. 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). Postdoctoral Scholar (60% FTE). Insight Net center for infectious disease forecasting and outbreak analytics. Research role: operational modeling, forecasting pipeline development, and computational infrastructure.

  • NSF EEID / UKRI UK--US Collaboration Grant ($4.05M / 5 years)

    Multi-scale infection dynamics from cells to landscapes: FMD in African buffalo. Senior Personnel (from 2024). Research role: mathematical model development and parameterization of within-host viral and immune dynamics.

  • Zuckerman Postdoctoral Scholarship ($120K total)

    Co-evolution of Cultural and Genetic Traits. Principal Investigator. Competitive postdoctoral fellowship; authored and defended research proposal.

Operational Modeling

  • 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.

  • COVID-19 Scenario Modeling Hub

    ACCIDDA. Support. Data cleaning and assimilation in support of ACCIDDA’s health heterogeneities COVID-19 round.

  • 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.

Research Software -- Lead Developer

  • OP System (Operator-Partitioned System)

    ACCIDDA. Declarative governing equation specification compiler for structured dynamical systems. Transforms YAML model definitions into callable numerics consumed by OP Engine or other solvers.

  • pp-eigentest

    Posterior predictive eigenvalue testing framework for determining signal rank in covariance and Gram matrices. Supports ordered hypothesis testing, family-wise error-rate control, and false discovery rate control.

  • Model Criticism (Python + Julia)

    Observable-based model calibration and criticism framework. Uses model worlds with known ground truth to tune inference pipelines—scoring rules, observable weights, and model settings—so that when applied to real data where latent structure is unobserved, the pipeline transfers reliably. Python implementation wraps scoringrules, pymoo, arviz, SALib, and optuna. Julia implementation wraps Metaheuristics.jl, ParetoSmooth.jl, QuasiMonteCarlo.jl, and GlobalSensitivity.jl with native scoring rules.

  • OP Engine (Operator-Partitioned Engine)

    ACCIDDA. Numerical simulation engine for mechanistic models of biological and epidemiological systems. Supports ODE, PDE, and hybrid operator-splitting solvers with pluggable backends.

  • vbpca-py

    Variational Bayesian PCA for incomplete data with native missing-data handling, uncertainty quantification, and C++-accelerated kernels; compatible with scikit-learn.

Research Software -- Collaborative Infrastructure

  • FlepiMoP2 (Flexible Epidemic Modeling Pipeline 2)

    ACCIDDA. Contributor to the redesign of a modular epidemic modeling and simulation pipeline for forecasting and scenario analysis.

  • TabularEpi

    UNC / ACCIDDA. Rule-based tabular epidemic simulator. Conducted systematic performance benchmarking that identified critical architectural bottlenecks, motivating an ongoing refactor to a vectorized backend.

  • FlepiMoP (Flexible Epidemic Modeling Pipeline)

    Hopkins IDD / ACCIDDA. Developed modular ODE solver interfaces; implemented PyMC-based Bayesian inference module for operational influenza modeling; benchmarking identified vectorization-driven performance gains of 5–20x, informing FlepiMoP2 architecture.

Invited Talks and Seminars

  • 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

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

    Department of Mathematics, University of Louisiana at Lafayette. Awarded to two graduate students annually (approximately 50 graduate students total).

  • 2021

    Society for Mathematical Biology Annual Meeting

  • 2019

    Louisiana Sea Grant

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)

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).