skip to main content


Search for: All records

Creators/Authors contains: "Ionides, Edward"

Note: When clicking on a Digital Object Identifier (DOI) number, you will be taken to an external site maintained by the publisher. Some full text articles may not yet be available without a charge during the embargo (administrative interval).
What is a DOI Number?

Some links on this page may take you to non-federal websites. Their policies may differ from this site.

  1. Parameter learning for high-dimensional, partially observed, and nonlinear stochastic processes is a methodological challenge. Spatiotemporal disease transmission systems provide examples of such processes giving rise to open inference problems. We propose the iterated block particle filter (IBPF) algorithm for learning high-dimensional parameters over graphical state space models with general state spaces, measures, transition densities and graph structure. Theoretical performance guarantees are obtained on beating the curse of dimensionality (COD), algorithm convergence, and likelihood maximization. Experiments on a highly nonlinear and non-Gaussian spatiotemporal model for measles transmission reveal that the iterated ensemble Kalman filter algorithm (Li et al., 2020) is ineffective and the iterated filtering algorithm (Ionides et al., 2015) suffers from the COD, while our IBPF algorithm beats COD consistently across various experiments with different metrics. 
    more » « less
  2. Predicting arbovirus re-emergence remains challenging in regions with limited off-season transmission and intermittent epidemics. Current mathematical models treat the depletion and replenishment of susceptible (non-immune) hosts as the principal drivers of re-emergence, based on established understanding of highly transmissible childhood diseases with frequent epidemics. We extend an analytical approach to determine the number of ‘skip’ years preceding re-emergence for diseases with continuous seasonal transmission, population growth and under-reporting. Re-emergence times are shown to be highly sensitive to small changes in low R 0 (secondary cases produced from a primary infection in a fully susceptible population). We then fit a stochastic Susceptible–Infected–Recovered (SIR) model to observed case data for the emergence of dengue serotype DENV1 in Rio de Janeiro. This aggregated city-level model substantially over-estimates observed re-emergence times either in terms of skips or outbreak probability under forward simulation. The inability of susceptible depletion and replenishment to explain re-emergence under ‘well-mixed’ conditions at a city-wide scale demonstrates a key limitation of SIR aggregated models, including those applied to other arboviruses. The predictive uncertainty and high skip sensitivity to epidemiological parameters suggest a need to investigate the relevant spatial scales of susceptible depletion and the scaling of microscale transmission dynamics to formulate simpler models that apply at coarse resolutions. 
    more » « less