Predicting arbovirus re-emergence remains challenging in regions with limited off-season transmis... more 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 <i>R</i><sub>0</sub> (secondary cases produced from a primary infection in a fully susceptible population). We then fit a stochastic (Sir) Susceptible–Infected–Recovered model to observed case data for the emergence of dengue serotype DENV1 in Rio de Janeiro. This aggregated city-level model substantially over-estimates obser...
Motivating plug-and-play inference for cell motility • Multiple models have been proposed for cel... more Motivating plug-and-play inference for cell motility • Multiple models have been proposed for cell movements. • If the choice of model matters, one wants to compare previous suggestions and investigate improvements. • Wanted: an inference framework for general classes of dynamic models. • Simulation-based methods offer generality. They can carry out likelihood-based, feature-based or Bayesian inference. • Modern simulation-based inference methods do not generate long trajectories, but make cunning use of many carefully selected short simulations. Such methods are said to be Plug-and-play.
Transportation Research Record: Journal of the Transportation Research Board, 2016
This research summarized the effect of cell phone restrictions on the prevalence of cell phone us... more This research summarized the effect of cell phone restrictions on the prevalence of cell phone use and motor vehicle crashes involving young drivers. Multiple databases were searched with the use of terms related to cell phone restrictions, the prevalence of cell phone use, crashes, and young drivers. Fifty-three abstracts were reviewed. Eleven studies met the inclusion criteria. Six studies examined changes in the prevalence of cell phone use before and after a restriction was imposed; five studies used changes in crash rates as the outcome. The majority of prevalence studies found no change in young drivers’ cell phone use following the introduction of a restriction. Crash studies using multistate samples reported significant reductions in fatal crashes; single-state studies reported no change or small increases in crashes. Restrictions appeared to have no long-term effect on the prevalence of cell phone use among novice drivers. Conflicting findings from crash studies reflected d...
Looking myopically at the larger features of the likelihood function, ab- sent some ne detail, ca... more Looking myopically at the larger features of the likelihood function, ab- sent some ne detail, can theoretically improve maximum likelihood estimation. Such estimators are, in fact, used routinely, since numerical techniques for maxi- mizing a computationally expensive likelihood function or for maximizing a Monte Carlo approximation to a likelihood function may be unable to investigate small scale behavior of the
Abstract: Statistical Analysis of Cell MotionbyEdward Luke IonidesDoctor of Philosophy in Statist... more Abstract: Statistical Analysis of Cell MotionbyEdward Luke IonidesDoctor of Philosophy in StatisticsUniversity of California, BerkeleyProfessor David R. Brillinger, ChairCertain biological experiments investigating cell motion result in time lapse video microscopydata which may be modeled using stochastic di#erential equations. Thesemodels suggest statistics for quantifying experimental results and testing relevanthypotheses, and carry implications for the qualitative behavior of cells and ...
Statistical inference for high-dimensional partially observed, nonlinear, stochastic processes is... more Statistical inference for high-dimensional partially observed, nonlinear, stochastic processes is a methodological challenge with applications including spatiotemporal analysis of epidemiological and ecological systems. Standard particle filter algorithms, which provide an effective approach for general low-dimensional partially observed Markov processes, suffer from a curse of dimensionality that limits their applicability beyond low-dimensional systems. We show that many independent Monte Carlo calculations, none of which, by itself, attempts to solve the filtering problem, can be combined to give a global filtering solution that theoretically beats the curse of dimensionality under weak coupling conditions. The independent Monte Carlo calculations are called islands, and the corresponding algorithm is called a basic island filter (BIF). Carrying out an operation called adapted simulation on each island results in a variant called an adapted simulation island filter (ASIF). Adapte...
Predicting arbovirus re-emergence remains challenging in regions with limited off-season transmis... more 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 <i>R</i><sub>0</sub> (secondary cases produced from a primary infection in a fully susceptible population). We then fit a stochastic (Sir) Susceptible–Infected–Recovered model to observed case data for the emergence of dengue serotype DENV1 in Rio de Janeiro. This aggregated city-level model substantially over-estimates obser...
Motivating plug-and-play inference for cell motility • Multiple models have been proposed for cel... more Motivating plug-and-play inference for cell motility • Multiple models have been proposed for cell movements. • If the choice of model matters, one wants to compare previous suggestions and investigate improvements. • Wanted: an inference framework for general classes of dynamic models. • Simulation-based methods offer generality. They can carry out likelihood-based, feature-based or Bayesian inference. • Modern simulation-based inference methods do not generate long trajectories, but make cunning use of many carefully selected short simulations. Such methods are said to be Plug-and-play.
Transportation Research Record: Journal of the Transportation Research Board, 2016
This research summarized the effect of cell phone restrictions on the prevalence of cell phone us... more This research summarized the effect of cell phone restrictions on the prevalence of cell phone use and motor vehicle crashes involving young drivers. Multiple databases were searched with the use of terms related to cell phone restrictions, the prevalence of cell phone use, crashes, and young drivers. Fifty-three abstracts were reviewed. Eleven studies met the inclusion criteria. Six studies examined changes in the prevalence of cell phone use before and after a restriction was imposed; five studies used changes in crash rates as the outcome. The majority of prevalence studies found no change in young drivers’ cell phone use following the introduction of a restriction. Crash studies using multistate samples reported significant reductions in fatal crashes; single-state studies reported no change or small increases in crashes. Restrictions appeared to have no long-term effect on the prevalence of cell phone use among novice drivers. Conflicting findings from crash studies reflected d...
Looking myopically at the larger features of the likelihood function, ab- sent some ne detail, ca... more Looking myopically at the larger features of the likelihood function, ab- sent some ne detail, can theoretically improve maximum likelihood estimation. Such estimators are, in fact, used routinely, since numerical techniques for maxi- mizing a computationally expensive likelihood function or for maximizing a Monte Carlo approximation to a likelihood function may be unable to investigate small scale behavior of the
Abstract: Statistical Analysis of Cell MotionbyEdward Luke IonidesDoctor of Philosophy in Statist... more Abstract: Statistical Analysis of Cell MotionbyEdward Luke IonidesDoctor of Philosophy in StatisticsUniversity of California, BerkeleyProfessor David R. Brillinger, ChairCertain biological experiments investigating cell motion result in time lapse video microscopydata which may be modeled using stochastic di#erential equations. Thesemodels suggest statistics for quantifying experimental results and testing relevanthypotheses, and carry implications for the qualitative behavior of cells and ...
Statistical inference for high-dimensional partially observed, nonlinear, stochastic processes is... more Statistical inference for high-dimensional partially observed, nonlinear, stochastic processes is a methodological challenge with applications including spatiotemporal analysis of epidemiological and ecological systems. Standard particle filter algorithms, which provide an effective approach for general low-dimensional partially observed Markov processes, suffer from a curse of dimensionality that limits their applicability beyond low-dimensional systems. We show that many independent Monte Carlo calculations, none of which, by itself, attempts to solve the filtering problem, can be combined to give a global filtering solution that theoretically beats the curse of dimensionality under weak coupling conditions. The independent Monte Carlo calculations are called islands, and the corresponding algorithm is called a basic island filter (BIF). Carrying out an operation called adapted simulation on each island results in a variant called an adapted simulation island filter (ASIF). Adapte...
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