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Incorporating Particle Filtering and System Dynamic Modelling in Infection Transmission of Measles and Pertussis

dc.contributor.advisorOsgood, Nathaniel D.
dc.contributor.committeeMemberDutchyn, Christopher
dc.contributor.committeeMemberStanley, Kevin G.
dc.contributor.committeeMemberSaini, Vineet
dc.creatorLi, Xiaoyan 1982-
dc.creator.orcid0000-0002-4206-098X 2018
dc.description.abstractChildhood viral and bacterial infections remain an important public problem, and research into their dynamics has broader scientific implications for understanding both dynamical systems and associated methodologies at the population level. Measles and pertussis are two important childhood infectious diseases. Measles is a highly transmissible disease and is one of the leading causes of death among young children under 5 globally. Pertussis (whooping cough) is another common childhood infectious disease, which is most harmful for babies and young children and can be deadly. While the use of ongoing surveillance data and - recently - dynamic models offer insight on measles (or pertussis) dynamics, both suffer notable shortcomings when applied to measles (or pertussis) outbreak prediction. In this thesis, I apply the Sequential Monte Carlo approach of particle filtering, incorporating reported measles and pertussis incidence for Saskatchewan during the pre-vaccination era, using an adaptation of a previously contributed measles and pertussis compartmental models. To secure further insight, I also perform particle filtering on age structured adaptations of the models. For some models, I further consider two different methods of configuring the contact matrix. The results indicate that, when used with a suitable dynamic model, particle filtering can offer high predictive capacity for measles and pertussis dynamics and outbreak occurrence in a low vaccination context. Based on the most competitive model as evaluated by predictive accuracy, I have performed prediction and outbreak classification analysis. The prediction results demonstrated that the most competitive models could predict the measles and pertussis outbreak patterns and classify whether there will be an outbreak or not in the next month (Area under the ROC Curve of measles is 0.89, while pertussis is 0.91). I conclude that anticipating the outbreak dynamics of measles and pertussis in low vaccination regions by applying particle filtering with simple measles and pertussis transmission models, and incorporating time series of reported case counts, is a valuable technique to assist public health authorities in estimating risk and magnitude of measles and pertussis outbreaks. Such approach offers particularly strong value proposition for other pathogens with little-known dynamics, important latent drivers, and in the context of the growing number of high-velocity electronic data sources. Strong additional benefits are also likely to be realized from extending the application of this technique to highly vaccinated populations.
dc.subjectParticle Filter
dc.subjectsystem dynamics
dc.subjectage structured model
dc.subjectcontact matrix
dc.subjectMachine Learning
dc.subjectcompartmental model
dc.subjectlatent state
dc.subjectSequential Monte Carlo method
dc.titleIncorporating Particle Filtering and System Dynamic Modelling in Infection Transmission of Measles and Pertussis
local.embargo.terms2020-02-05 Science Science of Saskatchewan of Science (M.Sc.)


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