Over the past few decades, various computational and mathematical methodologies have been proposed for forecasting seasonal epidemics. In recent years, the deadly effects of enormous pandemics such as the H1N1 influenza virus, Ebola, and Zika, have compelled scientists to find new ways to improve the reliability and accuracy of epidemic forecasts. The improvement and variety of these prediction methods are undeniable. Nevertheless, many challenges remain unresolved in the path of forecasting the outbreaks using surveillance data. Obtaining the clean real-time data has always been an obstacle. Moreover, the surveillance data is usually noisy and handling the uncertainty of the observed data is a major issue for forecasting algorithms. Correct modeling assumptions regarding the nature of the infectious disease is another dilemma. Oversimplified models could lead to inaccurate forecasts, whereas more complicated methods require additional computational resources and information. Without those, the model may not be able to converge to a unique optimum solution. Through the last decade, there has been a significant effort towards achieving better epidemic forecasting algorithms. However, the lack of standard, well-defined evaluating metrics impedes a fair judgment on the proposed methods. This dissertation is divided into two parts. In the first part, we present a Bayesian particle filter calibration framework integrated with an agent-based model to forecast the epidemic trend of diseases like flu and Ebola. Our approach uses Bayesian statistics to estimate the underlying disease model parameters given the observed data and handle the uncertainty in the reasoning. An individual-based model with different intervention strategies could result in a large number of unknown parameters that should be properly calibrated. As particle filter could collapse in very large-scale systems (curse-of-dimensionality problem), achieving the optimum solution becomes more challenging. Our proposed particle filter framework utilizes machine learning concepts to restrain the intractable search space. It incorporates a smart analyzer in the state dynamics unit that examines the predicted and observed data using machine learning techniques to guide the direction and amount of perturbation of each parameter in the searching process. The second part of this dissertation focuses on providing standard evaluation measures for evaluating epidemic forecasts. We present an end-to-end framework that introduces epidemiologically relevant features (Epi-features), error measures, and ranking schema as the main modules of the evaluation process. Lastly, we provide the evaluation framework as a software package named Epi-Evaluator and demonstrate the potentials and capabilities of the framework by applying it to the output of different forecasting methods. / PHD / Epidemics impose substantial costs to societies by deteriorating the public health and disrupting economic trends. In recent years, the deadly effects of wide-spread pandemics such as H1N1, Ebola, and Zika, have compelled scientists to find new ways to improve the reliability and accuracy of epidemic forecasts. The reliable prediction of future pandemics and providing efficient intervention plans for health care providers could prevent or control disease propagations. Over the last decade, there has been a significant effort towards achieving better epidemic forecasting algorithms. The mission, however, is far from accomplished. Moreover, there has been no significant leap towards standard, well-defined evaluating metrics and criteria for a fair performance judgment between the proposed methods. This dissertation is divided into two parts. In the first part, we present a Bayesian particle filter calibration framework integrated with an agent-based model to forecast the epidemic trend of diseases like flu and Ebola. We model the disease propagation via a large scale agent-based model that simulates the disease spread across the contact network of people. The contact network consists of millions of nodes and is constructed based on demographic information of individuals achieved from the census data. The agent-based model’s configurations are mostly unknown parameters that should be properly calibrated. We present a Bayesian particle filter calibration approach to estimate the underlying disease model parameters given the observed data and handle the uncertainty in the reasoning. As particle filter could collapse in very large-scale systems, achieving the optimum solution becomes more challenging. Our proposed particle filter framework utilizes machine learning concepts to restrain the intractable search space. It incorporates a smart analyzer unit that examines the predicted and observed data using machine learning techniques to guide the direction and amount of perturbation of each parameter in the searching process. The second part of this dissertation focuses on providing standard evaluation measures for evaluating and comparing epidemic forecasts. We present a framework that introduces epidemiologically relevant features (Epi-features), error measures, and ranking schema as the main modules of the evaluation process. Lastly, we provide the evaluation framework as a software package named Epi-Evaluator and demonstrate the potentials and capabilities of the framework by applying it to the output of different forecasting methods.

In recent years, several methods have been proposed for real-time modeling and forecasting of the epidemic curve. These methods range from simple compartmental models to complex agent-based models. In this dissertation, we present a model-based reasoning approach to forecasting the epidemic curve and estimating underlying disease model parameters. The method is based on building an epidemic library consisting of past and simulated influenza outbreaks. During an influenza epidemic, we use a combination of statistical, optimization and modeling techniques to either assign the epidemic to one of the cases in the library or propose parameters for modeling the epidemic. The method is presented in four steps. First, we discuss a sensitivity analysis study evaluating how minute changes in the disease model parameters influence the dynamics of simulated epidemics. Next, we present a supervised classification method for predicting the epidemic curve. The epidemic curve is forecasted by matching the partial surveillance curve to at least one of the epidemics in the library. We expand on the classification approach by presenting a method which identifies epidemics similar or different from those in the library. Lastly, we discuss a simulation optimization method for estimating model parameters to forecast the epidemic curve of an epidemic distinct from those in the library. / Ph. D.

Most epidemiological systems described in the literature are built for evaluation and analysis of specific diseases, such as Influenza-like-illness. The modeling environments that support these systems are implemented for specific diseases and epidemiological models. Hence they are not reusable or extendable. This thesis focuses on the design and development of an integrated analytical environment with flexible data integration methodologies and multi-level web services for evaluation and forecasting of various epidemics in different regions of the world. The environment supports analysis of epidemics based on any combination of disease, surveillance sources, epidemiological models, geographic regions and demographic factors. The environment also supports evaluation and forecasting of epidemics when various policy-level and behavioral interventions are applied, that may inhibit the spread of an epidemic. First, we describe data integration methodologies and schema design, for flexible experiment design, storage and query retrieval mechanisms related to large scale epidemic data. We describe novel techniques for data transformation, optimization, pre-computation and automation that enable flexibility, extendibility and efficiency required in different categories of query processing. Second, we describe the design and engineering of adaptable middleware platforms based on service-oriented paradigms for interactive workflow, communication, and decoupled integration. This supports large-scale multi-user applications with provision for online analysis of interventions as well as analytical processing of forecast computations. Using a service-oriented architecture, we have provided a platform-as-a-service representation for evaluation and forecasting of epidemics. We demonstrate the applicability of our integrated environment through development of the applications, DISIMS and EpiCaster. DISIMS is an interactive web-based system for evaluating the effects of dynamic intervention strategies on epidemic propagation. EpiCaster is a situation assessment and forecasting tool for projecting the state of evolving epidemics such as flu and Ebola in different regions of the world. We discuss how our platform uses existing technologies to solve a novel problem in epidemiology, and provides a unique solution on which different applications can be built for analyzing epidemic containment strategies. / Ph. D.