On the 3 M's of Epidemic Forecasting: Methods, Measures, and Metrics
| dc.contributor.author | Tabataba, Farzaneh Sadat | en |
| dc.contributor.committeechair | Marathe, Madhav Vishnu | en |
| dc.contributor.committeechair | Lewis, Bryan L. | en |
| dc.contributor.committeemember | Vullikanti, Anil Kumar S. | en |
| dc.contributor.committeemember | Brownstein, John S. | en |
| dc.contributor.committeemember | Ramakrishnan, Naren | en |
| dc.contributor.committeemember | Higdon, David | en |
| dc.contributor.department | Computer Science | en |
| dc.date.accessioned | 2019-05-31T06:00:26Z | en |
| dc.date.available | 2019-05-31T06:00:26Z | en |
| dc.date.issued | 2017-12-06 | en |
| dc.description.abstract | 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. | en |
| dc.description.abstractgeneral | 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. | en |
| dc.description.degree | PHD | en |
| dc.format.medium | ETD | en |
| dc.identifier.other | vt_gsexam:13173 | en |
| dc.identifier.uri | http://hdl.handle.net/10919/89646 | en |
| dc.publisher | Virginia Tech | en |
| dc.rights | In Copyright | en |
| dc.rights.uri | http://rightsstatements.org/vocab/InC/1.0/ | en |
| dc.subject | Epidemic forecasting | en |
| dc.subject | Data assimilation | en |
| dc.subject | Calibration | en |
| dc.subject | Forecast Evaluation | en |
| dc.title | On the 3 M's of Epidemic Forecasting: Methods, Measures, and Metrics | en |
| dc.type | Dissertation | en |
| thesis.degree.discipline | Computer Science and Applications | en |
| thesis.degree.grantor | Virginia Polytechnic Institute and State University | en |
| thesis.degree.level | doctoral | en |
| thesis.degree.name | PHD | en |
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