Improving surveillance and prediction of emerging and re-emerging infectious diseases

Infectious diseases are emerging at an unprecedent rate in recent years, such as the flu pandemic initialized from Mexico in 2009, the 2014 Ebola epidemic in West Africa, and the 2016-2017 expansion of Zika across Americas. They rarely happened previously and thus lack resources and data to detect and predict their spread. This highlights the challenges in emerging an re-emerging infectious disease surveillance. In the dissertation, I mainly put efforts in developing methods for early detection of such diseases, and assessing predictive power of various models in early phase of an epidemic. In Chapter 2, I developed a two-layer early detection framework which provides early warning of emerging epidemics based on the idea of anomaly detection. The framework could evaluate and identify data sources to achieve the best performance automatically from available data, such as data from the Internet and public health surveillance systems. I demonstrated the framework using historical influenza data in the US, and found that the optimal combination of predictors includes data sources from Google search query and Wikipedia page view. The optimized system is able to detect the onset of seasonal influenza outbreaks an average of 16.4 weeks in advance, and the second wave of the 2009 flu pandemic 5 weeks ahead. In Chapter 3, I extended the framework in Chapter 2 to identify large dengue outbreaks from small ones. The results show that the framework could personalize optimal combinations of predictors for different locations, and an optimal combination for one location might not perform well for other locations. In Chapter 4, I investigated the contribution of different population structures to total epidemic incidence, peak intensity and timing, and also explored the ability of various models with different population structures in predicting epidemic dynamics. The results suggest that heterogeneous contact pattern and direct contacts dominate the evolution of epidemics, and a homogeneous model is not able to provide reliable prediction for an epidemic. In summary, my dissertation not only provides method frameworks for building early detection systems for emerging and re-emerging infectious diseases, but also gives insight to the effects of various models in predicting epidemics.Cellular and Molecular Biolog

Algorithmic futures

In the last few years, tracking systems that harvest web data to identify trends, calculate predictions, and warn about potential epidemic outbreaks have proliferated. These systems integrate crowdsourced data and digital traces, collecting information from a variety of online sources, and they promise to change the way governments, institutions, and individuals understand and respond to health concerns. This article examines some of the conceptual and practical challenges raised by the online algorithmic tracking of disease by focusing on the case of Google Flu Trends (GFT). Launched in 2008, GFT was Google’s flagship syndromic surveillance system, specializing in ‘real-time’ tracking of outbreaks of influenza. GFT mined massive amounts of data about online search behavior to extract patterns and anticipate the future of viral activity. But it did a poor job, and Google shut the system down in 2015. This paper focuses on GFT’s shortcomings, which were particularly severe during flu epidemics, when GFT struggled to make sense of the unexpected surges in the number of search queries. I suggest two reasons for GFT’s difficulties. First, it failed to keep track of the dynamics of contagion, at once biological and digital, as it affected what I call here the ‘googling crowds’. Search behavior during epidemics in part stems from a sort of viral anxiety not easily amenable to algorithmic anticipation, to the extent that the algorithm’s predictive capacity remains dependent on past data and patterns. Second, I suggest that GFT’s troubles were the result of how it collected data and performed what I call ‘epidemic reality’. GFT’s data became severed from the processes Google aimed to track, and the data took on a life of their own: a trackable life, in which there was little flu left. The story of GFT, I suggest, offers insight into contemporary tensions between the indomitable intensity of collective life and stubborn attempts at its algorithmic formalization

Improved forecasts of influenza-associated hospitalization rates with Google Search Trends

Reliable forecasts of influenza-associated hospitalizations during seasonal outbreaks can help health systems better prepare for patient surges. Within the USA, public health surveillance systems collect and distribute near real-time weekly hospitalization rates, a key observational metric that makes real-time forecast of this outcome possible. In this paper, we describe a method to forecast hospitalization rates using a population level transmission model in combination with a data assimilation technique. Using this method, we generated retrospective forecasts of hospitalization rates for five age groups and the overall population during five seasons in the USA and quantified forecast accuracy for both near-term and seasonal targets. Additionally, we describe methods to correct for under-reporting of hospitalization rates (backcast) and to estimate hospitalization rates from publicly available online search trends data (nowcast). Forecasts based on surveillance rates alone were reasonably accurate in predicting peak hospitalization rates (within ± 25% of the actual peak rate, three weeks before peak). The error in predicting rates one to four weeks ahead, remained constant for the duration of the seasons, even during periods of increased influenza incidence. An improvement in forecast quality across all age groups, seasons and targets was observed when backcasts and nowcasts supplemented surveillance data. These results suggest that the model-inference framework can provide reasonably accurate real-time forecasts of influenza hospitalizations; backcasts and nowcasts offer a way to improve system tolerance to observational errors

Disaster and Pandemic Management Using Machine Learning: A Survey

This article provides a literature review of state-of-the-art machine learning (ML) algorithms for disaster and pandemic management. Most nations are concerned about disasters and pandemics, which, in general, are highly unlikely events. To date, various technologies, such as IoT, object sensing, UAV, 5G, and cellular networks, smartphone-based system, and satellite-based systems have been used for disaster and pandemic management. ML algorithms can handle multidimensional, large volumes of data that occur naturally in environments related to disaster and pandemic management and are particularly well suited for important related tasks, such as recognition and classification. ML algorithms are useful for predicting disasters and assisting in disaster management tasks, such as determining crowd evacuation routes, analyzing social media posts, and handling the post-disaster situation. ML algorithms also find great application in pandemic management scenarios, such as predicting pandemics, monitoring pandemic spread, disease diagnosis, etc. This article first presents a tutorial on ML algorithms. It then presents a detailed review of several ML algorithms and how we can combine these algorithms with other technologies to address disaster and pandemic management. It also discusses various challenges, open issues and, directions for future research