Browsing by Author "Chakraborty, Prithwish"

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    Data-Driven Methods for Modeling and Predicting Multivariate Time Series using Surrogates
    Chakraborty, Prithwish (Virginia Tech, 2016-07-05)
    Modeling and predicting multivariate time series data has been of prime interest to researchers for many decades. Traditionally, time series prediction models have focused on finding attributes that have consistent correlations with target variable(s). However, diverse surrogate signals, such as News data and Twitter chatter, are increasingly available which can provide real-time information albeit with inconsistent correlations. Intelligent use of such sources can lead to early and real-time warning systems such as Google Flu Trends. Furthermore, the target variables of interest, such as public heath surveillance, can be noisy. Thus models built for such data sources should be flexible as well as adaptable to changing correlation patterns. In this thesis we explore various methods of using surrogates to generate more reliable and timely forecasts for noisy target signals. We primarily investigate three key components of the forecasting problem viz. (i) short-term forecasting where surrogates can be employed in a now-casting framework, (ii) long-term forecasting problem where surrogates acts as forcing parameters to model system dynamics and, (iii) robust drift models that detect and exploit 'changepoints' in surrogate-target relationship to produce robust models. We explore various 'physical' and 'social' surrogate sources to study these sub-problems, primarily to generate real-time forecasts for endemic diseases. On modeling side, we employed matrix factorization and generalized linear models to detect short-term trends and explored various Bayesian sequential analysis methods to model long-term effects. Our research indicates that, in general, a combination of surrogates can lead to more robust models. Interestingly, our findings indicate that under specific scenarios, particular surrogates can decrease overall forecasting accuracy - thus providing an argument towards the use of 'Good data' against 'Big data'.
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    A framework for evaluating epidemic forecasts
    Tabataba, Farzaneh Sadat; Chakraborty, Prithwish; Ramakrishnan, Naren; Venkatramanan, Srinivasan; Chen, Jiangzhuo; Lewis, Bryan L.; Marathe, Madhav V. (2017-05-15)
    Background Over the past few decades, numerous forecasting methods have been proposed in the field of epidemic forecasting. Such methods can be classified into different categories such as deterministic vs. probabilistic, comparative methods vs. generative methods, and so on. In some of the more popular comparative methods, researchers compare observed epidemiological data from the early stages of an outbreak with the output of proposed models to forecast the future trend and prevalence of the pandemic. A significant problem in this area is the lack of standard well-defined evaluation measures to select the best algorithm among different ones, as well as for selecting the best possible configuration for a particular algorithm. Results In this paper we present an evaluation framework which allows for combining different features, error measures, and ranking schema to evaluate forecasts. We describe the various epidemic features (Epi-features) included to characterize the output of forecasting methods and provide suitable error measures that could be used to evaluate the accuracy of the methods with respect to these Epi-features. We focus on long-term predictions rather than short-term forecasting and demonstrate the utility of the framework by evaluating six forecasting methods for predicting influenza in the United States. Our results demonstrate that different error measures lead to different rankings even for a single Epi-feature. Further, our experimental analyses show that no single method dominates the rest in predicting all Epi-features when evaluated across error measures. As an alternative, we provide various Consensus Ranking schema that summarize individual rankings, thus accounting for different error measures. Since each Epi-feature presents a different aspect of the epidemic, multiple methods need to be combined to provide a comprehensive forecast. Thus we call for a more nuanced approach while evaluating epidemic forecasts and we believe that a comprehensive evaluation framework, as presented in this paper, will add value to the computational epidemiology community.
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    Temporal Topic Modeling to Assess Associations between News Trends and Infectious Disease Outbreaks
    Ghosh, Saurav; Chakraborty, Prithwish; Nsoesie, Elaine O.; Cohn, Emily; Mekaru, Sumiko R.; Brownstein, John S.; Ramakrishnan, Naren (Nature, 2017-01-19)
    In retrospective assessments, internet news reports have been shown to capture early reports of unknown infectious disease transmission prior to official laboratory confirmation. In general, media interest and reporting peaks and wanes during the course of an outbreak. In this study, we quantify the extent to which media interest during infectious disease outbreaks is indicative of trends of reported incidence. We introduce an approach that uses supervised temporal topic models to transform large corpora of news articles into temporal topic trends. The key advantages of this approach include: applicability to a wide range of diseases and ability to capture disease dynamics, including seasonality, abrupt peaks and troughs. We evaluated the method using data from multiple infectious disease outbreaks reported in the United States of America (U.S.), China, and India. We demonstrate that temporal topic trends extracted from disease-related news reports successfully capture the dynamics of multiple outbreaks such as whooping cough in U.S. (2012), dengue outbreaks in India (2013) and China (2014). Our observations also suggest that, when news coverage is uniform, efficient modeling of temporal topic trends using time-series regression techniques can estimate disease case counts with increased precision before official reports by health organizations.
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    What to know before forecasting the flu
    Chakraborty, Prithwish; Lewis, Bryan L.; Eubank, Stephen; Brownstein, John S.; Marathe, Madhav V.; Ramakrishnan, Naren (PLOS, 2018-10-12)
    Accurate and timely influenza (flu) forecasting has gained significant traction in recent times. If done well, such forecasting can aid in deploying effective public health measures. Unlike other statistical or machine learning problems, however, flu forecasting brings unique challenges and considerations stemming from the nature of the surveillance apparatus and the end utility of forecasts. This article presents a set of considerations for flu forecasters to take into account prior to applying forecasting algorithms.