Flexible Modeling of Epidemics with an Empirical Bayes Framework

Brooks, Logan; Farrow, David; Hyun, Sangwon; Tibshirani, Ryan J.; Rosenfeld, Roni

doi:10.1371/journal.pcbi.1004382

Cited by 106 publications

(127 citation statements)

References 39 publications

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“…Similar approaches have been used previously to forecast influenza [29,30] and dengue [21]. Here, the respective weights for each candidate trajectory were determined using Bayesian model averaging (BMA), a statistical method that is commonly used to combine information from competing models [31 -33], and was adapted by Raftery et al [34] for use with dynamic weather forecasts.…”

Section: Forecast Methods 2: Bayesian Weighted Outbreaksmentioning

confidence: 99%

Superensemble forecasts of dengue outbreaks

Yamana¹,

Kandula²,

Shaman³

2016

J. R. Soc. Interface.

111

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In recent years, a number of systems capable of predicting future infectious disease incidence have been developed. As more of these systems are operationalized, it is important that the forecasts generated by these different approaches be formally reconciled so that individual forecast error and bias are reduced. Here we present a first example of such multi-system, or superensemble, forecast. We develop three distinct systems for predicting dengue, which are applied retrospectively to forecast outbreak characteristics in San Juan, Puerto Rico. We then use Bayesian averaging methods to combine the predictions from these systems and create superensemble forecasts. We demonstrate that on average, the superensemble approach produces more accurate forecasts than those made from any of the individual forecasting systems.

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Section: Forecast Methods 2: Bayesian Weighted Outbreaksmentioning

confidence: 99%

Superensemble forecasts of dengue outbreaks

Yamana¹,

Kandula²,

Shaman³

2016

J. R. Soc. Interface.

111

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“…These traces of disease observations are embedded in search queries [5, 7, 9, 12, 14, 17, 21, 25, 26, 31, 32, 33, 39, 49, 50, 53, 59, 63, 64, 71, 72 73, 77, 78, 81, 85, 87, 90, 97, 103, 104, 109, 119, 126, 127, 131, 132, 141, 142, 144, 146, 157, 158, 162, 163, 166, 168, 169, 170, 173, 177, 179, 180, 182], social media messages [1, 2, 8, 10, 20, 36, 40, 41, 42, 46, 51, 60, 62, 68, 76, 84, 89, 92, 93, 115, 116, 118, 123, 124, 148, 149, 151, 176], web server access logs [57, 79, 101, 105], and combinations thereof [13, 19, 30, 91, 136, 143, 167]. …”

Section: Related Workmentioning

confidence: 99%

“…The disease surveillance work cited above has been applied to a wide variety of infectious and non-infectious conditions: allergies [87], asthma [136, 176], avian influenza [25], cancer [39], chicken pox [109, 126], chikungunya [109], chlamydia [42, 78, 109], cholera [36, 57], dengue [7, 31, 32, 57, 62, 109], diabetes [42, 60], dysentery [180], Ebola [5, 57], erythromelalgia [63], food poisoning [12], gastroenteritis [45, 50, 71, 126], gonorrhea [77, 78, 109], hand foot and mouth disease [26, 167], heart disease [51, 60], hepatitis [109], HIV/AIDS [57, 76, 177, 180], influenza [1, 2, 8, 9, 10, 13, 19, 20, 21, 30, 33, 40, 41, 43, 46, 48, 53, 57, 59, 68, 72, 73, 79, 81, 84, 85, 89, 90, 91, 92, 93, 97, 101, 103, 104, 105, 109, 115, 116, 118, 123, 124, 126, 131, 132, 141, 14...…”

Section: Related Workmentioning

confidence: 99%

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Measuring Global Disease with Wikipedia

Priedhorsky

Osthus

Daughton

et al. 2017

Proceedings of the 2017 ACM Conference on Computer Supported Cooperative Work and Social Computing

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Effective disease monitoring provides a foundation for effective public health systems. This has historically been accomplished with patient contact and bureaucratic aggregation, which tends to be slow and expensive. Recent internet-based approaches promise to be real-time and cheap, with few parameters. However, the question of when and how these approaches work remains open. We addressed this question using Wikipedia access logs and category links. Our experiments, replicable and extensible using our open source code and data, test the effect of semantic article filtering, amount of training data, forecast horizon, and model staleness by comparing across 6 diseases and 4 countries using thousands of individual models. We found that our minimal-configuration, language-agnostic article selection process based on semantic relatedness is effective for improving predictions, and that our approach is relatively insensitive to the amount and age of training data. We also found, in contrast to prior work, very little forecasting value, and we argue that this is consistent with theoretical considerations about the nature of forecasting. These mixed results lead us to propose that the currently observational field of internet-based disease surveillance must pivot to include theoretical models of information flow as well as controlled experiments based on simulations of disease.

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“…Advance knowledge about the location, timing, peak intensity, and potential number of infected will help public health stakeholders in taking proactive disease containment and management efforts [1,2,3]. Health organizations such as the CDC have recognized this fact, and have sponsored several competitions and workshops to encourage development of viable prediction models [7,8,13].…”

Section: Introductionmentioning

confidence: 99%