COFFEE: COVID-19 Forecasts using Fast Evaluations and Estimation
This document details the methodology of the Los Alamos National Laboratory COVID-19 forecasting model, COFFEE (COVID-19 Forecasts using Fast Evaluations and Estimation).
stat.ME↗
arXiv subjects
Geoffrey Fairchild
Publications and source records attributed to Geoffrey Fairchild.
"Thought I'd Share First" and Other Conspiracy Theory Tweets from the COVID-19 Infodemic: Exploratory Study
Background: The COVID-19 outbreak has left many people isolated within their homes; these people are turning to social media for news and social connection, which leaves them vulnerable to believing and sharing misinformation. Health-related misinformation threatens adherence to public health messaging, and monitoring its spread on social media is critical to understanding the evolution of ideas that have potentially negative public health impacts. Results: Analysis using model-labeled data was beneficial for increasing the proportion of data matching misinformation indicators. Random forest classifier metrics varied across the four conspiracy theories considered (F1 scores between 0.347 and 0.857); this performance increased as the given conspiracy theory was more narrowly defined. We showed that misinformation tweets demonstrate more negative sentiment when compared to nonmisinformation tweets and that theories evolve over time, incorporating details from unrelated conspiracy theories as well as real-world events. Conclusions: Although we focus here on health-related misinformation, this combination of approaches is not specific to public health and is valuable for characterizing misinformation in general, which is an important first step in creating targeted messaging to counteract its spread. Initial messaging should aim to preempt generalized misinformation before it becomes widespread, while later messaging will need to target evolving conspiracy theories and the new facets of each as they become incorporated.
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Time Series Methods and Ensemble Models to Nowcast Dengue at the State Level in Brazil
Predicting an infectious disease can help reduce its impact by advising public health interventions and personal preventive measures. Novel data streams, such as Internet and social media data, have recently been reported to benefit infectious disease prediction. As a case study of dengue in Brazil, we have combined multiple traditional and non-traditional, heterogeneous data streams (satellite imagery, Internet, weather, and clinical surveillance data) across its 27 states on a weekly basis over seven years. For each state, we nowcast dengue based on several time series models, which vary in complexity and inclusion of exogenous data. The top-performing model varies by state, motivating our consideration of ensemble approaches to automatically combine these models for better outcomes at the state level. Model comparisons suggest that predictions often improve with the addition of exogenous data, although similar performance can be attained by including only one exogenous data stream (either weather data or the novel satellite data) rather than combining all of them. Our results demonstrate that Brazil can be nowcasted at the state level with high accuracy and confidence, inform the utility of each individual data stream, and reveal potential geographic contributors to predictive performance. Our work can be extended to other spatial levels of Brazil, vector-borne diseases, and countries, so that the spread of infectious disease can be more effectively curbed.
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Nowcasting Influenza Incidence with CDC Web Traffic Data: A Demonstration Using a Novel Data Set
Influenza epidemics result in a public health and economic burden around the globe. Traditional surveillance techniques, which rely on doctor visits, provide data with a delay of 1-2 weeks. A means of obtaining real-time data and forecasting future outbreaks is desirable to provide more timely responses to influenza epidemics. In this work, we present the first implementation of a novel data set by demonstrating its ability to supplement traditional disease surveillance at multiple spatial resolutions. We use Internet traffic data from the Centers for Disease Control and Prevention (CDC) website to determine the potential usability of this data source. We test the traffic generated by ten influenza-related pages in eight states and nine census divisions within the United States and compare it against clinical surveillance data. Our results yield $r^2$ = 0.955 in the most successful case, promising results for some cases, and unsuccessful results for other cases. These results demonstrate that Internet data may be able to complement traditional influenza surveillance in some cases but not in others. Specifically, our results show that the CDC website traffic may inform national and division-level models but not models for each individual state. In addition, our results show better agreement when the data were broken up by seasons instead of aggregated over several years. In the interest of scientific transparency to further the understanding of when Internet data streams are an appropriate supplemental data source, we also include negative results (i.e., unsuccessful models). We anticipate that this work will lead to more complex nowcasting and forecasting models using this data stream.
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Epidemiological data challenges: planning for a more robust future through data standards
Accessible epidemiological data are of great value for emergency preparedness and response, understanding disease progression through a population, and building statistical and mechanistic disease models that enable forecasting. The status quo, however, renders acquiring and using such data difficult in practice. In many cases, a primary way of obtaining epidemiological data is through the internet, but the methods by which the data are presented to the public often differ drastically among institutions. As a result, there is a strong need for better data sharing practices. This paper identifies, in detail and with examples, the three key challenges one encounters when attempting to acquire and use epidemiological data: 1) interfaces, 2) data formatting, and 3) reporting. These challenges are used to provide suggestions and guidance for improvement as these systems evolve in the future. If these suggested data and interface recommendations were adhered to, epidemiological and public health analysis, modeling, and informatics work would be significantly streamlined, which can in turn yield better public health decision-making capabilities.
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Eliciting Disease Data from Wikipedia Articles
Traditional disease surveillance systems suffer from several disadvantages, including reporting lags and antiquated technology, that have caused a movement towards internet-based disease surveillance systems. Internet systems are particularly attractive for disease outbreaks because they can provide data in near real-time and can be verified by individuals around the globe. However, most existing systems have focused on disease monitoring and do not provide a data repository for policy makers or researchers. In order to fill this gap, we analyzed Wikipedia article content. We demonstrate how a named-entity recognizer can be trained to tag case counts, death counts, and hospitalization counts in the article narrative that achieves an F1 score of 0.753. We also show, using the 2014 West African Ebola virus disease epidemic article as a case study, that there are detailed time series data that are consistently updated that closely align with ground truth data. We argue that Wikipedia can be used to create the first community-driven open-source emerging disease detection, monitoring, and repository system.
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Forecasting the 2013--2014 Influenza Season using Wikipedia
Infectious diseases are one of the leading causes of morbidity and mortality around the world; thus, forecasting their impact is crucial for planning an effective response strategy. According to the Centers for Disease Control and Prevention (CDC), seasonal influenza affects between 5% to 20% of the U.S. population and causes major economic impacts resulting from hospitalization and absenteeism. Understanding influenza dynamics and forecasting its impact is fundamental for developing prevention and mitigation strategies. We combine modern data assimilation methods with Wikipedia access logs and CDC influenza like illness (ILI) reports to create a weekly forecast for seasonal influenza. The methods are applied to the 2013--2014 influenza season but are sufficiently general to forecast any disease outbreak, given incidence or case count data. We adjust the initialization and parametrization of a disease model and show that this allows us to determine systematic model bias. In addition, we provide a way to determine where the model diverges from observation and evaluate forecast accuracy. Wikipedia article access logs are shown to be highly correlated with historical ILI records and allow for accurate prediction of ILI data several weeks before it becomes available. The results show that prior to the peak of the flu season, our forecasting method projected the actual outcome with a high probability. However, since our model does not account for re-infection or multiple strains of influenza, the tail of the epidemic is not predicted well after the peak of flu season has past.
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Global disease monitoring and forecasting with Wikipedia
Infectious disease is a leading threat to public health, economic stability, and other key social structures. Efforts to mitigate these impacts depend on accurate and timely monitoring to measure the risk and progress of disease. Traditional, biologically-focused monitoring techniques are accurate but costly and slow; in response, new techniques based on social internet data such as social media and search queries are emerging. These efforts are promising, but important challenges in the areas of scientific peer review, breadth of diseases and countries, and forecasting hamper their operational usefulness. We examine a freely available, open data source for this use: access logs from the online encyclopedia Wikipedia. Using linear models, language as a proxy for location, and a systematic yet simple article selection procedure, we tested 14 location-disease combinations and demonstrate that these data feasibly support an approach that overcomes these challenges. Specifically, our proof-of-concept yields models with $r^2$ up to 0.92, forecasting value up to the 28 days tested, and several pairs of models similar enough to suggest that transferring models from one location to another without re-training is feasible. Based on these preliminary results, we close with a research agenda designed to overcome these challenges and produce a disease monitoring and forecasting system that is significantly more effective, robust, and globally comprehensive than the current state of the art.
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