681 research outputs found
Prediction of infectious disease epidemics via weighted density ensembles
Accurate and reliable predictions of infectious disease dynamics can be
valuable to public health organizations that plan interventions to decrease or
prevent disease transmission. A great variety of models have been developed for
this task, using different model structures, covariates, and targets for
prediction. Experience has shown that the performance of these models varies;
some tend to do better or worse in different seasons or at different points
within a season. Ensemble methods combine multiple models to obtain a single
prediction that leverages the strengths of each model. We considered a range of
ensemble methods that each form a predictive density for a target of interest
as a weighted sum of the predictive densities from component models. In the
simplest case, equal weight is assigned to each component model; in the most
complex case, the weights vary with the region, prediction target, week of the
season when the predictions are made, a measure of component model uncertainty,
and recent observations of disease incidence. We applied these methods to
predict measures of influenza season timing and severity in the United States,
both at the national and regional levels, using three component models. We
trained the models on retrospective predictions from 14 seasons (1997/1998 -
2010/2011) and evaluated each model's prospective, out-of-sample performance in
the five subsequent influenza seasons. In this test phase, the ensemble methods
showed overall performance that was similar to the best of the component
models, but offered more consistent performance across seasons than the
component models. Ensemble methods offer the potential to deliver more reliable
predictions to public health decision makers.Comment: 20 pages, 6 figure
The Dynamics of Real-Time Online Information and Disease Progression: Understanding Spatial Heterogeneity in the Relationship
The re-emergence of infectious diseases such as measles and polio is creating logistics challenges for the state authorities to curb their spread and contain them. (CL, 2015) Real-time surveillance of infectious diseases is important to detect possible epidemics in advance to prevent shortages of medications (FDA, 2018). The outbreak of an infectious disease creates panic in the community and is accompanied by a sudden increase in the online interest in knowing more about the disease and its symptoms. Prior studies have found a strong relationship between web-based information and disease outbreak but the influence of dynamics of web-based information in real-time is often not considered (Zhang, 2017). The dynamics or rate of change of the online interest in a disease can inform or misinform about perspective cases of the disease in a region. Oftentimes, especially in this connected world individuals overreact to the situation which may send spurious online signals regarding the disease progression. Hence, we study the relationship between the dynamics of online information and the infectious disease outbreak. We also investigate if this relationship could be influenced by regional demographic factors. We analyze weekly online interest dynamics for five infectious diseases over a period of three years across 50 states of the United States. We control for several factors (including weather, demographics, and travelers) and utilize hierarchical functional data models to incorporate real-time dynamics and clustering at the regional level. Preliminary findings suggest that online interest dynamics have a significant relationship with disease outbreak and the effect is segregated at the regional level. These findings are important to develop a system for real-time surveillance and account for the influence of heterogonous online interest during an endemic outbreak
Stat Med
Seasonal influenza infects between 10 and 50 million people in the United States every year. Accurate forecasts of influenza and influenza-like illness (ILI) have been named by the CDC as an important tool to fight the damaging effects of these epidemics. Multi-model ensembles make accurate forecasts of seasonal influenza, but current operational ensemble forecasts are static: they require an abundance of past ILI data and assign fixed weights to component models at the beginning of a season, but do not update weights as new data on component model performance is collected. We propose an adaptive ensemble that (i) does not initially need data to combine forecasts and (ii) finds optimal weights which are updated week-by-week throughout the influenza season. We take a regularized likelihood approach and investigate this regularizer's ability to impact adaptive ensemble performance. After finding an optimal regularization value, we compare our adaptive ensemble to an equal-weighted and static ensemble. Applied to forecasts of short-term ILI incidence at the regional and national level, our adaptive model outperforms an equal-weighted ensemble and has similar performance to the static ensemble using only a fraction of the data available to the static ensemble. Needing no data at the beginning of an epidemic, an adaptive ensemble can quickly train and forecast an outbreak, providing a practical tool to public health officials looking for a forecast to conform to unique features of a specific season.R35 GM119582/GM/NIGMS NIH HHSUnited States/U01 IP001122/IP/NCIRD CDC HHSUnited States
Data-Centric Epidemic Forecasting: A Survey
The COVID-19 pandemic has brought forth the importance of epidemic
forecasting for decision makers in multiple domains, ranging from public health
to the economy as a whole. While forecasting epidemic progression is frequently
conceptualized as being analogous to weather forecasting, however it has some
key differences and remains a non-trivial task. The spread of diseases is
subject to multiple confounding factors spanning human behavior, pathogen
dynamics, weather and environmental conditions. Research interest has been
fueled by the increased availability of rich data sources capturing previously
unobservable facets and also due to initiatives from government public health
and funding agencies. This has resulted, in particular, in a spate of work on
'data-centered' solutions which have shown potential in enhancing our
forecasting capabilities by leveraging non-traditional data sources as well as
recent innovations in AI and machine learning. This survey delves into various
data-driven methodological and practical advancements and introduces a
conceptual framework to navigate through them. First, we enumerate the large
number of epidemiological datasets and novel data streams that are relevant to
epidemic forecasting, capturing various factors like symptomatic online
surveys, retail and commerce, mobility, genomics data and more. Next, we
discuss methods and modeling paradigms focusing on the recent data-driven
statistical and deep-learning based methods as well as on the novel class of
hybrid models that combine domain knowledge of mechanistic models with the
effectiveness and flexibility of statistical approaches. We also discuss
experiences and challenges that arise in real-world deployment of these
forecasting systems including decision-making informed by forecasts. Finally,
we highlight some challenges and open problems found across the forecasting
pipeline.Comment: 67 pages, 12 figure
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