skip to main content
US FlagAn official website of the United States government
dot gov icon
Official websites use .gov
A .gov website belongs to an official government organization in the United States.
https lock icon
Secure .gov websites use HTTPS
A lock ( lock ) or https:// means you've safely connected to the .gov website. Share sensitive information only on official, secure websites.


Title: Geospatial forecasting of COVID-19 spread and risk of reaching hospital capacity
Prompt surveillance and forecasting of COVID-19 spread are of critical importance for slowing down the pandemic and for the success of any public mitigation efforts. However, as with any infectious disease with rapid transmission and high virulence, lack of COVID-19 observations for near-real-time forecasting is still the key challenge obstructing operational disease prediction and control. In this context, we can follow the two approaches to forecasting COVID-19 dynamics: based on mechanistic models and based on machine learning. Mechanistic models are better in capturing an epidemiological curve, using a low amount of data, and describing the overall trajectory of the disease dynamics, hence, providing long-term insights into where the disease might go. Machine learning, in turn, can provide more precise data-driven forecasts especially in the short-term horizons, while suffering from limited interpretability and usually requiring backlog history on the infectious disease. We propose a unified reinforcement learning framework that combines the two approaches. That is, long-term trajectory forecasts are used in machine learning techniques to forecast local variability which is not captured by the mechanistic model.  more » « less
Award ID(s):
2027793 2027802
PAR ID:
10284524
Author(s) / Creator(s):
; ; ; ; ;
Date Published:
Journal Name:
SIGSPATIAL Special
Volume:
12
Issue:
2
ISSN:
1946-7729
Page Range / eLocation ID:
25 to 32
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
More Like this
  1. null (Ed.)
    Abstract Background Ensemble modeling aims to boost the forecasting performance by systematically integrating the predictive accuracy across individual models. Here we introduce a simple-yet-powerful ensemble methodology for forecasting the trajectory of dynamic growth processes that are defined by a system of non-linear differential equations with applications to infectious disease spread. Methods We propose and assess the performance of two ensemble modeling schemes with different parametric bootstrapping procedures for trajectory forecasting and uncertainty quantification. Specifically, we conduct sequential probabilistic forecasts to evaluate their forecasting performance using simple dynamical growth models with good track records including the Richards model, the generalized-logistic growth model, and the Gompertz model. We first test and verify the functionality of the method using simulated data from phenomenological models and a mechanistic transmission model. Next, the performance of the method is demonstrated using a diversity of epidemic datasets including scenario outbreak data of the Ebola Forecasting Challenge and real-world epidemic data outbreaks of including influenza, plague, Zika, and COVID-19. Results We found that the ensemble method that randomly selects a model from the set of individual models for each time point of the trajectory of the epidemic frequently outcompeted the individual models as well as an alternative ensemble method based on the weighted combination of the individual models and yields broader and more realistic uncertainty bounds for the trajectory envelope, achieving not only better coverage rate of the 95% prediction interval but also improved mean interval scores across a diversity of epidemic datasets. Conclusion Our new methodology for ensemble forecasting outcompete component models and an alternative ensemble model that differ in how the variance is evaluated for the generation of the prediction intervals of the forecasts. 
    more » « less
  2. The integration of viral genomic data into public health surveillance has revolutionized our ability to track and forecast infectious disease dynamics. This review addresses two critical aspects of infectious disease forecasting and monitoring: the methodological workflow for epidemic forecasting and the transformative role of molecular surveillance. We first present a detailed approach for validating epidemic models, emphasizing an iterative workflow that utilizes ordinary differential equation (ODE)-based models to investigate and forecast disease dynamics. We recommend a more structured approach to model validation, systematically addressing key stages such as model calibration, assessment of structural and practical parameter identifiability, and effective uncertainty propagation in forecasts. Furthermore, we underscore the importance of incorporating multiple data streams by applying both simulated and real epidemiological data from the COVID-19 pandemic to produce more reliable forecasts with quantified uncertainty. Additionally, we emphasize the pivotal role of viral genomic data in tracking transmission dynamics and pathogen evolution. By leveraging advanced computational tools such as Bayesian phylogenetics and phylodynamics, researchers can more accurately estimate transmission clusters and reconstruct outbreak histories, thereby improving data-driven modeling and forecasting and informing targeted public health interventions. Finally, we discuss the transformative potential of integrating molecular epidemiology with mathematical modeling to complement and enhance epidemic forecasting and optimize public health strategies. 
    more » « less
  3. The COVID-19 pandemic represents the most significant public health disaster since the 1918 influenza pandemic. During pandemics such as COVID-19, timely and reliable spatiotemporal forecasting of epidemic dynamics is crucial. Deep learning-based time series models for forecasting have recently gained popularity and have been successfully used for epidemic forecasting. Here we focus on the design and analysis of deep learning-based models for COVID-19 forecasting. We implement multiple recurrent neural network-based deep learning models and combine them using the stacking ensemble technique. In order to incorporate the effects of multiple factors in COVID-19 spread, we consider multiple sources such as COVID-19 confirmed and death case count data and testing data for better predictions. To overcome the sparsity of training data and to address the dynamic correlation of the disease, we propose clustering-based training for high-resolution forecasting. The methods help us to identify the similar trends of certain groups of regions due to various spatio-temporal effects. We examine the proposed method for forecasting weekly COVID-19 new confirmed cases at county-, state-, and country-level. A comprehensive comparison between different time series models in COVID-19 context is conducted and analyzed. The results show that simple deep learning models can achieve comparable or better performance when compared with more complicated models. We are currently integrating our methods as a part of our weekly forecasts that we provide state and federal authorities. 
    more » « less
  4. Short-term forecasts of the dynamics of coronavirus disease 2019 (COVID-19) in the period up to its decline following mass vaccination was a task that received much attention but proved difficult to do with high accuracy. However, the availability of standardized forecasts and versioned datasets from this period allows for continued work in this area. Here, we introduce the Gaussian infection state space with time dependence (GISST) forecasting model. We evaluate its performance in one to four weeks ahead forecasts of COVID-19 cases, hospital admissions and deaths in the state of California made with official reports of COVID-19, Google’s mobility reports and vaccination data available each week. Evaluation of these forecasts with a weighted interval score shows them to consistently outperform a naive baseline forecast and often score closer to or better than a high-performing ensemble forecaster. The GISST model also provides parameter estimates for a compartmental model of COVID-19 dynamics, includes a regression submodel for the transmission rate and allows for parameters to vary over time according to a random walk. GISST provides a novel, balanced combination of computational efficiency, model interpretability and applicability to large multivariate datasets that may prove useful in improving the accuracy of infectious disease forecasts. 
    more » « less
  5. The increased availability of datasets during the COVID-19 pandemic enabled machine-learning approaches for modeling and forecasting infectious diseases. However, such approaches are known to amplify the bias in the data they are trained on. Bias in such input data like clinical case data for COVID-19 is difficult to measure due to disparities in testing availability, reporting standards, and healthcare access among different populations and regions. Furthermore, the way such biases may propagate through the modeling pipeline to decision-making is relatively unknown. Therefore, we present a system that leverages a highly detailed agent-based model (ABM) of infectious disease spread in a city to simulate the collection of biased clinical case data where the bias is known. Our system allows users to load either a pre-selected region or select their own (using OpenStreetMap data for the environment and census data for the population), specify population and infectious disease parameters, and the degree(s) to which different populations will be overrepresented or underrepresented in the case data. In addition to the system, we provide a large number of benchmark datasets that produce case data at different levels of bias for different regions. Wehope that infectious disease modelers will use these datasets to investigate how well their models are robust to data bias or whether their model is overfit to biased data. 
    more » « less