Reliable, short-term forecasts of traditional public health reporting streams (such as cases, hospitalizations, and deaths) are a key ingredient in effective public health decision-making during a pandemic. Since April 2020, our research group has worked with data partners to collect, curate, and make publicly available numerous real-time COVID-19 indicators, providing multiple views of pandemic activity. This paper studies the utility of these indicators from a forecasting perspective. We focus on five indicators, derived from medical insurance claims data, web search queries, and online survey responses. For each indicator, we ask whether its inclusion in a simple model leads to improved predictive accuracy relative to a similar model excluding it. We consider both probabilistic forecasting of confirmed COVID-19 case rates and binary prediction of case "hotspots". Since the values of indicators (and case rates) are commonly revised over time, we take special care to ensure that the data provided to a forecaster is the version that would have been available at the time the forecast was made. Our analysis shows that consistent but modest gains in predictive accuracy are obtained by using these indicators, and furthermore, these gains are related to periods in which the auxiliary indicators behave as "leading indicators" of case rates.

/pdf/can-auxiliary-indicators-improve-covid-19-forecasting-and-4gifeqdfko.pdf

Can Auxiliary Indicators Improve COVID-19 Forecasting and Hotspot Prediction?

With COVID-19 affecting every country globally and changing everyday life, the ability to forecast the spread of the disease is more important than any previous epidemic. The conventional methods of disease-spread modeling, compartmental models, are based on the assumption of spatiotemporal homogeneity of the spread of the virus, which may cause forecasting to underperform, especially at high spatial resolutions. In this paper, we approach the forecasting task with an alternative technique—spatiotemporal machine learning. We present COVID-LSTM, a data-driven model based on a long short-term memory deep learning architecture for forecasting COVID-19 incidence at the county level in the USA. We use the weekly number of new positive cases as temporal input, and hand-engineered spatial features from Facebook movement and connectedness datasets to capture the spread of the disease in time and space. COVID-LSTM outperforms the COVID-19 Forecast Hub’s Ensemble model (COVIDhub-ensemble) on our 17-week evaluation period, making it the first model to be more accurate than the COVIDhub-ensemble over one or more forecast periods. Over the 4-week forecast horizon, our model is on average 50 cases per county more accurate than the COVIDhub-ensemble. We highlight that the underutilization of data-driven forecasting of disease spread prior to COVID-19 is likely due to the lack of sufficient data available for previous diseases, in addition to the recent advances in machine learning methods for spatiotemporal forecasting. We discuss the impediments to the wider uptake of data-driven forecasting, and whether it is likely that more deep learning-based models will be used in the future. 

/pdf/a-spatiotemporal-machine-learning-approach-to-forecasting-1i5n9m93.pdf

A spatiotemporal machine learning approach to forecasting COVID-19 incidence at the county level in the USA

With COVID-19 affecting every country globally and changing everyday life, the ability to forecast the spread of the disease is more important than any previous epidemic. The conventional methods of disease-spread modeling, compartmental models, are based on the assumption of spatiotemporal homogeneity of the spread of the virus, which may cause forecasting to underperform, especially at high spatial resolutions. In this paper we approach the forecasting task with an alternative technique -- spatiotemporal machine learning. We present COVID-LSTM, a data-driven model based on a Long Short-term Memory deep learning architecture for forecasting COVID-19 incidence at the county-level in the US. We use the weekly number of new positive cases as temporal input, and hand-engineered spatial features from Facebook movement and connectedness datasets to capture the spread of the disease in time and space. 
COVID-LSTM outperforms the COVID-19 Forecast Hub's Ensemble model (COVIDhub-ensemble) on our 17-week evaluation period, making it the first model to be more accurate than the COVIDhub-ensemble over one or more forecast periods. Over the 4-week forecast horizon, our model is on average 50 cases per county more accurate than the COVIDhub-ensemble. We highlight that the underutilization of data-driven forecasting of disease spread prior to COVID-19 is likely due to the lack of sufficient data available for previous diseases, in addition to the recent advances in machine learning methods for spatiotemporal forecasting. We discuss the impediments to the wider uptake of data-driven forecasting, and whether it is likely that more deep learning-based models will be used in the future.

A spatiotemporal machine learning approach to forecasting COVID-19 incidence at the county level in the United States.

The COVID-19 pandemic presented enormous data challenges in the United States. Policy makers, epidemiological modelers, and health researchers all require up-to-date data on the pandemic and relevant public behavior, ideally at fine spatial and temporal resolution. The COVIDcast API is our attempt to fill this need: operational since April 2020, it provides open access to both traditional public health surveillance signals (cases, deaths, and hospitalizations) and many auxiliary indicators of COVID-19 activity, such as signals extracted from de-identified medical claims data, massive online surveys, cell phone mobility data, and internet search trends. These are available at a fine geographic resolution (mostly at the county level) and are updated daily. The COVIDcast API also tracks all revisions to historical data, allowing modelers to account for the frequent revisions and backfill that are common for many public health data sources. All of the data is available in a common format through the API and accompanying R and Python software packages. This paper describes the data sources and signals, and provides examples demonstrating that the auxiliary signals in the COVIDcast API present information relevant to tracking COVID activity, augmenting traditional public health reporting and empowering research and decision-making.

https://www.medrxiv.org/content/medrxiv/early/2021/07/16/2021.07.12.21259660.full.pdf

Jimi Kim

Papers

An Open Repository of Real-Time COVID-19 Indicators