The ability to quickly learn fundamentals about a new infectious disease, such as how it is transmitted, the incubation period, and related symptoms, is crucial in any novel pandemic. For instance, rapid identification of symptoms can enable interventions for dampening the spread of the disease. Traditionally, symptoms are learned from research publications associated with clinical studies. However, clinical studies are often slow and time intensive, and hence delays can have dire consequences in a rapidly spreading pandemic like we have seen with COVID-19. In this article, we introduce SymptomID, a modular artificial intelligence–based framework for rapid identification of symptoms associated with novel pandemics using publicly available news reports. SymptomID is built using the state-of-the-art natural language processing model (Bidirectional Encoder Representations for Transformers) to extract symptoms from publicly available news reports and cluster-related symptoms together to remove redundancy. Our proposed framework requires minimal training data, because it builds on a pre-trained language model. In this study, we present a case study of SymptomID using news articles about the current COVID-19 pandemic. Our COVID-19 symptom extraction module, trained on 225 articles, achieves an F1 score of over 0.8. SymptomID can correctly identify well-established symptoms (e.g., “fever” and “cough”) and less-prevalent symptomsmore »
A semi-parametric, state-space compartmental model with time-dependent parameters for forecasting COVID-19 cases, hospitalizations and deaths
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.
- Award ID(s):
- 2027786
- Publication Date:
- NSF-PAR ID:
- 10349576
- Journal Name:
- Journal of The Royal Society Interface
- Volume:
- 19
- Issue:
- 187
- ISSN:
- 1742-5662
- Sponsoring Org:
- National Science Foundation
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Abstract Background The COVID-19 outbreak in Wuhan started in December 2019 and was under control by the end of March 2020 with a total of 50,006 confirmed cases by the implementation of a series of nonpharmaceutical interventions (NPIs) including unprecedented lockdown of the city. This study analyzes the complete outbreak data from Wuhan, assesses the impact of these public health interventions, and estimates the asymptomatic, undetected and total cases for the COVID-19 outbreak in Wuhan. Methods By taking different stages of the outbreak into account, we developed a time-dependent compartmental model to describe the dynamics of disease transmission and case detection and reporting. Model coefficients were parameterized by using the reported cases and following key events and escalated control strategies. Then the model was used to calibrate the complete outbreak data by using the Monte Carlo Markov Chain (MCMC) method. Finally we used the model to estimate asymptomatic and undetected cases and approximate the overall antibody prevalence level. Results We found that the transmission rate between Jan 24 and Feb 1, 2020, was twice as large as that before the lockdown on Jan 23 and 67.6 % (95% CI [0.584,0.759]) of detectable infections occurred during this period. Based on themore »
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Accepted Manuscript1.0
- Publisher's Version of Record
- https://doi.org/10.1098/rsif.2021.0702
