Approximate Bayesian computation for an explicit-duration hidden Markov model of COVID-19 hospital trajectories

Date: April 28, 2021
Journal: Proceedings of Machine Learning Research
Citation: Visani, G. M., Lee, A. H., Nguyen, C., Kent, D. M., Wong, J. B., Cohen, J. T., & Hughes, M. C. (2021). Approximate Bayesian Computation for an Explicit-Duration Hidden Markov Model of COVID-19 Hospital Trajectories. arXiv preprint arXiv:2105.00773.


We address the problem of modeling constrained hospital resources in the midst of the COVID-19 pandemic in order to inform decision-makers of future demand and assess the societal value of possible interventions. For broad applicability, we focus on the common yet challenging scenario where patient-level data for a region of interest are not available. Instead, given daily admissions counts, we model aggregated counts of observed resource use, such as the number of patients in the general ward, in the intensive care unit, or on a ventilator. In order to explain how individual patient trajectories produce these counts, we propose an aggregate count explicit-duration hidden Markov model, nicknamed the ACED-HMM, with an interpretable, compact parameterization. We develop an Approximate Bayesian Computation approach that draws samples from the posterior distribution over the model’s transition and duration parameters given aggregate counts from a specific location, thus adapting the model to a region or individual hospital site of interest. Samples from this posterior can then be used to produce future forecasts of any counts of interest. Using data from the United States and the United Kingdom, we show our mechanistic approach provides competitive probabilistic forecasts for the future even as the dynamics of the pandemic shift. Furthermore, we show how our model provides insight about recovery probabilities or length of stay distributions, and we suggest its potential to answer challenging what-if questions about the societal value of possible interventions. 

More Publications