Leveraging network structure to improve pooled testing efficiency.

Screening is a powerful tool for infection control, allowing for infectious individuals, whether they be symptomatic or asymptomatic, to be identified and isolated. The resource burden of regular and comprehensive screening can often be prohibitive, however. One such measure to address this is pooled testing, whereby groups of individuals are each given a composite test; should a group receive a positive diagnostic test result, those comprising the group are then tested individually. Infectious disease is spread through a transmission network, and this paper shows how assigning individuals to pools based on this underlying network can improve the efficiency of the pooled testing strategy, thereby reducing the resource burden. We designed a simulated annealing algorithm to improve the pooled testing efficiency as measured by the ratio of the expected number of correct classifications to the expected number of tests performed. We then evaluated our approach using an agent-based model designed to simulate the spread of SARS-CoV-2 in a school setting. Our results suggest that our approach can decrease the number of tests required to regularly screen the student body, and that these reductions are quite robust to assigning pools based on partially observed or noisy versions of the network.

Inferring patient transfer networks between healthcare facilities

Constructing accurate patient transfer networks between hospitals is critical for understanding the spread of healthcare associated infections through statistical and mathematical modeling, and for determining optimal screening and treatment strategies. The Healthcare Cost & Utilization Project (HCUP) State Inpatient Databases (SID) provide valuable information on patient transfers from publicly obtainable claims databases, yet often give an incomplete picture due to missingness of patient tracking identifiers. We designed a novel imputation algorithm that enabled us to estimate the true number of patient transfers between each pair of hospitals in a state over a specified time period and age group in the presence of these missing identifiers. We then validated the algorithm's performance through a series of simulation experiments using the HCUP SID, and finally tested the algorithm on multiple states' genuine data. Our proposed method significantly reduced the total mean squared error in predicting the true number of transfers amongst hospitals for all simulation experiments, and it also yielded epidemic simulations that more closely approximated those corresponding to the true patient transfer network.

Simulation-free estimation of an individual-based SEIR model for evaluating nonpharmaceutical interventions with an application to COVID-19 in the District of Columbia.

The ongoing COVID-19 pandemic has overwhelmingly demonstrated the need to accurately evaluate the effects of implementing new or altering existing nonpharmaceutical interventions. Since these interventions applied at the societal level cannot be evaluated through traditional experimental means, public health officials and other decision makers must rely on statistical and mathematical epidemiological models. Nonpharmaceutical interventions are typically focused on contacts between members of a population, and yet most epidemiological models rely on homogeneous mixing which has repeatedly been shown to be an unrealistic representation of contact patterns. An alternative approach is individual based models (IBMs), but these are often time intensive and computationally expensive to implement, requiring a high degree of expertise and computational resources. More often, decision makers need to know the effects of potential public policy decisions in a very short time window using limited resources. This paper presents a computation algorithm for an IBM designed to evaluate nonpharmaceutical interventions. By utilizing recursive relationships, our method can quickly compute the expected epidemiological outcomes even for large populations based on any arbitrary contact network. We utilize our methods to evaluate the effects of various mitigation measures in the District of Columbia, USA, at various times and to various degrees. Rcode for our method is provided in the supplementry material, thereby allowing others to utilize our approach for other regions.