Fast and Efficient Data Science Techniques for COVID-19 Group Testing
Volume 19, Issue 3 (2021), pp. 390–408
Pub. online: 26 March 2021
Type: Statistical Data Science
Received
17 December 2020
17 December 2020
Accepted
5 March 2021
5 March 2021
Published
26 March 2021
26 March 2021
Abstract
Researchers and public officials tend to agree that until a vaccine is readily available, stopping SARS-CoV-2 transmission is the name of the game. Testing is the key to preventing the spread, especially by asymptomatic individuals. With testing capacity restricted, group testing is an appealing alternative for comprehensive screening and has recently received FDA emergency authorization. This technique tests pools of individual samples, thereby often requiring fewer testing resources while potentially providing multiple folds of speedup. We approach group testing from a data science perspective and offer two contributions. First, we provide an extensive empirical comparison of modern group testing techniques based on simulated data. Second, we propose a simple one-round method based on ${\ell _{1}}$-norm sparse recovery, which outperforms current state-of-the-art approaches at certain disease prevalence rates.
Supplementary material
Supplementary MaterialThe code supplement (Kutateladze and Seregina, 2020) is available in Google Colab environment. It is written in Python and readily allows to replicate all the graphs provided, as well as produce additional exercises.
References
FDA (2020). Emergency Authorization for Sample Pooling. https://www.fda.gov/news-events/press-announcements/coronavirus-covid-19-update-fda-issues-first-emergency-authorization-sample-pooling-diagnostic.
Kutateladze V, Seregina E (2020). Code supplement to “Fast and Efficient Data Science Techniques for COVID-19 Group Testing. https://tinyurl.com/y4vo86sb.
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Worldometer (2020). US SARS-CoV-2 cases. https://www.worldometers.info/coronavirus/country/us/.
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