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Fast and Efficient Data Science Techniques for COVID-19 Group Testing
Volume 19, Issue 3 (2021), pp. 390–408
Varlam Kutateladze ORCID icon link to view author Varlam Kutateladze details   Ekaterina Seregina ORCID icon link to view author Ekaterina Seregina details  

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https://doi.org/10.6339/21-JDS1011
Pub. online: 26 March 2021      Type: Statistical Data Science     

Received
17 December 2020
Accepted
5 March 2021
Published
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 Material
The 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

 
Abdalhamid B, Bilder CR, McCutchen EL, Hinrichs SH, Koepsell SA, Iwen PC (2020). Assessment of specimen pooling to conserve SARS CoV-2 testing resources. American Journal of Clinical Pathology, 153(6): 715–718.
 
Aldridge M, Johnson O, Scarlett J (2016). Improved group testing rates with constant column weight designs. In: 2016 IEEE International Symposium on Information Theory (ISIT), 1381–1385.
 
Bandeira AS, Dobriban E, Mixon DG, Sawin WF (2013). Certifying the restricted isometry property is hard. IEEE Transactions on Information Theory, 59(6): 3448–3450.
 
Baraniuk R, Davenport M, DeVore R, Wakin M (2008). A simple proof of the restricted isometry property for random matrices. Constructive Approximation, 28(3): 253–263.
 
Candes EJ, Romberg J, Tao T (2006). Robust uncertainty principles: Exact signal reconstruction from highly incomplete frequency information. IEEE Transactions on Information Theory, 52(2): 489–509.
 
Chan CL, Che PH, Jaggi S, Saligrama V (2011). Non-adaptive probabilistic group testing with noisy measurements: Near-optimal bounds with efficient algorithms. In: 2011 49th Annual Allerton Conference on Communication, Control, and Computing (Allerton), 1832–1839.
 
Donoho DL (2006). Compressed sensing. IEEE Transactions on Information Theory, 52(4): 1289–1306.
 
Dorfman R (1943). The detection of defective members of large populations. Ann. Math. Statist., 14(4): 436–440.
 
Emmanuel JC, Bassett MT, Smith HJ, Jacobs JA (1988). Pooling of sera for human immunodeficiency virus (hiv) testing: An economical method for use in developing countries. Journal of Clinical Pathology, 41(5): 582–585.
 
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.
 
Ghosh S, Agarwal R, Rehan M, Pathak S, Agarwal P, Gupta Y, et al. (2020). A compressed sensing approach to group-testing for COVID-19 detection.
 
Hogan CA, Sahoo MK, Pinsky BA (2020). Sample pooling as a strategy to detect community transmission of SARS-CoV-2. JAMA, 323(19): 1967–1969.
 
Hughes-Oliver JM (2006). Pooling Experiments for Blood Screening and Drug Discovery. 48–68. Springer, New York, New York, NY.
 
Johnson O, Aldridge M, Scarlett J (2019). Performance of group testing algorithms with near-constant tests per item. IEEE Transactions on Information Theory, 65(2): 707–723.
 
Kutateladze V, Seregina E (2020). Code supplement to “Fast and Efficient Data Science Techniques for COVID-19 Group Testing. https://tinyurl.com/y4vo86sb.
 
Litvak E, Tu XM, Pagano M (1994). Screening for the presence of a disease by pooling sera samples.
 
Mutesa L, Ndishimye P, Butera Y, Souopgui J, Uwineza A, Rutayisire R, et al. (2020). A strategy for finding people infected with SARS-CoV-2: optimizing pooled testing at low prevalence. medRxiv preprint: https://doi.org/10.1101/2020.05.02.20087924.
 
Chen S, Donoho D (1994). Basis pursuit. In: Proceedings of 1994 28th Asilomar Conference on Signals, Systems and Computers, volume 1, 41–44. 1.
 
Sobel M, Groll PA (1959). Group testing to eliminate efficiently all defectives in a binomial sample. Bell System Technical Journal, 38(5): 1179–1252.
 
Sterrett A (1957). On the detection of defective members of large populations. The Annals of Mathematical Statistics, 28(4): 1033–1036.
 
Taylor SM, Juliano JJ, Trottman PA, Griffin JB, Landis SH, Kitsa P, et al. (2010). High-throughput pooling and real-time pcr-based strategy for malaria detection. Journal of Clinical Microbiology, 48(2): 512–519.
 
Van TT, Miller J, Warshauer DM, Reisdorf E, Jernigan D, Humes R, et al. (2012). Pooling nasopharyngeal/throat swab specimens to increase testing capacity for influenza viruses by pcr. Journal of Clinical Microbiology, 50(3): 891–896.
 
Worldometer (2020). US SARS-CoV-2 cases. https://www.worldometers.info/coronavirus/country/us/.
 
Yelin I, Aharony N, Shaer-Tamar E, Argoetti A, Messer E, Berenbaum D, et al. (2020). Evaluation of COVID-19 rt-qpcr test in multi-sample pools. medRxiv preprint: https://doi.org/10.1101/2020.03.26.20039438.
 
Yi J, Mudumbai R, Xu W (2020). Low-cost and high-throughput testing of COVID-19 viruses and antibodies via compressed sensing: System concepts and computational experiments.

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© 2021 The Author(s)
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Keywords
compressed sensing coronavirus lasso pooled testing SARS-CoV-2 sensing matrix sparse recovery

Funding
This research did not receive any specific grant from funding agencies in the public, commercial, or not-for-profit sectors. Declarations of interest: none.

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