A Compressed Sensing Approach to Pooled RT-PCR Testing for COVID-19 Detection

Ghosh, Sabyasachi; Agarwal, Rishi; Rehan, Mohammad Ali; Pathak, Shreya; Agarwal, Preeti; Gupta, Yash; Consul, Sarthak; Gupta, Nimay; Ritika,; Goenka, Ritesh; Rajwade, Ajit; Gopalkrishnan, Manoj

doi:10.1109/ojsp.2021.3075913

Cited by 57 publications

(29 citation statements)

References 50 publications

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“…Figure 18 shows a comparison of tropical group testing to Tapestry [Gho+21]. Under the same number of patients (D = 10), the same matrix dimension (45 × 105), and no delay (ℓ = 0), we can also achieve 99% sensitivity and 95% specificity.…”

Section: %mentioning

confidence: 99%

Tropical Group Testing

Wang¹,

Gabrys²,

Vardy³

2022

Preprint

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Polymerase chain reaction (PCR) testing is the gold standard for diagnosing COVID-19. PCR amplifies the virus DNA 40 times to produce measurements of viral loads that span seven orders of magnitude. Unfortunately, the outputs of these tests are imprecise and therefore quantitative group testing methods, which rely on precise measurements, are not applicable. Motivated by the ever-increasing demand to identify individuals infected with SARS-CoV-19, we propose a new model that leverages tropical arithmetic to characterize the PCR testing process. Our proposed framework, termed tropical group testing, overcomes existing limitations of quantitative group testing by allowing for imprecise test measurements. In many cases, some of which are highlighted in this work, tropical group testing is provably more powerful than traditional binary group testing in that it requires fewer tests than classical approaches, while additionally providing a mechanism to identify the viral load of each infected individual. It is also empirically stronger than related works that have attempted to combine PCR, quantitative group testing, and compressed sensing.

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Section: %mentioning

confidence: 99%

Tropical Group Testing

Wang¹,

Gabrys²,

Vardy³

2022

Preprint

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“…In instances where testing must be conducted in massive numbers, pooling tests have been used [81][82][83][84][85][86]. This type of testing is designed to estimate the "best" pool size for testing under uncertainty.…”

Section: A Screening Testing Strategiesmentioning

confidence: 99%

Optimization in the Context of COVID-19 Prediction and Control: A Literature Review

et al. 2021

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This paper presents an overview of some key results from a body of optimization studies that are specifically related to COVID-19, as reported in the literature during 2020-2021. As shown in this paper, optimization studies in the context of COVID-19 have been used for many aspects of the pandemic. From these studies, it is observed that since COVID-19 is a multifaceted problem, it cannot be studied from a single perspective or framework, and neither can the related optimization models. Four new and different frameworks are proposed that capture the essence of analyzing COVID-19 (or any pandemic for that matter) and the relevant optimization models. These are: (i) microscale vs. macroscale perspective; (ii) early stages vs. later stages perspective; (iii) aspects with direct vs. indirect relationship to COVID-19; and (iv) compartmentalized perspective. To limit the scope of the review, only optimization studies related to the prediction and control of COVID-19 are considered (public health focused), and which utilize formal optimization techniques or machine learning approaches. In this context and to the best of our knowledge, this survey paper is the first in the literature with a focus on the prediction and control related optimization studies. These studies include optimization of screening testing strategies, prediction, prevention and control, resource management, vaccination prioritization, and decision support tools. Upon reviewing the literature, this paper identifies current gaps and major challenges that hinder the closure of these gaps and provides some insights into future research directions.

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“…In these solutions a sample is shared between two or more pools in same stage rather than only one pool. Recently, a method using Kirkman Triples, known as "Tapestry pooling" has been proposed by 9 . In this strategy too the samples are distributed in different groups in same stage.…”

Section: A Pooled or Group Testingmentioning

confidence: 99%

A unified picture of Balance puzzles and Group testing: Some lessons from quantum mechanics for the pandemic

Waghela

2021

Preprint

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Balance (Counterfeit coin) puzzles have been part of recreational mathematics for a few decades.A particular type of Counterfeit coin puzzle is known in the literature as the "Beam balance puzzle".An abstract solution to it is provided by Iwama et.al as a modification of the Bernstein-Vazirani algorithm, making use of quantum parallelism and entanglement. Moreover, during this pandemic, group testing has proved to be an efficient algorithm to save time and cost of testing specimens for the presence of infection. In this article, we propose a "Binary Spring Balance" (BSB) puzzle, to facilitate a unified picture of the counterfeit coin problem and the testing for infection problem, as both aim to reduce the number of queries. We then showcase two solutions to the BSB problem, one using bits and other using classical-qubits ('cebits") for querying. Both solutions are demonstrated using circuits. In this pursuit, we develop a modified optical implementation of Bernstein-Vazirani algorithm using only polarizers (no need of beam splitters), which has sur-prisingly not yet been proposed earlier. Under the pretext of this demonstration we question why we have not yet developed testing mechanisms inspired by Bernstein-Vazirani algorithm for the pandemic, as they solve the problem in single query, they have no issues related to prevalence of infection in the population, nor are they plagued by the issue of dilution of samples due to pooling. The modified implementation of Bernstein-Vazirani algorithm using polarizers can also be a cost-effective demonstration in an undergraduate lab.

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A Compressed Sensing Approach to Pooled RT-PCR Testing for COVID-19 Detection

Cited by 57 publications

References 50 publications

Tropical Group Testing

Tropical Group Testing

Optimization in the Context of COVID-19 Prediction and Control: A Literature Review

A unified picture of Balance puzzles and Group testing: Some lessons from quantum mechanics for the pandemic

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