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Register a new userGroup testing for overlapping communities
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Added by
Tao Guo
Publication date
2020
fields
Informatics Engineering
and research's language is
English
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In this paper, we propose algorithms that leverage a known community structure to make group testing more efficient. We consider a population organized in connected communities: each individual participates in one or more communities, and the infection probability of each individual depends on the communities (s)he participates in. Use cases include students who participate in several classes, and workers who share common spaces. Group testing reduces the number of tests needed to identify the infected individuals by pooling diagnostic samples and testing them together. We show that making testing algorithms aware of the community structure, can significantly reduce the number of tests needed both for adaptive and non-adaptive group testing.
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In this paper, we propose algorithms that leverage a known community structure to make group testing more efficient. We consider a population organized in disjoint communities: each individual participates in a community, and its infection probability depends on the community (s)he participates in. Use cases include families, students who participate in several classes, and workers who share common spaces. Group testing reduces the number of tests needed to identify the infected individuals by pooling diagnostic samples and testing them together. We show that if we design the testing strategy taking into account the community structure, we can significantly reduce the number of tests needed for adaptive and non-adaptive group testing, and can improve the reliability in cases where tests are noisy.
We will discuss superimposed codes and non-adaptive group testing designs arising from the potentialities of compressed genotyping models in molecular biology. The given paper was motivated by the 30th anniversary of Dyachkov-Rykov recurrent upper bound on the rate of superimposed codes published in 1982. We were also inspired by recent results obtained for non-adaptive threshold group testing which develop the theory of superimposed codes
The goal of threshold group testing is to identify up to $d$ defective items among a population of $n$ items, where $d$ is usually much smaller than $n$. A test is positive if it has at least $u$ defective items and negative otherwise. Our objective is to identify defective items in sublinear time the number of items, e.g., $mathrm{poly}(d, ln{n}),$ by using the number of tests as low as possible. In this paper, we reduce the number of tests to $O left( h times frac{d^2 ln^2{n}}{mathsf{W}^2(d ln{n})} right)$ and the decoding time to $O left( mathrm{dec}_0 times h right),$ where $mathrm{dec}_0 = O left( frac{d^{3.57} ln^{6.26}{n}}{mathsf{W}^{6.26}(d ln{n})} right) + O left( frac{d^6 ln^4{n}}{mathsf{W}^4(d ln{n})} right)$, $h = Oleft( frac{d_0^2 ln{frac{n}{d_0}}}{(1-p)^2} right)$ , $d_0 = max{u, d - u }$, $p in [0, 1),$ and $mathsf{W}(x) = Theta left( ln{x} - ln{ln{x}} right).$ If the number of tests is increased to $Oleft( h times frac{d^2ln^3{n}}{mathsf{W}^2(d ln{n})} right),$ the decoding complexity is reduced to $O left(mathrm{dec}_1 times h right),$ where $mathrm{dec}_1 = max left{ frac{d^2 ln^3{n}}{mathsf{W}^2(d ln{n})}, frac{ud ln^4{n}}{mathsf{W}^3(d ln{n})} right}.$ Moreover, our proposed scheme is capable of handling errors in test outcomes.
The task of non-adaptive group testing is to identify up to $d$ defective items from $N$ items, where a test is positive if it contains at least one defective item, and negative otherwise. If there are $t$ tests, they can be represented as a $t times N$ measurement matrix. We have answered the question of whether there exists a scheme such that a larger measurement matrix, built from a given $ttimes N$ measurement matrix, can be used to identify up to $d$ defective items in time $O(t log_2{N})$. In the meantime, a $t times N$ nonrandom measurement matrix with $t = O left(frac{d^2 log_2^2{N}}{(log_2(dlog_2{N}) - log_2{log_2(dlog_2{N})})^2} right)$ can be obtained to identify up to $d$ defective items in time $mathrm{poly}(t)$. This is much better than the best well-known bound, $t = O left( d^2 log_2^2{N} right)$. For the special case $d = 2$, there exists an efficient nonrandom construction in which at most two defective items can be identified in time $4log_2^2{N}$ using $t = 4log_2^2{N}$ tests. Numerical results show that our proposed scheme is more practical than existing ones, and experimental results confirm our theoretical analysis. In particular, up to $2^{7} = 128$ defective items can be identified in less than $16$s even for $N = 2^{100}$.
Identification of up to $d$ defective items and up to $h$ inhibitors in a set of $n$ items is the main task of non-adaptive group testing with inhibitors. To efficiently reduce the cost of this Herculean task, a subset of the $n$ items is formed and then tested. This is called textit{group testing}. A test outcome on a subset of items is positive if the subset contains at least one defective item and no inhibitors, and negative otherwise. We present two decoding schemes for efficiently identifying the defective items and the inhibitors in the presence of $e$ erroneous outcomes in time $mathsf{poly}(d, h, e, log_2{n})$, which is sublinear to the number of items $n$. This decoding complexity significantly improves the state-of-the-art schemes in which the decoding time is linear to the number of items $n$, i.e., $mathsf{poly}(d, h, e, n)$. Moreover, each column of the measurement matrices associated with the proposed schemes can be nonrandomly generated in polynomial order of the number of rows. As a result, one can save space for storing them. Simulation results confirm our theoretical analysis. When the number of items is sufficiently large, the decoding time in our proposed scheme is smallest in comparison with existing work. In addition, when some erroneous outcomes are allowed, the number of tests in the proposed scheme is often smaller than the number of tests in existing work.
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