GROTESQUE: Noisy Group Testing (Quick and Efficient)

Group-testing refers to the problem of identifying (with high probability) a (small) subset of $D$ defectives from a (large) set of $N$ items via a "small" number of "pooled" tests. For ease of presentation in this work we focus on the regime when D = \cO{N^{1-\gap}} for some \gap > 0. The tests may be noiseless or noisy, and the testing procedure may be adaptive (the pool defining a test may depend on the outcome of a previous test), or non-adaptive (each test is performed independent of the outcome of other tests). A rich body of literature demonstrates that $\Theta(D\log(N))$ tests are information-theoretically necessary and sufficient for the group-testing problem, and provides algorithms that achieve this performance. However, it is only recently that reconstruction algorithms with computational complexity that is sub-linear in $N$ have started being investigated (recent work by \cite{GurI:04,IndN:10, NgoP:11} gave some of the first such algorithms). In the scenario with adaptive tests with noisy outcomes, we present the first scheme that is simultaneously order-optimal (up to small constant factors) in both the number of tests and the decoding complexity (\cO{D\log(N)} in both the performance metrics). The total number of stages of our adaptive algorithm is "small" (\cO{\log(D)}). Similarly, in the scenario with non-adaptive tests with noisy outcomes, we present the first scheme that is simultaneously near-optimal in both the number of tests and the decoding complexity (via an algorithm that requires \cO{D\log(D)\log(N)} tests and has a decoding complexity of {${\cal O}(D(\log N+\log^{2}D))$}. Finally, we present an adaptive algorithm that only requires 2 stages, and for which both the number of tests and the decoding complexity scale as {${\cal O}(D(\log N+\log^{2}D))$}. For all three settings the probability of error of our algorithms scales as \cO{1/(poly(D)}.Comment: 26 pages, 5 figure

Learning Immune-Defectives Graph through Group Tests

This paper deals with an abstraction of a unified problem of drug discovery and pathogen identification. Pathogen identification involves identification of disease-causing biomolecules. Drug discovery involves finding chemical compounds, called lead compounds, that bind to pathogenic proteins and eventually inhibit the function of the protein. In this paper, the lead compounds are abstracted as inhibitors, pathogenic proteins as defectives, and the mixture of "ineffective" chemical compounds and non-pathogenic proteins as normal items. A defective could be immune to the presence of an inhibitor in a test. So, a test containing a defective is positive iff it does not contain its "associated" inhibitor. The goal of this paper is to identify the defectives, inhibitors, and their "associations" with high probability, or in other words, learn the Immune Defectives Graph (IDG) efficiently through group tests. We propose a probabilistic non-adaptive pooling design, a probabilistic two-stage adaptive pooling design and decoding algorithms for learning the IDG. For the two-stage adaptive-pooling design, we show that the sample complexity of the number of tests required to guarantee recovery of the inhibitors, defectives, and their associations with high probability, i.e., the upper bound, exceeds the proposed lower bound by a logarithmic multiplicative factor in the number of items. For the non-adaptive pooling design too, we show that the upper bound exceeds the proposed lower bound by at most a logarithmic multiplicative factor in the number of items.Comment: Double column, 17 pages. Updated with tighter lower bounds and other minor edit

On Detecting Some Defective Items in Group Testing

Group testing is an approach aimed at identifying up to $d$ defective items among a total of $n$ elements. This is accomplished by examining subsets to determine if at least one defective item is present. In our study, we focus on the problem of identifying a subset of $\ell\leq d$ defective items. We develop upper and lower bounds on the number of tests required to detect $\ell$ defective items in both the adaptive and non-adaptive settings while considering scenarios where no prior knowledge of $d$ is available, and situations where an estimate of $d$ or at least some non-trivial upper bound on $d$ is available. When no prior knowledge on $d$ is available, we prove a lower bound of $\Omega(\frac{\ell \log^2n}{\log \ell +\log\log n})$ tests in the randomized non-adaptive settings and an upper bound of $O(\ell \log^2 n)$ for the same settings. Furthermore, we demonstrate that any non-adaptive deterministic algorithm must ask $\Theta(n)$ tests, signifying a fundamental limitation in this scenario. For adaptive algorithms, we establish tight bounds in different scenarios. In the deterministic case, we prove a tight bound of $\Theta(\ell\log{(n/\ell)})$. Moreover, in the randomized settings, we derive a tight bound of $\Theta(\ell\log{(n/d)})$. When $d$, or at least some non-trivial estimate of $d$, is known, we prove a tight bound of $\Theta(d\log (n/d))$ for the deterministic non-adaptive settings, and $\Theta(\ell\log(n/d))$ for the randomized non-adaptive settings. In the adaptive case, we present an upper bound of $O(\ell \log (n/\ell))$ for the deterministic settings, and a lower bound of $\Omega(\ell\log(n/d)+\log n)$. Additionally, we establish a tight bound of $\Theta(\ell \log(n/d))$ for the randomized adaptive settings

Non-adaptive Group Testing on Graphs

Grebinski and Kucherov (1998) and Alon et al. (2004-2005) study the problem of learning a hidden graph for some especial cases, such as hamiltonian cycle, cliques, stars, and matchings. This problem is motivated by problems in chemical reactions, molecular biology and genome sequencing. In this paper, we present a generalization of this problem. Precisely, we consider a graph G and a subgraph H of G and we assume that G contains exactly one defective subgraph isomorphic to H. The goal is to find the defective subgraph by testing whether an induced subgraph contains an edge of the defective subgraph, with the minimum number of tests. We present an upper bound for the number of tests to find the defective subgraph by using the symmetric and high probability variation of Lov\'asz Local Lemma