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

Pooling spaces associated with finite geometry

AbstractMotivated by the works of Ngo and Du [H. Ngo, D. Du, A survey on combinatorial group testing algorithms with applications to DNA library screening, DIMACS Series in Discrete Mathematics and Theoretical Computer Science 55 (2000) 171–182], the notion of pooling spaces was introduced [T. Huang, C. Weng, Pooling spaces and non-adaptive pooling designs, Discrete Mathematics 282 (2004) 163–169] for a systematic way of constructing pooling designs; note that geometric lattices are among pooling spaces. This paper attempts to draw possible connections from finite geometry and distance regular graphs to pooling spaces: including the projective spaces, the affine spaces, the attenuated spaces, and a few families of geometric lattices associated with the orbits of subspaces under finite classical groups, and associated with d-bounded distance-regular graphs

Derandomization and Group Testing

The rapid development of derandomization theory, which is a fundamental area in theoretical computer science, has recently led to many surprising applications outside its initial intention. We will review some recent such developments related to combinatorial group testing. In its most basic setting, the aim of group testing is to identify a set of "positive" individuals in a population of items by taking groups of items and asking whether there is a positive in each group. In particular, we will discuss explicit constructions of optimal or nearly-optimal group testing schemes using "randomness-conducting" functions. Among such developments are constructions of error-correcting group testing schemes using randomness extractors and condensers, as well as threshold group testing schemes from lossless condensers.Comment: Invited Paper in Proceedings of 48th Annual Allerton Conference on Communication, Control, and Computing, 201

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

Optimal Nested Test Plan for Combinatorial Quantitative Group Testing

We consider the quantitative group testing problem where the objective is to identify defective items in a given population based on results of tests performed on subsets of the population. Under the quantitative group testing model, the result of each test reveals the number of defective items in the tested group. The minimum number of tests achievable by nested test plans was established by Aigner and Schughart in 1985 within a minimax framework. The optimal nested test plan offering this performance, however, was not obtained. In this work, we establish the optimal nested test plan in closed form. This optimal nested test plan is also order optimal among all test plans as the population size approaches infinity. Using heavy-hitter detection as a case study, we show via simulation examples orders of magnitude improvement of the group testing approach over two prevailing sampling-based approaches in detection accuracy and counter consumption. Other applications include anomaly detection and wideband spectrum sensing in cognitive radio systems

Unconstraining Graph-Constrained Group Testing

In network tomography, one goal is to identify a small set of failed links in a network using as little information as possible. One way of setting up this problem is called graph-constrained group testing. Graph-constrained group testing is a variant of the classical combinatorial group testing problem, where the tests that one is allowed are additionally constrained by a graph. In this case, the graph is given by the underlying network topology. The main contribution of this work is to show that for most graphs, the constraints imposed by the graph are no constraint at all. That is, the number of tests required to identify the failed links in graph-constrained group testing is near-optimal even for the corresponding group testing problem with no graph constraints. Our approach is based on a simple randomized construction of tests. To analyze our construction, we prove new results about the size of giant components in randomly sparsified graphs. Finally, we provide empirical results which suggest that our connected-subgraph tests perform better not just in theory but also in practice, and in particular perform better on a real-world network topology