A framework for generalized group testing with inhibitors and its potential application in neuroscience

The main goal of group testing with inhibitors (GTI) is to efficiently identify a small number of defective items and inhibitor items in a large set of items. A test on a subset of items is positive if the subset satisfies some specific properties. Inhibitor items cancel the effects of defective items, which often make the outcome of a test containing defective items negative. Different GTI models can be formulated by considering how specific properties have different cancellation effects. This work introduces generalized GTI (GGTI) in which a new type of items is added, i.e., hybrid items. A hybrid item plays the roles of both defectives items and inhibitor items. Since the number of instances of GGTI is large (more than 7 million), we introduce a framework for classifying all types of items non-adaptively, i.e., all tests are designed in advance. We then explain how GGTI can be used to classify neurons in neuroscience. Finally, we show how to realize our proposed scheme in practice

Efficiently Decodable Non-Adaptive Threshold Group Testing

We consider non-adaptive threshold group testing for identification of up to $d$ defective items in a set of $n$ items, where a test is positive if it contains at least $2 \leq u \leq d$ defective items, and negative otherwise. The defective items can be identified using $t = O \left( \left( \frac{d}{u} \right)^u \left( \frac{d}{d - u} \right)^{d-u} \left(u \log{\frac{d}{u}} + \log{\frac{1}{\epsilon}} \right) \cdot d^2 \log{n} \right)$ tests with probability at least $1 - \epsilon$ for any $\epsilon > 0$ or $t = O \left( \left( \frac{d}{u} \right)^u \left( \frac{d}{d -u} \right)^{d - u} d^3 \log{n} \cdot \log{\frac{n}{d}} \right)$ tests with probability 1. The decoding time is $t \times \mathrm{poly}(d^2 \log{n})$. This result significantly improves the best known results for decoding non-adaptive threshold group testing: $O(n\log{n} + n \log{\frac{1}{\epsilon}})$ for probabilistic decoding, where $\epsilon > 0$, and $O(n^u \log{n})$ for deterministic decoding

Asymptotics of Fingerprinting and Group Testing: Tight Bounds from Channel Capacities

In this work we consider the large-coalition asymptotics of various fingerprinting and group testing games, and derive explicit expressions for the capacities for each of these models. We do this both for simple decoders (fast but suboptimal) and for joint decoders (slow but optimal). For fingerprinting, we show that if the pirate strategy is known, the capacity often decreases linearly with the number of colluders, instead of quadratically as in the uninformed fingerprinting game. For many attacks the joint capacity is further shown to be strictly higher than the simple capacity. For group testing, we improve upon known results about the joint capacities, and derive new explicit asymptotics for the simple capacities. These show that existing simple group testing algorithms are suboptimal, and that simple decoders cannot asymptotically be as efficient as joint decoders. For the traditional group testing model, we show that the gap between the simple and joint capacities is a factor 1.44 for large numbers of defectives.Comment: 14 pages, 6 figure

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 sequential fingerprinting: Wald vs. Tardos

We study sequential collusion-resistant fingerprinting, where the fingerprinting code is generated in advance but accusations may be made between rounds, and show that in this setting both the dynamic Tardos scheme and schemes building upon Wald's sequential probability ratio test (SPRT) are asymptotically optimal. We further compare these two approaches to sequential fingerprinting, highlighting differences between the two schemes. Based on these differences, we argue that Wald's scheme should in general be preferred over the dynamic Tardos scheme, even though both schemes have their merits. As a side result, we derive an optimal sequential group testing method for the classical model, which can easily be generalized to different group testing models.Comment: 12 pages, 10 figure

Capacities and Capacity-Achieving Decoders for Various Fingerprinting Games

Combining an information-theoretic approach to fingerprinting with a more constructive, statistical approach, we derive new results on the fingerprinting capacities for various informed settings, as well as new log-likelihood decoders with provable code lengths that asymptotically match these capacities. The simple decoder built against the interleaving attack is further shown to achieve the simple capacity for unknown attacks, and is argued to be an improved version of the recently proposed decoder of Oosterwijk et al. With this new universal decoder, cut-offs on the bias distribution function can finally be dismissed. Besides the application of these results to fingerprinting, a direct consequence of our results to group testing is that (i) a simple decoder asymptotically requires a factor 1.44 more tests to find defectives than a joint decoder, and (ii) the simple decoder presented in this paper provably achieves this bound.Comment: 13 pages, 2 figure