We study non-adaptive pooling strategies for detection of rare faulty items. Given a binary sparse N dimensional signal x, how to construct a sparse binary M × N pooling matrix F such that the signal can be reconstructed from the smallest possible number M of measurements y = Fx? We show that a very small number of measurements is possible for random spatially coupled design of pools F. Our design might find application in genetic screening or compressed genotyping. We show that our results are robust with respect to the uncertainty in the matrix F when some elements are mistaken.
The reconstruction algorithm that is most commonly used in compressed sensing and that has been also discussed several times for reconstruction in group testing and pooling experiments @cite_4 @cite_17 @cite_7 is based on a linear relaxation of the problem to real signal components @math . One then minimizes the @math -norm of the signal under the constraints @math . This is a convex problem that can be solved efficiently using linear programing. In what follows we will use the @math reconstruction as a reference benchmark to demonstrate the improvement that can be achieved using our pooling design and the belief propagation based reconstruction.
@cite_4 @cite_7 @cite_17
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We study the compressed sensing reconstruction problem for a broad class of random, band-diagonal sensing matrices. This construction is inspired by the idea of spatial coupling in coding theory. As demonstrated heuristically and numerically by KrzakalaEtAl , message passing algorithms can effectively solve the reconstruction problem for spatially coupled measurements with undersampling rates close to the fraction of non-zero coordinates. We use an approximate message passing (AMP) algorithm and analyze it through the state evolution method. We give a rigorous proof that this approach is successful as soon as the undersampling rate @math exceeds the (upper) R 'enyi information dimension of the signal, @math . More precisely, for a sequence of signals of diverging dimension @math whose empirical distribution converges to @math , reconstruction is with high probability successful from @math measurements taken according to a band diagonal matrix. For sparse signals, i.e., sequences of dimension @math and @math non-zero entries, this implies reconstruction from @math measurements. For discrete' signals, i.e., signals whose coordinates take a fixed finite set of values, this implies reconstruction from @math measurements. The result is robust with respect to noise, does not apply uniquely to random signals, but requires the knowledge of the empirical distribution of the signal @math . Accurate signal recovery or image reconstruction from indirect and possibly undersampled data is a topic of considerable interest; for example, the literature in the recent field of compressed sensing is already quite immense. This paper applies a smoothing technique and an accelerated first-order algorithm, both from Nesterov [Math. Program. Ser. A, 103 (2005), pp. 127-152], and demonstrates that this approach is ideally suited for solving large-scale compressed sensing reconstruction problems as (1) it is computationally efficient, (2) it is accurate and returns solutions with several correct digits, (3) it is flexible and amenable to many kinds of reconstruction problems, and (4) it is robust in the sense that its excellent performance across a wide range of problems does not depend on the fine tuning of several parameters. Comprehensive numerical experiments on realistic signals exhibiting a large dynamic range show that this algorithm compares favorably with recently proposed state-of-the-art methods. We also apply the algorithm to solve other problems for which there are fewer alternatives, such as total-variation minimization and convex programs seeking to minimize the @math norm of @math under constraints, in which @math is not diagonal. The code is available online as a free package in the MATLAB language. We study the compressed sensing reconstruction problem for a broad class of random, band-diagonal sensing matrices. This construction is inspired by the idea of spatial coupling in coding theory. As demonstrated heuristically and numerically by Krzakala [30], message passing algorithms can effectively solve the reconstruction problem for spatially coupled measurements with undersampling rates close to the fraction of nonzero coordinates. We use an approximate message passing (AMP) algorithm and analyze it through the state evolution method. We give a rigorous proof that this approach is successful as soon as the undersampling rate δ exceeds the (upper) Renyi information dimension of the signal, d(pX). More precisely, for a sequence of signals of diverging dimension n whose empirical distribution converges to pX, reconstruction is with high probability successful from d(pX) n+o(n) measurements taken according to a band diagonal matrix. For sparse signals, i.e., sequences of dimension n and k(n) nonzero entries, this implies reconstruction from k(n)+o(n) measurements. For “discrete” signals, i.e., signals whose coordinates take a fixed finite set of values, this implies reconstruction from o(n) measurements. The result is robust with respect to noise, does not apply uniquely to random signals, but requires the knowledge of the empirical distribution of the signal pX. In sparse approximation theory, the fundamental problem is to reconstruct a signal A∈ℝn from linear measurements 〈Aψi〉 with respect to a dictionary of ψi's. Recently, there is focus on the novel direction of Compressed Sensing [9] where the reconstruction can be done with very few—O(k logn)—linear measurements over a modified dictionary if the signal is compressible, that is, its information is concentrated in k coefficients with the original dictionary. In particular, these results [9, 4, 23] prove that there exists a single O(k logn) ×n measurement matrix such that any such signal can be reconstructed from these measurements, with error at most O(1) times the worst case error for the class of such signals. Compressed sensing has generated tremendous excitement both because of the sophisticated underlying Mathematics and because of its potential applications In this paper, we address outstanding open problems in Compressed Sensing. Our main result is an explicit construction of a non-adaptive measurement matrix and the corresponding reconstruction algorithm so that with a number of measurements polynomial in k, logn, 1 e, we can reconstruct compressible signals. This is the first known polynomial time explicit construction of any such measurement matrix. In addition, our result improves the error guarantee from O(1) to 1 + e and improves the reconstruction time from poly(n) to poly(k logn) Our second result is a randomized construction of O(kpolylog (n)) measurements that work for each signal with high probability and gives per-instance approximation guarantees rather than over the class of all signals. Previous work on Compressed Sensing does not provide such per-instance approximation guarantees; our result improves the best known number of measurements known from prior work in other areas including Learning Theory [20, 21], Streaming algorithms [11, 12, 6] and Complexity Theory [1] for this case Our approach is combinatorial. In particular, we use two parallel sets of group tests, one to filter and the other to certify and estimate; the resulting algorithms are quite simple to implement