Distributed classifier based on genetically engineered bacterial cell cultures

We describe a conceptual design of a distributed classifier formed by a population of genetically engineered microbial cells. The central idea is to create a complex classifier from a population of weak or simple classifiers. We create a master population of cells with randomized synthetic biosensor circuits that have a broad range of sensitivities towards chemical signals of interest that form the input vectors subject to classification. The randomized sensitivities are achieved by constructing a library of synthetic gene circuits with randomized control sequences (e.g. ribosome-binding sites) in the front element. The training procedure consists in re-shaping of the master population in such a way that it collectively responds to the "positive" patterns of input signals by producing above-threshold output (e.g. fluorescent signal), and below-threshold output in case of the "negative" patterns. The population re-shaping is achieved by presenting sequential examples and pruning the population using either graded selection/counterselection or by fluorescence-activated cell sorting (FACS). We demonstrate the feasibility of experimental implementation of such system computationally using a realistic model of the synthetic sensing gene circuits.Comment: 31 pages, 9 figure

Proceedings of the second "international Traveling Workshop on Interactions between Sparse models and Technology" (iTWIST'14)

The implicit objective of the biennial "international - Traveling Workshop on Interactions between Sparse models and Technology" (iTWIST) is to foster collaboration between international scientific teams by disseminating ideas through both specific oral/poster presentations and free discussions. For its second edition, the iTWIST workshop took place in the medieval and picturesque town of Namur in Belgium, from Wednesday August 27th till Friday August 29th, 2014. The workshop was conveniently located in "The Arsenal" building within walking distance of both hotels and town center. iTWIST'14 has gathered about 70 international participants and has featured 9 invited talks, 10 oral presentations, and 14 posters on the following themes, all related to the theory, application and generalization of the "sparsity paradigm": Sparsity-driven data sensing and processing; Union of low dimensional subspaces; Beyond linear and convex inverse problem; Matrix/manifold/graph sensing/processing; Blind inverse problems and dictionary learning; Sparsity and computational neuroscience; Information theory, geometry and randomness; Complexity/accuracy tradeoffs in numerical methods; Sparsity? What's next?; Sparse machine learning and inference.Comment: 69 pages, 24 extended abstracts, iTWIST'14 website: http://sites.google.com/site/itwist1

Subspace Methods for Joint Sparse Recovery

We propose robust and efficient algorithms for the joint sparse recovery problem in compressed sensing, which simultaneously recover the supports of jointly sparse signals from their multiple measurement vectors obtained through a common sensing matrix. In a favorable situation, the unknown matrix, which consists of the jointly sparse signals, has linearly independent nonzero rows. In this case, the MUSIC (MUltiple SIgnal Classification) algorithm, originally proposed by Schmidt for the direction of arrival problem in sensor array processing and later proposed and analyzed for joint sparse recovery by Feng and Bresler, provides a guarantee with the minimum number of measurements. We focus instead on the unfavorable but practically significant case of rank-defect or ill-conditioning. This situation arises with limited number of measurement vectors, or with highly correlated signal components. In this case MUSIC fails, and in practice none of the existing methods can consistently approach the fundamental limit. We propose subspace-augmented MUSIC (SA-MUSIC), which improves on MUSIC so that the support is reliably recovered under such unfavorable conditions. Combined with subspace-based greedy algorithms also proposed and analyzed in this paper, SA-MUSIC provides a computationally efficient algorithm with a performance guarantee. The performance guarantees are given in terms of a version of restricted isometry property. In particular, we also present a non-asymptotic perturbation analysis of the signal subspace estimation that has been missing in the previous study of MUSIC.Comment: submitted to IEEE transactions on Information Theory, revised versio

From Sparse Signals to Sparse Residuals for Robust Sensing

One of the key challenges in sensor networks is the extraction of information by fusing data from a multitude of distinct, but possibly unreliable sensors. Recovering information from the maximum number of dependable sensors while specifying the unreliable ones is critical for robust sensing. This sensing task is formulated here as that of finding the maximum number of feasible subsystems of linear equations, and proved to be NP-hard. Useful links are established with compressive sampling, which aims at recovering vectors that are sparse. In contrast, the signals here are not sparse, but give rise to sparse residuals. Capitalizing on this form of sparsity, four sensing schemes with complementary strengths are developed. The first scheme is a convex relaxation of the original problem expressed as a second-order cone program (SOCP). It is shown that when the involved sensing matrices are Gaussian and the reliable measurements are sufficiently many, the SOCP can recover the optimal solution with overwhelming probability. The second scheme is obtained by replacing the initial objective function with a concave one. The third and fourth schemes are tailored for noisy sensor data. The noisy case is cast as a combinatorial problem that is subsequently surrogated by a (weighted) SOCP. Interestingly, the derived cost functions fall into the framework of robust multivariate linear regression, while an efficient block-coordinate descent algorithm is developed for their minimization. The robust sensing capabilities of all schemes are verified by simulated tests.Comment: Under review for publication in the IEEE Transactions on Signal Processing (revised version