Rapid Sequence Identification of Potential Pathogens Using Techniques from Sparse Linear Algebra

The decreasing costs and increasing speed and accuracy of DNA sample collection, preparation, and sequencing has rapidly produced an enormous volume of genetic data. However, fast and accurate analysis of the samples remains a bottleneck. Here we present D$^{4}$RAGenS, a genetic sequence identification algorithm that exhibits the Big Data handling and computational power of the Dynamic Distributed Dimensional Data Model (D4M). The method leverages linear algebra and statistical properties to increase computational performance while retaining accuracy by subsampling the data. Two run modes, Fast and Wise, yield speed and precision tradeoffs, with applications in biodefense and medical diagnostics. The D$^{4}$RAGenS analysis algorithm is tested over several datasets, including three utilized for the Defense Threat Reduction Agency (DTRA) metagenomic algorithm contest

Multidimensional Index Modulation in Wireless Communications

In index modulation schemes, information bits are conveyed through indexing of transmission entities such as antennas, subcarriers, times slots, precoders, subarrays, and radio frequency (RF) mirrors. Index modulation schemes are attractive for their advantages such as good performance, high rates, and hardware simplicity. This paper focuses on index modulation schemes in which multiple transmission entities, namely, {\em antennas}, {\em time slots}, and {\em RF mirrors}, are indexed {\em simultaneously}. Recognizing that such multidimensional index modulation schemes encourage sparsity in their transmit signal vectors, we propose efficient signal detection schemes that use compressive sensing based reconstruction algorithms. Results show that, for a given rate, improved performance is achieved when the number of indexed transmission entities is increased. We also explore indexing opportunities in {\em load modulation}, which is a modulation scheme that offers power efficiency and reduced RF hardware complexity advantages in multiantenna systems. Results show that indexing space and time in load modulated multiantenna systems can achieve improved performance

Grid-free compressive beamforming

The direction-of-arrival (DOA) estimation problem involves the localization of a few sources from a limited number of observations on an array of sensors, thus it can be formulated as a sparse signal reconstruction problem and solved efficiently with compressive sensing (CS) to achieve high-resolution imaging. On a discrete angular grid, the CS reconstruction degrades due to basis mismatch when the DOAs do not coincide with the angular directions on the grid. To overcome this limitation, a continuous formulation of the DOA problem is employed and an optimization procedure is introduced, which promotes sparsity on a continuous optimization variable. The DOA estimation problem with infinitely many unknowns, i.e., source locations and amplitudes, is solved over a few optimization variables with semidefinite programming. The grid-free CS reconstruction provides high-resolution imaging even with non-uniform arrays, single-snapshot data and under noisy conditions as demonstrated on experimental towed array data.Comment: 14 pages, 8 figures, journal pape