Linear Transformations for Randomness Extraction

Information-efficient approaches for extracting randomness from imperfect sources have been extensively studied, but simpler and faster ones are required in the high-speed applications of random number generation. In this paper, we focus on linear constructions, namely, applying linear transformation for randomness extraction. We show that linear transformations based on sparse random matrices are asymptotically optimal to extract randomness from independent sources and bit-fixing sources, and they are efficient (may not be optimal) to extract randomness from hidden Markov sources. Further study demonstrates the flexibility of such constructions on source models as well as their excellent information-preserving capabilities. Since linear transformations based on sparse random matrices are computationally fast and can be easy to implement using hardware like FPGAs, they are very attractive in the high-speed applications. In addition, we explore explicit constructions of transformation matrices. We show that the generator matrices of primitive BCH codes are good choices, but linear transformations based on such matrices require more computational time due to their high densities.Comment: 2 columns, 14 page

Coarse-graining in retrodictive quantum state tomography

Quantum state tomography often operates in the highly idealised scenario of assuming perfect measurements. The errors implied by such an approach are entwined with other imperfections relating to the information processing protocol or application of interest. We consider the problem of retrodicting the quantum state of a system, existing prior to the application of random but known phase errors, allowing those errors to be separated and removed. The continuously random nature of the errors implies that there is only one click per measurement outcome -- a feature having a drastically adverse effect on data-processing times. We provide a thorough analysis of coarse-graining under various reconstruction algorithms, finding dramatic increases in speed for only modest sacrifices in fidelity

Bacterial Community Reconstruction Using A Single Sequencing Reaction

Bacteria are the unseen majority on our planet, with millions of species and comprising most of the living protoplasm. While current methods enable in-depth study of a small number of communities, a simple tool for breadth studies of bacterial population composition in a large number of samples is lacking. We propose a novel approach for reconstruction of the composition of an unknown mixture of bacteria using a single Sanger-sequencing reaction of the mixture. This method is based on compressive sensing theory, which deals with reconstruction of a sparse signal using a small number of measurements. Utilizing the fact that in many cases each bacterial community is comprised of a small subset of the known bacterial species, we show the feasibility of this approach for determining the composition of a bacterial mixture. Using simulations, we show that sequencing a few hundred base-pairs of the 16S rRNA gene sequence may provide enough information for reconstruction of mixtures containing tens of species, out of tens of thousands, even in the presence of realistic measurement noise. Finally, we show initial promising results when applying our method for the reconstruction of a toy experimental mixture with five species. Our approach may have a potential for a practical and efficient way for identifying bacterial species compositions in biological samples.Comment: 28 pages, 12 figure