4,424 research outputs found

    PEAR: PEriodic And fixed Rank separation for fast fMRI

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    In functional MRI (fMRI), faster acquisition via undersampling of data can improve the spatial-temporal resolution trade-off and increase statistical robustness through increased degrees-of-freedom. High quality reconstruction of fMRI data from undersampled measurements requires proper modeling of the data. We present an fMRI reconstruction approach based on modeling the fMRI signal as a sum of periodic and fixed rank components, for improved reconstruction from undersampled measurements. We decompose the fMRI signal into a component which a has fixed rank and a component consisting of a sum of periodic signals which is sparse in the temporal Fourier domain. Data reconstruction is performed by solving a constrained problem that enforces a fixed, moderate rank on one of the components, and a limited number of temporal frequencies on the other. Our approach is coined PEAR - PEriodic And fixed Rank separation for fast fMRI. Experimental results include purely synthetic simulation, a simulation with real timecourses and retrospective undersampling of a real fMRI dataset. Evaluation was performed both quantitatively and visually versus ground truth, comparing PEAR to two additional recent methods for fMRI reconstruction from undersampled measurements. Results demonstrate PEAR's improvement in estimating the timecourses and activation maps versus the methods compared against at acceleration ratios of R=8,16 (for simulated data) and R=6.66,10 (for real data). PEAR results in reconstruction with higher fidelity than when using a fixed-rank based model or a conventional Low-rank+Sparse algorithm. We have shown that splitting the functional information between the components leads to better modeling of fMRI, over state-of-the-art methods

    Sampling from a system-theoretic viewpoint

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    This paper studies a system-theoretic approach to the problem of reconstructing an analog signal from its samples. The idea, borrowed from earlier treatments in the control literature, is to address the problem as a hybrid model-matching problem in which performance is measured by system norms. \ud \ud The paper is split into three parts. In Part I we present the paradigm and revise the lifting technique, which is our main technical tool. In Part II optimal samplers and holds are designed for various analog signal reconstruction problems. In some cases one component is fixed while the remaining are designed, in other cases all three components are designed simultaneously. No causality requirements are imposed in Part II, which allows to use frequency domain arguments, in particular the lifted frequency response as introduced in Part I. In Part III the main emphasis is placed on a systematic incorporation of causality constraints into the optimal design of reconstructors. We consider reconstruction problems, in which the sampling (acquisition) device is given and the performance is measured by the L2L^2-norm of the reconstruction error. The problem is solved under the constraint that the optimal reconstructor is ll-causal for a given l0,l\geq 0, i.e., that its impulse response is zero in the time interval (,lh),(-\infty,-l h), where hh is the sampling period. We derive a closed-form state-space solution of the problem, which is based on the spectral factorization of a rational transfer function

    Inelastic transport theory from first-principles: methodology and applications for nanoscale devices

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    We describe a first-principles method for calculating electronic structure, vibrational modes and frequencies, electron-phonon couplings, and inelastic electron transport properties of an atomic-scale device bridging two metallic contacts under nonequilibrium conditions. The method extends the density-functional codes SIESTA and TranSIESTA that use atomic basis sets. The inelastic conductance characteristics are calculated using the nonequilibrium Green's function formalism, and the electron-phonon interaction is addressed with perturbation theory up to the level of the self-consistent Born approximation. While these calculations often are computationally demanding, we show how they can be approximated by a simple and efficient lowest order expansion. Our method also addresses effects of energy dissipation and local heating of the junction via detailed calculations of the power flow. We demonstrate the developed procedures by considering inelastic transport through atomic gold wires of various lengths, thereby extending the results presented in [Frederiksen et al., Phys. Rev. Lett. 93, 256601 (2004)]. To illustrate that the method applies more generally to molecular devices, we also calculate the inelastic current through different hydrocarbon molecules between gold electrodes. Both for the wires and the molecules our theory is in quantitative agreement with experiments, and characterizes the system-specific mode selectivity and local heating.Comment: 24 pages, 17 figure

    Sampling from a system-theoretic viewpoint: Part I - Concepts and tools

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    This paper is first in a series of papers studying a system-theoretic approach to the problem of reconstructing an analog signal from its samples. The idea, borrowed from earlier treatments in the control literature, is to address the problem as a hybrid model-matching problem in which performance is measured by system norms. In this paper we present the paradigm and revise underlying technical tools, such as the lifting technique and some topics of the operator theory. This material facilitates a systematic and unified treatment of a wide range of sampling and reconstruction problems, recovering many hitherto considered different solutions and leading to new results. Some of these applications are discussed in the second part

    Quantization and Compressive Sensing

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    Quantization is an essential step in digitizing signals, and, therefore, an indispensable component of any modern acquisition system. This book chapter explores the interaction of quantization and compressive sensing and examines practical quantization strategies for compressive acquisition systems. Specifically, we first provide a brief overview of quantization and examine fundamental performance bounds applicable to any quantization approach. Next, we consider several forms of scalar quantizers, namely uniform, non-uniform, and 1-bit. We provide performance bounds and fundamental analysis, as well as practical quantizer designs and reconstruction algorithms that account for quantization. Furthermore, we provide an overview of Sigma-Delta (ΣΔ\Sigma\Delta) quantization in the compressed sensing context, and also discuss implementation issues, recovery algorithms and performance bounds. As we demonstrate, proper accounting for quantization and careful quantizer design has significant impact in the performance of a compressive acquisition system.Comment: 35 pages, 20 figures, to appear in Springer book "Compressed Sensing and Its Applications", 201

    Conservation and specialization in PAS domain dynamics

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    The PAS (Per-ARNT-Sim) superfamily is presented as a well-suited study case to demonstrate how comparison of functional motions among distant homologous proteins with conserved fold characteristics may give insight into their functional specialization. Based on the importance of structural flexibility of the receptive structures in anticipating the signal-induced conformational changes of these sensory systems, the dynamics of these structures were analysed. Molecular dynamics was proved to be an effective method to obtain a reliable picture of the dynamics of the crystal structures of HERG, phy3, PYP and FixL, provided that an extensive conformational space sampling is performed. Other reliable sources of dynamic information were the ensembles of NMR structures of hPASK, HIF-2α and PYP. Essential dynamics analysis was successfully employed to extract the relevant information from the sampled conformational spaces. Comparison of motion patterns in the essential subspaces, based on the structural alignment, allowed identification of the specialized region in each domain. This appears to be evolved in the superfamily by following a specific trend, that also suggests the presence of a limited number of general solutions adopted by the PAS domains to sense external signals. These findings may give insight into unknown mechanisms of PAS domains and guide further experimental studies. © The Author 2005. Published by Oxford University Press. All rights reserved

    Signal Reconstruction via H-infinity Sampled-Data Control Theory: Beyond the Shannon Paradigm

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    This paper presents a new method for signal reconstruction by leveraging sampled-data control theory. We formulate the signal reconstruction problem in terms of an analog performance optimization problem using a stable discrete-time filter. The proposed H-infinity performance criterion naturally takes intersample behavior into account, reflecting the energy distributions of the signal. We present methods for computing optimal solutions which are guaranteed to be stable and causal. Detailed comparisons to alternative methods are provided. We discuss some applications in sound and image reconstruction
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