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Results for “Parallel Algorithms”

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PubMed2000

Speckle tracking for multi-dimensional flow estimation.

Speckle tracking methods overcome the major limitations of current Doppler methods for flow imaging and quantification: angle dependence and aliasing. In this paper, we review the development of speckle tracking, with particular attention to the advantages and limitations of two-dimensional algorithms that use a single transducer aperture. Ensemble tracking, a recent speckle tracking method based upon parallel receive processing, is described. Experimental results with ensemble tracking indicate the ability to measure laminar flow in a phantom at a beam-vessel angle of 60 degrees, which had not been possible with previous 2D speckle tracking methods. Finally, important areas for future research in speckle tracking are briefly summarized.

Algorithms↗

PubMed2007

Bayesian parallel imaging with edge-preserving priors.

Existing parallel MRI methods are limited by a fundamental trade-off in that suppressing noise introduces aliasing artifacts. Bayesian methods with an appropriately chosen image prior offer a promising alternative; however, previous methods with spatial priors assume that intensities vary smoothly over the entire image, resulting in blurred edges. Here we introduce an edge-preserving prior (EPP) that instead assumes that intensities are piecewise smooth, and propose a new approach to efficiently compute its Bayesian estimate. The estimation task is formulated as an optimization problem that requires a nonconvex objective function to be minimized in a space with thousands of dimensions. As a result, traditional continuous minimization methods cannot be applied. This optimization task is closely related to some problems in the field of computer vision for which discrete optimization methods have been developed in the last few years. We adapt these algorithms, which are based on graph cuts, to address our optimization problem. The results of several parallel imaging experiments on brain and torso regions performed under challenging conditions with high acceleration factors are shown and compared with the results of conventional sensitivity encoding (SENSE) methods. An empirical analysis indicates that the proposed method visually improves overall quality compared to conventional methods.

Algorithms↗

PubMed1994

Detection of jumps in single-channel data containing subconductance levels.

Detection algorithms are widely used for the analysis of single-channel data because they remove the background noise from the measured current signal and reconstruct the noise-free time series. Standard detection algorithms assume channels switching only between zero and full conductance. Many types of channels, however, show subconductance levels. A new detection algorithm for data containing sublevels, the so-called sublevel Hinkley-detector (SHD), calculates several test values in parallel, one for each possible jump. The velocity of increase has a maximum for the correct jump. This feature is used to detect the jump and to diagnose the new level of current. Because patch-clamp data are always filtered by an antialiasing low-pass filter before sampling, the algorithm is supplemented by a special diagnosis phase accounting for the distortion of the originally rectangular jumps. Along with the reconstructed (noise-free) time series the SHD also gives a matrix of the transition counts between the levels. This matrix is a useful statistical tool for the decision whether the observed channel(s) have in fact a subconductance conformation or if there are simply several channels of different conductivity contained within the patch.

Algorithms↗

PubMed2005

Analytical fan-beam and cone-beam reconstruction algorithms with uniform attenuation correction for SPECT.

In this paper, we developed an analytical fan-beam reconstruction algorithm that compensates for uniform attenuation in SPECT. The new fan-beam algorithm is in the form of backprojection first, then filtering, and is mathematically exact. The algorithm is based on three components. The first one is the established generalized central-slice theorem, which relates the 1D Fourier transform of a set of arbitrary data and the 2D Fourier transform of the backprojected image. The second one is the fact that the backprojection of the fan-beam measurements is identical to the backprojection of the parallel measurements of the same object with the same attenuator. The third one is the stable analytical reconstruction algorithm for uniformly attenuated Radon data, developed by Metz and Pan. The fan-beam algorithm is then extended into a cone-beam reconstruction algorithm, where the orbit of the focal point of the cone-beam imaging geometry is a circle. This orbit geometry does not satisfy Tuy's condition and the obtained cone-beam algorithm is an approximation. In the cone-beam algorithm, the cone-beam data are first backprojected into the 3D image volume; then a slice-by-slice filtering is performed. This slice-by-slice filtering procedure is identical to that of the fan-beam algorithm. Both the fan-beam and cone-beam algorithms are efficient, and computer simulations are presented. The new cone-beam algorithm is compared with Bronnikov's cone-beam algorithm, and it is shown to have better performance with noisy projections.

Algorithms↗

PubMed1991

Isotropic connections generate functional asymmetrical behavior in visual cortical cells.

1. We study the relationship between structure and function in inhibitory long-range interactions in visual cortex. The sharpening of orientation tuning with "cross-orientation inhibition" is used as an example to discuss anisotropies that are generated by long-range connections. 2. In this study, as opposed to the detailed cortex model described in a previous report, a model of the cortical orientation column structure is proposed in which cortical cells are described only by their orientation preference. 3. We present results using different geometric arrangements of orientation columns. In the simplest case, straight parallel orientation columns were used. We also utilized more realistic, curved columns generated by a simple algorithm. The results were confirmed by the study of a patch of real column structure, determined experimentally by Swindale et al. 4. A given cell receives functionally defined cross-orientation inhibition if the cell receives inhibitory input that is strongest along its nonpreferred orientation. On the other hand, a cell is said to receive structurally defined cross-orientation inhibition if the inhibition arises from source cells with an orientation preference orthogonal to that of the target cell. Even though those definitions seem to describe similar situations, we show that, in the general case, structurally defined cross-orientation inhibition does not efficiently sharpen orientation selectivity. In particular, for straight and parallel columns, structurally defined cross-orientation inhibition results in unequal amounts of inhibition for whole cell populations with different preferred orientations. 5. In more realistic column structures, we studied the question of whether structural cross-orientation inhibition could be implemented in a more efficient way. However, for the majority of cells, it is demonstrated that their nonpreferred stimulus will not preferably excite "cross-oriented" cells. Thus structural cross-orientation inhibition is not efficient in real cortical columns. 6. We propose a new mechanism called circular inhibition. In this connection scheme, a target cell receives inhibitory input from source cells that are located at a given distance (the same for all cells) from the target cell. Circular inhibition can be regarded as two-dimensional long-range lateral inhibition. As opposed to structural cross-orientation inhibition, this mechanism does not introduce unwanted anisotropies in the orientation tuning of the target cells. It is also conceptually much simpler and developmentally advantageous. It is shown that this connection scheme results in a net functional cross-orientation inhibition in all realistic column geometries. The inhibitory tuning strength obtained with circular inhibition is weak and similar to that measured in reality.(ABSTRACT TRUNCATED AT 400 WORDS)

Algorithms↗

PubMed1999

Protein tertiary structure prediction using a branch and bound algorithm.

We report a new method for predicting protein tertiary structure from sequence and secondary structure information. The predictions result from global optimization of a potential energy function, including van der Waals, hydrophobic, and excluded volume terms. The optimization algorithm, which is based on the alphaBB method developed by Floudas and coworkers (Costas and Floudas, J Chem Phys 1994;100:1247-1261), uses a reduced model of the protein and is implemented in both distance and dihedral angle space, enabling a side-by-side comparison of methodologies. For a set of eight small proteins, representing the three basic types--all alpha, all beta, and mixed alpha/beta--the algorithm locates low-energy native-like structures (less than 6A root mean square deviation from the native coordinates) starting from an unfolded state. Serial and parallel implementations of this methodology are discussed.

Algorithms↗

PubMed1992

The two polypeptide chains in fibronectin are joined in antiparallel fashion: NMR structural characterization.

The fibronectin C-terminal interchain disulfide-linked heptapeptide dimer (Val-Asn-Cys-Pro-Ile-Glu-Cys)2 has been investigated via 1H NMR spectroscopy in both water and dimethyl sulfoxide (DMSO) solutions. Proton Overhauser experiments in DMSO indicate unambiguously that the two fibronectin polypeptide chains are linked head-to-tail (N-terminus to C-terminus), in an antiparallel fashion. It is found that the structure of the peptide is extended. From the 1H NMR interproton distance and angle constraints, the preferred mean (time-averaged) conformations in both H2O and DMSO were derived using distance geometry and molecular mechanics algorithms. The two conformations, although significantly dissimilar, exhibit the common feature of a structurally parallel (as opposed to chemically antiparallel) fibronectin alpha/beta chain array.

Amino Acid Sequence↗

PubMed1998

Patenting computer-designed peptides.

The problem of designing new peptides that possess specific properties, such as bactericidal activity, is of wide interest. Recently, attention has focused on the use of Computer-Aided Molecular Design techniques in parallel with more traditional 'synthesise and test' methods. These techniques may typically use Genetic Algorithms to optimise molecules based on Neural Network models that predict activity. In this paper we describe a successful application of this Molecular Design methodology that has resulted in novel bactericidal peptides of real value. A key issue for commercial utilisation of such results is the ability to protect the intellectual property rights associated with the discovery of new molecules. Typically peptide patents use structural templates of amino acid hydrophobicity-hydrophilicity that define highly regular peptide patent spaces. In an extension of established patenting practice we describe a patent application that uses a Neural Net predictive model to define the regions of peptide space that we claim within the patent. This formalism makes no a priori assumptions about the regularity of the patent space. A preliminary comparative investigation of the shape and size of this and other bactericidal peptide patent spaces is conducted.

Algorithms↗

PubMed2002

Further development and validation of empirical scoring functions for structure-based binding affinity prediction.

New empirical scoring functions have been developed to estimate the binding affinity of a given protein-ligand complex with known three-dimensional structure. These scoring functions include terms accounting for van der Waals interaction, hydrogen bonding, deformation penalty, and hydrophobic effect. A special feature is that three different algorithms have been implemented to calculate the hydrophobic effect term, which results in three parallel scoring functions. All three scoring functions are calibrated through multivariate regression analysis of a set of 200 protein-ligand complexes and they reproduce the binding free energies of the entire training set with standard deviations of 2.2 kcal/mol, 2.1 kcal/mol, and 2.0 kcal/mol, respectively. These three scoring functions are further combined into a consensus scoring function, X-CSCORE. When tested on an independent set of 30 protein-ligand complexes. X-CSCORE is able to predict their binding free energies with a standard deviation of 2.2 kcal/mol. The potential application of X-CSCORE to molecular docking is also investigated. Our results show that this consensus scoring function improves the docking accuracy considerably when compared to the conventional force field computation used for molecular docking.

Binding Sites↗

PubMed1992

Coupled map lattices as computational systems.

The coupled map lattice (CML) as a mathematical model for a computer is considered. Using the theory of synchronous concurrent algorithms, it is shown that the CML is a valid new model for a parallel deterministic analog machine, but that, in principle, such a CML computer does not generate computations that cannot be reproduced by the standard mathematical models for computing on real numbers. The analysis is based on new general mathematical definitions of CMLs, and an axiomatic approach to determining which models of computation can be used to simulate CMLs.

Journal Article↗

PubMed1995

Filtered backprojection reconstruction of combined parallel beam and cone beam SPECT data.

The reconstruction problem for a combined parallel beam (PB) and cone beam (CB) imaging geometry has been addressed. The general algorithm (CB-FBP) of Defrise and Clack has been applied to this geometry and shown to provide accurate images as expected. A second algorithm specifically tailored to the PB-CB geometry was developed. It uses the general principles of the CB-FBP method to combine a shift-variant filtering of the PB data with a standard reconstruction of the CB data using the algorithm of Feldkamp, Davis and Kress (FDK). This 'mixed' algorithm has the advantage of fewer interpolation steps, thereby reducing reconstruction time and providing more accurate reconstructions. The algorithms were applied to noiseless data from a computer-generated 3D Shepp phantom. Both the CB-FBP algorithm and the mixed algorithm successfully combine the CB and the PB data to correct the well known artefacts observed when reconstructing CB data acquired with a circular orbit. The mixed algorithm is about twice as fast as CB-FBP and results in better image quality, due to decreased discretization errors. However, the two algorithms yield comparable image quality when applied to a disc phantom measured with a two-headed SPECT system.

Algorithms↗

PubMed2006

MZmine: toolbox for processing and visualization of mass spectrometry based molecular profile data.

SUMMARY: New additional methods are presented for processing and visualizing mass spectrometry based molecular profile data, implemented as part of the recently introduced MZmine software. They include new features and extensions such as support for mzXML data format, capability to perform batch processing for large number of files, support for parallel processing, new methods for calculating peak areas using post-alignment peak picking algorithm and implementation of Sammon's mapping and curvilinear distance analysis for data visualization and exploratory analysis. AVAILABILITY: MZmine is available under GNU Public license from http://mzmine.sourceforge.net/.

Computer Graphics↗

PubMedDate not supplied

Retrospective registration of PET and MR brain images: an algorithm and its stereotactic validation.

OBJECTIVE: We present a validation study of an algorithm for retrospective registration of PET and MR brain images. MATERIALS AND METHODS: This algorithm involves two steps. In the first step, the two volumes are reformatted by aligning their interhemispheric fissure planes (midsagittal plane). In the second step, the corresponding planes parallel to the midsagittal plane are further aligned in the reformatted volumes to produce a 3D rigid body registration of the two original volumes. It is an efficient algorithm because both steps are performed in 2D spaces, and in each step only a small number of landmarks are required. A user-friendly system has been implemented to facilitate easy and fast processing of registration and reformatting of image volumes. The accuracy of this algorithm is validated using clinical scans of neurosurgical patients with a stereotaxic frame attached to their skull. The frame-based stereotaxic system provides an effective method for transforming image coordinates from different image volumes into a common coordinate system. This common coordinate system is used for assessing the spatial correspondence of each pixel in the registered image volumes. Validation using the stereotaxic image volumes enables objective estimation of retrospective registration accuracy. RESULTS: Analysis of 11 MR/PET image pairs indicates that our registration method not only is efficient but also provides adequate accuracy for most clinical evaluation of PET studies. CONCLUSION: We have implemented and validated an efficient algorithm for retrospective registration of PET and MR brain images.

Adult↗

PubMed2005

A power efficient electronic implant for a visual cortical neuroprosthesis.

An integrated microstimulator designed for a cortical visual prosthesis is presented, along with a pixel reordering algorithm, together minimizing the peak total current and voltage required for stimulation of large numbers of electrodes at a high rate. In order to maximize the available voltage for stimulation at a given supply voltage for generating biphasic pulses, the device uses monopolar stimulation, where the return electrode voltage is dynamically varied. Thus, the voltage available for stimulation is maximized, as opposed to the conventional fixed return voltage monopolar approach, and impedance is significantly lower than can be achieved using bipolar stimulation with microelectrodes. This enables the use of a low voltage power supply, minimizing power consumption of the device. An important constraint resulting from this stimulation strategy, however, is that current generation needs to be simultaneous and in-phase for all active parallel channels, imposing heavy stress on the wireless power recovery and regulation circuitry in large electrode count systems such as a visual prosthesis. An ordering algorithm to be implemented in the external controller of the prosthesis is then proposed. Based on the data for each frame of the video signal to be transmitted to the implant, the algorithm minimizes the total generated current standard deviation between time multiplexed stimulations by determining the most appropriate combination of parallel stimulation channels to be activated simultaneously. A stimulator prototype has been implemented in CMOS technology and successfully tested. Execution of the external controller reordering algorithm on an application specific hardware architecture has been verified using a System-On-Chip development platform. A near 75% decrease in the total stimulation current standard deviation was observed with a one-pass algorithm, whereas a recursive variation of the algorithm resulted in a greater than 95% decrease of the same variable.

Algorithms↗

PubMed2001

Efficiency of parallel direct optimization.

Tremendous progress has been made at the level of sequential computation in phylogenetics. However, little attention has been paid to parallel computation. Parallel computing is particularly suited to phylogenetics because of the many ways large computational problems can be broken into parts that can be analyzed concurrently. In this paper, we investigate the scaling factors and efficiency of random addition and tree refinement strategies using the direct optimization software, POY, on a small (10 slave processors) and a large (256 slave processors) cluster of networked PCs running LINUX. These algorithms were tested on several data sets composed of DNA and morphology ranging from 40 to 500 taxa. Various algorithms in POY show fundamentally different properties within and between clusters. All algorithms are efficient on the small cluster for the 40-taxon data set. On the large cluster, multibuilding exhibits excellent parallel efficiency, whereas parallel building is inefficient. These results are independent of data set size. Branch swapping in parallel shows excellent speed-up for 16 slave processors on the large cluster. However, there is no appreciable speed-up for branch swapping with the further addition of slave processors (>16). This result is independent of data set size. Ratcheting in parallel is efficient with the addition of up to 32 processors in the large cluster. This result is independent of data set size.

Algorithms↗

PubMed2006

Parallel computations on pedigree data through mapping to configurable computing devices.

Pedigree data structures have a number of applications in genetics, including the estimation of allelic or haplotype probabilities in humans and agricultural species, and the estimation of breeding values in agricultural species. Sequential algorithms for general purpose CPU-based computers are commonly used, but are inadequate for some tasks on large data sets. We show that pedigree data can be directly represented on Field Programmable Gate Arrays (FPGA), allowing highly efficient massively parallel simulation of the flow of genes. Operating on the whole pedigree in parallel, the transmission of genes can occur for all individuals in a single clock cycle. By using FPGA, the algorithms to estimate inbreeding coefficients and allelic probabilities are shown to operate hundreds to thousands of times faster than the corresponding sequentially based algorithms. Where problems can be largely represented in an integer form, FPGA provide an efficient platform for computations on pedigree data.

Algorithms↗

PubMed2002

Feature decomposition architectures for neural networks: algorithms, error bounds, and applications.

In recent years, systems consisting of multiple modular neural networks have attracted substantial interest in the neural networks community because of various advantages they offer over a single large monolithic network. In this paper, we propose two basic feature decomposition models (namely, parallel model and tandem model) in which each of the neural network modules processes a disjoint subset of the input features. A novel feature decomposition algorithm is introduced to partition the input space into disjoint subsets solely based on the available training data. Under certain assumptions, the approximation error due to decomposition can be proved to be bounded by any desired small value over a compact set. Finally, the performance of feature decomposition networks is compared with that of a monolithic network in real world bench mark pattern recognition and modeling problems.

Algorithms↗

PubMed2005

Maximum-likelihood methods for phylogeny estimation.

Maximum-likelihood (ML) estimation of phylogenies has reached a rather high level of sophistication because of algorithmic advances, improvements in models of sequence evolution, and improvements in statistical approaches and application of cluster computing. Here, I provide a brief basic background in application of the general principle of ML estimation to phylogenetics and provide an example of selecting among a nested set of ML models using a dynamic approach to hierarchical likelihood-ratio tests. I focus attention on PAUP* because it provides unique ease of switching among alternative optimality criteria (e.g., minimum evolution, parsimony, and ML). Further, examples of parametric bootstrap tests are provided that demonstrate statistical tests of phylogenetic hypotheses and model adequacy, in an absolute rather than relative sense. The increasing availability of clustered, parallelized computation makes use of such parametric approaches feasible.

Algorithms↗