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At least 235 records · Page 13Linked to original sources

PubMed1992

Three-dimensional SPECT reconstruction of combined cone beam and parallel beam data.

Single photon emission computed tomography (SPECT) using cone beam (CB) collimation exhibits increased sensitivity compared with acquisition geometries using parallel (P) hole collimation. However, CB collimation has a smaller field-of-view which may result in truncated projections and image artifacts. A primary objective of this work is to investigate maximum likelihood-expectation maximization (ML-EM) methods to reconstruct simultaneously acquired parallel and cone beam (P&CB) SPECT data. Simultaneous P&CB acquisition can be performed with commercially available triple camera systems by using two cone-beam collimators and a single parallel-hole collimator. The loss in overall sensitivity (relative to the use of three CB collimators) is about 15 to 20%. We have developed three methods to combine P&CB data using modified ML-EM algorithms. The first method consists of using both data sets to reconstruct a single intermediate image after each iteration using the ML-EM algorithm. The other two iterative algorithms combine intermediate parallel beam (PB) and CB source estimates to enhance image quality. For these methods, a PB estimate and a CB estimate are obtained for the first iteration. The second method consists of summing the PB and CB estimates for each subsequent iteration to obtain new PB and CB estimates. The third method is similar to the second method, with the exception that the new PB estimate simply is set equal to the PB estimate after each iteration. The combined source estimate is used in each subsequent iteration step of the EM algorithm. These algorithms are evaluated using projection data simulated using a Monte Carlo SPECT model. The P&CB SPECT images demonstrate marked improvement as compared with the CB-only reconstruction, particularly when the projections are truncated.

Algorithms↗

PubMed2005

Parallel magnetic resonance imaging with adaptive radius in k-space (PARS): constrained image reconstruction using k-space locality in radiofrequency coil encoded data.

A parallel image reconstruction algorithm is presented that exploits the k-space locality in radiofrequency (RF) coil encoded data. In RF coil encoding, information relevant to reconstructing an omitted datum rapidly diminishes as a function of k-space separation between the omitted datum and the acquired signal data. The proposed method, parallel magnetic resonance imaging with adaptive radius in k-space (PARS), harnesses this physical property of RF coil encoding via a sliding-kernel approach. Unlike generalized parallel imaging approaches that might typically involve inverting a prohibitively large matrix for arbitrary sampling trajectories, the PARS sliding-kernel approach creates manageable and distributable independent matrices to be inverted, achieving both computational efficiency and numerical stability. An empirical method designed to measure total error power is described, and the total error power of PARS reconstructions is studied over a range of k-space radii and accelerations, revealing "minimal-error" conditions at comparatively modest k-space radii. PARS reconstructions of undersampled in vivo Cartesian and non-Cartesian data sets are shown and are compared selectively with traditional SENSE reconstructions. Various characteristics of the PARS k-space locality constraint (such as the tradeoff between signal-to-noise ratio and artifact power and the relationship with iterative parallel conjugate gradient approaches or nonparallel gridding approaches) are discussed.

Algorithms↗

PubMed2003

Complete graph conjecture for inner-core electrons: homogeneous index case.

The complete graph conjecture that encodes the inner-core electrons of atoms with principal quantum number n >or= 2 with complete graphs, and especially with odd complete graphs, is discussed. This conjecture is used to derive new values for the molecular connectivity and pseudoconnectivity basis indices of hydrogen-suppressed chemical pseudographs. For atoms with n = 2 the new values derived with this conjecture are coincident with the old ones. The modeling ability of the new homogeneous basis indices, and of the higher-order terms, is tested and compared with previous modeling studies, which are centered on basis indices that are either based on quantum concepts or partially based on this new conjecture for the inner-core electrons. Two similar algorithms have been proposed with this conjecture, and they parallel the two "quantum" algorithms put forward by molecular connectivity for atoms with n > 2. Nine properties of five classes of compounds have been tested: the molecular polarizabilities of a class of organic compounds, the dipole moment, molar refraction, boiling points, ionization energies, and parachor of a series of halomethanes, the lattice enthalpy of metal halides, the rates of hydrogen abstraction of chlorofluorocarbons, and the pED(50) of phenylalkylamines. The two tested algorithms based on the odd complete graph conjecture give rise to a highly interesting model of the nine properties, and three of them can even be modeled by the same set of basis indices. Interesting is the role of some basis indices all along the model.

Journal Article↗

PubMedDate not supplied

Coevolving solutions to the shortest common superstring problem.

The shortest common superstring (SCS) problem, known to be NP-Complete, seeks the shortest string that contains all strings from a given set. In this paper we compare four approaches for finding solutions to the SCS problem: a standard genetic algorithm, a novel cooperative-coevolutionary algorithm, a benchmark greedy algorithm, and a parallel coevolutionary-greedy approach. We show the coevolutionary approach produces the best results, and discuss directions for future research.

Algorithms↗

PubMedDate not supplied

Interactive stereoscopic rendering of volumetric environments.

We present an efficient stereoscopic rendering algorithm supporting interactive navigation through large-scale 3D voxel-based environments. In this algorithm, most of the pixel values of the right image are derived from the left image by a fast 3D warping based on a specific stereoscopic projection geometry. An accelerated volumetric ray casting then fills the remaining gaps in the warped right image. Our algorithm has been parallelized on a multiprocessor by employing effective task partitioning schemes and achieved a high cache coherency and load balancing. We also extend our stereoscopic rendering to include view-dependent shading and transparency effects. We have applied our algorithm in two virtual navigation systems, flythrough over terrain and virtual colonoscopy, and reached interactive stereoscopic rendering rates of more than 10 frames per second on a 16-processor SGI Challenge.

Algorithms↗

PubMed2004

Molecular solutions for the subset-sum problem on DNA-based supercomputing.

In this paper our main purpose is to give molecular solutions for the subset-sum problem. In order to achieve this, we propose a DNA-based algorithm of an n-bit parallel adder and a DNA-based algorithm of an n-bit parallel comparator to formally verify our designed molecular solutions for the subset-sum problem.

Algorithms↗

PubMed2004

Determination of a unique solution to parallel proton transfer reactions using the genetic algorithm.

Kinetic analysis of the dynamics as measured in multiequilibria systems is readily attained by curve-fitting methodologies, a treatment that can accurately retrace the shape of the measured signal. Still, these reconstructions are not related to the detailed mechanism of the process. In this study we subjected multiple proton transfer reactions to rigorous kinetic analysis, which consists of solving a set of coupled-nonlinear differential rate equations. The manual analysis of such systems can be biased by the operator; thus the analysis calls for impartial corroboration. What is more, there is no assurance that such a complex system has a unique solution. In this study, we used the Genetic Algorithm to investigate whether the solution of the system will converge into a single global minimum in the multidimensional parameter space. The experimental system consisted of proton transfer between four proton-binding sites with seven independent adjustable parameters. The results of the search indicate that the solution is unique and all adjustable parameters converge into a single minimum in the multidimensional parameter space, thus corroborating the accuracy of the manual analysis.

Algorithms↗

PubMed2006

Dynamic programming algorithms for comparing multineuronal spike trains via cost-based metrics and alignments.

Cost-based metrics formalize notions of distance, or dissimilarity, between two spike trains, and are applicable to single- and multineuronal responses. As such, these metrics have been used to characterize neural variability and neural coding. By examining the structure of an efficient algorithm [Aronov D, 2003. Fast algorithm for the metric-space analysis of simultaneous responses of multiple single neurons. J Neurosci Methods 124(2), 175-79] implementing a metric for multineuronal responses, we determine criteria for its generalization, and identify additional efficiencies that are applicable when related dissimilarity measures are computed in parallel. The generalized algorithm provides the means to test a wide range of coding hypotheses.

Action Potentials↗

PubMed1997

DNA solution of the maximal clique problem.

The maximal clique problem has been solved by means of molecular biology techniques. A pool of DNA molecules corresponding to the total ensemble of six-vertex cliques was built, followed by a series of selection processes. The algorithm is highly parallel and has satisfactory fidelity. This work represents further evidence for the ability of DNA computing to solve NP-complete search problems.

Algorithms↗

PubMed1985

Detection of binocular disparities.

A stereo correspondence algorithm designed to perform matching on figurally similar images (arising in normal human binocular vision) is described. It is based on the observation that the operational principles underlying biological stereo disparity detection seem to be extremely general and few in number instead of an extended set of specific "constraints". We identify one general characteristic of objects in the three dimensional world and use it to formulate a simple noniterative, parallel and local algorithm that successfully detects disparities generated by opaque as well as transparent surfaces.

Humans↗

PubMed1992

A parallel implementation of the backward error propagation neural network training algorithm: experiments in event identification.

An artificial neural-network-based (ANN) event detection and alarm generation system has been developed to aid clinicians in the identification of critical events commonly occurring in the anesthesia breathing circuit. To detect breathing circuit problems, the system monitored CO2 gas concentration, gas flow, and airway pressure. Various parameters were extracted from each of these input waveforms and fed into an artificial neural network. To develop truly robust ANNs, investigators are required to train their networks on large training data sets, requiring enormous computing power. We implemented a parallel version of the backward error propagation neural network training algorithm in the widely portable parallel programming language C-Linda. A maximum speedup of 4.06 was obtained with six processors. This speedup represents a reduction in total run-time from 6.4 to 1.5 h. By reducing the total run time of the computation through parallelism, we were able to optimize many of the neural network's initial parameters. We conclude that use of the master-worker model of parallel computation is an excellent method for speeding up the backward error propagation neural network training algorithm.

Algorithms↗

PubMed2006

Active catheter tracking using parallel MRI and real-time image reconstruction.

In this work active MR catheter tracking with automatic slice alignment was combined with an autocalibrated parallel imaging technique. Using an optimized generalized autocalibrating partially parallel acquisitions (GRAPPA) algorithm with an acceleration factor of 2, we were able to reduce the acquisition time per image by 34%. To accelerate real-time GRAPPA image reconstruction, the coil sensitivities were updated only after slice reorientation. For a 2D trueFISP acquisition (160 x 256 matrix, 80% phase matrix, half Fourier acquisition, TR = 3.7 ms, GRAPPA factor = 2) real-time image reconstruction was achieved with up to six imaging coils. In a single animal experiment the method was used to steer a catheter from the vena cava through the beating heart into the pulmonary vasculature at an image update rate of about five images per second. Under all slice orientations, parallel image reconstruction was accomplished with only minor image artifacts, and the increased temporal resolution provided a sharp delineation of intracardial structures, such as the papillary muscle.

Algorithms↗

PubMed2000

A PARAFAC algorithm using penalty diagonalization error (PDE) for three-way data array resolution.

A modified parallel factors analysis (PARAFAC) algorithm with the penalty diagnolization error (PDE) was developed. This algorithm can overcome the slow convergence problem of the traditional PARAFAC method and is insensitive to the number of components, i.e., it is much faster than PARAFAC and insensitive to overestimation of the dimensionality of the model. The characteristic performance was demonstrated by treating simulated and real excitation-emission fluorescence data for samples of naphthalene, 1-naphthol and 2-naphthol with satisfactory results.

Journal Article↗

PubMed1987

Treatment of axial data in three-dimensional PET.

Improved axial spatial resolution in positron emission tomography (PET) scanners will lead to reduced sensitivity unless the axial acceptance angle for the coincidences is kept constant. A large acceptance angle, however, violates assumptions made in most reconstruction algorithms, which reconstruct parallel independent slices, rather than a three-dimensional volume. Two methods of treating the axial information from a volume PET scanner are presented. Qualitative and quantitative errors introduced by the approximations are examined for simulated objects with sharp boundaries and for a more anatomically realistic distribution with smooth activity gradients.

Algorithms↗

PubMed1992

A parallel implementation of a multi-state Kalman filtering algorithm to detect ECG arrhythmias.

Detecting arrhythmias from the electrocardiogram (ECG) is of great importance for the continued development of intelligent cardiovascular monitors (ICM). An ICM's main goal is to present to the clinician a 'high-level' analysis of the patient's condition (e.g., the patient is slightly hypovolemic) based upon 'low-level' physiologic signals (e.g., blood pressure, heart rate, etc.). This paper reports on a parallel implementation of a multi-state Kalman filtering algorithm, within a prototype ICM, to help detect ECG arrhythmias. Preliminary test results show that the parallel, multi-state implementation performed exactly as the original sequential version. Several different rhythm disturbances were correctly identified after 3-5 beats. We conclude that our parallel implementation of the multi-state Kalman filter provides a faster and still reliable means of accurately detecting ECG arrhythmias in real-time.

Algorithms↗

PubMed1997

RAGA: RNA sequence alignment by genetic algorithm.

We describe a new approach for accurately aligning two homologous RNA sequences when the secondary structure of one of them is known. To do so we developed two software packages, called RAGA and PRAGA, which use a genetic algorithm approach to optimize the alignments. RAGA is mainly an extension of SAGA, an earlier package for multiple protein sequence alignment. In PRAGA several genetic algorithms run in parallel and exchange individual solutions. This method allows us to optimize an objective function that describes the quality of a RNA pairwise alignment, taking into account both primary and secondary structure, including pseudoknots. We report results obtained using PRAGA on nine test cases of pairs of eukaryotic small subunit rRNA sequence (nuclear and mitochondrial).

Algorithms↗

PubMed2002

Theory and practice of parallel direct optimization.

Our ability to collect and distribute genomic and other biological data is growing at a staggering rate (Pagel, 1999). However, the synthesis of these data into knowledge of evolution is incomplete. Phylogenetic systematics provides a unifying intellectual approach to understanding evolution but presents formidable computational challenges. A fundamental goal of systematics, the generation of evolutionary trees, is typically approached as two distinct NP-complete problems: multiple sequence alignment and phylogenetic tree search. The number of cells in a multiple alignment matrix are exponentially related to sequence length. In addition, the number of evolutionary trees expands combinatorially with respect to the number of organisms or sequences to be examined. Biologically interesting datasets are currently comprised of hundreds of taxa and thousands of nucleotides and morphological characters. This standard will continue to grow with the advent of highly automated sequencing and development of character databases. Three areas of innovation are changing how evolutionary computation can be addressed: (1) novel concepts for determination of sequence homology, (2) heuristics and shortcuts in tree-search algorithms, and (3) parallel computing. In this paper and the online software documentation we describe the basic usage of parallel direct optimization as implemented in the software POY (ftp://ftp.amnh.org/pub/molecular/poy).

Animals↗

PubMed2026

MethylModes: computationally efficient detection of multimodal distributions in DNA methylation data.

SUMMARY: MethylModes is an R package and Shiny application to identify multimodal distributions in human DNA methylation at individual CpG sites. Multimodal distributions, which can be the result of nearby genetic variation, environmental exposures, or assay artifacts, are susceptible to confounding and important to identify for methylation analysis. MethylModes is easily incorporated into existing quality control pipelines of array-based DNA methylation data. The underlying algorithm uses kernel smoothing of probe-level data to locate the number and location of peaks. The algorithm can be parallelized across probes for efficient implementation at genome-scale. We provide a case study implementation of MethylModes in the Health and Retirement Study as well as the Airwave Health Monitoring Study. AVAILABILITY AND IMPLEMENTATION: MethylModes is available on GitHub at https://github.com/lutiffan/methylModes as an R package wrapping an R Shiny application. We include a toy dataset to validate installation. The codebase is also published on Zenodo at https://doi.org/10.5281/zenodo.17448517.

DNA Methylation↗