PubMed Health⌕ Search

SEARCH · PubMed Health

Results for “Parallel Algorithms”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 469 records · Page 26Linked to original sources
PubMed2002

Computational reconstruction of images from holograms.

The equations to reconstruct an image plane from a hologram are developed. This development is carried out for planes parallel to the hologram, which allows fast computation through the use of fast Fourier transforms. Algorithms for a digital computer are developed so images can be reconstructed, both with and without the Fresnel approximation, from a digitized hologram without the need for three-dimensional optical reconstruction equipment. Examples of holographically recorded images of marine micro-organisms are shown. A computational method for counting the number of micro-organisms in the holographically recorded volume is developed, and an example is provided.

Journal Article↗
PubMed2003

Two-dimensional correlation analysis in application to a kinetic model of parallel reactions.

By applying generalized two-dimensional (2D) correlation analysis as reported by Noda, we have systematically studied a kinetic model of parallel reactions. Given the related rate constants and absorption coefficients, the correlation between reactant and products are analyzed. The reactant-reactant, reactant-product, and product-product pairs are found to be synchronously correlated, and their intensities increase with increase of the rate constant and the absorption coefficient. On the other hand, only the reactant-product pairs show in the asynchronous spectra. Their intensities also depend proportionally on the rate constant and the absorption coefficient. The influence of signal-to-noise ratio (S/N) and overlapped spectra are further discussed. The resulting synchronous and asynchronous correlation spectra for the kinetic model appear to be weakly influenced by poor quality of the signal when the reference spectrum is set at zero. The ratio of asynchronous to synchronous correlation intensity yields a coherence spectrum. This spectrum remains a constant intensity for all the correlated peaks, being free from the influence of rate constant and absorption coefficient as well as being weakly disturbed by a small S/N ratio. It also provides a way to evaluate the extent of spectral overlap between two peaks. The coherence spectrum is useful to characterize the type of parallel reactions.

Algorithms↗
PubMed2002

[Effectiveness of endovideosurgical technology in diagnosis and treatment of patient with hemoblastoses].

Results of using endovideosurgical technology for diagnosis and treatment of hematological diseases in 123 patients are described. It was shown that laparoscopy is highly effective parallel with ultrasound examination and tomography in a complex diagnostic program. Using the developed diagnostic algorithm was shown to be very expedient for making primary diagnosis, recurrent diseases and control of the effectiveness of chemotherapy. Endovideosurgical interventions were shown to be less invasive and safe in hematological patients. Laparoscopy is an alternative to diagnostic laparotomy which is often used in this group of patients.

Adult↗
PubMed1997

Dynamic three-dimensional echocardiography: a new era in ultrasound technology.

The use of noninvasive methods to visualise the heart has had an extraordinary development over the last decade, with echocardiography demonstrating a particularly fast growth. Despite its unquestionable role in the diagnosis of heart disease and in the management of cardiac patients, it does have some limitations, both in the morphological visualisation, as well as in the functional assessment of the heart, such as blood flow, quantification of intracardiac volumes, etc. The recent development of dynamic three-dimensional (3D) echocardiography from two dimensional images has opened new perspectives in the study of cardiac pathophysiology. There are basically two methods of displaying three dimensional data sets: (1) a two-dimensional display from individual selected cut planes (any-plane echocardiography) or from parallel short axis cuts; (2) a volume rendered technique: from any defined cut plane, different algorithms are applied to represent the information in space. There are several potential clinical applications of 3D such as the measurement and serial follow-up of left ventricular volumes; in valvular heart disease (the abnormalities can be delineated more precisely and in greater detail than conventional imaging, including a detailed definition of mitral apparatus in mitral stenosis), in mitral valve prolapse both leaflets can be seen from the left atrial view and in endocarditis it can aid in deciding when and how to intervene; in complex congenital heart disease, such as reconstruction of double outlet right ventricle, left-sided obstructive and regurgitant lesions and subaortic obstructive cases, in atrial and ventricular septal defects, displaying size, geometry and relationships to other structures; another expression of cardiac disorders are blood flow disturbances (visualisation of flows in 3D could allow a better qualitative and quantitative assessment of their size and severity; the pictures so far generated allow a good perception of the size and shape of mitral, aortic and tricuspid regurgitation jets, by examining them from a new perspective, it also has the potential to display the flow convergence zone and quantify the regurgitant volume). Recent studies have clearly demonstrated the feasibility of performing three-dimensional imaging in a variety of cardiac diseases, but continued development of ultrasound technology must be made to improve better image resolution. The prolonged acquisition time is the most important limiting factor that currently restricts the routine use of 3D echocardiography. The development of faster computers will shorten the time needed for image acquisition, postprocessing, and data analysis, contributing to the goal of easy access and wide use. With improvements in computer technology and production of interactive software, 3D echocardiography will provide a dynamic view of the surgical anatomy of the heart. Thus, the three-dimensional reconstruction concept has the potential to and diagnostic assessment of cardiac pathology in every facet.

Cardiovascular Diseases↗
PubMed2002

A parallel mixture of SVMs for very large scale problems.

Support vector machines (SVMs) are the state-of-the-art models for many classification problems, but they suffer from the complexity of their training algorithm, which is at least quadratic with respect to the number of examples. Hence, it is hopeless to try to solve real-life problems having more than a few hundred thousand examples with SVMs. This article proposes a new mixture of SVMs that can be easily implemented in parallel and where each SVM is trained on a small subset of the whole data set. Experiments on a large benchmark data set (Forest) yielded significant time improvement (time complexity appears empirically to locally grow linearly with the number of examples). In addition, and surprisingly, a significant improvement in generalization was observed.

Algorithms↗
PubMed1998

Astigmatic single photon emission computed tomography imaging with a displaced center of rotation.

A filtered backprojection algorithm is developed for single photon emission computed tomography (SPECT) imaging with an astigmatic collimator having a displaced center of rotation. The astigmatic collimator has two perpendicular focal lines, one that is parallel to the axis of rotation of the gamma camera and one that is perpendicular to this axis. Using SPECT simulations of projection data from a hot rod phantom and point source arrays, it is found that a lack of incorporation of the mechanical shift in the reconstruction algorithm causes errors and artifacts in reconstructed SPECT images. The collimator and acquisition parameters in the astigmatic reconstruction formula, which include focal lengths, radius of rotation, and mechanical shifts, are often partly unknown and can be determined using the projections of a point source at various projection angles. The accurate determination of these parameters by a least squares fitting technique using projection data from numerically simulated SPECT acquisitions is studied. These studies show that the accuracy of parameter determination is improved as the distance between the point source and the axis of rotation of the gamma camera is increased. The focal length of the focal line perpendicular to the axis of rotation is determined more accurately than the focal length to the focal line parallel to this axis.

Algorithms↗
PubMed2001

Rebinning-based algorithms for helical cone-beam CT.

Several image reconstruction algorithms based on rebinning have been proposed recently for helical cone-beam CT. These algorithms separate the 3D reconstruction into a set of independent 2D reconstructions for a set of surfaces: planar or non-planar surfaces are defined and then reconstructed using 2D filtered backprojection from a 2D fan-beam or parallel-beam set of data estimated from the cone-beam (CB) measurements. The first part of this paper presents a unified derivation of rebinning algorithms for planar and non-planar surfaces. An integral equation is derived for the surface allowing the best rebinning and an iterative algorithm converging to the solution of that equation is given. The second part presents an efficient method to correct the residual reconstruction artefacts observed with rebinning algorithms when the cone-angle is too large for the required accuracy. This correction algorithm involves a CB backprojection and the reconstruction time is slightly longer than for the zero-boundary (ZB) method.

Algorithms↗
PubMed1999

Parallel image segmentation using the L4 network.

Each processing element in the outer plexiform layer of the fly's (Musca domestica) compound eye has a single copy of a monopolar cell called L4 whose function is still unknown. This paper proposes that L4 acts as an image segmentor receiving data from the L1 and L2 cell layer above it. The photoreceptor terminals R1 through R6 and L1 and L2 form a cartridge with shunting current inhibition that enhances contrast at the first synaptic contact. The photoreceptors feeding their respective terminals share a common optical axis. What was realized for this entire structure that led up to and included L1 and L2, was that it forms a single processing element which outputs a weighted function based on current shunting between the photoreceptor axon terminals around L1 and L2. Thus the basic biological 'algorithm' that this paper proposes for L1 and L2 involves a summation of the differences between a central reference cell (referred to as Rref) and the six neighboring photoreceptor terminals R1-R6 within the cartridge of L1 and L2. Simulation implementing this simple algorithm on a hexagonal packed matrix in Matlab, suggest that objects with even small differences in intensity with the background, can readily be distinguished from the background. This high pass filter biological model allows edge detection and segmentation, independent of scale in a parallel, modular fashion. Implementation of such a biological algorithm using analog circuitry forms a preprocessing unit that introduces virtually no delay in the processing of image information, in comparison to present DSP techniques, that require iterative approaches and costly computing time.

Algorithms↗
PubMed2004

Facilitating arrhythmia simulation: the method of quantitative cellular automata modeling and parallel running.

BACKGROUND: Many arrhythmias are triggered by abnormal electrical activity at the ionic channel and cell level, and then evolve spatio-temporally within the heart. To understand arrhythmias better and to diagnose them more precisely by their ECG waveforms, a whole-heart model is required to explore the association between the massively parallel activities at the channel/cell level and the integrative electrophysiological phenomena at organ level. METHODS: We have developed a method to build large-scale electrophysiological models by using extended cellular automata, and to run such models on a cluster of shared memory machines. We describe here the method, including the extension of a language-based cellular automaton to implement quantitative computing, the building of a whole-heart model with Visible Human Project data, the parallelization of the model on a cluster of shared memory computers with OpenMP and MPI hybrid programming, and a simulation algorithm that links cellular activity with the ECG. RESULTS: We demonstrate that electrical activities at channel, cell, and organ levels can be traced and captured conveniently in our extended cellular automaton system. Examples of some ECG waveforms simulated with a 2-D slice are given to support the ECG simulation algorithm. A performance evaluation of the 3-D model on a four-node cluster is also given. CONCLUSIONS: Quantitative multicellular modeling with extended cellular automata is a highly efficient and widely applicable method to weave experimental data at different levels into computational models. This process can be used to investigate complex and collective biological activities that can be described neither by their governing differentiation equations nor by discrete parallel computation. Transparent cluster computing is a convenient and effective method to make time-consuming simulation feasible. Arrhythmias, as a typical case, can be effectively simulated with the methods described.

Anisotropy↗
PubMed2002

Proteins wriggle.

We propose an algorithmic strategy for improving the efficiency of Monte Carlo searches for the low-energy states of proteins. Our strategy is motivated by a model of how proteins alter their shapes. In our model, when proteins fold under physiological conditions, their backbone dihedral angles change synchronously in groups of four or more to avoid steric clashes and respect the kinematic conservation laws. They wriggle; they do not thrash. We describe a simple algorithm that can be used to incorporate wriggling in Monte Carlo simulations of protein folding. We have tested this wriggling algorithm against a code in which the dihedral angles are varied independently (thrashing). Our standard of success is the average root-mean-square distance (rmsd) between the alpha-carbons of the folding protein and those of its native structure. After 100,000 Monte Carlo sweeps, the relative decrease in the mean rmsd, as one switches from thrashing to wriggling, rises from 11% for the protein 3LZM with 164 amino acids (aa) to 40% for the protein 1A1S with 313 aa and 47% for the protein 16PK with 415 aa. These results suggest that wriggling is useful and that its utility increases with the size of the protein. One may implement wriggling on a parallel computer or a computer farm.

Algorithms↗
PubMed1998

Molecular evidence for parallel evolution of adaptive syndromes in fig-breeding Lissocephala (Drosophilidae).

Afrotropical Lissocephala (Drosophilidae) breed strictly in syconia (figs) of Ficus (Moraceae) and have accordingly evolved specific features including modified female and eggshell morphologies, ovipositing, larval foraging, and mating behaviors. These various traits may exist as two or three alternative states. Each species displays a specific suite of traits so closely coordinated with one another that alternative states of the overall suites of traits can be seen as "adaptive syndromes." Three clear-cut adaptive syndromes can be recognized while two taxonomic lineages (juncta and sanu species groups) are traditionally accepted on the basis of male terminalia. A crucial evolutionary question results from the consideration that ecological clusters and taxonomic groups have conflicting compositions: the three syndromes are found in the juncta group while two of them occur in the sanu group. To resolve this conflict, we present molecular data which provide a robust phylogeny: mitochondrial DNA (12S + 16S ribosomal DNA and cytochrome b) sequence data are in agreement with one another regardless of the algorithm used. All molecular data consistently support male terminalia dichotomy. Such a level of consistency unambiguously indicates that parallel evolution of adaptive syndromes occurred. Thus, homoplasy may affect morphological and behavioral traits concomitantly when these are involved in a network of functional relationships.

Adaptation, Physiological↗
PubMed2001

Advanced single-slice rebinning for tilted spiral cone-beam CT.

Future medical CT scanners and today's micro CT scanners demand cone-beam reconstruction algorithms that are capable of reconstructing data acquired from a tilted spiral trajectory where the vector of rotation is not necessarily parallel to the vector of table increment. For the medical CT scanner this case of nonparallel object motion is met for nonzero gantry tilt: the table moves into a direction that is not perpendicular to the plane of rotation. Since this is not a special application of medical CT but rather a daily routine in head exams, there is a strong need for corresponding reconstruction algorithms. In contrast to medical CT, where the special case of nonperpendicular motion is used on purpose, micro CT scanners cannot avoid aberrations of the rotational axis and the table increment vector due to alignment problems. Especially for those micro CT scanners that have the lifting stage mounted on the rotation table (in contrast to setups where the lifting stage holds the rotation table), this kind of misalignment is equivalent to a gantry tilt. We therefore generalize the advanced single-slice rebinning algorithm (ASSR), which is considered a very promising approach for medical cone-beam reconstruction due to its high image quality and its high reconstruction speed [Med. Phys. 27, 754-772 (2000)], to the case of tilted gantries. We evaluate this extended ASSR approach (which we will denote as ASSR+, for convenience) in comparison to the original ASSR algorithm using simulated phantom data for reconstruction. For the case of nonparallel object motion ASSR+ shows significant improvements over ASSR, however, its computational complexity is slightly increased due to the broken symmetry of the spiral trajectory.

Algorithms↗
PubMedDate not supplied

Monte Carlo methods for small molecule high-throughput experimentation.

By analogy with Monte Carlo algorithms, we propose new strategies for design and redesign of small molecule libraries in high-throughput experimentation, or combinatorial chemistry. Several Monte Carlo methods are examined, including Metropolis, three types of biased schemes, and composite moves that include swapping or parallel tempering. Among them, the biased Monte Carlo schemes exhibit particularly high efficiency in locating optimal compounds. The Monte Carlo strategies are compared to a genetic algorithm approach. Although the best compounds identified by the genetic algorithm are comparable to those from the better Monte Carlo schemes, the diversity of favorable compounds identified is reduced by roughly 60%.

Journal Article↗
PubMed1994

A comparison of three electron planning algorithms for a 16 MeV electron beam.

PURPOSE: We report results of a comparison of three electron planning algorithms, an Age-Diffusion Pencil beam algorithm and two (2-D) and three dimensional (3-D) Hogstrom pencil beam algorithms, using simple 2 x 2 cm air and hard bone inhomogeneities and a complex anthropomorphic head and neck phantom. METHODS AND MATERIALS: The simple inhomogeneities have variable dimensions outside the plane of calculation to test the effects of out of plane scattering on 2-D algorithms, compared with dose measured by film below the inhomogeneity in the dose fall-off range. Comparisons are also made of a parotid treatment field for 16 MeV electrons, and the dose measured by high sensitivity thermoluminescent dosimeters in the head and neck phantom. RESULTS: Behind the simple inhomogeneities, the electron algorithms are found to underestimate the dose behind the air cavity by up to 40% and overestimated the dose behind bone by up to 30%. In the head phantom, the presence of inhomogeneities also presents problems for the algorithms, with overestimations of dose of up to 20% found behind bone-tissue interfaces, apparently due to shielding by high density bone. Overestimations of up to 17% are also found beside interfaces parallel to the beam. Underestimations of dose of up to 10% are found on the beam-side of interfaces, due to under-prediction of backscattered electrons. All three investigated algorithms underestimate the dose by up to 20% behind extreme surface curvature. One algorithm is found to underestimate the dose in the falloff region while another overestimates the dose around the 90% isodose. CONCLUSION: Clinicians should be aware of the limitations of their planning systems.

Algorithms↗
PubMed1999

Inexpensive, semi-automated system for measuring mechanical properties of soft tissues.

Stiffness and strength are important properties of many tissues, but standard material-testing equipment is expensive, often ill-suited for testing soft tissues, and rarely accessible to biologists. We describe a system built around a microcomputer and an electronic balance which is particularly well-suited for measuring stress and strain in small samples of soft tissue. We use a discarded floppy disk drive as a linear actuator to strain the sample, while an electronic balance measures the tension (used to calculate stress). We give an algorithm for a program to drive a microcomputer which controls the floppy disk drive via its parallel port and records the balance measurements via its serial port. We used this system to obtain stress-strain curves from a sample of latex rubber and a sample of soft insect cuticle. Three tests of the rubber sample gave nearly identical results, with smooth, J-shaped stress-strain curves. The stress-strain curves gave a modulus elasticity value of 1.72 Mpa over the steep, straight region, well within the range for natural latex rubber. We also tested a sample of abdominal cuticle from a caterpillar (Manduca sexta). The caterpillar cuticle had a J-shaped stress-strain curve with a modulus of elasticity of 2.11 Mpa over the steep part of the curve. J. Exp. Zool. 284:374-378, 1999.

Animals↗
PubMed1985

Design and fitting of neural network transfer functions.

An algorithm is presented which (a) allows construction of mathematical models involving arbitrary combinations of linear cascades, parallel pathways, and feedback loops, (b) computes a total transfer function of the system, (c) performs a least-squares optimization of model parameters to best fit the model to experimental data, and (d) provides a measure of goodness-of-fit to the data. The technique has been employed to construct and test models of neural networks which mimic a class of responses observed in the cat vestibular nuclei in response to tilt, namely responses which show both a gain increase and progressive phase lag as the stimulation frequency goes from 0.01 to 2 Hz. A network consisting of a simple gain element in parallel with an inhibitory high-pass filtered version of the input provided a satisfactory fit to these data.

Animals↗
PubMed1984

Evoked potential techniques in the evaluation of visual function.

Visual evoked potentials (VEPs) can be used in a multitude of ways to assess the various levels of visual processing. The human visual system consists of multiple, parallel channels which process different information, and each channel constitutes a set of sequential processes. An algorithm of sequential steps that can be used to assess visual function is reviewed. The pathophysiology of retinal, anterior visual pathways and retrochiasmal pathways can be objectively evaluated by VEPs.

Adolescent↗