Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Parallel Algorithms”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

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

At least 775 records · Page 43Linked to original sources
PubMed1979

Rapid analysis of hematology image data: the ADC-500 preprocessor.

A sequential, pipeline processor (that we have named the ADC-500 preprocessor) has been developed which scene segments the three color image data from the ADC-500 optics one image element at a time, groups together image elements from each object in the scene and extracts features from each object. The processing occurs at television frame rates, requiring 16.7 msec to process the entire image. This speed was instrumental in allowing the ADC-500 automated differential analyzer to perform routine 500-cell differentials. The preprocessor also contains hardware which simplifies compilation of the three color histograms. The segmentation algorithms implemented in the preprocessor are multicolor extensions of the classical monochrome density histogram threshold method. For most cell image analysis tasks, a sequential pipeline processor of this type should be more economical and as fast or faster than a parallel processor.

Blood Cells↗
PubMed1993

Hidden Markov models and iterative aligners: study of their equivalence and possibilities.

There are many shared attributes between existing iterative aligners and Hidden Markov Model (HMM). A learning algorithm of HMM called Viterbi is the same as the iteration of DP-matching of iterative aligners. HMM aligners can use the result of an iterative aligner initially, incorporate the similarity score of amino acids, and apply the detailed gap cost systems to improve the matching accuracy. On the other hand, the iterative aligner can inherit the modeling capability of HMM, and provide the better representation of the proteins than motifs. In this paper, we present an overview of several iterative aligners which include the parallel iterative aligner of ICOT and the HMM aligner of Haussler's group. We compare the merits and shortcomings of these aligners. This comparison enables us to formulate a better, more advanced aligner through proper integration of the iterative technique and HMM technique.

Algorithms↗
PubMed1998

Analysis of 3D transient blood flow passing through an artificial aortic valve by Lattice-Boltzmann methods.

The development of flow instabilities due to high Reynolds number flow in artificial heart valve geometries inducing high strain rates and stresses often leads to hemolysis and related highly undesired effects. Geometric and functional optimization of artificial heart valves is therefore mandatory. In addition to experimental work in this field it is meanwhile possible to obtain increasing insight into flow dynamics by computer simulation of refined model problems. After giving an introductory overview we report the results of the simulation of three-dimensional transient physiological flows in fixed geometries similar to a CarboMedics bileaflet heart valve at different opening angles. The visualization of emerging complicated flow patterns gives detailed information about the transient history of the systems dynamical stability. Stress analysis indicates temporal shear stress peaks even far away from walls. The mathematical approach used is the Lattice Boltzmann method. We obtained reasonable results for velocity and shear stress fields. The code is implemented on parallel hardware in order to decrease computation time. Finally, we discuss problems, shortcomings and possible extensions of our approach.

Algorithms↗
PubMed2004

Folding probabilities: a novel approach to folding transitions and the two-dimensional Ising-model.

The theoretical concept of folding probability, p(fold), has proven to be a useful means to characterize the kinetics of protein folding. Here, we illustrate the practical importance of p(fold) and demonstrate how it can be determined theoretically. We derive a general analytical expression for p(fold) and show how it can be estimated from simulations for systems where the transition rates between the relevant microstates are not known. By analyzing the Ising model we are able to determine the scaling behavior of the numerical error in the p(fold) estimate as function of the number of analyzed Monte Carlo runs. We apply our method to a simple, newly developed protein folding model for the formation of alpha helices. It is demonstrated that our technique highly parallelizes the calculation of p(fold) and that it is orders of magnitude more efficient than conventional approaches.

Algorithms↗
PubMed2004

Synchronization of trajectories in canonical molecular-dynamics simulations: observation, explanation, and exploitation.

For two methods commonly used to achieve canonical-ensemble sampling in a molecular-dynamics simulation, the Langevin thermostat and the Andersen [H. C. Andersen, J. Chem. Phys. 72, 2384 (1980)] thermostat, we observe, as have others, synchronization of initially independent trajectories in the same potential basin when the same random number sequence is employed. For the first time, we derive the time dependence of this synchronization for a harmonic well and show that the rate of synchronization is proportional to the thermostat coupling strength at weak coupling and inversely proportional at strong coupling with a peak in between. Explanations for the synchronization and the coupling dependence are given for both thermostats. Observation of the effect for a realistic 97-atom system indicates that this phenomenon is quite general. We discuss some of the implications of this effect and propose that it can be exploited to develop new simulation techniques. We give three examples: efficient thermalization (a concept which was also noted by Fahy and Hamann [S. Fahy and D. R. Hamann, Phys. Rev. Lett. 69, 761 (1992)]), time-parallelization of a trajectory in an infrequent-event system, and detecting transitions in an infrequent-event system.

Algorithms↗
PubMed2002

A note on sample size calculation for mean comparisons based on noncentral t-statistics.

One-sample and two-sample t-tests are commonly used in analyzing data from clinical trials in comparing mean responses from two drug products. During the planning stage of a clinical study, a crucial step is the sample size calculation, i.e., the determination of the number of subjects (patients) needed to achieve a desired power (e.g., 80%) for detecting a clinically meaningful difference in the mean drug responses. Based on noncentral t-distributions, we derive some sample size calculation formulas for testing equality, testing therapeutic noninferiority/superiority, and testing therapeutic equivalence, under the popular one-sample design, two-sample parallel design, and two-sample crossover design. Useful tables are constructed and some examples are given for illustration.

Algorithms↗
PubMed1996

Reduction of computational complexity in the butterfly search technique.

In the butterfly search technique, echoes from repeated firings of a transducer are resampled along a set of predetermined trajectories of constant velocities, called "butterfly lines," because of their intersection and crossing at a reference range. The slope of the trajectory on which the sampled signals satisfy a predetermined criterion appropriate for the type of signal in question, provides an estimate of the velocity of the target. The search for this trajectory is called "butterfly search," which can be carried out efficiently in a parallel processing scheme. The estimator can be based on the radio frequency (RF) A-lines, the envelopes, or the quadrature components. The butterfly search on quadrature components has shown outstanding noise immunity, even with relatively few successive scan lines, and was found to outperform all the common time domain and Doppler techniques in simulations and experiments with strong noise. It can be simply implemented using elementary digital signal processing hardware. However, it is possible to further improve upon its computational complexity to make the technique even simpler to implement, without any complex multipliers in the parallel channels. In this paper, we present some modifications that significantly reduce the computational complexity of butterfly search on quadrature components.

Algorithms↗
PubMed2003

The transtheoretical model applied to an oral self-care behavioral change: development and testing of instruments for stages of change and decisional balance.

PURPOSE: The Transtheoretical Model is a theory-based approach for conceptualizing behavioral change. Inherent in this model is the determination and use of appropriate interventions to assist clients in improving their health behaviors. In the Transtheoretical Model, behavioral change progresses through a series of stages (precontemplation, contemplation, preparation, action, and maintenance) where movement from stage to stage is dependent upon decisional balance (the pros and cons that influence the decision). The purpose of this study was to develop instruments to test the validity and reliability of two components of the Transtheoretical Model--stages of change and decisional balance--as they relate to a new application in oral self-care behavior. An additional purpose was to determine if there was an association between these two components that would be applicable to a specific oral self-care behavior. METHODS: A three-part questionnaire was developed consisting of 1) stages of change instrument (4 items), 2) decisional balance instrument (40 items), and 3) demographic and dental experience information (9 items). Regular interdental cleaning was chosen as a behavior representing a commitment to oral self-care. The study population consisted of 709 subjects aged 35 to 55 who were recruited from 17 dental practices. RESULTS: A 70% (n = 521) response rate was obtained. Based upon the stages of change portion of the questionnaire, nearly 60% (n = 309) of the subjects were in the maintenance stage, while 21% (n = 109) were in precontemplation, with the rest distributed among the other stages. Reliability of the instrument was established with Kappa scoring. The decisional balance instrument was subjected to factor analysis resulting in a final decisional balance instrument of 28 items. There was a statistically significant relationship between the two components of stages of change and decisional balance. CONCLUSIONS: Stages of change and decisional balance instruments were developed and shown to be valid and reliable. Based upon the oral self-care behavior defined in this study, these instruments can identify an individual's current behavior and assess readiness to change by analyzing the distribution of the pros and cons a person considers when making a behavioral change. Understanding a client's behavioral stage would enable the practitioner to select and provide appropriate interventions. Further research should focus upon development of stage-appropriate intervention strategies and techniques, in order to move individuals along the continuum of stages toward behavioral change. Additionally, research with parallel and diverse populations is indicated.

Adult↗
PubMedDate not supplied

Similarity searching in databases of three-dimensional molecules and macromolecules.

This paper discusses algorithmic techniques for measuring the degree of similarity between pairs of three-dimensional (3-D) chemical molecules represented by interatomic distance matrices. A comparison of four methods for the calculation of 3-D structural similarity suggests that the most effective one is a procedure that identifies pairs of atoms, one from each of the molecules that are being compared, that lie at the center of geometrically-related volumes of 3-D space. This atom mapping method enables the calculation of a wide range of types of intermolecular similarity coefficient, including measures that are based on physicochemical data. Massively-parallel implementations of the method are discussed, using the AMT Distributed Array Processor, that achieve a substantial increase in performance when compared with a sequential implementation on a UNIX workstation. Current work involves the use of angular information and the extension of the method to field-based similarity searching. Similarity searching in 3-D macromolecules is effected by the use of a maximal common subgraph (MCS) isomorphism algorithm with a novel, graph-based representation of the tertiary structures of proteins. This algorithm is being used to identify similarities between the 3-D structures of proteins in the Brookhaven Protein Data Bank; its use is exemplified by searches involving the NAD-binding fold motif.

Algorithms↗
PubMed2003

Cool walking: a new Markov chain Monte Carlo sampling method.

Effective relaxation processes for difficult systems like proteins or spin glasses require special simulation techniques that permit barrier crossing to ensure ergodic sampling. Numerous adaptations of the venerable Metropolis Monte Carlo (MMC) algorithm have been proposed to improve its sampling efficiency, including various hybrid Monte Carlo (HMC) schemes, and methods designed specifically for overcoming quasi-ergodicity problems such as Jump Walking (J-Walking), Smart Walking (S-Walking), Smart Darting, and Parallel Tempering. We present an alternative to these approaches that we call Cool Walking, or C-Walking. In C-Walking two Markov chains are propagated in tandem, one at a high (ergodic) temperature and the other at a low temperature. Nonlocal trial moves for the low temperature walker are generated by first sampling from the high-temperature distribution, then performing a statistical quenching process on the sampled configuration to generate a C-Walking jump move. C-Walking needs only one high-temperature walker, satisfies detailed balance, and offers the important practical advantage that the high and low-temperature walkers can be run in tandem with minimal degradation of sampling due to the presence of correlations. To make the C-Walking approach more suitable to real problems we decrease the required number of cooling steps by attempting to jump at intermediate temperatures during cooling. We further reduce the number of cooling steps by utilizing "windows" of states when jumping, which improves acceptance ratios and lowers the average number of cooling steps. We present C-Walking results with comparisons to J-Walking, S-Walking, Smart Darting, and Parallel Tempering on a one-dimensional rugged potential energy surface in which the exact normalized probability distribution is known. C-Walking shows superior sampling as judged by two ergodic measures.

Journal Article↗
PubMed1985

Cortical ultrastructure of Coleps bicuspis Noland, 1925 and the phylogeny of the class Prostomatea (Ciliophora).

The ultrastructure of Coleps bicuspis Noland, 1925 is described. The ciliate is a typical prostomate: the somatic kinetid is a monokinetid with a postciliary ribbon at triple 9, a kinetodesmal fibril originating near triplets 5, 6, 7 and an apparently radial transverse ribbon at triplet 4. The oral area is circular and has three brosse kineties associated with it. The brosse kineties are composed of dikinetids whose anterior kinetosome bears a tangential transverse ribbon and whose posterior kinetosome bears the fibrillar associates typical of a somatic monokinetid. The oral dikinetids are oriented parallel to the circumference of the oral cavity, which is surrounded by oral papillae and oral ridges. Pairs of nematodesmata, originating from oral dikinetid kinetosomes, are typically triangular in transection. A phylogeny of rhabdophoran ciliates is presented using the mixed parsimony algorithm and is discussed with reference to the systematic revisions of the phylum Ciliophora.

Animals↗
PubMed2000

SPLASH: structural pattern localization analysis by sequential histograms.

MOTIVATION: The discovery of sparse amino acid patterns that match repeatedly in a set of protein sequences is an important problem in computational biology. Statistically significant patterns, that is patterns that occur more frequently than expected, may identify regions that have been preserved by evolution and which may therefore play a key functional or structural role. Sparseness can be important because a handful of non-contiguous residues may play a key role, while others, in between, may be changed without significant loss of function or structure. Similar arguments may be applied to conserved DNA patterns. Available sparse pattern discovery algorithms are either inefficient or impose limitations on the type of patterns that can be discovered. RESULTS: This paper introduces a deterministic pattern discovery algorithm, called Splash, which can find sparse amino or nucleic acid patterns matching identically or similarly in a set of protein or DNA sequences. Sparse patterns of any length, up to the size of the input sequence, can be discovered without significant loss in performances. Splash is extremely efficient and embarrassingly parallel by nature. Large databases, such as a complete genome or the non-redundant SWISS-PROT database can be processed in a few hours on a typical workstation. Alternatively, a protein family or superfamily, with low overall homology, can be analyzed to discover common functional or structural signatures. Some examples of biologically interesting motifs discovered by Splash are reported for the histone I and for the G-Protein Coupled Receptor families. Due to its efficiency, Splash can be used to systematically and exhaustively identify conserved regions in protein family sets. These can then be used to build accurate and sensitive PSSM or HMM models for sequence analysis. AVAILABILITY: Splash is available to non-commercial research centers upon request, conditional on the signing of a test field agreement. CONTACT: acal@us.ibm.com, Splash main page http://www.research.ibm.com/splash

Algorithms↗
PubMed2000

Algorithms for estimating blood velocities using ultrasound.

Ultrasound has been used intensively for the last 15 years for studying the hemodynamics of the human body. Systems for determining both the velocity distribution at one point of interest (spectral systems) and for displaying a map of velocity in real time have been constructed. A number of schemes have been developed for performing the estimation, and the various approaches are described. The current systems only display the velocity along the ultrasound beam direction and a velocity transverse to the beam is not detected. This is a major problem in these systems, since most blood vessels are parallel to the skin surface. Angling the transducer will often disturb the flow, and new techniques for finding transverse velocities are needed. The various approaches for determining transverse velocities will be explained. This includes techniques using two-dimensional correlation (speckle tracking), multiple beams, and the new transverse modulation technique. The different advantages and disadvantages of the approaches are explained.

Algorithms↗
PubMed1993

Automated tuning of a closed-loop hand grasp neuroprosthesis.

An automated tuning algorithm was developed to reduce the time and skill required to tune a closed-loop hand grasp neuroprosthesis. The time reduction results from simultaneous tuning of four gain parameters controlling the dynamic response of the system, and from automation of the calculation and decision processes. The new tuning method is therefore an automated parallel tuning method, replacing a manual sequential method in which only one parameter at a time was tuned. RMS error between the step input and the grasp output is minimized, with absence of oscillation as a constraint. The difference between the system's RMS ramp tracking errors for the two tuning methods was less than 1% of the ramp size regardless of the initial values of the parameters, implying that the tuning methods were equivalent. However, the parallel tuning method was faster and required fewer trials than the sequential method. The capability of the closed-loop system to regulate grasp output in the presence of disturbances was compared with the capability without feedback. Patients were instructed to either grasp an object at a certain force level or to match a certain grasp opening. They would then lock their command at a fixed value, and either remain immobile to test time dependence or pronate and supinate their forearm to test postural disturbances. With closed-loop control, the grasp output was better regulated in the presence of disturbances, with an average output variance 60% lower than without feedback control.

Algorithms↗
PubMed1998

Reduced test time by early identification of patients requiring atropine during dobutamine stress echocardiography.

In a randomized, controlled clinical trial, we evaluated the ability of an algorithm to identify, before peak stress, patients who will ultimately require atropine during dobutamine stress echocardiography. The effects of early atropine administration on test duration, atropine dose, dobutamine dose, and heart rate response also were studied. Compared with conventional atropine administration at peak dobutamine infusion, early atropine administration reduced test duration 8% (1.1 minutes, p = 0.02) and total dobutamine use 11% (0.41 mg/kg, p = 0.02) but required 90% more atropine (0.36 mg, p < 0.001). Conventional atropine administration resulted in a late, rapid rise in both heart rate and rate-pressure product. However, the heart rate and rate-pressure product curves for patients receiving early atropine paralleled those seen in patients not requiring atropine during dobutamine stress echocardiography. In conclusion, early atropine administration provides a more balanced stress and reduces test duration, thus decreasing total exposure to dobutamine and potentially increasing test efficiency.

Algorithms↗
PubMed2000

Activation linearity and parallelism of the superficial quadriceps across the isometric intensity spectrum.

The purpose of this study was to assess neuromuscular activation of the three superficial portions of the quadriceps femoris muscles during linearly increasing isometric contraction intensities. Thirty healthy volunteers were assessed for isometric electromyographic (EMG) activity of the vastus medialis (VM), vastus lateralis (VL), and rectus femoris (RF) muscles with the knee at 60 degrees of flexion. For 5 s, subjects performed isometric contractions equivalent to 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, and 90% of the average of three maximal voluntary contractions (MVC), in random order. Full-wave rectified and integrated EMG signals over the middle 3 s of each contraction were expressed as a percentage of the activity recorded during the three averaged MVCs. One sample t-tests and 95% confidence intervals were calculated at each relative torque level. A two-factor analysis of variance (muscle by intensity) with repeated measures was performed to evaluate parallel activation across the intensity levels. Activation linearity was assessed via regression analysis for each muscle. VM activation was shown to be significantly lower than expected at 20-70% MVC. VL and RF activations were significantly higher than expected at 10% MVC, and RF EMG was less than expected at 40-70% MVC. EMG of VM was shown to increase significantly more than VL and RF from 80% to 90% MVC. Significant linear and quadratic relations were also demonstrated for all three muscles. Parallel activation of the superficial quadriceps muscles occurred from low to moderate intensities, whereas convergence was noted at near maximal intensities.

Adult↗
PubMed2004

Three-dimensional reconstruction of biological objects' internal structure heterogeneity from the set of ultrasonic tomograms.

The paper presents the method of the three-dimensional reconstruction of biological objects' internal structure heterogeneity based on the ultrasonic examination of a woman's breast biopsy phantom. The phantom is made of quasi-homogeneous dense gel in which drops of lesions, characterized by fixed sizes and two different acoustic impedances, were dipped at random. For the purpose of this research a special measurement setup was elaborated, enabling a non-invasive in vitro imaging of biological objects' internal structure in cross-sections for fixed levels, by means of ultrasound transmission tomography (UTT) using the parallel-ray projection geometry of scanning. The two-dimensional images of the local values of ultrasonic wave's propagation velocity in the phantom's internal structure (ultrasonic tomograms) were reconstructed for fixed levels (by using the convolution and back-projection algorithm) from the measurements of average values of ultrasonic signals' runtime propagated from many directions around the object dipped in water. Analyzing the values of particular pixels and using an appropriate image processing technique, in effect the three-dimensional image of heterogeneity boundaries in the examined phantom's internal structure was computer-reconstructed. The obtained results are compatible with the specification provided by the phantom's producer in terms of sizes and acoustic parameters of lesions, which can simulate pathological changes and of the gel imitating the healthy tissue. It means that the method presented, after an appropriate modification and development of the measurement setup with an aim to accelerate the object scanning process and thus provide an opportunity for non-invasive in vivo examinations, could be applied for detecting and diagnosing tumors in women's breasts.

Breast Neoplasms↗
PubMed2002

A blood vessel exposed to ultrasound: a mathematical simulation of the temperature field.

In this article we present a mathematical simulation of the temperature field in and around a blood vessel when it is sonicated by a focused ultrasound beam. A simplified geometry is considered: a cylindrical blood vessel is embedded in tissue parallel to a flat skin surface. The ultrasound transducer is placed on the skin above the blood vessel, perpendicular to the skin surface. The 3D geometry of the problem is simplified by transformation, which maps the domain into a parallelepiped. A computational algorithm and computer program were developed. The simulation provides the conditions for successful occlusion of a blood vessel and demonstrates the significant role of the blood flow rate on the temperature difference between the vessel wall and the surrounding tissue. Comparing the predictions with published experimental data tested the validity of the method.

Blood Flow Velocity↗