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Results for “Parallel Algorithms”

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PubMed1997

High-performance computing and networking as tools for accurate emission computed tomography reconstruction.

It is well known that the quantitative potential of emission computed tomography (ECT) relies on the ability to compensate for resolution, attenuation and scatter effects. Reconstruction algorithms which are able to take these effects into account are highly demanding in terms of computing resources. The reported work aimed to investigate the use of a parallel high-performance computing platform for ECT reconstruction taking into account an accurate model of the acquisition of single-photon emission tomographic (SPET) data. An iterative algorithm with an accurate model of the variable system response was ported on the MIMD (Multiple Instruction Multiple Data) parallel architecture of a 64-node Cray T3D massively parallel computer. The system was organized to make it easily accessible even from low-cost PC-based workstations through standard TCP/IP networking. A complete brain study of 30 (64x64) slices could be reconstructed from a set of 90 (64x64) projections with ten iterations of the conjugate gradients algorithm in 9 s, corresponding to an actual speed-up factor of 135. This work demonstrated the possibility of exploiting remote high-performance computing and networking resources from hospital sites by means of low-cost workstations using standard communication protocols without particular problems for routine use. The achievable speed-up factors allow the assessment of the clinical benefit of advanced reconstruction techniques which require a heavy computational burden for the compensation effects such as variable spatial resolution, scatter and attenuation. The possibility of using the same software on the same hardware platform with data acquired in different laboratories with various kinds of SPET instrumentation is appealing for software quality control and for the evaluation of the clinical impact of the reconstruction methods.

Algorithms↗

PubMed2006

DIESEL-MP2: a new program to perform large-scale multireference-MP2 computations.

This article presents a new MR-MP2 code (Multi-Reference Møller-Plesset 2nd order) suitable for the computation MR-MP2 energies of extended systems with strong near degeneracy effects (e.g., open shell systems). It is based on the DIESEL program package developed by Hanrath and Engels. Due to improved algorithms the new code is able to handle systems with 400-500 basis functions and more than 100 electrons. The code is made for parallel computers with distributed memory, but can also be run on local machines. It possesses two integral interfaces (MOLCAS, TURBOMOLE). The algorithms are briefly introduced and timings for the Neocarzinostatin chromophore are presented. The efficiencies of the codes obtained with Intel or GNU compilers are compared.

Algorithms↗

PubMed2003

Asynchronously parallelized percolation on distributed machines.

We propose a powerful method based on the Hoshen-Kopelman algorithm for simulating percolation asynchronously on distributed machines. Our method demands very little of hardware and yet we are able to make high precision measurements on very large lattices. We implement our method to calculate various cluster size distributions on large lattices of different aspect ratios spanning three orders of magnitude for two-dimensional site and bond percolation. We find that the nonuniversal constants in the scaling function for the cluster size distribution apparently satisfy a scaling relation, and that the moment ratios for the largest cluster size distribution reveal a characteristic aspect ratio at r approximately 9.

Journal Article↗

PubMed2000

An algorithm for the treatment of schizophrenia in the correctional setting: the Forensic Algorithm Project.

The Forensic Algorithm Project (FAP) was born of the need for a holistic approach in the treatment of the inmate with schizophrenia. Schizophrenia was chosen as the first entity to be addressed by the algorithm because of its refractory nature and high rate of recidivism in the correctional setting. Schizophrenia is regarded as a spectrum disorder, with symptom clusters and behaviors ranging from positive to negative symptoms to neurocognitive dysfunction and affective instability. Furthermore, the clinical picture is clouded by Axis II symptomatology (particularly prominent in the inmate population), comorbid Axis I disorders, and organicity. Four subgroups of schizophrenia were created to coincide with common clinical presentations in the forensic inpatient facility and also to parallel 4 tracks of intervention, consisting of pharmacologic management and programming recommendations. The algorithm begins with any antipsychotic medication and proceeds to atypical neuroleptic usage, augmentation with other psychotropic agents, and, finally, the use of clozapine as the common pathway for refractory schizophrenia. Outcome measurement of pharmacologic intervention is assessed every 6 weeks through the use of a 4-item subscale, specific for each forensic subgroup. A "floating threshold" of 40% symptom severity reduction on Positive and Negative Syndrome Scale and Brief Psychiatric Rating Scale items over a 6-week period is considered an indication for neuroleptic continuation. The forensic algorithm differs from other clinical practice guidelines in that specific programming in certain prison environments is stipulated. Finally, a social commentary on the importance of state-of-the-art psychiatric treatment for all members of society is woven into the clinical tapestry of this article.

Algorithms↗

PubMed2006

[The use of head CT scan in adult trauma victims: an algorithm].

INTRODUCTION: The purpose of this study was to identify, through recursive partitioning, clinically relevant criteria which predict the need for acute neurosurgical intervention in a group of patients with mild head injury. MATERIALS AND METHODS: A retrospective cohort of all adult patients, from April 2000 to March 2001, who sustained a blunt trauma and underwent head CT scan, was reviewed. The following inclusion criteria for mild head injury were used: initial Glasgow Coma Scale (GCS) ranging from 13 to 15; no loss of consciousness lasting more than one hour; no obvious skull fracture; a cranial CT scan performed. We collected demographic and trauma related data, interventions and outcome. Univariate and multivariate analyses were undertaken. In parallel, recursive partitioning was carried out using all variables to elaborate a decision algorithm. RESULTS: There were 405 patients in the sample. CT identified lesions in 12% of patients. Twelve patients (3%) required acute neurosurgical intervention. The recursive partitioning analysis identified three significant sequential nodes: deterioration of the GCS; an initial GCS of 13 vs 14 or 15; and the presence of associated injuries or comorbid conditions. CONCLUSIONS: A simple three step rule predicts the need for acute neurosurgical intervention based on clinical findings: a deteriorating GCS; an initial GCS of 13; and the presence of associated injuries or comorbid conditions.

Adolescent↗

PubMedDate not supplied

Visualisation of synchronous firing in multi-dimensional spike trains.

The gravity transform algorithm is used to study the dependencies in firing of multi-dimensional spike trains. The pros and cons of this algorithm are discussed and the necessity for improved representation of output data is demonstrated. Parallel coordinates are introduced to visualise the results of the gravity transform and principal component analysis (PCA) is used to reduce the quantity of data represented whilst minimising loss of information.

Action Potentials↗

PubMed2005

DMLC leaf-pair optimal control for mobile, deforming target.

Existing algorithms of dynamic control of independent pairs of leaves allow optimal DMLC delivery of IMRT to rigid targets translating parallel to leaf trajectories. However, in numerous cases of radiotherapy treatments simplifying assumptions of rigid-like motions of targets and surrounding tissues are clearly not satisfied. Therefore algorithms have to be developed that allow one to control MLC so that predetermined intensities are delivered to various points in targets that experience compression and expansion at the time of irradiation. Moreover, it is desirable for such algorithms to ensure that delivery of modulated intensity map will be done with minimal expense of monitor units. Derivation of the algorithm that optimizes the DMLC IMRT to mobile, deforming target is presented in this paper. [To illustrate the general algorithm two representative examples of DMLC IMRT delivery to deforming targets are presented in full detail.] Finally, similarities and differences between solutions for immobile targets, for moving, rigid targets and for moving, deforming targets are discussed.

Algorithms↗

PubMed1998

A cluster computer system for the analysis and classification of massively large biomedical image data.

The current trend in medical image acquisition is towards the generation of image datasets which are massively large, either because they exhibit fine x, y, or z resolution, are volumetric, are multispectral, or a combination of all of the preceding. Such images pose a significant computational challenge in their analysis, not only in terms of data throughput, but also in terms of platform costs and simplicity. In this paper we describe the role of a cluster of workstations together with two quite different application programming interfaces (APIs) in the quantitative analysis of anatomic image data from the visible human project using an MRF-Gibbs classification algorithm. We describe the typical architecture of a cluster computer, two API options and the parallelization of the MRF-Gibbs procedure for the cluster. Finally, we show speedup results obtained on the cluster and sample classifications of visible human data.

Algorithms↗

PubMed2000

Modified genetic algorithm resolves ambiguous NOE restraints and reduces unsightly NOE violations.

In an ideal world, every NOE cross peak would have a unique assignment. However, the interpretation of NOE peaks is frequently complicated by overlapping resonances. In theory, ambiguous assignments could be resolved by performing separate structure calculations with each possible interpretation. Unfortunately, this would require an astronomical amount of computing time. A modified genetic algorithm has been developed that efficiently resolves hundreds of ambiguous restraints in parallel. Each NOE assignment becomes a gene that can be passed on to a new generation. New individuals are constructed by making a constraint lists from a subset of the genes. The constraint lists are then tested for self-consistency by using molecular dynamics to generate new structures for each list. To a first-degree approximation, there is enough information retained in each list to determine the global fold of the protein. Self-consistent constraint lists receive higher scores and their genes (or NOEs) stand a better chance of surviving into the next generation. The process selects NOEs that are consistent with the global fold. Under normal conditions, the program converges in 3 to 8 generations using 70 structures per generation. The final constraints are self-consistent and contain almost no residual NOE violations.

Algorithms↗

PubMed2006

EMAN2: an extensible image processing suite for electron microscopy.

EMAN is a scientific image processing package with a particular focus on single particle reconstruction from transmission electron microscopy (TEM) images. It was first released in 1999, and new versions have been released typically 2-3 times each year since that time. EMAN2 has been under development for the last two years, with a completely refactored image processing library, and a wide range of features to make it much more flexible and extensible than EMAN1. The user-level programs are better documented, more straightforward to use, and written in the Python scripting language, so advanced users can modify the programs' behavior without any recompilation. A completely rewritten 3D transformation class simplifies translation between Euler angle standards and symmetry conventions. The core C++ library has over 500 functions for image processing and associated tasks, and it is modular with introspection capabilities, so programmers can add new algorithms with minimal effort and programs can incorporate new capabilities automatically. Finally, a flexible new parallelism system has been designed to address the shortcomings in the rigid system in EMAN1.

Algorithms↗

PubMed2002

Image reconstruction algorithm for a rotating slat collimator.

A slat collimator in single photon emission computed tomography consists of a set of parallel slats. As the collimator spins, the detector measures a one-dimensional projection data set. A complete data set can be obtained by rotating the detector/collimator assembly around the object (patient) while the collimator spins continuously. The measured projection data are assumed to be weighted planar integrals of the object. This paper describes the development of an approximate three-dimensional image reconstruction algorithm for a rotating/spinning slat collimator. This algorithm is in filtered backprojection form. Computer simulations were performed to verify the effectiveness of the algorithm.

Algorithms↗

PubMed2005

A three-dimensional weighted cone beam filtered backprojection (CB-FBP) algorithm for image reconstruction in volumetric CT under a circular source trajectory.

The original FDK algorithm proposed for cone beam (CB) image reconstruction under a circular source trajectory has been extensively employed in medical and industrial imaging applications. With increasing cone angle, CB artefacts in images reconstructed by the original FDK algorithm deteriorate, since the circular trajectory does not satisfy the so-called data sufficiency condition (DSC). A few 'circular plus' trajectories have been proposed in the past to help the original FDK algorithm to reduce CB artefacts by meeting the DSC. However, the circular trajectory has distinct advantages over other scanning trajectories in practical CT imaging, such as head imaging, breast imaging, cardiac, vascular and perfusion applications. In addition to looking into the DSC, another insight into the CB artefacts existing in the original FDK algorithm is the inconsistency between conjugate rays that are 180 degrees apart in view angle (namely conjugate ray inconsistency). The conjugate ray inconsistency is pixel dependent, varying dramatically over pixels within the image plane to be reconstructed. However, the original FDK algorithm treats all conjugate rays equally, resulting in CB artefacts that can be avoided if appropriate weighting strategies are exercised. Along with an experimental evaluation and verification, a three-dimensional (3D) weighted axial cone beam filtered backprojection (CB-FBP) algorithm is proposed in this paper for image reconstruction in volumetric CT under a circular source trajectory. Without extra trajectories supplemental to the circular trajectory, the proposed algorithm applies 3D weighting on projection data before 3D backprojection to reduce conjugate ray inconsistency by suppressing the contribution from one of the conjugate rays with a larger cone angle. Furthermore, the 3D weighting is dependent on the distance between the reconstruction plane and the central plane determined by the circular trajectory. The proposed 3D weighted axial CB-FBP algorithm can be implemented in either the native CB geometry or the so-called cone-parallel geometry. By taking the cone-parallel geometry as an example, the experimental evaluation shows that, up to a moderate cone angle corresponding to a detector dimension of 64 x 0.625 mm, the CB artefacts can be substantially suppressed by the proposed algorithm, while advantages of the original FDK algorithm, such as the filtered backprojection algorithm structure, 1D ramp filtering and data manipulation efficiency, are maintained.

Algorithms↗

PubMedDate not supplied

High-performance electron tomography of complex biological specimens.

We have evaluated reconstruction methods using smooth basis functions in the electron tomography of complex biological specimens. In particular, we have investigated series expansion methods, with special emphasis on parallel computation. Among the methods investigated, the component averaging techniques have proven to be most efficient and have generally shown fast convergence rates. The use of smooth basis functions provides the reconstruction algorithms with an implicit regularization mechanism, very appropriate for noisy conditions. Furthermore, we have applied high-performance computing (HPC) techniques to address the computational requirements demanded by the reconstruction of large volumes. One of the standard techniques in parallel computing, domain decomposition, has yielded an effective computational algorithm which hides the latencies due to interprocessor communication. We present comparisons with weighted back-projection (WBP), one of the standard reconstruction methods in the areas of computational demand and reconstruction quality under noisy conditions. These techniques yield better results, according to objective measures of quality, than the weighted backprojection techniques after a very few iterations. As a consequence, the combination of efficient iterative algorithms and HPC techniques has proven to be well suited to the reconstruction of large biological specimens in electron tomography, yielding solutions in reasonable computation times.

Algorithms↗

PubMed2002

Can the stages of change for smoking acquisition be measured reliably in adolescents?

BACKGROUND: was to examine the reliability of the algorithm. METHODS: As part of a randomized controlled trial, 3,930 adolescents completed a paper version of the algorithm questions and a differently worded computerized version on the same day: a parallel form reliability assessment. In a separate assessment, another group of 118 adolescents completed 2 identical paper versions of the same questionnaire 2 weeks apart: a test-retest reliability assessment. Kappa (kappa) for agreement for stage and the individual questions were calculated. Logistic regression was used to examine whether demographic characteristics, smoking status, and stage predicted agreement for stage. RESULTS: Kappa (95% confidence intervals) for stage was 0.57 (0.55-0.60) in the first assessment and 0.46 (0.28-0.63) in the second assessment, indicating moderate reliability. The question concerning trying smoking in the next 6 months was moderately reliable, but that concerning trying within the next thirty days was poorly reliable. Acquisition precontemplation was significantly more reliably coded than all other stages. Demographic characteristics did not predict reliability. CONCLUSIONS: The algorithm reliably allocates individuals into acquisition precontemplation, but for all other stages, its reliability is fair.

Adolescent↗

PubMedDate not supplied

Techniques for the rapid display and manipulation of 3-D biomedical data.

The use of fully interactive 3-D workstations with true real-time performance will become increasingly common as technology matures and economical commercial systems become available. This paper provides a comprehensive introduction to high speed approaches to the display and manipulation of 3-D medical objects obtained from tomographic data acquisition systems such as CT, MR, and PET. A variety of techniques are outlined including the use of software on conventional minicomputers, hardware assist devices such as array processors and programmable frame buffers, and special purpose computer architecture for dedicated high performance systems. While both algorithms and architectures are addressed, the major theme centers around the utilization of hardware-based approaches including parallel processors for the implementation of true real-time systems.

Algorithms↗

PubMedDate not supplied

Fault location of two-parallel transmission line for double phase-to-earth fault using one-terminal data.

An accurate algorithm for fault location of double phase-to-earth fault on transmission line of direct ground neutral system is presented. The algorithm, which employs the faulted phase network and zero-sequence network as fault-location model in which the source impedance at the remote end is not involved, effectively eliminates the effect of load flow and fault resistance on the accuracy of fault location. The algorithm achieves accurate location by measuring only one local end data and is used in a procedure that provides automatic determination of faulted types and phases, and does not require the engineer to specify them. Simulation results showed the effectiveness of the algorithm under the condition of double phase-to-earth fault.

Algorithms↗

PubMed2005

Inherently self-calibrating non-Cartesian parallel imaging.

The use of self-calibrating techniques in parallel magnetic resonance imaging eliminates the need for coil sensitivity calibration scans and avoids potential mismatches between calibration scans and subsequent accelerated acquisitions (e.g., as a result of patient motion). Most examples of self-calibrating Cartesian parallel imaging techniques have required the use of modified k-space trajectories that are densely sampled at the center and more sparsely sampled in the periphery. However, spiral and radial trajectories offer inherent self-calibrating characteristics because of their densely sampled center. At no additional cost in acquisition time and with no modification in scanning protocols, in vivo coil sensitivity maps may be extracted from the densely sampled central region of k-space. This work demonstrates the feasibility of self-calibrated spiral and radial parallel imaging using a previously described iterative non-Cartesian sensitivity encoding algorithm.

Algorithms↗

PubMed2006

Parallel RF transmission in MRI.

Following the development of parallel imaging, parallel transmission describes the use of multiple RF transmit coils. Parallel transmission can be applied to improve RF excitation, in particular, multidimensional, spatially selective RF excitation. For instance, parallel transmission is able to shorten spatially selective RF pulses in two or three dimensions, or to minimize the occurring SAR. One potential major application might be the compensation of patient-induced B(1) inhomogeneities, particularly at high main fields. This paper provides an overview of selected aspects of this new transmission approach. The basic principles of parallel transmission are discussed, initial experimental proofs are described, and the impact of error propagation on coil design for parallel transmission is outlined.

Algorithms↗