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 1,675 records · Page 93Linked to original sources
PubMed1994

Distributed machine learning: scaling up with coarse-grained parallelism.

Machine learning methods are becoming accepted as additions to the biologists data-analysis tool kit. However, scaling these techniques up to large data sets, such as those in biological and medical domains, is problematic in terms of both the required computational search effort and required memory (and the detrimental effects of excessive swapping). Our approach to tackling the problem of scaling up to large datasets is to take advantage of the ubiquitous workstation networks that are generally available in scientific and engineering environments. This paper introduces the notion of the invariant-partitioning property--that for certain evaluation criteria it is possible to partition a data set across multiple processors such that any rule that is satisfactory over the entire data set will also be satisfactory on at least one subset. In addition, by taking advantage of cooperation through interprocess communication, it is possible to build distributed learning algorithms such that only rules that are satisfactory over the entire data set will be learned. We describe a distributed learning system, CorPRL, that takes advantage of the invariant-partitioning property to learn from very large data sets, and present results demonstrating CorPRL's effectiveness in analyzing data from two databases.

Database Management Systems↗
PubMed1995

A novel transverse gradient coil design for high-resolution MR imaging.

The authors describe a new gradient coil design for high resolution human, animal, specimen, or phantom imaging with high gradient efficiency and a large region of excellent gradient uniformity. Important features of our new design are the simple analytical description of the wire patterns that comprise the design, and ease of construction. Wires are spaced in a sinusoidal distribution around the circumference of the cylinder, and curved in an arcsin shape along the length of the cylinder. This coil produces a magnetic field pointing in a direction transverse to the axis of the coil with a gradient in the direction parallel to the axis of the coil. The same arcsin coil can be used to create a magnetic field pointing in a direction parallel to its axis with a gradient in a direction perpendicular to the coil axis. A prototype coil was constructed; field and inductance calculations were verified. Geometric variations on this coil design were modeled and their performance characteristics compared. This coil design is ideal for rapid implementation of a transverse gradient coil, since no specialized design software is required.

Algorithms↗
PubMed2004

Expert knowledge-guided segmentation system for brain MRI.

We describe an automated 3-D segmentation system for in vivo brain magnetic resonance images (MRI). Our segmentation method combines a variety of filtering, segmentation, and registration techniques and makes maximum use of the available a priori biomedical expertise, both in an implicit and an explicit form. We approach the issue of boundary finding as a process of fitting a group of deformable templates (simplex mesh surfaces) to the contours of the target structures. These templates evolve in parallel, supervised by a series of rules derived from analyzing the template's dynamics and from medical experience. The templates are also constrained by knowledge on the expected textural and shape properties of the target structures. We apply our system to segment four brain structures (corpus callosum, ventricles, hippocampus, and caudate nuclei) and discuss its robustness to imaging characteristics and acquisition noise.

Algorithms↗
PubMed1995

Role of prostate-specific antigen density after applying age-specific prostate-specific antigen reference ranges.

OBJECTIVES: To determine the potential role of prostate-specific antigen (PSA) density (PSAD) in the early detection of prostate carcinoma if we apply age-specific PSA reference ranges (2.5 ng/mL or less for ages 40 to 49 years, 3.5 or less for ages 50 to 59, 4.5 or less for ages 60 to 69, and 6.5 or less for ages 70 to 79. METHODS: We retrospectively reviewed 3234 cases referred to us by urologists for transrectal ultrasound (TRUS) between January 1, 1991, and September 28, 1993. We included 2429 patients in the study, ages 40 to 79 years, with Hybritech or Abbott IMx serum PSA determinations and without previously diagnosed prostate cancer. We performed digital rectal examination (DRE) and TRUS in all cases, and TRUS-guided biopsies when indicated. We used stringent criteria to define 736 cases without clinical evidence of malignancy that were designated as a "benign group." RESULTS: In the benign group, we found serum PSA to increase with age in parallel with the increase in prostate volume with age (r = 0.25 and r = 0.26, respectively). The association between serum PSA and prostate volume was stronger (r = 0.46). Using multiple regression analysis, prostate volume accounted for 18% of the variation in serum PSA, whereas age accounted for only an additional 2%. PSAD, which directly relates serum PSA to prostate volume, showed a weak association with age (r = 0.1). In the entire study population of 2429 cases, 555 patients had negative DRE and TRUS results and a serum PSA level between the age-specific upper limit of normal and 10.0 ng/mL. According to the proposed age-specific algorithm, these patients would have required automatic biopsies. Of these, 315 cases (56.8%) still had a PSAD of less than 0.15. We performed biopsies in 108 of these 315 and detected only two cancers, for a positive biopsy rate (PBR) of 1.9%. The remaining 240 cases had a PSAD of 0.15 or higher, and we performed biopsies in 217 of these cases and detected 59 cancers, for a PBR of 27.2%. CONCLUSIONS: The use of age-specific PSA reference ranges does not totally account for the effect of prostate volume on serum PSA. Therefore PSAD can still be used to reduce safely the number of biopsies performed in patients with negative DRE and TRUS results and a serum PSA level 10.0 ng/mL or less and above the age-specific upper limit of normal.

Adult↗
PubMed1997

National Institute of Mental Health Collaborative Multimodal Treatment Study of Children with ADHD (the MTA). Design challenges and choices.

The Collaborative Multimodal Treatment Study of Children with Attention Deficit Hyperactivity Disorder (ADHD), the MTA, is the first child multisite cooperative agreement treatment study of children conducted by the National Institute of Mental Health, Rockville, Md. It examines the long-term effectiveness of medication vs behavioral treatment vs both for treatment of ADHD and compares state-of-the-art treatment with routine community care. In a parallel-groups design, 576 children (age, 7-9 years) with ADHD (96 at each site) are thoroughly assessed and randomized to 4 conditions: (1) medication alone, (2) psychosocial treatment alone, (3) the combination of both, (4) or community comparison. The first 3 groups are treated for 14 months and all are reassessed periodically for 24 months. Designers met the following challenges: framing clinically relevant primary questions; defining the target population; choice, intensity, and integration and combination of treatments for fair comparisons; combining scientific controls and standardization with clinical flexibility; and implementing a controlled clinical trial in a nonclinical setting (school) controlled by others. Innovative solutions included extensive decision algorithms and manualized adaptations of treatments to specific needs.

Attention Deficit Disorder with Hyperactivity↗
PubMed1999

Single-shot diffusion measurement in laser-polarized Gas.

A single-shot pulsed gradient stimulated echo sequence is introduced to address the challenges of diffusion measurements of laser polarized 3He and 129Xe gas. Laser polarization enhances the NMR sensitivity of these noble gases by >10(3), but creates an unstable, nonthermal polarization that is not readily renewable. A new method is presented which permits parallel acquisition of the several measurements required to determine a diffusive attenuation curve. The NMR characterization of a sample's diffusion behavior can be accomplished in a single measurement, using only a single polarization step. As a demonstration, the diffusion coefficient of a sample of laser-polarized 129Xe gas is measured via this method.

Algorithms↗
PubMed2001

Applicability of the single equivalent point dipole model to represent a spatially distributed bio-electrical source.

Although the single equivalent point dipole model has been used to represent well-localised bio-electrical sources, in realistic situations the source is distributed. Consequently, position estimates of point dipoles determined by inverse algorithms suffer from systematic error due to the non-exact applicability of the inverse model. In realistic situations, this systematic error cannot be avoided, a limitation that is independent of the complexity of the torso model used. This study quantitatively investigates the intrinsic limitations in the assignment of a location to the equivalent dipole due to distributed electrical source. To simulate arrhythmic activity in the heart, a model of a wave of depolarisation spreading from a focal source over the surface of a spherical shell is used. The activity is represented by a sequence of concentric belt sources (obtained by slicing the shell with a sequence of parallel plane pairs), with constant dipole moment per unit length (circumferentially) directed parallel to the propagation direction. The distributed source is represented by N dipoles at equal arc lengths along the belt. The sum of the dipole potentials is calculated at predefined electrode locations. The inverse problem involves finding a single equivalent point dipole that best reproduces the electrode potentials due to the distributed source. The inverse problem is implemented by minimising the chi2 per degree of freedom. It is found that the trajectory traced by the equivalent dipole is sensitive to the location of the spherical shell relative to the fixed electrodes. It is shown that this trajectory does not coincide with the sequence of geometrical centres of the consecutive belt sources. For distributed sources within a bounded spherical medium, displaced from the sphere's centre by 40% of the sphere's radius, it is found that the error in the equivalent dipole location varies from 3 to 20% for sources with size between 5 and 50% of the sphere's radius. Finally, a method is devised to obtain the size of the distributed source during the cardiac cycle.

Computer Simulation↗
PubMed2006

Structural identifiability of physiologically based pharmacokinetic models.

When starting a project in drug kinetics it is necessary to test a priori whether there is sufficient information in the experimental input-output design to estimate unique values of internal rate constants. This is an important test if the pharmacokinetics of a drug are to be characterised in some way by the parameter values estimated from the observed plasma or blood concentration profile. Various modifications of the well-perfused Physiologically Based Pharmacokinetic model (PBPK) are considered here. More complex PBPK models can be considered to consist of subsystems, representing groups of tissues, which are connected in parallel to the central compartment. A novel method of structural identifiability analysis is presented here that considers these subsystems individually. This makes analysis of subsequently modified models much simpler. It is found in a number of cases that these more complex systems remain globally identifiable and at worst reduce to locally identifiable for the additional parameters. A caveat is added about having more than one eliminating peripheral tissue.

Algorithms↗
PubMed2000

Na(+)-K(+)-ATPase-mediated basolateral rubidium uptake in the maturing rabbit cortical collecting duct.

Within the renal cortical collecting duct (CCD), transepithelial Na(+) absorption and K(+) secretion are linked to basolateral Na(+)-K(+)-ATPase activity. Our purpose was to examine the developmental changes in basolateral Na(+)-K(+)-ATPase-mediated (86)rubidium (Rb) uptake, its inhibitor sensitivity and relationship to pump hydrolytic activity and Na(+) transport. Multiple CCDs ( approximately 6 mm) from maturing rabbits were affixed to coverslips, preincubated at 37 degrees C for 10 min (+/-1-2.5 mM ouabain or 10 or 100 micro M Schering-28080, an inhibitor of H(+)-K(+)-ATPase), and then transferred to prewarmed incubation solution containing tracer amounts of (86)Rb (+/-inhibitors). After 1 min at 37 degrees C, tubular samples were rinsed and permeabilized and isotope counts were measured to calculate basolateral Rb uptake. Ouabain-inhibitable Rb uptake, an index of basolateral Na(+)-K(+) pump activity, increased approximately 3-fold during the 1st 8 wk of postnatal life (P < 0.03). The approximately 2-fold increase in absolute rate of Rb uptake between 1 and 6 wk (2.64 +/- 0.45 to 5.02 +/- 0.32 pmol. min(-1). mm(-1)) did not reach statistical significance. The rate of basolateral Rb uptake increased further after the 6th wk of life to 7.29 +/- 0.53 pmol. min(-1). mm(-1) in adult animals (P < 0.03 vs. 6 wk). Schering-28080 failed to inhibit Rb uptake, implying that functional H(+)-K(+)-ATPase is absent at the basolateral membrane. Na(+)-K(+)-ATPase hydrolytic activity, determined by using a microassay that measured inorganic phosphate release from [gamma-(32)P]ATP under maximum velocity (V(max)) conditions, also increased in the differentiating CCD (from 316.2 +/- 44.4 pmol. h(-1). mm(-1) at 2 wk to 555.9 +/- 105.1 at 4 wk to 789.7 +/- 145.0 at 6 wk; r = 1.0 by linear regression analysis; P < 0.005). The parallel approximately 2.5-fold increases in Na(+)-K(+)-ATPase activity and ouabain-sensitive Rb uptake between 2- and 6-wk postnatal age suggest that the developmental increase in basolateral transport capacity is due predominantly to an increase in enzyme abundance. The signals mediating the developmental increase in Na(+)-K(+)-ATPase activity in the CCD remain to be defined.

Algorithms↗
PubMed1994

Some approaches to the analysis of recurrent event data.

Methodological research in biostatistics has been dominated over the last twenty years by further development of Cox's regression model for life tables and of Nelder and Wedderburn's formulation of generalized linear models. In both of these areas the need to address the problems introduced by subject level heterogeneity has provided a major motivation, and the analysis of data concerning recurrent events has been widely discussed within both frameworks. This paper reviews this work, drawing together the parallel development of 'marginal' and 'conditional' approaches in survival analysis and in generalized linear models. Frailty models are shown to be a special case of a random effects generalization of generalized linear models, whereas marginal models for multivariate failure time data are more closely related to the generalized estimating equation approach to longitudinal generalized linear models. Computational methods for inference are discussed, including the Bayesian Markov chain Monte Carlo approach.

Algorithms↗
PubMed2004

Experimental evaluation of an anisotropic scattering model of a slab geometry.

A model has been developed based on random walk theory that allows the diffusion of light along a principal axis to differ from that in orthogonal directions. We present expressions that describe the time-resolved intensity measured across a slab and on the surface of a semi-infinite medium for a principal axis oriented parallel or perpendicular to the surface. The model of time-resolved transmittance is compared with experimental data acquired by use of a phantom consisting of wax fibers arranged within a solid cube of resin. It is shown that a single set of optical parameters is sufficient to model the experimental measurements acquired across all three orientations of the cube.

Algorithms↗
PubMed2003

Mechanobiology of soft skeletal tissue differentiation--a computational approach of a fiber-reinforced poroelastic model based on homogeneous and isotropic simplifications.

The material properties of multipotent mesenchymal tissue change dramatically during the differentiation process associated with skeletal regeneration. Using a mechanobiological tissue differentiation concept, and homogeneous and isotropic simplifications of a fiber-reinforced poroelastic model of soft skeletal tissues, we have developed a mathematical approach for describing time-dependent material property changes during the formation of cartilage, fibrocartilage, and fibrous tissue under various loading histories. In this approach, intermittently imposed fluid pressure and tensile strain regulate proteoglycan synthesis and collagen fibrillogenesis, assembly, cross-linking, and alignment to cause changes in tissue permeability (k), compressive aggregate modulus (H(A)), and tensile elastic modulus (E). In our isotropic model, k represents the permeability in the least permeable direction (perpendicular to the fibers) and E represents the tensile elastic modulus in the stiffest direction (parallel to the fibers). Cyclic fluid pressure causes an increase in proteoglycan synthesis, resulting in a decrease in k and increase in H(A) caused by the hydrophilic nature and large size of the aggregating proteoglycans. It further causes a slight increase in E owing to the stiffness added by newly synthesized type II collagen. Tensile strain increases the density, size, alignment, and cross-linking of collagen fibers thereby increasing E while also decreasing k as a result of an increased flow path length. The Poisson's ratio of the solid matrix, nu(s), is assumed to remain constant (near zero) for all soft tissues. Implementing a computer algorithm based on these concepts, we simulate progressive changes in material properties for differentiating tissues. Beginning with initial values of E=0.05 MPa, H(A)=0 MPa, and k=1 x 10(-13) m(4)/Ns for multipotent mesenchymal tissue, we predict final values of E=11 MPa, H(A)=1 MPa, and k=4.8 x 10(-15) m(4)/Ns for articular cartilage, E=339 MPa, H(A)=1 MPa, and k=9.5 x 10(-16) m(4)/Ns for fibrocartilage, and E=1,000 MPa, H(A)=0 MPa, and k=7.5 x 10(-16) m(4)/Ns for fibrous tissue. These final values are consistent with the values reported by other investigators and the time-dependent acquisition of these values is consistent with current knowledge of the differentiation process.

Algorithms↗
PubMed1994

Evaluation and quality control of a commercial 3-D dose compensator system.

A commercially available software/hardware system for automated design and fabrication of three-dimensional dose compensator molds has been tested for accuracy and precision as well as for its ability to provide adequate dose compensation at depth. To date, we have used this system to treat more than 50 patients with either head and neck or lung malignancies. In 19 head and neck patients (38 compensators) the use of a customized compensator resulted in an average reduction of dose variance in the target volume from 13.8% (range of 7%-21%) with uncompensated parallel-opposed fields to 4.5% (2%-7%) with custom-compensated parallel-opposed fields. A similar reduction was seen in the dose variation across lung tumor volumes. The custom compensators were also tested for accuracy of fabrication and positioning; both were found to be accurate within +/- 1 mm of the design specifications for all compensators tested. Last, the dosimetric properties of the compensators were studied. The ratios of measured open-beam dose profiles to measured compensated-beam dose profiles were compared with the ratio of similar profiles calculated with a treatment planning system. These ratios were equal within +/- 2.9%, thus providing evidence of the fidelity of the compensator to its design and the accuracy of the treatment planning algorithm that designs 34 each compensator.

Algorithms↗
PubMed2006

Exploiting application locality to design low-complexity, highly performing, and power-aware embedded classifiers.

Temporal and spatial locality of the inputs, i.e., the property allowing a classifier to receive the same samples over time--or samples belonging to a neighborhood--with high probability, can be translated into the design of embedded classifiers. The outcome is a computational complexity and power aware design particularly suitable for implementation. A classifier based on the gated-parallel family has been found particularly suitable for exploiting locality properties: Subclassifiers are generally small, independent each other, and controlled by a master-enabling module granting that only a subclassifier is active at a time, the others being switched off. By exploiting locality properties we obtain classifiers with accuracy comparable with the ones designed without integrating locality but gaining a significant reduction in computational complexity and power consumption.

Algorithms↗
PubMed2003

Bounds on the number of hidden neurons in three-layer binary neural networks.

This paper investigates an important problem concerning the complexity of three-layer binary neural networks (BNNs) with one hidden layer. The neuron in the studied BNNs employs a hard limiter activation function with only integer weights and an integer threshold. The studies are focused on implementations of arbitrary Boolean functions which map from [0, 1]n into [0, 1]. A deterministic algorithm called set covering algorithm (SCA) is proposed for the construction of a three-layer BNN to implement an arbitrary Boolean function. The SCA is based on a unit sphere covering (USC) of the Hamming space (HS) which is chosen in advance. It is proved that for the implementation of an arbitrary Boolean function of n-variables (n > or = 3) by using SCA, [3L/2] hidden neurons are necessary and sufficient, where L is the number of unit spheres contained in the chosen USC of the n-dimensional HS. It is shown that by using SCA, the number of hidden neurons required is much less than that by using a two-parallel hyperplane method. In order to indicate the potential ability of three-layer BNNs, a lower bound on the required number of hidden neurons which is derived by using the method of estimating the Vapnik-Chervonenkis (VC) dimension is also given.

Neural Networks, Computer↗
PubMed2002

Patchy distribution fields: a zigzag survey design and reconstruction adequacy.

A mathematical model was used to examine the effects of a zigzag survey design on the adequacy of reconstructing patchy distribution fields. The model simulates fish or plankton patches (or gaps) of different shapes and spatial orientations, and an acoustic survey by a set of transects forming a zigzag. Adequacy of the reconstructed fields to those originally generated was evaluated by calculating their correlations (r). A priori information on the autocorrelation radius for the field in the direction of a survey (R) allows optimization of survey design and the algorithm of data analysis. A patchy field can be reconstructed properly (r > 0.80) if the distance between transects D < (1.0-1.5)R. If a priori information on the field is not available, the autocorrelation radius should be determined when reconstructing the field, i.e. a posteriori. In cases of field movement, the criterion for choosing a survey direction is based on the relationship between the dimension of moving patches in the direction of movement and that of the surveyed area. The results obtained indicate that, for a fixed transect spacing, zigzag pattern allow less adequate reconstruction of an original distribution field (in cases of both immovable and movable fields) than corresponding parallel pattern.

Acoustics↗
PubMed2006

A Bayesian framework for extracting human gait using strong prior knowledge.

Extracting full-body motion of walking people from monocular video sequences in complex, real-world environments is an important and difficult problem, going beyond simple tracking, whose satisfactory solution demands an appropriate balance between use of prior knowledge and learning from data. We propose a consistent Bayesian framework for introducing strong prior knowledge into a system for extracting human gait. In this work, the strong prior is built from a simple articulated model having both time-invariant (static) and time-variant (dynamic) parameters. The model is easily modified to cater to situations such as walkers wearing clothing that obscures the limbs. The statistics of the parameters are learned from high-quality (indoor laboratory) data and the Bayesian framework then allows us to "bootstrap" to accurate gait extraction on the noisy images typical of cluttered, outdoor scenes. To achieve automatic fitting, we use a hidden Markov model to detect the phases of images in a walking cycle. We demonstrate our approach on silhouettes extracted from fronto-parallel ("sideways on") sequences of walkers under both high-quality indoor and noisy outdoor conditions. As well as high-quality data with synthetic noise and occlusions added, we also test walkers with rucksacks, skirts, and trench coats. Results are quantified in terms of chamfer distance and average pixel error between automatically extracted body points and corresponding hand-labeled points. No one part of the system is novel in itself, but the overall framework makes it feasible to extract gait from very much poorer quality image sequences than hitherto. This is confirmed by comparing person identification by gait using our method and a well-established baseline recognition algorithm.

Algorithms↗
PubMed2005

Reconfigurable systems for sequence alignment and for general dynamic programming.

Reconfigurable systolic arrays can be adapted to efficiently resolve a wide spectrum of computational problems; parallelism is naturally explored in systolic arrays and reconfigurability allows for redefinition of the interconnections and operations even during run time (dynamically). We present a reconfigurable systolic architecture that can be applied for the efficient treatment of several dynamic programming methods for resolving well-known problems, such as global and local sequence alignment, approximate string matching and longest common subsequence. The dynamicity of the reconfigurability was found to be useful for practical applications in the construction of sequence alignments. A VHDL (VHSIC hardware description language) version of this new architecture was implemented on an APEX FPGA (Field programmable gate array). It would be several magnitudes faster than the software algorithm alternatives.

Algorithms↗