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PubMed2003

Directed geometrical worm algorithm applied to the quantum rotor model.

We discuss the implementation of a directed geometrical worm algorithm for the study of quantum link-current models. In this algorithm the Monte Carlo updates are made through the biased reptation of a worm through the lattice. A directed algorithm is an algorithm where, during the construction of the worm, the probability for erasing the immediately preceding part of the worm, when adding a new part, is minimal. We introduce a simple numerical procedure for minimizing this probability. The procedure only depends on appropriately defined local probabilities and should be generally applicable. Furthermore, we show how correlation functions C(r,tau) can be straightforwardly obtained from the probability of a worm to reach a site (r,tau) away from its starting point independent of whether or not a directed version of the algorithm is used. Detailed analytical proofs of the validity of the Monte Carlo algorithms are presented for both the directed and undirected geometrical worm algorithms. Results for autocorrelation times and Green's functions are presented for the quantum rotor model.

Journal Article↗

PubMed1997

Spiral CT artifact that simulates aortic dissection: image reconstruction with use of 180 degrees and 360 degrees linear-interpolation algorithms.

PURPOSE: To evaluate a computed tomographic (CT) artifact that simulates aortic dissection. MATERIALS AND METHODS: Two groups of 65 patients underwent spiral CT of the chest for reasons other than suspected aortic dissection. In each group, two series of images (10-mm sections) were reconstructed with use of a 180 degrees or 360 degrees linear-interpolation algorithm. Series of images were read by two radiologists, and variance between interpretations was statistically measured. RESULTS: Among series of images, artifacts were seen on 21-26 (32%-40%) with use of a 180 degrees algorithm and 41 (63%) and 44 (68%) with use of a 360 degrees algorithm. Concordance between reviewers was fair (kappa = 0.58, 0.59) or good (kappa = 0.65) with use of a 180 degrees algorithm and excellent (kappa = 0.92) with use of a 360 degrees algorithm. In one group, with use of a 180 degrees algorithm, two series of reconstructed images were separated by 5 mm; artifact was observed on seven (11%) CT studies (on both series of images) and was located along the left or left anterior side of the aorta. CONCLUSION: To reduce the frequency of a spiral CT artifact that simulates aortic dissection, two series of segmented images can be reconstructed with a change of image position along the z axis of the aorta and use of a 180 degrees linear-interpolation algorithm.

Adult↗

PubMed2002

Double three-step phase-shifting algorithm.

We describe what we believe is a new phase-shifting algorithm called a double three-step algorithm developed to reduce the measurement error of a three-dimensional shape-measurement system, which is based on digital fringe-projection and phase-shifting techniques. After comparing the performance of different existing phase-shifting algorithms, we present the new double three-step algorithm based on the error analysis of the standard three-step algorithm. In this algorithm, three-step phase shifting is done twice with an initial phase offset of 60 degrees between them, and the two obtained phase maps are averaged to generate the final phase map. Both theoretical and experimental results showed that this new algorithm worked well in significantly reducing the measurement error.

Journal Article↗

PubMed2002

Parallel image restoration with a two-dimensional likelihood-based algorithm.

We describe a pixelwise parallel algorithm for the restoration of images that have been corrupted by a low-pass optical channel and additive noise. This new algorithm is based on an iterative soft-decision method of error correction (i.e., turbo decoding) and offers performance on binary-valued imagery that is comparable to the Viterbi algorithm. We quantify the restoration performance of this new algorithm on random binary imagery for which it is superior to both the Wiener filter and the projection onto convex sets algorithms over a wide range of channels. For typical optical channels, the new algorithm is within 0.5 dB of the two-dimensional Viterbi restoration method [J. Opt. Soc. Am. A 17, 265 (2000)]. We also demonstrate the extension of our new algorithm to correlated and gray-scale images using vector quantization to mitigate the associated complexity burden. A highly parallel focal-plane implementation is also discussed, and a design study is presented to quantify the capabilities of such a VLSI hardware solution. We find that video-rate restoration on 252 x 252 pixel images is possible using current technology.

Journal Article↗

PubMed2002

Deriving inherent optical properties from water color: a multiband quasi-analytical algorithm for optically deep waters.

For open ocean and coastal waters, a multiband quasi-analytical algorithm is developed to retrieve absorption and backscattering coefficients, as well as absorption coefficients of phytoplankton pigments and gelbstoff. This algorithm is based on remote-sensing reflectance models derived from the radiative transfer equation, and values of total absorption and backscattering coefficients are analytically calculated from values of remote-sensing reflectance. In the calculation of total absorption coefficient, no spectral models for pigment and gelbstoff absorption coefficients are used. Actually those absorption coefficients are spectrally decomposed from the derived total absorption coefficient in a separate calculation. The algorithm is easy to understand and simple to implement. It can be applied to data from past and current satellite sensors, as well as to data from hyperspectral sensors. There are only limited empirical relationships involved in the algorithm, and they are for less important properties, which implies that the concept and details of the algorithm could be applied to many data for oceanic observations. The algorithm is applied to simulated data and field data, both non-case1, to test its performance, and the results are quite promising. More independent tests with field-measured data are desired to validate and improve this algorithm.

Journal Article↗

PubMed2003

Relaxed ordered-subset algorithm for penalized-likelihood image restoration.

The expectation-maximization (EM) algorithm for maximum-likelihood image recovery is guaranteed to converge, but it converges slowly. Its ordered-subset version (OS-EM) is used widely in tomographic image reconstruction because of its order-of-magnitude acceleration compared with the EM algorithm, but it does not guarantee convergence. Recently the ordered-subset, separable-paraboloidal-surrogate (OS-SPS) algorithm with relaxation has been shown to converge to the optimal point while providing fast convergence. We adapt the relaxed OS-SPS algorithm to the problem of image restoration. Because data acquisition in image restoration is different from that in tomography, we employ a different strategy for choosing subsets, using pixel locations rather than projection angles. Simulation results show that the relaxed OS-SPS algorithm can provide an order-of-magnitude acceleration over the EM algorithm for image restoration. This new algorithm now provides the speed and guaranteed convergence necessary for efficient image restoration.

Journal Article↗

PubMed1979

An algorithm for the operational assessment of adverse drug reactions. II. Demonstration of reproducibility and validity.

The reproducibility and validity of an algorithm for diagnosis of adverse drug reactions (ADRs) were tested in a clinical spectrum of 30 suspect cases. Using a questionnaire derived from the algorithm the three algorithm developers (nonexperts) agreed on the probability of ADR in 67% of cases, with pair-wise agreement varying from 73% to 87%. The pair-wise agreement of two clinical pharmacologic experts rose from 47% without the algorithm to 63% with the algorithm, with Kw, a chance-corrected index of weighted agreement, increasing from 0.26 to 0.57. The algorithmic assessments of the three nonexperts agreed with expert consensus in 80% to 83% of cases. The ADR algorithm appears to provide a reproducible and valid method of evaluating the likelihood of ADRs in individual patients. Its use can help improve the diagnostic and epidemiologic approach to these important, complex clinical phenomena.

Adult↗

PubMed1979

An algorithm for the operational assessment of adverse drug reactions. III. Results of tests among clinicians.

To determine how practicing clinicians use a recently developed algorithm for the diagnostic assessment of suspected adverse drug reactions (ADRs), eight clinicians--four board-certified, practicing physicians and four interns--rated the likelihood of 30 suspected ADRs. Each physician reviewed the case summaries, first using implicit clinical judgment and two months later by means of the ADR algorithm. The algorithm significantly improved the reproducibility of the senior clinicians' assessments as compared with their implicit assessments; however, the improvement in the interns' assessments with the algorithm was not significant. The validity of the physicians' assessments, which was measured by comparing their ratings with a consensus rating of the three algorithm developers, was also significantly improved by the use of the algorithm. When used by practicing clinicians, the algorithm improves the reproducibility and validity of their assessments of ADRs and should provide a more precise diagnostic approach to these complex clinical phenomena.

Child↗

PubMed1998

A cost-saving algorithm for children hospitalized for status asthmaticus.

OBJECTIVE: To test the ability of an assessment-driven algorithm for treatment of pediatric status asthmaticus to reduce length and cost of hospitalization. DESIGN: Nonrandomized, prospective, controlled trial. SETTING: Tertiary care children's hospital. PATIENTS: Children aged 1 to 18 years hospitalized for status asthmaticus; 104 were treated using the asthma care algorithm (intervention) and 97 using unstructured standard treatment (control). INTERVENTION: Patients were treated using either an assessment-based algorithm or standard care practices. The algorithm group was treated with standard medications (aerosolized albuterol, systemic corticosteroids, epinephrine, ipratropium) administered at a frequency driven by the patient's clinical condition. Specific criteria were outlined for decreasing or augmenting therapy, transferring to intensive care, and discharging to home. A unique patient record containing assessments, algorithm cues, and a treatment record was used. Intervention group patients were interviewed by telephone 1 week after discharge. MAIN OUTCOME MEASURES: Hospital length of stay, cost per hospitalization, relapse rate, protocol adherence. RESULTS: Average hospital stay for intervention patients was significantly shorter than for control patients (2.0 vs 2.9 days, P<.001). Although intervention patients received fewer aerosolized albuterol doses than controls, there was no difference in short-term relapse rate between groups. The intervention saved more than $700 per patient in hospital charges. Adherence to the protocol was excellent, with only 8 variances per patient stay out of more than 150 opportunities. CONCLUSION: An intensive, assessment-driven algorithm for pediatric status asthmaticus significantly reduces hospital length of stay and costs without increasing morbidity.

Adolescent↗

PubMed1996

Development of a multivariate statistical algorithm to analyze human cervical tissue fluorescence spectra acquired in vivo.

BACKGROUND AND OBJECTIVE: A general multivariate statistical algorithm has been developed to analyze the diagnostic content of cervical tissue fluorescence spectra acquired in vivo. MATERIALS AND METHODS: The primary steps of the algorithm are to: (1) preprocess the data to reduce inter-patient and intra-patient variation of tissue spectra within a diagnostic category, without a priori information, (2) dimensionally reduce the preprocessed fluorescence emission spectrum with minimal information loss and use it to select the minimum number of the original emission variables of the fluorescence spectrum required to achieve classification with negligible decrease in predictive ability, and (3) assign a posterior probability to the diagnosis of each sample, so that samples with relative uncertain diagnosis can be reevaluated by a clinician. The algorithm was tested retrospectively and prospectively on cervical tissue spectra acquired from 476 sites from 92 patients at 337 nm excitation. RESULTS: The algorithm based on the entire fluorescence spectrum differentiates squamous intraepithelial lesions (SILs) from normal squamous epithelia and inflammation with an average sensitivity and specificity of 88% +/- 1.4 and 70% +/- 1, respectively. The average sensitivity and specificity of the identical algorithm based on intensity selected at only two emission wavelengths is 88% +/- 1.4 and 71% +/- 1.4, respectively. CONCLUSION: The multivariate statistical algorithm based on both types of spectral inputs at 337 nm excitation has a similar sensitivity and significantly improved specificity relative to colposcopy in expert hands.

Algorithms↗

PubMed1998

AmbiPack: a systematic algorithm for packing of macromolecular structures with ambiguous distance constraints.

The determination of structures of multimers presents interesting new challenges. The structure(s) of the individual monomers must be found and the transformations to produce the packing interfaces must be described. A substantial difficulty results from ambiguities in assigning intermolecular distance measurements (from nuclear magnetic resonance, for example) to particular intermolecular interfaces in the structure. Here we present a rapid and efficient method to solve the packing and the assignment problems simultaneously given rigid monomer structures and (potentially ambiguous) intermolecular distance measurements. A promising application of this algorithm is to couple it with a monomer searching protocol such that each monomer structure consistent with intramolecular constraints can be subsequently input to the current algorithm to check whether it is consistent with (potentially ambiguous) intermolecular constraints. The algorithm AmbiPack uses a hierarchical division of the search space and the branch-and-bound algorithm to eliminate infeasible regions of the space. Local search methods are then focused on the remaining space. The algorithm generally runs faster as more constraints are included because more regions of the search space can be eliminated. This is not the case for other methods, for which additional constraints increase the complexity of the search space. The algorithm presented is guaranteed to find all solutions to a predetermined resolution. This resolution can be chosen arbitrarily to produce outputs at various level of detail. Illustrative applications are presented for the P22 tailspike protein (a trimer) and portions of beta-amyloid (an ordered aggregate).

Algorithms↗

PubMed1994

Brief communication: bone remodeling rates: a test of an algorithm for estimating missing osteons.

Frost (1987a) proposed an algorithm for estimating the number of missing osteons that correspond to observed osteon population densities (OPD). Such an algorithm should allow more accurate estimates of bone remodeling rates for skeletal remains for which in vivo labeling is not possible. In order to validate the algorithm, it was tested on an autopsy sample of 44 ribs. Estimates of activation frequency (mu RC) and bone remodeling rate (Vf,r,t) using the new algorithm are in reasonable agreement with age-matched tetracycline-based values. Although mean values for activation frequencies (mu RC) and bone formation rate (Vf,r,t) generated by the algorithm were generally lower, they fell below 1 standard error for only an age category that included all ages above the 5th decade. It is now appropriate to apply the algorithm to archaeological skeletal remains.

Age Determination by Skeleton↗

PubMed1995

An evaluation of numerical integration algorithms for the estimation of the area under the curve (AUC) in pharmacokinetic studies.

Six numerical integration algorithms based on linear and log trapezoidal methods as well as four cubic-spline methods were proposed for estimation of area under the curve (AUC). These six different algorithms were implemented using IMSL/IDL command language and evaluated using data simulated under five different dosing conditions and two different sampling conditions. Comparisons between AUC estimations using these six different algorithms and the theoretical results were made in terms of both overall AUC values and the superimposability of the concentration-time profiles. In well designed studies with ample data points, the algorithm based on IMSL/IDL function CSSHAPE with concavity preservation gave the best performance. In contrast, when the frequency of blood collection was limited, the algorithm based on the log trapezoidal rule proved to be stable with reasonable accuracy, and is recommended as the practical method for numerical interpolation and integration in pharmacokinetic studies. Algorithms based on the combination of the log trapezoidal rule and cubic-spline methods using IMSL/IDL function CSSHAPE can be developed to enhance overall performance.

Algorithms↗

PubMedDate not supplied

The sampling properties of some distance geometry algorithms applied to unconstrained polypeptide chains: a study of 1830 independently computed conformations.

In this paper we study the statistical geometry of ensembles of poly (L-alanine) conformations computed by several different distance geometry algorithms. Since basic theory only permits us to predict the statistical properties of such ensembles a priori when the distance constraints have a very simple form, the only constraints used for these calculations are those necessary to obtain reasonable bond lengths and angles, together with a lack of short- and long-range atomic overlaps. The geometric properties studied include the squared end-to-end distance and radius of gyration of the computed conformations, in addition to the usual rms coordinate and phi/psi angle deviations among these conformations. The distance geometry algorithms evaluated include several variations of the well-known embed algorithm, together with optimizations of the torsion angles using the ellipsoid and variable target function algorithms. The conclusions may be summarized as follows: First, the distribution with which the trial distances are chosen in most implementations of the embed algorithm is not appropriate when no long-range upper bounds on the distances are present, because it leads to unjustifiably expanded conformations. Second, chosing the trial distances independently of one another leads to a lack of variation in the degree of expansion, which in turn produces a relatively low rms square coordinate difference among the members of the ensemble. Third, when short-range steric constraints are present, torsion angle optimizations that start from conformations obtained by choosing their phi/psi angles randomly with a uniform distribution between -180 degrees and +180 degrees do not converge to conformations whose angles are uniformly distributed over the sterically allowed regions of the phi/psi plane. Finally, in an appendix we show how the sampling obtained with the embed algorithm can be substantially improved upon by the proper application of existing methodology.

Algorithms↗

PubMed2002

Spatial independent component analysis of functional MRI time-series: to what extent do results depend on the algorithm used?

Independent component analysis (ICA) has been successfully employed to decompose functional MRI (fMRI) time-series into sets of activation maps and associated time-courses. Several ICA algorithms have been proposed in the neural network literature. Applied to fMRI, these algorithms might lead to different spatial or temporal readouts of brain activation. We compared the two ICA algorithms that have been used so far for spatial ICA (sICA) of fMRI time-series: the Infomax (Bell and Sejnowski [1995]: Neural Comput 7:1004-1034) and the Fixed-Point (Hyvärinen [1999]: Adv Neural Inf Proc Syst 10:273-279) algorithms. We evaluated the Infomax- and Fixed Point-based sICA decompositions of simulated motor, and real motor and visual activation fMRI time-series using an ensemble of measures. Log-likelihood (McKeown et al. [1998]: Hum Brain Mapp 6:160-188) was used as a measure of how significantly the estimated independent sources fit the statistical structure of the data; receiver operating characteristics (ROC) and linear correlation analyses were used to evaluate the algorithms' accuracy of estimating the spatial layout and the temporal dynamics of simulated and real activations; cluster sizing calculations and an estimation of a residual gaussian noise term within the components were used to examine the anatomic structure of ICA components and for the assessment of noise reduction capabilities. Whereas both algorithms produced highly accurate results, the Fixed-Point outperformed the Infomax in terms of spatial and temporal accuracy as long as inferential statistics were employed as benchmarks. Conversely, the Infomax sICA was superior in terms of global estimation of the ICA model and noise reduction capabilities. Because of its adaptive nature, the Infomax approach appears to be better suited to investigate activation phenomena that are not predictable or adequately modelled by inferential techniques.

Adult↗

PubMedDate not supplied

Using algorithms in rehabilitation nursing: an educational strategy.

The purpose of this article is to describe the use of algorithms in the specialty practice of rehabilitation nursing. Algorithms are particularly useful for the nurse who is new to rehabilitation because they can offer guidance in some important aspects of clinical decision making. In this article, the authors include information on the historical uses of algorithms, the benefits of using algorithms, and the ways in which algorithms are developed. Examples are also included, and suggestions for further development of algorithms in rehabilitation nursing are proposed.

Algorithms↗

PubMedDate not supplied

Correspondence of closest gradient voxels--a robust registration algorithm.

A robust, automatic volume registration algorithm based on intensity gradients is presented. This algorithm can successfully perform registrations under conditions of unrelated intervolume voxel intensities, significant object displacements, and/or significant amounts of missing data. It also allows the user to visualize the registration convergence, clearly illustrating any source of registration errors. This algorithm consists of a matching algorithm based on iteratively finding the correspondence of the closest voxels containing a high three-dimensional intensity gradient magnitude. This algorithm was tested by registering T2-weighted MR volumes that had undergone varying displacement transformations to simultaneously acquired proton-density volumes. These transformations involved rotations of up to 25 degrees followed by translations of up to 25 mm along the axis of rotation. For all registrations, the mean registration error was less than one-fifth of a voxel and the mean registration time was less than 30 minutes. In conclusion, this algorithm is shown to be a powerful method of sequence-independent MR volume registration that is simple to both use and understand.

Algorithms↗

PubMed2003

Deconvolution algorithm based on automatic cutoff frequency selection for EPR imaging.

The large line-width associated with electron paramagnetic resonance imaging (EPRI) requires effective algorithms to deconvolve the true spatial profiles of spins from the measured projection data. The commonly used Fourier transform (FT) deconvolution algorithm is easy to implement but suffers from the division-by-zero problem. As a result, a couple of parameters are used to control the deconvolution performance. However, this is inconvenient and the deconvolution results are subject to the experience of the operators. In the present work we examined FT deconvolution for EPRI, and proposed an automatic algorithm to determine the cutoff frequency by calculating the piecewise variance of the division result of the Fourier amplitude spectra. The deconvolution algorithm and the filtered back-projection image reconstruction algorithm were implemented and validated using 3D phantom and in vivo imaging data. It was clearly observed that the image resolution improved after deconvolution with the proposed algorithm.

Algorithms↗