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Results for “Measuring algorithm”

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PubMed2004

Finding relevant sequences in time series containing crisp, interval, and fuzzy interval data.

Finding similar sequences in time series has received much attention and is a widely studied topic. Most existing approaches in the time series area focus on the efficiency of algorithms but seldom provide a means to handle imprecise data. In this paper, a more general approach is proposed to measure the distance of time sequences containing crisp values, intervals, and fuzzy intervals as well. The concept of distance measurement and its associated dynamic-programming-based algorithms are described. In addition to finding the sequences with similar evolving trends, a means of finding the sequences with opposite evolving tendencies is also proposed, which is usually omitted in current related research but could be of great interest to many users.

Algorithms↗

PubMed2002

Iterative reconstruction algorithm for optoacoustic imaging.

Optoacoustic imaging is based on the generation of thermoelastic stress waves by heating an object in an optically heterogeneous medium with a short laser pulse. The stress waves contain information about the distribution of structures with preferential optical absorption. Detection of the waves with an array of broadband ultrasound detectors at the surface of the medium and applying a backprojection algorithm is used to create a map of absorbed energy inside the medium. With conventional reconstruction methods a large number of detector elements and filtering of the signals are necessary to reduce backprojection artifacts. As an alternative this study proposes an iterative procedure. The algorithm is designed to minimize the error between measured signals and signals calculated from the reconstructed image. In experiments using broadband optical ultrasound detectors and in simulations the algorithm was used to obtain three-dimensional images of multiple optoacoustic sources. With signals from a planar array of 3x3 detector elements a significant improvement was observed after about 10 iterations compared to the simple radial backprojection. Compared to conventional methods using filtered backprojection, the iterative method is computationally more intensive but requires less time and instrumentation for signal acquisition.

Journal Article↗

PubMed1999

A modified definition of Sov, a segment-based measure for protein secondary structure prediction assessment.

We present a measure for the evaluation of secondary structure prediction methods that is based on secondary structure segments rather than individual residues. The algorithm is an extension of the segment overlap measure Sov, originally defined by Rost et al. (J Mol Biol 1994;235:13-26). The new definition of Sov corrects the normalization procedure and improves Sov's ability to discriminate between similar and dissimilar segment distributions. The method has been comprehensively tested during the second Critical Assessment of Techniques for Protein Structure Prediction (CASP2). Here, we describe the underlying concepts, modifications to the original definition, and their significance.

Algorithms↗

PubMed2002

Estimation of an errors-in-variables regression model when the variances of the measurement errors vary between the observations.

It is common in the analysis of aggregate data in epidemiology that the variances of the aggregate observations are available. The analysis of such data leads to a measurement error situation, where the known variances of the measurement errors vary between the observations. Assuming multivariate normal distribution for the 'true' observations and normal distributions for the measurement errors, we derive a simple EM algorithm for obtaining maximum likelihood estimates of the parameters of the multivariate normal distributions. The results also facilitate the estimation of regression parameters between the variables as well as the 'true' values of the observations. The approach is applied to re-estimate recent results of the WHO MONICA Project on cardiovascular disease and its risk factors, where the original estimation of the regression coefficients did not adjust for the regression attenuation caused by the measurement errors.

Algorithms↗

PubMed1999

Some characteristics of solid-state and photo-stimulable phosphor detectors for intra-oral radiography.

The general aim of the study was to evaluate and compare different solid-state and photo-stimulable phosphor systems for digital intra-oral radiography and to compare different generations of some of the systems. The evaluations concerned physical and psychophysical performance, subjective image quality and the influence of image processing. Physical performance was tested by means of large area transfer characteristics, noise, contrast, and modulation transfer function. For the physical performance it was found that grey level values in images from solid-state systems decreased faster with increasing exposure than in images from photo-stimulable phosphor systems. Noise increased with increased exposure for both solid-state and photo-stimulable phosphor systems. Solid-state systems reached their highest contrast index at lower doses than the photo-stimulable phosphor systems. Solid-state systems had better resolving power due to higher contrast and smaller pixel sizes than the PSP systems. The resolving power of the photo-stimulable phosphor systems improved when the images were enhanced. Psychophysical tests were performed by determining the sensitivity of the systems for detecting small mass differences in test objects. It was found that when contrast enhancement were applied lower exposures could be used to detect low contrast objects in images from both solid-state and photo-stimulable phosphor systems. Blooming effects deteriorated images from solid-state systems at lower doses than burn-out effects deteriorated conventional radiographs or images from a photo-stimulable phosphor system. Some improvement in physical and psychophysical performance could be seen in the new generation of solid-state systems. Subjective image quality was tested by visual grading analysis in which observers graded the visibility of structures important for the diagnosis of common dental diseases. All systems produced diagnostically acceptable image quality but the photo-stimulable phosphor systems over a much wider exposure range than the solid-state systems. Histogram equalization did not improve image quality. A common diagnostic task; measurement of marginal bone level around implants, was used to study the influence of image processing. Radiographic measurements of bone height around implants in images from a photo-stimulable phosphor system was as accurate and precise as film images. Image processing was found to be task dependent. For a specific task, related to marginal bone height measurements around implants, a strong edge enhancement algorithm was found to be best.

Absorptiometry, Photon↗

PubMed2005

Differences in oscillometric non-invasive blood pressure measurements recorded by different revisions of the Philips Component Monitoring System.

OBJECTIVE: To investigate whether a simulator can detect differences in oscillometric noninvasive blood pressure measurements in different revisions of the Philips Component Monitoring System. Philips revised the intraarterial-based algorithm with software revision C.0, and added an auscultation-based algorithm in revision C.1. METHODS: Three methods were adopted. Firstly, differences were assessed using the Dynatech Nevada CuffLink simulator. Five noninvasive blood pressure modules were tested on monitors with software revision C (software revision prior to C.0) and revision C.0. Monitor C.1 allows the selection of the original intraarterial algorithm (as for revision C), the improved intraarterial (revision C.0) or auscultation; two noninvasive blood pressure modules were tested on it.Secondly, pressures were recorded simultaneously from a participant's left and right arms by monitors C and C.0. The monitors were then swapped between arms and a second set of six pressures were recorded. The two sets were subtracted to calculate the differences between monitors, removing interarm differences. The experiment was carried out on two participants.Thirdly, pressures were recorded from three participants with a simultaneous reference auscultatory measurement. Six sets of simultaneous oscillometric and auscultatory determinations were recorded from monitors C and C.0. RESULTS AND CONCLUSIONS: All three methods revealed that the 'original' intraarterial-based algorithm in revision C recorded lower systolic, diastolic and mean arterial pressures than revision C.0, with the difference in diastolic pressure being the greatest. The difference in diastolic pressures between C and C.0 was up to 15 mmHg. The simulator evaluation finding of higher systolic and diastolic pressures recorded by the revised intraarterial algorithm (C.1 option 3) than by the auscultation-based algorithm (C.1 option 2) is in qualitative agreement with the regression equations of the clinical validation studies. The results suggest that simulators can identify the existence of differing algorithms used to measure blood pressure by the CMS monitor. Philips has continued to develop the algorithms used to determine the pressure by the oscillometric method. While significantly different pressures were recorded by the different revisions, it is interesting that each revision passed clinical validation studies.

Algorithms↗

PubMed1988

DESIGN: computerized optimization of experimental design for estimating Kd and Bmax in ligand binding experiments. I. Homologous and heterologous binding to one or two classes of sites.

We have developed a versatile computer program for optimization of ligand binding experiments (e.g., radioreceptor assay system for hormones, drugs, etc.). This optimization algorithm is based on an overall measure of precision of the parameter estimates (D-optimality). The program DESIGN uses an exact mathematical model of the equilibrium ligand binding system with up to two ligands binding to any number of classes of binding sites. The program produces a minimal list of the optimal ligand concentrations for use in the binding experiment. This potentially reduces the time and cost necessary to perform a binding experiment. The program allows comparison of any proposed experimental design with the D-optimal design or with assay protocols in current use. The level of nonspecific binding is regarded as an unknown parameter of the system, along with the affinity constant (Kd) and binding capacity (Bmax). Selected parameters can be fixed at constant values and thereby excluded from the optimization algorithm. Emphasis may be placed on improving the precision of a single parameter or on improving the precision of all the parameters simultaneously. We present optimal designs for several of the more commonly used assay protocols (saturation binding with a single labeled ligand, competition or displacement curve, one or two classes of binding sites), and evaluate the robustness of these designs to changes in parameter values of the underlying models. We also derive the theoretical D-optimal design for the saturation binding experiment with a homogeneous receptor class.

Binding Sites↗

PubMed2001

SVDMAN--singular value decomposition analysis of microarray data.

SUMMARY: We have developed two novel methods for Singular Value Decomposition analysis (SVD) of microarray data. The first is a threshold-based method for obtaining gene groups, and the second is a method for obtaining a measure of confidence in SVD analysis. Gene groups are obtained by identifying elements of the left singular vectors, or gene coefficient vectors, that are greater in magnitude than the threshold W N(-1/2), where N is the number of genes, and W is a weight factor whose default value is 3. The groups are non-exclusive and may contain genes of opposite (i.e. inversely correlated) regulatory response. The confidence measure is obtained by systematically deleting assays from the data set, interpolating the SVD of the reduced data set to reconstruct the missing assay, and calculating the Pearson correlation between the reconstructed assay and the original data. This confidence measure is applicable when each experimental assay corresponds to a value of parameter that can be interpolated, such as time, dose or concentration. Algorithms for the grouping method and the confidence measure are available in a software application called SVD Microarray ANalysis (SVDMAN). In addition to calculating the SVD for generic analysis, SVDMAN provides a new means for using microarray data to develop hypotheses for gene associations and provides a measure of confidence in the hypotheses, thus extending current SVD research in the area of global gene expression analysis.

Algorithms↗

PubMed2001

Novel methods for quantifying soft tissue changes after orthognathic surgery.

Laser scanners are becoming increasingly important as a tool for quantifying the outcome of facial surgery. However, few computer algorithms have been developed for this purpose. Researchers have either measured the differences in the positions of (manually located) landmarks, or have taken radial measurements of the distances between surfaces. Neither of these techniques provides satisfactory information about the shape changes between surfaces. In this paper, alternative methods are proposed and their performance is compared with that of the radial method. Tests on two patients show that the Correspondences by Sensitivity to Movement (CSM) and closest point algorithms provide the most realistic measurements of the differences between two surfaces. The CSM method was found to be useful for pinpointing areas where the shape has changed.

Adult↗

PubMed2005

Inference of missing SNPs and information quantity measurements for haplotype blocks.

MOTIVATION: Missing data in genotyping single nucleotide polymorphism (SNP) spots are common. High-throughput genotyping methods usually have a high rate of missing data. For example, the published human chromosome 21 data by Patil et al. contains about 20% missing SNPs. Inferring missing SNPs using the haplotype block structure is promising but difficult because the haplotype block boundaries are not well defined. Here we propose a global algorithm to overcome this difficulty. RESULTS: First, we propose to use entropy as a measure of haplotype diversity. We show that the entropy measure combined with a dynamic programming algorithm produces better haplotype block partitions than other measures. Second, based on the entropy measure, we propose a two-step iterative partition-inference algorithm for the inference of missing SNPs. At the first step, we apply the dynamic programming algorithm to partition haplotypes into blocks. At the second step, we use an iterative process similar to the expectation-maximization algorithm to infer missing SNPs in each haplotype block so as to minimize the block entropy. The algorithm iterates these two steps until the total block entropy is minimized. We test our algorithm in several experimental data sets. The results show that the global approach significantly improves the accuracy of the inference. AVAILABILITY: Upon request.

Algorithms↗

PubMed1983

Automated radioautographic grain counting. Correction for grain overlap.

An algorithm is described for the calculation of radioautographic cell grain count from measurements of total cell nuclear area and total grain area. This algorithm provides a statistical correction for grain overlap that is based on the solution to the occupancy problem in probability theory. This method permits the use of automated grain counting over a wide range of grain counts per cell, and extends the useful dynamic range of radioautographic grain counting to well over 200 grains/cell.

Autoradiography↗

PubMed2006

Evaluation of a commercial electron treatment planning system based on Monte Carlo techniques (eMC).

A commercial electron beam treatment planning system on the basis of a Monte Carlo algorithm (Varian Eclipse, eMC V7.2.35) was evaluated. Measured dose distributions were used for comparison with dose distributions predicted by eMC calculations. Tests were carried out for various applicators and field sizes, irregular shaped cut outs and an inhomogeneity phantom for energies between 6 Me V and 22 MeV Monitor units were calculated for all applicator/energy combinations and field sizes down to 3 cm diameter and source-to-surface distances of 100 cm and 110 cm. A mass-density-to-Hounsfield-Units calibration was performed to compare dose distributions calculated with a default and an individual calibration. The relationship between calculation parameters of the eMC and the resulting dose distribution was studied in detail. Finally, the algorithm was also applied to a clinical case (boost treatment of the breast) to reveal possible problems in the implementation. For standard geometries there was a good agreement between measurements and calculations, except for profiles for low energies (6 MeV) and high energies (18 Me V 22 MeV), in which cases the algorithm overestimated the dose off-axis in the high-dose region. For energies of 12 MeV and higher there were oscillations in the plateau region of the corresponding depth dose curves calculated with a grid size of 1 mm. With irregular cut outs, an overestimation of the dose was observed for small slits and low energies (4% for 6 MeV), as well as for asymmetric cases and extended source-to-surface distances (12% for SSD = 120 cm). While all monitor unit calculations for SSD = 100 cm were within 3% compared to measure-ments, there were large deviations for small cut outs and source-to-surface distances larger than 100 cm (7%for a 3 cm diameter cut-out and a source-to-surface distance of 10 cm).

Algorithms↗

PubMed1989

Tracking time-varying properties of the systemic vascular bed.

The problem of tracking changes in viscoelastic properties of the systemic arterial bed is considered and a recursive estimation procedure, belonging to the class of output-error algorithms with adjustable compensator, is developed and discussed. By means of computer simulations, suitable values are determined for the key design variable which controls the tradeoff between tracking ability and noise sensitivity of the algorithm. In this way, the algorithm allows on-line estimation of arterial compliance, peripheral resistance, and characteristic impedance on the basis of aortic pressure and flow signals. Furthermore, the results obtained from data numerically simulated, as well as measured on a mock circulatory system, demonstrate that the dominant arterial time-constant can be tracked by the algorithm using only measurements of the aortic pressure during diastole.

Algorithms↗

PubMed1999

Simultaneous maximum a posteriori reconstruction of attenuation and activity distributions from emission sinograms.

In order to perform attenuation correction in emission tomography an attenuation map is required. We propose a new method to compute this map directly from the emission sinogram, eliminating the transmission scan from the acquisition protocol. The problem is formulated as an optimization task where the objective function is a combination of the likelihood and an a priori probability. The latter uses a Gibbs prior distribution to encourage local smoothness and a multimodal distribution for the attenuation coefficients. Since the attenuation process is different in positron emission tomography (PET) and single photon emission tomography (SPECT), a separate algorithm for each case is derived. The method has been tested on mathematical phantoms and on a few clinical studies. For PET, good agreement was found between the images obtained with transmission measurements and those produced by the new algorithm in an abdominal study. For SPECT, promising simulation results have been obtained for nonhomogeneous attenuation due to the presence of the lungs.

Abdomen↗

PubMed1992

6R instrumented spatial linkages for anatomical joint motion measurement--Part 2: Calibration.

The six-revolute-joint instrumented spatial linkage (6R ISL) is often the measurement system of choice for monitoring motion of anatomical joints. However, due to tolerances of the linkage parameters, the system may not be as accurate as desired. A calibration algorithm and associated calibration device have been developed to refine the initial measurements of the ISL's mechanical and electrical parameters so that the measurement of six-degree-of-freedom motion will be most accurate within the workspace of the anatomical joint. The algorithm adjusts the magnitudes of selected linkage parameters to reduce the squared differences between the six known and calculated anatomical position parameters at all the calibration positions. Weighting is permitted so as to obtain a linkage parameter set that is specialized for measuring certain anatomical position parameters. Output of the algorithm includes estimates of the measuring system accuracy. For a particular knee-motion-measuring ISL and calibration device, several interdependent design parameter relationships have been identified. These interdependent relationships are due to the configuration of the ISL and calibration device, the number of calibration positions, and the limited resolution of the devices that monitor the position of the linkage joints. It is shown that if interdependence is not eliminated, then the resulting ISL parameter set will not be accurate in measuring motion outside of the calibration positions, even though these positions are within the ISL workspace.

Algorithms↗

PubMed2004

Tooth segmentation of dental study models using range images.

The accurate segmentation of the teeth from the digitized representation of a dental study model is an important component in computer-based algorithms for orthodontic feature detection and measurement and in the simulation of orthodontic procedures such as tooth rearrangement. This paper presents an automated method for tooth segmentation from the three-dimensional (3-D) digitized image captured by a laser scanner. We avoid the complexity of directly processing 3-D mesh data by proposing the innovative idea of detecting features on two range images computed from the 3-D image. The dental arch is first obtained from the plan-view range image. Using the arch as the reference, a panoramic range image of the dental model can be computed. The interstices between the teeth are detected separately in the two range images, and results from both views are combined for a determination of interstice locations and orientations. Finally, the teeth are separated from the gums by delineating the gum margin. The algorithm was tested on 34 dental models representing a variety of malocclusions and was found to be robust and accurate.

Algorithms↗

PubMed2003

Genomic expression discovery predicts pathways and opposing functions behind phenotypes.

Discovering states of genetic expression that are true to a high degree of certainty is likely to predict gene function behind biological phenotypes. The states of expression (up- or down-regulated) of 19200 cDNAs in 10 meningiomas are compared with normal brain by an algorithm that detects only 1 false measurement per 192000; 364 genes are discovered. The expression data accurately predict activation of signaling pathways and link gene function to specific phenotypes. Meningiomas appear to acquire aberrant phenotypes by disturbing the balanced expression of molecules that promote opposing functions. The findings expose interconnected genes and propose a role of genomic expression discovery in functional genomics of living systems.

Algorithms↗

PubMed1998

Analytical shape computation of macromolecules: II. Inaccessible cavities in proteins.

The structures of proteins are well-packed, yet they contain numerous cavities which play key roles in accommodating small molecules, or enabling conformational changes. From high-resolution structures it is possible to identify these cavities. We have developed a precise algorithm based on alpha shapes for measuring space-filling-based molecular models (such as van der Waals, solvent accessible, and molecular surface descriptions). We applied this method for accurate computation of the surface area and volume of cavities in several proteins. In addition, all of the atoms/residues lining the cavities are identified. We use this method to study the structure and the stability of proteins, as well as to locate cavities that could contain structural water molecules in the proton transport pathway in the membrane protein bacteriorhodopsin.

Algorithms↗