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PubMed2005

Removal of eye blinking artifact from the electro-encephalogram, incorporating a new constrained blind source separation algorithm.

A robust constrained blind source separation (CBSS) algorithm has been developed as an effective means to remove ocular artifacts (OAs) from electro-encephalograms (EEGs). Currently, clinicians reject a data segment if the patient blinked or spoke during the observation interval. The rejected data segment could contain important information masked by the artifact. In the CBSS technique, a reference signal was exploited as a constraint. The constrained problem was then converted to an unconstrained problem by means of non-linear penalty functions weighted by the penalty terms. This led to the modification of the overall cost function, which was then minimised with the natural gradient algorithm. The effectiveness of the algorithm was also examined for the removal of other interfering signals such as electrocardiograms. The CBSS algorithm was tested with ten sets of data containing OAs. The proposed algorithm yielded, on average, a 19% performance improvement over Parra's BSS algorithm for removing OAs.

Algorithms↗

PubMed1993

In vitro comparison of different signal processing algorithms used in laser Doppler flowmetry.

The paper reports the results of investigations comparing the relative in vitro responses of different signal processing algorithms commonly employed in laser Doppler flowmetry (LDF). A versatile laser Doppler system is described which enabled complex signal processing to be implemented relatively simply using digital analysis. The flexibility of the system allowed a variety of processing algorithms to be studied by simply characterising the algorithm of interest under software control using a personal computer. An in vitro physical model is also presented which was used to maintain reproducible fluid flows. Flows of particles were studied in a physical model using both a near-infra-red (NIR) diode and an He/Ne laser source. The results show that frequency-weighted algorithms are responsive to both particle velocity and concentration, whereas non-weighted algorithms respond to concentration only. The linearity of the velocity response is critically dependent on both the dimensions of the in vitro model and the frequency bandwidth of the signal-processing algorithm.

Algorithms↗

PubMed2001

[Mode-switching algorithms: programming and usefulness].

BACKGROUND: Automatic mode switching is defined as the ability of a pacemaker to reprogram itself from tracking to non-tracking mode in response to atrial tachyarrhythmias, and to regain tracking mode as soon as the tachyarrhythmia terminates. In contrast to upper rate behavior, mode switching does not only limit atrial tracking at a certain rate but actively drives the ventricular pacing rate back to lower rate or sensor rate as long as the atrial tachyarrhythmia persists. In contrast to DDD with mode switch, AV synchrony may be lost in DDIR mode if the sinus rate exceeds the sensor rate. DDD pacing with mode switching represents a valuable option in patients with AV block and paroxysmal atrial tachyarrhythmias. It may prevent the transition from paroxysmal to permanent atrial fibrillation after AV node ablation to a higher extent than VVI(R) pacing. On the other hand, patients with sinus node disease and normal AV conduction may benefit from DDIR mode with long AV interval. Mode switching should provide a rapid, sensitive and specific detection of atrial tachyarrhythmias, fast switch to non-tracking mode without ventricular pacing at the upper rate limit, adequate ventricular rate during the atrial tachyarrhythmia, rapid, sensitive and specific detection of conversion to sinus rhythm and fast switch back to tracking mode. In addition, oscillations between DDD and DDI mode with sudden ventricular rate changes should be avoided. MODE-SWITCHING ALGORITHMS: To achieve these aims, different mode-switching algorithms have been developed which all show specific disadvantages: reliable but slow response to atrial tachyarrhythmias, fast but unspecific switch to non-tracking mode, mode oscillations, inclination to inadequate mode-switching due to ventricular far-field sensing, failure to perform modeswitching during atrial flutter or intermittent atrial undersensing. Some of these problems can be avoided by careful atrial lead implantation providing atrial signals above 2 mV and avoiding ventricular far-field signals. Programming of mode-switching related parameters (e.g. atrial rate and number of fast beats required for mode switch), atrial blanking times, and atrial sensitivity can solve some of the problems with mode switching. Clinical results show a strong influence of device programming and atrial undersensing on mode-switching performance. Some data suggest a superiority of fast mode-switching algorithms with regard to clinical symptoms. However, loss of AV synchrony during sinus rhythm due to premature or inadequate mode switching may limit the benefit of fast mode switching. FURTHER DEVELOPMENTS: Improved performance may be achieved by a combination of different mode-switching algorithms (e.g. one algorithm for detection of atrial fibrillation, another one for detection of atrial flutter). In addition, programmability of several algorithms (e.g. mean atrial rate, beat-to-beat, x out of y) within the same device and atrial cycle-dependent sensitivity adjustment similar to automatic gain control in implantable defibrillators may further increase the clinical use of automatic mode switching.

Algorithms↗

PubMed2003

[Comparison of algorithms for management of the difficult airway].

Management of the difficult airway and maintenance of the oxygenation are the most important tasks of the anaesthetist. Respiratory problems are still the most important single cause for anaesthesia-related accidents with poor outcome. Algorithms are step-wise procedures developed from a great number of recommendations and are well suited to automation and training procedures. There is strong agreement among consultants that specific strategies lead to improved outcome, although, strictly speaking the degree of benefit on airway management cannot be clearly determined. Several anaesthesia societies, including the American Society of Anesthesiology,have developed their own algorithms for management of the difficult airway. The comparison of published algorithms shows that the management of the anticipated difficult airway has to be performed in the awake patient and fiberoptic intubation is a crucial part of that procedure. There are different techniques (different blades, guide wire, laryngeal mask, fiber optics) for the management of the unanticipated difficult airway. The laryngeal mask, transtracheal access and the Combitube are recommended for the management of the cannot intubate, cannot ventilate situation. More important than the questions which algorithm, which technique and which instruments should be used,is that each department has and practices its own algorithm. This strongly depends on local circumstances and personal preferences. Daily practice is the condition for the successful use in an emergency situation. The management is easier if one uses a simple algorithm and as few instruments as possible.

Algorithms↗

PubMed2000

Interest of the ordered subsets expectation maximization (OS-EM) algorithm in pinhole single-photon emission tomography reconstruction: a phantom study.

Pinhole single-photon emission tomography (SPET) has been proposed to improve the trade-off between sensitivity and resolution for small organs located in close proximity to the pinhole aperture. This technique is hampered by artefacts in the non-central slices. These artefacts are caused by truncation and by the fact that the pinhole SPET data collected in a circular orbit do not contain sufficient information for exact reconstruction. The ordered subsets expectation maximization (OS-EM) algorithm is a potential solution to these problems. In this study a three-dimensional OS-EM algorithm was implemented for data acquired on a single-head gamma camera equipped with a pinhole collimator (PH OS-EM). The aim of this study was to compare the PH OS-EM algorithm with the filtered back-projection algorithm of Feldkamp, Davis and Kress (FDK) and with the conventional parallel-hole geometry as a whole, using a line source phantom, Picker's thyroid phantom and a phantom mimicking the human cervical column. Correction for the angular dependency of the sensitivity in the pinhole geometry was based on a uniform flood acquisition. The projection data were shifted according to the measured centre of rotation. No correction was made for attenuation, scatter or distance-dependent camera resolution. The resolution measured with the line source phantom showed a significant improvement with PH OS-EM as compared with FDK, especially in the axial direction. Using Picker's thyroid phantom, one iteration with eight subsets was sufficient to obtain images with similar noise levels in uniform regions of interest to those obtained with the FDK algorithm. With these parameters the reconstruction time was 2.5 times longer than for the FDK method. Furthermore, there was a reduction in the artefacts caused by the circular orbit SPET acquisition. The images obtained from the phantom mimicking the human cervical column indicated that the improvement in image quality with PH OS-EM is relevant for future clinical use and that the improvements obtained using the OS-EM algorithm are more significant for the pinhole geometry than for the conventional parallel-hole geometry. We conclude that PH OS-EM is a practical and promising alternative for pinhole SPET reconstruction.

Algorithms↗

PubMed2004

Multi-detector row computed tomography of the heart: does a multi-segment reconstruction algorithm improve left ventricular volume measurements?

A multi-segment cardiac image reconstruction algorithm in multi-detector row computed tomography (MDCT) was evaluated regarding temporal resolution and determination of left ventricular (LV) volumes and global LV function. MDCT and cine magnetic resonance (CMR) imaging were performed in 12 patients with known or suspected coronary artery disease. Patients gave informed written consent for the MDCT and the CMR exam. MDCT data were reconstructed using the standard adaptive cardiac volume (ACV) algorithm as well as a multi-segment algorithm utilizing data from three, five and seven rotations. LV end-diastolic (LV-EDV) and end-systolic volumes and ejection fraction (LV-EF) were determined from short-axis image reformations and compared to CMR data. Mean temporal resolution achieved was 192+/-24 ms using the ACV algorithm and improved significantly utilizing the three, five and seven data segments to 139+/-12, 113+/-13 and 96+/-11 ms (P<0.001 for each). Mean LV-EDV was without significant differences using the ACV algorithm, the multi-segment approach and CMR imaging. Despite improved temporal resolution with multi-segment image reconstruction, end-systolic volumes were less accurately measured (mean differences 3.9+/-11.8 ml to 8.1+/-13.9 ml), resulting in a consistent underestimation of LV-EF by 2.3-5.4% in comparison to CMR imaging (Bland-Altman analysis). Multi-segment image reconstruction improves temporal resolution compared to the standard ACV algorithm, but this does not result in a benefit for determination of LV volume and function.

Adult↗

PubMed2005

The centroidal algorithm in molecular similarity and diversity calculations on confidential datasets.

Chemical structure provides exhaustive description of a compound, but it is often proprietary and thus an impediment in the exchange of information. For example, structure disclosure is often needed for the selection of most similar or dissimilar compounds. Authors propose a centroidal algorithm based on structural fragments (screens) that can be efficiently used for the similarity and diversity selections without disclosing structures from the reference set. For an increased security purposes, authors recommend that such set contains at least some tens of structures. Analysis of reverse engineering feasibility showed that the problem difficulty grows with decrease of the screen's radius. The algorithm is illustrated with concrete calculations on known steroidal, quinoline, and quinazoline drugs. We also investigate a problem of scaffold identification in combinatorial library dataset. The results show that relatively small screens of radius equal to 2 bond lengths perform well in the similarity sorting, while radius 4 screens yield better results in diversity sorting. The software implementation of the algorithm taking SDF file with a reference set generates screens of various radii which are subsequently used for the similarity and diversity sorting of external SDFs. Since the reverse engineering of the reference set molecules from their screens has the same difficulty as the RSA asymmetric encryption algorithm, generated screens can be stored openly without further encryption. This approach ensures an end user transfers only a set of structural fragments and no other data. Like other algorithms of encryption, the centroid algorithm cannot give 100% guarantee of protecting a chemical structure from dataset, but probability of initial structure identification is very small-order of 10(-40) in typical cases.

Algorithms↗

PubMed2005

Randomized and parallel algorithms for distance matrix calculations in multiple sequence alignment.

Multiple sequence alignment (MSA) is a vital problem in biology. Optimal alignment of multiple sequences becomes impractical even for a modest number of sequences since the general version of the problem is NP-hard. Because of the high time complexity of traditional MSA algorithms, even today's fast computers are not able to solve the problem for large number of sequences. In this paper we present a randomized algorithm to calculate distance matrices, which is a major step in many multiple sequence alignment algorithms. The basic idea employed is sampling (along the lines of). We also illustrate how to parallelize this algorithm. In Section we introduce the problem of multiple sequence alignments. In Section we provide a discussion on various methods that have been employed in the literature for Multiple Sequence Alignment. In this section we also introduce our new sampling approach. We extend our randomized algorithm to the case of non-uniform length sequences as well. We show that our algorithms are amenable to parallelism in Section. In Section we back up our claim of speedup and accuracy with empirical data and examples. In Section we provide some concluding remarks.

Algorithms↗

PubMed1992

An endoscopic retrograde cholangiopancreatography (ERCP)-based algorithm for the management of pancreatic pseudocysts.

In the treatment of pancreatic pseudocysts, percutaneous and endoscopic drainage have, in certain cases, become alternatives to surgery. However, each treatment modality carries risks of complications and recurrences that may be minimized by the appropriate allocation of therapy. This article proposes the use of an endoscopic retrograde cholangiopancreatography (ERCP)-based algorithm as a means to allocate pseudocyst therapy based on the findings of pancreatic duct obstruction or pseudocyst communication. To evaluate this algorithm, the records of a series of patients with pancreatic pseudocysts seen at Duke University Medical Center from 1984 to 1990 were reviewed. Of 102 patients, 73 had symptomatic pseudocysts that required treatment. Forty of the 69 elective interventions were preceded by ERCPs and retrospectively applied to the algorithm. The number of adverse outcomes (treatment failures + complications) of the group that followed the algorithm was 3 of 26 (12%), while the number of adverse outcomes of the group that did not follow the algorithm was 6 of 14 (43%) (p less than 0.04 by Fisher's exact test). These two subgroups were similar in all other characteristics examined. Therefore, this ERCP-based algorithm may be used to allocate pseudocyst treatment; however, a prospective trial is necessary to prove its efficacy.

Algorithms↗

PubMed1991

A parallelizing algorithm for computing solutions to arbitrarily branched cable neuron models.

An algorithm for the solution of branching one-dimensional cable neuron models is presented. The algorithm is based on solving the finite-difference approximations to a cable or compartmental model of a neuron with a time implicit integration scheme. The algorithm solves the linear system of equations that must be solved at each time step with implicit algorithms via an "exact domain decomposition." This domain decomposition allows the solution of the unbranched and branching regions of the neuron to be done separately and permits a wide variety of possible implementations on parallel computers. Similarly, the separation of the straight and branched regions allows the solution of these two problems to be accomplished with linear system algorithms optimized for each class of problems. In contrast to other widely used methods (Hines, M. (1984) Int. J. Biomed. Comput., 15: 69-75), this algorithm can be used with arbitrary branching geometries, even those which contain closed loops.

Algorithms↗

PubMed1993

Algorithms for detection and measurement of spontaneous events.

The development of the personal computer and its mass storage capabilities has enabled long-term digitization of voltage records at high sampling rates. This paper presents a program that employs algorithms to analyze a sampled record for spontaneously occurring events. A detection algorithm employs amplitude and temporal parameters to identify the onsets of these events. Other algorithms then characterize size and shape features of these events. Examples of the results of these algorithms are given for intracellularly recorded excitatory postsynaptic potentials (EPSPs). These algorithms permit rapid and accurate quantitation of tens of thousands of events that may occur over many minutes. It is suggested that this set of algorithms may be applied to biological events other than synaptic potentials.

Algorithms↗

PubMed1994

An algorithm to detect low incidence arrhythmic events in electrocardiographic records from ambulatory patients.

An algorithm was devised to detect low incidence arrhythmic events in electrocardiograms obtained during ambulatory monitoring. The algorithm incorporated baseline correction and R wave detection. The RR interval was used to identify tachycardia, bradycardia, and premature ventricular beats. Only a few beats before and after the arrhythmic event were stored. The software was evaluated on a prototype hardware system which consisted of an Intel 86/30 single board computer with a suitable analog pre-processor and an analog to digital converter. The algorithm was used to determine the incidence and type of arrhythmia in records from an ambulatory electrocardiogram (ECG) database and from a cardiac exercise laboratory. These results were compared to annotations on the records which were assumed to be correct. Standard criteria used previously to evaluate algorithms designed for arrhythmia detection were sensitivity, specificity, and diagnostic accuracy. Sensitivities ranging from 77 to 100%, specificities from 94 to 100%, and diagnostic accuracies from 92 to 100% were obtained on the different data sets. These results compare favourably with published results based on more elaborate algorithms. By circumventing the need to make a continuous record of the ECG, the algorithm could form the basis for a compact monitoring device for the detection of arrhythmic events which are so infrequent that standard 24-h Holter monitoring is insufficient.

Algorithms↗

PubMed1996

Implementation of OSPOP, an algorithm for the estimation of optimal sampling times in pharmacokinetics by the ED, EID and API criteria.

The most common approach to optimize the sampling schedule in parameter estimation experiments is the D-optimality criterion, which consists in maximizing the determinant of the Fisher information matrix (max det F). In order to incorporate prior parameter uncertainty in the optimal design, other criteria have been proposed: The ED = max E (det F), EID = min E (l/det F) and API = max E (log det F) criteria, where the expectation is with respect to the given prior distribution of the parameters. Previously described algorithm for the estimation of optimal sampling times according to these criteria are adaptive random search (ARS), a robust and global but slow optimizer for API, and stochastic gradient (SG), a fast but local optimizer for ED and EID. We implemented an algorithm named OSPOP 1.0, based on non-adaptive random search (RS) followed by stochastic gradient to determine optimal sampling times for parameter estimation in various pharmacokinetic models according to ED, EID and API criteria. Prior distributions are allowed to be uniform, normal or lognormal. This algorithm combines the robustness of RS and the speediness of SG (convergence is obtained in a few minutes on a microcomputer). The results of the SG algorithm have been compared to those described in the literature using the ARS algorithm on a one compartment model with first- order absorption and were very similar. Also, the CPU time needed by SG and ARS algorithms were compared and the former proved to be much faster. Then, it has been applied to a five parameters stochastic model with zero-order absorption rate and Weibull-distributed residence times which was shown to describe adequately the kinetics of metacycline in humans. Population pharmacokinetic parameters of metacycline were estimated from a six subject pilot study, by the iterative two-staged method, using ADAPT II repeatedly. Optimal sampling times were determined with each criterion (ED, EID, API) with a multivariate normal prior parameter distribution. Six to seven distinct sampling times could be estimated. Higher numbers of samples revealed coalescing of design points.

Algorithms↗

PubMed1994

Evolutionary algorithms and a fractal inverse problem.

Over the past 30 years, algorithms that model natural evolution have generated robust search methods. These so-called evolutionary algorithms have been successfully applied to a wide range of problems. This paper discusses two types of evolutionary algorithms and their application to a problem in shape representation. Genetic algorithms and evolutionary programming, although both based on evolutionary principles, each place different emphasis on what drives the evolutionary process. While genetic algorithms rely on mimicking specific genotypic transformations, evolutionary programming emphasizes phenotypic adaptation. Results presented show the success of evolutionary programming in solving an example of a fractal inverse problem, but indicate that a genetic algorithm is not as successful. Reasons for this disparity are discussed.

Algorithms↗

PubMed1995

An iterative filtered backprojection inverse treatment planning algorithm for tomotherapy.

PURPOSE: An inverse treatment planning algorithm for tomotherapy is described. METHODS AND MATERIALS: The algorithm iteratively computes a set of nonnegative beam intensity profiles that minimizes the least-square residual dose defined in the target and selected normal tissue regions of interest. At each iteration the residual dose distribution is transformed into a set of residual beam profiles using an inversion method derived from filtered backprojection image reconstruction theory. These "residual" profiles are used to correct the current beam profile estimates resulting in new profile estimates. Adaptive filtering is incorporated into the inversion model so that the gross structure of the dose distribution is optimized during initial iterations of the algorithm, and the fine structure corresponding to edges is obtained at later iterations. A three dimensional, kernel based, convolutions/superposition dose model is used to compute dose during each iteration. RESULTS: Two clinically relevant treatment planning examples are presented illustrating the use of the algorithm for planning conformal radiotherapy of the breast and the prostate. Solutions are generally achieved in 10-20 iterations requiring about 20 h of CPU time using a midrange workstation. The majority of the calculation time is spent on the three-dimensional dose calculation. CONCLUSIONS: The inverse treatment planning algorithm is a useful research tool for exploring the potential of tomotherapy for conformal radiotherapy. Further work is needed to (a) achieve clinically acceptable computation times; (b) verify the algorithm using multileaf collimator technology; and (c) extend the method to biological objectives.

Algorithms↗

PubMedDate not supplied

SiMCAL 1 algorithm for analysis of gene expression data related to the phosphatidylserine receptor.

OBJECTIVE: SiMCAL 1 (simple multilevel clustering and linking, version 1) is a novel clustering algorithm for time-series microarray data, presented here with an application to a specific data set. The purpose of the algorithm is to present a complete feature set not found in either Jarvis-Patrick clustering, from which it is derived, or in other popular clustering methods such as hierarchical and k-means. The data concern the activity of the phosphatidylserine receptor (PSR) which is believed to be a crucial molecular switch in the mediation of inflammatory response in apoptosis and lysis. By analyzing the behavior of PSR-related genes in mouse macrophages, we hope to elucidate the mechanisms involved in this important biological process. METHODS AND MATERIALS: SiMCAL 1 is implemented in the Python programming language using the Numerical Python extensions, and the data are stored using the MySQL database management system. The data are derived from exposures of multiple Affymetrix mouse gene microarray chips to elevated levels of PSR antibody and control conditions. Code and data are available at (accessed: 17 January 2005). RESULTS: The algorithm meets its objectives: it is simple, in that it is computationally inexpensive; it is multilevel, in that it provides a small number of clearly defined hierarchical levels of clusters; and it offers linking between clusters at the same level in each hierarchy. Clustering and linking results indicate previously unknown co-regulation for genes expressing PGH synthase (COX2) and PGE2, appear to confirm increased production of proteins for clearance of apoptotic cells in the presence of PSR antibody, and correspond to other findings regarding the temporal relationship between PGE2 production and B cell proliferation and differentiation. These results are promising but should be taken as highly preliminary. CONCLUSION: Both the algorithm and its application to this problem show great potential for future development. We plan to improve and extend the SiMCAL family of algorithms, and to obtain new data so that the algorithm(s) may be further applied to this and other problems of interest.

Algorithms↗

PubMed2005

Evaluation of the DotMap algorithm for locating analytes of interest based on mass spectral similarity in data collected using comprehensive two-dimensional gas chromatography coupled with time-of-flight mass spectrometry.

Comprehensive two-dimensional gas chromatography coupled with time-of-flight mass spectrometry (GC x GC-TOF-MS) is a highly selective technique ideal for the analysis of complex mixtures. The instrument yields an abundance of data, with complete mass spectral scans at every time point in the GC x GC separation space. The development and application of appropriate tools for data mining is essential in making sense of the wealth of information available. An algorithm for locating analytes of interest based on mass spectral similarity in GC x GC-TOF-MS data, called DotMap, has been previously reported and is rigorously evaluated herein. A thorough investigation into the performance characteristics of DotMap, including the performance near the limit of detection and dynamic range of the algorithm as well as the capacity of the algorithm to deal with peak overlap, is investigated using jet fuel as a complex sample matrix. For instance, the algorithm can successfully identify a spiked compound at the single microg/ml level in a jet fuel sample with an overlapping interferent. The performance of the DotMap algorithm in situations with very limited mass spectral selectivity, specifically in the evaluation of spectra from isomer compounds, as well as the ability to tune DotMap results to provide the location of a specific analyte or of a class of compounds is demonstrated. The DotMap algorithm is demonstrated to be a sensitive tool that is useful in the analysis of complex mixtures and which possesses the capacity to be easily "tuned" to discern the location of analytes of interest.

Algorithms↗

PubMed2004

Seizure detection: evaluation of the Reveal algorithm.

OBJECTIVE: The aim of this study is to evaluate an improved seizure detection algorithm and to compare with two other algorithms and human experts. METHODS: 672 seizures from 426 epilepsy patients were examined with the (new) Reveal algorithm which utilizes 3 methods, novel in their application to seizure detection: Matching Pursuit, small neural network-rules and a new connected-object hierarchical clustering algorithm. RESULTS: Reveal had a sensitivity of 76% with a false positive rate of 0.11/h. Two other algorithms (Sensa and CNet) were tested and had sensitivities of 35.4 and 48.2% and false positive rates of 0.11/h and 0.75/h, respectively. CONCLUSIONS: This study validates the Reveal algorithm, and shows it to compare favorably with other methods. SIGNIFICANCE: Improved seizure detection can improve patient care in both the epilepsy monitoring unit and the intensive care unit.

Adolescent↗