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PubMed1995

An innovative dicrotic notch detection algorithm which combines rule-based logic with digital signal processing techniques.

Automated, real-time localization of the dicrotic notch, a component of the arterial pressure waveform, represents a deceptively complex problem in computerized biomedical signal processing. The high-frequency nature of the notch can make it difficult to distinguish from artifactual noise or from other high-frequency physiological components of the waveform. In addition, the contour of the notch varies with vascular status and with propagation through arterial beds, requiring any detection algorithm to recognize various possible notch conformations. Finally, location of the notch along the waveform may vary widely depending on other hemodynamic variables, further complicating detection algorithms. We have reviewed various published algorithms and have implemented a number of them to determine the strengths and shortcomings of each. We then developed a reliable and accurate hybrid algorithm which utilizes the strengths of the various algorithmic approaches reviewed; after analyzing the waveform, the algorithm selects the most appropriate method for accurate notch localization based on a series of waveform features. The application of rule-based logic represents a relatively unique approach to digital signal processing.

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PubMed2000

A decentralized multichannel length transformation algorithm and its parallel implementation for real-time ECG monitoring.

Multichannel algorithms have been developed for more accurate analysis of electrocardiograms (ECGs). Their benefit is the ability to use the information contained in all simultaneously acquired channels. In this paper we present a multichannel version of a nonsyntactic algorithm, based on length transformation. The proposed algorithm uses a decentralized schema for combining the results derived from each individual lead, instead of a global/centralized one (a spatial vector approach). Its performance was evaluated using the CSE database and real ECGs acquired by a 12-lead cardiograph. The results are also compared with previous-single-channel and multichannel-versions of the algorithm, showing a better performance. Since a multichannel algorithm is always a time-consuming task, it is rarely used in real-time monitoring systems. Motivated by this observation, we designed a parallel implementation of the proposed algorithm and tested its ability to be used in such systems.

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PubMed1996

Multiple sequence information for threading algorithms.

Threading algorithms attempt to solve the inverse protein folding problem: given a group of structures and a sequence, identify the structure that is most compatible with this sequence. A recent study of this class of algorithms by S. J. Wodak and colleagues suggests that while threading algorithms are capable of recognizing many folding motifs, their performance in truly blind predictions is disappointing, and the underlying alignments upon which the selections are based are frequently errant. To help overcome this problem we have developed a Test of Optimal Mutagenesis algorithm (TOM) that exploits information inherent in the variation between several homologues in a multiple sequence alignment. This information is used to help select the correct structural motif for the sequence from a database of known structures. A total of 305 high-resolution structures were selected to represent the set of known folds; 56 proteins were chosen that had at least one close structural match in this set. To test TOM, we attempted to determine which of the 305 folds was a match to each of the 56 protein sequences. TOM correctly predicts a close structural match for 45% of these proteins. THREADER, an algorithm chosen as a literature standard, correctly matched 20% of the test set. By comparing the performance of TOM, THREADER, and TOM NOVAR (a version of TOM without variability information), we conclude that the tendency of an amino acid to be buried or exposed is the dominant determinant of the success of threading algorithms. In addition, the structural alignments produced by TOM suggest that the exact alignment of just 30 to 50% of the residues in a sequence with the correct fold is necessary to select it as the highest scoring match in a set of folds.

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PubMed1992

A motion correction algorithm for an image realignment programme useful for sequential radionuclide renography.

The correction of organ movements in sequential radionuclide renography was done using an iterative algorithm that, by means of a set of rectangular regions of interest (ROIs), did not require any anatomical marker or manual elaboration of frames. The realignment programme here proposed is quite independent of the spatial and temporal distribution of activity and analyses the rotational movement in a simplified but reliable way. The position of the object inside a frame is evaluated by choosing the best ROI in a set of ROIs shifted 1 pixel around the central one. Statistical tests have to be ful-filled by the algorithm in order to activate the realignment procedure. Validation of the algorithm was done for different acquisition set-ups and organ movements. Results, summarized in Table 1, show that in about 90% of the simulated experiments the algorithm is able to correct the movements of the object with a maximum error less or equal to 1 pixel limit. The usefulness of the realignment programme was demonstrated with sequential radionuclide renography as a typical clinical application. The algorithm-corrected curves of a 1-year-old patient were completely different from those obtained without a motion correction procedure. The algorithm may be applicable also to other types of scintigraphic examinations, besides functional imaging in which the realignment of frames of the dynamic sequence was an intrinsic demand.

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PubMed1994

An evaluation of the accelerated expectation maximization algorithms for single-photon emission tomography image reconstruction.

We previously reported that brain single-photon emission tomography (SPET) images could be improved by using an attenuation coefficient map constructed with transmission data and the iterative expectation maximization (EM) algorithm. However, the conventional EM algorithm (CEM) typically requires 30-80 iterations to provide acceptable results, limiting its clinical applicability. Several methods have been proposed to accelerate the EM algorithm. The purpose of this study was to search for a practical method for accelerating the EM algorithm. The methods investigated here include the accelerated EM algorithm (ACEM) using additive correction, ACEM using multiplicative correction, and Tanaka's filtered iterative reconstruction method (FIR). These methods were assessed by simulated SPET studies of a phantom incorporating nonuniform attenuation and by reference to clinical brain SPET data. In the simulation studies, the above methods were evaluated by using three parameters (root mean square error, log likelihood value, and contrast recovery coefficient); the results showed that FIR had an advantage over other methods in terms of all parameters. The results obtained using the clinical data demonstrated that FIR could reconstruct acceptable images in only five iterations. These results show that FIR offers significant advantages over CEM or other ACEMs, indicating that FIR can make the EM algorithm practical for clinical use in SPET.

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PubMed1995

Classification-algorithm evaluation: five performance measures based on confusion matrices.

OBJECTIVE: The objective of this paper is to introduce, explain, and extend methods for comparing the performance of classification algorithms using error tallies obtained on properly sized, populated, and labeled data sets. METHODS: Two distinct contexts of classification are defined, involving "objects-by-inspection" and "objects-by-segmentation." In the former context, the total number of objects to be classified is unambiguously and self-evidently defined. In the latter, there is troublesome ambiguity. All five of the measures of performance here considered are based on confusion matrices, tables of counts revealing the extent of an algorithm's "confusion" regarding the true classifications. A proper measure of classification-algorithm performance must meet four requirements. A proper measure should obey six additional constraints. RESULTS: Four traditional measures of performance are critiqued in terms of the requirements and constraints. Each measure meets the requirements, but fails to obey at least one of the constraints. A nontraditional measure of algorithm performance, the normalized mutual information (NMI), is therefore introduced. Based on the NMI, methods for comparing algorithm performance using confusion matrices are devised. CONCLUSIONS: The five performance measures lead to similar inferences when comparing a trio of QRS-detection algorithms using a large data set. The modified NMI is preferred, however, because it obeys each of the constraints and is the most conservative measure of performance.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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