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PubMed1985

A new algorithm for voltage clamp by iteration: a learning control of a nonlinear neuronal system.

Voltage-clamp of excitable membrane allows the measurement of membrane currents associated with electrical potential changes across the membrane. However, it has been impossible in practice to apply the conventional analog feedback voltage-clamp circuits to single electrode voltage clamping in central neurons. The reason for this is that the feedback system becomes unstable because of the positive feedback required for compensation of capacitative loss through the wall of the microelectrode. Park et al. (1981) proposed a new iterative technique to solve this problem. It requires that the potential to be clamped repeats itself with little or no change. The amount of current needed to clamp the membrane potential is not determined at once, but in a step-wise, trial and error fashion in the course of a set of repetitions. Since the feedback loop is open in real time, the system has great stability, and this advantage can be exploited in single electrode preparations. The computation algorithm which calculates the current waveform based on the voltage deviation during the last trial is the central part of the iterative voltage-clamp system. In this paper, we propose a new algorithm, which has several theoretical and practical advantages over the original one proposed by Park et al. First, two parameters used in the new algorithm are predetermined by a current-clamp experiment. Second, the speed of convergence of the new algorithm is faster than that of the Park's original algorithm. This was shown by computer simulation of iterative voltage clamp of artificial membrane following Hodgkin-Huxley equations for squid axon membrane and Rall's compartment model for a neuron with dendrites. Finally, we offer proof that the new algorithm is certain to converge for the general cases of voltage-clamp experiments with active membrane properties, synaptic membranes, etc. Consequently, the new algorithm for iterative voltage clamp is very suitable for single electrode voltage clamp in the central neurons. The new algorithm has been successfully applied to voltage-clamp experiments on rubrospinal neurons of cats (Tsukahara, Murakami, Kawato, Oda, and Etoh, in preparation).

Animals↗

PubMed1985

Identification and estimation algorithm for stochastic neural system. II.

The algorithm for identifying the stochastic neural system and estimating the system process which reflects the dynamics of the neural network are presented in this paper. The analogous algorithm has been proposed in our preceding paper (Nakao et al., 1984), which was based on the randomly missed observations of a system process only. Since the previous algorithm mentioned above was subject to an unfavorable effect of consecutively missed observations, to reduce such an effect the algorithm proposed here is designed additionally to observe an intensity process in a neural spike train as the information for the estimation. The algorithm is constructed with the extended Kalman filters because it is naturally expected that a nonlinear and time variant structure is necessary for the filters to realize the observation of an intensity process by means of mapping from a system process to an intensity process. The performance of the algorithm is examined by applying it to some artificial neural systems and also to cat's visual nervous systems. The results in these applications are thought to prove the effectiveness of the algorithm proposed here and its superiority to the algorithm proposed previously.

Animals↗

PubMed1991

Classification of postoperative cardiac patients: comparative evaluation of four algorithms.

Four classification algorithms based on Bayes' rule for minimum error are compared by evaluating their ability to recognize high- and normal-risk cardio-surgical patients. These algorithms differ in the modelling of the probability density function (pdf) for each class and include: (a) two parametric algorithms based on the assumption of normal pdf; (b) two non-parametric algorithms using Parzen multidimensional approximation of pdf with normal kernels. In each case, classes with both equal and different covariance matrices were considered. A set of 200 patients in the 6 h immediately following cardiac surgery has been used to test the performance of the algorithms. For each patient the three measured variables most effective in representing the difference between the two classes were considered. We found that the two algorithms which explicitly incorporate the information on the different sample covariance between the physiological variables existing in the two classes generally provide better recognition of high- and normal-risk patients. Of these two algorithms the parametric one appears extremely attractive for practical applications, since it exhibits slightly better performance in spite of its great simplicity.

Algorithms↗

PubMed1992

Fast ECG data compression algorithms suitable for microprocessor systems.

ECG data compression techniques have received extensive attention in ECG analysis. Numerous data compression algorithms for ECG signals have been proposed during the last three decades. We describe two algorithms based on the scan-along polygonal approximation algorithm (SAPA) that are suitable for multichannel ECG data reduction on a microprocessor-based system. One represents a modification of SAPA (MSAPA) which adopts the method of integer division table searching to speed up data reduction; the other (CSAPA) combines MSAPA and TP, a turning-point algorithm, to preserve ST segment signals. Results show that our algorithms achieve a compression ratio of more than 5:1 and a percent rms difference (PRD) to the original signal of less than 3.5%. In addition, the maximum execution time of MSAPA for processing one data point is about 50 microseconds. Moreover, the CSAPA algorithm retains all of the details of the ST segment, which are important in ischaemia diagnosis, by employing the TP algorithm.

Algorithms↗

PubMed2026

Singletrack: an algorithm for improving memory consumption and performance of gap-affine sequence alignment.

MOTIVATION: Advances in DNA sequencing have outpaced advances in computation, making sequence alignment a major bottleneck in genome data analyses. Classical dynamic programming (DP) algorithms are particularly memory-intensive, especially when computing gap-affine and dual gap-affine alignments. Existing strategies to reduce memory consumption often sacrifice speed or alignment accuracy. RESULTS: We present Singletrack, an efficient algorithm for backtrace gap-affine and dual gap-affine alignments that requires storing a single DP matrix while preserving optimal alignment results. Compared to classical DP algorithms, Singletrack removes the need to store additional matrices (i.e. 2 for gap-affine and 4 for dual gap-affine), significantly reducing memory consumption and, in turn, reducing pressure on the memory hierarchy and improving overall performance. Most importantly, Singletrack is a general backtrace method compatible with state-of-the-art DP-based algorithms and heuristics, such as the Suzuki-Kasahara (SK) and the Wavefront Alignment (WFA) algorithms. We demonstrate that Singletrack reduces memory consumption for both SK and WFA algorithms, lowering SK usage by 2× and 4× and WFA usage by 3× and 5× for gap-affine and dual gap-affine alignments, respectively. Moreover, replacing KSW2's memory-reduction technique with Singletrack accelerates its SK implementation by up to 1.4× at the cost of doubling memory consumption, while Singletrack increases the performance of the WFA implementation in WFA2-lib by 1.2-2.1×. Compared to the efficient linear-memory BiWFA algorithm, the Singletrack-accelerated version of WFA trades a practical increase in memory usage for up to 5.2× higher performance. AVAILABILITY AND IMPLEMENTATION: The Singletrack implementations presented in this work are available on Zenodo (DOI: 10.5281/zenodo.18770585) and GitHub (https://github.com/LorienLV/singletrack).

Algorithms↗

PubMed1989

A microcomputer algorithm for solving first-order compartmental models involving recycling.

A general algorithm for solving first-order compartmental models including recycling systems has been developed and its implementation on a microcomputer is described. Matrix algebra is used to obtain for any compartmental model an analytical solution, which is expressed as the exponential of a matrix of rate constants. A special technique is used in the algorithm to enable this exponential to be evaluated with a rapidly converging series. Truncation errors incurred in this process are estimated automatically. Thus, in an extreme case, where these errors may be significant, the appropriate action can be taken. Given a particular model, the user enters the model parameters into a rate matrix according to a simple rule. The algorithm then uses this matrix to solve the model, and thus no specialized mathematical knowledge is needed. The algorithm is given in a short BASIC program (60 lines) listed in an appendix. No additional software is required. By running this program on a standard microcomputer, the user can solve models of any complexity: those up to 15 compartments in seconds and those up to 30 compartments within a minute. The algorithm is thus ideally suited to solve kinetic models describing the transport of radionuclides in the environment or the translocation of elements in biological systems such as the metabolic models recommended by the International Commission on Radiological Protection (ICRP). Given the initial amount of material in each compartment at time t = 0, together with its radioactive decay constant, the algorithm gives both the amount in each compartment at any future time t and the number of disintegrations that will have occurred in each compartment up to time t. The computer program, shown in an appendix, could easily be used to calculate disintegrations over any time interval of interest, or to predict the quantities or fractions of an intake expected to be present in any in vivo or excretion compartments of interest. Thus, the algorithm can be useful in both the design and conduct of bioassay and internal dose assessment procedures.

Algorithms↗

PubMed1990

Algorithms for separating the speech of interfering talkers: evaluations with voiced sentences, and normal-hearing and hearing-impaired listeners.

Two signal-processing algorithms, derived from those described by Stubbs and Summerfield [R.J. Stubbs and Q. Summerfield, J. Acoust. Soc. Am. 84, 1236-1249 (1988)], were used to separate the voiced speech of two talkers speaking simultaneously, at similar intensities, in a single channel. Both algorithms use fundamental frequency (FO) as the basis for segregation. One attenuates the interfering voice by filtering the cepstrum of the signal. The other is a hybrid algorithm that combines cepstral filtering with the technique of harmonic selection [T.W. Parsons, J. Acoust. Soc. Am. 60, 911-918 (1976)]. The algorithms were evaluated and compared in perceptual experiments involving listeners with normal hearing and listeners with cochlear hearing impairments. In experiment 1 the processing was used to separate voiced sentences spoken on a monotone. Both algorithms gave significant increases in intelligibility to both groups of listeners. The improvements were equivalent to an increase of 3-4 dB in the effective signal-to-noise ratio (SNR). In experiment 2 the processing was used to separate voiced sentences spoken with time-varying intonation. For normal-hearing listeners, cepstral filtering gave a significant increase in intelligibility, while the hybrid algorithm gave an increase that was on the margins of significance (p = 0.06). The improvements were equivalent to an increase of 2-3 dB in the effective SNR. For impaired listeners, no intelligibility improvements were demonstrated with intoned sentences. The decrease in performance for intoned material is attributed to limitations of the algorithms when FO is nonstationary.

Algorithms↗

PubMed1986

Formal connections between lightness algorithms.

The computational problem underlying color vision is to recover the invariant surface-spectral-reflectance properties of an object. Lightness algorithms, which recover an approximation to surface reflectance in independent wavelength channels, have been proposed as one method to compute color. This paper clarifies and formalizes the lightness problem by proposing a new formulation of the intensity equation on which lightness algorithms are based and by identifying and discussing two basic subproblems of lightness and color computation: spatial decomposition and spectral normalization of the intensity signal. Several lightness algorithms are reviewed, and a new extension (the multiple-scales algorithm) of one of them is proposed. The main computational result is that each of the lightness algorithms may be derived from a single mathematical formula, under different conditions, which, in turn, imply limitations for the implementation of lightness algorithms by man or machine. In particular, the algorithms share certain limitations on their implementation that follow from the physical constraints imposed on the statement of the problem and the boundary conditions applied in its solution.

Algorithms↗

PubMed1991

Evaluation of a comprehensive algorithm for blunt and penetrating thoracic and abdominal trauma.

The objective was to develop a single branched-chain decision tree for both blunt and penetrating thoracic and abdominal trauma and to test its feasibility to track clinical decisions. The algorithm consisted of 14 specific patient management loops and 31 decision nodes. During a 4-month period, the management decisions and clinical course of 434 trauma patients were prospectively observed. Thirty-four patients had no signs of life on arrival to the emergency department (ED) and were excluded from the statistical evaluation; the remaining 400 patients constituted the study group. The mean Injury Severity Score (ISS), Penetrating Abdominal Trauma Index (PATI), and Trauma Score (TS) scores in the series were 21 +/- 10, 34 +/- 12, and 13 +/- 3. The overall patient mortality of the study group was 17 per cent; it was 61 per cent in those patients with major deviations from the algorithm and 6 per cent in patients who complied with the algorithm. The ISS, PATI, and TS scores were 29 +/- 9, 32 +/- 12, and 13 +/- 2 in patients with deviations and 20 +/- 10, 37 +/- 12, and 14 +/- 2 in patients who complied with the algorithm. Of the 37 patients who died with major deviations from the algorithm, the deviation was directly contributory to death in 21 cases (57%) and probably contributory in another 14 cases (38%). There were 108 patients with ISS scores between 20 and 50. In this group, mortality was 55 per cent when a major deviation occurred and 5 per cent without major deviations from the algorithm. The authors conclude that the survival of trauma patients may be improved by following the specific management criteria outlined by the algorithm.

Abdominal Injuries↗

PubMed1989

A selective mapping algorithm for computer analysis of voided urine cell images.

One of the fundamental targets of the automated image analysis of cytologic preparations is the reduction of computer classification errors due to cells or other objects that do not lend themselves to image segmentation or that have morphologic features that may mislead the cell classification schemes. In prior work from this laboratory, the achievement of this goal was attempted by hierarchical analysis of sequential microscopic objects at high resolution. This paper reports on the successful development and implementation of an automated "selective mapping algorithm" that selects cells at low power for further analysis and eliminates a large proportion of unwanted "objects." The algorithm classifies the objects and extracts appropriate features from a 256 X 240 digital image obtained via a 10 X planachromatic objective. The five-node binary tree classifier used in this triage is described. The algorithm was trained and tested initially on 501 visually classified microscopic "objects," resulting in a correct acceptance rate of 61.3% and correct rejection rate of 81.3%. The selective mapping algorithm was subsequently integrated into the video-based image analysis system constructed at the Montefiore Medical Center for the diagnostic evaluation of sediments of voided urine. The algorithm was then tested on ten cytocentrifuge preparations for a preliminary evaluation of its performance. Up to 100 "objects" per case were selected by the algorithm for further classification by the computer at high power. Of the 810 "objects" selected by the selective mapping algorithm, 344 (42.5%) were classified by the computer at high resolution as cells of diagnostic value ("WELL" cells) and 466 were rejected.(ABSTRACT TRUNCATED AT 250 WORDS)

Algorithms↗

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↗

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↗

PubMed1989

An automated iterative algorithm for the quantitative analysis of in vivo spectra based on the simplex optimization method.

The success in utilizing in vivo NMR to identify and/or monitor metabolic abnormalities will be determined in large part on the reliability with which the spectral parameters of the metabolites present can be measured. For these reasons it is clear that there is a need for the development of algorithms with which to obtain quantitatively reliable estimates of the spectral parameters of the peaks present. In this report we describe an adaptation of the simplex algorithm which we have found useful in fitting in vivo spectral data in the frequency domain. This simplex algorithm was implemented on an IBM-PC AT compatible computer. We evaluated the simplex algorithm on three representative kinds of spectral data: a simulated spectrum, 31P spectrum of normal calf muscle, and the 31P spectrum of a pediatric patient with a brain tumor. In each case we generated a set of spectra by adding varying amounts of noise. On the basis of our simulations and the two examples discussed, we conclude that the simplex method generates parameters which are reliable estimates of the areas of the peaks present when the signal-to-noise is above 8:1 for phosphocreatine. We found that the speed of convergence of the algorithm was improved by overestimating the linewidths of the peaks present. We also found that the method converged more rapidly in the presence of a moderate amount of noise. We conclude that the algorithm described here can provide a robust method with which to analyze in vivo spectra in a quantitative manner. Because the method requires little user intervention, it lends itself to implementation in a semi-, or fully, automated fashion.

Algorithms↗

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.

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↗

PubMed1990

Comparative accuracy of the vectorcardiogram and electrocardiogram in the localization of the accessory pathway in patients with Wolff-Parkinson-White syndrome: validation of a new vectorcardiographic algorithm by intraoperative epicardial mapping and electrophysiologic studies.

The scalar electrocardiograms (ECGs) and vectorcardiograms (VCGs) of 41 patients with Wolff-Parkinson-White (WPW) syndrome were used to compare the accuracy of these techniques in the identification of the site of preexcitation. The location of the accessory pathway (AP) was determined by endocavitary electrophysiologic studies in all patients and the location was confirmed during intraoperative epicardial mapping in 28 of them. The ECGs were classified according to Gallagher's criteria and with Milstein's algorithm, whereas the VCGs were classified according to a new two-step algorithm. The presence of multiple accessory pathways and coexisting myocardial infarctions were major limitations in both the VCG and ECG classification procedures. In patients with a single accessory pathway, three AP localizations (right free ventricular wall, posterior, or left free ventricular wall) were identified with the first step of the VCG algorithm, with an overall sensitivity (96.5%), specificity (90.7%), and positive predictive values (80%) that were greater than those obtained with the ECG Milstein algorithm (77.1%, 91.5%, and 75%, respectively). The second step of the VCG algorithm made it possible to identify an AP location in one of the following sites: anterior right, lateral right, posterior right, posterior left, lateral left, or anterior left ventricle. The overall sensitivity, specificity, and positive predictive values were greater for the second step of the VCG algorithm than for the ECG criteria proposed by Gallagher (43.6% versus 39.3%, 92.1% versus 87.4%, and 51.5% versus 33.3%, respectively). It was concluded that the VCG seems to be more specific and sensitive than the ECG in the identification of the preexcitation site and should be given preference in the initial evaluation of the WPW syndrome.

Adult↗