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PubMed1991

Volume rendering and connectivity algorithms for MR angiography.

Several display algorithms for three-dimensional angiographic data are evaluated. The mathematical analysis assumes additive Gaussian noise to predict the background distribution function for maximum intensity projection, sum projection, and connectivity display methods. In the maximum intensity projection method the mean noise level increases with the number of voxels in the ray, while in the sum projection the noise distribution width increases with the projection thickness, but the mean level remains constant. Comparisons of maximum intensity projection, sum projection, and connectivity algorithms applied to an MR angiogram of the circle of Willis are made. Measurements of the noise distribution are in agreement with the analysis. Algorithms combining connectivity with maximum intensity and sum projection are also evaluated. In these methods, a projection image is created using only the voxels marked by connectivity, typically with a 6% threshold of the data. Fine vessels are resolved and background noise is reduced in agreement with the analysis.

Algorithms↗

PubMed1989

Describing protein structure: a general algorithm yielding complete helicoidal parameters and a unique overall axis.

We present a general and mathematically rigorous algorithm which allows the helicoidal structure of a protein to be calculated starting from the atomic coordinates of its peptide backbone. This algorithm yields a unique curved axis which quantifies the folding of the backbone and a full set of helicoidal parameters describing the location of each peptide unit. The parameters obtained form a complete and independent set and can therefore be used for analyzing, comparing, or reconstructing protein backbone geometry. This algorithm has been implemented in a computer program named P-Curve. Several examples of its possible applications are discussed.

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PubMed1992

CLIX: a search algorithm for finding novel ligands capable of binding proteins of known three-dimensional structure.

A computer algorithm, CLIX, capable of searching a crystallographic data-base of small molecules for candidates which have both steric and chemical likelihood of binding a protein of known three-dimensional structure is presented. The algorithm is a significant advance over previous strategies which consider solely steric or chemical requirements for binding. The algorithm is shown to be capable of predicting the correct binding geometry of sialic acid to a mutant influenza-virus hemagglutinin and of proposing a number of potential new ligands to this protein.

Algorithms↗

PubMed1992

A new algorithm for the identification of multiple input Wiener systems.

Multiple-input Wiener systems consist of two or more linear dynamic elements, whose outputs are transformed by a multiple-input static non-linearity. Korenberg (1985) demonstrated that the linear elements of these systems can be estimated using either a first order input-output cross-covariance or a slice of the second, or higher, order input-output cross-covariance function. Korenberg's work used a multiple input LNL structure, in which the output of the static nonlinearity was then filtered by a linear dynamic system. In this paper we show that by restricting our study to the slightly simpler Wiener structure, it is possible to improve the linear subsystem estimates obtained from the measured cross-covariance functions. Three algorithms, which taken together can identify any multiple-input Wiener system, have been developed. We present the theory underlying these algorithms and detail their implementation. Simulation results are then presented which demonstrate that the algorithms are robust in the presence of output noise, and provide good estimates of the system dynamics under a wide set of conditions.

Algorithms↗

PubMed1988

Solving a combinatorial problem via self-organizing process: an application of the Kohonen algorithm to the traveling salesman problem.

We present an application of the Kohonen algorithm to the traveling salesman problem: Using only this algorithm, without energy function nor any parameter chosen "ad hoc", we found good suboptimal tours. We give a neural model version of this algorithm, closer to classical neural networks. This is illustrated with various numerical examples.

Algorithms↗

PubMed1991

[Algorithms, brains, computer. What they know and what not. II].

In order to say something substantial about the fundamental limits of machines (especially of computers) and of human calculations, we must explicate the concept of algorithm. Such an explication is provided by the Turing machine. Thus, problems have been discovered which cannot be solved algorithmically. For other problems there are problem-solving procedures, but no elegant algorithms. That men are fundamentally superior to machines has not been shown as yet.

Algorithms↗

PubMedDate not supplied

Methods of decision analysis: protocols, decision trees, and algorithms in medicine.

Algorithms, decision trees, and protocols are defined and explained since they constitute an accepted part of clinical decision analysis and application to clinical care. Algorithms are particularly useful for common clinical problems where uncertainties are unlikely. Decision trees are helpful when--as usually occurs in difficult clinical decisions--there are problems in probability. Clinical protocols, which, at best, are based on algorithms and decision trees, provide instruction of how to best treat a patient given the strict definitions of the clinical problem. These techniques are, in essence, merely graphic representations of a logical scientific approach to clinical problems. Criticisms of these techniques center on their rigidity and the automatic unthinking cookbook medicine they might sponsor. It is concluded that if these techniques are wisely designed and, even more importantly, wisely administered with an understanding flexibility, they can lead to both economy and patient benefit.

Algorithms↗

PubMed1989

Algorithms for the optimal identification of segment neighborhoods.

Two algorithms for the efficient identification of segment neighborhoods are presented. A segment neighborhood is a set of contiguous residues that share common features. Two procedures are developed to efficiently find estimates for the parameters of the model that describe these features and for the residues that define the boundaries of each segment neighborhood. The algorithms can accept nearly any model of segment neighborhood, and can be applied with a broad class of best fit functions including least squares and maximum likelihood. The algorithms successively identify the most important features of the sequence. The application of one of these methods to the haemagglutinin protein of influenza virus reveals a possible mechanism for conformational change through the finding of a break in a strong heptad repeat structure.

Algorithms↗

PubMed1992

An O (N2 log N) restriction map comparison and search algorithm.

We present an O (R log P) time, O (M+P2) space algorithm for searching a restriction map with M sites for the best matches to a shorter map with P sites, where R, the number of matching site pairs, is bounded by MP. As first proposed by Waterman et al. (1984, Nucl. Acids Res. 12, 237-242) the objective function used to score matches is additive in the number of unaligned sites and the discrepancies in the distances between adjacent aligned sites. Our algorithm is basically a sparse dynamic programming computation in which "candidate lists" are used to model the future contribution of all previously computed entries to those yet to be computed. A simple modification to the algorithm computes the distance between two restriction maps with M and N sites, respectively, in O (MN (log M+log N)) time.

Algorithms↗

PubMed1990

Breath detection algorithm in digital computers.

An algorithm for the detection and delineation of breaths is described. The proposed algorithm takes into account the different, common modes of ventilation like the pressure controlled, volume controlled and patient triggered modes of ventilation. Airway flow curve is used as the basic delineator and the airway pressure and the Co2 concentration curves are used to confirm the delineation. A flow chart is also included to explain the algorithm. The detailed explanation and modifications, for additional confirmation and for the selections of constants, to check for the rise or fall of the pressure and Co2 curves, are also included.

Algorithms↗

PubMed2025

Optimising parent selection in plant breeding: comparing metaheuristic algorithms for genotype building.

Stacking desirable haplotypes across the genome to develop superior genotypes has been implemented in several crop species. A major challenge in Optimal Haplotype Selection is identifying a set of parents that collectively contain all desirable haplotypes, a complex combinatorial problem with countless possibilities. In this study, we evaluated the performance of metaheuristic search algorithms (MSAs)-genetic algorithm (GA), differential evolution (DE), particle swarm optimisation (PSO), and simulated annealing (SA) for optimising parent selection under two genotype building (GB) objectives: Optimal Haplotype Selection (OHS) and Optimal Population Value (OPV). Using a diverse wheat population of 583 lines genotyped for 29,972 SNPs, forming 7645 haplotype blocks and phenotyped for stripe rust scores, we assessed each algorithm's performance across fitness optimisation, convergence speed, and computational efficiency. GA consistently achieved high fitness and rapid convergence, while DE showed robustness but required longer runtime and careful tuning. PSO performed well under the OHS criterion but was less effective for OPV. SA, although computationally lighter, was less consistent in finding optimal solutions. Simulation over 100 breeding cycles showed that OHS outperformed both OPV and GEBV-based selection in long-term genetic gain and diversity retention. OHS maintained heterozygosity and additive variance, which are key for sustainable improvement, while GEBV selection led to early allele fixation. Our findings underscore the potential of GB strategies that prioritise the collective performance of parent sets rather than individual ranking to enhance selection outcomes in genomic-assisted breeding programmes.

Plant Breeding↗

PubMed1991

Determination of pulse wave velocities with computerized algorithms.

Careful determination of pulse wave velocity is important in the study of arterial viscoelastic properties, wave reflections, and ventricular-arterial interactions. In spite of its increasingly widespread use, there is as yet no standardized method for its determination. Most studies have manually identified the transit time of the pressure wave front as it travels over a known distance in the arterial system, but the issues of accuracy and reproducibility have not been addressed. This study was designed to investigate the efficacy of four computerized algorithms in the determination of pulse wave velocities in invasive as well as in noninvasive pressure determinations. The four methods were the identification of: (1) the point of minimum diastolic pressure, (2) the point at which the first derivative of pressure is maximum, (3) the point at which the second derivative of pressure is maximum, and (4) the point yielded by the intersection of a line tangent to the initial systolic upstroke of the pressure tracing and a horizontal line through the minimum point. High-fidelity aortic pressure recordings were obtained in 26 patients with a multi-sensor micromanometer catheter. Noninvasive brachial and radial pressure waveforms were recorded in 11 volunteers with external piezoelectric transducers. The results show that the first derivative method consistently provided results that were different from the other methods for both the invasive and noninvasive methods because of changes in the structure of the upstroke as the arterial pulse propagates distally. Although the minimum method worked well for the invasive determinations, it was erratic with the noninvasive determinations, probably because of the higher amount of noise and reflection in the latter. Among the four algorithms, the second derivative and the intersecting tangents methods worked well with both invasive and noninvasive determinations with mean variation coefficients of less than 7% and correlation coefficients between the methods of greater than 0.90 for all data. In conclusion, computerized algorithms allow accurate determination of pulse wave velocity in invasively and noninvasively measured arterial pressure waveforms.

Adult↗

PubMed1989

International application of a new probability algorithm for the diagnosis of coronary artery disease.

A new discriminant function model for estimating probabilities of angiographic coronary disease was tested for reliability and clinical utility in 3 patient test groups. This model, derived from the clinical and noninvasive test results of 303 patients undergoing angiography at the Cleveland Clinic in Cleveland, Ohio, was applied to a group of 425 patients undergoing angiography at the Hungarian Institute of Cardiology in Budapest, Hungary (disease prevalence 38%); 200 patients undergoing angiography at the Veterans Administration Medical Center in Long Beach, California (disease prevalence 75%); and 143 such patients from the University Hospitals in Zurich and Basel, Switzerland (disease prevalence 84%). The probabilities that resulted from the application of the Cleveland algorithm were compared with those derived by applying a Bayesian algorithm derived from published medical studies called CADENZA to the same 3 patient test groups. Both algorithms overpredicted the probability of disease at the Hungarian and American centers. Overprediction was more pronounced with the use of CADENZA (average overestimation 16 vs 10% and 11 vs 5%, p less than 0.001). In the Swiss group, the discriminant function underestimated (by 7%) and CADENZA slightly overestimated (by 2%) disease probability. Clinical utility, assessed as the percentage of patients correctly classified, was modestly superior for the new discriminant function as compared with CADENZA in the Hungarian group and similar in the American and Swiss groups. It was concluded that coronary disease probabilities derived from discriminant functions are reliable and clinically useful when applied to patients with chest pain syndromes and intermediate disease prevalence.

Algorithms↗

PubMed1992

Echocardiographic algorithms for admission and predischarge prediction of mortality in acute myocardial infarction.

To develop improved prognostic algorithms for routine bedside use in acute myocardial infarction (AMI), the prognostic value concerning 2- and 12-month mortality of an early (within 72 hours after AMI) resting echocardiogram was defined in 201 consecutive patients. The relation between (1) the clinical variables (age, sex, prior and repeat AMI, arrhythmias, cardiac arrest, early [less than 72 hours after AMI] and late heart failure, early and maximal in-hospital Killip class, and maximal creatine kinase-MB isoenzyme), (2) early myocardial performance by echocardiography, and (3) mortality was characterized by Kaplan-Meier survival curves and receiver-operating characteristic curves based on Cox regression model. Only age and clinical heart failure in terms of the maximal in-hospital Killip class had independent predictive value of death (p less than 0.05) when an early echocardiographic estimate of left ventricular ejection fraction (LVEF) was included in the multivariate statistical models. The following 2 optimized algorithms for admission and predischarge calculation of risk of mortality at 2 and 12 months were developed based on the Cox model, using combinations of age, maximal Killip class and early echocardiographic LVEF: mortality at 2 months = 1 - exp - [0.051 x exp [0.044 x (age -60) - (0.117 x (LVEF - 40)]]; and mortality at 1 year = 1 - exp - [0.101 x exp [0.408 x (maxKillip - 1) - (0.061 x (LVEF - 40)]]. Discriminative power for prediction of mortality of the predischarge algorithm in an independent population of 195 patients 5 days after AMI compared favorably with that obtained in the original population, confirming the validity of the proposed method of prognostication.

Adult↗

PubMed1992

Analysis of the circular dichroism spectrum of proteins using the convex constraint algorithm: a practical guide.

Due to the time scale of circular dichroism (CD) measurements, it is theoretically possible to deconvolute such a spectrum if the pure CD spectra differ significantly from one another. In the last decade several methods have been published aiming at obtaining the conformational weights, or percentages (which are the coefficients for a linear combination) of the so-called typical secondary structural elements making up the three-dimensional structure of proteins. Two methods that can be used to determine the secondary structures of proteins are described here. The first method, called LINCOMB, is a simple algorithm based on a least-squares fit with a set of reference spectra representing the known secondary structures and yielding an estimation of weights attributed to alpha-helix, beta-pleated sheet (mainly antiparallel), beta-turns, unordered form, and aromatic/disulfide (or nonpeptide) contributions of the protein being analyzed. This method requires a "template" or reference curve set, which was obtained from the second method. The second method, "convex constraint analysis," is a general deconvolution method for a CD spectra set of any variety of conformational type. The algorithm, based on a set of three constraints, is able to deconvolute a set of CD curves to its common "pure"-component curves and conformational weights. To analyze a single CD spectrum with this method, the spectrum is appended to the data set used as a reference data set. As a way to determine the reliability of the algorithm and provide a guideline to its usage, some applications are presented.

Algorithms↗

PubMed1989

An algorithm for the quantification of ST-T segment variability.

A template boundary algorithm which quantitatively determines repolarization (ST-T segment) variability in a normal population has been developed. The algorithm defines an initial ST-T template for comparison with successive beats. Variability is quantified using boundary limits around the template which are widened, when necessary, to included incoming ST-T segments. The boundaries at the end of each hour are stored and the collection of boundaries over a set of normal subjects quantifies the normal variation over the entire ST-T segment. The algorithm can be used to determine prospectively normal ST-T variability based on a regression analysis of R-wave or T-wave amplitude, and QT interval. Application of these boundary predictions should be useful in distinguishing repolarization changes secondary to ischemia from normal variability.

Algorithms↗

PubMed1990

Utility of an algorithm in differentiating spontaneous from secondary bacterial peritonitis.

To prospectively assess the value of an algorithm in differentiating spontaneous from secondary bacterial peritonitis, we performed serial paracenteses in 43 episodes of ascitic fluid infection (28 spontaneous and 15 secondary) in 40 patients. The algorithm involved identification of (a) secondary peritonitis associated with gut perforation, based on previously proposed criteria in patients with neutrocytic ascites (ascitic fluid total protein greater than 1 g/dl, glucose less than 50 mg/dl, and lactate dehydrogenase greater than the upper limit of normal for serum) and (b) separation of spontaneous from secondary peritonitis (unassociated with perforation) based on the response of the ascitic fluid cell count to antibiotic therapy. The perforation criteria had 100% sensitivity in detecting episodes of actual gut perforation; their specificity, however, was low (45%). After 48 h of treatment the concentration of ascitic fluid neutrophils was below the baseline pretreatment value in all episodes of spontaneous peritonitis but in only two thirds of the patients with secondary peritonitis. This algorithm is useful in (a) identifying patients who have infected ascites associated with perforation of an intraabdominal viscus, and (b) differentiating spontaneous from nonperforation secondary peritonitis on the basis of the response of the ascitic fluid cell count to appropriate antibiotic therapy. The optimal time for repeat paracentesis in patients with infected ascites appears to be 48 h after initiation of treatment.

Algorithms↗

PubMed1986

A simple algorithm for assisting medical diagnosis.

This is a description of an algorithm to assist in the selection of the most probable diagnosis of a given patient. This algorithm is based on the comparison of a scaled column vector of the symptoms displayed by the patient, and of each column of symptoms appearing in a disease matrix. Moreover, the same algorithm gives the degree of similarity of the diseases compared by the differential diagnosis, as well as the hierarchic order of the symptoms that characterise any disease.

Algorithms↗