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PubMed2006

Combined genetic algorithm and multiple linear regression (GA-MLR) optimizer: Application to multi-exponential fluorescence decay surface.

The optimization approach based on the genetic algorithm (GA) combined with multiple linear regression (MLR) method, is discussed. The GA-MLR optimizer is designed for the nonlinear least-squares problems in which the model functions are linear combinations of nonlinear functions. GA optimizes the nonlinear parameters, and the linear parameters are calculated from MLR. GA-MLR is an intuitive optimization approach and it exploits all advantages of the genetic algorithm technique. This optimization method results from an appropriate combination of two well-known optimization methods. The MLR method is embedded in the GA optimizer and linear and nonlinear model parameters are optimized in parallel. The MLR method is the only one strictly mathematical "tool" involved in GA-MLR. The GA-MLR approach simplifies and accelerates considerably the optimization process because the linear parameters are not the fitted ones. Its properties are exemplified by the analysis of the kinetic biexponential fluorescence decay surface corresponding to a two-excited-state interconversion process. A short discussion of the variable projection (VP) algorithm, designed for the same class of the optimization problems, is presented. VP is a very advanced mathematical formalism that involves the methods of nonlinear functionals, algebra of linear projectors, and the formalism of Fréchet derivatives and pseudo-inverses. Additional explanatory comments are added on the application of recently introduced the GA-NR optimizer to simultaneous recovery of linear and weakly nonlinear parameters occurring in the same optimization problem together with nonlinear parameters. The GA-NR optimizer combines the GA method with the NR method, in which the minimum-value condition for the quadratic approximation to chi(2), obtained from the Taylor series expansion of chi(2), is recovered by means of the Newton-Raphson algorithm. The application of the GA-NR optimizer to model functions which are multi-linear combinations of nonlinear functions, is indicated. The VP algorithm does not distinguish the weakly nonlinear parameters from the nonlinear ones and it does not apply to the model functions which are multi-linear combinations of nonlinear functions.

Algorithms↗

PubMed1999

Pressure and flow fields in the hinge region of bileaflet mechanical heart valves.

BACKGROUND AND AIM OF THE STUDY: Recent clinical thrombotic experiences with the Medtronic Parallel (MP) bileaflet heart valve have highlighted the need for new methods to assess preclinical valve hinge flow. The aim of the current study was to investigate hinge pivot flow fields in bileaflet mechanical heart valves using flow visualization in scaled x5 magnification transparent polymer models and computational fluid dynamic (CFD) analysis using CFD 2000 STORM code. METHODS: Polymeric x5 flow models of the On-X, St. Jude Medical (SJM) and MP bileaflet heart valves were constructed using laser stereolithography to replicate the interior geometry while maintaining realistic manufacturing tolerances. Each hinge flow experiment was carried out by installing the transparent x5 model in a pulsatile flow loop, which was designed according to Womersley number similitude requirements. Motions of suspended microparticles in the valve hinge area, recorded by laser imaging techniques, were used to visualize hinge flow. Experimentally measured parameters were used as input for CFD analysis. CFD simulations were made by solving the Navier-Stokes equation using a finite volume method with the pressure-based algorithm for continuity, and a pressure-implicit with splitting of operators (PISO) algorithm for pressure-velocity coupling. Moving grid methodology was employed to simulate periodic motion of the valve leaflets. CFD hinge flow results were visualized on four parallel planes at different depths in the hinge socket. The hinge flow patterns of the three types of bileaflet heart valve design are discussed. RESULTS: Prominent vortex formation and stagnant flow areas were noticed in the pivot region of the MP valve. Vortices persisted throughout both the forward- and reverse-flow phases. These flow structures were not observed in the hinge areas of the SJM and On-X valves. CONCLUSIONS: Vortex formation observed in the MP valve may contribute to the high thrombogenic potential of this valve. The absence of such vortices and areas of stagnant flow in the On-X and SJM valves indicate that hinge flow conditions in these valves do not favor mechanically induced thrombogenesis or thromboembolic events.

Biocompatible Materials↗

PubMed1997

Recovery of protein structure from contact maps.

BACKGROUND: Prediction of a protein's structure from its amino acid sequence is a key issue in molecular biology. While dynamics, performed in the space of two-dimensional contact maps, eases the necessary conformational search, it may also lead to maps that do not correspond to any real three-dimensional structure. To remedy this, an efficient procedure is needed to reconstruct three-dimensional conformations from their contact maps. RESULTS: We present an efficient algorithm to recover the three-dimensional structure of a protein from its contact map representation. We show that when a physically realizable map is used as target, our method generates a structure whose contact map is essentially similar to the target. furthermore, the reconstructed and original structures are similar up to the resolution of the contact map representation. Next, we use nonphysical target maps, obtained by corrupting a physical one; in this case, our method essentially recovers the underlying physical map and structure. Hence, our algorithm will help to fold proteins, using dynamics in the space of contact maps. Finally, we investigate the manner in which the quality of the recovered structure degrades when the number of contacts is reduced. CONCLUSIONS: The procedure is capable of assigning quickly and reliably a three-dimensional structure to a given contact map. It is well suited for use in parallel with dynamics in contact map space to project a contact map onto its closest physically allowed structural counterpart.

Algorithms↗

PubMed2007

One-bit-matching theorem for ICA, convex-concave programming on polyhedral set, and distribution approximation for combinatorics.

According to the proof by Liu, Chiu, and Xu (2004) on the so-called one-bit-matching conjecture (Xu, Cheung, and Amari, 1998a), all the sources can be separated as long as there is an one-to-one same-sign correspondence between the kurtosis signs of all source probability density functions (pdf's) and the kurtosis signs of all model pdf's, which is widely believed and implicitly supported by many empirical studies. However, this proof is made only in a weak sense that the conjecture is true when the global optimal solution of an independent component analysis criterion is reached. Thus, it cannot support the successes of many existing iterative algorithms that usually converge at one of the local optimal solutions. This article presents a new mathematical proof that is obtained in a strong sense that the conjecture is also true when any one of local optimal solutions is reached in helping to investigating convex-concave programming on a polyhedral set. Theorems are also provided not only on partial separation of sources when there is a partial matching between the kurtosis signs, but also on an interesting duality of maximization and minimization on source separation. Moreover, corollaries are obtained on an interesting duality, with supergaussian sources separated by maximization and subgaussian sources separated by minimization. Also, a corollary is obtained to confirm the symmetric orthogonalization implementation of the kurtosis extreme approach for separating multiple sources in parallel, which works empirically but lacks mathematical proof. Furthermore, a linkage has been set up to combinatorial optimization from a distribution approximation perspective and a Stiefel manifold perspective, with algorithms that guarantee convergence as well as satisfaction of constraints.

Algorithms↗

PubMed1994

Establishing specific retrovirus-free breeding colonies of macaques: an approach to primary screening and surveillance.

For reasons of occupational safety and animal health, as well as to improve the quality of nonhuman primates used in biomedical research, the establishment and maintenance of specific retrovirus-free breeding colonies of macaques (genus Macaca) are now high priorities. Sensitive and specific screening tests are now available for use in identifying macaques infected with the exogenous simian retroviruses simian immunodeficiency virus (SIV), simian T-lymphotropic virus (STLV), and simian type D retrovirus (SRV/D). A testing algorithm of repeated antibody screening by enzyme immunoassay with confirmatory testing of enzyme immunoassay-reactive sera by Western blot (immunoblot) has proved adequate for identification and exclusion of SIV- and STLV-infected animals in five facilities. In follow-up testing of animals seronegative on primary screening, seroconversions to these two viruses have been rare (0% and < 0.01%, respectively). The testing algorithm for SRV/D must include virus isolation in addition to antibody screening, as some SRV/D-infected animals lack detectable antibody or exhibit a prolonged interval between infection and seroconversion. This parallel testing for SRV/D antibody and virus is critical, especially during primary screening of potential specific pathogen-free stock obtained from external sources. "Indeterminate" immunoblot results, particularly for SRV/D, continue to pose a problem of interpretation. However, preliminary results indicate that newer diagnostic test methods, such as polymerase chain reaction for amplification of proviral DNA, will be useful in resolving SRV/D infection status and will contribute substantially to specific pathogen-free colony development and maintenance.

Algorithms↗

PubMed1993

An investigation of the accuracy in measuring the body center of pressure in a standing posture with a force plate.

It has been reported that accuracy in the measured point of force application depends on the position and magnitude of load. The aim of this study is to investigate the error in measuring the body center of pressure in a standing posture with a force plate and to improve the accuracy by proposing a correction algorithm. The measurement of the point of force application with a calibrated load demonstrated its co-ordinates, which were scaled down towards the zero co-ordinate and moved parallel relative to the true co-ordinates. This trend was exaggerated with any decrease in magnitude of the load. The root mean square (r.m.s.) and maximum of errors at light load of 10 kg were 10 and 18 mm in the X axis, and 6 and 12 mm in the Y axis, respectively. The error seems to result from such causes as (i) non-linearity of the load cell, (ii) deformation of the top plate due to load application and (iii) differences in characteristics among individual load cells, including amplifiers. A mathematical representation of the measured point of force application accounting for these causes of error has been made and an algorithm for estimating the true point at any magnitude of load with only one correction equation is proposed. Actual correction of the measured point demonstrated an expected improvement in the r.m.s. error to less than 1 mm at any magnitude of load greater than 10 kg and the validity of this algorithm was confirmed.

Algorithms↗

PubMed2000

Efficient and scalable Pareto optimization by evolutionary local selection algorithms.

Local selection is a simple selection scheme in evolutionary computation. Individual fitnesses are accumulated over time and compared to a fixed threshold, rather than to each other, to decide who gets to reproduce. Local selection, coupled with fitness functions stemming from the consumption of finite shared environmental resources, maintains diversity in a way similar to fitness sharing. However, it is more efficient than fitness sharing and lends itself to parallel implementations for distributed tasks. While local selection is not prone to premature convergence, it applies minimal selection pressure to the population. Local selection is, therefore, particularly suited to Pareto optimization or problem classes where diverse solutions must be covered. This paper introduces ELSA, an evolutionary algorithm employing local selection and outlines three experiments in which ELSA is applied to multiobjective problems: a multimodal graph search problem, and two Pareto optimization problems. In all these experiments, ELSA significantly outperforms other well-known evolutionary algorithms. The paper also discusses scalability, parameter dependence, and the potential distributed applications of the algorithm.

Algorithms↗

PubMed2004

Range image segmentation into planar and quadric surfaces using an improved robust estimator and genetic algorithm.

This paper presents a novel range image segmentation method employing an improved robust estimator to iteratively detect and extract distinct planar and quadric surfaces. Our robust estimator extends M-estimator Sample Consensus/Random Sample Consensus (MSAC/RANSAC) to use local surface orientation information, enhancing the accuracy of inlier/outlier classification when processing noisy range data describing multiple structures. An efficient approximation to the true geometric distance between a point and a quadric surface also contributes to effectively reject weak surface hypotheses and avoid the extraction of false surface components. Additionally, a genetic algorithm was specifically designed to accelerate the optimization process of surface extraction, while avoiding premature convergence. We present thorough experimental results with quantitative evaluation against ground truth. The segmentation algorithm was applied to three real range image databases and competes favorably against eleven other segmenters using the most popular evaluation framework in the literature. Our approach lends itself naturally to parallel implementation and application in real-time tasks. The method fits well, into several of today's applications in man-made environments, such as target detection and autonomous navigation, for which obstacle detection, but not description or reconstruction, is required. It can also be extended to process point clouds resulting from range image registration.

Algorithms↗

PubMed2004

Simultaneous measurement of surface shape and variation in optical thickness of a transparent parallel plate in wavelength-scanning Fizeau interferometer.

Wavelength-scanning interferometry permits the simultaneous measurement of variations in surface shape and optical thickness of a nearly parallel plate. Interference signals from both surfaces of the test plate can be separated in frequency space; however, these frequencies are shifted from the expected frequency by the refractive-index dispersion of the test plate and any nonlinearity that is due to wavelength scanning. Conventional Fourier analysis is sensitive to this detuning of the signal frequency and suffers from multiple-beam interference noise. We propose new wavelength-scanning algorithms that permit a large tolerance for dispersion of the test plate and nonlinearity of scanning. Two 19-sample algorithms that suppress multiple-interference noise up to the second order of the reflectance of the test plate are presented. Experimental results show that the variation in surface shape and optical thickness of a glass parallel plate of 250-mm diameter was measured with a resolution of 1-2 nm rms.

Journal Article↗

PubMed2004

Linear scaling computation of the Fock matrix. VII. Parallel computation of the Coulomb matrix.

We present parallelization of a quantum-chemical tree-code for linear scaling computation of the Coulomb matrix. Equal time partition is used to load balance computation of the Coulomb matrix. Equal time partition is a measurement based algorithm for domain decomposition that exploits small variation of the density between self-consistent-field cycles to achieve load balance. Efficiency of the equal time partition is illustrated by several tests involving both finite and periodic systems. It is found that equal time partition is able to deliver 91%-98% efficiency with 128 processors in the most time consuming part of the Coulomb matrix calculation. The current parallel quantum chemical tree code is able to deliver 63%-81% overall efficiency on 128 processors with fine grained parallelism (less than two heavy atoms per processor).

Journal Article↗

PubMed2001

Catatonia: syndrome or schizophrenia subtype? Recognition and treatment.

Two views of catatonia influence clinical practice. In the classical European view, adopted by DSM classifications, the signs of catatonia indicate a form of schizophrenia. In the syndromal view, the signs of catatonia are motor signs that are readily identified in many psychiatric disorders. Catatonia is a parallel behavior phenomenon to delusions (in thought) and delirium (in cognition). The syndromic view includes the neuroleptic malignant syndrome. It encourages a different treatment algorithm, the use of benzodiazepines and electroconvulsive therapy, to replace the customary use of antipsychotic drugs alone. The benefits of such treatment warrant the recommended change in concept and classification.

Catatonia↗

PubMed2006

Scalable implementation of analytic gradients for second-order Z-averaged perturbation theory using the distributed data interface.

The analytic gradient expression for second-order Z-averaged perturbation theory is revised and its parallel implementation is described in detail. The distributed data interface is used to access molecular-orbital integral arrays stored in distributed memory. The algorithm is designed to maximize the use of local data and reduce communication costs. The iterative solution and the preconditioner used to induce the convergence of the coupled-perturbed Hartree-Fock equations are presented. Several illustrative timing examples are discussed.

Journal Article↗

PubMed1994

The effects of experimental malnutrition on albumin metabolism and distribution in rabbits.

In order to determine the extent to which the concentration of albumin in plasma is maintained at the expense of the extravascular pool during protein-energy malnutrition, the rates of exchange between albumin in plasma (IA) and the extravascular pool (EA) and consequently the distribution of albumin between intravascular and extravascular pools (expressed as EA:IA) were measured in protein-energy-depleted and control rabbits. The fractional rates of synthesis (FSR) and catabolism (FCR), the concentration of albumin and the plasma volume (PV) were also measured. In animals in which protein-energy intake was reduced by 58% the concentration of albumin in plasma remained unchanged, whereas FCR decreased by 38% and FSR by 30%. No significant changes in EA:IA or PV were found. We conclude that albumin concentration during protein-energy depletion is not maintained at the expense of extravascular albumin, but by parallel changes in the rates of catabolism and synthesis.

Algorithms↗

PubMed2003

Automatic registration of microarray images. I. Rectangular grid.

MOTIVATION: The analysis of high-throughput experiment data provided by microarrays becomes increasingly more and more important part of modern biological science. Microarrays allow to conduct genotyping or gene expression experiments on hundreds of thousands of test genes in parallel. Because of the large and constantly growing amount of experimental data the necessity of efficiency, robustness and complete automation of microarray image analysis algorithms is gaining significant attention in the field of microarray processing. RESULTS: The author presents here an efficient and completely automatic image registration algorithm (that is an algorithm for spots and blocks indexing) that allows to process a wide variety of microarray slides with different parameters of grid and block spacing as well as spot sizes. The algorithm scales linearly with the grid size, the time complexity is O(M), where M is number of rows x number of columns. It can successfully cope with local and global distortions of the grid, such as focal distortions and non-orthogonal transformations. The algorithm has been tested both on CCD and scanned images and showed very good performance-the processing time of a single slide with 44 blocks of 200 x 200 grid points (or 1 760 000 grid points total) was about 10 s. AVAILABILITY: The test implementation of the algorithm will be available upon request for academics. SUPPLEMENTARY INFORMATION: http://fleece.ucsd.edu/~vit/Registration_Supplement.pdf

Algorithms↗

PubMed2001

Complete 3-D reconstruction of dental cast shape using perceptual grouping.

To achieve the complete three-dimensional (3-D) data retrieval of the shape of dentition, dental casts were measured from four directions; occlusal, right, left, and labial sides using a line laser scanner. Reconstruction of the entire shape, including undercuts and tooth crowding area, was attempted by applying a perceptual grouping algorithm, which is one of pattern-recognition theories. In the data measured from occlusal, right and left sides, the rows of measurements were parallel to the frontal plane, and three-directionally combined data (3-DC data) was accomplished by affine transformation. While, in the labial side, transformation to the frontal plane was done since rows of the measured data were parallel to the sagittal plane. To combine the labial data with the 3-DC data and reconstruct the complete image, rearrangement of the order of the data in the file was attempted by applying the perceptual grouping. That is, the minimum total length of data combining was examined by considering the factor of proximity and continuity between the data. The most appropriate order of data combining and recognition of islands were accomplished. Using a computer graphic (CG) with a wire-frame model, complicated regions such as anterior segments showing tooth crowding and undercut area were found to be successfully reconstructed without any data defects. The accuracy of reconstruction was ascertained by comparing the characteristic distances between apexes of molars in the reconstructed model with the real cast. The difference was within 0.3 mm, and present method for dental cast reconstruction is considered to be satisfactory for the present purpose such as orthodontics.

Dental Casting Technique↗

PubMed2001

Leaf sequencing with secondary beam blocking under leaf positioning constraints for continuously modulated radiotherapy beams.

The creation of arbitrary photon fluence patterns for intensity modulated radiotherapy is addressed. The proposed method is intended for a class of multileaf collimators with a requirement for minimum leaf separation. Unlike the solution of Convery and Webb in which discrete beam intensity modulation was assumed, the present method deals with continuous modulation or that consisting of infinitely small bixels. The method begins with the time-optimal solution of Spirou-Stein-Svensson disregarding the minimum gap requirement. Subsequently, the gaps are restored by mobilizing the secondary beam blocking devices to prevent overexposure resulting from the leaf separation process. The secondary beam blocking is provided by means of two orthogonal backup diaphragms that are computer controlled. The results indicate that the method can be used to accurately deliver the desired modulation while satisfying the leaf positioning constraints. Furthermore, an example is presented which illustrates the efficacy of using the horizontal backup diaphragms (moving in perpendicular direction of the leaves) in addition to the vertical backup diaphragms (moving in the parallel direction of the leaves) to generate zero fluence regions.

Algorithms↗

PubMed1989

Nuclear medicine in the 1990s: a quantitative physiological approach.

This paper describes the potential advantages to medical diagnosis and treatment that might be obtained from the wider application of positron emission tomography as a clinical tool. Developments along the lines suggested here will require a radical change in thinking from both clinicians and the medically related scientific community in the UK and some enlightened and resourceful funding from a mixture of charitable, industrial and government sources. If these ideas are to be pursued successfully, then the work must start now on a much wider scale than is presently perceived in the UK, and close collaboration between physicists, engineers, chemists, biochemists, clinicians and industrialists is needed. Furthermore, it is imperative that the scientific developments now underway in silicon technology, parallel data processors, biochemical and pharmacological processes and even high-temperature superconductors be kept under close and constant review by those associated with the technological advancements of medicine, so that the value of such developments is rapidly transferred to applications to medicine. This must include closer relationships between academic medicine and science than is the general rule in the UK at present. In conclusion, the scenario presented here includes the installation of regional cyclotron facilities to provide a large number of institutions in the UK with positron-emitter labelled radiopharmaceuticals. Additionally, agents labelled with radionuclides from in-house generators and other already existing higher-energy cyclotrons will provide a versatile and valuable range of radiopharmaceuticals for the study of human disease. These developments must be supported by the manufacture of lower-cost positron camera systems, as suggested here, connected to high-data-rate parallel processors to provide images of body function and to determine the effects brought about by disease. These images may then be processed using algorithms based on kinetic models of the body systems to provide information about the basic biochemical and physiological processes of the body. Such a development could have a profound effect on our knowledge of human disease and on our ability to control and treat it successfully.

Forecasting↗

PubMed2001

Computer-aided method for calculating animal configurations during social interactions from two-dimensional coordinates of color-marked body parts.

In an experiment investigating the impact of preweaning social experience on later social behavior in pigs, we were interested in the mutual spatial positions of pigs during paired social interactions. To obtain these data, we applied a different colored mark to the head and back of each of 2 pigs per group and videotaped the pigs' interactions. We used the EthoVision tracking system to provide x,y coordinates of the four colored marks every 0.2 sec. This paper describes the structure and functioning of a FoxPro program designed to clean the raw data and use it to identify the mutual body positions of the 2 animals at 0.2-sec intervals. Cleaning the data was achieved by identifying invalid data points and replacing them by interpolations. An algorithm was then applied to extract three variables from the coordinates: (1) whether the two pigs were in body contact; (2) the mutual orientation (parallel, antiparallel, or perpendicular) of the two pigs; and (3) whether the pig in the "active" position made snout contact in front of, or behind, the ear base of the other pig. Using these variables, we were able to identify five interaction types: Pig A attacks, Pig B attacks, undecided head-to-head position, "clinch" resting position, or no contact. To assess the reliability of the automatic system, a randomly chosen 5-min videotaped interaction was scored for mutual positions both visually (by 2 independent observers) and automatically. Good agreement was found between the data from the 2 observers and between each observer's data and the data from the automated system, as assessed using Cohen's kappa coefficients.

Animals↗