Advanced Targeting Cost Function Design for Evolutionary Optimization of Control of Logistic Equation

NASA Astrophysics Data System (ADS)

Senkerik, Roman; Zelinka, Ivan; Davendra, Donald; Oplatkova, Zuzana

2010-06-01

This research deals with the optimization of the control of chaos by means of evolutionary algorithms. This work is aimed on an explanation of how to use evolutionary algorithms (EAs) and how to properly define the advanced targeting cost function (CF) securing very fast and precise stabilization of desired state for any initial conditions. As a model of deterministic chaotic system, the one dimensional Logistic equation was used. The evolutionary algorithm Self-Organizing Migrating Algorithm (SOMA) was used in four versions. For each version, repeated simulations were conducted to outline the effectiveness and robustness of used method and targeting CF.

Integrated Multiscale Modeling of Molecular Computing Devices

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gregory Beylkin

2012-03-23

Significant advances were made on all objectives of the research program. We have developed fast multiresolution methods for performing electronic structure calculations with emphasis on constructing efficient representations of functions and operators. We extended our approach to problems of scattering in solids, i.e. constructing fast algorithms for computing above the Fermi energy level. Part of the work was done in collaboration with Robert Harrison and George Fann at ORNL. Specific results (in part supported by this grant) are listed here and are described in greater detail. (1) We have implemented a fast algorithm to apply the Green's function for themore » free space (oscillatory) Helmholtz kernel. The algorithm maintains its speed and accuracy when the kernel is applied to functions with singularities. (2) We have developed a fast algorithm for applying periodic and quasi-periodic, oscillatory Green's functions and those with boundary conditions on simple domains. Importantly, the algorithm maintains its speed and accuracy when applied to functions with singularities. (3) We have developed a fast algorithm for obtaining and applying multiresolution representations of periodic and quasi-periodic Green's functions and Green's functions with boundary conditions on simple domains. (4) We have implemented modifications to improve the speed of adaptive multiresolution algorithms for applying operators which are represented via a Gaussian expansion. (5) We have constructed new nearly optimal quadratures for the sphere that are invariant under the icosahedral rotation group. (6) We obtained new results on approximation of functions by exponential sums and/or rational functions, one of the key methods that allows us to construct separated representations for Green's functions. (7) We developed a new fast and accurate reduction algorithm for obtaining optimal approximation of functions by exponential sums and/or their rational representations.« less

Parameter Search Algorithms for Microwave Radar-Based Breast Imaging: Focal Quality Metrics as Fitness Functions.

PubMed

O'Loughlin, Declan; Oliveira, Bárbara L; Elahi, Muhammad Adnan; Glavin, Martin; Jones, Edward; Popović, Milica; O'Halloran, Martin

2017-12-06

Inaccurate estimation of average dielectric properties can have a tangible impact on microwave radar-based breast images. Despite this, recent patient imaging studies have used a fixed estimate although this is known to vary from patient to patient. Parameter search algorithms are a promising technique for estimating the average dielectric properties from the reconstructed microwave images themselves without additional hardware. In this work, qualities of accurately reconstructed images are identified from point spread functions. As the qualities of accurately reconstructed microwave images are similar to the qualities of focused microscopic and photographic images, this work proposes the use of focal quality metrics for average dielectric property estimation. The robustness of the parameter search is evaluated using experimental dielectrically heterogeneous phantoms on the three-dimensional volumetric image. Based on a very broad initial estimate of the average dielectric properties, this paper shows how these metrics can be used as suitable fitness functions in parameter search algorithms to reconstruct clear and focused microwave radar images.

Online Coregularization for Multiview Semisupervised Learning

PubMed Central

Li, Guohui; Huang, Kuihua

2013-01-01

We propose a novel online coregularization framework for multiview semisupervised learning based on the notion of duality in constrained optimization. Using the weak duality theorem, we reduce the online coregularization to the task of increasing the dual function. We demonstrate that the existing online coregularization algorithms in previous work can be viewed as an approximation of our dual ascending process using gradient ascent. New algorithms are derived based on the idea of ascending the dual function more aggressively. For practical purpose, we also propose two sparse approximation approaches for kernel representation to reduce the computational complexity. Experiments show that our derived online coregularization algorithms achieve risk and accuracy comparable to offline algorithms while consuming less time and memory. Specially, our online coregularization algorithms are able to deal with concept drift and maintain a much smaller error rate. This paper paves a way to the design and analysis of online coregularization algorithms. PMID:24194680

Fronts propagating with curvature dependent speed: Algorithms based on Hamilton-Jacobi formulations

NASA Technical Reports Server (NTRS)

Osher, Stanley; Sethian, James A.

1987-01-01

New numerical algorithms are devised (PSC algorithms) for following fronts propagating with curvature-dependent speed. The speed may be an arbitrary function of curvature, and the front can also be passively advected by an underlying flow. These algorithms approximate the equations of motion, which resemble Hamilton-Jacobi equations with parabolic right-hand-sides, by using techniques from the hyperbolic conservation laws. Non-oscillatory schemes of various orders of accuracy are used to solve the equations, providing methods that accurately capture the formation of sharp gradients and cusps in the moving fronts. The algorithms handle topological merging and breaking naturally, work in any number of space dimensions, and do not require that the moving surface be written as a function. The methods can be used also for more general Hamilton-Jacobi-type problems. The algorithms are demonstrated by computing the solution to a variety of surface motion problems.

Network compensation for missing sensors

NASA Technical Reports Server (NTRS)

Ahumada, Albert J., Jr.; Mulligan, Jeffrey B.

1991-01-01

A network learning translation invariance algorithm to compute interpolation functions is presented. This algorithm with one fixed receptive field can construct a linear transformation compensating for gain changes, sensor position jitter, and sensor loss when there are enough remaining sensors to adequately sample the input images. However, when the images are undersampled and complete compensation is not possible, the algorithm need to be modified. For moderate sensor losses, the algorithm works if the transformation weight adjustment is restricted to the weights to output units affected by the loss.

Convergence and objective functions of some fault/noise-injection-based online learning algorithms for RBF networks.

PubMed

Ho, Kevin I-J; Leung, Chi-Sing; Sum, John

2010-06-01

In the last two decades, many online fault/noise injection algorithms have been developed to attain a fault tolerant neural network. However, not much theoretical works related to their convergence and objective functions have been reported. This paper studies six common fault/noise-injection-based online learning algorithms for radial basis function (RBF) networks, namely 1) injecting additive input noise, 2) injecting additive/multiplicative weight noise, 3) injecting multiplicative node noise, 4) injecting multiweight fault (random disconnection of weights), 5) injecting multinode fault during training, and 6) weight decay with injecting multinode fault. Based on the Gladyshev theorem, we show that the convergence of these six online algorithms is almost sure. Moreover, their true objective functions being minimized are derived. For injecting additive input noise during training, the objective function is identical to that of the Tikhonov regularizer approach. For injecting additive/multiplicative weight noise during training, the objective function is the simple mean square training error. Thus, injecting additive/multiplicative weight noise during training cannot improve the fault tolerance of an RBF network. Similar to injective additive input noise, the objective functions of other fault/noise-injection-based online algorithms contain a mean square error term and a specialized regularization term.

Algorithms and programming tools for image processing on the MPP:3

NASA Technical Reports Server (NTRS)

Reeves, Anthony P.

1987-01-01

This is the third and final report on the work done for NASA Grant 5-403 on Algorithms and Programming Tools for Image Processing on the MPP:3. All the work done for this grant is summarized in the introduction. Work done since August 1986 is reported in detail. Research for this grant falls under the following headings: (1) fundamental algorithms for the MPP; (2) programming utilities for the MPP; (3) the Parallel Pascal Development System; and (4) performance analysis. In this report, the results of two efforts are reported: region growing, and performance analysis of important characteristic algorithms. In each case, timing results from MPP implementations are included. A paper is included in which parallel algorithms for region growing on the MPP is discussed. These algorithms permit different sized regions to be merged in parallel. Details on the implementation and peformance of several important MPP algorithms are given. These include a number of standard permutations, the FFT, convolution, arbitrary data mappings, image warping, and pyramid operations, all of which have been implemented on the MPP. The permutation and image warping functions have been included in the standard development system library.

Research on the Optimization Method of Arm Movement in the Assembly Workshop Based on Ergonomics

NASA Astrophysics Data System (ADS)

Hu, X. M.; Qu, H. W.; Xu, H. J.; Yang, L.; Yu, C. C.

2017-12-01

In order to improve the work efficiency and comfortability, Ergonomics is used to research the work of the operator in the assembly workshop. An optimization algorithm of arm movement in the assembly workshop is proposed. In the algorithm, a mathematical model of arm movement is established based on multi rigid body movement model and D-H method. The solution of inverse kinematics equation on arm movement is solved through kinematics theory. The evaluation functions of each joint movement and the whole arm movement are given based on the comfortability of human body joint. The solution method of the optimal arm movement posture based on the evaluation functions is described. The software CATIA is used to verify that the optimal arm movement posture is valid in an example and the experimental result show the effectiveness of the algorithm.

Co-evolution for Problem Simplification

NASA Technical Reports Server (NTRS)

Haith, Gary L.; Lohn, Jason D.; Cplombano, Silvano P.; Stassinopoulos, Dimitris

1999-01-01

This paper explores a co-evolutionary approach applicable to difficult problems with limited failure/success performance feedback. Like familiar "predator-prey" frameworks this algorithm evolves two populations of individuals - the solutions (predators) and the problems (prey). The approach extends previous work by rewarding only the problems that match their difficulty to the level of solut,ion competence. In complex problem domains with limited feedback, this "tractability constraint" helps provide an adaptive fitness gradient that, effectively differentiates the candidate solutions. The algorithm generates selective pressure toward the evolution of increasingly competent solutions by rewarding solution generality and uniqueness and problem tractability and difficulty. Relative (inverse-fitness) and absolute (static objective function) approaches to evaluating problem difficulty are explored and discussed. On a simple control task, this co-evolutionary algorithm was found to have significant advantages over a genetic algorithm with either a static fitness function or a fitness function that changes on a hand-tuned schedule.

MR-guided dynamic PET reconstruction with the kernel method and spectral temporal basis functions

NASA Astrophysics Data System (ADS)

Novosad, Philip; Reader, Andrew J.

2016-06-01

Recent advances in dynamic positron emission tomography (PET) reconstruction have demonstrated that it is possible to achieve markedly improved end-point kinetic parameter maps by incorporating a temporal model of the radiotracer directly into the reconstruction algorithm. In this work we have developed a highly constrained, fully dynamic PET reconstruction algorithm incorporating both spectral analysis temporal basis functions and spatial basis functions derived from the kernel method applied to a co-registered T1-weighted magnetic resonance (MR) image. The dynamic PET image is modelled as a linear combination of spatial and temporal basis functions, and a maximum likelihood estimate for the coefficients can be found using the expectation-maximization (EM) algorithm. Following reconstruction, kinetic fitting using any temporal model of interest can be applied. Based on a BrainWeb T1-weighted MR phantom, we performed a realistic dynamic [18F]FDG simulation study with two noise levels, and investigated the quantitative performance of the proposed reconstruction algorithm, comparing it with reconstructions incorporating either spectral analysis temporal basis functions alone or kernel spatial basis functions alone, as well as with conventional frame-independent reconstruction. Compared to the other reconstruction algorithms, the proposed algorithm achieved superior performance, offering a decrease in spatially averaged pixel-level root-mean-square-error on post-reconstruction kinetic parametric maps in the grey/white matter, as well as in the tumours when they were present on the co-registered MR image. When the tumours were not visible in the MR image, reconstruction with the proposed algorithm performed similarly to reconstruction with spectral temporal basis functions and was superior to both conventional frame-independent reconstruction and frame-independent reconstruction with kernel spatial basis functions. Furthermore, we demonstrate that a joint spectral/kernel model can also be used for effective post-reconstruction denoising, through the use of an EM-like image-space algorithm. Finally, we applied the proposed algorithm to reconstruction of real high-resolution dynamic [11C]SCH23390 data, showing promising results.

MR-guided dynamic PET reconstruction with the kernel method and spectral temporal basis functions.

PubMed

Novosad, Philip; Reader, Andrew J

2016-06-21

Recent advances in dynamic positron emission tomography (PET) reconstruction have demonstrated that it is possible to achieve markedly improved end-point kinetic parameter maps by incorporating a temporal model of the radiotracer directly into the reconstruction algorithm. In this work we have developed a highly constrained, fully dynamic PET reconstruction algorithm incorporating both spectral analysis temporal basis functions and spatial basis functions derived from the kernel method applied to a co-registered T1-weighted magnetic resonance (MR) image. The dynamic PET image is modelled as a linear combination of spatial and temporal basis functions, and a maximum likelihood estimate for the coefficients can be found using the expectation-maximization (EM) algorithm. Following reconstruction, kinetic fitting using any temporal model of interest can be applied. Based on a BrainWeb T1-weighted MR phantom, we performed a realistic dynamic [(18)F]FDG simulation study with two noise levels, and investigated the quantitative performance of the proposed reconstruction algorithm, comparing it with reconstructions incorporating either spectral analysis temporal basis functions alone or kernel spatial basis functions alone, as well as with conventional frame-independent reconstruction. Compared to the other reconstruction algorithms, the proposed algorithm achieved superior performance, offering a decrease in spatially averaged pixel-level root-mean-square-error on post-reconstruction kinetic parametric maps in the grey/white matter, as well as in the tumours when they were present on the co-registered MR image. When the tumours were not visible in the MR image, reconstruction with the proposed algorithm performed similarly to reconstruction with spectral temporal basis functions and was superior to both conventional frame-independent reconstruction and frame-independent reconstruction with kernel spatial basis functions. Furthermore, we demonstrate that a joint spectral/kernel model can also be used for effective post-reconstruction denoising, through the use of an EM-like image-space algorithm. Finally, we applied the proposed algorithm to reconstruction of real high-resolution dynamic [(11)C]SCH23390 data, showing promising results.

Unsteady Solution of Non-Linear Differential Equations Using Walsh Function Series

NASA Technical Reports Server (NTRS)

Gnoffo, Peter A.

2015-01-01

Walsh functions form an orthonormal basis set consisting of square waves. The discontinuous nature of square waves make the system well suited for representing functions with discontinuities. The product of any two Walsh functions is another Walsh function - a feature that can radically change an algorithm for solving non-linear partial differential equations (PDEs). The solution algorithm of non-linear differential equations using Walsh function series is unique in that integrals and derivatives may be computed using simple matrix multiplication of series representations of functions. Solutions to PDEs are derived as functions of wave component amplitude. Three sample problems are presented to illustrate the Walsh function series approach to solving unsteady PDEs. These include an advection equation, a Burgers equation, and a Riemann problem. The sample problems demonstrate the use of the Walsh function solution algorithms, exploiting Fast Walsh Transforms in multi-dimensions (O(Nlog(N))). Details of a Fast Walsh Reciprocal, defined here for the first time, enable inversion of aWalsh Symmetric Matrix in O(Nlog(N)) operations. Walsh functions have been derived using a fractal recursion algorithm and these fractal patterns are observed in the progression of pairs of wave number amplitudes in the solutions. These patterns are most easily observed in a remapping defined as a fractal fingerprint (FFP). A prolongation of existing solutions to the next highest order exploits these patterns. The algorithms presented here are considered a work in progress that provide new alternatives and new insights into the solution of non-linear PDEs.

Genetic Algorithm for Solving Fuzzy Shortest Path Problem in a Network with mixed fuzzy arc lengths

NASA Astrophysics Data System (ADS)

Mahdavi, Iraj; Tajdin, Ali; Hassanzadeh, Reza; Mahdavi-Amiri, Nezam; Shafieian, Hosna

2011-06-01

We are concerned with the design of a model and an algorithm for computing a shortest path in a network having various types of fuzzy arc lengths. First, we develop a new technique for the addition of various fuzzy numbers in a path using α -cuts by proposing a linear least squares model to obtain membership functions for the considered additions. Then, using a recently proposed distance function for comparison of fuzzy numbers. we propose a new approach to solve the fuzzy APSPP using of genetic algorithm. Examples are worked out to illustrate the applicability of the proposed model.

Output-Sensitive Construction of Reeb Graphs.

PubMed

Doraiswamy, H; Natarajan, V

2012-01-01

The Reeb graph of a scalar function represents the evolution of the topology of its level sets. This paper describes a near-optimal output-sensitive algorithm for computing the Reeb graph of scalar functions defined over manifolds or non-manifolds in any dimension. Key to the simplicity and efficiency of the algorithm is an alternate definition of the Reeb graph that considers equivalence classes of level sets instead of individual level sets. The algorithm works in two steps. The first step locates all critical points of the function in the domain. Critical points correspond to nodes in the Reeb graph. Arcs connecting the nodes are computed in the second step by a simple search procedure that works on a small subset of the domain that corresponds to a pair of critical points. The paper also describes a scheme for controlled simplification of the Reeb graph and two different graph layout schemes that help in the effective presentation of Reeb graphs for visual analysis of scalar fields. Finally, the Reeb graph is employed in four different applications-surface segmentation, spatially-aware transfer function design, visualization of interval volumes, and interactive exploration of time-varying data.

Genetic Algorithm Approaches for Actuator Placement

NASA Technical Reports Server (NTRS)

Crossley, William A.

2000-01-01

This research investigated genetic algorithm approaches for smart actuator placement to provide aircraft maneuverability without requiring hinged flaps or other control surfaces. The effort supported goals of the Multidisciplinary Design Optimization focus efforts in NASA's Aircraft au program. This work helped to properly identify various aspects of the genetic algorithm operators and parameters that allow for placement of discrete control actuators/effectors. An improved problem definition, including better definition of the objective function and constraints, resulted from this research effort. The work conducted for this research used a geometrically simple wing model; however, an increasing number of potential actuator placement locations were incorporated to illustrate the ability of the GA to determine promising actuator placement arrangements. This effort's major result is a useful genetic algorithm-based approach to assist in the discrete actuator/effector placement problem.

On the Satisfaction of Modulus and Ambiguity Function Constraints in Radar Waveform Optimization for Detection

DTIC Science & Technology

2010-06-01

sense that the two waveforms are as close as possible in a Euclidean sense . Li et al. [33] later devised an algorithm that provides the optimal waveform...respectively), and the SWORD algorithm in [33]. These algorithms were designed for the problem of detecting a known signal in the presence of wide- sense ... sensing , astronomy, crystallography, signal processing, and image processing. (See references in the works cited below for examples.) In the general

A dynamic data source selection system for smartwatch platform.

PubMed

Nemati, Ebrahim; Sideris, Konstantinos; Kalantarian, Haik; Sarrafzadeh, Majid

2016-08-01

A novel data source selection algorithm is proposed for ambulatory activity tracking of elderly people. The algorithm introduces the concept of dynamic switching between the data collection modules (a smartwatch and a smartphone) to improve accuracy and battery life using contextual information. We show that by making offloading decisions as a function of activity, the proposed algorithm improves power consumption and accuracy of the previous work by 7 hours and 5% respectively compared to the baseline.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Omet, M.; Michizono, S.; Matsumoto, T.

We report the development and implementation of four FPGA-based predistortion-type klystron linearization algorithms. Klystron linearization is essential for the realization of ILC, since it is required to operate the klystrons 7% in power below their saturation. The work presented was performed in international collaborations at the Fermi National Accelerator Laboratory (FNAL), USA and the Deutsches Elektronen Synchrotron (DESY), Germany. With the newly developed algorithms, the generation of correction factors on the FPGA was improved compared to past algorithms, avoiding quantization and decreasing memory requirements. At FNAL, three algorithms were tested at the Advanced Superconducting Test Accelerator (ASTA), demonstrating a successfulmore » implementation for one algorithm and a proof of principle for two algorithms. Furthermore, the functionality of the algorithm implemented at DESY was demonstrated successfully in a simulation.« less

An item-oriented recommendation algorithm on cold-start problem

NASA Astrophysics Data System (ADS)

Qiu, Tian; Chen, Guang; Zhang, Zi-Ke; Zhou, Tao

2011-09-01

Based on a hybrid algorithm incorporating the heat conduction and probability spreading processes (Proc. Natl. Acad. Sci. U.S.A., 107 (2010) 4511), in this letter, we propose an improved method by introducing an item-oriented function, focusing on solving the dilemma of the recommendation accuracy between the cold and popular items. Differently from previous works, the present algorithm does not require any additional information (e.g., tags). Further experimental results obtained in three real datasets, RYM, Netflix and MovieLens, show that, compared with the original hybrid method, the proposed algorithm significantly enhances the recommendation accuracy of the cold items, while it keeps the recommendation accuracy of the overall and the popular items. This work might shed some light on both understanding and designing effective methods for long-tailed online applications of recommender systems.

Parana Basin Structure from Multi-Objective Inversion of Surface Wave and Receiver Function by Competent Genetic Algorithm

NASA Astrophysics Data System (ADS)

An, M.; Assumpcao, M.

2003-12-01

The joint inversion of receiver function and surface wave is an effective way to diminish the influences of the strong tradeoff among parameters and the different sensitivity to the model parameters in their respective inversions, but the inversion problem becomes more complex. Multi-objective problems can be much more complicated than single-objective inversion in the model selection and optimization. If objectives are involved and conflicting, models can be ordered only partially. In this case, Pareto-optimal preference should be used to select solutions. On the other hand, the inversion to get only a few optimal solutions can not deal properly with the strong tradeoff between parameters, the uncertainties in the observation, the geophysical complexities and even the incompetency of the inversion technique. The effective way is to retrieve the geophysical information statistically from many acceptable solutions, which requires more competent global algorithms. Competent genetic algorithms recently proposed are far superior to the conventional genetic algorithm and can solve hard problems quickly, reliably and accurately. In this work we used one of competent genetic algorithms, Bayesian Optimization Algorithm as the main inverse procedure. This algorithm uses Bayesian networks to draw out inherited information and can use Pareto-optimal preference in the inversion. With this algorithm, the lithospheric structure of Paran"› basin is inverted to fit both the observations of inter-station surface wave dispersion and receiver function.

Gaussian-input Gaussian mixture model for representing density maps and atomic models.

PubMed

Kawabata, Takeshi

2018-07-01

A new Gaussian mixture model (GMM) has been developed for better representations of both atomic models and electron microscopy 3D density maps. The standard GMM algorithm employs an EM algorithm to determine the parameters. It accepted a set of 3D points with weights, corresponding to voxel or atomic centers. Although the standard algorithm worked reasonably well; however, it had three problems. First, it ignored the size (voxel width or atomic radius) of the input, and thus it could lead to a GMM with a smaller spread than the input. Second, the algorithm had a singularity problem, as it sometimes stopped the iterative procedure due to a Gaussian function with almost zero variance. Third, a map with a large number of voxels required a long computation time for conversion to a GMM. To solve these problems, we have introduced a Gaussian-input GMM algorithm, which considers the input atoms or voxels as a set of Gaussian functions. The standard EM algorithm of GMM was extended to optimize the new GMM. The new GMM has identical radius of gyration to the input, and does not suddenly stop due to the singularity problem. For fast computation, we have introduced a down-sampled Gaussian functions (DSG) by merging neighboring voxels into an anisotropic Gaussian function. It provides a GMM with thousands of Gaussian functions in a short computation time. We also have introduced a DSG-input GMM: the Gaussian-input GMM with the DSG as the input. This new algorithm is much faster than the standard algorithm. Copyright © 2018 The Author(s). Published by Elsevier Inc. All rights reserved.

Automatic measurement of voice onset time using discriminative structured prediction.

PubMed

Sonderegger, Morgan; Keshet, Joseph

2012-12-01

A discriminative large-margin algorithm for automatic measurement of voice onset time (VOT) is described, considered as a case of predicting structured output from speech. Manually labeled data are used to train a function that takes as input a speech segment of an arbitrary length containing a voiceless stop, and outputs its VOT. The function is explicitly trained to minimize the difference between predicted and manually measured VOT; it operates on a set of acoustic feature functions designed based on spectral and temporal cues used by human VOT annotators. The algorithm is applied to initial voiceless stops from four corpora, representing different types of speech. Using several evaluation methods, the algorithm's performance is near human intertranscriber reliability, and compares favorably with previous work. Furthermore, the algorithm's performance is minimally affected by training and testing on different corpora, and remains essentially constant as the amount of training data is reduced to 50-250 manually labeled examples, demonstrating the method's practical applicability to new datasets.

An improved Bayesian tensor regularization and sampling algorithm to track neuronal fiber pathways in the language circuit.

PubMed

Mishra, Arabinda; Anderson, Adam W; Wu, Xi; Gore, John C; Ding, Zhaohua

2010-08-01

The purpose of this work is to design a neuronal fiber tracking algorithm, which will be more suitable for reconstruction of fibers associated with functionally important regions in the human brain. The functional activations in the brain normally occur in the gray matter regions. Hence the fibers bordering these regions are weakly myelinated, resulting in poor performance of conventional tractography methods to trace the fiber links between them. A lower fractional anisotropy in this region makes it even difficult to track the fibers in the presence of noise. In this work, the authors focused on a stochastic approach to reconstruct these fiber pathways based on a Bayesian regularization framework. To estimate the true fiber direction (propagation vector), the a priori and conditional probability density functions are calculated in advance and are modeled as multivariate normal. The variance of the estimated tensor element vector is associated with the uncertainty due to noise and partial volume averaging (PVA). An adaptive and multiple sampling of the estimated tensor element vector, which is a function of the pre-estimated variance, overcomes the effect of noise and PVA in this work. The algorithm has been rigorously tested using a variety of synthetic data sets. The quantitative comparison of the results to standard algorithms motivated the authors to implement it for in vivo DTI data analysis. The algorithm has been implemented to delineate fibers in two major language pathways (Broca's to SMA and Broca's to Wernicke's) across 12 healthy subjects. Though the mean of standard deviation was marginally bigger than conventional (Euler's) approach [P. J. Basser et al., "In vivo fiber tractography using DT-MRI data," Magn. Reson. Med. 44(4), 625-632 (2000)], the number of extracted fibers in this approach was significantly higher. The authors also compared the performance of the proposed method to Lu's method [Y. Lu et al., "Improved fiber tractography with Bayesian tensor regularization," Neuroimage 31(3), 1061-1074 (2006)] and Friman's stochastic approach [O. Friman et al., "A Bayesian approach for stochastic white matter tractography," IEEE Trans. Med. Imaging 25(8), 965-978 (2006)]. Overall performance of the approach is found to be superior to above two methods, particularly when the signal-to-noise ratio was low. The authors observed that an adaptive sampling of the tensor element vectors, estimated as a function of the variance in a Bayesian framework, can effectively delineate neuronal fibers to analyze the structure-function relationship in human brain. The simulated and in vivo results are in good agreement with the theoretical aspects of the algorithm.

A Kind of Nonlinear Programming Problem Based on Mixed Fuzzy Relation Equations Constraints

NASA Astrophysics Data System (ADS)

Li, Jinquan; Feng, Shuang; Mi, Honghai

In this work, a kind of nonlinear programming problem with non-differential objective function and under the constraints expressed by a system of mixed fuzzy relation equations is investigated. First, some properties of this kind of optimization problem are obtained. Then, a polynomial-time algorithm for this kind of optimization problem is proposed based on these properties. Furthermore, we show that this algorithm is optimal for the considered optimization problem in this paper. Finally, numerical examples are provided to illustrate our algorithms.

Self Improving Methods for Materials and Process Design

DTIC Science & Technology

1998-08-31

using inductive coupling techniques. The first phase of the work focuses on developing an artificial neural network learning for function approximation...developing an artificial neural network learning algorithm for time-series prediction. The third phase of the work focuses on model selection. We have

A novel approach for analyzing fuzzy system reliability using different types of intuitionistic fuzzy failure rates of components.

PubMed

Kumar, Mohit; Yadav, Shiv Prasad

2012-03-01

This paper addresses the fuzzy system reliability analysis using different types of intuitionistic fuzzy numbers. Till now, in the literature, to analyze the fuzzy system reliability, it is assumed that the failure rates of all components of a system follow the same type of fuzzy set or intuitionistic fuzzy set. However, in practical problems, such type of situation rarely occurs. Therefore, in the present paper, a new algorithm has been introduced to construct the membership function and non-membership function of fuzzy reliability of a system having components following different types of intuitionistic fuzzy failure rates. Functions of intuitionistic fuzzy numbers are calculated to construct the membership function and non-membership function of fuzzy reliability via non-linear programming techniques. Using the proposed algorithm, membership functions and non-membership functions of fuzzy reliability of a series system and a parallel systems are constructed. Our study generalizes the various works of the literature. Numerical examples are given to illustrate the proposed algorithm. Copyright © 2011 ISA. Published by Elsevier Ltd. All rights reserved.

A Genetic Algorithm for the Generation of Packetization Masks for Robust Image Communication

PubMed Central

Zapata-Quiñones, Katherine; Duran-Faundez, Cristian; Gutiérrez, Gilberto; Lecuire, Vincent; Arredondo-Flores, Christopher; Jara-Lipán, Hugo

2017-01-01

Image interleaving has proven to be an effective solution to provide the robustness of image communication systems when resource limitations make reliable protocols unsuitable (e.g., in wireless camera sensor networks); however, the search for optimal interleaving patterns is scarcely tackled in the literature. In 2008, Rombaut et al. presented an interesting approach introducing a packetization mask generator based in Simulated Annealing (SA), including a cost function, which allows assessing the suitability of a packetization pattern, avoiding extensive simulations. In this work, we present a complementary study about the non-trivial problem of generating optimal packetization patterns. We propose a genetic algorithm, as an alternative to the cited work, adopting the mentioned cost function, then comparing it to the SA approach and a torus automorphism interleaver. In addition, we engage the validation of the cost function and provide results attempting to conclude about its implication in the quality of reconstructed images. Several scenarios based on visual sensor networks applications were tested in a computer application. Results in terms of the selected cost function and image quality metric PSNR show that our algorithm presents similar results to the other approaches. Finally, we discuss the obtained results and comment about open research challenges. PMID:28452934

An Efficient Augmented Lagrangian Method for Statistical X-Ray CT Image Reconstruction.

PubMed

Li, Jiaojiao; Niu, Shanzhou; Huang, Jing; Bian, Zhaoying; Feng, Qianjin; Yu, Gaohang; Liang, Zhengrong; Chen, Wufan; Ma, Jianhua

2015-01-01

Statistical iterative reconstruction (SIR) for X-ray computed tomography (CT) under the penalized weighted least-squares criteria can yield significant gains over conventional analytical reconstruction from the noisy measurement. However, due to the nonlinear expression of the objective function, most exiting algorithms related to the SIR unavoidably suffer from heavy computation load and slow convergence rate, especially when an edge-preserving or sparsity-based penalty or regularization is incorporated. In this work, to address abovementioned issues of the general algorithms related to the SIR, we propose an adaptive nonmonotone alternating direction algorithm in the framework of augmented Lagrangian multiplier method, which is termed as "ALM-ANAD". The algorithm effectively combines an alternating direction technique with an adaptive nonmonotone line search to minimize the augmented Lagrangian function at each iteration. To evaluate the present ALM-ANAD algorithm, both qualitative and quantitative studies were conducted by using digital and physical phantoms. Experimental results show that the present ALM-ANAD algorithm can achieve noticeable gains over the classical nonlinear conjugate gradient algorithm and state-of-the-art split Bregman algorithm in terms of noise reduction, contrast-to-noise ratio, convergence rate, and universal quality index metrics.

FPGA-based Klystron linearization implementations in scope of ILC

DOE PAGES

Omet, M.; Michizono, S.; Matsumoto, T.; ...

2015-01-23

We report the development and implementation of four FPGA-based predistortion-type klystron linearization algorithms. Klystron linearization is essential for the realization of ILC, since it is required to operate the klystrons 7% in power below their saturation. The work presented was performed in international collaborations at the Fermi National Accelerator Laboratory (FNAL), USA and the Deutsches Elektronen Synchrotron (DESY), Germany. With the newly developed algorithms, the generation of correction factors on the FPGA was improved compared to past algorithms, avoiding quantization and decreasing memory requirements. At FNAL, three algorithms were tested at the Advanced Superconducting Test Accelerator (ASTA), demonstrating a successfulmore » implementation for one algorithm and a proof of principle for two algorithms. Furthermore, the functionality of the algorithm implemented at DESY was demonstrated successfully in a simulation.« less

Common spatial pattern combined with kernel linear discriminate and generalized radial basis function for motor imagery-based brain computer interface applications

NASA Astrophysics Data System (ADS)

Hekmatmanesh, Amin; Jamaloo, Fatemeh; Wu, Huapeng; Handroos, Heikki; Kilpeläinen, Asko

2018-04-01

Brain Computer Interface (BCI) can be a challenge for developing of robotic, prosthesis and human-controlled systems. This work focuses on the implementation of a common spatial pattern (CSP) base algorithm to detect event related desynchronization patterns. Utilizing famous previous work in this area, features are extracted by filter bank with common spatial pattern (FBCSP) method, and then weighted by a sensitive learning vector quantization (SLVQ) algorithm. In the current work, application of the radial basis function (RBF) as a mapping kernel of linear discriminant analysis (KLDA) method on the weighted features, allows the transfer of data into a higher dimension for more discriminated data scattering by RBF kernel. Afterwards, support vector machine (SVM) with generalized radial basis function (GRBF) kernel is employed to improve the efficiency and robustness of the classification. Averagely, 89.60% accuracy and 74.19% robustness are achieved. BCI Competition III, Iva data set is used to evaluate the algorithm for detecting right hand and foot imagery movement patterns. Results show that combination of KLDA with SVM-GRBF classifier makes 8.9% and 14.19% improvements in accuracy and robustness, respectively. For all the subjects, it is concluded that mapping the CSP features into a higher dimension by RBF and utilization GRBF as a kernel of SVM, improve the accuracy and reliability of the proposed method.

Superiorized algorithm for reconstruction of CT images from sparse-view and limited-angle polyenergetic data

NASA Astrophysics Data System (ADS)

Humphries, T.; Winn, J.; Faridani, A.

2017-08-01

Recent work in CT image reconstruction has seen increasing interest in the use of total variation (TV) and related penalties to regularize problems involving reconstruction from undersampled or incomplete data. Superiorization is a recently proposed heuristic which provides an automatic procedure to ‘superiorize’ an iterative image reconstruction algorithm with respect to a chosen objective function, such as TV. Under certain conditions, the superiorized algorithm is guaranteed to find a solution that is as satisfactory as any found by the original algorithm with respect to satisfying the constraints of the problem; this solution is also expected to be superior with respect to the chosen objective. Most work on superiorization has used reconstruction algorithms which assume a linear measurement model, which in the case of CT corresponds to data generated from a monoenergetic x-ray beam. Many CT systems generate x-rays from a polyenergetic spectrum, however, in which the measured data represent an integral of object attenuation over all energies in the spectrum. This inconsistency with the linear model produces the well-known beam hardening artifacts, which impair analysis of CT images. In this work we superiorize an iterative algorithm for reconstruction from polyenergetic data, using both TV and an anisotropic TV (ATV) penalty. We apply the superiorized algorithm in numerical phantom experiments modeling both sparse-view and limited-angle scenarios. In our experiments, the superiorized algorithm successfully finds solutions which are as constraints-compatible as those found by the original algorithm, with significantly reduced TV and ATV values. The superiorized algorithm thus produces images with greatly reduced sparse-view and limited angle artifacts, which are also largely free of the beam hardening artifacts that would be present if a superiorized version of a monoenergetic algorithm were used.

Experimental realization of a one-way quantum computer algorithm solving Simon's problem.

PubMed

Tame, M S; Bell, B A; Di Franco, C; Wadsworth, W J; Rarity, J G

2014-11-14

We report an experimental demonstration of a one-way implementation of a quantum algorithm solving Simon's problem-a black-box period-finding problem that has an exponential gap between the classical and quantum runtime. Using an all-optical setup and modifying the bases of single-qubit measurements on a five-qubit cluster state, key representative functions of the logical two-qubit version's black box can be queried and solved. To the best of our knowledge, this work represents the first experimental realization of the quantum algorithm solving Simon's problem. The experimental results are in excellent agreement with the theoretical model, demonstrating the successful performance of the algorithm. With a view to scaling up to larger numbers of qubits, we analyze the resource requirements for an n-qubit version. This work helps highlight how one-way quantum computing provides a practical route to experimentally investigating the quantum-classical gap in the query complexity model.

An integral conservative gridding--algorithm using Hermitian curve interpolation.

PubMed

Volken, Werner; Frei, Daniel; Manser, Peter; Mini, Roberto; Born, Ernst J; Fix, Michael K

2008-11-07

The problem of re-sampling spatially distributed data organized into regular or irregular grids to finer or coarser resolution is a common task in data processing. This procedure is known as 'gridding' or 're-binning'. Depending on the quantity the data represents, the gridding-algorithm has to meet different requirements. For example, histogrammed physical quantities such as mass or energy have to be re-binned in order to conserve the overall integral. Moreover, if the quantity is positive definite, negative sampling values should be avoided. The gridding process requires a re-distribution of the original data set to a user-requested grid according to a distribution function. The distribution function can be determined on the basis of the given data by interpolation methods. In general, accurate interpolation with respect to multiple boundary conditions of heavily fluctuating data requires polynomial interpolation functions of second or even higher order. However, this may result in unrealistic deviations (overshoots or undershoots) of the interpolation function from the data. Accordingly, the re-sampled data may overestimate or underestimate the given data by a significant amount. The gridding-algorithm presented in this work was developed in order to overcome these problems. Instead of a straightforward interpolation of the given data using high-order polynomials, a parametrized Hermitian interpolation curve was used to approximate the integrated data set. A single parameter is determined by which the user can control the behavior of the interpolation function, i.e. the amount of overshoot and undershoot. Furthermore, it is shown how the algorithm can be extended to multidimensional grids. The algorithm was compared to commonly used gridding-algorithms using linear and cubic interpolation functions. It is shown that such interpolation functions may overestimate or underestimate the source data by about 10-20%, while the new algorithm can be tuned to significantly reduce these interpolation errors. The accuracy of the new algorithm was tested on a series of x-ray CT-images (head and neck, lung, pelvis). The new algorithm significantly improves the accuracy of the sampled images in terms of the mean square error and a quality index introduced by Wang and Bovik (2002 IEEE Signal Process. Lett. 9 81-4).

Thermodynamic properties of solvated peptides from selective integrated tempering sampling with a new weighting factor estimation algorithm

NASA Astrophysics Data System (ADS)

Shen, Lin; Xie, Liangxu; Yang, Mingjun

2017-04-01

Conformational sampling under rugged energy landscape is always a challenge in computer simulations. The recently developed integrated tempering sampling, together with its selective variant (SITS), emerges to be a powerful tool in exploring the free energy landscape or functional motions of various systems. The estimation of weighting factors constitutes a critical step in these methods and requires accurate calculation of partition function ratio between different thermodynamic states. In this work, we propose a new adaptive update algorithm to compute the weighting factors based on the weighted histogram analysis method (WHAM). The adaptive-WHAM algorithm with SITS is then applied to study the thermodynamic properties of several representative peptide systems solvated in an explicit water box. The performance of the new algorithm is validated in simulations of these solvated peptide systems. We anticipate more applications of this coupled optimisation and production algorithm to other complicated systems such as the biochemical reactions in solution.

Computational complexities and storage requirements of some Riccati equation solvers

NASA Technical Reports Server (NTRS)

Utku, Senol; Garba, John A.; Ramesh, A. V.

1989-01-01

The linear optimal control problem of an nth-order time-invariant dynamic system with a quadratic performance functional is usually solved by the Hamilton-Jacobi approach. This leads to the solution of the differential matrix Riccati equation with a terminal condition. The bulk of the computation for the optimal control problem is related to the solution of this equation. There are various algorithms in the literature for solving the matrix Riccati equation. However, computational complexities and storage requirements as a function of numbers of state variables, control variables, and sensors are not available for all these algorithms. In this work, the computational complexities and storage requirements for some of these algorithms are given. These expressions show the immensity of the computational requirements of the algorithms in solving the Riccati equation for large-order systems such as the control of highly flexible space structures. The expressions are also needed to compute the speedup and efficiency of any implementation of these algorithms on concurrent machines.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dall-Anese, Emiliano; Simonetto, Andrea

This paper focuses on the design of online algorithms based on prediction-correction steps to track the optimal solution of a time-varying constrained problem. Existing prediction-correction methods have been shown to work well for unconstrained convex problems and for settings where obtaining the inverse of the Hessian of the cost function can be computationally affordable. The prediction-correction algorithm proposed in this paper addresses the limitations of existing methods by tackling constrained problems and by designing a first-order prediction step that relies on the Hessian of the cost function (and do not require the computation of its inverse). Analytical results are establishedmore » to quantify the tracking error. Numerical simulations corroborate the analytical results and showcase performance and benefits of the algorithms.« less

Generalized and efficient algorithm for computing multipole energies and gradients based on Cartesian tensors

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lin, Dejun, E-mail: dejun.lin@gmail.com

2015-09-21

Accurate representation of intermolecular forces has been the central task of classical atomic simulations, known as molecular mechanics. Recent advancements in molecular mechanics models have put forward the explicit representation of permanent and/or induced electric multipole (EMP) moments. The formulas developed so far to calculate EMP interactions tend to have complicated expressions, especially in Cartesian coordinates, which can only be applied to a specific kernel potential function. For example, one needs to develop a new formula each time a new kernel function is encountered. The complication of these formalisms arises from an intriguing and yet obscured mathematical relation between themore » kernel functions and the gradient operators. Here, I uncover this relation via rigorous derivation and find that the formula to calculate EMP interactions is basically invariant to the potential kernel functions as long as they are of the form f(r), i.e., any Green’s function that depends on inter-particle distance. I provide an algorithm for efficient evaluation of EMP interaction energies, forces, and torques for any kernel f(r) up to any arbitrary rank of EMP moments in Cartesian coordinates. The working equations of this algorithm are essentially the same for any kernel f(r). Recently, a few recursive algorithms were proposed to calculate EMP interactions. Depending on the kernel functions, the algorithm here is about 4–16 times faster than these algorithms in terms of the required number of floating point operations and is much more memory efficient. I show that it is even faster than a theoretically ideal recursion scheme, i.e., one that requires 1 floating point multiplication and 1 addition per recursion step. This algorithm has a compact vector-based expression that is optimal for computer programming. The Cartesian nature of this algorithm makes it fit easily into modern molecular simulation packages as compared with spherical coordinate-based algorithms. A software library based on this algorithm has been implemented in C++11 and has been released.« less

A new numerical method for inverse Laplace transforms used to obtain gluon distributions from the proton structure function

NASA Astrophysics Data System (ADS)

Block, Martin M.; Durand, Loyal

2011-11-01

We recently derived a very accurate and fast new algorithm for numerically inverting the Laplace transforms needed to obtain gluon distributions from the proton structure function F2^{γ p}(x,Q2). We numerically inverted the function g( s), s being the variable in Laplace space, to G( v), where v is the variable in ordinary space. We have since discovered that the algorithm does not work if g( s)→0 less rapidly than 1/ s as s→∞, e.g., as 1/ s β for 0< β<1. In this note, we derive a new numerical algorithm for such cases, which holds for all positive and non-integer negative values of β. The new algorithm is exact if the original function G( v) is given by the product of a power v β-1 and a polynomial in v. We test the algorithm numerically for very small positive β, β=10-6 obtaining numerical results that imitate the Dirac delta function δ( v). We also devolve the published MSTW2008LO gluon distribution at virtuality Q 2=5 GeV2 down to the lower virtuality Q 2=1.69 GeV2. For devolution, β is negative, giving rise to inverse Laplace transforms that are distributions and not proper functions. This requires us to introduce the concept of Hadamard Finite Part integrals, which we discuss in detail.

A Log-Scaling Fault Tolerant Agreement Algorithm for a Fault Tolerant MPI

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hursey, Joshua J; Naughton, III, Thomas J; Vallee, Geoffroy R

The lack of fault tolerance is becoming a limiting factor for application scalability in HPC systems. The MPI does not provide standardized fault tolerance interfaces and semantics. The MPI Forum's Fault Tolerance Working Group is proposing a collective fault tolerant agreement algorithm for the next MPI standard. Such algorithms play a central role in many fault tolerant applications. This paper combines a log-scaling two-phase commit agreement algorithm with a reduction operation to provide the necessary functionality for the new collective without any additional messages. Error handling mechanisms are described that preserve the fault tolerance properties while maintaining overall scalability.

Application of a Noise Adaptive Contrast Sensitivity Function to Image Data Compression

NASA Astrophysics Data System (ADS)

Daly, Scott J.

1989-08-01

The visual contrast sensitivity function (CSF) has found increasing use in image compression as new algorithms optimize the display-observer interface in order to reduce the bit rate and increase the perceived image quality. In most compression algorithms, increasing the quantization intervals reduces the bit rate at the expense of introducing more quantization error, a potential image quality degradation. The CSF can be used to distribute this error as a function of spatial frequency such that it is undetectable by the human observer. Thus, instead of being mathematically lossless, the compression algorithm can be designed to be visually lossless, with the advantage of a significantly reduced bit rate. However, the CSF is strongly affected by image noise, changing in both shape and peak sensitivity. This work describes a model of the CSF that includes these changes as a function of image noise level by using the concepts of internal visual noise, and tests this model in the context of image compression with an observer study.

Graphical programming interface: A development environment for MRI methods.

PubMed

Zwart, Nicholas R; Pipe, James G

2015-11-01

To introduce a multiplatform, Python language-based, development environment called graphical programming interface for prototyping MRI techniques. The interface allows developers to interact with their scientific algorithm prototypes visually in an event-driven environment making tasks such as parameterization, algorithm testing, data manipulation, and visualization an integrated part of the work-flow. Algorithm developers extend the built-in functionality through simple code interfaces designed to facilitate rapid implementation. This article shows several examples of algorithms developed in graphical programming interface including the non-Cartesian MR reconstruction algorithms for PROPELLER and spiral as well as spin simulation and trajectory visualization of a FLORET example. The graphical programming interface framework is shown to be a versatile prototyping environment for developing numeric algorithms used in the latest MR techniques. © 2014 Wiley Periodicals, Inc.

[A diagnostic algorithm and treatment procedure in disordered vital functions in newborns admitted to a resuscitation ward].

PubMed

Ostreĭkov, I F; Podkopaev, V N; Moiseev, D B; Karpysheva, E V; Markova, L A; Sizov, S V

1997-01-01

Total mortality decreased by 2.5 times in the wards for intensive care of the newborns in the Tushino Pediatric Hospital in 1996 and is now 7.6%. Such results are due to a complex of measures, one such measure being the development and introduction of an algorithm for the diagnosis and treatment of newborns hospitalized in intensive care wards. The algorithm facilitates the work of the staff, helps earlier diagnose a disease, and, hence, carry out timely scientifically based therapy.

Parameter identification for nonlinear aerodynamic systems

NASA Technical Reports Server (NTRS)

Pearson, Allan E.

1992-01-01

Continuing work on frequency analysis for transfer function identification is discussed. A new study was initiated into a 'weighted' least squares algorithm within the context of the Fourier modulating function approach. The first phase of applying these techniques to the F-18 flight data is nearing completion, and these results are summarized.

Energy design for protein-protein interactions

PubMed Central

Ravikant, D. V. S.; Elber, Ron

2011-01-01

Proteins bind to other proteins efficiently and specifically to carry on many cell functions such as signaling, activation, transport, enzymatic reactions, and more. To determine the geometry and strength of binding of a protein pair, an energy function is required. An algorithm to design an optimal energy function, based on empirical data of protein complexes, is proposed and applied. Emphasis is made on negative design in which incorrect geometries are presented to the algorithm that learns to avoid them. For the docking problem the search for plausible geometries can be performed exhaustively. The possible geometries of the complex are generated on a grid with the help of a fast Fourier transform algorithm. A novel formulation of negative design makes it possible to investigate iteratively hundreds of millions of negative examples while monotonically improving the quality of the potential. Experimental structures for 640 protein complexes are used to generate positive and negative examples for learning parameters. The algorithm designed in this work finds the correct binding structure as the lowest energy minimum in 318 cases of the 640 examples. Further benchmarks on independent sets confirm the significant capacity of the scoring function to recognize correct modes of interactions. PMID:21842951

Saturation: An efficient iteration strategy for symbolic state-space generation

NASA Technical Reports Server (NTRS)

Ciardo, Gianfranco; Luettgen, Gerald; Siminiceanu, Radu; Bushnell, Dennis M. (Technical Monitor)

2001-01-01

This paper presents a novel algorithm for generating state spaces of asynchronous systems using Multi-valued Decision Diagrams. In contrast to related work, the next-state function of a system is not encoded as a single Boolean function, but as cross-products of integer functions. This permits the application of various iteration strategies to build a system's state space. In particular, this paper introduces a new elegant strategy, called saturation, and implements it in the tool SMART. On top of usually performing several orders of magnitude faster than existing BDD-based state-space generators, the algorithm's required peak memory is often close to the nal memory needed for storing the overall state spaces.

An improved algorithm of fiber tractography demonstrates postischemic cerebral reorganization

NASA Astrophysics Data System (ADS)

Liu, Xiao-dong; Lu, Jie; Yao, Li; Li, Kun-cheng; Zhao, Xiao-jie

2008-03-01

In vivo white matter tractography by diffusion tensor imaging (DTI) accurately represents the organizational architecture of white matter in the vicinity of brain lesions and especially ischemic brain. In this study, we suggested an improved fiber tracking algorithm based on TEND, called TENDAS, for tensor deflection with adaptive stepping, which had been introduced a stepping framework for interpreting the algorithm behavior as a function of the tensor shape (linear-shaped or not) and tract history. The propagation direction at each step was given by the deflection vector. TENDAS tractography was used to examine a 17-year-old recovery patient with congenital right hemisphere artery stenosis combining with fMRI. Meaningless picture location was used as spatial working memory task in this study. We detected the shifted functional localization to the contralateral homotypic cortex and more prominent and extensive left-sided parietal and medial frontal cortical activations which were used directly as seed mask for tractography for the reconstruction of individual spatial parietal pathways. Comparing with the TEND algorithms, TENDAS shows smoother and less sharp bending characterization of white matter architecture of the parietal cortex. The results of this preliminary study were twofold. First, TENDAS may provide more adaptability and accuracy in reconstructing certain anatomical features, whereas it is very difficult to verify tractography maps of white matter connectivity in the living human brain. Second, our study indicates that combination of TENDAS and fMRI provide a unique image of functional cortical reorganization and structural modifications of postischemic spatial working memory.

On multiple crack identification by ultrasonic scanning

NASA Astrophysics Data System (ADS)

Brigante, M.; Sumbatyan, M. A.

2018-04-01

The present work develops an approach which reduces operator equations arising in the engineering problems to the problem of minimizing the discrepancy functional. For this minimization, an algorithm of random global search is proposed, which is allied to some genetic algorithms. The efficiency of the method is demonstrated by the solving problem of simultaneous identification of several linear cracks forming an array in an elastic medium by using the circular Ultrasonic scanning.

Development of Artificial Neural Network Model for Diesel Fuel Properties Prediction using Vibrational Spectroscopy.

PubMed

Bolanča, Tomislav; Marinović, Slavica; Ukić, Sime; Jukić, Ante; Rukavina, Vinko

2012-06-01

This paper describes development of artificial neural network models which can be used to correlate and predict diesel fuel properties from several FTIR-ATR absorbances and Raman intensities as input variables. Multilayer feed forward and radial basis function neural networks have been used to rapid and simultaneous prediction of cetane number, cetane index, density, viscosity, distillation temperatures at 10% (T10), 50% (T50) and 90% (T90) recovery, contents of total aromatics and polycyclic aromatic hydrocarbons of commercial diesel fuels. In this study two-phase training procedures for multilayer feed forward networks were applied. While first phase training algorithm was constantly the back propagation one, two second phase training algorithms were varied and compared, namely: conjugate gradient and quasi Newton. In case of radial basis function network, radial layer was trained using K-means radial assignment algorithm and three different radial spread algorithms: explicit, isotropic and K-nearest neighbour. The number of hidden layer neurons and experimental data points used for the training set have been optimized for both neural networks in order to insure good predictive ability by reducing unnecessary experimental work. This work shows that developed artificial neural network models can determine main properties of diesel fuels simultaneously based on a single and fast IR or Raman measurement.

The Performance of Short-Term Heart Rate Variability in the Detection of Congestive Heart Failure

PubMed Central

Barros, Allan Kardec; Ohnishi, Noboru

2016-01-01

Congestive heart failure (CHF) is a cardiac disease associated with the decreasing capacity of the cardiac output. It has been shown that the CHF is the main cause of the cardiac death around the world. Some works proposed to discriminate CHF subjects from healthy subjects using either electrocardiogram (ECG) or heart rate variability (HRV) from long-term recordings. In this work, we propose an alternative framework to discriminate CHF from healthy subjects by using HRV short-term intervals based on 256 RR continuous samples. Our framework uses a matching pursuit algorithm based on Gabor functions. From the selected Gabor functions, we derived a set of features that are inputted into a hybrid framework which uses a genetic algorithm and k-nearest neighbour classifier to select a subset of features that has the best classification performance. The performance of the framework is analyzed using both Fantasia and CHF database from Physionet archives which are, respectively, composed of 40 healthy volunteers and 29 subjects. From a set of nonstandard 16 features, the proposed framework reaches an overall accuracy of 100% with five features. Our results suggest that the application of hybrid frameworks whose classifier algorithms are based on genetic algorithms has outperformed well-known classifier methods. PMID:27891509

Robust dynamic myocardial perfusion CT deconvolution for accurate residue function estimation via adaptive-weighted tensor total variation regularization: a preclinical study.

PubMed

Zeng, Dong; Gong, Changfei; Bian, Zhaoying; Huang, Jing; Zhang, Xinyu; Zhang, Hua; Lu, Lijun; Niu, Shanzhou; Zhang, Zhang; Liang, Zhengrong; Feng, Qianjin; Chen, Wufan; Ma, Jianhua

2016-11-21

Dynamic myocardial perfusion computed tomography (MPCT) is a promising technique for quick diagnosis and risk stratification of coronary artery disease. However, one major drawback of dynamic MPCT imaging is the heavy radiation dose to patients due to its dynamic image acquisition protocol. In this work, to address this issue, we present a robust dynamic MPCT deconvolution algorithm via adaptive-weighted tensor total variation (AwTTV) regularization for accurate residue function estimation with low-mA s data acquisitions. For simplicity, the presented method is termed 'MPD-AwTTV'. More specifically, the gains of the AwTTV regularization over the original tensor total variation regularization are from the anisotropic edge property of the sequential MPCT images. To minimize the associative objective function we propose an efficient iterative optimization strategy with fast convergence rate in the framework of an iterative shrinkage/thresholding algorithm. We validate and evaluate the presented algorithm using both digital XCAT phantom and preclinical porcine data. The preliminary experimental results have demonstrated that the presented MPD-AwTTV deconvolution algorithm can achieve remarkable gains in noise-induced artifact suppression, edge detail preservation, and accurate flow-scaled residue function and MPHM estimation as compared with the other existing deconvolution algorithms in digital phantom studies, and similar gains can be obtained in the porcine data experiment.

Robust dynamic myocardial perfusion CT deconvolution for accurate residue function estimation via adaptive-weighted tensor total variation regularization: a preclinical study

NASA Astrophysics Data System (ADS)

Zeng, Dong; Gong, Changfei; Bian, Zhaoying; Huang, Jing; Zhang, Xinyu; Zhang, Hua; Lu, Lijun; Niu, Shanzhou; Zhang, Zhang; Liang, Zhengrong; Feng, Qianjin; Chen, Wufan; Ma, Jianhua

2016-11-01

Dynamic myocardial perfusion computed tomography (MPCT) is a promising technique for quick diagnosis and risk stratification of coronary artery disease. However, one major drawback of dynamic MPCT imaging is the heavy radiation dose to patients due to its dynamic image acquisition protocol. In this work, to address this issue, we present a robust dynamic MPCT deconvolution algorithm via adaptive-weighted tensor total variation (AwTTV) regularization for accurate residue function estimation with low-mA s data acquisitions. For simplicity, the presented method is termed ‘MPD-AwTTV’. More specifically, the gains of the AwTTV regularization over the original tensor total variation regularization are from the anisotropic edge property of the sequential MPCT images. To minimize the associative objective function we propose an efficient iterative optimization strategy with fast convergence rate in the framework of an iterative shrinkage/thresholding algorithm. We validate and evaluate the presented algorithm using both digital XCAT phantom and preclinical porcine data. The preliminary experimental results have demonstrated that the presented MPD-AwTTV deconvolution algorithm can achieve remarkable gains in noise-induced artifact suppression, edge detail preservation, and accurate flow-scaled residue function and MPHM estimation as compared with the other existing deconvolution algorithms in digital phantom studies, and similar gains can be obtained in the porcine data experiment.

A Hybrid Adaptive Routing Algorithm for Event-Driven Wireless Sensor Networks

PubMed Central

Figueiredo, Carlos M. S.; Nakamura, Eduardo F.; Loureiro, Antonio A. F.

2009-01-01

Routing is a basic function in wireless sensor networks (WSNs). For these networks, routing algorithms depend on the characteristics of the applications and, consequently, there is no self-contained algorithm suitable for every case. In some scenarios, the network behavior (traffic load) may vary a lot, such as an event-driven application, favoring different algorithms at different instants. This work presents a hybrid and adaptive algorithm for routing in WSNs, called Multi-MAF, that adapts its behavior autonomously in response to the variation of network conditions. In particular, the proposed algorithm applies both reactive and proactive strategies for routing infrastructure creation, and uses an event-detection estimation model to change between the strategies and save energy. To show the advantages of the proposed approach, it is evaluated through simulations. Comparisons with independent reactive and proactive algorithms show improvements on energy consumption. PMID:22423207

A hybrid adaptive routing algorithm for event-driven wireless sensor networks.

PubMed

Figueiredo, Carlos M S; Nakamura, Eduardo F; Loureiro, Antonio A F

2009-01-01

Routing is a basic function in wireless sensor networks (WSNs). For these networks, routing algorithms depend on the characteristics of the applications and, consequently, there is no self-contained algorithm suitable for every case. In some scenarios, the network behavior (traffic load) may vary a lot, such as an event-driven application, favoring different algorithms at different instants. This work presents a hybrid and adaptive algorithm for routing in WSNs, called Multi-MAF, that adapts its behavior autonomously in response to the variation of network conditions. In particular, the proposed algorithm applies both reactive and proactive strategies for routing infrastructure creation, and uses an event-detection estimation model to change between the strategies and save energy. To show the advantages of the proposed approach, it is evaluated through simulations. Comparisons with independent reactive and proactive algorithms show improvements on energy consumption.

Comparison of multihardware parallel implementations for a phase unwrapping algorithm

NASA Astrophysics Data System (ADS)

Hernandez-Lopez, Francisco Javier; Rivera, Mariano; Salazar-Garibay, Adan; Legarda-Sáenz, Ricardo

2018-04-01

Phase unwrapping is an important problem in the areas of optical metrology, synthetic aperture radar (SAR) image analysis, and magnetic resonance imaging (MRI) analysis. These images are becoming larger in size and, particularly, the availability and need for processing of SAR and MRI data have increased significantly with the acquisition of remote sensing data and the popularization of magnetic resonators in clinical diagnosis. Therefore, it is important to develop faster and accurate phase unwrapping algorithms. We propose a parallel multigrid algorithm of a phase unwrapping method named accumulation of residual maps, which builds on a serial algorithm that consists of the minimization of a cost function; minimization achieved by means of a serial Gauss-Seidel kind algorithm. Our algorithm also optimizes the original cost function, but unlike the original work, our algorithm is a parallel Jacobi class with alternated minimizations. This strategy is known as the chessboard type, where red pixels can be updated in parallel at same iteration since they are independent. Similarly, black pixels can be updated in parallel in an alternating iteration. We present parallel implementations of our algorithm for different parallel multicore architecture such as CPU-multicore, Xeon Phi coprocessor, and Nvidia graphics processing unit. In all the cases, we obtain a superior performance of our parallel algorithm when compared with the original serial version. In addition, we present a detailed comparative performance of the developed parallel versions.

Multimodal optimization by using hybrid of artificial bee colony algorithm and BFGS algorithm

NASA Astrophysics Data System (ADS)

Anam, S.

2017-10-01

Optimization has become one of the important fields in Mathematics. Many problems in engineering and science can be formulated into optimization problems. They maybe have many local optima. The optimization problem with many local optima, known as multimodal optimization problem, is how to find the global solution. Several metaheuristic methods have been proposed to solve multimodal optimization problems such as Particle Swarm Optimization (PSO), Genetics Algorithm (GA), Artificial Bee Colony (ABC) algorithm, etc. The performance of the ABC algorithm is better than or similar to those of other population-based algorithms with the advantage of employing a fewer control parameters. The ABC algorithm also has the advantages of strong robustness, fast convergence and high flexibility. However, it has the disadvantages premature convergence in the later search period. The accuracy of the optimal value cannot meet the requirements sometimes. Broyden-Fletcher-Goldfarb-Shanno (BFGS) algorithm is a good iterative method for finding a local optimum. Compared with other local optimization methods, the BFGS algorithm is better. Based on the advantages of the ABC algorithm and the BFGS algorithm, this paper proposes a hybrid of the artificial bee colony algorithm and the BFGS algorithm to solve the multimodal optimization problem. The first step is that the ABC algorithm is run to find a point. In the second step is that the point obtained by the first step is used as an initial point of BFGS algorithm. The results show that the hybrid method can overcome from the basic ABC algorithm problems for almost all test function. However, if the shape of function is flat, the proposed method cannot work well.

High quality 4D cone-beam CT reconstruction using motion-compensated total variation regularization

NASA Astrophysics Data System (ADS)

Zhang, Hua; Ma, Jianhua; Bian, Zhaoying; Zeng, Dong; Feng, Qianjin; Chen, Wufan

2017-04-01

Four dimensional cone-beam computed tomography (4D-CBCT) has great potential clinical value because of its ability to describe tumor and organ motion. But the challenge in 4D-CBCT reconstruction is the limited number of projections at each phase, which result in a reconstruction full of noise and streak artifacts with the conventional analytical algorithms. To address this problem, in this paper, we propose a motion compensated total variation regularization approach which tries to fully explore the temporal coherence of the spatial structures among the 4D-CBCT phases. In this work, we additionally conduct motion estimation/motion compensation (ME/MC) on the 4D-CBCT volume by using inter-phase deformation vector fields (DVFs). The motion compensated 4D-CBCT volume is then viewed as a pseudo-static sequence, of which the regularization function was imposed on. The regularization used in this work is the 3D spatial total variation minimization combined with 1D temporal total variation minimization. We subsequently construct a cost function for a reconstruction pass, and minimize this cost function using a variable splitting algorithm. Simulation and real patient data were used to evaluate the proposed algorithm. Results show that the introduction of additional temporal correlation along the phase direction can improve the 4D-CBCT image quality.

A Probabilistic Model of Social Working Memory for Information Retrieval in Social Interactions.

PubMed

Li, Liyuan; Xu, Qianli; Gan, Tian; Tan, Cheston; Lim, Joo-Hwee

2018-05-01

Social working memory (SWM) plays an important role in navigating social interactions. Inspired by studies in psychology, neuroscience, cognitive science, and machine learning, we propose a probabilistic model of SWM to mimic human social intelligence for personal information retrieval (IR) in social interactions. First, we establish a semantic hierarchy as social long-term memory to encode personal information. Next, we propose a semantic Bayesian network as the SWM, which integrates the cognitive functions of accessibility and self-regulation. One subgraphical model implements the accessibility function to learn the social consensus about IR-based on social information concept, clustering, social context, and similarity between persons. Beyond accessibility, one more layer is added to simulate the function of self-regulation to perform the personal adaptation to the consensus based on human personality. Two learning algorithms are proposed to train the probabilistic SWM model on a raw dataset of high uncertainty and incompleteness. One is an efficient learning algorithm of Newton's method, and the other is a genetic algorithm. Systematic evaluations show that the proposed SWM model is able to learn human social intelligence effectively and outperforms the baseline Bayesian cognitive model. Toward real-world applications, we implement our model on Google Glass as a wearable assistant for social interaction.

Research on WNN Modeling for Gold Price Forecasting Based on Improved Artificial Bee Colony Algorithm

PubMed Central

2014-01-01

Gold price forecasting has been a hot issue in economics recently. In this work, wavelet neural network (WNN) combined with a novel artificial bee colony (ABC) algorithm is proposed for this gold price forecasting issue. In this improved algorithm, the conventional roulette selection strategy is discarded. Besides, the convergence statuses in a previous cycle of iteration are fully utilized as feedback messages to manipulate the searching intensity in a subsequent cycle. Experimental results confirm that this new algorithm converges faster than the conventional ABC when tested on some classical benchmark functions and is effective to improve modeling capacity of WNN regarding the gold price forecasting scheme. PMID:24744773

ClusterViz: A Cytoscape APP for Cluster Analysis of Biological Network.

PubMed

Wang, Jianxin; Zhong, Jiancheng; Chen, Gang; Li, Min; Wu, Fang-xiang; Pan, Yi

2015-01-01

Cluster analysis of biological networks is one of the most important approaches for identifying functional modules and predicting protein functions. Furthermore, visualization of clustering results is crucial to uncover the structure of biological networks. In this paper, ClusterViz, an APP of Cytoscape 3 for cluster analysis and visualization, has been developed. In order to reduce complexity and enable extendibility for ClusterViz, we designed the architecture of ClusterViz based on the framework of Open Services Gateway Initiative. According to the architecture, the implementation of ClusterViz is partitioned into three modules including interface of ClusterViz, clustering algorithms and visualization and export. ClusterViz fascinates the comparison of the results of different algorithms to do further related analysis. Three commonly used clustering algorithms, FAG-EC, EAGLE and MCODE, are included in the current version. Due to adopting the abstract interface of algorithms in module of the clustering algorithms, more clustering algorithms can be included for the future use. To illustrate usability of ClusterViz, we provided three examples with detailed steps from the important scientific articles, which show that our tool has helped several research teams do their research work on the mechanism of the biological networks.

Decorating surfaces with bidirectional texture functions.

PubMed

Zhou, Kun; Du, Peng; Wang, Lifeng; Matsushita, Yasuyuki; Shi, Jiaoying; Guo, Baining; Shum, Heung-Yeung

2005-01-01

We present a system for decorating arbitrary surfaces with bidirectional texture functions (BTF). Our system generates BTFs in two steps. First, we automatically synthesize a BTF over the target surface from a given BTF sample. Then, we let the user interactively paint BTF patches onto the surface such that the painted patches seamlessly integrate with the background patterns. Our system is based on a patch-based texture synthesis approach known as quilting. We present a graphcut algorithm for BTF synthesis on surfaces and the algorithm works well for a wide variety of BTF samples, including those which present problems for existing algorithms. We also describe a graphcut texture painting algorithm for creating new surface imperfections (e.g., dirt, cracks, scratches) from existing imperfections found in input BTF samples. Using these algorithms, we can decorate surfaces with real-world textures that have spatially-variant reflectance, fine-scale geometry details, and surfaces imperfections. A particularly attractive feature of BTF painting is that it allows us to capture imperfections of real materials and paint them onto geometry models. We demonstrate the effectiveness of our system with examples.

Grey Wolf based control for speed ripple reduction at low speed operation of PMSM drives.

PubMed

Djerioui, Ali; Houari, Azeddine; Ait-Ahmed, Mourad; Benkhoris, Mohamed-Fouad; Chouder, Aissa; Machmoum, Mohamed

2018-03-01

Speed ripple at low speed-high torque operation of Permanent Magnet Synchronous Machine (PMSM) drives is considered as one of the major issues to be treated. The presented work proposes an efficient PMSM speed controller based on Grey Wolf (GW) algorithm to ensure a high-performance control for speed ripple reduction at low speed operation. The main idea of the proposed control algorithm is to propose a specific objective function in order to incorporate the advantage of fast optimization process of the GW optimizer. The role of GW optimizer is to find the optimal input controls that satisfy the speed tracking requirements. The synthesis methodology of the proposed control algorithm is detailed and the feasibility and performances of the proposed speed controller is confirmed by simulation and experimental results. The GW algorithm is a model-free controller and the parameters of its objective function are easy to be tuned. The GW controller is compared to PI one on real test bench. Then, the superiority of the first algorithm is highlighted. Copyright © 2018 ISA. Published by Elsevier Ltd. All rights reserved.

Advanced End-to-end Simulation for On-board Processing (AESOP)

NASA Technical Reports Server (NTRS)

Mazer, Alan S.

1994-01-01

Developers of data compression algorithms typically use their own software together with commercial packages to implement, evaluate and demonstrate their work. While convenient for an individual developer, this approach makes it difficult to build on or use another's work without intimate knowledge of each component. When several people or groups work on different parts of the same problem, the larger view can be lost. What's needed is a simple piece of software to stand in the gap and link together the efforts of different people, enabling them to build on each other's work, and providing a base for engineers and scientists to evaluate the parts as a cohesive whole and make design decisions. AESOP (Advanced End-to-end Simulation for On-board Processing) attempts to meet this need by providing a graphical interface to a developer-selected set of algorithms, interfacing with compiled code and standalone programs, as well as procedures written in the IDL and PV-Wave command languages. As a proof of concept, AESOP is outfitted with several data compression algorithms integrating previous work on different processors (AT&T DSP32C, TI TMS320C30, SPARC). The user can specify at run-time the processor on which individual parts of the compression should run. Compressed data is then fed through simulated transmission and uncompression to evaluate the effects of compression parameters, noise and error correction algorithms. The following sections describe AESOP in detail. Section 2 describes fundamental goals for usability. Section 3 describes the implementation. Sections 4 through 5 describe how to add new functionality to the system and present the existing data compression algorithms. Sections 6 and 7 discuss portability and future work.

Efficient Green's Function Reaction Dynamics (GFRD) simulations for diffusion-limited, reversible reactions

NASA Astrophysics Data System (ADS)

Bashardanesh, Zahedeh; Lötstedt, Per

2018-03-01

In diffusion controlled reversible bimolecular reactions in three dimensions, a dissociation step is typically followed by multiple, rapid re-association steps slowing down the simulations of such systems. In order to improve the efficiency, we first derive an exact Green's function describing the rate at which an isolated pair of particles undergoing reversible bimolecular reactions and unimolecular decay separates beyond an arbitrarily chosen distance. Then the Green's function is used in an algorithm for particle-based stochastic reaction-diffusion simulations for prediction of the dynamics of biochemical networks. The accuracy and efficiency of the algorithm are evaluated using a reversible reaction and a push-pull chemical network. The computational work is independent of the rates of the re-associations.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Goodwin, D. L.; Kuprov, Ilya, E-mail: i.kuprov@soton.ac.uk

Quadratic convergence throughout the active space is achieved for the gradient ascent pulse engineering (GRAPE) family of quantum optimal control algorithms. We demonstrate in this communication that the Hessian of the GRAPE fidelity functional is unusually cheap, having the same asymptotic complexity scaling as the functional itself. This leads to the possibility of using very efficient numerical optimization techniques. In particular, the Newton-Raphson method with a rational function optimization (RFO) regularized Hessian is shown in this work to require fewer system trajectory evaluations than any other algorithm in the GRAPE family. This communication describes algebraic and numerical implementation aspects (matrixmore » exponential recycling, Hessian regularization, etc.) for the RFO Newton-Raphson version of GRAPE and reports benchmarks for common spin state control problems in magnetic resonance spectroscopy.« less

A proposed study of multiple scattering through clouds up to 1 THz

NASA Technical Reports Server (NTRS)

Gerace, G. C.; Smith, E. K.

1992-01-01

A rigorous computation of the electromagnetic field scattered from an atmospheric liquid water cloud is proposed. The recent development of a fast recursive algorithm (Chew algorithm) for computing the fields scattered from numerous scatterers now makes a rigorous computation feasible. A method is presented for adapting this algorithm to a general case where there are an extremely large number of scatterers. It is also proposed to extend a new binary PAM channel coding technique (El-Khamy coding) to multiple levels with non-square pulse shapes. The Chew algorithm can be used to compute the transfer function of a cloud channel. Then the transfer function can be used to design an optimum El-Khamy code. In principle, these concepts can be applied directly to the realistic case of a time-varying cloud (adaptive channel coding and adaptive equalization). A brief review is included of some preliminary work on cloud dispersive effects on digital communication signals and on cloud liquid water spectra and correlations.

Robust dynamic myocardial perfusion CT deconvolution using adaptive-weighted tensor total variation regularization

NASA Astrophysics Data System (ADS)

Gong, Changfei; Zeng, Dong; Bian, Zhaoying; Huang, Jing; Zhang, Xinyu; Zhang, Hua; Lu, Lijun; Feng, Qianjin; Liang, Zhengrong; Ma, Jianhua

2016-03-01

Dynamic myocardial perfusion computed tomography (MPCT) is a promising technique for diagnosis and risk stratification of coronary artery disease by assessing the myocardial perfusion hemodynamic maps (MPHM). Meanwhile, the repeated scanning of the same region results in a relatively large radiation dose to patients potentially. In this work, we present a robust MPCT deconvolution algorithm with adaptive-weighted tensor total variation regularization to estimate residue function accurately under the low-dose context, which is termed `MPD-AwTTV'. More specifically, the AwTTV regularization takes into account the anisotropic edge property of the MPCT images compared with the conventional total variation (TV) regularization, which can mitigate the drawbacks of TV regularization. Subsequently, an effective iterative algorithm was adopted to minimize the associative objective function. Experimental results on a modified XCAT phantom demonstrated that the present MPD-AwTTV algorithm outperforms and is superior to other existing deconvolution algorithms in terms of noise-induced artifacts suppression, edge details preservation and accurate MPHM estimation.

Variational data assimilation schemes for transport and transformation models of atmospheric chemistry

NASA Astrophysics Data System (ADS)

Penenko, Alexey; Penenko, Vladimir; Tsvetova, Elena; Antokhin, Pavel

2016-04-01

The work is devoted to data assimilation algorithm for atmospheric chemistry transport and transformation models. In the work a control function is introduced into the model source term (emission rate) to provide flexibility to adjust to data. This function is evaluated as the constrained minimum of the target functional combining a control function norm with a norm of the misfit between measured data and its model-simulated analog. Transport and transformation processes model is acting as a constraint. The constrained minimization problem is solved with Euler-Lagrange variational principle [1] which allows reducing it to a system of direct, adjoint and control function estimate relations. This provides a physically-plausible structure of the resulting analysis without model error covariance matrices that are sought within conventional approaches to data assimilation. High dimensionality of the atmospheric chemistry models and a real-time mode of operation demand for computational efficiency of the data assimilation algorithms. Computational issues with complicated models can be solved by using a splitting technique. Within this approach a complex model is split to a set of relatively independent simpler models equipped with a coupling procedure. In a fine-grained approach data assimilation is carried out quasi-independently on the separate splitting stages with shared measurement data [2]. In integrated schemes data assimilation is carried out with respect to the split model as a whole. We compare the two approaches both theoretically and numerically. Data assimilation on the transport stage is carried out with a direct algorithm without iterations. Different algorithms to assimilate data on nonlinear transformation stage are compared. In the work we compare data assimilation results for both artificial and real measurement data. With these data we study the impact of transformation processes and data assimilation to the performance of the modeling system [3]. The work has been partially supported by RFBR grant 14-01-00125 and RAS Presidium II.4P. References: [1] Penenko V.V., Tsvetova E.A., Penenko A.V. Development of variational approach for direct and inverse problems of atmospheric hydrodynamics and chemistry // IZVESTIYA ATMOSPHERIC AND OCEANIC PHYSICS, 2015, v 51 , p. 311 - 319 [2] A.V. Penenko and V.V. Penenko. Direct data assimilation method for convection-diffusion models based on splitting scheme. Computational technologies, 19(4):69-83, 2014. [3] A. Penenko; V. Penenko; R. Nuterman; A. Baklanov and A. Mahura Direct variational data assimilation algorithm for atmospheric chemistry data with transport and transformation model, Proc. SPIE 9680, 21st International Symposium Atmospheric and Ocean Optics: Atmospheric Physics, 968076 (November 19, 2015); doi:10.1117/12.2206008;http://dx.doi.org/10.1117/12.2206008

Non-Algorithmic Quantitative Problem Solving in University Physical Chemistry: A Correlation Study of the Role of Selective Cognitive Factors

ERIC Educational Resources Information Center

Tsaparlis, Georgios

2005-01-01

This work provides a correlation study of the role of the following cognitive variables on problem solving in elementary physical chemistry: scientific reasoning (level of intellectual development/developmental level), working-memory capacity, functional mental ("M") capacity, and disembedding ability (i.e., degree of perceptual field…

Performances of the New Real Time Tsunami Detection Algorithm applied to tide gauges data

NASA Astrophysics Data System (ADS)

Chierici, F.; Embriaco, D.; Morucci, S.

2017-12-01

Real-time tsunami detection algorithms play a key role in any Tsunami Early Warning System. We have developed a new algorithm for tsunami detection (TDA) based on the real-time tide removal and real-time band-pass filtering of seabed pressure time series acquired by Bottom Pressure Recorders. The TDA algorithm greatly increases the tsunami detection probability, shortens the detection delay and enhances detection reliability with respect to the most widely used tsunami detection algorithm, while containing the computational cost. The algorithm is designed to be used also in autonomous early warning systems with a set of input parameters and procedures which can be reconfigured in real time. We have also developed a methodology based on Monte Carlo simulations to test the tsunami detection algorithms. The algorithm performance is estimated by defining and evaluating statistical parameters, namely the detection probability, the detection delay, which are functions of the tsunami amplitude and wavelength, and the occurring rate of false alarms. In this work we present the performance of the TDA algorithm applied to tide gauge data. We have adapted the new tsunami detection algorithm and the Monte Carlo test methodology to tide gauges. Sea level data acquired by coastal tide gauges in different locations and environmental conditions have been used in order to consider real working scenarios in the test. We also present an application of the algorithm to the tsunami event generated by Tohoku earthquake on March 11th 2011, using data recorded by several tide gauges scattered all over the Pacific area.

Threshold matrix for digital halftoning by genetic algorithm optimization

NASA Astrophysics Data System (ADS)

Alander, Jarmo T.; Mantere, Timo J.; Pyylampi, Tero

1998-10-01

Digital halftoning is used both in low and high resolution high quality printing technologies. Our method is designed to be mainly used for low resolution ink jet marking machines to produce both gray tone and color images. The main problem with digital halftoning is pink noise caused by the human eye's visual transfer function. To compensate for this the random dot patterns used are optimized to contain more blue than pink noise. Several such dot pattern generator threshold matrices have been created automatically by using genetic algorithm optimization, a non-deterministic global optimization method imitating natural evolution and genetics. A hybrid of genetic algorithm with a search method based on local backtracking was developed together with several fitness functions evaluating dot patterns for rectangular grids. By modifying the fitness function, a family of dot generators results, each with its particular statistical features. Several versions of genetic algorithms, backtracking and fitness functions were tested to find a reasonable combination. The generated threshold matrices have been tested by simulating a set of test images using the Khoros image processing system. Even though the work was focused on developing low resolution marking technology, the resulting family of dot generators can be applied also in other halftoning application areas including high resolution printing technology.

Improved Quantum Artificial Fish Algorithm Application to Distributed Network Considering Distributed Generation.

PubMed

Du, Tingsong; Hu, Yang; Ke, Xianting

2015-01-01

An improved quantum artificial fish swarm algorithm (IQAFSA) for solving distributed network programming considering distributed generation is proposed in this work. The IQAFSA based on quantum computing which has exponential acceleration for heuristic algorithm uses quantum bits to code artificial fish and quantum revolving gate, preying behavior, and following behavior and variation of quantum artificial fish to update the artificial fish for searching for optimal value. Then, we apply the proposed new algorithm, the quantum artificial fish swarm algorithm (QAFSA), the basic artificial fish swarm algorithm (BAFSA), and the global edition artificial fish swarm algorithm (GAFSA) to the simulation experiments for some typical test functions, respectively. The simulation results demonstrate that the proposed algorithm can escape from the local extremum effectively and has higher convergence speed and better accuracy. Finally, applying IQAFSA to distributed network problems and the simulation results for 33-bus radial distribution network system show that IQAFSA can get the minimum power loss after comparing with BAFSA, GAFSA, and QAFSA.

Improved Quantum Artificial Fish Algorithm Application to Distributed Network Considering Distributed Generation

PubMed Central

Hu, Yang; Ke, Xianting

2015-01-01

An improved quantum artificial fish swarm algorithm (IQAFSA) for solving distributed network programming considering distributed generation is proposed in this work. The IQAFSA based on quantum computing which has exponential acceleration for heuristic algorithm uses quantum bits to code artificial fish and quantum revolving gate, preying behavior, and following behavior and variation of quantum artificial fish to update the artificial fish for searching for optimal value. Then, we apply the proposed new algorithm, the quantum artificial fish swarm algorithm (QAFSA), the basic artificial fish swarm algorithm (BAFSA), and the global edition artificial fish swarm algorithm (GAFSA) to the simulation experiments for some typical test functions, respectively. The simulation results demonstrate that the proposed algorithm can escape from the local extremum effectively and has higher convergence speed and better accuracy. Finally, applying IQAFSA to distributed network problems and the simulation results for 33-bus radial distribution network system show that IQAFSA can get the minimum power loss after comparing with BAFSA, GAFSA, and QAFSA. PMID:26447713

Fuel management optimization using genetic algorithms and code independence

DOE Office of Scientific and Technical Information (OSTI.GOV)

DeChaine, M.D.; Feltus, M.A.

1994-12-31

Fuel management optimization is a hard problem for traditional optimization techniques. Loading pattern optimization is a large combinatorial problem without analytical derivative information. Therefore, methods designed for continuous functions, such as linear programming, do not always work well. Genetic algorithms (GAs) address these problems and, therefore, appear ideal for fuel management optimization. They do not require derivative information and work well with combinatorial. functions. The GAs are a stochastic method based on concepts from biological genetics. They take a group of candidate solutions, called the population, and use selection, crossover, and mutation operators to create the next generation of bettermore » solutions. The selection operator is a {open_quotes}survival-of-the-fittest{close_quotes} operation and chooses the solutions for the next generation. The crossover operator is analogous to biological mating, where children inherit a mixture of traits from their parents, and the mutation operator makes small random changes to the solutions.« less

An interior-point method for total variation regularized positron emission tomography image reconstruction

NASA Astrophysics Data System (ADS)

Bai, Bing

2012-03-01

There has been a lot of work on total variation (TV) regularized tomographic image reconstruction recently. Many of them use gradient-based optimization algorithms with a differentiable approximation of the TV functional. In this paper we apply TV regularization in Positron Emission Tomography (PET) image reconstruction. We reconstruct the PET image in a Bayesian framework, using Poisson noise model and TV prior functional. The original optimization problem is transformed to an equivalent problem with inequality constraints by adding auxiliary variables. Then we use an interior point method with logarithmic barrier functions to solve the constrained optimization problem. In this method, a series of points approaching the solution from inside the feasible region are found by solving a sequence of subproblems characterized by an increasing positive parameter. We use preconditioned conjugate gradient (PCG) algorithm to solve the subproblems directly. The nonnegativity constraint is enforced by bend line search. The exact expression of the TV functional is used in our calculations. Simulation results show that the algorithm converges fast and the convergence is insensitive to the values of the regularization and reconstruction parameters.

A Functional-Genetic Scheme for Seizure Forecasting in Canine Epilepsy.

PubMed

Bou Assi, Elie; Nguyen, Dang K; Rihana, Sandy; Sawan, Mohamad

2018-06-01

The objective of this work is the development of an accurate seizure forecasting algorithm that considers brain's functional connectivity for electrode selection. We start by proposing Kmeans-directed transfer function, an adaptive functional connectivity method intended for seizure onset zone localization in bilateral intracranial EEG recordings. Electrodes identified as seizure activity sources and sinks are then used to implement a seizure-forecasting algorithm on long-term continuous recordings in dogs with naturally-occurring epilepsy. A precision-recall genetic algorithm is proposed for feature selection in line with a probabilistic support vector machine classifier. Epileptic activity generators were focal in all dogs confirming the diagnosis of focal epilepsy in these animals while sinks spanned both hemispheres in 2 of 3 dogs. Seizure forecasting results show performance improvement compared to previous studies, achieving average sensitivity of 84.82% and time in warning of 0.1. Achieved performances highlight the feasibility of seizure forecasting in canine epilepsy. The ability to improve seizure forecasting provides promise for the development of EEG-triggered closed-loop seizure intervention systems for ambulatory implantation in patients with refractory epilepsy.

Final Technical Report [Scalable methods for electronic excitations and optical responses of nanostructures: mathematics to algorithms to observables

DOE Office of Scientific and Technical Information (OSTI.GOV)

Saad, Yousef

2014-03-19

The master project under which this work is funded had as its main objective to develop computational methods for modeling electronic excited-state and optical properties of various nanostructures. The specific goals of the computer science group were primarily to develop effective numerical algorithms in Density Functional Theory (DFT) and Time Dependent Density Functional Theory (TDDFT). There were essentially four distinct stated objectives. The first objective was to study and develop effective numerical algorithms for solving large eigenvalue problems such as those that arise in Density Functional Theory (DFT) methods. The second objective was to explore so-called linear scaling methods ormore » Methods that avoid diagonalization. The third was to develop effective approaches for Time-Dependent DFT (TDDFT). Our fourth and final objective was to examine effective solution strategies for other problems in electronic excitations, such as the GW/Bethe-Salpeter method, and quantum transport problems.« less

Efficient Compressed Sensing Based MRI Reconstruction using Nonconvex Total Variation Penalties

NASA Astrophysics Data System (ADS)

Lazzaro, D.; Loli Piccolomini, E.; Zama, F.

2016-10-01

This work addresses the problem of Magnetic Resonance Image Reconstruction from highly sub-sampled measurements in the Fourier domain. It is modeled as a constrained minimization problem, where the objective function is a non-convex function of the gradient of the unknown image and the constraints are given by the data fidelity term. We propose an algorithm, Fast Non Convex Reweighted (FNCR), where the constrained problem is solved by a reweighting scheme, as a strategy to overcome the non-convexity of the objective function, with an adaptive adjustment of the penalization parameter. We propose a fast iterative algorithm and we can prove that it converges to a local minimum because the constrained problem satisfies the Kurdyka-Lojasiewicz property. Moreover the adaptation of non convex l0 approximation and penalization parameters, by means of a continuation technique, allows us to obtain good quality solutions, avoiding to get stuck in unwanted local minima. Some numerical experiments performed on MRI sub-sampled data show the efficiency of the algorithm and the accuracy of the solution.

Composition-based classification of short metagenomic sequences elucidates the landscapes of taxonomic and functional enrichment of microorganisms

PubMed Central

Liu, Jiemeng; Wang, Haifeng; Yang, Hongxing; Zhang, Yizhe; Wang, Jinfeng; Zhao, Fangqing; Qi, Ji

2013-01-01

Compared with traditional algorithms for long metagenomic sequence classification, characterizing microorganisms’ taxonomic and functional abundance based on tens of millions of very short reads are much more challenging. We describe an efficient composition and phylogeny-based algorithm [Metagenome Composition Vector (MetaCV)] to classify very short metagenomic reads (75–100 bp) into specific taxonomic and functional groups. We applied MetaCV to the Meta-HIT data (371-Gb 75-bp reads of 109 human gut metagenomes), and this single-read-based, instead of assembly-based, classification has a high resolution to characterize the composition and structure of human gut microbiota, especially for low abundance species. Most strikingly, it only took MetaCV 10 days to do all the computation work on a server with five 24-core nodes. To our knowledge, MetaCV, benefited from the strategy of composition comparison, is the first algorithm that can classify millions of very short reads within affordable time. PMID:22941634

Stochastic subset selection for learning with kernel machines.

PubMed

Rhinelander, Jason; Liu, Xiaoping P

2012-06-01

Kernel machines have gained much popularity in applications of machine learning. Support vector machines (SVMs) are a subset of kernel machines and generalize well for classification, regression, and anomaly detection tasks. The training procedure for traditional SVMs involves solving a quadratic programming (QP) problem. The QP problem scales super linearly in computational effort with the number of training samples and is often used for the offline batch processing of data. Kernel machines operate by retaining a subset of observed data during training. The data vectors contained within this subset are referred to as support vectors (SVs). The work presented in this paper introduces a subset selection method for the use of kernel machines in online, changing environments. Our algorithm works by using a stochastic indexing technique when selecting a subset of SVs when computing the kernel expansion. The work described here is novel because it separates the selection of kernel basis functions from the training algorithm used. The subset selection algorithm presented here can be used in conjunction with any online training technique. It is important for online kernel machines to be computationally efficient due to the real-time requirements of online environments. Our algorithm is an important contribution because it scales linearly with the number of training samples and is compatible with current training techniques. Our algorithm outperforms standard techniques in terms of computational efficiency and provides increased recognition accuracy in our experiments. We provide results from experiments using both simulated and real-world data sets to verify our algorithm.

SU-E-T-446: Group-Sparsity Based Angle Generation Method for Beam Angle Optimization

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gao, H

2015-06-15

Purpose: This work is to develop the effective algorithm for beam angle optimization (BAO), with the emphasis on enabling further improvement from existing treatment-dependent templates based on clinical knowledge and experience. Methods: The proposed BAO algorithm utilizes a priori beam angle templates as the initial guess, and iteratively generates angular updates for this initial set, namely angle generation method, with improved dose conformality that is quantitatively measured by the objective function. That is, during each iteration, we select “the test angle” in the initial set, and use group-sparsity based fluence map optimization to identify “the candidate angle” for updating “themore » test angle”, for which all the angles in the initial set except “the test angle”, namely “the fixed set”, are set free, i.e., with no group-sparsity penalty, and the rest of angles including “the test angle” during this iteration are in “the working set”. And then “the candidate angle” is selected with the smallest objective function value from the angles in “the working set” with locally maximal group sparsity, and replaces “the test angle” if “the fixed set” with “the candidate angle” has a smaller objective function value by solving the standard fluence map optimization (with no group-sparsity regularization). Similarly other angles in the initial set are in turn selected as “the test angle” for angular updates and this chain of updates is iterated until no further new angular update is identified for a full loop. Results: The tests using the MGH public prostate dataset demonstrated the effectiveness of the proposed BAO algorithm. For example, the optimized angular set from the proposed BAO algorithm was better the MGH template. Conclusion: A new BAO algorithm is proposed based on the angle generation method via group sparsity, with improved dose conformality from the given template. Hao Gao was partially supported by the NSFC (#11405105), the 973 Program (#2015CB856000) and the Shanghai Pujiang Talent Program (#14PJ1404500)« less

Tailored Algorithm for Sensitivity Enhancement of Gas Concentration Sensors Based on Tunable Laser Absorption Spectroscopy.

PubMed

Vargas-Rodriguez, Everardo; Guzman-Chavez, Ana Dinora; Baeza-Serrato, Roberto

2018-06-04

In this work, a novel tailored algorithm to enhance the overall sensitivity of gas concentration sensors based on the Direct Absorption Tunable Laser Absorption Spectroscopy (DA-ATLAS) method is presented. By using this algorithm, the sensor sensitivity can be custom-designed to be quasi constant over a much larger dynamic range compared with that obtained by typical methods based on a single statistics feature of the sensor signal output (peak amplitude, area under the curve, mean or RMS). Additionally, it is shown that with our algorithm, an optimal function can be tailored to get a quasi linear relationship between the concentration and some specific statistics features over a wider dynamic range. In order to test the viability of our algorithm, a basic C 2 H 2 sensor based on DA-ATLAS was implemented, and its experimental measurements support the simulated results provided by our algorithm.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tumuluru, Jaya Shankar; McCulloch, Richard Chet James

In this work a new hybrid genetic algorithm was developed which combines a rudimentary adaptive steepest ascent hill climbing algorithm with a sophisticated evolutionary algorithm in order to optimize complex multivariate design problems. By combining a highly stochastic algorithm (evolutionary) with a simple deterministic optimization algorithm (adaptive steepest ascent) computational resources are conserved and the solution converges rapidly when compared to either algorithm alone. In genetic algorithms natural selection is mimicked by random events such as breeding and mutation. In the adaptive steepest ascent algorithm each variable is perturbed by a small amount and the variable that caused the mostmore » improvement is incremented by a small step. If the direction of most benefit is exactly opposite of the previous direction with the most benefit then the step size is reduced by a factor of 2, thus the step size adapts to the terrain. A graphical user interface was created in MATLAB to provide an interface between the hybrid genetic algorithm and the user. Additional features such as bounding the solution space and weighting the objective functions individually are also built into the interface. The algorithm developed was tested to optimize the functions developed for a wood pelleting process. Using process variables (such as feedstock moisture content, die speed, and preheating temperature) pellet properties were appropriately optimized. Specifically, variables were found which maximized unit density, bulk density, tapped density, and durability while minimizing pellet moisture content and specific energy consumption. The time and computational resources required for the optimization were dramatically decreased using the hybrid genetic algorithm when compared to MATLAB's native evolutionary optimization tool.« less

Reliable Adaptive Data Aggregation Route Strategy for a Trade-off between Energy and Lifetime in WSNs

PubMed Central

Guo, Wenzhong; Hong, Wei; Zhang, Bin; Chen, Yuzhong; Xiong, Naixue

2014-01-01

Mobile security is one of the most fundamental problems in Wireless Sensor Networks (WSNs). The data transmission path will be compromised for some disabled nodes. To construct a secure and reliable network, designing an adaptive route strategy which optimizes energy consumption and network lifetime of the aggregation cost is of great importance. In this paper, we address the reliable data aggregation route problem for WSNs. Firstly, to ensure nodes work properly, we propose a data aggregation route algorithm which improves the energy efficiency in the WSN. The construction process achieved through discrete particle swarm optimization (DPSO) saves node energy costs. Then, to balance the network load and establish a reliable network, an adaptive route algorithm with the minimal energy and the maximum lifetime is proposed. Since it is a non-linear constrained multi-objective optimization problem, in this paper we propose a DPSO with the multi-objective fitness function combined with the phenotype sharing function and penalty function to find available routes. Experimental results show that compared with other tree routing algorithms our algorithm can effectively reduce energy consumption and trade off energy consumption and network lifetime. PMID:25215944

An optimal algorithm for reconstructing images from binary measurements

NASA Astrophysics Data System (ADS)

Yang, Feng; Lu, Yue M.; Sbaiz, Luciano; Vetterli, Martin

2010-01-01

We have studied a camera with a very large number of binary pixels referred to as the gigavision camera [1] or the gigapixel digital film camera [2, 3]. Potential advantages of this new camera design include improved dynamic range, thanks to its logarithmic sensor response curve, and reduced exposure time in low light conditions, due to its highly sensitive photon detection mechanism. We use maximum likelihood estimator (MLE) to reconstruct a high quality conventional image from the binary sensor measurements of the gigavision camera. We prove that when the threshold T is "1", the negative loglikelihood function is a convex function. Therefore, optimal solution can be achieved using convex optimization. Base on filter bank techniques, fast algorithms are given for computing the gradient and the multiplication of a vector and Hessian matrix of the negative log-likelihood function. We show that with a minor change, our algorithm also works for estimating conventional images from multiple binary images. Numerical experiments with synthetic 1-D signals and images verify the effectiveness and quality of the proposed algorithm. Experimental results also show that estimation performance can be improved by increasing the oversampling factor or the number of binary images.

Orbit Clustering Based on Transfer Cost

NASA Technical Reports Server (NTRS)

Gustafson, Eric D.; Arrieta-Camacho, Juan J.; Petropoulos, Anastassios E.

2013-01-01

We propose using cluster analysis to perform quick screening for combinatorial global optimization problems. The key missing component currently preventing cluster analysis from use in this context is the lack of a useable metric function that defines the cost to transfer between two orbits. We study several proposed metrics and clustering algorithms, including k-means and the expectation maximization algorithm. We also show that proven heuristic methods such as the Q-law can be modified to work with cluster analysis.

Methodology for the inference of gene function from phenotype data.

PubMed

Ascensao, Joao A; Dolan, Mary E; Hill, David P; Blake, Judith A

2014-12-12

Biomedical ontologies are increasingly instrumental in the advancement of biological research primarily through their use to efficiently consolidate large amounts of data into structured, accessible sets. However, ontology development and usage can be hampered by the segregation of knowledge by domain that occurs due to independent development and use of the ontologies. The ability to infer data associated with one ontology to data associated with another ontology would prove useful in expanding information content and scope. We here focus on relating two ontologies: the Gene Ontology (GO), which encodes canonical gene function, and the Mammalian Phenotype Ontology (MP), which describes non-canonical phenotypes, using statistical methods to suggest GO functional annotations from existing MP phenotype annotations. This work is in contrast to previous studies that have focused on inferring gene function from phenotype primarily through lexical or semantic similarity measures. We have designed and tested a set of algorithms that represents a novel methodology to define rules for predicting gene function by examining the emergent structure and relationships between the gene functions and phenotypes rather than inspecting the terms semantically. The algorithms inspect relationships among multiple phenotype terms to deduce if there are cases where they all arise from a single gene function. We apply this methodology to data about genes in the laboratory mouse that are formally represented in the Mouse Genome Informatics (MGI) resource. From the data, 7444 rule instances were generated from five generalized rules, resulting in 4818 unique GO functional predictions for 1796 genes. We show that our method is capable of inferring high-quality functional annotations from curated phenotype data. As well as creating inferred annotations, our method has the potential to allow for the elucidation of unforeseen, biologically significant associations between gene function and phenotypes that would be overlooked by a semantics-based approach. Future work will include the implementation of the described algorithms for a variety of other model organism databases, taking full advantage of the abundance of available high quality curated data.

An algorithm on simultaneous optimization of performance and mass parameters of open-cycle liquid-propellant engine of launch vehicles

NASA Astrophysics Data System (ADS)

Eskandari, M. A.; Mazraeshahi, H. K.; Ramesh, D.; Montazer, E.; Salami, E.; Romli, F. I.

2017-12-01

In this paper, a new method for the determination of optimum parameters of open-cycle liquid-propellant engine of launch vehicles is introduced. The parameters affecting the objective function, which is the ratio of specific impulse to gross mass of the launch vehicle, are chosen to achieve maximum specific impulse as well as minimum mass for the structure of engine, tanks, etc. The proposed algorithm uses constant integration of thrust with respect to time for launch vehicle with specific diameter and length to calculate the optimum working condition. The results by this novel algorithm are compared to those obtained from using Genetic Algorithm method and they are also validated against the results of existing launch vehicle.

Research on infrared small-target tracking technology under complex background

NASA Astrophysics Data System (ADS)

Liu, Lei; Wang, Xin; Chen, Jilu; Pan, Tao

2012-10-01

In this paper, some basic principles and the implementing flow charts of a series of algorithms for target tracking are described. On the foundation of above works, a moving target tracking software base on the OpenCV is developed by the software developing platform MFC. Three kinds of tracking algorithms are integrated in this software. These two tracking algorithms are Kalman Filter tracking method and Camshift tracking method. In order to explain the software clearly, the framework and the function are described in this paper. At last, the implementing processes and results are analyzed, and those algorithms for tracking targets are evaluated from the two aspects of subjective and objective. This paper is very significant in the application of the infrared target tracking technology.

An empirical comparative study on biological age estimation algorithms with an application of Work Ability Index (WAI).

PubMed

Cho, Il Haeng; Park, Kyung S; Lim, Chang Joo

2010-02-01

In this study, we described the characteristics of five different biological age (BA) estimation algorithms, including (i) multiple linear regression, (ii) principal component analysis, and somewhat unique methods developed by (iii) Hochschild, (iv) Klemera and Doubal, and (v) a variant of Klemera and Doubal's method. The objective of this study is to find the most appropriate method of BA estimation by examining the association between Work Ability Index (WAI) and the differences of each algorithm's estimates from chronological age (CA). The WAI was found to be a measure that reflects an individual's current health status rather than the deterioration caused by a serious dependency with the age. Experiments were conducted on 200 Korean male participants using a BA estimation system developed principally under the concept of non-invasive, simple to operate and human function-based. Using the empirical data, BA estimation as well as various analyses including correlation analysis and discriminant function analysis was performed. As a result, it had been confirmed by the empirical data that Klemera and Doubal's method with uncorrelated variables from principal component analysis produces relatively reliable and acceptable BA estimates. 2009 Elsevier Ireland Ltd. All rights reserved.

On the Green's function of the partially diffusion-controlled reversible ABCD reaction for radiation chemistry codes

NASA Astrophysics Data System (ADS)

Plante, Ianik; Devroye, Luc

2015-09-01

Several computer codes simulating chemical reactions in particles systems are based on the Green's functions of the diffusion equation (GFDE). Indeed, many types of chemical systems have been simulated using the exact GFDE, which has also become the gold standard for validating other theoretical models. In this work, a simulation algorithm is presented to sample the interparticle distance for partially diffusion-controlled reversible ABCD reaction. This algorithm is considered exact for 2-particles systems, is faster than conventional look-up tables and uses only a few kilobytes of memory. The simulation results obtained with this method are compared with those obtained with the independent reaction times (IRT) method. This work is part of our effort in developing models to understand the role of chemical reactions in the radiation effects on cells and tissues and may eventually be included in event-based models of space radiation risks. However, as many reactions are of this type in biological systems, this algorithm might play a pivotal role in future simulation programs not only in radiation chemistry, but also in the simulation of biochemical networks in time and space as well.

Multi Objective Optimization of Yarn Quality and Fibre Quality Using Evolutionary Algorithm

NASA Astrophysics Data System (ADS)

Ghosh, Anindya; Das, Subhasis; Banerjee, Debamalya

2013-03-01

The quality and cost of resulting yarn play a significant role to determine its end application. The challenging task of any spinner lies in producing a good quality yarn with added cost benefit. The present work does a multi-objective optimization on two objectives, viz. maximization of cotton yarn strength and minimization of raw material quality. The first objective function has been formulated based on the artificial neural network input-output relation between cotton fibre properties and yarn strength. The second objective function is formulated with the well known regression equation of spinning consistency index. It is obvious that these two objectives are conflicting in nature i.e. not a single combination of cotton fibre parameters does exist which produce maximum yarn strength and minimum cotton fibre quality simultaneously. Therefore, it has several optimal solutions from which a trade-off is needed depending upon the requirement of user. In this work, the optimal solutions are obtained with an elitist multi-objective evolutionary algorithm based on Non-dominated Sorting Genetic Algorithm II (NSGA-II). These optimum solutions may lead to the efficient exploitation of raw materials to produce better quality yarns at low costs.

Using Functional or Structural Magnetic Resonance Images and Personal Characteristic Data to Identify ADHD and Autism

PubMed Central

Ghiassian, Sina; Greiner, Russell; Jin, Ping; Brown, Matthew R. G.

2016-01-01

A clinical tool that can diagnose psychiatric illness using functional or structural magnetic resonance (MR) brain images has the potential to greatly assist physicians and improve treatment efficacy. Working toward the goal of automated diagnosis, we propose an approach for automated classification of ADHD and autism based on histogram of oriented gradients (HOG) features extracted from MR brain images, as well as personal characteristic data features. We describe a learning algorithm that can produce effective classifiers for ADHD and autism when run on two large public datasets. The algorithm is able to distinguish ADHD from control with hold-out accuracy of 69.6% (over baseline 55.0%) using personal characteristics and structural brain scan features when trained on the ADHD-200 dataset (769 participants in training set, 171 in test set). It is able to distinguish autism from control with hold-out accuracy of 65.0% (over baseline 51.6%) using functional images with personal characteristic data when trained on the Autism Brain Imaging Data Exchange (ABIDE) dataset (889 participants in training set, 222 in test set). These results outperform all previously presented methods on both datasets. To our knowledge, this is the first demonstration of a single automated learning process that can produce classifiers for distinguishing patients vs. controls from brain imaging data with above-chance accuracy on large datasets for two different psychiatric illnesses (ADHD and autism). Working toward clinical applications requires robustness against real-world conditions, including the substantial variability that often exists among data collected at different institutions. It is therefore important that our algorithm was successful with the large ADHD-200 and ABIDE datasets, which include data from hundreds of participants collected at multiple institutions. While the resulting classifiers are not yet clinically relevant, this work shows that there is a signal in the (f)MRI data that a learning algorithm is able to find. We anticipate this will lead to yet more accurate classifiers, over these and other psychiatric disorders, working toward the goal of a clinical tool for high accuracy differential diagnosis. PMID:28030565

Adaptive non-linear control for cancer therapy through a Fokker-Planck observer.

PubMed

Shakeri, Ehsan; Latif-Shabgahi, Gholamreza; Esmaeili Abharian, Amir

2018-04-01

In recent years, many efforts have been made to present optimal strategies for cancer therapy through the mathematical modelling of tumour-cell population dynamics and optimal control theory. In many cases, therapy effect is included in the drift term of the stochastic Gompertz model. By fitting the model with empirical data, the parameters of therapy function are estimated. The reported research works have not presented any algorithm to determine the optimal parameters of therapy function. In this study, a logarithmic therapy function is entered in the drift term of the Gompertz model. Using the proposed control algorithm, the therapy function parameters are predicted and adaptively adjusted. To control the growth of tumour-cell population, its moments must be manipulated. This study employs the probability density function (PDF) control approach because of its ability to control all the process moments. A Fokker-Planck-based non-linear stochastic observer will be used to determine the PDF of the process. A cost function based on the difference between a predefined desired PDF and PDF of tumour-cell population is defined. Using the proposed algorithm, the therapy function parameters are adjusted in such a manner that the cost function is minimised. The existence of an optimal therapy function is also proved. The numerical results are finally given to demonstrate the effectiveness of the proposed method.

Implementation of the ground level enhancement alert software at NMDB database

NASA Astrophysics Data System (ADS)

Mavromichalaki, Helen; Souvatzoglou, George; Sarlanis, Christos; Mariatos, George; Papaioannou, Athanasios; Belov, Anatoly; Eroshenko, Eugenia; Yanke, Victor; NMDB Team

2010-11-01

The European Commission is supporting the real-time database for high-resolution neutron monitor measurements (NMDB) as an e-Infrastructures project in the Seventh Framework Programme in the Capacities section. The realization of the NMDB will provide the opportunity for several applications most of which will be implemented in real-time. An important application will be the establishment of an Alert signal when dangerous solar particle events are heading to the Earth, resulting into a ground level enhancement (GLE) registered by neutron monitors (NMs). The cosmic ray community has been occupied with the question of establishing such an Alert for many years and recently several groups succeeded in creating a proper algorithm capable of detecting space weather threats in an off-line mode. A lot of original work has been done to this direction and every group working in this field performed routine runs for all GLE cases, resulting into statistical analyses of GLE events. The next step was to make this algorithm as accurate as possible and most importantly, working in real-time. This was achieved when, during the last GLE observed so far, a real-time GLE Alert signal was produced. In this work, the steps of this procedure as well as the functionality of this algorithm for both the scientific community and users are being discussed. Nevertheless, the transition of the Alert algorithm to the NMDB is also being discussed.

A study of hydrogen diffusion flames using PDF turbulence model

NASA Technical Reports Server (NTRS)

Hsu, Andrew T.

1991-01-01

The application of probability density function (pdf) turbulence models is addressed in this work. For the purpose of accurate prediction of turbulent combustion, an algorithm that combines a conventional CFD flow solver with the Monte Carlo simulation of the pdf evolution equation has been developed. The algorithm has been validated using experimental data for a heated turbulent plane jet. The study of H2-F2 diffusion flames has been carried out using this algorithm. Numerical results compared favorably with experimental data. The computuations show that the flame center shifts as the equivalence ratio changes, and that for the same equivalence ratio, similarity solutions for flames exist.

Modified Newton-Raphson GRAPE methods for optimal control of spin systems

NASA Astrophysics Data System (ADS)

Goodwin, D. L.; Kuprov, Ilya

2016-05-01

Quadratic convergence throughout the active space is achieved for the gradient ascent pulse engineering (GRAPE) family of quantum optimal control algorithms. We demonstrate in this communication that the Hessian of the GRAPE fidelity functional is unusually cheap, having the same asymptotic complexity scaling as the functional itself. This leads to the possibility of using very efficient numerical optimization techniques. In particular, the Newton-Raphson method with a rational function optimization (RFO) regularized Hessian is shown in this work to require fewer system trajectory evaluations than any other algorithm in the GRAPE family. This communication describes algebraic and numerical implementation aspects (matrix exponential recycling, Hessian regularization, etc.) for the RFO Newton-Raphson version of GRAPE and reports benchmarks for common spin state control problems in magnetic resonance spectroscopy.

Developing a New Wireless Sensor Network Platform and Its Application in Precision Agriculture

PubMed Central

Aquino-Santos, Raúl; González-Potes, Apolinar; Edwards-Block, Arthur; Virgen-Ortiz, Raúl Alejandro

2011-01-01

Wireless sensor networks are gaining greater attention from the research community and industrial professionals because these small pieces of “smart dust” offer great advantages due to their small size, low power consumption, easy integration and support for “green” applications. Green applications are considered a hot topic in intelligent environments, ubiquitous and pervasive computing. This work evaluates a new wireless sensor network platform and its application in precision agriculture, including its embedded operating system and its routing algorithm. To validate the technological platform and the embedded operating system, two different routing strategies were compared: hierarchical and flat. Both of these routing algorithms were tested in a small-scale network applied to a watermelon field. However, we strongly believe that this technological platform can be also applied to precision agriculture because it incorporates a modified version of LORA-CBF, a wireless location-based routing algorithm that uses cluster-based flooding. Cluster-based flooding addresses the scalability concerns of wireless sensor networks, while the modified LORA-CBF routing algorithm includes a metric to monitor residual battery energy. Furthermore, results show that the modified version of LORA-CBF functions well with both the flat and hierarchical algorithms, although it functions better with the flat algorithm in a small-scale agricultural network. PMID:22346622

Developing a new wireless sensor network platform and its application in precision agriculture.

PubMed

Aquino-Santos, Raúl; González-Potes, Apolinar; Edwards-Block, Arthur; Virgen-Ortiz, Raúl Alejandro

2011-01-01

Wireless sensor networks are gaining greater attention from the research community and industrial professionals because these small pieces of "smart dust" offer great advantages due to their small size, low power consumption, easy integration and support for "green" applications. Green applications are considered a hot topic in intelligent environments, ubiquitous and pervasive computing. This work evaluates a new wireless sensor network platform and its application in precision agriculture, including its embedded operating system and its routing algorithm. To validate the technological platform and the embedded operating system, two different routing strategies were compared: hierarchical and flat. Both of these routing algorithms were tested in a small-scale network applied to a watermelon field. However, we strongly believe that this technological platform can be also applied to precision agriculture because it incorporates a modified version of LORA-CBF, a wireless location-based routing algorithm that uses cluster-based flooding. Cluster-based flooding addresses the scalability concerns of wireless sensor networks, while the modified LORA-CBF routing algorithm includes a metric to monitor residual battery energy. Furthermore, results show that the modified version of LORA-CBF functions well with both the flat and hierarchical algorithms, although it functions better with the flat algorithm in a small-scale agricultural network.

Modeling cortical circuits.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rohrer, Brandon Robinson; Rothganger, Fredrick H.; Verzi, Stephen J.

2010-09-01

The neocortex is perhaps the highest region of the human brain, where audio and visual perception takes place along with many important cognitive functions. An important research goal is to describe the mechanisms implemented by the neocortex. There is an apparent regularity in the structure of the neocortex [Brodmann 1909, Mountcastle 1957] which may help simplify this task. The work reported here addresses the problem of how to describe the putative repeated units ('cortical circuits') in a manner that is easily understood and manipulated, with the long-term goal of developing a mathematical and algorithmic description of their function. The approachmore » is to reduce each algorithm to an enhanced perceptron-like structure and describe its computation using difference equations. We organize this algorithmic processing into larger structures based on physiological observations, and implement key modeling concepts in software which runs on parallel computing hardware.« less

Probabilistic DHP adaptive critic for nonlinear stochastic control systems.

PubMed

Herzallah, Randa

2013-06-01

Following the recently developed algorithms for fully probabilistic control design for general dynamic stochastic systems (Herzallah & Káarnáy, 2011; Kárný, 1996), this paper presents the solution to the probabilistic dual heuristic programming (DHP) adaptive critic method (Herzallah & Káarnáy, 2011) and randomized control algorithm for stochastic nonlinear dynamical systems. The purpose of the randomized control input design is to make the joint probability density function of the closed loop system as close as possible to a predetermined ideal joint probability density function. This paper completes the previous work (Herzallah & Káarnáy, 2011; Kárný, 1996) by formulating and solving the fully probabilistic control design problem on the more general case of nonlinear stochastic discrete time systems. A simulated example is used to demonstrate the use of the algorithm and encouraging results have been obtained. Copyright © 2013 Elsevier Ltd. All rights reserved.

Noise-tolerant parity learning with one quantum bit

NASA Astrophysics Data System (ADS)

Park, Daniel K.; Rhee, June-Koo K.; Lee, Soonchil

2018-03-01

Demonstrating quantum advantage with less powerful but more realistic devices is of great importance in modern quantum information science. Recently, a significant quantum speedup was achieved in the problem of learning a hidden parity function with noise. However, if all data qubits at the query output are completely depolarized, the algorithm fails. In this work, we present a quantum parity learning algorithm that exhibits quantum advantage as long as one qubit is provided with nonzero polarization in each query. In this scenario, the quantum parity learning naturally becomes deterministic quantum computation with one qubit. Then the hidden parity function can be revealed by performing a set of operations that can be interpreted as measuring nonlocal observables on the auxiliary result qubit having nonzero polarization and each data qubit. We also discuss the source of the quantum advantage in our algorithm from the resource-theoretic point of view.

Finite time convergent learning law for continuous neural networks.

PubMed

Chairez, Isaac

2014-02-01

This paper addresses the design of a discontinuous finite time convergent learning law for neural networks with continuous dynamics. The neural network was used here to obtain a non-parametric model for uncertain systems described by a set of ordinary differential equations. The source of uncertainties was the presence of some external perturbations and poor knowledge of the nonlinear function describing the system dynamics. A new adaptive algorithm based on discontinuous algorithms was used to adjust the weights of the neural network. The adaptive algorithm was derived by means of a non-standard Lyapunov function that is lower semi-continuous and differentiable in almost the whole space. A compensator term was included in the identifier to reject some specific perturbations using a nonlinear robust algorithm. Two numerical examples demonstrated the improvements achieved by the learning algorithm introduced in this paper compared to classical schemes with continuous learning methods. The first one dealt with a benchmark problem used in the paper to explain how the discontinuous learning law works. The second one used the methane production model to show the benefits in engineering applications of the learning law proposed in this paper. Copyright © 2013 Elsevier Ltd. All rights reserved.

Models of performance of evolutionary program induction algorithms based on indicators of problem difficulty.

PubMed

Graff, Mario; Poli, Riccardo; Flores, Juan J

2013-01-01

Modeling the behavior of algorithms is the realm of evolutionary algorithm theory. From a practitioner's point of view, theory must provide some guidelines regarding which algorithm/parameters to use in order to solve a particular problem. Unfortunately, most theoretical models of evolutionary algorithms are difficult to apply to realistic situations. However, in recent work (Graff and Poli, 2008, 2010), where we developed a method to practically estimate the performance of evolutionary program-induction algorithms (EPAs), we started addressing this issue. The method was quite general; however, it suffered from some limitations: it required the identification of a set of reference problems, it required hand picking a distance measure in each particular domain, and the resulting models were opaque, typically being linear combinations of 100 features or more. In this paper, we propose a significant improvement of this technique that overcomes the three limitations of our previous method. We achieve this through the use of a novel set of features for assessing problem difficulty for EPAs which are very general, essentially based on the notion of finite difference. To show the capabilities or our technique and to compare it with our previous performance models, we create models for the same two important classes of problems-symbolic regression on rational functions and Boolean function induction-used in our previous work. We model a variety of EPAs. The comparison showed that for the majority of the algorithms and problem classes, the new method produced much simpler and more accurate models than before. To further illustrate the practicality of the technique and its generality (beyond EPAs), we have also used it to predict the performance of both autoregressive models and EPAs on the problem of wind speed forecasting, obtaining simpler and more accurate models that outperform in all cases our previous performance models.

Intelligent neural network and fuzzy logic control of industrial and power systems

NASA Astrophysics Data System (ADS)

Kuljaca, Ognjen

The main role played by neural network and fuzzy logic intelligent control algorithms today is to identify and compensate unknown nonlinear system dynamics. There are a number of methods developed, but often the stability analysis of neural network and fuzzy control systems was not provided. This work will meet those problems for the several algorithms. Some more complicated control algorithms included backstepping and adaptive critics will be designed. Nonlinear fuzzy control with nonadaptive fuzzy controllers is also analyzed. An experimental method for determining describing function of SISO fuzzy controller is given. The adaptive neural network tracking controller for an autonomous underwater vehicle is analyzed. A novel stability proof is provided. The implementation of the backstepping neural network controller for the coupled motor drives is described. Analysis and synthesis of adaptive critic neural network control is also provided in the work. Novel tuning laws for the system with action generating neural network and adaptive fuzzy critic are given. Stability proofs are derived for all those control methods. It is shown how these control algorithms and approaches can be used in practical engineering control. Stability proofs are given. Adaptive fuzzy logic control is analyzed. Simulation study is conducted to analyze the behavior of the adaptive fuzzy system on the different environment changes. A novel stability proof for adaptive fuzzy logic systems is given. Also, adaptive elastic fuzzy logic control architecture is described and analyzed. A novel membership function is used for elastic fuzzy logic system. The stability proof is proffered. Adaptive elastic fuzzy logic control is compared with the adaptive nonelastic fuzzy logic control. The work described in this dissertation serves as foundation on which analysis of particular representative industrial systems will be conducted. Also, it gives a good starting point for analysis of learning abilities of adaptive and neural network control systems, as well as for the analysis of the different algorithms such as elastic fuzzy systems.

End-point detection in potentiometric titration by continuous wavelet transform.

PubMed

Jakubowska, Małgorzata; Baś, Bogusław; Kubiak, Władysław W

2009-10-15

The aim of this work was construction of the new wavelet function and verification that a continuous wavelet transform with a specially defined dedicated mother wavelet is a useful tool for precise detection of end-point in a potentiometric titration. The proposed algorithm does not require any initial information about the nature or the type of analyte and/or the shape of the titration curve. The signal imperfection, as well as random noise or spikes has no influence on the operation of the procedure. The optimization of the new algorithm was done using simulated curves and next experimental data were considered. In the case of well-shaped and noise-free titration data, the proposed method gives the same accuracy and precision as commonly used algorithms. But, in the case of noisy or badly shaped curves, the presented approach works good (relative error mainly below 2% and coefficients of variability below 5%) while traditional procedures fail. Therefore, the proposed algorithm may be useful in interpretation of the experimental data and also in automation of the typical titration analysis, specially in the case when random noise interfere with analytical signal.

A New Model for Solving Time-Cost-Quality Trade-Off Problems in Construction

PubMed Central

Fu, Fang; Zhang, Tao

2016-01-01

A poor quality affects project makespan and its total costs negatively, but it can be recovered by repair works during construction. We construct a new non-linear programming model based on the classic multi-mode resource constrained project scheduling problem considering repair works. In order to obtain satisfactory quality without a high increase of project cost, the objective is to minimize total quality cost which consists of the prevention cost and failure cost according to Quality-Cost Analysis. A binary dependent normal distribution function is adopted to describe the activity quality; Cumulative quality is defined to determine whether to initiate repair works, according to the different relationships among activity qualities, namely, the coordinative and precedence relationship. Furthermore, a shuffled frog-leaping algorithm is developed to solve this discrete trade-off problem based on an adaptive serial schedule generation scheme and adjusted activity list. In the program of the algorithm, the frog-leaping progress combines the crossover operator of genetic algorithm and a permutation-based local search. Finally, an example of a construction project for a framed railway overpass is provided to examine the algorithm performance, and it assist in decision making to search for the appropriate makespan and quality threshold with minimal cost. PMID:27911939

Comparison between different direct search optimization algorithms in the calibration of a distributed hydrological model

NASA Astrophysics Data System (ADS)

Campo, Lorenzo; Castelli, Fabio; Caparrini, Francesca

2010-05-01

The modern distributed hydrological models allow the representation of the different surface and subsurface phenomena with great accuracy and high spatial and temporal resolution. Such complexity requires, in general, an equally accurate parametrization. A number of approaches have been followed in this respect, from simple local search method (like Nelder-Mead algorithm), that minimize a cost function representing some distance between model's output and available measures, to more complex approaches like dynamic filters (such as the Ensemble Kalman Filter) that carry on an assimilation of the observations. In this work the first approach was followed in order to compare the performances of three different direct search algorithms on the calibration of a distributed hydrological balance model. The direct search family can be defined as that category of algorithms that make no use of derivatives of the cost function (that is, in general, a black box) and comprehend a large number of possible approaches. The main benefit of this class of methods is that they don't require changes in the implementation of the numerical codes to be calibrated. The first algorithm is the classical Nelder-Mead, often used in many applications and utilized as reference. The second algorithm is a GSS (Generating Set Search) algorithm, built in order to guarantee the conditions of global convergence and suitable for a parallel and multi-start implementation, here presented. The third one is the EGO algorithm (Efficient Global Optimization), that is particularly suitable to calibrate black box cost functions that require expensive computational resource (like an hydrological simulation). EGO minimizes the number of evaluations of the cost function balancing the need to minimize a response surface that approximates the problem and the need to improve the approximation sampling where prediction error may be high. The hydrological model to be calibrated was MOBIDIC, a complete balance distributed model developed at the Department of Civil and Environmental Engineering of the University of Florence. Discussion on the comparisons between the effectiveness of the different algorithms on different cases of study on Central Italy basins is provided.

Fairness in optimizing bus-crew scheduling process.

PubMed

Ma, Jihui; Song, Cuiying; Ceder, Avishai Avi; Liu, Tao; Guan, Wei

2017-01-01

This work proposes a model considering fairness in the problem of crew scheduling for bus drivers (CSP-BD) using a hybrid ant-colony optimization (HACO) algorithm to solve it. The main contributions of this work are the following: (a) a valid approach for cases with a special cost structure and constraints considering the fairness of working time and idle time; (b) an improved algorithm incorporating Gamma heuristic function and selecting rules. The relationships of each cost are examined with ten bus lines collected from the Beijing Public Transport Holdings (Group) Co., Ltd., one of the largest bus transit companies in the world. It shows that unfair cost is indirectly related to common cost, fixed cost and extra cost and also the unfair cost approaches to common and fixed cost when its coefficient is twice of common cost coefficient. Furthermore, the longest time for the tested bus line with 1108 pieces, 74 blocks is less than 30 minutes. The results indicate that the HACO-based algorithm can be a feasible and efficient optimization technique for CSP-BD, especially with large scale problems.

Linear-scaling time-dependent density-functional theory beyond the Tamm-Dancoff approximation: Obtaining efficiency and accuracy with in situ optimised local orbitals.

PubMed

Zuehlsdorff, T J; Hine, N D M; Payne, M C; Haynes, P D

2015-11-28

We present a solution of the full time-dependent density-functional theory (TDDFT) eigenvalue equation in the linear response formalism exhibiting a linear-scaling computational complexity with system size, without relying on the simplifying Tamm-Dancoff approximation (TDA). The implementation relies on representing the occupied and unoccupied subspaces with two different sets of in situ optimised localised functions, yielding a very compact and efficient representation of the transition density matrix of the excitation with the accuracy associated with a systematic basis set. The TDDFT eigenvalue equation is solved using a preconditioned conjugate gradient algorithm that is very memory-efficient. The algorithm is validated on a small test molecule and a good agreement with results obtained from standard quantum chemistry packages is found, with the preconditioner yielding a significant improvement in convergence rates. The method developed in this work is then used to reproduce experimental results of the absorption spectrum of bacteriochlorophyll in an organic solvent, where it is demonstrated that the TDA fails to reproduce the main features of the low energy spectrum, while the full TDDFT equation yields results in good qualitative agreement with experimental data. Furthermore, the need for explicitly including parts of the solvent into the TDDFT calculations is highlighted, making the treatment of large system sizes necessary that are well within reach of the capabilities of the algorithm introduced here. Finally, the linear-scaling properties of the algorithm are demonstrated by computing the lowest excitation energy of bacteriochlorophyll in solution. The largest systems considered in this work are of the same order of magnitude as a variety of widely studied pigment-protein complexes, opening up the possibility of studying their properties without having to resort to any semiclassical approximations to parts of the protein environment.

QuateXelero: An Accelerated Exact Network Motif Detection Algorithm

PubMed Central

Khakabimamaghani, Sahand; Sharafuddin, Iman; Dichter, Norbert; Koch, Ina; Masoudi-Nejad, Ali

2013-01-01

Finding motifs in biological, social, technological, and other types of networks has become a widespread method to gain more knowledge about these networks’ structure and function. However, this task is very computationally demanding, because it is highly associated with the graph isomorphism which is an NP problem (not known to belong to P or NP-complete subsets yet). Accordingly, this research is endeavoring to decrease the need to call NAUTY isomorphism detection method, which is the most time-consuming step in many existing algorithms. The work provides an extremely fast motif detection algorithm called QuateXelero, which has a Quaternary Tree data structure in the heart. The proposed algorithm is based on the well-known ESU (FANMOD) motif detection algorithm. The results of experiments on some standard model networks approve the overal superiority of the proposed algorithm, namely QuateXelero, compared with two of the fastest existing algorithms, G-Tries and Kavosh. QuateXelero is especially fastest in constructing the central data structure of the algorithm from scratch based on the input network. PMID:23874498

MRI-based dynamic tracking of an untethered ferromagnetic microcapsule navigating in liquid

NASA Astrophysics Data System (ADS)

Dahmen, Christian; Belharet, Karim; Folio, David; Ferreira, Antoine; Fatikow, Sergej

2016-04-01

The propulsion of ferromagnetic objects by means of MRI gradients is a promising approach to enable new forms of therapy. In this work, necessary techniques are presented to make this approach work. This includes path planning algorithms working on MRI data, ferromagnetic artifact imaging and a tracking algorithm which delivers position feedback for the ferromagnetic objects, and a propulsion sequence to enable interleaved magnetic propulsion and imaging. Using a dedicated software environment, integrating path-planning methods and real-time tracking, a clinical MRI system is adapted to provide this new functionality for controlled interventional targeted therapeutic applications. Through MRI-based sensing analysis, this article aims to propose a framework to plan a robust pathway to enhance the navigation ability to reach deep locations in the human body. The proposed approaches are validated with different experiments.

Evolutionary Algorithms Approach to the Solution of Damage Detection Problems

NASA Astrophysics Data System (ADS)

Salazar Pinto, Pedro Yoajim; Begambre, Oscar

2010-09-01

In this work is proposed a new Self-Configured Hybrid Algorithm by combining the Particle Swarm Optimization (PSO) and a Genetic Algorithm (GA). The aim of the proposed strategy is to increase the stability and accuracy of the search. The central idea is the concept of Guide Particle, this particle (the best PSO global in each generation) transmits its information to a particle of the following PSO generation, which is controlled by the GA. Thus, the proposed hybrid has an elitism feature that improves its performance and guarantees the convergence of the procedure. In different test carried out in benchmark functions, reported in the international literature, a better performance in stability and accuracy was observed; therefore the new algorithm was used to identify damage in a simple supported beam using modal data. Finally, it is worth noting that the algorithm is independent of the initial definition of heuristic parameters.

Novel trace chemical detection algorithms: a comparative study

NASA Astrophysics Data System (ADS)

Raz, Gil; Murphy, Cara; Georgan, Chelsea; Greenwood, Ross; Prasanth, R. K.; Myers, Travis; Goyal, Anish; Kelley, David; Wood, Derek; Kotidis, Petros

2017-05-01

Algorithms for standoff detection and estimation of trace chemicals in hyperspectral images in the IR band are a key component for a variety of applications relevant to law-enforcement and the intelligence communities. Performance of these methods is impacted by the spectral signature variability due to presence of contaminants, surface roughness, nonlinear dependence on abundances as well as operational limitations on the compute platforms. In this work we provide a comparative performance and complexity analysis of several classes of algorithms as a function of noise levels, error distribution, scene complexity, and spatial degrees of freedom. The algorithm classes we analyze and test include adaptive cosine estimator (ACE and modifications to it), compressive/sparse methods, Bayesian estimation, and machine learning. We explicitly call out the conditions under which each algorithm class is optimal or near optimal as well as their built-in limitations and failure modes.

The q-G method : A q-version of the Steepest Descent method for global optimization.

PubMed

Soterroni, Aline C; Galski, Roberto L; Scarabello, Marluce C; Ramos, Fernando M

2015-01-01

In this work, the q-Gradient (q-G) method, a q-version of the Steepest Descent method, is presented. The main idea behind the q-G method is the use of the negative of the q-gradient vector of the objective function as the search direction. The q-gradient vector, or simply the q-gradient, is a generalization of the classical gradient vector based on the concept of Jackson's derivative from the q-calculus. Its use provides the algorithm an effective mechanism for escaping from local minima. The q-G method reduces to the Steepest Descent method when the parameter q tends to 1. The algorithm has three free parameters and it is implemented so that the search process gradually shifts from global exploration in the beginning to local exploitation in the end. We evaluated the q-G method on 34 test functions, and compared its performance with 34 optimization algorithms, including derivative-free algorithms and the Steepest Descent method. Our results show that the q-G method is competitive and has a great potential for solving multimodal optimization problems.

CUFID-query: accurate network querying through random walk based network flow estimation.

PubMed

Jeong, Hyundoo; Qian, Xiaoning; Yoon, Byung-Jun

2017-12-28

Functional modules in biological networks consist of numerous biomolecules and their complicated interactions. Recent studies have shown that biomolecules in a functional module tend to have similar interaction patterns and that such modules are often conserved across biological networks of different species. As a result, such conserved functional modules can be identified through comparative analysis of biological networks. In this work, we propose a novel network querying algorithm based on the CUFID (Comparative network analysis Using the steady-state network Flow to IDentify orthologous proteins) framework combined with an efficient seed-and-extension approach. The proposed algorithm, CUFID-query, can accurately detect conserved functional modules as small subnetworks in the target network that are expected to perform similar functions to the given query functional module. The CUFID framework was recently developed for probabilistic pairwise global comparison of biological networks, and it has been applied to pairwise global network alignment, where the framework was shown to yield accurate network alignment results. In the proposed CUFID-query algorithm, we adopt the CUFID framework and extend it for local network alignment, specifically to solve network querying problems. First, in the seed selection phase, the proposed method utilizes the CUFID framework to compare the query and the target networks and to predict the probabilistic node-to-node correspondence between the networks. Next, the algorithm selects and greedily extends the seed in the target network by iteratively adding nodes that have frequent interactions with other nodes in the seed network, in a way that the conductance of the extended network is maximally reduced. Finally, CUFID-query removes irrelevant nodes from the querying results based on the personalized PageRank vector for the induced network that includes the fully extended network and its neighboring nodes. Through extensive performance evaluation based on biological networks with known functional modules, we show that CUFID-query outperforms the existing state-of-the-art algorithms in terms of prediction accuracy and biological significance of the predictions.

SU-FF-T-668: A Simple Algorithm for Range Modulation Wheel Design in Proton Therapy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nie, X; Nazaryan, Vahagn; Gueye, Paul

2009-06-01

Purpose: To develop a simple algorithm in designing the range modulation wheel to generate a very smooth Spread-Out Bragg peak (SOBP) for proton therapy.Method and Materials: A simple algorithm has been developed to generate the weight factors in corresponding pristine Bragg peaks which composed a smooth SOBP in proton therapy. We used a modified analytical Bragg peak function based on Monte Carol simulation tool-kits of Geant4 as pristine Bragg peaks input in our algorithm. A simple METLAB(R) Quad Program was introduced to optimize the cost function in our algorithm. Results: We found out that the existed analytical function of Braggmore » peak can't directly use as pristine Bragg peak dose-depth profile input file in optimization of the weight factors since this model didn't take into account of the scattering factors introducing from the range shifts in modifying the proton beam energies. We have done Geant4 simulations for proton energy of 63.4 MeV with a 1.08 cm SOBP for variation of pristine Bragg peaks which composed this SOBP and modified the existed analytical Bragg peak functions for their peak heights, ranges of R{sub 0}, and Gaussian energies {sigma}{sub E}. We found out that 19 pristine Bragg peaks are enough to achieve a flatness of 1.5% of SOBP which is the best flatness in the publications. Conclusion: This work develops a simple algorithm to generate the weight factors which is used to design a range modulation wheel to generate a smooth SOBP in protonradiation therapy. We have found out that a medium number of pristine Bragg peaks are enough to generate a SOBP with flatness less than 2%. It is potential to generate data base to store in the treatment plan to produce a clinic acceptable SOBP by using our simple algorithm.« less

A genetic algorithms approach for altering the membership functions in fuzzy logic controllers

NASA Technical Reports Server (NTRS)

Shehadeh, Hana; Lea, Robert N.

1992-01-01

Through previous work, a fuzzy control system was developed to perform translational and rotational control of a space vehicle. This problem was then re-examined to determine the effectiveness of genetic algorithms on fine tuning the controller. This paper explains the problems associated with the design of this fuzzy controller and offers a technique for tuning fuzzy logic controllers. A fuzzy logic controller is a rule-based system that uses fuzzy linguistic variables to model human rule-of-thumb approaches to control actions within a given system. This 'fuzzy expert system' features rules that direct the decision process and membership functions that convert the linguistic variables into the precise numeric values used for system control. Defining the fuzzy membership functions is the most time consuming aspect of the controller design. One single change in the membership functions could significantly alter the performance of the controller. This membership function definition can be accomplished by using a trial and error technique to alter the membership functions creating a highly tuned controller. This approach can be time consuming and requires a great deal of knowledge from human experts. In order to shorten development time, an iterative procedure for altering the membership functions to create a tuned set that used a minimal amount of fuel for velocity vector approach and station-keep maneuvers was developed. Genetic algorithms, search techniques used for optimization, were utilized to solve this problem.

The decoding of Reed-Solomon codes

NASA Technical Reports Server (NTRS)

Mceliece, R. J.

1988-01-01

Reed-Solomon (RS) codes form an important part of the high-rate downlink telemetry system for the Magellan mission, and the RS decoding function for this project will be done by DSN. Although the basic idea behind all Reed-Solomon decoding algorithms was developed by Berlekamp in 1968, there are dozens of variants of Berlekamp's algorithm in current use. An attempt to restore order is made by presenting a mathematical theory which explains the working of almost all known RS decoding algorithms. The key innovation that makes this possible is the unified approach to the solution of the key equation, which simultaneously describes the Berlekamp, Berlekamp-Massey, Euclid, and continued fractions approaches. Additionally, a detailed analysis is made of what can happen to a generic RS decoding algorithm when the number of errors and erasures exceeds the code's designed correction capability, and it is shown that while most published algorithms do not detect as many of these error-erasure patterns as possible, by making a small change in the algorithms, this problem can be overcome.

Optical network unit placement in Fiber-Wireless (FiWi) access network by Moth-Flame optimization algorithm

NASA Astrophysics Data System (ADS)

Singh, Puja; Prakash, Shashi

2017-07-01

Hybrid wireless-optical broadband access network (WOBAN) or Fiber-Wireless (FiWi) is the integration of wireless access network and optical network. This hybrid multi-domain network adopts the advantages of wireless and optical domains and serves the demand of technology savvy users. FiWi exhibits the properties of cost effectiveness, robustness, flexibility, high capacity, reliability and is self organized. Optical Network Unit (ONU) placement problem in FiWi contributes in simplifying the network design and enhances the performance in terms of cost efficiency and increased throughput. Several individual-based algorithms, such as Simulated Annealing (SA), Tabu Search, etc. have been suggested for ONU placement, but these algorithms suffer from premature convergence (trapping in a local optima). The present research work undertakes the deployment of FiWi and proposes a novel nature-inspired heuristic paradigm called Moth-Flame optimization (MFO) algorithm for multiple optical network units' placement. MFO is a population based algorithm. Population-based algorithms are better in handling local optima avoidance. The simulation results are compared with the existing Greedy and Simulated Annealing algorithms to optimize the position of ONUs. To the best of our knowledge, MFO algorithm has been used for the first time in this domain, moreover it has been able to provide very promising and competitive results. The performance of MFO algorithm has been analyzed by varying the 'b' parameter. MFO algorithm results in faster convergence than the existing strategies of Greedy and SA and returns a lower value of overall cost function. The results exhibit the dependence of the objective function on the distribution of wireless users also.

Online Pairwise Learning Algorithms.

PubMed

Ying, Yiming; Zhou, Ding-Xuan

2016-04-01

Pairwise learning usually refers to a learning task that involves a loss function depending on pairs of examples, among which the most notable ones are bipartite ranking, metric learning, and AUC maximization. In this letter we study an online algorithm for pairwise learning with a least-square loss function in an unconstrained setting of a reproducing kernel Hilbert space (RKHS) that we refer to as the Online Pairwise lEaRning Algorithm (OPERA). In contrast to existing works (Kar, Sriperumbudur, Jain, & Karnick, 2013 ; Wang, Khardon, Pechyony, & Jones, 2012 ), which require that the iterates are restricted to a bounded domain or the loss function is strongly convex, OPERA is associated with a non-strongly convex objective function and learns the target function in an unconstrained RKHS. Specifically, we establish a general theorem that guarantees the almost sure convergence for the last iterate of OPERA without any assumptions on the underlying distribution. Explicit convergence rates are derived under the condition of polynomially decaying step sizes. We also establish an interesting property for a family of widely used kernels in the setting of pairwise learning and illustrate the convergence results using such kernels. Our methodology mainly depends on the characterization of RKHSs using its associated integral operators and probability inequalities for random variables with values in a Hilbert space.

Artificial intelligence tools for pattern recognition

NASA Astrophysics Data System (ADS)

Acevedo, Elena; Acevedo, Antonio; Felipe, Federico; Avilés, Pedro

2017-06-01

In this work, we present a system for pattern recognition that combines the power of genetic algorithms for solving problems and the efficiency of the morphological associative memories. We use a set of 48 tire prints divided into 8 brands of tires. The images have dimensions of 200 x 200 pixels. We applied Hough transform to obtain lines as main features. The number of lines obtained is 449. The genetic algorithm reduces the number of features to ten suitable lines that give thus the 100% of recognition. Morphological associative memories were used as evaluation function. The selection algorithms were Tournament and Roulette wheel. For reproduction, we applied one-point, two-point and uniform crossover.

Detection theory applied to high intensity focused ultrasound (HIFU) treatment evaluation

NASA Astrophysics Data System (ADS)

Sanghvi, Narendra; Wunderlich, Adam; Seip, Ralf; Tavakkoli, Jahangir; Dines, Kris; Baily, Michael; Crum, Lawrence

2003-04-01

The aim of this work is to develop a HIFU treatment evaluation algorithm based on 1-D pulse/echo (P/E) ultrasound data taken during HIFU exposures. The algorithm is applicable to large treatment volumes resulting from several overlapping elementary exposures. Treatments consisted of multiple HIFU exposures with an on-time of 3 seconds each, spaced 3 mm apart, and an off-time of 6 seconds in between HIFU exposures. The HIFU was paused for approximately 70 milliseconds every 0.5 seconds, while P/E data was acquired along the beam axis, using a confocal imaging transducer. Data was collected from multiple in vitro and in vivo tissue treatments, including shams. The cumulative energy change in the P/E data was found for every HIFU exposure, as a function of depth. Subsequently, a likelihood ratio test with a fixed false alarm rate was used to derive a positive or negative lesion creation decision for that position. For false alarm rates less than 5%, positive treatment outcomes were consistently detected for better than 90% of the HIFU exposures. In addition, the algorithm outcome correlated to the applied HIFU intensity level. Lesion formation was therefore successfully detected as a function of dosage. [Work supported by NIH SBIR Grant 2 R 44 CA 83244-02.

Log-linear model based behavior selection method for artificial fish swarm algorithm.

PubMed

Huang, Zhehuang; Chen, Yidong

2015-01-01

Artificial fish swarm algorithm (AFSA) is a population based optimization technique inspired by social behavior of fishes. In past several years, AFSA has been successfully applied in many research and application areas. The behavior of fishes has a crucial impact on the performance of AFSA, such as global exploration ability and convergence speed. How to construct and select behaviors of fishes are an important task. To solve these problems, an improved artificial fish swarm algorithm based on log-linear model is proposed and implemented in this paper. There are three main works. Firstly, we proposed a new behavior selection algorithm based on log-linear model which can enhance decision making ability of behavior selection. Secondly, adaptive movement behavior based on adaptive weight is presented, which can dynamically adjust according to the diversity of fishes. Finally, some new behaviors are defined and introduced into artificial fish swarm algorithm at the first time to improve global optimization capability. The experiments on high dimensional function optimization showed that the improved algorithm has more powerful global exploration ability and reasonable convergence speed compared with the standard artificial fish swarm algorithm.

Robust Algorithms for on Minor-Free Graphs Based on the Sherali-Adams Hierarchy

NASA Astrophysics Data System (ADS)

Magen, Avner; Moharrami, Mohammad

This work provides a Linear Programming-based Polynomial Time Approximation Scheme (PTAS) for two classical NP-hard problems on graphs when the input graph is guaranteed to be planar, or more generally Minor Free. The algorithm applies a sufficiently large number (some function of when approximation is required) of rounds of the so-called Sherali-Adams Lift-and-Project system. needed to obtain a -approximation, where f is some function that depends only on the graph that should be avoided as a minor. The problem we discuss are the well-studied problems, the and problems. An curious fact we expose is that in the world of minor-free graph, the is harder in some sense than the.

OpenMM 7: Rapid development of high performance algorithms for molecular dynamics

PubMed Central

Swails, Jason; Zhao, Yutong; Beauchamp, Kyle A.; Wang, Lee-Ping; Stern, Chaya D.; Brooks, Bernard R.; Pande, Vijay S.

2017-01-01

OpenMM is a molecular dynamics simulation toolkit with a unique focus on extensibility. It allows users to easily add new features, including forces with novel functional forms, new integration algorithms, and new simulation protocols. Those features automatically work on all supported hardware types (including both CPUs and GPUs) and perform well on all of them. In many cases they require minimal coding, just a mathematical description of the desired function. They also require no modification to OpenMM itself and can be distributed independently of OpenMM. This makes it an ideal tool for researchers developing new simulation methods, and also allows those new methods to be immediately available to the larger community. PMID:28746339

Management of unmanned moving sensors through human decision layers: a bi-level optimization process with calls to costly sub-processes

NASA Astrophysics Data System (ADS)

Dambreville, Frédéric

2013-10-01

While there is a variety of approaches and algorithms for optimizing the mission of an unmanned moving sensor, there are much less works which deal with the implementation of several sensors within a human organization. In this case, the management of the sensors is done through at least one human decision layer, and the sensors management as a whole arises as a bi-level optimization process. In this work, the following hypotheses are considered as realistic: Sensor handlers of first level plans their sensors by means of elaborated algorithmic tools based on accurate modelling of the environment; Higher level plans the handled sensors according to a global observation mission and on the basis of an approximated model of the environment and of the first level sub-processes. This problem is formalized very generally as the maximization of an unknown function, defined a priori by sampling a known random function (law of model error). In such case, each actual evaluation of the function increases the knowledge about the function, and subsequently the efficiency of the maximization. The issue is to optimize the sequence of value to be evaluated, in regards to the evaluation costs. There is here a fundamental link with the domain of experiment design. Jones, Schonlau and Welch proposed a general method, the Efficient Global Optimization (EGO), for solving this problem in the case of additive functional Gaussian law. In our work, a generalization of the EGO is proposed, based on a rare event simulation approach. It is applied to the aforementioned bi-level sensor planning.

Differential Evolution algorithm applied to FSW model calibration

NASA Astrophysics Data System (ADS)

Idagawa, H. S.; Santos, T. F. A.; Ramirez, A. J.

2014-03-01

Friction Stir Welding (FSW) is a solid state welding process that can be modelled using a Computational Fluid Dynamics (CFD) approach. These models use adjustable parameters to control the heat transfer and the heat input to the weld. These parameters are used to calibrate the model and they are generally determined using the conventional trial and error approach. Since this method is not very efficient, we used the Differential Evolution (DE) algorithm to successfully determine these parameters. In order to improve the success rate and to reduce the computational cost of the method, this work studied different characteristics of the DE algorithm, such as the evolution strategy, the objective function, the mutation scaling factor and the crossover rate. The DE algorithm was tested using a friction stir weld performed on a UNS S32205 Duplex Stainless Steel.

Object Detection Based on Template Matching through Use of Best-So-Far ABC

PubMed Central

2014-01-01

Best-so-far ABC is a modified version of the artificial bee colony (ABC) algorithm used for optimization tasks. This algorithm is one of the swarm intelligence (SI) algorithms proposed in recent literature, in which the results demonstrated that the best-so-far ABC can produce higher quality solutions with faster convergence than either the ordinary ABC or the current state-of-the-art ABC-based algorithm. In this work, we aim to apply the best-so-far ABC-based approach for object detection based on template matching by using the difference between the RGB level histograms corresponding to the target object and the template object as the objective function. Results confirm that the proposed method was successful in both detecting objects and optimizing the time used to reach the solution. PMID:24812556

Progress Implementing a Model-Based Iterative Reconstruction Algorithm for Ultrasound Imaging of Thick Concrete

DOE Office of Scientific and Technical Information (OSTI.GOV)

Almansouri, Hani; Johnson, Christi R; Clayton, Dwight A

All commercial nuclear power plants (NPPs) in the United States contain concrete structures. These structures provide important foundation, support, shielding, and containment functions. Identification and management of aging and the degradation of concrete structures is fundamental to the proposed long-term operation of NPPs. Concrete structures in NPPs are often inaccessible and contain large volumes of massively thick concrete. While acoustic imaging using the synthetic aperture focusing technique (SAFT) works adequately well for thin specimens of concrete such as concrete transportation structures, enhancements are needed for heavily reinforced, thick concrete. We argue that image reconstruction quality for acoustic imaging in thickmore » concrete could be improved with Model-Based Iterative Reconstruction (MBIR) techniques. MBIR works by designing a probabilistic model for the measurements (forward model) and a probabilistic model for the object (prior model). Both models are used to formulate an objective function (cost function). The final step in MBIR is to optimize the cost function. Previously, we have demonstrated a first implementation of MBIR for an ultrasonic transducer array system. The original forward model has been upgraded to account for direct arrival signal. Updates to the forward model will be documented and the new algorithm will be assessed with synthetic and empirical samples.« less

Retrospective Cost Adaptive Control with Concurrent Closed-Loop Identification

NASA Astrophysics Data System (ADS)

Sobolic, Frantisek M.

Retrospective cost adaptive control (RCAC) is a discrete-time direct adaptive control algorithm for stabilization, command following, and disturbance rejection. RCAC is known to work on systems given minimal modeling information which is the leading numerator coefficient and any nonminimum-phase (NMP) zeros of the plant transfer function. This information is normally needed a priori and is key in the development of the filter, also known as the target model, within the retrospective performance variable. A novel approach to alleviate the need for prior modeling of both the leading coefficient of the plant transfer function as well as any NMP zeros is developed. The extension to the RCAC algorithm is the use of concurrent optimization of both the target model and the controller coefficients. Concurrent optimization of the target model and controller coefficients is a quadratic optimization problem in the target model and controller coefficients separately. However, this optimization problem is not convex as a joint function of both variables, and therefore nonconvex optimization methods are needed. Finally, insights within RCAC that include intercalated injection between the controller numerator and the denominator, unveil the workings of RCAC fitting a specific closed-loop transfer function to the target model. We exploit this interpretation by investigating several closed-loop identification architectures in order to extract this information for use in the target model.

Progress implementing a model-based iterative reconstruction algorithm for ultrasound imaging of thick concrete

NASA Astrophysics Data System (ADS)

Almansouri, Hani; Johnson, Christi; Clayton, Dwight; Polsky, Yarom; Bouman, Charles; Santos-Villalobos, Hector

2017-02-01

All commercial nuclear power plants (NPPs) in the United States contain concrete structures. These structures provide important foundation, support, shielding, and containment functions. Identification and management of aging and the degradation of concrete structures is fundamental to the proposed long-term operation of NPPs. Concrete structures in NPPs are often inaccessible and contain large volumes of massively thick concrete. While acoustic imaging using the synthetic aperture focusing technique (SAFT) works adequately well for thin specimens of concrete such as concrete transportation structures, enhancements are needed for heavily reinforced, thick concrete. We argue that image reconstruction quality for acoustic imaging in thick concrete could be improved with Model-Based Iterative Reconstruction (MBIR) techniques. MBIR works by designing a probabilistic model for the measurements (forward model) and a probabilistic model for the object (prior model). Both models are used to formulate an objective function (cost function). The final step in MBIR is to optimize the cost function. Previously, we have demonstrated a first implementation of MBIR for an ultrasonic transducer array system. The original forward model has been upgraded to account for direct arrival signal. Updates to the forward model will be documented and the new algorithm will be assessed with synthetic and empirical samples.

Development of an analytical guidance algorithm for lunar descent

NASA Astrophysics Data System (ADS)

Chomel, Christina Tvrdik

In recent years, NASA has indicated a desire to return humans to the moon. With NASA planning manned missions within the next couple of decades, the concept development for these lunar vehicles has begun. The guidance, navigation, and control (GN&C) computer programs that will perform the function of safely landing a spacecraft on the moon are part of that development. The lunar descent guidance algorithm takes the horizontally oriented spacecraft from orbital speeds hundreds of kilometers from the desired landing point to the landing point at an almost vertical orientation and very low speed. Existing lunar descent GN&C algorithms date back to the Apollo era with little work available for implementation since then. Though these algorithms met the criteria of the 1960's, they are cumbersome today. At the basis of the lunar descent phase are two elements: the targeting, which generates a reference trajectory, and the real-time guidance, which forces the spacecraft to fly that trajectory. The Apollo algorithm utilizes a complex, iterative, numerical optimization scheme for developing the reference trajectory. The real-time guidance utilizes this reference trajectory in the form of a quartic rather than a more general format to force the real-time trajectory errors to converge to zero; however, there exist no guarantees under any conditions for this convergence. The proposed algorithm implements a purely analytical targeting algorithm used to generate two-dimensional trajectories "on-the-fly"' or to retarget the spacecraft to another landing site altogether. It is based on the analytical solutions to the equations for speed, downrange, and altitude as a function of flight path angle and assumes two constant thrust acceleration curves. The proposed real-time guidance algorithm has at its basis the three-dimensional non-linear equations of motion and a control law that is proven to converge under certain conditions through Lyapunov analysis to a reference trajectory formatted as a function of downrange, altitude, speed, and flight path angle. The two elements of the guidance algorithm are joined in Monte Carlo analysis to prove their robustness to initial state dispersions and mass and thrust errors. The robustness of the retargeting algorithm is also demonstrated.

Evaluating High-Degree-and-Order Gravitational Harmonics and its Application to the State Predictions of a Lunar Orbiting Satellite

NASA Astrophysics Data System (ADS)

Song, Young-Joo; Kim, Bang-Yeop

2015-09-01

In this work, an efficient method with which to evaluate the high-degree-and-order gravitational harmonics of the nonsphericity of a central body is described and applied to state predictions of a lunar orbiter. Unlike the work of Song et al. (2010), which used a conventional computation method to process gravitational harmonic coefficients, the current work adapted a well-known recursion formula that directly uses fully normalized associated Legendre functions to compute the acceleration due to the non-sphericity of the moon. With the formulated algorithms, the states of a lunar orbiting satellite are predicted and its performance is validated in comparisons with solutions obtained from STK/Astrogator. The predicted differences in the orbital states between STK/Astrogator and the current work all remain at a position of less than 1 m with velocity accuracy levels of less than 1 mm/s, even with different orbital inclinations. The effectiveness of the current algorithm, in terms of both the computation time and the degree of accuracy degradation, is also shown in comparisons with results obtained from earlier work. It is expected that the proposed algorithm can be used as a foundation for the development of an operational flight dynamics subsystem for future lunar exploration missions by Korea. It can also be used to analyze missions which require very close operations to the moon.

Optimization of digital breast tomosynthesis (DBT) acquisition parameters for human observers: effect of reconstruction algorithms

NASA Astrophysics Data System (ADS)

Zeng, Rongping; Badano, Aldo; Myers, Kyle J.

2017-04-01

We showed in our earlier work that the choice of reconstruction methods does not affect the optimization of DBT acquisition parameters (angular span and number of views) using simulated breast phantom images in detecting lesions with a channelized Hotelling observer (CHO). In this work we investigate whether the model-observer based conclusion is valid when using humans to interpret images. We used previously generated DBT breast phantom images and recruited human readers to find the optimal geometry settings associated with two reconstruction algorithms, filtered back projection (FBP) and simultaneous algebraic reconstruction technique (SART). The human reader results show that image quality trends as a function of the acquisition parameters are consistent between FBP and SART reconstructions. The consistent trends confirm that the optimization of DBT system geometry is insensitive to the choice of reconstruction algorithm. The results also show that humans perform better in SART reconstructed images than in FBP reconstructed images. In addition, we applied CHOs with three commonly used channel models, Laguerre-Gauss (LG) channels, square (SQR) channels and sparse difference-of-Gaussian (sDOG) channels. We found that LG channels predict human performance trends better than SQR and sDOG channel models for the task of detecting lesions in tomosynthesis backgrounds. Overall, this work confirms that the choice of reconstruction algorithm is not critical for optimizing DBT system acquisition parameters.

Key Generation for Fast Inversion of the Paillier Encryption Function

NASA Astrophysics Data System (ADS)

Hirano, Takato; Tanaka, Keisuke

We study fast inversion of the Paillier encryption function. Especially, we focus only on key generation, and do not modify the Paillier encryption function. We propose three key generation algorithms based on the speeding-up techniques for the RSA encryption function. By using our algorithms, the size of the private CRT exponent is half of that of Paillier-CRT. The first algorithm employs the extended Euclidean algorithm. The second algorithm employs factoring algorithms, and can construct the private CRT exponent with low Hamming weight. The third algorithm is a variant of the second one, and has some advantage such as compression of the private CRT exponent and no requirement for factoring algorithms. We also propose the settings of the parameters for these algorithms and analyze the security of the Paillier encryption function by these algorithms against known attacks. Finally, we give experimental results of our algorithms.

Learning about Functions through Learner-Generated Examples

ERIC Educational Resources Information Center

Dinkelman, Martha O.; Cavey, Laurie O.

2015-01-01

In many mathematics classrooms, the teacher provides "worked examples" to demonstrate how students should perform certain algorithms or processes. Some students find it difficult to generalize from the examples that teachers provide and cannot apply what they have learned in new situations (Watson and Mason 2002). Instead, teachers might…

Combined Tensor Fitting and TV Regularization in Diffusion Tensor Imaging Based on a Riemannian Manifold Approach.

PubMed

Baust, Maximilian; Weinmann, Andreas; Wieczorek, Matthias; Lasser, Tobias; Storath, Martin; Navab, Nassir

2016-08-01

In this paper, we consider combined TV denoising and diffusion tensor fitting in DTI using the affine-invariant Riemannian metric on the space of diffusion tensors. Instead of first fitting the diffusion tensors, and then denoising them, we define a suitable TV type energy functional which incorporates the measured DWIs (using an inverse problem setup) and which measures the nearness of neighboring tensors in the manifold. To approach this functional, we propose generalized forward- backward splitting algorithms which combine an explicit and several implicit steps performed on a decomposition of the functional. We validate the performance of the derived algorithms on synthetic and real DTI data. In particular, we work on real 3D data. To our knowledge, the present paper describes the first approach to TV regularization in a combined manifold and inverse problem setup.

Graphical Environment Tools for Application to Gamma-Ray Energy Tracking Arrays

DOE Office of Scientific and Technical Information (OSTI.GOV)

Todd, Richard A.; Radford, David C.

2013-12-30

Highly segmented, position-sensitive germanium detector systems are being developed for nuclear physics research where traditional electronic signal processing with mixed analog and digital function blocks would be enormously complex and costly. Future systems will be constructed using pipelined processing of high-speed digitized signals as is done in the telecommunications industry. Techniques which provide rapid algorithm and system development for future systems are desirable. This project has used digital signal processing concepts and existing graphical system design tools to develop a set of re-usable modular functions and libraries targeted for the nuclear physics community. Researchers working with complex nuclear detector arraysmore » such as the Gamma-Ray Energy Tracking Array (GRETA) have been able to construct advanced data processing algorithms for implementation in field programmable gate arrays (FPGAs) through application of these library functions using intuitive graphical interfaces.« less

Global navigation satellite system receiver for weak signals under all dynamic conditions

NASA Astrophysics Data System (ADS)

Ziedan, Nesreen Ibrahim

The ability of the Global Navigation Satellite System (GNSS) receiver to work under weak signal and various dynamic conditions is required in some applications. For example, to provide a positioning capability in wireless devices, or orbit determination of Geostationary and high Earth orbit satellites. This dissertation develops Global Positioning System (GPS) receiver algorithms for such applications. Fifteen algorithms are developed for the GPS C/A signal. They cover all the receiver main functions, which include acquisition, fine acquisition, bit synchronization, code and carrier tracking, and navigation message decoding. They are integrated together, and they can be used in any software GPS receiver. They also can be modified to fit any other GPS or GNSS signals. The algorithms have new capabilities. The processing and memory requirements are considered in the design to allow the algorithms to fit the limited resources of some applications; they do not require any assisting information. Weak signals can be acquired in the presence of strong interfering signals and under high dynamic conditions. The fine acquisition, bit synchronization, and tracking algorithms are based on the Viterbi algorithm and Extended Kalman filter approaches. The tracking algorithms capabilities increase the time to lose lock. They have the ability to adaptively change the integration length and the code delay separation. More than one code delay separation can be used in the same time. Large tracking errors can be detected and then corrected by a re-initialization and an acquisition-like algorithms. Detecting the navigation message is needed to increase the coherent integration; decoding it is needed to calculate the navigation solution. The decoding algorithm utilizes the message structure to enable its decoding for signals with high Bit Error Rate. The algorithms are demonstrated using simulated GPS C/A code signals, and TCXO clocks. The results have shown the algorithms ability to reliably work with 15 dB-Hz signals and acceleration over 6 g.

One cutting plane algorithm using auxiliary functions

NASA Astrophysics Data System (ADS)

Zabotin, I. Ya; Kazaeva, K. E.

2016-11-01

We propose an algorithm for solving a convex programming problem from the class of cutting methods. The algorithm is characterized by the construction of approximations using some auxiliary functions, instead of the objective function. Each auxiliary function bases on the exterior penalty function. In proposed algorithm the admissible set and the epigraph of each auxiliary function are embedded into polyhedral sets. In connection with the above, the iteration points are found by solving linear programming problems. We discuss the implementation of the algorithm and prove its convergence.

Demyelinating and ischemic brain diseases: detection algorithm through regular magnetic resonance images

NASA Astrophysics Data System (ADS)

Castillo, D.; Samaniego, René; Jiménez, Y.; Cuenca, L.; Vivanco, O.; Rodríguez-Álvarez, M. J.

2017-09-01

This work presents the advance to development of an algorithm for automatic detection of demyelinating lesions and cerebral ischemia through magnetic resonance images, which have contributed in paramount importance in the diagnosis of brain diseases. The sequences of images to be used are T1, T2, and FLAIR. Brain demyelination lesions occur due to damage of the myelin layer of nerve fibers; and therefore this deterioration is the cause of serious pathologies such as multiple sclerosis (MS), leukodystrophy, disseminated acute encephalomyelitis. Cerebral or cerebrovascular ischemia is the interruption of the blood supply to the brain, thus interrupting; the flow of oxygen and nutrients needed to maintain the functioning of brain cells. The algorithm allows the differentiation between these lesions.

A collaborative filtering approach for protein-protein docking scoring functions.

PubMed

Bourquard, Thomas; Bernauer, Julie; Azé, Jérôme; Poupon, Anne

2011-04-22

A protein-protein docking procedure traditionally consists in two successive tasks: a search algorithm generates a large number of candidate conformations mimicking the complex existing in vivo between two proteins, and a scoring function is used to rank them in order to extract a native-like one. We have already shown that using Voronoi constructions and a well chosen set of parameters, an accurate scoring function could be designed and optimized. However to be able to perform large-scale in silico exploration of the interactome, a near-native solution has to be found in the ten best-ranked solutions. This cannot yet be guaranteed by any of the existing scoring functions. In this work, we introduce a new procedure for conformation ranking. We previously developed a set of scoring functions where learning was performed using a genetic algorithm. These functions were used to assign a rank to each possible conformation. We now have a refined rank using different classifiers (decision trees, rules and support vector machines) in a collaborative filtering scheme. The scoring function newly obtained is evaluated using 10 fold cross-validation, and compared to the functions obtained using either genetic algorithms or collaborative filtering taken separately. This new approach was successfully applied to the CAPRI scoring ensembles. We show that for 10 targets out of 12, we are able to find a near-native conformation in the 10 best ranked solutions. Moreover, for 6 of them, the near-native conformation selected is of high accuracy. Finally, we show that this function dramatically enriches the 100 best-ranking conformations in near-native structures.

A Collaborative Filtering Approach for Protein-Protein Docking Scoring Functions

PubMed Central

Bourquard, Thomas; Bernauer, Julie; Azé, Jérôme; Poupon, Anne

2011-01-01

A protein-protein docking procedure traditionally consists in two successive tasks: a search algorithm generates a large number of candidate conformations mimicking the complex existing in vivo between two proteins, and a scoring function is used to rank them in order to extract a native-like one. We have already shown that using Voronoi constructions and a well chosen set of parameters, an accurate scoring function could be designed and optimized. However to be able to perform large-scale in silico exploration of the interactome, a near-native solution has to be found in the ten best-ranked solutions. This cannot yet be guaranteed by any of the existing scoring functions. In this work, we introduce a new procedure for conformation ranking. We previously developed a set of scoring functions where learning was performed using a genetic algorithm. These functions were used to assign a rank to each possible conformation. We now have a refined rank using different classifiers (decision trees, rules and support vector machines) in a collaborative filtering scheme. The scoring function newly obtained is evaluated using 10 fold cross-validation, and compared to the functions obtained using either genetic algorithms or collaborative filtering taken separately. This new approach was successfully applied to the CAPRI scoring ensembles. We show that for 10 targets out of 12, we are able to find a near-native conformation in the 10 best ranked solutions. Moreover, for 6 of them, the near-native conformation selected is of high accuracy. Finally, we show that this function dramatically enriches the 100 best-ranking conformations in near-native structures. PMID:21526112

A Comparative Study of Probability Collectives Based Multi-agent Systems and Genetic Algorithms

NASA Technical Reports Server (NTRS)

Huang, Chien-Feng; Wolpert, David H.; Bieniawski, Stefan; Strauss, Charles E. M.

2005-01-01

We compare Genetic Algorithms (GA's) with Probability Collectives (PC), a new framework for distributed optimization and control. In contrast to GA's, PC-based methods do not update populations of solutions. Instead they update an explicitly parameterized probability distribution p over the space of solutions. That updating of p arises as the optimization of a functional of p. The functional is chosen so that any p that optimizes it should be p peaked about good solutions. The PC approach works in both continuous and discrete problems. It does not suffer from the resolution limitation of the finite bit length encoding of parameters into GA alleles. It also has deep connections with both game theory and statistical physics. We review the PC approach using its motivation as the information theoretic formulation of bounded rationality for multi-agent systems. It is then compared with GA's on a diverse set of problems. To handle high dimensional surfaces, in the PC method investigated here p is restricted to a product distribution. Each distribution in that product is controlled by a separate agent. The test functions were selected for their difficulty using either traditional gradient descent or genetic algorithms. On those functions the PC-based approach significantly outperforms traditional GA's in both rate of descent, trapping in false minima, and long term optimization.

A Temperature Compensation Method for Piezo-Resistive Pressure Sensor Utilizing Chaotic Ions Motion Algorithm Optimized Hybrid Kernel LSSVM.

PubMed

Li, Ji; Hu, Guoqing; Zhou, Yonghong; Zou, Chong; Peng, Wei; Alam Sm, Jahangir

2016-10-14

A piezo-resistive pressure sensor is made of silicon, the nature of which is considerably influenced by ambient temperature. The effect of temperature should be eliminated during the working period in expectation of linear output. To deal with this issue, an approach consists of a hybrid kernel Least Squares Support Vector Machine (LSSVM) optimized by a chaotic ions motion algorithm presented. To achieve the learning and generalization for excellent performance, a hybrid kernel function, constructed by a local kernel as Radial Basis Function (RBF) kernel, and a global kernel as polynomial kernel is incorporated into the Least Squares Support Vector Machine. The chaotic ions motion algorithm is introduced to find the best hyper-parameters of the Least Squares Support Vector Machine. The temperature data from a calibration experiment is conducted to validate the proposed method. With attention on algorithm robustness and engineering applications, the compensation result shows the proposed scheme outperforms other compared methods on several performance measures as maximum absolute relative error, minimum absolute relative error mean and variance of the averaged value on fifty runs. Furthermore, the proposed temperature compensation approach lays a foundation for more extensive research.

Interacting with target tracking algorithms in a gaze-enhanced motion video analysis system

NASA Astrophysics Data System (ADS)

Hild, Jutta; Krüger, Wolfgang; Heinze, Norbert; Peinsipp-Byma, Elisabeth; Beyerer, Jürgen

2016-05-01

Motion video analysis is a challenging task, particularly if real-time analysis is required. It is therefore an important issue how to provide suitable assistance for the human operator. Given that the use of customized video analysis systems is more and more established, one supporting measure is to provide system functions which perform subtasks of the analysis. Recent progress in the development of automated image exploitation algorithms allow, e.g., real-time moving target tracking. Another supporting measure is to provide a user interface which strives to reduce the perceptual, cognitive and motor load of the human operator for example by incorporating the operator's visual focus of attention. A gaze-enhanced user interface is able to help here. This work extends prior work on automated target recognition, segmentation, and tracking algorithms as well as about the benefits of a gaze-enhanced user interface for interaction with moving targets. We also propose a prototypical system design aiming to combine both the qualities of the human observer's perception and the automated algorithms in order to improve the overall performance of a real-time video analysis system. In this contribution, we address two novel issues analyzing gaze-based interaction with target tracking algorithms. The first issue extends the gaze-based triggering of a target tracking process, e.g., investigating how to best relaunch in the case of track loss. The second issue addresses the initialization of tracking algorithms without motion segmentation where the operator has to provide the system with the object's image region in order to start the tracking algorithm.

Motion artifact removal algorithm by ICA for e-bra: a women ECG measurement system

NASA Astrophysics Data System (ADS)

Kwon, Hyeokjun; Oh, Sechang; Varadan, Vijay K.

2013-04-01

Wearable ECG(ElectroCardioGram) measurement systems have increasingly been developing for people who suffer from CVD(CardioVascular Disease) and have very active lifestyles. Especially, in the case of female CVD patients, several abnormal CVD symptoms are accompanied with CVDs. Therefore, monitoring women's ECG signal is a significant diagnostic method to prevent from sudden heart attack. The E-bra ECG measurement system from our previous work provides more convenient option for women than Holter monitor system. The e-bra system was developed with a motion artifact removal algorithm by using an adaptive filter with LMS(least mean square) and a wandering noise baseline detection algorithm. In this paper, ICA(independent component analysis) algorithms are suggested to remove motion artifact factor for the e-bra system. Firstly, the ICA algorithms are developed with two kinds of statistical theories: Kurtosis, Endropy and evaluated by performing simulations with a ECG signal created by sgolayfilt function of MATLAB, a noise signal including 0.4Hz, 1.1Hz and 1.9Hz, and a weighed vector W estimated by kurtosis or entropy. A correlation value is shown as the degree of similarity between the created ECG signal and the estimated new ECG signal. In the real time E-Bra system, two pseudo signals are extracted by multiplying with a random weighted vector W, the measured ECG signal from E-bra system, and the noise component signal by noise extraction algorithm from our previous work. The suggested ICA algorithm basing on kurtosis or entropy is used to estimate the new ECG signal Y without noise component.

Quantum annealing for combinatorial clustering

NASA Astrophysics Data System (ADS)

Kumar, Vaibhaw; Bass, Gideon; Tomlin, Casey; Dulny, Joseph

2018-02-01

Clustering is a powerful machine learning technique that groups "similar" data points based on their characteristics. Many clustering algorithms work by approximating the minimization of an objective function, namely the sum of within-the-cluster distances between points. The straightforward approach involves examining all the possible assignments of points to each of the clusters. This approach guarantees the solution will be a global minimum; however, the number of possible assignments scales quickly with the number of data points and becomes computationally intractable even for very small datasets. In order to circumvent this issue, cost function minima are found using popular local search-based heuristic approaches such as k-means and hierarchical clustering. Due to their greedy nature, such techniques do not guarantee that a global minimum will be found and can lead to sub-optimal clustering assignments. Other classes of global search-based techniques, such as simulated annealing, tabu search, and genetic algorithms, may offer better quality results but can be too time-consuming to implement. In this work, we describe how quantum annealing can be used to carry out clustering. We map the clustering objective to a quadratic binary optimization problem and discuss two clustering algorithms which are then implemented on commercially available quantum annealing hardware, as well as on a purely classical solver "qbsolv." The first algorithm assigns N data points to K clusters, and the second one can be used to perform binary clustering in a hierarchical manner. We present our results in the form of benchmarks against well-known k-means clustering and discuss the advantages and disadvantages of the proposed techniques.

Delaunay-based derivative-free optimization for efficient minimization of time-averaged statistics of turbulent flows

NASA Astrophysics Data System (ADS)

Beyhaghi, Pooriya

2016-11-01

This work considers the problem of the efficient minimization of the infinite time average of a stationary ergodic process in the space of a handful of independent parameters which affect it. Problems of this class, derived from physical or numerical experiments which are sometimes expensive to perform, are ubiquitous in turbulence research. In such problems, any given function evaluation, determined with finite sampling, is associated with a quantifiable amount of uncertainty, which may be reduced via additional sampling. This work proposes the first algorithm of this type. Our algorithm remarkably reduces the overall cost of the optimization process for problems of this class. Further, under certain well-defined conditions, rigorous proof of convergence is established to the global minimum of the problem considered.

Discrete-Time Demodulator Architectures for Free-Space Broadband Optical Pulse-Position Modulation

NASA Technical Reports Server (NTRS)

Gray, A. A.; Lee, C.

2004-01-01

The objective of this work is to develop discrete-time demodulator architectures for broadband optical pulse-position modulation (PPM) that are capable of processing Nyquist or near-Nyquist data rates. These architectures are motivated by the numerous advantages of realizing communications demodulators in digital very large scale integrated (VLSI) circuits. The architectures are developed within a framework that encompasses a large body of work in optical communications, synchronization, and multirate discrete-time signal processing and are constrained by the limitations of the state of the art in digital hardware. This work attempts to create a bridge between theoretical communication algorithms and analysis for deep-space optical PPM and modern digital VLSI. The primary focus of this work is on the synthesis of discrete-time processing architectures for accomplishing the most fundamental functions required in PPM demodulators, post-detection filtering, synchronization, and decision processing. The architectures derived are capable of closely approximating the theoretical performance of the continuous-time algorithms from which they are derived. The work concludes with an outline of the development path that leads to hardware.

FPGA implementation of sparse matrix algorithm for information retrieval

NASA Astrophysics Data System (ADS)

Bojanic, Slobodan; Jevtic, Ruzica; Nieto-Taladriz, Octavio

2005-06-01

Information text data retrieval requires a tremendous amount of processing time because of the size of the data and the complexity of information retrieval algorithms. In this paper the solution to this problem is proposed via hardware supported information retrieval algorithms. Reconfigurable computing may adopt frequent hardware modifications through its tailorable hardware and exploits parallelism for a given application through reconfigurable and flexible hardware units. The degree of the parallelism can be tuned for data. In this work we implemented standard BLAS (basic linear algebra subprogram) sparse matrix algorithm named Compressed Sparse Row (CSR) that is showed to be more efficient in terms of storage space requirement and query-processing timing over the other sparse matrix algorithms for information retrieval application. Although inverted index algorithm is treated as the de facto standard for information retrieval for years, an alternative approach to store the index of text collection in a sparse matrix structure gains more attention. This approach performs query processing using sparse matrix-vector multiplication and due to parallelization achieves a substantial efficiency over the sequential inverted index. The parallel implementations of information retrieval kernel are presented in this work targeting the Virtex II Field Programmable Gate Arrays (FPGAs) board from Xilinx. A recent development in scientific applications is the use of FPGA to achieve high performance results. Computational results are compared to implementations on other platforms. The design achieves a high level of parallelism for the overall function while retaining highly optimised hardware within processing unit.

ABCluster: the artificial bee colony algorithm for cluster global optimization.

PubMed

Zhang, Jun; Dolg, Michael

2015-10-07

Global optimization of cluster geometries is of fundamental importance in chemistry and an interesting problem in applied mathematics. In this work, we introduce a relatively new swarm intelligence algorithm, i.e. the artificial bee colony (ABC) algorithm proposed in 2005, to this field. It is inspired by the foraging behavior of a bee colony, and only three parameters are needed to control it. We applied it to several potential functions of quite different nature, i.e., the Coulomb-Born-Mayer, Lennard-Jones, Morse, Z and Gupta potentials. The benchmarks reveal that for long-ranged potentials the ABC algorithm is very efficient in locating the global minimum, while for short-ranged ones it is sometimes trapped into a local minimum funnel on a potential energy surface of large clusters. We have released an efficient, user-friendly, and free program "ABCluster" to realize the ABC algorithm. It is a black-box program for non-experts as well as experts and might become a useful tool for chemists to study clusters.

Parallelization of Nullspace Algorithm for the computation of metabolic pathways

PubMed Central

Jevremović, Dimitrije; Trinh, Cong T.; Srienc, Friedrich; Sosa, Carlos P.; Boley, Daniel

2011-01-01

Elementary mode analysis is a useful metabolic pathway analysis tool in understanding and analyzing cellular metabolism, since elementary modes can represent metabolic pathways with unique and minimal sets of enzyme-catalyzed reactions of a metabolic network under steady state conditions. However, computation of the elementary modes of a genome- scale metabolic network with 100–1000 reactions is very expensive and sometimes not feasible with the commonly used serial Nullspace Algorithm. In this work, we develop a distributed memory parallelization of the Nullspace Algorithm to handle efficiently the computation of the elementary modes of a large metabolic network. We give an implementation in C++ language with the support of MPI library functions for the parallel communication. Our proposed algorithm is accompanied with an analysis of the complexity and identification of major bottlenecks during computation of all possible pathways of a large metabolic network. The algorithm includes methods to achieve load balancing among the compute-nodes and specific communication patterns to reduce the communication overhead and improve efficiency. PMID:22058581

Modelling soil water retention using support vector machines with genetic algorithm optimisation.

PubMed

Lamorski, Krzysztof; Sławiński, Cezary; Moreno, Felix; Barna, Gyöngyi; Skierucha, Wojciech; Arrue, José L

2014-01-01

This work presents point pedotransfer function (PTF) models of the soil water retention curve. The developed models allowed for estimation of the soil water content for the specified soil water potentials: -0.98, -3.10, -9.81, -31.02, -491.66, and -1554.78 kPa, based on the following soil characteristics: soil granulometric composition, total porosity, and bulk density. Support Vector Machines (SVM) methodology was used for model development. A new methodology for elaboration of retention function models is proposed. Alternative to previous attempts known from literature, the ν-SVM method was used for model development and the results were compared with the formerly used the C-SVM method. For the purpose of models' parameters search, genetic algorithms were used as an optimisation framework. A new form of the aim function used for models parameters search is proposed which allowed for development of models with better prediction capabilities. This new aim function avoids overestimation of models which is typically encountered when root mean squared error is used as an aim function. Elaborated models showed good agreement with measured soil water retention data. Achieved coefficients of determination values were in the range 0.67-0.92. Studies demonstrated usability of ν-SVM methodology together with genetic algorithm optimisation for retention modelling which gave better performing models than other tested approaches.

SPOTting model parameters using a ready-made Python package

NASA Astrophysics Data System (ADS)

Houska, Tobias; Kraft, Philipp; Breuer, Lutz

2015-04-01

The selection and parameterization of reliable process descriptions in ecological modelling is driven by several uncertainties. The procedure is highly dependent on various criteria, like the used algorithm, the likelihood function selected and the definition of the prior parameter distributions. A wide variety of tools have been developed in the past decades to optimize parameters. Some of the tools are closed source. Due to this, the choice for a specific parameter estimation method is sometimes more dependent on its availability than the performance. A toolbox with a large set of methods can support users in deciding about the most suitable method. Further, it enables to test and compare different methods. We developed the SPOT (Statistical Parameter Optimization Tool), an open source python package containing a comprehensive set of modules, to analyze and optimize parameters of (environmental) models. SPOT comes along with a selected set of algorithms for parameter optimization and uncertainty analyses (Monte Carlo, MC; Latin Hypercube Sampling, LHS; Maximum Likelihood, MLE; Markov Chain Monte Carlo, MCMC; Scuffled Complex Evolution, SCE-UA; Differential Evolution Markov Chain, DE-MCZ), together with several likelihood functions (Bias, (log-) Nash-Sutcliff model efficiency, Correlation Coefficient, Coefficient of Determination, Covariance, (Decomposed-, Relative-, Root-) Mean Squared Error, Mean Absolute Error, Agreement Index) and prior distributions (Binomial, Chi-Square, Dirichlet, Exponential, Laplace, (log-, multivariate-) Normal, Pareto, Poisson, Cauchy, Uniform, Weibull) to sample from. The model-independent structure makes it suitable to analyze a wide range of applications. We apply all algorithms of the SPOT package in three different case studies. Firstly, we investigate the response of the Rosenbrock function, where the MLE algorithm shows its strengths. Secondly, we study the Griewank function, which has a challenging response surface for optimization methods. Here we see simple algorithms like the MCMC struggling to find the global optimum of the function, while algorithms like SCE-UA and DE-MCZ show their strengths. Thirdly, we apply an uncertainty analysis of a one-dimensional physically based hydrological model build with the Catchment Modelling Framework (CMF). The model is driven by meteorological and groundwater data from a Free Air Carbon Enrichment (FACE) experiment in Linden (Hesse, Germany). Simulation results are evaluated with measured soil moisture data. We search for optimal parameter sets of the van Genuchten-Mualem function and find different equally optimal solutions with some of the algorithms. The case studies reveal that the implemented SPOT methods work sufficiently well. They further show the benefit of having one tool at hand that includes a number of parameter search methods, likelihood functions and a priori parameter distributions within one platform independent package.

Detecting non-orthology in the COGs database and other approaches grouping orthologs using genome-specific best hits.

PubMed

Dessimoz, Christophe; Boeckmann, Brigitte; Roth, Alexander C J; Gonnet, Gaston H

2006-01-01

Correct orthology assignment is a critical prerequisite of numerous comparative genomics procedures, such as function prediction, construction of phylogenetic species trees and genome rearrangement analysis. We present an algorithm for the detection of non-orthologs that arise by mistake in current orthology classification methods based on genome-specific best hits, such as the COGs database. The algorithm works with pairwise distance estimates, rather than computationally expensive and error-prone tree-building methods. The accuracy of the algorithm is evaluated through verification of the distribution of predicted cases, case-by-case phylogenetic analysis and comparisons with predictions from other projects using independent methods. Our results show that a very significant fraction of the COG groups include non-orthologs: using conservative parameters, the algorithm detects non-orthology in a third of all COG groups. Consequently, sequence analysis sensitive to correct orthology assignments will greatly benefit from these findings.

Formation control of robotic swarm using bounded artificial forces.

PubMed

Qin, Long; Zha, Yabing; Yin, Quanjun; Peng, Yong

2013-01-01

Formation control of multirobot systems has drawn significant attention in the recent years. This paper presents a potential field control algorithm, navigating a swarm of robots into a predefined 2D shape while avoiding intermember collisions. The algorithm applies in both stationary and moving targets formation. We define the bounded artificial forces in the form of exponential functions, so that the behavior of the swarm drove by the forces can be adjusted via selecting proper control parameters. The theoretical analysis of the swarm behavior proves the stability and convergence properties of the algorithm. We further make certain modifications upon the forces to improve the robustness of the swarm behavior in the presence of realistic implementation considerations. The considerations include obstacle avoidance, local minima, and deformation of the shape. Finally, detailed simulation results validate the efficiency of the proposed algorithm, and the direction of possible futrue work is discussed in the conclusions.

Formation Control of Robotic Swarm Using Bounded Artificial Forces

PubMed Central

Zha, Yabing; Peng, Yong

2013-01-01

Formation control of multirobot systems has drawn significant attention in the recent years. This paper presents a potential field control algorithm, navigating a swarm of robots into a predefined 2D shape while avoiding intermember collisions. The algorithm applies in both stationary and moving targets formation. We define the bounded artificial forces in the form of exponential functions, so that the behavior of the swarm drove by the forces can be adjusted via selecting proper control parameters. The theoretical analysis of the swarm behavior proves the stability and convergence properties of the algorithm. We further make certain modifications upon the forces to improve the robustness of the swarm behavior in the presence of realistic implementation considerations. The considerations include obstacle avoidance, local minima, and deformation of the shape. Finally, detailed simulation results validate the efficiency of the proposed algorithm, and the direction of possible futrue work is discussed in the conclusions. PMID:24453809

Fully Decentralized Semi-supervised Learning via Privacy-preserving Matrix Completion.

PubMed

Fierimonte, Roberto; Scardapane, Simone; Uncini, Aurelio; Panella, Massimo

2016-08-26

Distributed learning refers to the problem of inferring a function when the training data are distributed among different nodes. While significant work has been done in the contexts of supervised and unsupervised learning, the intermediate case of Semi-supervised learning in the distributed setting has received less attention. In this paper, we propose an algorithm for this class of problems, by extending the framework of manifold regularization. The main component of the proposed algorithm consists of a fully distributed computation of the adjacency matrix of the training patterns. To this end, we propose a novel algorithm for low-rank distributed matrix completion, based on the framework of diffusion adaptation. Overall, the distributed Semi-supervised algorithm is efficient and scalable, and it can preserve privacy by the inclusion of flexible privacy-preserving mechanisms for similarity computation. The experimental results and comparison on a wide range of standard Semi-supervised benchmarks validate our proposal.

GPU Accelerated Browser for Neuroimaging Genomics.

PubMed

Zigon, Bob; Li, Huang; Yao, Xiaohui; Fang, Shiaofen; Hasan, Mohammad Al; Yan, Jingwen; Moore, Jason H; Saykin, Andrew J; Shen, Li

2018-04-25

Neuroimaging genomics is an emerging field that provides exciting opportunities to understand the genetic basis of brain structure and function. The unprecedented scale and complexity of the imaging and genomics data, however, have presented critical computational bottlenecks. In this work we present our initial efforts towards building an interactive visual exploratory system for mining big data in neuroimaging genomics. A GPU accelerated browsing tool for neuroimaging genomics is created that implements the ANOVA algorithm for single nucleotide polymorphism (SNP) based analysis and the VEGAS algorithm for gene-based analysis, and executes them at interactive rates. The ANOVA algorithm is 110 times faster than the 4-core OpenMP version, while the VEGAS algorithm is 375 times faster than its 4-core OpenMP counter part. This approach lays a solid foundation for researchers to address the challenges of mining large-scale imaging genomics datasets via interactive visual exploration.

Application of a derivative-free global optimization algorithm to the derivation of a new time integration scheme for the simulation of incompressible turbulence

NASA Astrophysics Data System (ADS)

Alimohammadi, Shahrouz; Cavaglieri, Daniele; Beyhaghi, Pooriya; Bewley, Thomas R.

2016-11-01

This work applies a recently developed Derivative-free optimization algorithm to derive a new mixed implicit-explicit (IMEX) time integration scheme for Computational Fluid Dynamics (CFD) simulations. This algorithm allows imposing a specified order of accuracy for the time integration and other important stability properties in the form of nonlinear constraints within the optimization problem. In this procedure, the coefficients of the IMEX scheme should satisfy a set of constraints simultaneously. Therefore, the optimization process, at each iteration, estimates the location of the optimal coefficients using a set of global surrogates, for both the objective and constraint functions, as well as a model of the uncertainty function of these surrogates based on the concept of Delaunay triangulation. This procedure has been proven to converge to the global minimum of the constrained optimization problem provided the constraints and objective functions are twice differentiable. As a result, a new third-order, low-storage IMEX Runge-Kutta time integration scheme is obtained with remarkably fast convergence. Numerical tests are then performed leveraging the turbulent channel flow simulations to validate the theoretical order of accuracy and stability properties of the new scheme.

Effective structural descriptors for natural and engineered radioactive waste confinement barriers

NASA Astrophysics Data System (ADS)

Lemmens, Laurent; Rogiers, Bart; De Craen, Mieke; Laloy, Eric; Jacques, Diederik; Huysmans, Marijke; Swennen, Rudy; Urai, Janos L.; Desbois, Guillaume

2017-04-01

The microstructure of a radioactive waste confinement barrier strongly influences its flow and transport properties. Numerical flow and transport simulations for these porous media at the pore scale therefore require input data that describe the microstructure as accurately as possible. To date, no imaging method can resolve all heterogeneities within important radioactive waste confinement barrier materials as hardened cement paste and natural clays at the micro scale (nm-cm). Therefore, it is necessary to merge information from different 2D and 3D imaging methods using porous media reconstruction techniques. To qualitatively compare the results of different reconstruction techniques, visual inspection might suffice. To quantitatively compare training-image based algorithms, Tan et al. (2014) proposed an algorithm using an analysis of distance. However, the ranking of the algorithm depends on the choice of the structural descriptor, in their case multiple-point or cluster-based histograms. We present here preliminary work in which we will review different structural descriptors and test their effectiveness, for capturing the main structural characteristics of radioactive waste confinement barrier materials, to determine the descriptors to use in the analysis of distance. The investigated descriptors are particle size distributions, surface area distributions, two point probability functions, multiple point histograms, linear functions and two point cluster functions. The descriptor testing consists of stochastically generating realizations from a reference image using the simulated annealing optimization procedure introduced by Karsanina et al. (2015). This procedure basically minimizes the differences between pre-specified descriptor values associated with the training image and the image being produced. The most efficient descriptor set can therefore be identified by comparing the image generation quality among the tested descriptor combinations. The assessment of the quality of the simulations will be made by combining all considered descriptors. Once the set of the most efficient descriptors is determined, they can be used in the analysis of distance, to rank different reconstruction algorithms in a more objective way in future work. Karsanina MV, Gerke KM, Skvortsova EB, Mallants D (2015) Universal Spatial Correlation Functions for Describing and Reconstructing Soil Microstructure. PLoS ONE 10(5): e0126515. doi:10.1371/journal.pone.0126515 Tan, Xiaojin, Pejman Tahmasebi, and Jef Caers. "Comparing training-image based algorithms using an analysis of distance." Mathematical Geosciences 46.2 (2014): 149-169.

One algorithm to rule them all? An evaluation and discussion of ten eye movement event-detection algorithms.

PubMed

Andersson, Richard; Larsson, Linnea; Holmqvist, Kenneth; Stridh, Martin; Nyström, Marcus

2017-04-01

Almost all eye-movement researchers use algorithms to parse raw data and detect distinct types of eye movement events, such as fixations, saccades, and pursuit, and then base their results on these. Surprisingly, these algorithms are rarely evaluated. We evaluated the classifications of ten eye-movement event detection algorithms, on data from an SMI HiSpeed 1250 system, and compared them to manual ratings of two human experts. The evaluation focused on fixations, saccades, and post-saccadic oscillations. The evaluation used both event duration parameters, and sample-by-sample comparisons to rank the algorithms. The resulting event durations varied substantially as a function of what algorithm was used. This evaluation differed from previous evaluations by considering a relatively large set of algorithms, multiple events, and data from both static and dynamic stimuli. The main conclusion is that current detectors of only fixations and saccades work reasonably well for static stimuli, but barely better than chance for dynamic stimuli. Differing results across evaluation methods make it difficult to select one winner for fixation detection. For saccade detection, however, the algorithm by Larsson, Nyström and Stridh (IEEE Transaction on Biomedical Engineering, 60(9):2484-2493,2013) outperforms all algorithms in data from both static and dynamic stimuli. The data also show how improperly selected algorithms applied to dynamic data misestimate fixation and saccade properties.

Non-equilibrium Green's functions method: Non-trivial and disordered leads

NASA Astrophysics Data System (ADS)

He, Yu; Wang, Yu; Klimeck, Gerhard; Kubis, Tillmann

2014-11-01

The non-equilibrium Green's function algorithm requires contact self-energies to model charge injection and extraction. All existing approaches assume infinitely periodic leads attached to a possibly quite complex device. This contradicts today's realistic devices in which contacts are spatially inhomogeneous, chemically disordered, and impacting the overall device characteristics. This work extends the complex absorbing potentials method for arbitrary, ideal, or non-ideal leads in atomistic tight binding representation. The algorithm is demonstrated on a Si nanowire with periodic leads, a graphene nanoribbon with trumpet shape leads, and devices with leads of randomly alloyed Si0.5Ge0.5. It is found that alloy randomness in the leads can reduce the predicted ON-state current of Si0.5Ge0.5 transistors by 45% compared to conventional lead methods.

Orbit-orbit relativistic correction calculated with all-electron molecular explicitly correlated Gaussians.

PubMed

Stanke, Monika; Palikot, Ewa; Kȩdziera, Dariusz; Adamowicz, Ludwik

2016-12-14

An algorithm for calculating the first-order electronic orbit-orbit magnetic interaction correction for an electronic wave function expanded in terms of all-electron explicitly correlated molecular Gaussian (ECG) functions with shifted centers is derived and implemented. The algorithm is tested in calculations concerning the H 2 molecule. It is also applied in calculations for LiH and H 3 + molecular systems. The implementation completes our work on the leading relativistic correction for ECGs and paves the way for very accurate ECG calculations of ground and excited potential energy surfaces (PESs) of small molecules with two and more nuclei and two and more electrons, such as HeH - , H 3 + , HeH 2 + , and LiH 2 + . The PESs will be used to determine rovibrational spectra of the systems.

Inverse estimation of the spheroidal particle size distribution using Ant Colony Optimization algorithms in multispectral extinction technique

NASA Astrophysics Data System (ADS)

He, Zhenzong; Qi, Hong; Wang, Yuqing; Ruan, Liming

2014-10-01

Four improved Ant Colony Optimization (ACO) algorithms, i.e. the probability density function based ACO (PDF-ACO) algorithm, the Region ACO (RACO) algorithm, Stochastic ACO (SACO) algorithm and Homogeneous ACO (HACO) algorithm, are employed to estimate the particle size distribution (PSD) of the spheroidal particles. The direct problems are solved by the extended Anomalous Diffraction Approximation (ADA) and the Lambert-Beer law. Three commonly used monomodal distribution functions i.e. the Rosin-Rammer (R-R) distribution function, the normal (N-N) distribution function, and the logarithmic normal (L-N) distribution function are estimated under dependent model. The influence of random measurement errors on the inverse results is also investigated. All the results reveal that the PDF-ACO algorithm is more accurate than the other three ACO algorithms and can be used as an effective technique to investigate the PSD of the spheroidal particles. Furthermore, the Johnson's SB (J-SB) function and the modified beta (M-β) function are employed as the general distribution functions to retrieve the PSD of spheroidal particles using PDF-ACO algorithm. The investigation shows a reasonable agreement between the original distribution function and the general distribution function when only considering the variety of the length of the rotational semi-axis.

Think globally and solve locally: secondary memory-based network learning for automated multi-species function prediction

PubMed Central

2014-01-01

Background Network-based learning algorithms for automated function prediction (AFP) are negatively affected by the limited coverage of experimental data and limited a priori known functional annotations. As a consequence their application to model organisms is often restricted to well characterized biological processes and pathways, and their effectiveness with poorly annotated species is relatively limited. A possible solution to this problem might consist in the construction of big networks including multiple species, but this in turn poses challenging computational problems, due to the scalability limitations of existing algorithms and the main memory requirements induced by the construction of big networks. Distributed computation or the usage of big computers could in principle respond to these issues, but raises further algorithmic problems and require resources not satisfiable with simple off-the-shelf computers. Results We propose a novel framework for scalable network-based learning of multi-species protein functions based on both a local implementation of existing algorithms and the adoption of innovative technologies: we solve “locally” the AFP problem, by designing “vertex-centric” implementations of network-based algorithms, but we do not give up thinking “globally” by exploiting the overall topology of the network. This is made possible by the adoption of secondary memory-based technologies that allow the efficient use of the large memory available on disks, thus overcoming the main memory limitations of modern off-the-shelf computers. This approach has been applied to the analysis of a large multi-species network including more than 300 species of bacteria and to a network with more than 200,000 proteins belonging to 13 Eukaryotic species. To our knowledge this is the first work where secondary-memory based network analysis has been applied to multi-species function prediction using biological networks with hundreds of thousands of proteins. Conclusions The combination of these algorithmic and technological approaches makes feasible the analysis of large multi-species networks using ordinary computers with limited speed and primary memory, and in perspective could enable the analysis of huge networks (e.g. the whole proteomes available in SwissProt), using well-equipped stand-alone machines. PMID:24843788

Analytic reconstruction of magnetic resonance imaging signal obtained from a periodic encoding field.

PubMed

Rybicki, F J; Hrovat, M I; Patz, S

2000-09-01

We have proposed a two-dimensional PERiodic-Linear (PERL) magnetic encoding field geometry B(x,y) = g(y)y cos(q(x)x) and a magnetic resonance imaging pulse sequence which incorporates two fields to image a two-dimensional spin density: a standard linear gradient in the x dimension, and the PERL field. Because of its periodicity, the PERL field produces a signal where the phase of the two dimensions is functionally different. The x dimension is encoded linearly, but the y dimension appears as the argument of a sinusoidal phase term. Thus, the time-domain signal and image spin density are not related by a two-dimensional Fourier transform. They are related by a one-dimensional Fourier transform in the x dimension and a new Bessel function integral transform (the PERL transform) in the y dimension. The inverse of the PERL transform provides a reconstruction algorithm for the y dimension of the spin density from the signal space. To date, the inverse transform has been computed numerically by a Bessel function expansion over its basis functions. This numerical solution used a finite sum to approximate an infinite summation and thus introduced a truncation error. This work analytically determines the basis functions for the PERL transform and incorporates them into the reconstruction algorithm. The improved algorithm is demonstrated by (1) direct comparison between the numerically and analytically computed basis functions, and (2) reconstruction of a known spin density. The new solution for the basis functions also lends proof of the system function for the PERL transform under specific conditions.

Comparing the ISO-recommended and the cumulative data-reduction algorithms in S-on-1 laser damage test by a reverse approach method

NASA Astrophysics Data System (ADS)

Zorila, Alexandru; Stratan, Aurel; Nemes, George

2018-01-01

We compare the ISO-recommended (the standard) data-reduction algorithm used to determine the surface laser-induced damage threshold of optical materials by the S-on-1 test with two newly suggested algorithms, both named "cumulative" algorithms/methods, a regular one and a limit-case one, intended to perform in some respects better than the standard one. To avoid additional errors due to real experiments, a simulated test is performed, named the reverse approach. This approach simulates the real damage experiments, by generating artificial test-data of damaged and non-damaged sites, based on an assumed, known damage threshold fluence of the target and on a given probability distribution function to induce the damage. In this work, a database of 12 sets of test-data containing both damaged and non-damaged sites was generated by using four different reverse techniques and by assuming three specific damage probability distribution functions. The same value for the threshold fluence was assumed, and a Gaussian fluence distribution on each irradiated site was considered, as usual for the S-on-1 test. Each of the test-data was independently processed by the standard and by the two cumulative data-reduction algorithms, the resulting fitted probability distributions were compared with the initially assumed probability distribution functions, and the quantities used to compare these algorithms were determined. These quantities characterize the accuracy and the precision in determining the damage threshold and the goodness of fit of the damage probability curves. The results indicate that the accuracy in determining the absolute damage threshold is best for the ISO-recommended method, the precision is best for the limit-case of the cumulative method, and the goodness of fit estimator (adjusted R-squared) is almost the same for all three algorithms.

Correction of motion artifacts and serial correlations for real-time functional near-infrared spectroscopy

PubMed Central

Barker, Jeffrey W.; Rosso, Andrea L.; Sparto, Patrick J.; Huppert, Theodore J.

2016-01-01

Abstract. Functional near-infrared spectroscopy (fNIRS) is a relatively low-cost, portable, noninvasive neuroimaging technique for measuring task-evoked hemodynamic changes in the brain. Because fNIRS can be applied to a wide range of populations, such as children or infants, and under a variety of study conditions, including those involving physical movement, gait, or balance, fNIRS data are often confounded by motion artifacts. Furthermore, the high sampling rate of fNIRS leads to high temporal autocorrelation due to systemic physiology. These two factors can reduce the sensitivity and specificity of detecting hemodynamic changes. In a previous work, we showed that these factors could be mitigated by autoregressive-based prewhitening followed by the application of an iterative reweighted least squares algorithm offline. This current work extends these same ideas to real-time analysis of brain signals by modifying the linear Kalman filter, resulting in an algorithm for online estimation that is robust to systemic physiology and motion artifacts. We evaluated the performance of the proposed method via simulations of evoked hemodynamics that were added to experimental resting-state data, which provided realistic fNIRS noise. Last, we applied the method post hoc to data from a standing balance task. Overall, the new method showed good agreement with the analogous offline algorithm, in which both methods outperformed ordinary least squares methods. PMID:27226974

Fast Nonlinear Generalized Inversion of Gravity Data with Application to the Three-Dimensional Crustal Density Structure of Sichuan Basin, Southwest China

NASA Astrophysics Data System (ADS)

Wang, Jun; Meng, Xiaohong; Li, Fang

2017-11-01

Generalized inversion is one of the important steps in the quantitative interpretation of gravity data. With appropriate algorithm and parameters, it gives a view of the subsurface which characterizes different geological bodies. However, generalized inversion of gravity data is time consuming due to the large amount of data points and model cells adopted. Incorporating of various prior information as constraints deteriorates the above situation. In the work discussed in this paper, a method for fast nonlinear generalized inversion of gravity data is proposed. The fast multipole method is employed for forward modelling. The inversion objective function is established with weighted data misfit function along with model objective function. The total objective function is solved by a dataspace algorithm. Moreover, depth weighing factor is used to improve depth resolution of the result, and bound constraint is incorporated by a transfer function to limit the model parameters in a reliable range. The matrix inversion is accomplished by a preconditioned conjugate gradient method. With the above algorithm, equivalent density vectors can be obtained, and interpolation is performed to get the finally density model on the fine mesh in the model domain. Testing on synthetic gravity data demonstrated that the proposed method is faster than conventional generalized inversion algorithm to produce an acceptable solution for gravity inversion problem. The new developed inversion method was also applied for inversion of the gravity data collected over Sichuan basin, southwest China. The established density structure in this study helps understanding the crustal structure of Sichuan basin and provides reference for further oil and gas exploration in this area.

Log-Linear Model Based Behavior Selection Method for Artificial Fish Swarm Algorithm

PubMed Central

Huang, Zhehuang; Chen, Yidong

2015-01-01

Artificial fish swarm algorithm (AFSA) is a population based optimization technique inspired by social behavior of fishes. In past several years, AFSA has been successfully applied in many research and application areas. The behavior of fishes has a crucial impact on the performance of AFSA, such as global exploration ability and convergence speed. How to construct and select behaviors of fishes are an important task. To solve these problems, an improved artificial fish swarm algorithm based on log-linear model is proposed and implemented in this paper. There are three main works. Firstly, we proposed a new behavior selection algorithm based on log-linear model which can enhance decision making ability of behavior selection. Secondly, adaptive movement behavior based on adaptive weight is presented, which can dynamically adjust according to the diversity of fishes. Finally, some new behaviors are defined and introduced into artificial fish swarm algorithm at the first time to improve global optimization capability. The experiments on high dimensional function optimization showed that the improved algorithm has more powerful global exploration ability and reasonable convergence speed compared with the standard artificial fish swarm algorithm. PMID:25691895

Impact of MPEG-4 3D mesh coding on watermarking algorithms for polygonal 3D meshes

NASA Astrophysics Data System (ADS)

Funk, Wolfgang

2004-06-01

The MPEG-4 multimedia standard addresses the scene-based composition of audiovisual objects. Natural and synthetic multimedia content can be mixed and transmitted over narrow and broadband communication channels. Synthetic natural hybrid coding (SNHC) within MPEG-4 provides tools for 3D mesh coding (3DMC). We investigate the robustness of two different 3D watermarking algorithms for polygonal meshes with respect to 3DMC. The first algorithm is a blind detection scheme designed for labelling applications that require high bandwidth and low robustness. The second algorithm is a robust non-blind one-bit watermarking scheme intended for copyright protection applications. Both algorithms have been proposed by Benedens. We expect 3DMC to have an impact on the watermarked 3D meshes, as the algorithms used for our simulations work on vertex coordinates to encode the watermark. We use the 3DMC implementation provided with the MPEG-4 reference software and the Princeton Shape Benchmark model database for our simulations. The watermarked models are sent through the 3DMC encoder and decoder, and the watermark decoding process is performed. For each algorithm under consideration we examine the detection properties as a function of the quantization of the vertex coordinates.

Embracing equifinality with efficiency: Limits of Acceptability sampling using the DREAM(LOA) algorithm

NASA Astrophysics Data System (ADS)

Vrugt, Jasper A.; Beven, Keith J.

2018-04-01

This essay illustrates some recent developments to the DiffeRential Evolution Adaptive Metropolis (DREAM) MATLAB toolbox of Vrugt (2016) to delineate and sample the behavioural solution space of set-theoretic likelihood functions used within the GLUE (Limits of Acceptability) framework (Beven and Binley, 1992, 2014; Beven and Freer, 2001; Beven, 2006). This work builds on the DREAM(ABC) algorithm of Sadegh and Vrugt (2014) and enhances significantly the accuracy and CPU-efficiency of Bayesian inference with GLUE. In particular it is shown how lack of adequate sampling in the model space might lead to unjustified model rejection.

Solid Rocket Fuel Constitutive Theory and Polymer Cure

NASA Technical Reports Server (NTRS)

Ream, Robert

2006-01-01

Solid Rocket Fuel is a complex composite material for which no general constitutive theory, based on first principles, has been developed. One of the principles such a relation would depend on is the morphology of the binder. A theory of polymer curing is required to determine this morphology. During work on such a theory an algorithm was developed for counting the number of ways a polymer chain could assemble. The methods used to develop and check this algorithm led to an analytic solution to the problem. This solution is used in a probability distribution function which characterizes the morphology of the polymer.

Extended capture range for focus-diverse phase retrieval in segmented aperture systems using geometrical optics.

PubMed

Jurling, Alden S; Fienup, James R

2014-03-01

Extending previous work by Thurman on wavefront sensing for segmented-aperture systems, we developed an algorithm for estimating segment tips and tilts from multiple point spread functions in different defocused planes. We also developed methods for overcoming two common modes for stagnation in nonlinear optimization-based phase retrieval algorithms for segmented systems. We showed that when used together, these methods largely solve the capture range problem in focus-diverse phase retrieval for segmented systems with large tips and tilts. Monte Carlo simulations produced a rate of success better than 98% for the combined approach.

Naturally Inspired Firefly Controller For Stabilization Of Double Inverted Pendulum

NASA Astrophysics Data System (ADS)

Srikanth, Kavirayani; Nagesh, Gundavarapu

2015-12-01

A double inverted pendulum plant as an established model that is analyzed as part of this work was tested under the influence of time delay, where the controller was fine tuned using a firefly algorithm taking into considering the fitness function of variation of the cart position and to minimize the cart position displacement and still stabilize it effectively. The naturally inspired algorithm which imitates the fireflies definitely is an energy efficient method owing to the inherent logic of the way the fireflies respond collectively and has shown that critical time delays makes the system healthy.

Efficient algorithm for multiconfiguration pair-density functional theory with application to the heterolytic dissociation energy of ferrocene

NASA Astrophysics Data System (ADS)

Sand, Andrew M.; Truhlar, Donald G.; Gagliardi, Laura

2017-01-01

The recently developed multiconfiguration pair-density functional theory (MC-PDFT) combines multiconfiguration wave function theory with a density functional that depends on the on-top pair density of an electronic system. In an MC-PDFT calculation, there are two steps: a conventional multiconfiguration self-consistent-field (MCSCF) calculation and a post-MCSCF evaluation of the energy with an on-top density functional. In this work, we present the details of the MC-PDFT algorithm that avoids steeply scaling steps that are present in other post-self-consistent-field multireference calculations of dynamic correlation energy. We demonstrate the favorable scaling by considering systems of H2 molecules with active spaces of several different sizes. We then apply the MC-PDFT method to calculate the heterolytic dissociation enthalpy of ferrocene. We find that MC-PDFT yields results that are at least as accurate as complete active space second-order perturbation theory and are more stable with respect to basis set, but at a fraction of the cost in both time and memory.

Efficient algorithm for multiconfiguration pair-density functional theory with application to the heterolytic dissociation energy of ferrocene.

PubMed

Sand, Andrew M; Truhlar, Donald G; Gagliardi, Laura

2017-01-21

The recently developed multiconfiguration pair-density functional theory (MC-PDFT) combines multiconfiguration wave function theory with a density functional that depends on the on-top pair density of an electronic system. In an MC-PDFT calculation, there are two steps: a conventional multiconfiguration self-consistent-field (MCSCF) calculation and a post-MCSCF evaluation of the energy with an on-top density functional. In this work, we present the details of the MC-PDFT algorithm that avoids steeply scaling steps that are present in other post-self-consistent-field multireference calculations of dynamic correlation energy. We demonstrate the favorable scaling by considering systems of H 2 molecules with active spaces of several different sizes. We then apply the MC-PDFT method to calculate the heterolytic dissociation enthalpy of ferrocene. We find that MC-PDFT yields results that are at least as accurate as complete active space second-order perturbation theory and are more stable with respect to basis set, but at a fraction of the cost in both time and memory.

Wind farm topology-finding algorithm considering performance, costs, and environmental impacts.

PubMed

Tazi, Nacef; Chatelet, Eric; Bouzidi, Youcef; Meziane, Rachid

2017-06-05

Optimal power in wind farms turns to be a modern problem for investors and decision makers; onshore wind farms are subject to performance and economic and environmental constraints. The aim of this work is to define the best installed capacity (best topology) with maximum performance and profits and consider environmental impacts as well. In this article, we continue the work recently done on wind farm topology-finding algorithm. The proposed resolution technique is based on finding the best topology of the system that maximizes the wind farm performance (availability) under the constraints of costs and capital investments. Global warming potential of wind farm is calculated and taken into account in the results. A case study is done using data and constraints similar to those collected from wind farm constructors, managers, and maintainers. Multi-state systems (MSS), universal generating function (UGF), wind, and load charge functions are applied. An economic study was conducted to assess the wind farm investment. Net present value (NPV) and levelized cost of energy (LCOE) were calculated for best topologies found.

Exact posterior computation in non-conjugate Gaussian location-scale parameters models

NASA Astrophysics Data System (ADS)

Andrade, J. A. A.; Rathie, P. N.

2017-12-01

In Bayesian analysis the class of conjugate models allows to obtain exact posterior distributions, however this class quite restrictive in the sense that it involves only a few distributions. In fact, most of the practical applications involves non-conjugate models, thus approximate methods, such as the MCMC algorithms, are required. Although these methods can deal with quite complex structures, some practical problems can make their applications quite time demanding, for example, when we use heavy-tailed distributions, convergence may be difficult, also the Metropolis-Hastings algorithm can become very slow, in addition to the extra work inevitably required on choosing efficient candidate generator distributions. In this work, we draw attention to the special functions as a tools for Bayesian computation, we propose an alternative method for obtaining the posterior distribution in Gaussian non-conjugate models in an exact form. We use complex integration methods based on the H-function in order to obtain the posterior distribution and some of its posterior quantities in an explicit computable form. Two examples are provided in order to illustrate the theory.

Locating structures and evolution pathways of reconstructed rutile TiO2(011) using genetic algorithm aided density functional theory calculations.

PubMed

Ding, Pan; Gong, Xue-Qing

2016-05-01

Titanium dioxide (TiO2) is an important metal oxide that has been used in many different applications. TiO2 has also been widely employed as a model system to study basic processes and reactions in surface chemistry and heterogeneous catalysis. In this work, we investigated the (011) surface of rutile TiO2 by focusing on its reconstruction. Density functional theory calculations aided by a genetic algorithm based optimization scheme were performed to extensively sample the potential energy surfaces of reconstructed rutile TiO2 structures that obey (2 × 1) periodicity. A lot of stable surface configurations were located, including the global-minimum configuration that was proposed previously. The wide variety of surface structures determined through the calculations performed in this work provide insight into the relationship between the atomic configuration of a surface and its stability. More importantly, several analytical schemes were proposed and tested to gauge the differences and similarities among various surface structures, aiding the construction of the complete pathway for the reconstruction process.

Linear-scaling time-dependent density-functional theory beyond the Tamm-Dancoff approximation: Obtaining efficiency and accuracy with in situ optimised local orbitals

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zuehlsdorff, T. J., E-mail: tjz21@cam.ac.uk; Payne, M. C.; Hine, N. D. M.

2015-11-28

We present a solution of the full time-dependent density-functional theory (TDDFT) eigenvalue equation in the linear response formalism exhibiting a linear-scaling computational complexity with system size, without relying on the simplifying Tamm-Dancoff approximation (TDA). The implementation relies on representing the occupied and unoccupied subspaces with two different sets of in situ optimised localised functions, yielding a very compact and efficient representation of the transition density matrix of the excitation with the accuracy associated with a systematic basis set. The TDDFT eigenvalue equation is solved using a preconditioned conjugate gradient algorithm that is very memory-efficient. The algorithm is validated on amore » small test molecule and a good agreement with results obtained from standard quantum chemistry packages is found, with the preconditioner yielding a significant improvement in convergence rates. The method developed in this work is then used to reproduce experimental results of the absorption spectrum of bacteriochlorophyll in an organic solvent, where it is demonstrated that the TDA fails to reproduce the main features of the low energy spectrum, while the full TDDFT equation yields results in good qualitative agreement with experimental data. Furthermore, the need for explicitly including parts of the solvent into the TDDFT calculations is highlighted, making the treatment of large system sizes necessary that are well within reach of the capabilities of the algorithm introduced here. Finally, the linear-scaling properties of the algorithm are demonstrated by computing the lowest excitation energy of bacteriochlorophyll in solution. The largest systems considered in this work are of the same order of magnitude as a variety of widely studied pigment-protein complexes, opening up the possibility of studying their properties without having to resort to any semiclassical approximations to parts of the protein environment.« less

Using Alternative Multiplication Algorithms to "Offload" Cognition

ERIC Educational Resources Information Center

Jazby, Dan; Pearn, Cath

2015-01-01

When viewed through a lens of embedded cognition, algorithms may enable aspects of the cognitive work of multi-digit multiplication to be "offloaded" to the environmental structure created by an algorithm. This study analyses four multiplication algorithms by viewing different algorithms as enabling cognitive work to be distributed…

Extreme-Scale Algorithms & Software Resilience (EASIR) Architecture-Aware Algorithms for Scalable Performance and Resilience on Heterogeneous Architectures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Demmel, James W.

This project addresses both communication-avoiding algorithms, and reproducible floating-point computation. Communication, i.e. moving data, either between levels of memory or processors over a network, is much more expensive per operation than arithmetic (measured in time or energy), so we seek algorithms that greatly reduce communication. We developed many new algorithms for both dense and sparse, and both direct and iterative linear algebra, attaining new communication lower bounds, and getting large speedups in many cases. We also extended this work in several ways: (1) We minimize writes separately from reads, since writes may be much more expensive than reads on emergingmore » memory technologies, like Flash, sometimes doing asymptotically fewer writes than reads. (2) We extend the lower bounds and optimal algorithms to arbitrary algorithms that may be expressed as perfectly nested loops accessing arrays, where the array subscripts may be arbitrary affine functions of the loop indices (eg A(i), B(i,j+k, k+3*m-7, …) etc.). (3) We extend our communication-avoiding approach to some machine learning algorithms, such as support vector machines. This work has won a number of awards. We also address reproducible floating-point computation. We define reproducibility to mean getting bitwise identical results from multiple runs of the same program, perhaps with different hardware resources or other changes that should ideally not change the answer. Many users depend on reproducibility for debugging or correctness. However, dynamic scheduling of parallel computing resources, combined with nonassociativity of floating point addition, makes attaining reproducibility a challenge even for simple operations like summing a vector of numbers, or more complicated operations like the Basic Linear Algebra Subprograms (BLAS). We describe an algorithm that computes a reproducible sum of floating point numbers, independent of the order of summation. The algorithm depends only on a subset of the IEEE Floating Point Standard 754-2008, uses just 6 words to represent a “reproducible accumulator,” and requires just one read-only pass over the data, or one reduction in parallel. New instructions based on this work are being considered for inclusion in the future IEEE 754-2018 floating-point standard, and new reproducible BLAS are being considered for the next version of the BLAS standard.« less

Optimization of multi-objective integrated process planning and scheduling problem using a priority based optimization algorithm

NASA Astrophysics Data System (ADS)

Ausaf, Muhammad Farhan; Gao, Liang; Li, Xinyu

2015-12-01

For increasing the overall performance of modern manufacturing systems, effective integration of process planning and scheduling functions has been an important area of consideration among researchers. Owing to the complexity of handling process planning and scheduling simultaneously, most of the research work has been limited to solving the integrated process planning and scheduling (IPPS) problem for a single objective function. As there are many conflicting objectives when dealing with process planning and scheduling, real world problems cannot be fully captured considering only a single objective for optimization. Therefore considering multi-objective IPPS (MOIPPS) problem is inevitable. Unfortunately, only a handful of research papers are available on solving MOIPPS problem. In this paper, an optimization algorithm for solving MOIPPS problem is presented. The proposed algorithm uses a set of dispatching rules coupled with priority assignment to optimize the IPPS problem for various objectives like makespan, total machine load, total tardiness, etc. A fixed sized external archive coupled with a crowding distance mechanism is used to store and maintain the non-dominated solutions. To compare the results with other algorithms, a C-matric based method has been used. Instances from four recent papers have been solved to demonstrate the effectiveness of the proposed algorithm. The experimental results show that the proposed method is an efficient approach for solving the MOIPPS problem.

Reliable clarity automatic-evaluation method for optical remote sensing images

NASA Astrophysics Data System (ADS)

Qin, Bangyong; Shang, Ren; Li, Shengyang; Hei, Baoqin; Liu, Zhiwen

2015-10-01

Image clarity, which reflects the sharpness degree at the edge of objects in images, is an important quality evaluate index for optical remote sensing images. Scholars at home and abroad have done a lot of work on estimation of image clarity. At present, common clarity-estimation methods for digital images mainly include frequency-domain function methods, statistical parametric methods, gradient function methods and edge acutance methods. Frequency-domain function method is an accurate clarity-measure approach. However, its calculation process is complicate and cannot be carried out automatically. Statistical parametric methods and gradient function methods are both sensitive to clarity of images, while their results are easy to be affected by the complex degree of images. Edge acutance method is an effective approach for clarity estimate, while it needs picking out the edges manually. Due to the limits in accuracy, consistent or automation, these existing methods are not applicable to quality evaluation of optical remote sensing images. In this article, a new clarity-evaluation method, which is based on the principle of edge acutance algorithm, is proposed. In the new method, edge detection algorithm and gradient search algorithm are adopted to automatically search the object edges in images. Moreover, The calculation algorithm for edge sharpness has been improved. The new method has been tested with several groups of optical remote sensing images. Compared with the existing automatic evaluation methods, the new method perform better both in accuracy and consistency. Thus, the new method is an effective clarity evaluation method for optical remote sensing images.

Modeling and analysis of solar distributed generation

NASA Astrophysics Data System (ADS)

Ortiz Rivera, Eduardo Ivan

Recent changes in the global economy are creating a big impact in our daily life. The price of oil is increasing and the number of reserves are less every day. Also, dramatic demographic changes are impacting the viability of the electric infrastructure and ultimately the economic future of the industry. These are some of the reasons that many countries are looking for alternative energy to produce electric energy. The most common form of green energy in our daily life is solar energy. To convert solar energy into electrical energy is required solar panels, dc-dc converters, power control, sensors, and inverters. In this work, a photovoltaic module, PVM, model using the electrical characteristics provided by the manufacturer data sheet is presented for power system applications. Experimental results from testing are showed, verifying the proposed PVM model. Also in this work, three maximum power point tracker, MPPT, algorithms would be presented to obtain the maximum power from a PVM. The first MPPT algorithm is a method based on the Rolle's and Lagrange's Theorems and can provide at least an approximate answer to a family of transcendental functions that cannot be solved using differential calculus. The second MPPT algorithm is based on the approximation of the proposed PVM model using fractional polynomials where the shape, boundary conditions and performance of the proposed PVM model are satisfied. The third MPPT algorithm is based in the determination of the optimal duty cycle for a dc-dc converter and the previous knowledge of the load or load matching conditions. Also, four algorithms to calculate the effective irradiance level and temperature over a photovoltaic module are presented in this work. The main reasons to develop these algorithms are for monitoring climate conditions, the elimination of temperature and solar irradiance sensors, reductions in cost for a photovoltaic inverter system, and development of new algorithms to be integrated with maximum power point tracking algorithms. Finally, several PV power applications will be presented like circuit analysis for a load connected to two different PV arrays, speed control for a do motor connected to a PVM, and a novel single phase photovoltaic inverter system using the Z-source converter.

Short-range density functional correlation within the restricted active space CI method

NASA Astrophysics Data System (ADS)

Casanova, David

2018-03-01

In the present work, I introduce a hybrid wave function-density functional theory electronic structure method based on the range separation of the electron-electron Coulomb operator in order to recover dynamic electron correlations missed in the restricted active space configuration interaction (RASCI) methodology. The working equations and the computational algorithm for the implementation of the new approach, i.e., RAS-srDFT, are presented, and the method is tested in the calculation of excitation energies of organic molecules. The good performance of the RASCI wave function in combination with different short-range exchange-correlation functionals in the computation of relative energies represents a quantitative improvement with respect to the RASCI results and paves the path for the development of RAS-srDFT as a promising scheme in the computation of the ground and excited states where nondynamic and dynamic electron correlations are important.

On strong homogeneity of a class of global optimization algorithms working with infinite and infinitesimal scales

NASA Astrophysics Data System (ADS)

Sergeyev, Yaroslav D.; Kvasov, Dmitri E.; Mukhametzhanov, Marat S.

2018-06-01

The necessity to find the global optimum of multiextremal functions arises in many applied problems where finding local solutions is insufficient. One of the desirable properties of global optimization methods is strong homogeneity meaning that a method produces the same sequences of points where the objective function is evaluated independently both of multiplication of the function by a scaling constant and of adding a shifting constant. In this paper, several aspects of global optimization using strongly homogeneous methods are considered. First, it is shown that even if a method possesses this property theoretically, numerically very small and large scaling constants can lead to ill-conditioning of the scaled problem. Second, a new class of global optimization problems where the objective function can have not only finite but also infinite or infinitesimal Lipschitz constants is introduced. Third, the strong homogeneity of several Lipschitz global optimization algorithms is studied in the framework of the Infinity Computing paradigm allowing one to work numerically with a variety of infinities and infinitesimals. Fourth, it is proved that a class of efficient univariate methods enjoys this property for finite, infinite and infinitesimal scaling and shifting constants. Finally, it is shown that in certain cases the usage of numerical infinities and infinitesimals can avoid ill-conditioning produced by scaling. Numerical experiments illustrating theoretical results are described.

chemf: A purely functional chemistry toolkit.

PubMed

Höck, Stefan; Riedl, Rainer

2012-12-20

Although programming in a type-safe and referentially transparent style offers several advantages over working with mutable data structures and side effects, this style of programming has not seen much use in chemistry-related software. Since functional programming languages were designed with referential transparency in mind, these languages offer a lot of support when writing immutable data structures and side-effects free code. We therefore started implementing our own toolkit based on the above programming paradigms in a modern, versatile programming language. We present our initial results with functional programming in chemistry by first describing an immutable data structure for molecular graphs together with a couple of simple algorithms to calculate basic molecular properties before writing a complete SMILES parser in accordance with the OpenSMILES specification. Along the way we show how to deal with input validation, error handling, bulk operations, and parallelization in a purely functional way. At the end we also analyze and improve our algorithms and data structures in terms of performance and compare it to existing toolkits both object-oriented and purely functional. All code was written in Scala, a modern multi-paradigm programming language with a strong support for functional programming and a highly sophisticated type system. We have successfully made the first important steps towards a purely functional chemistry toolkit. The data structures and algorithms presented in this article perform well while at the same time they can be safely used in parallelized applications, such as computer aided drug design experiments, without further adjustments. This stands in contrast to existing object-oriented toolkits where thread safety of data structures and algorithms is a deliberate design decision that can be hard to implement. Finally, the level of type-safety achieved by Scala highly increased the reliability of our code as well as the productivity of the programmers involved in this project.

chemf: A purely functional chemistry toolkit

PubMed Central

2012-01-01

Background Although programming in a type-safe and referentially transparent style offers several advantages over working with mutable data structures and side effects, this style of programming has not seen much use in chemistry-related software. Since functional programming languages were designed with referential transparency in mind, these languages offer a lot of support when writing immutable data structures and side-effects free code. We therefore started implementing our own toolkit based on the above programming paradigms in a modern, versatile programming language. Results We present our initial results with functional programming in chemistry by first describing an immutable data structure for molecular graphs together with a couple of simple algorithms to calculate basic molecular properties before writing a complete SMILES parser in accordance with the OpenSMILES specification. Along the way we show how to deal with input validation, error handling, bulk operations, and parallelization in a purely functional way. At the end we also analyze and improve our algorithms and data structures in terms of performance and compare it to existing toolkits both object-oriented and purely functional. All code was written in Scala, a modern multi-paradigm programming language with a strong support for functional programming and a highly sophisticated type system. Conclusions We have successfully made the first important steps towards a purely functional chemistry toolkit. The data structures and algorithms presented in this article perform well while at the same time they can be safely used in parallelized applications, such as computer aided drug design experiments, without further adjustments. This stands in contrast to existing object-oriented toolkits where thread safety of data structures and algorithms is a deliberate design decision that can be hard to implement. Finally, the level of type-safety achieved by Scala highly increased the reliability of our code as well as the productivity of the programmers involved in this project. PMID:23253942

Advisory Algorithm for Scheduling Open Sectors, Operating Positions, and Workstations

NASA Technical Reports Server (NTRS)

Bloem, Michael; Drew, Michael; Lai, Chok Fung; Bilimoria, Karl D.

2012-01-01

Air traffic controller supervisors configure available sector, operating position, and work-station resources to safely and efficiently control air traffic in a region of airspace. In this paper, an algorithm for assisting supervisors with this task is described and demonstrated on two sample problem instances. The algorithm produces configuration schedule advisories that minimize a cost. The cost is a weighted sum of two competing costs: one penalizing mismatches between configurations and predicted air traffic demand and another penalizing the effort associated with changing configurations. The problem considered by the algorithm is a shortest path problem that is solved with a dynamic programming value iteration algorithm. The cost function contains numerous parameters. Default values for most of these are suggested based on descriptions of air traffic control procedures and subject-matter expert feedback. The parameter determining the relative importance of the two competing costs is tuned by comparing historical configurations with corresponding algorithm advisories. Two sample problem instances for which appropriate configuration advisories are obvious were designed to illustrate characteristics of the algorithm. Results demonstrate how the algorithm suggests advisories that appropriately utilize changes in airspace configurations and changes in the number of operating positions allocated to each open sector. The results also demonstrate how the advisories suggest appropriate times for configuration changes.

Sign changes in sums of the Liouville function

NASA Astrophysics Data System (ADS)

Borwein, Peter; Ferguson, Ron; Mossinghoff, Michael J.

2008-09-01

The Liouville function λ(n) is the completely multiplicative function whose value is -1 at each prime. We develop some algorithms for computing the sum T(n)Dsum_{kD1}^n λ(k)/k , and use these methods to determine the smallest positive integer n where T(n)<0 . This answers a question originating in some work of Turan, who linked the behavior of T(n) to questions about the Riemann zeta function. We also study the problem of evaluating Polya's sum L(n)Dsum_{kD1}^nλ(k) , and we determine some new local extrema for this function, including some new positive values.

A new convergence analysis and perturbation resilience of some accelerated proximal forward-backward algorithms with errors

NASA Astrophysics Data System (ADS)

Reem, Daniel; De Pierro, Alvaro

2017-04-01

Many problems in science and engineering involve, as part of their solution process, the consideration of a separable function which is the sum of two convex functions, one of them possibly non-smooth. Recently a few works have discussed inexact versions of several accelerated proximal methods aiming at solving this minimization problem. This paper shows that inexact versions of a method of Beck and Teboulle (fast iterative shrinkable tresholding algorithm) preserve, in a Hilbert space setting, the same (non-asymptotic) rate of convergence under some assumptions on the decay rate of the error terms The notion of inexactness discussed here seems to be rather simple, but, interestingly, when comparing to related works, closely related decay rates of the errors terms yield closely related convergence rates. The derivation sheds some light on the somewhat mysterious origin of some parameters which appear in various accelerated methods. A consequence of the analysis is that the accelerated method is perturbation resilient, making it suitable, in principle, for the superiorization methodology. By taking this into account, we re-examine the superiorization methodology and significantly extend its scope. This work was supported by FAPESP 2013/19504-9. The second author was supported also by CNPq grant 306030/2014-4.

A Practical Computational Method for the Anisotropic Redshift-Space 3-Point Correlation Function

NASA Astrophysics Data System (ADS)

Slepian, Zachary; Eisenstein, Daniel J.

2018-04-01

We present an algorithm enabling computation of the anisotropic redshift-space galaxy 3-point correlation function (3PCF) scaling as N2, with N the number of galaxies. Our previous work showed how to compute the isotropic 3PCF with this scaling by expanding the radially-binned density field around each galaxy in the survey into spherical harmonics and combining these coefficients to form multipole moments. The N2 scaling occurred because this approach never explicitly required the relative angle between a galaxy pair about the primary galaxy. Here we generalize this work, demonstrating that in the presence of azimuthally-symmetric anisotropy produced by redshift-space distortions (RSD) the 3PCF can be described by two triangle side lengths, two independent total angular momenta, and a spin. This basis for the anisotropic 3PCF allows its computation with negligible additional work over the isotropic 3PCF. We also present the covariance matrix of the anisotropic 3PCF measured in this basis. Our algorithm tracks the full 5-D redshift-space 3PCF, uses an accurate line of sight to each triplet, is exact in angle, and easily handles edge correction. It will enable use of the anisotropic large-scale 3PCF as a probe of RSD in current and upcoming large-scale redshift surveys.

Discrete Sparse Coding.

PubMed

Exarchakis, Georgios; Lücke, Jörg

2017-11-01

Sparse coding algorithms with continuous latent variables have been the subject of a large number of studies. However, discrete latent spaces for sparse coding have been largely ignored. In this work, we study sparse coding with latents described by discrete instead of continuous prior distributions. We consider the general case in which the latents (while being sparse) can take on any value of a finite set of possible values and in which we learn the prior probability of any value from data. This approach can be applied to any data generated by discrete causes, and it can be applied as an approximation of continuous causes. As the prior probabilities are learned, the approach then allows for estimating the prior shape without assuming specific functional forms. To efficiently train the parameters of our probabilistic generative model, we apply a truncated expectation-maximization approach (expectation truncation) that we modify to work with a general discrete prior. We evaluate the performance of the algorithm by applying it to a variety of tasks: (1) we use artificial data to verify that the algorithm can recover the generating parameters from a random initialization, (2) use image patches of natural images and discuss the role of the prior for the extraction of image components, (3) use extracellular recordings of neurons to present a novel method of analysis for spiking neurons that includes an intuitive discretization strategy, and (4) apply the algorithm on the task of encoding audio waveforms of human speech. The diverse set of numerical experiments presented in this letter suggests that discrete sparse coding algorithms can scale efficiently to work with realistic data sets and provide novel statistical quantities to describe the structure of the data.

Plugin-docking system for autonomous charging using particle filter

NASA Astrophysics Data System (ADS)

Koyasu, Hiroshi; Wada, Masayoshi

2017-03-01

Autonomous charging of the robot battery is one of the key functions for the sake of expanding working areas of the robots. To realize it, most of existing systems use custom docking stations or artificial markers. By the other words, they can only charge on a few specific outlets. If the limit can be removed, working areas of the robots significantly expands. In this paper, we describe a plugin-docking system for the autonomous charging, which does not require any custom docking stations or artificial markers. A single camera is used for recognizing the 3D position of an outlet socket. A particle filter-based image tracking algorithm which is robust to the illumination change is applied. The algorithm is implemented on a robot with an omnidirectional moving system. The experimental results show the effectiveness of our system.

A Darwinian approach to control-structure design

NASA Technical Reports Server (NTRS)

Zimmerman, David C.

1993-01-01

Genetic algorithms (GA's), as introduced by Holland (1975), are one form of directed random search. The form of direction is based on Darwin's 'survival of the fittest' theories. GA's are radically different from the more traditional design optimization techniques. GA's work with a coding of the design variables, as opposed to working with the design variables directly. The search is conducted from a population of designs (i.e., from a large number of points in the design space), unlike the traditional algorithms which search from a single design point. The GA requires only objective function information, as opposed to gradient or other auxiliary information. Finally, the GA is based on probabilistic transition rules, as opposed to deterministic rules. These features allow the GA to attack problems with local-global minima, discontinuous design spaces and mixed variable problems, all in a single, consistent framework.

DD3MAT - a code for yield criteria anisotropy parameters identification.

NASA Astrophysics Data System (ADS)

Barros, P. D.; Carvalho, P. D.; Alves, J. L.; Oliveira, M. C.; Menezes, L. F.

2016-08-01

This work presents the main strategies and algorithms adopted in the DD3MAT inhouse code, specifically developed for identifying the anisotropy parameters. The algorithm adopted is based on the minimization of an error function, using a downhill simplex method. The set of experimental values can consider yield stresses and r -values obtained from in-plane tension, for different angles with the rolling direction (RD), yield stress and r -value obtained for biaxial stress state, and yield stresses from shear tests performed also for different angles to RD. All these values can be defined for a specific value of plastic work. Moreover, it can also include the yield stresses obtained from in-plane compression tests. The anisotropy parameters are identified for an AA2090-T3 aluminium alloy, highlighting the importance of the user intervention to improve the numerical fit.

Comparison of Classical and Lazy Approach in SCG Compiler

NASA Astrophysics Data System (ADS)

Jirák, Ota; Kolář, Dušan

2011-09-01

The existing parsing methods of scattered context grammar usually expand nonterminals deeply in the pushdown. This expansion is implemented by using either a linked list, or some kind of an auxiliary pushdown. This paper describes the parsing algorithm of an LL(1) scattered context grammar. The given algorithm merges two principles together. The first approach is a table-driven parsing method commonly used for parsing of the context-free grammars. The second is a delayed execution used in functional programming. The main part of this paper is a proof of equivalence between the common principle (the whole rule is applied at once) and our approach (execution of the rules is delayed). Therefore, this approach works with the pushdown top only. In the most cases, the second approach is faster than the first one. Finally, the future work is discussed.

Comparative assessment of techniques for initial pose estimation using monocular vision

NASA Astrophysics Data System (ADS)

Sharma, Sumant; D`Amico, Simone

2016-06-01

This work addresses the comparative assessment of initial pose estimation techniques for monocular navigation to enable formation-flying and on-orbit servicing missions. Monocular navigation relies on finding an initial pose, i.e., a coarse estimate of the attitude and position of the space resident object with respect to the camera, based on a minimum number of features from a three dimensional computer model and a single two dimensional image. The initial pose is estimated without the use of fiducial markers, without any range measurements or any apriori relative motion information. Prior work has been done to compare different pose estimators for terrestrial applications, but there is a lack of functional and performance characterization of such algorithms in the context of missions involving rendezvous operations in the space environment. Use of state-of-the-art pose estimation algorithms designed for terrestrial applications is challenging in space due to factors such as limited on-board processing power, low carrier to noise ratio, and high image contrasts. This paper focuses on performance characterization of three initial pose estimation algorithms in the context of such missions and suggests improvements.

A new stellar spectrum interpolation algorithm and its application to Yunnan-III evolutionary population synthesis models

NASA Astrophysics Data System (ADS)

Cheng, Liantao; Zhang, Fenghui; Kang, Xiaoyu; Wang, Lang

2018-05-01

In evolutionary population synthesis (EPS) models, we need to convert stellar evolutionary parameters into spectra via interpolation in a stellar spectral library. For theoretical stellar spectral libraries, the spectrum grid is homogeneous on the effective-temperature and gravity plane for a given metallicity. It is relatively easy to derive stellar spectra. For empirical stellar spectral libraries, stellar parameters are irregularly distributed and the interpolation algorithm is relatively complicated. In those EPS models that use empirical stellar spectral libraries, different algorithms are used and the codes are often not released. Moreover, these algorithms are often complicated. In this work, based on a radial basis function (RBF) network, we present a new spectrum interpolation algorithm and its code. Compared with the other interpolation algorithms that are used in EPS models, it can be easily understood and is highly efficient in terms of computation. The code is written in MATLAB scripts and can be used on any computer system. Using it, we can obtain the interpolated spectra from a library or a combination of libraries. We apply this algorithm to several stellar spectral libraries (such as MILES, ELODIE-3.1 and STELIB-3.2) and give the integrated spectral energy distributions (ISEDs) of stellar populations (with ages from 1 Myr to 14 Gyr) by combining them with Yunnan-III isochrones. Our results show that the differences caused by the adoption of different EPS model components are less than 0.2 dex. All data about the stellar population ISEDs in this work and the RBF spectrum interpolation code can be obtained by request from the first author or downloaded from http://www1.ynao.ac.cn/˜zhangfh.

Comparison study of reconstruction algorithms for prototype digital breast tomosynthesis using various breast phantoms.

PubMed

Kim, Ye-seul; Park, Hye-suk; Lee, Haeng-Hwa; Choi, Young-Wook; Choi, Jae-Gu; Kim, Hak Hee; Kim, Hee-Joung

2016-02-01

Digital breast tomosynthesis (DBT) is a recently developed system for three-dimensional imaging that offers the potential to reduce the false positives of mammography by preventing tissue overlap. Many qualitative evaluations of digital breast tomosynthesis were previously performed by using a phantom with an unrealistic model and with heterogeneous background and noise, which is not representative of real breasts. The purpose of the present work was to compare reconstruction algorithms for DBT by using various breast phantoms; validation was also performed by using patient images. DBT was performed by using a prototype unit that was optimized for very low exposures and rapid readout. Three algorithms were compared: a back-projection (BP) algorithm, a filtered BP (FBP) algorithm, and an iterative expectation maximization (EM) algorithm. To compare the algorithms, three types of breast phantoms (homogeneous background phantom, heterogeneous background phantom, and anthropomorphic breast phantom) were evaluated, and clinical images were also reconstructed by using the different reconstruction algorithms. The in-plane image quality was evaluated based on the line profile and the contrast-to-noise ratio (CNR), and out-of-plane artifacts were evaluated by means of the artifact spread function (ASF). Parenchymal texture features of contrast and homogeneity were computed based on reconstructed images of an anthropomorphic breast phantom. The clinical images were studied to validate the effect of reconstruction algorithms. The results showed that the CNRs of masses reconstructed by using the EM algorithm were slightly higher than those obtained by using the BP algorithm, whereas the FBP algorithm yielded much lower CNR due to its high fluctuations of background noise. The FBP algorithm provides the best conspicuity for larger calcifications by enhancing their contrast and sharpness more than the other algorithms; however, in the case of small-size and low-contrast microcalcifications, the FBP reduced detectability due to its increased noise. The EM algorithm yielded high conspicuity for both microcalcifications and masses and yielded better ASFs in terms of the full width at half maximum. The higher contrast and lower homogeneity in terms of texture analysis were shown in FBP algorithm than in other algorithms. The patient images using the EM algorithm resulted in high visibility of low-contrast mass with clear border. In this study, we compared three reconstruction algorithms by using various kinds of breast phantoms and patient cases. Future work using these algorithms and considering the type of the breast and the acquisition techniques used (e.g., angular range, dose distribution) should include the use of actual patients or patient-like phantoms to increase the potential for practical applications.

Porting ONETEP to graphical processing unit-based coprocessors. 1. FFT box operations.

PubMed

Wilkinson, Karl; Skylaris, Chris-Kriton

2013-10-30

We present the first graphical processing unit (GPU) coprocessor-enabled version of the Order-N Electronic Total Energy Package (ONETEP) code for linear-scaling first principles quantum mechanical calculations on materials. This work focuses on porting to the GPU the parts of the code that involve atom-localized fast Fourier transform (FFT) operations. These are among the most computationally intensive parts of the code and are used in core algorithms such as the calculation of the charge density, the local potential integrals, the kinetic energy integrals, and the nonorthogonal generalized Wannier function gradient. We have found that direct porting of the isolated FFT operations did not provide any benefit. Instead, it was necessary to tailor the port to each of the aforementioned algorithms to optimize data transfer to and from the GPU. A detailed discussion of the methods used and tests of the resulting performance are presented, which show that individual steps in the relevant algorithms are accelerated by a significant amount. However, the transfer of data between the GPU and host machine is a significant bottleneck in the reported version of the code. In addition, an initial investigation into a dynamic precision scheme for the ONETEP energy calculation has been performed to take advantage of the enhanced single precision capabilities of GPUs. The methods used here result in no disruption to the existing code base. Furthermore, as the developments reported here concern the core algorithms, they will benefit the full range of ONETEP functionality. Our use of a directive-based programming model ensures portability to other forms of coprocessors and will allow this work to form the basis of future developments to the code designed to support emerging high-performance computing platforms. Copyright © 2013 Wiley Periodicals, Inc.

LBP-based penalized weighted least-squares approach to low-dose cone-beam computed tomography reconstruction

NASA Astrophysics Data System (ADS)

Ma, Ming; Wang, Huafeng; Liu, Yan; Zhang, Hao; Gu, Xianfeng; Liang, Zhengrong

2014-03-01

Cone-beam computed tomography (CBCT) has attracted growing interest of researchers in image reconstruction. The mAs level of the X-ray tube current, in practical application of CBCT, is mitigated in order to reduce the CBCT dose. The lowering of the X-ray tube current, however, results in the degradation of image quality. Thus, low-dose CBCT image reconstruction is in effect a noise problem. To acquire clinically acceptable quality of image, and keep the X-ray tube current as low as achievable in the meanwhile, some penalized weighted least-squares (PWLS)-based image reconstruction algorithms have been developed. One representative strategy in previous work is to model the prior information for solution regularization using an anisotropic penalty term. To enhance the edge preserving and noise suppressing in a finer scale, a novel algorithm combining the local binary pattern (LBP) with penalized weighted leastsquares (PWLS), called LBP-PWLS-based image reconstruction algorithm, is proposed in this work. The proposed LBP-PWLS-based algorithm adaptively encourages strong diffusion on the local spot/flat region around a voxel and less diffusion on edge/corner ones by adjusting the penalty for cost function, after the LBP is utilized to detect the region around the voxel as spot, flat and edge ones. The LBP-PWLS-based reconstruction algorithm was evaluated using the sinogram data acquired by a clinical CT scanner from the CatPhan® 600 phantom. Experimental results on the noiseresolution tradeoff measurement and other quantitative measurements demonstrated its feasibility and effectiveness in edge preserving and noise suppressing in comparison with a previous PWLS reconstruction algorithm.

The challenge of understanding the brain: where we stand in 2015

PubMed Central

Lisman, John

2015-01-01

Starting with the work of Cajal more than 100 years ago, neuroscience has sought to understand how the cells of the brain give rise to cognitive functions. How far has neuroscience progressed in this endeavor? This Perspective assesses progress in elucidating five basic brain processes: visual recognition, long-term memory, short-term memory, action selection, and motor control. Each of these processes entails several levels of analysis: the behavioral properties, the underlying computational algorithm, and the cellular/network mechanisms that implement that algorithm. At this juncture, while many questions remain unanswered, achievements in several areas of research have made it possible to relate specific properties of brain networks to cognitive functions. What has been learned reveals, at least in rough outline, how cognitive processes can be an emergent property of neurons and their connections. PMID:25996132

Improving the convergence rate in affine registration of PET and SPECT brain images using histogram equalization.

PubMed

Salas-Gonzalez, D; Górriz, J M; Ramírez, J; Padilla, P; Illán, I A

2013-01-01

A procedure to improve the convergence rate for affine registration methods of medical brain images when the images differ greatly from the template is presented. The methodology is based on a histogram matching of the source images with respect to the reference brain template before proceeding with the affine registration. The preprocessed source brain images are spatially normalized to a template using a general affine model with 12 parameters. A sum of squared differences between the source images and the template is considered as objective function, and a Gauss-Newton optimization algorithm is used to find the minimum of the cost function. Using histogram equalization as a preprocessing step improves the convergence rate in the affine registration algorithm of brain images as we show in this work using SPECT and PET brain images.

Teaching and Learning Activity Sequencing System using Distributed Genetic Algorithms

NASA Astrophysics Data System (ADS)

Matsui, Tatsunori; Ishikawa, Tomotake; Okamoto, Toshio

The purpose of this study is development of a supporting system for teacher's design of lesson plan. Especially design of lesson plan which relates to the new subject "Information Study" is supported. In this study, we developed a system which generates teaching and learning activity sequences by interlinking lesson's activities corresponding to the various conditions according to the user's input. Because user's input is multiple information, there will be caused contradiction which the system should solve. This multiobjective optimization problem is resolved by Distributed Genetic Algorithms, in which some fitness functions are defined with reference models on lesson, thinking and teaching style. From results of various experiments, effectivity and validity of the proposed methods and reference models were verified; on the other hand, some future works on reference models and evaluation functions were also pointed out.

Non-equilibrium Green's functions method: Non-trivial and disordered leads

DOE Office of Scientific and Technical Information (OSTI.GOV)

He, Yu, E-mail: heyuyhe@gmail.com; Wang, Yu; Klimeck, Gerhard

2014-11-24

The non-equilibrium Green's function algorithm requires contact self-energies to model charge injection and extraction. All existing approaches assume infinitely periodic leads attached to a possibly quite complex device. This contradicts today's realistic devices in which contacts are spatially inhomogeneous, chemically disordered, and impacting the overall device characteristics. This work extends the complex absorbing potentials method for arbitrary, ideal, or non-ideal leads in atomistic tight binding representation. The algorithm is demonstrated on a Si nanowire with periodic leads, a graphene nanoribbon with trumpet shape leads, and devices with leads of randomly alloyed Si{sub 0.5}Ge{sub 0.5}. It is found that alloy randomnessmore » in the leads can reduce the predicted ON-state current of Si{sub 0.5}Ge{sub 0.5} transistors by 45% compared to conventional lead methods.« less

Optical properties reconstruction using the adjoint method based on the radiative transfer equation

NASA Astrophysics Data System (ADS)

Addoum, Ahmad; Farges, Olivier; Asllanaj, Fatmir

2018-01-01

An efficient algorithm is proposed to reconstruct the spatial distribution of optical properties in heterogeneous media like biological tissues. The light transport through such media is accurately described by the radiative transfer equation in the frequency-domain. The adjoint method is used to efficiently compute the objective function gradient with respect to optical parameters. Numerical tests show that the algorithm is accurate and robust to retrieve simultaneously the absorption μa and scattering μs coefficients for lowly and highly absorbing medium. Moreover, the simultaneous reconstruction of μs and the anisotropy factor g of the Henyey-Greenstein phase function is achieved with a reasonable accuracy. The main novelty in this work is the reconstruction of g which might open the possibility to image this parameter in tissues as an additional contrast agent in optical tomography.

Comparison of genetic algorithms with conjugate gradient methods

NASA Technical Reports Server (NTRS)

Bosworth, J. L.; Foo, N. Y.; Zeigler, B. P.

1972-01-01

Genetic algorithms for mathematical function optimization are modeled on search strategies employed in natural adaptation. Comparisons of genetic algorithms with conjugate gradient methods, which were made on an IBM 1800 digital computer, show that genetic algorithms display superior performance over gradient methods for functions which are poorly behaved mathematically, for multimodal functions, and for functions obscured by additive random noise. Genetic methods offer performance comparable to gradient methods for many of the standard functions.

Classification of Normal and Apoptotic Cells from Fluorescence Microscopy Images Using Generalized Polynomial Chaos and Level Set Function.

PubMed

Du, Yuncheng; Budman, Hector M; Duever, Thomas A

2016-06-01

Accurate automated quantitative analysis of living cells based on fluorescence microscopy images can be very useful for fast evaluation of experimental outcomes and cell culture protocols. In this work, an algorithm is developed for fast differentiation of normal and apoptotic viable Chinese hamster ovary (CHO) cells. For effective segmentation of cell images, a stochastic segmentation algorithm is developed by combining a generalized polynomial chaos expansion with a level set function-based segmentation algorithm. This approach provides a probabilistic description of the segmented cellular regions along the boundary, from which it is possible to calculate morphological changes related to apoptosis, i.e., the curvature and length of a cell's boundary. These features are then used as inputs to a support vector machine (SVM) classifier that is trained to distinguish between normal and apoptotic viable states of CHO cell images. The use of morphological features obtained from the stochastic level set segmentation of cell images in combination with the trained SVM classifier is more efficient in terms of differentiation accuracy as compared with the original deterministic level set method.

Implementation of the Hungarian Algorithm to Account for Ligand Symmetry and Similarity in Structure-Based Design

PubMed Central

2015-01-01

False negative docking outcomes for highly symmetric molecules are a barrier to the accurate evaluation of docking programs, scoring functions, and protocols. This work describes an implementation of a symmetry-corrected root-mean-square deviation (RMSD) method into the program DOCK based on the Hungarian algorithm for solving the minimum assignment problem, which dynamically assigns atom correspondence in molecules with symmetry. The algorithm adds only a trivial amount of computation time to the RMSD calculations and is shown to increase the reported overall docking success rate by approximately 5% when tested over 1043 receptor–ligand systems. For some families of protein systems the results are even more dramatic, with success rate increases up to 16.7%. Several additional applications of the method are also presented including as a pairwise similarity metric to compare molecules during de novo design, as a scoring function to rank-order virtual screening results, and for the analysis of trajectories from molecular dynamics simulation. The new method, including source code, is available to registered users of DOCK6 (http://dock.compbio.ucsf.edu). PMID:24410429

Fusion of multiple quadratic penalty function support vector machines (QPFSVM) for automated sea mine detection and classification

NASA Astrophysics Data System (ADS)

Dobeck, Gerald J.; Cobb, J. Tory

2002-08-01

The high-resolution sonar is one of the principal sensors used by the Navy to detect and classify sea mines in minehunting operations. For such sonar systems, substantial effort has been devoted to the development of automated detection and classification (D/C) algorithms. These have been spurred by several factors including (1) aids for operators to reduce work overload, (2) more optimal use of all available data, and (3) the introduction of unmanned minehunting systems. The environments where sea mines are typically laid (harbor areas, shipping lanes, and the littorals) give rise to many false alarms caused by natural, biologic, and man-made clutter. The objective of the automated D/C algorithms is to eliminate most of these false alarms while still maintaining a very high probability of mine detection and classification (PdPc). In recent years, the benefits of fusing the outputs of multiple D/C algorithms have been studied. We refer to this as Algorithm Fusion. The results have been remarkable, including reliable robustness to new environments. The Quadratic Penalty Function Support Vector Machine (QPFSVM) algorithm to aid in the automated detection and classification of sea mines is introduced in this paper. The QPFSVM algorithm is easy to train, simple to implement, and robust to feature space dimension. Outputs of successive SVM algorithms are cascaded in stages (fused) to improve the Probability of Classification (Pc) and reduce the number of false alarms. Even though our experience has been gained in the area of sea mine detection and classification, the principles described herein are general and can be applied to fusion of any D/C problem (e.g., automated medical diagnosis or automatic target recognition for ballistic missile defense).

A heuristic neural network initialization scheme for modeling nonlinear functions in engineering mechanics: continuous development

NASA Astrophysics Data System (ADS)

Pei, Jin-Song; Mai, Eric C.

2007-04-01

This paper introduces a continuous effort towards the development of a heuristic initialization methodology for constructing multilayer feedforward neural networks to model nonlinear functions. In this and previous studies that this work is built upon, including the one presented at SPIE 2006, the authors do not presume to provide a universal method to approximate arbitrary functions, rather the focus is given to the development of a rational and unambiguous initialization procedure that applies to the approximation of nonlinear functions in the specific domain of engineering mechanics. The applications of this exploratory work can be numerous including those associated with potential correlation and interpretation of the inner workings of neural networks, such as damage detection. The goal of this study is fulfilled by utilizing the governing physics and mathematics of nonlinear functions and the strength of the sigmoidal basis function. A step-by-step graphical procedure utilizing a few neural network prototypes as "templates" to approximate commonly seen memoryless nonlinear functions of one or two variables is further developed in this study. Decomposition of complex nonlinear functions into a summation of some simpler nonlinear functions is utilized to exploit this prototype-based initialization methodology. Training examples are presented to demonstrate the rationality and effciency of the proposed methodology when compared with the popular Nguyen-Widrow initialization algorithm. Future work is also identfied.

Autonomous Guidance Strategy for Spacecraft Formations and Reconfiguration Maneuvers

NASA Astrophysics Data System (ADS)

Wahl, Theodore P.

A guidance strategy for autonomous spacecraft formation reconfiguration maneuvers is presented. The guidance strategy is presented as an algorithm that solves the linked assignment and delivery problems. The assignment problem is the task of assigning the member spacecraft of the formation to their new positions in the desired formation geometry. The guidance algorithm uses an auction process (also called an "auction algorithm''), presented in the dissertation, to solve the assignment problem. The auction uses the estimated maneuver and time of flight costs between the spacecraft and targets to create assignments which minimize a specific "expense'' function for the formation. The delivery problem is the task of delivering the spacecraft to their assigned positions, and it is addressed through one of two guidance schemes described in this work. The first is a delivery scheme based on artificial potential function (APF) guidance. APF guidance uses the relative distances between the spacecraft, targets, and any obstacles to design maneuvers based on gradients of potential fields. The second delivery scheme is based on model predictive control (MPC); this method uses a model of the system dynamics to plan a series of maneuvers designed to minimize a unique cost function. The guidance algorithm uses an analytic linearized approximation of the relative orbital dynamics, the Yamanaka-Ankersen state transition matrix, in the auction process and in both delivery methods. The proposed guidance strategy is successful, in simulations, in autonomously assigning the members of the formation to new positions and in delivering the spacecraft to these new positions safely using both delivery methods. This guidance algorithm can serve as the basis for future autonomous guidance strategies for spacecraft formation missions.

Nuclear IHC enumeration: A digital phantom to evaluate the performance of automated algorithms in digital pathology.

PubMed

Niazi, Muhammad Khalid Khan; Abas, Fazly Salleh; Senaras, Caglar; Pennell, Michael; Sahiner, Berkman; Chen, Weijie; Opfer, John; Hasserjian, Robert; Louissaint, Abner; Shana'ah, Arwa; Lozanski, Gerard; Gurcan, Metin N

2018-01-01

Automatic and accurate detection of positive and negative nuclei from images of immunostained tissue biopsies is critical to the success of digital pathology. The evaluation of most nuclei detection algorithms relies on manually generated ground truth prepared by pathologists, which is unfortunately time-consuming and suffers from inter-pathologist variability. In this work, we developed a digital immunohistochemistry (IHC) phantom that can be used for evaluating computer algorithms for enumeration of IHC positive cells. Our phantom development consists of two main steps, 1) extraction of the individual as well as nuclei clumps of both positive and negative nuclei from real WSI images, and 2) systematic placement of the extracted nuclei clumps on an image canvas. The resulting images are visually similar to the original tissue images. We created a set of 42 images with different concentrations of positive and negative nuclei. These images were evaluated by four board certified pathologists in the task of estimating the ratio of positive to total number of nuclei. The resulting concordance correlation coefficients (CCC) between the pathologist and the true ratio range from 0.86 to 0.95 (point estimates). The same ratio was also computed by an automated computer algorithm, which yielded a CCC value of 0.99. Reading the phantom data with known ground truth, the human readers show substantial variability and lower average performance than the computer algorithm in terms of CCC. This shows the limitation of using a human reader panel to establish a reference standard for the evaluation of computer algorithms, thereby highlighting the usefulness of the phantom developed in this work. Using our phantom images, we further developed a function that can approximate the true ratio from the area of the positive and negative nuclei, hence avoiding the need to detect individual nuclei. The predicted ratios of 10 held-out images using the function (trained on 32 images) are within ±2.68% of the true ratio. Moreover, we also report the evaluation of a computerized image analysis method on the synthetic tissue dataset.

Automatic treatment plan re-optimization for adaptive radiotherapy guided with the initial plan DVHs

NASA Astrophysics Data System (ADS)

Li, Nan; Zarepisheh, Masoud; Uribe-Sanchez, Andres; Moore, Kevin; Tian, Zhen; Zhen, Xin; Jiang Graves, Yan; Gautier, Quentin; Mell, Loren; Zhou, Linghong; Jia, Xun; Jiang, Steve

2013-12-01

Adaptive radiation therapy (ART) can reduce normal tissue toxicity and/or improve tumor control through treatment adaptations based on the current patient anatomy. Developing an efficient and effective re-planning algorithm is an important step toward the clinical realization of ART. For the re-planning process, manual trial-and-error approach to fine-tune planning parameters is time-consuming and is usually considered unpractical, especially for online ART. It is desirable to automate this step to yield a plan of acceptable quality with minimal interventions. In ART, prior information in the original plan is available, such as dose-volume histogram (DVH), which can be employed to facilitate the automatic re-planning process. The goal of this work is to develop an automatic re-planning algorithm to generate a plan with similar, or possibly better, DVH curves compared with the clinically delivered original plan. Specifically, our algorithm iterates the following two loops. An inner loop is the traditional fluence map optimization, in which we optimize a quadratic objective function penalizing the deviation of the dose received by each voxel from its prescribed or threshold dose with a set of fixed voxel weighting factors. In outer loop, the voxel weighting factors in the objective function are adjusted according to the deviation of the current DVH curves from those in the original plan. The process is repeated until the DVH curves are acceptable or maximum iteration step is reached. The whole algorithm is implemented on GPU for high efficiency. The feasibility of our algorithm has been demonstrated with three head-and-neck cancer IMRT cases, each having an initial planning CT scan and another treatment CT scan acquired in the middle of treatment course. Compared with the DVH curves in the original plan, the DVH curves in the resulting plan using our algorithm with 30 iterations are better for almost all structures. The re-optimization process takes about 30 s using our in-house optimization engine. This work was originally presented at the 54th AAPM annual meeting in Charlotte, NC, July 29-August 2, 2012.

Nonnegative matrix factorization with the Itakura-Saito divergence: with application to music analysis.

PubMed

Févotte, Cédric; Bertin, Nancy; Durrieu, Jean-Louis

2009-03-01

This letter presents theoretical, algorithmic, and experimental results about nonnegative matrix factorization (NMF) with the Itakura-Saito (IS) divergence. We describe how IS-NMF is underlaid by a well-defined statistical model of superimposed gaussian components and is equivalent to maximum likelihood estimation of variance parameters. This setting can accommodate regularization constraints on the factors through Bayesian priors. In particular, inverse-gamma and gamma Markov chain priors are considered in this work. Estimation can be carried out using a space-alternating generalized expectation-maximization (SAGE) algorithm; this leads to a novel type of NMF algorithm, whose convergence to a stationary point of the IS cost function is guaranteed. We also discuss the links between the IS divergence and other cost functions used in NMF, in particular, the Euclidean distance and the generalized Kullback-Leibler (KL) divergence. As such, we describe how IS-NMF can also be performed using a gradient multiplicative algorithm (a standard algorithm structure in NMF) whose convergence is observed in practice, though not proven. Finally, we report a furnished experimental comparative study of Euclidean-NMF, KL-NMF, and IS-NMF algorithms applied to the power spectrogram of a short piano sequence recorded in real conditions, with various initializations and model orders. Then we show how IS-NMF can successfully be employed for denoising and upmix (mono to stereo conversion) of an original piece of early jazz music. These experiments indicate that IS-NMF correctly captures the semantics of audio and is better suited to the representation of music signals than NMF with the usual Euclidean and KL costs.

Prediction of interface residue based on the features of residue interaction network.

PubMed

Jiao, Xiong; Ranganathan, Shoba

2017-11-07

Protein-protein interaction plays a crucial role in the cellular biological processes. Interface prediction can improve our understanding of the molecular mechanisms of the related processes and functions. In this work, we propose a classification method to recognize the interface residue based on the features of a weighted residue interaction network. The random forest algorithm is used for the prediction and 16 network parameters and the B-factor are acting as the element of the input feature vector. Compared with other similar work, the method is feasible and effective. The relative importance of these features also be analyzed to identify the key feature for the prediction. Some biological meaning of the important feature is explained. The results of this work can be used for the related work about the structure-function relationship analysis via a residue interaction network model. Copyright © 2017 Elsevier Ltd. All rights reserved.

Mutually beneficial relationship in optimization between search-space smoothing and stochastic search

NASA Astrophysics Data System (ADS)

Hasegawa, Manabu; Hiramatsu, Kotaro

2013-10-01

The effectiveness of the Metropolis algorithm (MA) (constant-temperature simulated annealing) in optimization by the method of search-space smoothing (SSS) (potential smoothing) is studied on two types of random traveling salesman problems. The optimization mechanism of this hybrid approach (MASSS) is investigated by analyzing the exploration dynamics observed in the rugged landscape of the cost function (energy surface). The results show that the MA can be successfully utilized as a local search algorithm in the SSS approach. It is also clarified that the optimization characteristics of these two constituent methods are improved in a mutually beneficial manner in the MASSS run. Specifically, the relaxation dynamics generated by employing the MA work effectively even in a smoothed landscape and more advantage is taken of the guiding function proposed in the idea of SSS; this mechanism operates in an adaptive manner in the de-smoothing process and therefore the MASSS method maintains its optimization function over a wider temperature range than the MA.

Double-Group Particle Swarm Optimization and Its Application in Remote Sensing Image Segmentation

PubMed Central

Shen, Liang; Huang, Xiaotao; Fan, Chongyi

2018-01-01

Particle Swarm Optimization (PSO) is a well-known meta-heuristic. It has been widely used in both research and engineering fields. However, the original PSO generally suffers from premature convergence, especially in multimodal problems. In this paper, we propose a double-group PSO (DG-PSO) algorithm to improve the performance. DG-PSO uses a double-group based evolution framework. The individuals are divided into two groups: an advantaged group and a disadvantaged group. The advantaged group works according to the original PSO, while two new strategies are developed for the disadvantaged group. The proposed algorithm is firstly evaluated by comparing it with the other five popular PSO variants and two state-of-the-art meta-heuristics on various benchmark functions. The results demonstrate that DG-PSO shows a remarkable performance in terms of accuracy and stability. Then, we apply DG-PSO to multilevel thresholding for remote sensing image segmentation. The results show that the proposed algorithm outperforms five other popular algorithms in meta-heuristic-based multilevel thresholding, which verifies the effectiveness of the proposed algorithm. PMID:29724013

Double-Group Particle Swarm Optimization and Its Application in Remote Sensing Image Segmentation.

PubMed

Shen, Liang; Huang, Xiaotao; Fan, Chongyi

2018-05-01

Particle Swarm Optimization (PSO) is a well-known meta-heuristic. It has been widely used in both research and engineering fields. However, the original PSO generally suffers from premature convergence, especially in multimodal problems. In this paper, we propose a double-group PSO (DG-PSO) algorithm to improve the performance. DG-PSO uses a double-group based evolution framework. The individuals are divided into two groups: an advantaged group and a disadvantaged group. The advantaged group works according to the original PSO, while two new strategies are developed for the disadvantaged group. The proposed algorithm is firstly evaluated by comparing it with the other five popular PSO variants and two state-of-the-art meta-heuristics on various benchmark functions. The results demonstrate that DG-PSO shows a remarkable performance in terms of accuracy and stability. Then, we apply DG-PSO to multilevel thresholding for remote sensing image segmentation. The results show that the proposed algorithm outperforms five other popular algorithms in meta-heuristic-based multilevel thresholding, which verifies the effectiveness of the proposed algorithm.

Infrared small target detection technology based on OpenCV

NASA Astrophysics Data System (ADS)

Liu, Lei; Huang, Zhijian

2013-05-01

Accurate and fast detection of infrared (IR) dim target has very important meaning for infrared precise guidance, early warning, video surveillance, etc. In this paper, some basic principles and the implementing flow charts of a series of algorithms for target detection are described. These algorithms are traditional two-frame difference method, improved three-frame difference method, background estimate and frame difference fusion method, and building background with neighborhood mean method. On the foundation of above works, an infrared target detection software platform which is developed by OpenCV and MFC is introduced. Three kinds of tracking algorithms are integrated in this software. In order to explain the software clearly, the framework and the function are described in this paper. At last, the experiments are performed for some real-life IR images. The whole algorithm implementing processes and results are analyzed, and those algorithms for detection targets are evaluated from the two aspects of subjective and objective. The results prove that the proposed method has satisfying detection effectiveness and robustness. Meanwhile, it has high detection efficiency and can be used for real-time detection.

Infrared small target detection technology based on OpenCV

NASA Astrophysics Data System (ADS)

Liu, Lei; Huang, Zhijian

2013-09-01

Accurate and fast detection of infrared (IR) dim target has very important meaning for infrared precise guidance, early warning, video surveillance, etc. In this paper, some basic principles and the implementing flow charts of a series of algorithms for target detection are described. These algorithms are traditional two-frame difference method, improved three-frame difference method, background estimate and frame difference fusion method, and building background with neighborhood mean method. On the foundation of above works, an infrared target detection software platform which is developed by OpenCV and MFC is introduced. Three kinds of tracking algorithms are integrated in this software. In order to explain the software clearly, the framework and the function are described in this paper. At last, the experiments are performed for some real-life IR images. The whole algorithm implementing processes and results are analyzed, and those algorithms for detection targets are evaluated from the two aspects of subjective and objective. The results prove that the proposed method has satisfying detection effectiveness and robustness. Meanwhile, it has high detection efficiency and can be used for real-time detection.

Plate/shell structure topology optimization of orthotropic material for buckling problem based on independent continuous topological variables

NASA Astrophysics Data System (ADS)

Ye, Hong-Ling; Wang, Wei-Wei; Chen, Ning; Sui, Yun-Kang

2017-10-01

The purpose of the present work is to study the buckling problem with plate/shell topology optimization of orthotropic material. A model of buckling topology optimization is established based on the independent, continuous, and mapping method, which considers structural mass as objective and buckling critical loads as constraints. Firstly, composite exponential function (CEF) and power function (PF) as filter functions are introduced to recognize the element mass, the element stiffness matrix, and the element geometric stiffness matrix. The filter functions of the orthotropic material stiffness are deduced. Then these filter functions are put into buckling topology optimization of a differential equation to analyze the design sensitivity. Furthermore, the buckling constraints are approximately expressed as explicit functions with respect to the design variables based on the first-order Taylor expansion. The objective function is standardized based on the second-order Taylor expansion. Therefore, the optimization model is translated into a quadratic program. Finally, the dual sequence quadratic programming (DSQP) algorithm and the global convergence method of moving asymptotes algorithm with two different filter functions (CEF and PF) are applied to solve the optimal model. Three numerical results show that DSQP&CEF has the best performance in the view of structural mass and discretion.

Inferring consistent functional interaction patterns from natural stimulus FMRI data

PubMed Central

Sun, Jiehuan; Hu, Xintao; Huang, Xiu; Liu, Yang; Li, Kaiming; Li, Xiang; Han, Junwei; Guo, Lei

2014-01-01

There has been increasing interest in how the human brain responds to natural stimulus such as video watching in the neuroimaging field. Along this direction, this paper presents our effort in inferring consistent and reproducible functional interaction patterns under natural stimulus of video watching among known functional brain regions identified by task-based fMRI. Then, we applied and compared four statistical approaches, including Bayesian network modeling with searching algorithms: greedy equivalence search (GES), Peter and Clark (PC) analysis, independent multiple greedy equivalence search (IMaGES), and the commonly used Granger causality analysis (GCA), to infer consistent and reproducible functional interaction patterns among these brain regions. It is interesting that a number of reliable and consistent functional interaction patterns were identified by the GES, PC and IMaGES algorithms in different participating subjects when they watched multiple video shots of the same semantic category. These interaction patterns are meaningful given current neuroscience knowledge and are reasonably reproducible across different brains and video shots. In particular, these consistent functional interaction patterns are supported by structural connections derived from diffusion tensor imaging (DTI) data, suggesting the structural underpinnings of consistent functional interactions. Our work demonstrates that specific consistent patterns of functional interactions among relevant brain regions might reflect the brain's fundamental mechanisms of online processing and comprehension of video messages. PMID:22440644

A Comparison of Hybrid Approaches for Turbofan Engine Gas Path Fault Diagnosis

NASA Astrophysics Data System (ADS)

Lu, Feng; Wang, Yafan; Huang, Jinquan; Wang, Qihang

2016-09-01

A hybrid diagnostic method utilizing Extended Kalman Filter (EKF) and Adaptive Genetic Algorithm (AGA) is presented for performance degradation estimation and sensor anomaly detection of turbofan engine. The EKF is used to estimate engine component performance degradation for gas path fault diagnosis. The AGA is introduced in the integrated architecture and applied for sensor bias detection. The contributions of this work are the comparisons of Kalman Filters (KF)-AGA algorithms and Neural Networks (NN)-AGA algorithms with a unified framework for gas path fault diagnosis. The NN needs to be trained off-line with a large number of prior fault mode data. When new fault mode occurs, estimation accuracy by the NN evidently decreases. However, the application of the Linearized Kalman Filter (LKF) and EKF will not be restricted in such case. The crossover factor and the mutation factor are adapted to the fitness function at each generation in the AGA, and it consumes less time to search for the optimal sensor bias value compared to the Genetic Algorithm (GA). In a word, we conclude that the hybrid EKF-AGA algorithm is the best choice for gas path fault diagnosis of turbofan engine among the algorithms discussed.

Fault-Tolerant Algorithms for Connectivity Restoration in Wireless Sensor Networks.

PubMed

Zeng, Yali; Xu, Li; Chen, Zhide

2015-12-22

As wireless sensor network (WSN) is often deployed in a hostile environment, nodes in the networks are prone to large-scale failures, resulting in the network not working normally. In this case, an effective restoration scheme is needed to restore the faulty network timely. Most of existing restoration schemes consider more about the number of deployed nodes or fault tolerance alone, but fail to take into account the fact that network coverage and topology quality are also important to a network. To address this issue, we present two algorithms named Full 2-Connectivity Restoration Algorithm (F2CRA) and Partial 3-Connectivity Restoration Algorithm (P3CRA), which restore a faulty WSN in different aspects. F2CRA constructs the fan-shaped topology structure to reduce the number of deployed nodes, while P3CRA constructs the dual-ring topology structure to improve the fault tolerance of the network. F2CRA is suitable when the restoration cost is given the priority, and P3CRA is suitable when the network quality is considered first. Compared with other algorithms, these two algorithms ensure that the network has stronger fault-tolerant function, larger coverage area and better balanced load after the restoration.

Enabling the extended compact genetic algorithm for real-parameter optimization by using adaptive discretization.

PubMed

Chen, Ying-ping; Chen, Chao-Hong

2010-01-01

An adaptive discretization method, called split-on-demand (SoD), enables estimation of distribution algorithms (EDAs) for discrete variables to solve continuous optimization problems. SoD randomly splits a continuous interval if the number of search points within the interval exceeds a threshold, which is decreased at every iteration. After the split operation, the nonempty intervals are assigned integer codes, and the search points are discretized accordingly. As an example of using SoD with EDAs, the integration of SoD and the extended compact genetic algorithm (ECGA) is presented and numerically examined. In this integration, we adopt a local search mechanism as an optional component of our back end optimization engine. As a result, the proposed framework can be considered as a memetic algorithm, and SoD can potentially be applied to other memetic algorithms. The numerical experiments consist of two parts: (1) a set of benchmark functions on which ECGA with SoD and ECGA with two well-known discretization methods: the fixed-height histogram (FHH) and the fixed-width histogram (FWH) are compared; (2) a real-world application, the economic dispatch problem, on which ECGA with SoD is compared to other methods. The experimental results indicate that SoD is a better discretization method to work with ECGA. Moreover, ECGA with SoD works quite well on the economic dispatch problem and delivers solutions better than the best known results obtained by other methods in existence.

SU-E-I-01: Iterative CBCT Reconstruction with a Feature-Preserving Penalty

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lyu, Q; Li, B; Southern Medical University, Guangzhou

2015-06-15

Purpose: Low-dose CBCT is desired in various clinical applications. Iterative image reconstruction algorithms have shown advantages in suppressing noise in low-dose CBCT. However, due to the smoothness constraint enforced during the reconstruction process, edges may be blurred and image features may lose in the reconstructed image. In this work, we proposed a new penalty design to preserve image features in the image reconstructed by iterative algorithms. Methods: Low-dose CBCT is reconstructed by minimizing the penalized weighted least-squares (PWLS) objective function. Binary Robust Independent Elementary Features (BRIEF) of the image were integrated into the penalty of PWLS. BRIEF is a generalmore » purpose point descriptor that can be used to identify important features of an image. In this work, BRIEF distance of two neighboring pixels was used to weigh the smoothing parameter in PWLS. For pixels of large BRIEF distance, weaker smooth constraint will be enforced. Image features will be better preserved through such a design. The performance of the PWLS algorithm with BRIEF penalty was evaluated by a CatPhan 600 phantom. Results: The image quality reconstructed by the proposed PWLS-BRIEF algorithm is superior to that by the conventional PWLS method and the standard FDK method. At matched noise level, edges in PWLS-BRIEF reconstructed image are better preserved. Conclusion: This study demonstrated that the proposed PWLS-BRIEF algorithm has great potential on preserving image features in low-dose CBCT.« less

Projection decomposition algorithm for dual-energy computed tomography via deep neural network.

PubMed

Xu, Yifu; Yan, Bin; Chen, Jian; Zeng, Lei; Li, Lei

2018-03-15

Dual-energy computed tomography (DECT) has been widely used to improve identification of substances from different spectral information. Decomposition of the mixed test samples into two materials relies on a well-calibrated material decomposition function. This work aims to establish and validate a data-driven algorithm for estimation of the decomposition function. A deep neural network (DNN) consisting of two sub-nets is proposed to solve the projection decomposition problem. The compressing sub-net, substantially a stack auto-encoder (SAE), learns a compact representation of energy spectrum. The decomposing sub-net with a two-layer structure fits the nonlinear transform between energy projection and basic material thickness. The proposed DNN not only delivers image with lower standard deviation and higher quality in both simulated and real data, and also yields the best performance in cases mixed with photon noise. Moreover, DNN costs only 0.4 s to generate a decomposition solution of 360 × 512 size scale, which is about 200 times faster than the competing algorithms. The DNN model is applicable to the decomposition tasks with different dual energies. Experimental results demonstrated the strong function fitting ability of DNN. Thus, the Deep learning paradigm provides a promising approach to solve the nonlinear problem in DECT.

Classical and adaptive control of ex vivo skeletal muscle contractions using Functional Electrical Stimulation (FES)

PubMed Central

Shoemaker, Adam; Grange, Robert W.; Abaid, Nicole; Leonessa, Alexander

2017-01-01

Functional Electrical Stimulation is a promising approach to treat patients by stimulating the peripheral nerves and their corresponding motor neurons using electrical current. This technique helps maintain muscle mass and promote blood flow in the absence of a functioning nervous system. The goal of this work is to control muscle contractions from FES via three different algorithms and assess the most appropriate controller providing effective stimulation of the muscle. An open-loop system and a closed-loop system with three types of model-free feedback controllers were assessed for tracking control of skeletal muscle contractions: a Proportional-Integral (PI) controller, a Model Reference Adaptive Control algorithm, and an Adaptive Augmented PI system. Furthermore, a mathematical model of a muscle-mass-spring system was implemented in simulation to test the open-loop case and closed-loop controllers. These simulations were carried out and then validated through experiments ex vivo. The experiments included muscle contractions following four distinct trajectories: a step, sine, ramp, and square wave. Overall, the closed-loop controllers followed the stimulation trajectories set for all the simulated and tested muscles. When comparing the experimental outcomes of each controller, we concluded that the Adaptive Augmented PI algorithm provided the best closed-loop performance for speed of convergence and disturbance rejection. PMID:28273101

Global optimization framework for solar building design

NASA Astrophysics Data System (ADS)

Silva, N.; Alves, N.; Pascoal-Faria, P.

2017-07-01

The generative modeling paradigm is a shift from static models to flexible models. It describes a modeling process using functions, methods and operators. The result is an algorithmic description of the construction process. Each evaluation of such an algorithm creates a model instance, which depends on its input parameters (width, height, volume, roof angle, orientation, location). These values are normally chosen according to aesthetic aspects and style. In this study, the model's parameters are automatically generated according to an objective function. A generative model can be optimized according to its parameters, in this way, the best solution for a constrained problem is determined. Besides the establishment of an overall framework design, this work consists on the identification of different building shapes and their main parameters, the creation of an algorithmic description for these main shapes and the formulation of the objective function, respecting a building's energy consumption (solar energy, heating and insulation). Additionally, the conception of an optimization pipeline, combining an energy calculation tool with a geometric scripting engine is presented. The methods developed leads to an automated and optimized 3D shape generation for the projected building (based on the desired conditions and according to specific constrains). The approach proposed will help in the construction of real buildings that account for less energy consumption and for a more sustainable world.

Super-Encryption Implementation Using Monoalphabetic Algorithm and XOR Algorithm for Data Security

NASA Astrophysics Data System (ADS)

Rachmawati, Dian; Andri Budiman, Mohammad; Aulia, Indra

2018-03-01

The exchange of data that occurs offline and online is very vulnerable to the threat of data theft. In general, cryptography is a science and art to maintain data secrecy. An encryption is a cryptography algorithm in which data is transformed into cipher text, which is something that is unreadable and meaningless so it cannot be read or understood by other parties. In super-encryption, two or more encryption algorithms are combined to make it more secure. In this work, Monoalphabetic algorithm and XOR algorithm are combined to form a super- encryption. Monoalphabetic algorithm works by changing a particular letter into a new letter based on existing keywords while the XOR algorithm works by using logic operation XOR Since Monoalphabetic algorithm is a classical cryptographic algorithm and XOR algorithm is a modern cryptographic algorithm, this scheme is expected to be both easy-to-implement and more secure. The combination of the two algorithms is capable of securing the data and restoring it back to its original form (plaintext), so the data integrity is still ensured.

Image processing meta-algorithm development via genetic manipulation of existing algorithm graphs

NASA Astrophysics Data System (ADS)

Schalkoff, Robert J.; Shaaban, Khaled M.

1999-07-01

Automatic algorithm generation for image processing applications is not a new idea, however previous work is either restricted to morphological operates or impractical. In this paper, we show recent research result in the development and use of meta-algorithms, i.e. algorithms which lead to new algorithms. Although the concept is generally applicable, the application domain in this work is restricted to image processing. The meta-algorithm concept described in this paper is based upon out work in dynamic algorithm. The paper first present the concept of dynamic algorithms which, on the basis of training and archived algorithmic experience embedded in an algorithm graph (AG), dynamically adjust the sequence of operations applied to the input image data. Each node in the tree-based representation of a dynamic algorithm with out degree greater than 2 is a decision node. At these nodes, the algorithm examines the input data and determines which path will most likely achieve the desired results. This is currently done using nearest-neighbor classification. The details of this implementation are shown. The constrained perturbation of existing algorithm graphs, coupled with a suitable search strategy, is one mechanism to achieve meta-algorithm an doffers rich potential for the discovery of new algorithms. In our work, a meta-algorithm autonomously generates new dynamic algorithm graphs via genetic recombination of existing algorithm graphs. The AG representation is well suited to this genetic-like perturbation, using a commonly- employed technique in artificial neural network synthesis, namely the blueprint representation of graphs. A number of exam. One of the principal limitations of our current approach is the need for significant human input in the learning phase. Efforts to overcome this limitation are discussed. Future research directions are indicated.

Optimization of High-Dimensional Functions through Hypercube Evaluation

PubMed Central

Abiyev, Rahib H.; Tunay, Mustafa

2015-01-01

A novel learning algorithm for solving global numerical optimization problems is proposed. The proposed learning algorithm is intense stochastic search method which is based on evaluation and optimization of a hypercube and is called the hypercube optimization (HO) algorithm. The HO algorithm comprises the initialization and evaluation process, displacement-shrink process, and searching space process. The initialization and evaluation process initializes initial solution and evaluates the solutions in given hypercube. The displacement-shrink process determines displacement and evaluates objective functions using new points, and the search area process determines next hypercube using certain rules and evaluates the new solutions. The algorithms for these processes have been designed and presented in the paper. The designed HO algorithm is tested on specific benchmark functions. The simulations of HO algorithm have been performed for optimization of functions of 1000-, 5000-, or even 10000 dimensions. The comparative simulation results with other approaches demonstrate that the proposed algorithm is a potential candidate for optimization of both low and high dimensional functions. PMID:26339237

6.7 radio sky mapping from satellites at very low frequencies

NASA Technical Reports Server (NTRS)

Storey, L. R. O.

1991-01-01

Wave Distribution Function (WDF) analysis is a procedure for making sky maps of the sources of natural electromagnetic waves in space plasmas, given local measurements of some or all of the three magnetic and three electric field components. The work that still needs to be done on this subject includes solving basic methodological problems, translating the solution into efficient algorithms, and embodying the algorithms in computer software. One important scientific use of WDF analysis is to identify the mode of origin of plasmaspheric hiss. Some of the data from the Japanese satellite Akebono (EXOS D) are likely to be suitable for this purpose.

Radio sky mapping from satellites at very low frequencies

NASA Technical Reports Server (NTRS)

Storey, L. R. O.

1991-01-01

Wave Distribution Function (WDF) analysis is a procedure for making sky maps of the sources of natural electromagnetic waves in space plasmas, given local measurements of some or all of the three magnetic and three electric field components. The work that still needs to be done on this subject includes solving basic methodological problems, translating the solution into efficient algorithms, and embodying the algorithms in computer software. One important scientific use of WDF analysis is to identify the mode of origin of plasmaspheric hiss. Some of the data from the Japanese satellite Akebono (EXOS D) are likely to be suitable for this purpose.

Under-reported data analysis with INAR-hidden Markov chains.

PubMed

Fernández-Fontelo, Amanda; Cabaña, Alejandra; Puig, Pedro; Moriña, David

2016-11-20

In this work, we deal with correlated under-reported data through INAR(1)-hidden Markov chain models. These models are very flexible and can be identified through its autocorrelation function, which has a very simple form. A naïve method of parameter estimation is proposed, jointly with the maximum likelihood method based on a revised version of the forward algorithm. The most-probable unobserved time series is reconstructed by means of the Viterbi algorithm. Several examples of application in the field of public health are discussed illustrating the utility of the models. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

A grid spacing control technique for algebraic grid generation methods

NASA Technical Reports Server (NTRS)

Smith, R. E.; Kudlinski, R. A.; Everton, E. L.

1982-01-01

A technique which controls the spacing of grid points in algebraically defined coordinate transformations is described. The technique is based on the generation of control functions which map a uniformly distributed computational grid onto parametric variables defining the physical grid. The control functions are smoothed cubic splines. Sets of control points are input for each coordinate directions to outline the control functions. Smoothed cubic spline functions are then generated to approximate the input data. The technique works best in an interactive graphics environment where control inputs and grid displays are nearly instantaneous. The technique is illustrated with the two-boundary grid generation algorithm.

Efficient Modeling of Gravity Fields Caused by Sources with Arbitrary Geometry and Arbitrary Density Distribution

NASA Astrophysics Data System (ADS)

Wu, Leyuan

2018-01-01

We present a brief review of gravity forward algorithms in Cartesian coordinate system, including both space-domain and Fourier-domain approaches, after which we introduce a truly general and efficient algorithm, namely the convolution-type Gauss fast Fourier transform (Conv-Gauss-FFT) algorithm, for 2D and 3D modeling of gravity potential and its derivatives due to sources with arbitrary geometry and arbitrary density distribution which are defined either by discrete or by continuous functions. The Conv-Gauss-FFT algorithm is based on the combined use of a hybrid rectangle-Gaussian grid and the fast Fourier transform (FFT) algorithm. Since the gravity forward problem in Cartesian coordinate system can be expressed as continuous convolution-type integrals, we first approximate the continuous convolution by a weighted sum of a series of shifted discrete convolutions, and then each shifted discrete convolution, which is essentially a Toeplitz system, is calculated efficiently and accurately by combining circulant embedding with the FFT algorithm. Synthetic and real model tests show that the Conv-Gauss-FFT algorithm can obtain high-precision forward results very efficiently for almost any practical model, and it works especially well for complex 3D models when gravity fields on large 3D regular grids are needed.

Multiple sequence alignment using multi-objective based bacterial foraging optimization algorithm.

PubMed

Rani, R Ranjani; Ramyachitra, D

2016-12-01

Multiple sequence alignment (MSA) is a widespread approach in computational biology and bioinformatics. MSA deals with how the sequences of nucleotides and amino acids are sequenced with possible alignment and minimum number of gaps between them, which directs to the functional, evolutionary and structural relationships among the sequences. Still the computation of MSA is a challenging task to provide an efficient accuracy and statistically significant results of alignments. In this work, the Bacterial Foraging Optimization Algorithm was employed to align the biological sequences which resulted in a non-dominated optimal solution. It employs Multi-objective, such as: Maximization of Similarity, Non-gap percentage, Conserved blocks and Minimization of gap penalty. BAliBASE 3.0 benchmark database was utilized to examine the proposed algorithm against other methods In this paper, two algorithms have been proposed: Hybrid Genetic Algorithm with Artificial Bee Colony (GA-ABC) and Bacterial Foraging Optimization Algorithm. It was found that Hybrid Genetic Algorithm with Artificial Bee Colony performed better than the existing optimization algorithms. But still the conserved blocks were not obtained using GA-ABC. Then BFO was used for the alignment and the conserved blocks were obtained. The proposed Multi-Objective Bacterial Foraging Optimization Algorithm (MO-BFO) was compared with widely used MSA methods Clustal Omega, Kalign, MUSCLE, MAFFT, Genetic Algorithm (GA), Ant Colony Optimization (ACO), Artificial Bee Colony (ABC), Particle Swarm Optimization (PSO) and Hybrid Genetic Algorithm with Artificial Bee Colony (GA-ABC). The final results show that the proposed MO-BFO algorithm yields better alignment than most widely used methods. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Towards Batched Linear Solvers on Accelerated Hardware Platforms

DOE Office of Scientific and Technical Information (OSTI.GOV)

Haidar, Azzam; Dong, Tingzing Tim; Tomov, Stanimire

2015-01-01

As hardware evolves, an increasingly effective approach to develop energy efficient, high-performance solvers, is to design them to work on many small and independent problems. Indeed, many applications already need this functionality, especially for GPUs, which are known to be currently about four to five times more energy efficient than multicore CPUs for every floating-point operation. In this paper, we describe the development of the main one-sided factorizations: LU, QR, and Cholesky; that are needed for a set of small dense matrices to work in parallel. We refer to such algorithms as batched factorizations. Our approach is based on representingmore » the algorithms as a sequence of batched BLAS routines for GPU-contained execution. Note that this is similar in functionality to the LAPACK and the hybrid MAGMA algorithms for large-matrix factorizations. But it is different from a straightforward approach, whereby each of GPU's symmetric multiprocessors factorizes a single problem at a time. We illustrate how our performance analysis together with the profiling and tracing tools guided the development of batched factorizations to achieve up to 2-fold speedup and 3-fold better energy efficiency compared to our highly optimized batched CPU implementations based on the MKL library on a two-sockets, Intel Sandy Bridge server. Compared to a batched LU factorization featured in the NVIDIA's CUBLAS library for GPUs, we achieves up to 2.5-fold speedup on the K40 GPU.« less

Learning in engineered multi-agent systems

NASA Astrophysics Data System (ADS)

Menon, Anup

Consider the problem of maximizing the total power produced by a wind farm. Due to aerodynamic interactions between wind turbines, each turbine maximizing its individual power---as is the case in present-day wind farms---does not lead to optimal farm-level power capture. Further, there are no good models to capture the said aerodynamic interactions, rendering model based optimization techniques ineffective. Thus, model-free distributed algorithms are needed that help turbines adapt their power production on-line so as to maximize farm-level power capture. Motivated by such problems, the main focus of this dissertation is a distributed model-free optimization problem in the context of multi-agent systems. The set-up comprises of a fixed number of agents, each of which can pick an action and observe the value of its individual utility function. An individual's utility function may depend on the collective action taken by all agents. The exact functional form (or model) of the agent utility functions, however, are unknown; an agent can only measure the numeric value of its utility. The objective of the multi-agent system is to optimize the welfare function (i.e. sum of the individual utility functions). Such a collaborative task requires communications between agents and we allow for the possibility of such inter-agent communications. We also pay attention to the role played by the pattern of such information exchange on certain aspects of performance. We develop two algorithms to solve this problem. The first one, engineered Interactive Trial and Error Learning (eITEL) algorithm, is based on a line of work in the Learning in Games literature and applies when agent actions are drawn from finite sets. While in a model-free setting, we introduce a novel qualitative graph-theoretic framework to encode known directed interactions of the form "which agents' action affect which others' payoff" (interaction graph). We encode explicit inter-agent communications in a directed graph (communication graph) and, under certain conditions, prove convergence of agent joint action (under eITEL) to the welfare optimizing set. The main condition requires that the union of interaction and communication graphs be strongly connected; thus the algorithm combines an implicit form of communication (via interactions through utility functions) with explicit inter-agent communications to achieve the given collaborative goal. This work has kinship with certain evolutionary computation techniques such as Simulated Annealing; the algorithm steps are carefully designed such that it describes an ergodic Markov chain with a stationary distribution that has support over states where agent joint actions optimize the welfare function. The main analysis tool is perturbed Markov chains and results of broader interest regarding these are derived as well. The other algorithm, Collaborative Extremum Seeking (CES), uses techniques from extremum seeking control to solve the problem when agent actions are drawn from the set of real numbers. In this case, under the assumption of existence of a local minimizer for the welfare function and a connected undirected communication graph between agents, a result regarding convergence of joint action to a small neighborhood of a local optimizer of the welfare function is proved. Since extremum seeking control uses a simultaneous gradient estimation-descent scheme, gradient information available in the continuous action space formulation is exploited by the CES algorithm to yield improved convergence speeds. The effectiveness of this algorithm for the wind farm power maximization problem is evaluated via simulations. Lastly, we turn to a different question regarding role of the information exchange pattern on performance of distributed control systems by means of a case study for the vehicle platooning problem. In the vehicle platoon control problem, the objective is to design distributed control laws for individual vehicles in a platoon (or a road-train) that regulate inter-vehicle distances at a specified safe value while the entire platoon follows a leader-vehicle. While most of the literature on the problem deals with some inadequacy in control performance when the information exchange is of the nearest neighbor-type, we consider an arbitrary graph serving as information exchange pattern and derive a relationship between how a certain indicator of control performance is related to the information pattern. Such analysis helps in understanding qualitative features of the `right' information pattern for this problem.

Determination of photophysical parameters of chlorophyll {alpha} in photosynthetic organisms using the method of nonlinear laser fluorimetry

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gostev, T S; Fadeev, V V

2011-05-31

We study the possibility of solving the multiparameter inverse problem of nonlinear laser fluorimetry of molecular systems with high local concentration of fluorophores (by the example of chlorophyll {alpha} molecules in photosynthetic organisms). The algorithms are proposed that allow determination of up to four photophysical parameters of chlorophyll {alpha} from the experimental fluorescence saturation curves. The uniqueness and stability of the inverse problem solution obtained using the proposed algorithms were assessed numerically. The laser spectrometer, designed in the course of carrying out the work and aimed at nonlinear laser fluorimetry in the quasi-stationary and nonstationary excitation regimes is described. Themore » algorithms, proposed in this paper, are tested on pure cultures of microalgae Chlorella pyrenoidosa and Chlamydomonas reinhardtii under different functional conditions. (optical technologies in biophysics and medicine)« less

Experimental Investigation and Optimization of TIG Welding Parameters on Aluminum 6061 Alloy Using Firefly Algorithm

NASA Astrophysics Data System (ADS)

Kumar, Rishi; Mevada, N. Ramesh; Rathore, Santosh; Agarwal, Nitin; Rajput, Vinod; Sinh Barad, AjayPal

2017-08-01

To improve Welding quality of aluminum (Al) plate, the TIG Welding system has been prepared, by which Welding current, Shielding gas flow rate and Current polarity can be controlled during Welding process. In the present work, an attempt has been made to study the effect of Welding current, current polarity, and shielding gas flow rate on the tensile strength of the weld joint. Based on the number of parameters and their levels, the Response Surface Methodology technique has been selected as the Design of Experiment. For understanding the influence of input parameters on Ultimate tensile strength of weldment, ANOVA analysis has been carried out. Also to describe and optimize TIG Welding using a new metaheuristic Nature - inspired algorithm which is called as Firefly algorithm which was developed by Dr. Xin-She Yang at Cambridge University in 2007. A general formulation of firefly algorithm is presented together with an analytical, mathematical modeling to optimize the TIG Welding process by a single equivalent objective function.

Estimation of radiative and conductive properties of a semitransparent medium using genetic algorithms

NASA Astrophysics Data System (ADS)

Braiek, A.; Adili, A.; Albouchi, F.; Karkri, M.; Ben Nasrallah, S.

2016-06-01

The aim of this work is to simultaneously identify the conductive and radiative parameters of a semitransparent sample using a photothermal method associated with an inverse problem. The identification of the conductive and radiative proprieties is performed by the minimization of an objective function that represents the errors between calculated temperature and measured signal. The calculated temperature is obtained from a theoretical model built with the thermal quadrupole formalism. Measurement is obtained in the rear face of the sample whose front face is excited by a crenel of heat flux. For identification procedure, a genetic algorithm is developed and used. The genetic algorithm is a useful tool in the simultaneous estimation of correlated or nearly correlated parameters, which can be a limiting factor for the gradient-based methods. The results of the identification procedure show the efficiency and the stability of the genetic algorithm to simultaneously estimate the conductive and radiative properties of clear glass.

Collision of Physics and Software in the Monte Carlo Application Toolkit (MCATK)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sweezy, Jeremy Ed

2016-01-21

The topic is presented in a series of slides organized as follows: MCATK overview, development strategy, available algorithms, problem modeling (sources, geometry, data, tallies), parallelism, miscellaneous tools/features, example MCATK application, recent areas of research, and summary and future work. MCATK is a C++ component-based Monte Carlo neutron-gamma transport software library with continuous energy neutron and photon transport. Designed to build specialized applications and to provide new functionality in existing general-purpose Monte Carlo codes like MCNP, it reads ACE formatted nuclear data generated by NJOY. The motivation behind MCATK was to reduce costs. MCATK physics involves continuous energy neutron & gammamore » transport with multi-temperature treatment, static eigenvalue (k eff and α) algorithms, time-dependent algorithm, and fission chain algorithms. MCATK geometry includes mesh geometries and solid body geometries. MCATK provides verified, unit-test Monte Carlo components, flexibility in Monte Carlo application development, and numerous tools such as geometry and cross section plotters.« less

Optimization Methods in Sherpa

NASA Astrophysics Data System (ADS)

Siemiginowska, Aneta; Nguyen, Dan T.; Doe, Stephen M.; Refsdal, Brian L.

2009-09-01

Forward fitting is a standard technique used to model X-ray data. A statistic, usually assumed weighted chi^2 or Poisson likelihood (e.g. Cash), is minimized in the fitting process to obtain a set of the best model parameters. Astronomical models often have complex forms with many parameters that can be correlated (e.g. an absorbed power law). Minimization is not trivial in such setting, as the statistical parameter space becomes multimodal and finding the global minimum is hard. Standard minimization algorithms can be found in many libraries of scientific functions, but they are usually focused on specific functions. However, Sherpa designed as general fitting and modeling application requires very robust optimization methods that can be applied to variety of astronomical data (X-ray spectra, images, timing, optical data etc.). We developed several optimization algorithms in Sherpa targeting a wide range of minimization problems. Two local minimization methods were built: Levenberg-Marquardt algorithm was obtained from MINPACK subroutine LMDIF and modified to achieve the required robustness; and Nelder-Mead simplex method has been implemented in-house based on variations of the algorithm described in the literature. A global search Monte-Carlo method has been implemented following a differential evolution algorithm presented by Storn and Price (1997). We will present the methods in Sherpa and discuss their usage cases. We will focus on the application to Chandra data showing both 1D and 2D examples. This work is supported by NASA contract NAS8-03060 (CXC).

Modeling the Pulse Signal by Wave-Shape Function and Analyzing by Synchrosqueezing Transform

PubMed Central

Wang, Chun-Li; Yang, Yueh-Lung; Wu, Wen-Hsiang; Tsai, Tung-Hu; Chang, Hen-Hong

2016-01-01

We apply the recently developed adaptive non-harmonic model based on the wave-shape function, as well as the time-frequency analysis tool called synchrosqueezing transform (SST) to model and analyze oscillatory physiological signals. To demonstrate how the model and algorithm work, we apply them to study the pulse wave signal. By extracting features called the spectral pulse signature, and based on functional regression, we characterize the hemodynamics from the radial pulse wave signals recorded by the sphygmomanometer. Analysis results suggest the potential of the proposed signal processing approach to extract health-related hemodynamics features. PMID:27304979

Modeling the Pulse Signal by Wave-Shape Function and Analyzing by Synchrosqueezing Transform.

PubMed

Wu, Hau-Tieng; Wu, Han-Kuei; Wang, Chun-Li; Yang, Yueh-Lung; Wu, Wen-Hsiang; Tsai, Tung-Hu; Chang, Hen-Hong

2016-01-01

We apply the recently developed adaptive non-harmonic model based on the wave-shape function, as well as the time-frequency analysis tool called synchrosqueezing transform (SST) to model and analyze oscillatory physiological signals. To demonstrate how the model and algorithm work, we apply them to study the pulse wave signal. By extracting features called the spectral pulse signature, and based on functional regression, we characterize the hemodynamics from the radial pulse wave signals recorded by the sphygmomanometer. Analysis results suggest the potential of the proposed signal processing approach to extract health-related hemodynamics features.

A hardware-oriented algorithm for floating-point function generation

NASA Technical Reports Server (NTRS)

O'Grady, E. Pearse; Young, Baek-Kyu

1991-01-01

An algorithm is presented for performing accurate, high-speed, floating-point function generation for univariate functions defined at arbitrary breakpoints. Rapid identification of the breakpoint interval, which includes the input argument, is shown to be the key operation in the algorithm. A hardware implementation which makes extensive use of read/write memories is used to illustrate the algorithm.

Structural optimisation of cage induction motors using finite element analysis

NASA Astrophysics Data System (ADS)

Palko, S.

The current trend in motor design is to have highly efficient, low noise, low cost, and modular motors with a high power factor. High torque motors are useful in applications like servo motors, lifts, cranes, and rolling mills. This report contains a detailed review of different optimization methods applicable in various design problems. Special attention is given to the performance of different methods, when they are used with finite element analysis (FEA) as an objective function, and accuracy problems arising from the numerical simulations. Also an effective method for designing high starting torque and high efficiency motors is presented. The method described in this work utilizes FEA combined with algorithms for the optimization of the slot geometry. The optimization algorithm modifies the position of the nodal points in the element mesh. The number of independent variables ranges from 14 to 140 in this work.

Model-based minimization algorithm of a supercritical helium loop consumption subject to operational constraints

NASA Astrophysics Data System (ADS)

Bonne, F.; Bonnay, P.; Girard, A.; Hoa, C.; Lacroix, B.; Le Coz, Q.; Nicollet, S.; Poncet, J.-M.; Zani, L.

2017-12-01

Supercritical helium loops at 4.2 K are the baseline cooling strategy of tokamaks superconducting magnets (JT-60SA, ITER, DEMO, etc.). This loops work with cryogenic circulators that force a supercritical helium flow through the superconducting magnets in order that the temperature stay below the working range all along their length. This paper shows that a supercritical helium loop associated with a saturated liquid helium bath can satisfy temperature constraints in different ways (playing on bath temperature and on the supercritical flow), but that only one is optimal from an energy point of view (every Watt consumed at 4.2 K consumes at least 220 W of electrical power). To find the optimal operational conditions, an algorithm capable of minimizing an objective function (energy consumption at 5 bar, 5 K) subject to constraints has been written. This algorithm works with a supercritical loop model realized with the Simcryogenics [2] library. This article describes the model used and the results of constrained optimization. It will be possible to see that the changes in operating point on the temperature of the magnet (e.g. in case of a change in the plasma configuration) involves large changes on the cryodistribution optimal operating point. Recommendations will be made to ensure that the energetic consumption is kept as low as possible despite the changing operating point. This work is partially supported by EUROfusion Consortium through the Euratom Research and Training Program 20142018 under Grant 633053.

Determining A Purely Symbolic Transfer Function from Symbol Streams: Theory and Algorithms

DOE Office of Scientific and Technical Information (OSTI.GOV)

Griffin, Christopher H

Transfer function modeling is a \\emph{standard technique} in classical Linear Time Invariant and Statistical Process Control. The work of Box and Jenkins was seminal in developing methods for identifying parameters associated with classicalmore » $(r,s,k)$$ transfer functions. Discrete event systems are often \\emph{used} for modeling hybrid control structures and high-level decision problems. \\emph{Examples include} discrete time, discrete strategy repeated games. For these games, a \\emph{discrete transfer function in the form of} an accurate hidden Markov model of input-output relations \\emph{could be used to derive optimal response strategies.} In this paper, we develop an algorithm \\emph{for} creating probabilistic \\textit{Mealy machines} that act as transfer function models for discrete event dynamic systems (DEDS). Our models are defined by three parameters, $$(l_1, l_2, k)$ just as the Box-Jenkins transfer function models. Here $$l_1$$ is the maximal input history lengths to consider, $$l_2$$ is the maximal output history lengths to consider and $k$ is the response lag. Using related results, We show that our Mealy machine transfer functions are optimal in the sense that they maximize the mutual information between the current known state of the DEDS and the next observed input/output pair.« less

Biological network motif detection and evaluation

PubMed Central

2011-01-01

Background Molecular level of biological data can be constructed into system level of data as biological networks. Network motifs are defined as over-represented small connected subgraphs in networks and they have been used for many biological applications. Since network motif discovery involves computationally challenging processes, previous algorithms have focused on computational efficiency. However, we believe that the biological quality of network motifs is also very important. Results We define biological network motifs as biologically significant subgraphs and traditional network motifs are differentiated as structural network motifs in this paper. We develop five algorithms, namely, EDGEGO-BNM, EDGEBETWEENNESS-BNM, NMF-BNM, NMFGO-BNM and VOLTAGE-BNM, for efficient detection of biological network motifs, and introduce several evaluation measures including motifs included in complex, motifs included in functional module and GO term clustering score in this paper. Experimental results show that EDGEGO-BNM and EDGEBETWEENNESS-BNM perform better than existing algorithms and all of our algorithms are applicable to find structural network motifs as well. Conclusion We provide new approaches to finding network motifs in biological networks. Our algorithms efficiently detect biological network motifs and further improve existing algorithms to find high quality structural network motifs, which would be impossible using existing algorithms. The performances of the algorithms are compared based on our new evaluation measures in biological contexts. We believe that our work gives some guidelines of network motifs research for the biological networks. PMID:22784624

The Automated System of the Rhythm Analysis of the Educational Process in a Higher Educational Institution on the Basis of Aprioristic Data

ERIC Educational Resources Information Center

Pelin, Nicolae; Mironov, Vladimir

2008-01-01

In this article the problems of functioning algorithms development for system of the automated analysis of educational process rhythm in a higher educational institution are considered. Using the device of experiment planning for conducting the scientific researches, adapted methodologies, received by authors in the dissertational works at the…

Aerodynamic optimization of supersonic compressor cascade using differential evolution on GPU

NASA Astrophysics Data System (ADS)

Aissa, Mohamed Hasanine; Verstraete, Tom; Vuik, Cornelis

2016-06-01

Differential Evolution (DE) is a powerful stochastic optimization method. Compared to gradient-based algorithms, DE is able to avoid local minima but requires at the same time more function evaluations. In turbomachinery applications, function evaluations are performed with time-consuming CFD simulation, which results in a long, non affordable, design cycle. Modern High Performance Computing systems, especially Graphic Processing Units (GPUs), are able to alleviate this inconvenience by accelerating the design evaluation itself. In this work we present a validated CFD Solver running on GPUs, able to accelerate the design evaluation and thus the entire design process. An achieved speedup of 20x to 30x enabled the DE algorithm to run on a high-end computer instead of a costly large cluster. The GPU-enhanced DE was used to optimize the aerodynamics of a supersonic compressor cascade, achieving an aerodynamic loss minimization of 20%.

Simulation of an expanding plasma using the Boris algorithm

NASA Astrophysics Data System (ADS)

Neal, Luke; Aguirre, Evan; Steinberger, Thomas; Good, Timothy; Scime, Earl

2017-10-01

We present a Boris algorithm simulation in a cylindrical geometry of charged particle motion in a helicon plasma confined by a diverging magnetic field. Laboratory measurements of ion velocity distribution functions (ivdfs) provide evidence for acceleration of ions into the divergent field region in the center of the discharge. The increase in ion velocity is inconsistent with expectations for simple magnetic moment conservation given the magnetic field mirror ratio and is therefore attributed to the presence of a double layer in the literature. Using measured electric fields and ivdfs (at different radial locations across the entire plasma column) upstream and downstream of the divergent magnetic field region, we compare predictions for the downstream ivdfs to measurements. We also present predictions for the evolution of the electron velocity distribution function downstream of the divergent magnetic field. This work was supported by U.S. National Science Foundation Grant No. PHY-1360278.

Aerodynamic optimization of supersonic compressor cascade using differential evolution on GPU

DOE Office of Scientific and Technical Information (OSTI.GOV)

Aissa, Mohamed Hasanine; Verstraete, Tom; Vuik, Cornelis

Differential Evolution (DE) is a powerful stochastic optimization method. Compared to gradient-based algorithms, DE is able to avoid local minima but requires at the same time more function evaluations. In turbomachinery applications, function evaluations are performed with time-consuming CFD simulation, which results in a long, non affordable, design cycle. Modern High Performance Computing systems, especially Graphic Processing Units (GPUs), are able to alleviate this inconvenience by accelerating the design evaluation itself. In this work we present a validated CFD Solver running on GPUs, able to accelerate the design evaluation and thus the entire design process. An achieved speedup of 20xmore » to 30x enabled the DE algorithm to run on a high-end computer instead of a costly large cluster. The GPU-enhanced DE was used to optimize the aerodynamics of a supersonic compressor cascade, achieving an aerodynamic loss minimization of 20%.« less

Design of compactly supported wavelet to match singularities in medical images

NASA Astrophysics Data System (ADS)

Fung, Carrson C.; Shi, Pengcheng

2002-11-01

Analysis and understanding of medical images has important clinical values for patient diagnosis and treatment, as well as technical implications for computer vision and pattern recognition. One of the most fundamental issues is the detection of object boundaries or singularities, which is often the basis for further processes such as organ/tissue recognition, image registration, motion analysis, measurement of anatomical and physiological parameters, etc. The focus of this work involved taking a correlation based approach toward edge detection, by exploiting some of desirable properties of wavelet analysis. This leads to the possibility of constructing a bank of detectors, consisting of multiple wavelet basis functions of different scales which are optimal for specific types of edges, in order to optimally detect all the edges in an image. Our work involved developing a set of wavelet functions which matches the shape of the ramp and pulse edges. The matching algorithm used focuses on matching the edges in the frequency domain. It was proven that this technique could create matching wavelets applicable at all scales. Results have shown that matching wavelets can be obtained for the pulse edge while the ramp edge requires another matching algorithm.

Applications of information theory, genetic algorithms, and neural models to predict oil flow

NASA Astrophysics Data System (ADS)

Ludwig, Oswaldo; Nunes, Urbano; Araújo, Rui; Schnitman, Leizer; Lepikson, Herman Augusto

2009-07-01

This work introduces a new information-theoretic methodology for choosing variables and their time lags in a prediction setting, particularly when neural networks are used in non-linear modeling. The first contribution of this work is the Cross Entropy Function (XEF) proposed to select input variables and their lags in order to compose the input vector of black-box prediction models. The proposed XEF method is more appropriate than the usually applied Cross Correlation Function (XCF) when the relationship among the input and output signals comes from a non-linear dynamic system. The second contribution is a method that minimizes the Joint Conditional Entropy (JCE) between the input and output variables by means of a Genetic Algorithm (GA). The aim is to take into account the dependence among the input variables when selecting the most appropriate set of inputs for a prediction problem. In short, theses methods can be used to assist the selection of input training data that have the necessary information to predict the target data. The proposed methods are applied to a petroleum engineering problem; predicting oil production. Experimental results obtained with a real-world dataset are presented demonstrating the feasibility and effectiveness of the method.

Assessment of Data Fusion Algorithms for Earth Observation Change Detection Processes.

PubMed

Molina, Iñigo; Martinez, Estibaliz; Morillo, Carmen; Velasco, Jesus; Jara, Alvaro

2016-09-30

In this work a parametric multi-sensor Bayesian data fusion approach and a Support Vector Machine (SVM) are used for a Change Detection problem. For this purpose two sets of SPOT5-PAN images have been used, which are in turn used for Change Detection Indices (CDIs) calculation. For minimizing radiometric differences, a methodology based on zonal "invariant features" is suggested. The choice of one or the other CDI for a change detection process is a subjective task as each CDI is probably more or less sensitive to certain types of changes. Likewise, this idea might be employed to create and improve a "change map", which can be accomplished by means of the CDI's informational content. For this purpose, information metrics such as the Shannon Entropy and "Specific Information" have been used to weight the changes and no-changes categories contained in a certain CDI and thus introduced in the Bayesian information fusion algorithm. Furthermore, the parameters of the probability density functions (pdf's) that best fit the involved categories have also been estimated. Conversely, these considerations are not necessary for mapping procedures based on the discriminant functions of a SVM. This work has confirmed the capabilities of probabilistic information fusion procedure under these circumstances.

Optimization design of wind turbine drive train based on Matlab genetic algorithm toolbox

NASA Astrophysics Data System (ADS)

Li, R. N.; Liu, X.; Liu, S. J.

2013-12-01

In order to ensure the high efficiency of the whole flexible drive train of the front-end speed adjusting wind turbine, the working principle of the main part of the drive train is analyzed. As critical parameters, rotating speed ratios of three planetary gear trains are selected as the research subject. The mathematical model of the torque converter speed ratio is established based on these three critical variable quantity, and the effect of key parameters on the efficiency of hydraulic mechanical transmission is analyzed. Based on the torque balance and the energy balance, refer to hydraulic mechanical transmission characteristics, the transmission efficiency expression of the whole drive train is established. The fitness function and constraint functions are established respectively based on the drive train transmission efficiency and the torque converter rotating speed ratio range. And the optimization calculation is carried out by using MATLAB genetic algorithm toolbox. The optimization method and results provide an optimization program for exact match of wind turbine rotor, gearbox, hydraulic mechanical transmission, hydraulic torque converter and synchronous generator, ensure that the drive train work with a high efficiency, and give a reference for the selection of the torque converter and hydraulic mechanical transmission.

Designing synthetic networks in silico: a generalised evolutionary algorithm approach.

PubMed

Smith, Robert W; van Sluijs, Bob; Fleck, Christian

2017-12-02

Evolution has led to the development of biological networks that are shaped by environmental signals. Elucidating, understanding and then reconstructing important network motifs is one of the principal aims of Systems & Synthetic Biology. Consequently, previous research has focused on finding optimal network structures and reaction rates that respond to pulses or produce stable oscillations. In this work we present a generalised in silico evolutionary algorithm that simultaneously finds network structures and reaction rates (genotypes) that can satisfy multiple defined objectives (phenotypes). The key step to our approach is to translate a schema/binary-based description of biological networks into systems of ordinary differential equations (ODEs). The ODEs can then be solved numerically to provide dynamic information about an evolved networks functionality. Initially we benchmark algorithm performance by finding optimal networks that can recapitulate concentration time-series data and perform parameter optimisation on oscillatory dynamics of the Repressilator. We go on to show the utility of our algorithm by finding new designs for robust synthetic oscillators, and by performing multi-objective optimisation to find a set of oscillators and feed-forward loops that are optimal at balancing different system properties. In sum, our results not only confirm and build on previous observations but we also provide new designs of synthetic oscillators for experimental construction. In this work we have presented and tested an evolutionary algorithm that can design a biological network to produce desired output. Given that previous designs of synthetic networks have been limited to subregions of network- and parameter-space, the use of our evolutionary optimisation algorithm will enable Synthetic Biologists to construct new systems with the potential to display a wider range of complex responses.

GPU-based fast cone beam CT reconstruction from undersampled and noisy projection data via total variation.

PubMed

Jia, Xun; Lou, Yifei; Li, Ruijiang; Song, William Y; Jiang, Steve B

2010-04-01

Cone-beam CT (CBCT) plays an important role in image guided radiation therapy (IGRT). However, the large radiation dose from serial CBCT scans in most IGRT procedures raises a clinical concern, especially for pediatric patients who are essentially excluded from receiving IGRT for this reason. The goal of this work is to develop a fast GPU-based algorithm to reconstruct CBCT from undersampled and noisy projection data so as to lower the imaging dose. The CBCT is reconstructed by minimizing an energy functional consisting of a data fidelity term and a total variation regularization term. The authors developed a GPU-friendly version of the forward-backward splitting algorithm to solve this model. A multigrid technique is also employed. It is found that 20-40 x-ray projections are sufficient to reconstruct images with satisfactory quality for IGRT. The reconstruction time ranges from 77 to 130 s on an NVIDIA Tesla C1060 (NVIDIA, Santa Clara, CA) GPU card, depending on the number of projections used, which is estimated about 100 times faster than similar iterative reconstruction approaches. Moreover, phantom studies indicate that the algorithm enables the CBCT to be reconstructed under a scanning protocol with as low as 0.1 mA s/projection. Comparing with currently widely used full-fan head and neck scanning protocol of approximately 360 projections with 0.4 mA s/projection, it is estimated that an overall 36-72 times dose reduction has been achieved in our fast CBCT reconstruction algorithm. This work indicates that the developed GPU-based CBCT reconstruction algorithm is capable of lowering imaging dose considerably. The high computation efficiency in this algorithm makes the iterative CBCT reconstruction approach applicable in real clinical environments.

The comparison of automated clustering algorithms for resampling representative conformer ensembles with RMSD matrix.

PubMed

Kim, Hyoungrae; Jang, Cheongyun; Yadav, Dharmendra K; Kim, Mi-Hyun

2017-03-23

The accuracy of any 3D-QSAR, Pharmacophore and 3D-similarity based chemometric target fishing models are highly dependent on a reasonable sample of active conformations. Since a number of diverse conformational sampling algorithm exist, which exhaustively generate enough conformers, however model building methods relies on explicit number of common conformers. In this work, we have attempted to make clustering algorithms, which could find reasonable number of representative conformer ensembles automatically with asymmetric dissimilarity matrix generated from openeye tool kit. RMSD was the important descriptor (variable) of each column of the N × N matrix considered as N variables describing the relationship (network) between the conformer (in a row) and the other N conformers. This approach used to evaluate the performance of the well-known clustering algorithms by comparison in terms of generating representative conformer ensembles and test them over different matrix transformation functions considering the stability. In the network, the representative conformer group could be resampled for four kinds of algorithms with implicit parameters. The directed dissimilarity matrix becomes the only input to the clustering algorithms. Dunn index, Davies-Bouldin index, Eta-squared values and omega-squared values were used to evaluate the clustering algorithms with respect to the compactness and the explanatory power. The evaluation includes the reduction (abstraction) rate of the data, correlation between the sizes of the population and the samples, the computational complexity and the memory usage as well. Every algorithm could find representative conformers automatically without any user intervention, and they reduced the data to 14-19% of the original values within 1.13 s per sample at the most. The clustering methods are simple and practical as they are fast and do not ask for any explicit parameters. RCDTC presented the maximum Dunn and omega-squared values of the four algorithms in addition to consistent reduction rate between the population size and the sample size. The performance of the clustering algorithms was consistent over different transformation functions. Moreover, the clustering method can also be applied to molecular dynamics sampling simulation results.

The Modular Design and Production of an Intelligent Robot Based on a Closed-Loop Control Strategy.

PubMed

Zhang, Libo; Zhu, Junjie; Ren, Hao; Liu, Dongdong; Meng, Dan; Wu, Yanjun; Luo, Tiejian

2017-10-14

Intelligent robots are part of a new generation of robots that are able to sense the surrounding environment, plan their own actions and eventually reach their targets. In recent years, reliance upon robots in both daily life and industry has increased. The protocol proposed in this paper describes the design and production of a handling robot with an intelligent search algorithm and an autonomous identification function. First, the various working modules are mechanically assembled to complete the construction of the work platform and the installation of the robotic manipulator. Then, we design a closed-loop control system and a four-quadrant motor control strategy, with the aid of debugging software, as well as set steering gear identity (ID), baud rate and other working parameters to ensure that the robot achieves the desired dynamic performance and low energy consumption. Next, we debug the sensor to achieve multi-sensor fusion to accurately acquire environmental information. Finally, we implement the relevant algorithm, which can recognize the success of the robot's function for a given application. The advantage of this approach is its reliability and flexibility, as the users can develop a variety of hardware construction programs and utilize the comprehensive debugger to implement an intelligent control strategy. This allows users to set personalized requirements based on their needs with high efficiency and robustness.

Algorithm of composing the schedule of construction and installation works

NASA Astrophysics Data System (ADS)

Nehaj, Rustam; Molotkov, Georgij; Rudchenko, Ivan; Grinev, Anatolij; Sekisov, Aleksandr

2017-10-01

An algorithm for scheduling works is developed, in which the priority of the work corresponds to the total weight of the subordinate works, the vertices of the graph, and it is proved that for graphs of the tree type the algorithm is optimal. An algorithm is synthesized to reduce the search for solutions when drawing up schedules of construction and installation works, allocating a subset with the optimal solution of the problem of the minimum power, which is determined by the structure of its initial data and numerical values. An algorithm for scheduling construction and installation work is developed, taking into account the schedule for the movement of brigades, which is characterized by the possibility to efficiently calculate the values of minimizing the time of work performance by the parameters of organizational and technological reliability through the use of the branch and boundary method. The program of the computational algorithm was compiled in the MatLAB-2008 program. For the initial data of the matrix, random numbers were taken, uniformly distributed in the range from 1 to 100. It takes 0.5; 2.5; 7.5; 27 minutes to solve the problem. Thus, the proposed method for estimating the lower boundary of the solution is sufficiently accurate and allows efficient solution of the minimax task of scheduling construction and installation works.

Preconditioned Alternating Projection Algorithms for Maximum a Posteriori ECT Reconstruction

PubMed Central

Krol, Andrzej; Li, Si; Shen, Lixin; Xu, Yuesheng

2012-01-01

We propose a preconditioned alternating projection algorithm (PAPA) for solving the maximum a posteriori (MAP) emission computed tomography (ECT) reconstruction problem. Specifically, we formulate the reconstruction problem as a constrained convex optimization problem with the total variation (TV) regularization. We then characterize the solution of the constrained convex optimization problem and show that it satisfies a system of fixed-point equations defined in terms of two proximity operators raised from the convex functions that define the TV-norm and the constrain involved in the problem. The characterization (of the solution) via the proximity operators that define two projection operators naturally leads to an alternating projection algorithm for finding the solution. For efficient numerical computation, we introduce to the alternating projection algorithm a preconditioning matrix (the EM-preconditioner) for the dense system matrix involved in the optimization problem. We prove theoretically convergence of the preconditioned alternating projection algorithm. In numerical experiments, performance of our algorithms, with an appropriately selected preconditioning matrix, is compared with performance of the conventional MAP expectation-maximization (MAP-EM) algorithm with TV regularizer (EM-TV) and that of the recently developed nested EM-TV algorithm for ECT reconstruction. Based on the numerical experiments performed in this work, we observe that the alternating projection algorithm with the EM-preconditioner outperforms significantly the EM-TV in all aspects including the convergence speed, the noise in the reconstructed images and the image quality. It also outperforms the nested EM-TV in the convergence speed while providing comparable image quality. PMID:23271835

Functional validation and comparison framework for EIT lung imaging.

PubMed

Grychtol, Bartłomiej; Elke, Gunnar; Meybohm, Patrick; Weiler, Norbert; Frerichs, Inéz; Adler, Andy

2014-01-01

Electrical impedance tomography (EIT) is an emerging clinical tool for monitoring ventilation distribution in mechanically ventilated patients, for which many image reconstruction algorithms have been suggested. We propose an experimental framework to assess such algorithms with respect to their ability to correctly represent well-defined physiological changes. We defined a set of clinically relevant ventilation conditions and induced them experimentally in 8 pigs by controlling three ventilator settings (tidal volume, positive end-expiratory pressure and the fraction of inspired oxygen). In this way, large and discrete shifts in global and regional lung air content were elicited. We use the framework to compare twelve 2D EIT reconstruction algorithms, including backprojection (the original and still most frequently used algorithm), GREIT (a more recent consensus algorithm for lung imaging), truncated singular value decomposition (TSVD), several variants of the one-step Gauss-Newton approach and two iterative algorithms. We consider the effects of using a 3D finite element model, assuming non-uniform background conductivity, noise modeling, reconstructing for electrode movement, total variation (TV) reconstruction, robust error norms, smoothing priors, and using difference vs. normalized difference data. Our results indicate that, while variation in appearance of images reconstructed from the same data is not negligible, clinically relevant parameters do not vary considerably among the advanced algorithms. Among the analysed algorithms, several advanced algorithms perform well, while some others are significantly worse. Given its vintage and ad-hoc formulation backprojection works surprisingly well, supporting the validity of previous studies in lung EIT.

A new real-time tsunami detection algorithm

NASA Astrophysics Data System (ADS)

Chierici, F.; Embriaco, D.; Pignagnoli, L.

2016-12-01

Real-time tsunami detection algorithms play a key role in any Tsunami Early Warning System. We have developed a new algorithm for tsunami detection based on the real-time tide removal and real-time band-pass filtering of sea-bed pressure recordings. The algorithm greatly increases the tsunami detection probability, shortens the detection delay and enhances detection reliability, at low computational cost. The algorithm is designed to be used also in autonomous early warning systems with a set of input parameters and procedures which can be reconfigured in real time. We have also developed a methodology based on Monte Carlo simulations to test the tsunami detection algorithms. The algorithm performance is estimated by defining and evaluating statistical parameters, namely the detection probability, the detection delay, which are functions of the tsunami amplitude and wavelength, and the occurring rate of false alarms. Pressure data sets acquired by Bottom Pressure Recorders in different locations and environmental conditions have been used in order to consider real working scenarios in the test. We also present an application of the algorithm to the tsunami event which occurred at Haida Gwaii on October 28th, 2012 using data recorded by the Bullseye underwater node of Ocean Networks Canada. The algorithm successfully ran for test purpose in year-long missions onboard the GEOSTAR stand-alone multidisciplinary abyssal observatory, deployed in the Gulf of Cadiz during the EC project NEAREST and on NEMO-SN1 cabled observatory deployed in the Western Ionian Sea, operational node of the European research infrastructure EMSO.

A comparative study between control strategies for a solar sailcraft in an Earth-Mars transfer

NASA Astrophysics Data System (ADS)

Mainenti-Lopes, I.; Souza, L. C. Gadelha; De Sousa, Fabiano. L.

2016-10-01

The goal of this work was a comparative study of solar sail trajectory optimization using different control strategies. Solar sailcraft is propulsion system with great interest in space engineering, since it uses solar radiation to propulsion. So there is no need for propellant to be used, thus it can remains active throughout the entire transfer maneuver. This type of propulsion system opens the possibility to reduce the cost of exploration missions in the solar system. In its simplest configuration, a Flat Solar Sail (FSS) consists of a large and thin structure generally composed by a film fixed to flexible rods. The performance of these vehicles depends largely on the sails attitude relative to the Sun. Using a FSS as propulsion, an Earth-Mars transfer optimization problem was tackled by the algorithms GEOreal1 and GEOreal2 (Generalized Extremal Optimization with real codification). Those algorithms are Evolutionary Algorithms (AE) based on the theory of Self-Organized Criticality. They were used to optimize the FSS attitude angle so it could reach Mars orbit in minimum time. It was considered that the FSS could perform up to ten attitude maneuvers during orbital transfer. Moreover, the time between maneuvers can be different. So, the algorithms had to optimize an objective function with 20 design variables. The results obtained in this work were compared with previously results that considered constant values of time between maneuvers.

Protein complex prediction for large protein protein interaction networks with the Core&Peel method.

PubMed

Pellegrini, Marco; Baglioni, Miriam; Geraci, Filippo

2016-11-08

Biological networks play an increasingly important role in the exploration of functional modularity and cellular organization at a systemic level. Quite often the first tools used to analyze these networks are clustering algorithms. We concentrate here on the specific task of predicting protein complexes (PC) in large protein-protein interaction networks (PPIN). Currently, many state-of-the-art algorithms work well for networks of small or moderate size. However, their performance on much larger networks, which are becoming increasingly common in modern proteome-wise studies, needs to be re-assessed. We present a new fast algorithm for clustering large sparse networks: Core&Peel, which runs essentially in time and storage O(a(G)m+n) for a network G of n nodes and m arcs, where a(G) is the arboricity of G (which is roughly proportional to the maximum average degree of any induced subgraph in G). We evaluated Core&Peel on five PPI networks of large size and one of medium size from both yeast and homo sapiens, comparing its performance against those of ten state-of-the-art methods. We demonstrate that Core&Peel consistently outperforms the ten competitors in its ability to identify known protein complexes and in the functional coherence of its predictions. Our method is remarkably robust, being quite insensible to the injection of random interactions. Core&Peel is also empirically efficient attaining the second best running time over large networks among the tested algorithms. Our algorithm Core&Peel pushes forward the state-of the-art in PPIN clustering providing an algorithmic solution with polynomial running time that attains experimentally demonstrable good output quality and speed on challenging large real networks.

Validation of MODIS-derived bidirectional reflectivity retrieval algorithm in mid-infrared channel with field measurements.

PubMed

Tang, Bo-Hui; Wu, Hua-; Li, Zhao-Liang; Nerry, Françoise

2012-07-30

This work addressed the validation of the MODIS-derived bidirectional reflectivity retrieval algorithm in mid-infrared (MIR) channel, proposed by Tang and Li [Int. J. Remote Sens. 29, 4907 (2008)], with ground-measured data, which were collected from a field campaign that took place in June 2004 at the ONERA (Office National d'Etudes et de Recherches Aérospatiales) center of Fauga-Mauzac, on the PIRRENE (Programme Interdisciplinaire de Recherche sur la Radiométrie en Environnement Extérieur) experiment site [Opt. Express 15, 12464 (2007)]. The leaving-surface spectral radiances measured by a BOMEM (MR250 Series) Fourier transform interferometer were used to calculate the ground brightness temperatures with the combination of the inversion of the Planck function and the spectral response functions of MODIS channels 22 and 23, and then to estimate the ground brightness temperature without the contribution of the solar direct beam and the bidirectional reflectivity by using Tang and Li's proposed algorithm. On the other hand, the simultaneously measured atmospheric profiles were used to obtain the atmospheric parameters and then to calculate the ground brightness temperature without the contribution of the solar direct beam, based on the atmospheric radiative transfer equation in the MIR region. Comparison of those two kinds of brightness temperature obtained by two different methods indicated that the Root Mean Square Error (RMSE) between the brightness temperatures estimated respectively using Tang and Li's algorithm and the atmospheric radiative transfer equation is 1.94 K. In addition, comparison of the hemispherical-directional reflectances derived by Tang and Li's algorithm with those obtained from the field measurements showed that the RMSE is 0.011, which indicates that Tang and Li's algorithm is feasible to retrieve the bidirectional reflectivity in MIR channel from MODIS data.

ROBIN: a platform for evaluating automatic target recognition algorithms: II. Protocols used for evaluating algorithms and results obtained on the SAGEM DS database

NASA Astrophysics Data System (ADS)

Duclos, D.; Lonnoy, J.; Guillerm, Q.; Jurie, F.; Herbin, S.; D'Angelo, E.

2008-04-01

Over the five past years, the computer vision community has explored many different avenues of research for Automatic Target Recognition. Noticeable advances have been made and we are now in the situation where large-scale evaluations of ATR technologies have to be carried out, to determine what the limitations of the recently proposed methods are and to determine the best directions for future works. ROBIN, which is a project funded by the French Ministry of Defence and by the French Ministry of Research, has the ambition of being a new reference for benchmarking ATR algorithms in operational contexts. This project, headed by major companies and research centers involved in Computer Vision R&D in the field of Defense (Bertin Technologies, CNES, ECA, DGA, EADS, INRIA, ONERA, MBDA, SAGEM, THALES) recently released a large dataset of several thousands of hand-annotated infrared and RGB images of different targets in different situations. Setting up an evaluation campaign requires us to define, accurately and carefully, sets of data (both for training ATR algorithms and for their evaluation), tasks to be evaluated, and finally protocols and metrics for the evaluation. ROBIN offers interesting contributions to each one of these three points. This paper first describes, justifies and defines the set of functions used in the ROBIN competitions and relevant for evaluating ATR algorithms (Detection, Localization, Recognition and Identification). It also defines the metrics and the protocol used for evaluating these functions. In the second part of the paper, the results obtained by several state-of-the-art algorithms on the SAGEM DS database (a subpart of ROBIN) are presented and discussed

Mesh-free based variational level set evolution for breast region segmentation and abnormality detection using mammograms.

PubMed

Kashyap, Kanchan L; Bajpai, Manish K; Khanna, Pritee; Giakos, George

2018-01-01

Automatic segmentation of abnormal region is a crucial task in computer-aided detection system using mammograms. In this work, an automatic abnormality detection algorithm using mammographic images is proposed. In the preprocessing step, partial differential equation-based variational level set method is used for breast region extraction. The evolution of the level set method is done by applying mesh-free-based radial basis function (RBF). The limitation of mesh-based approach is removed by using mesh-free-based RBF method. The evolution of variational level set function is also done by mesh-based finite difference method for comparison purpose. Unsharp masking and median filtering is used for mammogram enhancement. Suspicious abnormal regions are segmented by applying fuzzy c-means clustering. Texture features are extracted from the segmented suspicious regions by computing local binary pattern and dominated rotated local binary pattern (DRLBP). Finally, suspicious regions are classified as normal or abnormal regions by means of support vector machine with linear, multilayer perceptron, radial basis, and polynomial kernel function. The algorithm is validated on 322 sample mammograms of mammographic image analysis society (MIAS) and 500 mammograms from digital database for screening mammography (DDSM) datasets. Proficiency of the algorithm is quantified by using sensitivity, specificity, and accuracy. The highest sensitivity, specificity, and accuracy of 93.96%, 95.01%, and 94.48%, respectively, are obtained on MIAS dataset using DRLBP feature with RBF kernel function. Whereas, the highest 92.31% sensitivity, 98.45% specificity, and 96.21% accuracy are achieved on DDSM dataset using DRLBP feature with RBF kernel function. Copyright © 2017 John Wiley & Sons, Ltd.

A method to optimize the processing algorithm of a computed radiography system for chest radiography.

PubMed

Moore, C S; Liney, G P; Beavis, A W; Saunderson, J R

2007-09-01

A test methodology using an anthropomorphic-equivalent chest phantom is described for the optimization of the Agfa computed radiography "MUSICA" processing algorithm for chest radiography. The contrast-to-noise ratio (CNR) in the lung, heart and diaphragm regions of the phantom, and the "system modulation transfer function" (sMTF) in the lung region, were measured using test tools embedded in the phantom. Using these parameters the MUSICA processing algorithm was optimized with respect to low-contrast detectability and spatial resolution. Two optimum "MUSICA parameter sets" were derived respectively for maximizing the CNR and sMTF in each region of the phantom. Further work is required to find the relative importance of low-contrast detectability and spatial resolution in chest images, from which the definitive optimum MUSICA parameter set can then be derived. Prior to this further work, a compromised optimum MUSICA parameter set was applied to a range of clinical images. A group of experienced image evaluators scored these images alongside images produced from the same radiographs using the MUSICA parameter set in clinical use at the time. The compromised optimum MUSICA parameter set was shown to produce measurably better images.

Optimising the production of succinate and lactate in Escherichia coli using a hybrid of artificial bee colony algorithm and minimisation of metabolic adjustment.

PubMed

Tang, Phooi Wah; Choon, Yee Wen; Mohamad, Mohd Saberi; Deris, Safaai; Napis, Suhaimi

2015-03-01

Metabolic engineering is a research field that focuses on the design of models for metabolism, and uses computational procedures to suggest genetic manipulation. It aims to improve the yield of particular chemical or biochemical products. Several traditional metabolic engineering methods are commonly used to increase the production of a desired target, but the products are always far below their theoretical maximums. Using numeral optimisation algorithms to identify gene knockouts may stall at a local minimum in a multivariable function. This paper proposes a hybrid of the artificial bee colony (ABC) algorithm and the minimisation of metabolic adjustment (MOMA) to predict an optimal set of solutions in order to optimise the production rate of succinate and lactate. The dataset used in this work was from the iJO1366 Escherichia coli metabolic network. The experimental results include the production rate, growth rate and a list of knockout genes. From the comparative analysis, ABCMOMA produced better results compared to previous works, showing potential for solving genetic engineering problems. Copyright © 2014 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

A-VCI: A flexible method to efficiently compute vibrational spectra

NASA Astrophysics Data System (ADS)

Odunlami, Marc; Le Bris, Vincent; Bégué, Didier; Baraille, Isabelle; Coulaud, Olivier

2017-06-01

The adaptive vibrational configuration interaction algorithm has been introduced as a new method to efficiently reduce the dimension of the set of basis functions used in a vibrational configuration interaction process. It is based on the construction of nested bases for the discretization of the Hamiltonian operator according to a theoretical criterion that ensures the convergence of the method. In the present work, the Hamiltonian is written as a sum of products of operators. The purpose of this paper is to study the properties and outline the performance details of the main steps of the algorithm. New parameters have been incorporated to increase flexibility, and their influence has been thoroughly investigated. The robustness and reliability of the method are demonstrated for the computation of the vibrational spectrum up to 3000 cm-1 of a widely studied 6-atom molecule (acetonitrile). Our results are compared to the most accurate up to date computation; we also give a new reference calculation for future work on this system. The algorithm has also been applied to a more challenging 7-atom molecule (ethylene oxide). The computed spectrum up to 3200 cm-1 is the most accurate computation that exists today on such systems.

A-VCI: A flexible method to efficiently compute vibrational spectra.

PubMed

Odunlami, Marc; Le Bris, Vincent; Bégué, Didier; Baraille, Isabelle; Coulaud, Olivier

2017-06-07

The adaptive vibrational configuration interaction algorithm has been introduced as a new method to efficiently reduce the dimension of the set of basis functions used in a vibrational configuration interaction process. It is based on the construction of nested bases for the discretization of the Hamiltonian operator according to a theoretical criterion that ensures the convergence of the method. In the present work, the Hamiltonian is written as a sum of products of operators. The purpose of this paper is to study the properties and outline the performance details of the main steps of the algorithm. New parameters have been incorporated to increase flexibility, and their influence has been thoroughly investigated. The robustness and reliability of the method are demonstrated for the computation of the vibrational spectrum up to 3000 cm -1 of a widely studied 6-atom molecule (acetonitrile). Our results are compared to the most accurate up to date computation; we also give a new reference calculation for future work on this system. The algorithm has also been applied to a more challenging 7-atom molecule (ethylene oxide). The computed spectrum up to 3200 cm -1 is the most accurate computation that exists today on such systems.

Identifying patients with poststroke mild cognitive impairment by pattern recognition of working memory load-related ERP.

PubMed

Li, Xiaoou; Yan, Yuning; Wei, Wenshi

2013-01-01

The early detection of subjects with probable cognitive deficits is crucial for effective appliance of treatment strategies. This paper explored a methodology used to discriminate between evoked related potential signals of stroke patients and their matched control subjects in a visual working memory paradigm. The proposed algorithm, which combined independent component analysis and orthogonal empirical mode decomposition, was applied to extract independent sources. Four types of target stimulus features including P300 peak latency, P300 peak amplitude, root mean square, and theta frequency band power were chosen. Evolutionary multiple kernel support vector machine (EMK-SVM) based on genetic programming was investigated to classify stroke patients and healthy controls. Based on 5-fold cross-validation runs, EMK-SVM provided better classification performance compared with other state-of-the-art algorithms. Comparing stroke patients with healthy controls using the proposed algorithm, we achieved the maximum classification accuracies of 91.76% and 82.23% for 0-back and 1-back tasks, respectively. Overall, the experimental results showed that the proposed method was effective. The approach in this study may eventually lead to a reliable tool for identifying suitable brain impairment candidates and assessing cognitive function.

Noise reduction for low-dose helical CT by 3D penalized weighted least-squares sinogram smoothing

NASA Astrophysics Data System (ADS)

Wang, Jing; Li, Tianfang; Lu, Hongbing; Liang, Zhengrong

2006-03-01

Helical computed tomography (HCT) has several advantages over conventional step-and-shoot CT for imaging a relatively large object, especially for dynamic studies. However, HCT may increase X-ray exposure significantly to the patient. This work aims to reduce the radiation by lowering the X-ray tube current (mA) and filtering the low-mA (or dose) sinogram noise. Based on the noise properties of HCT sinogram, a three-dimensional (3D) penalized weighted least-squares (PWLS) objective function was constructed and an optimal sinogram was estimated by minimizing the objective function. To consider the difference of signal correlation among different direction of the HCT sinogram, an anisotropic Markov random filed (MRF) Gibbs function was designed as the penalty. The minimization of the objection function was performed by iterative Gauss-Seidel updating strategy. The effectiveness of the 3D-PWLS sinogram smoothing for low-dose HCT was demonstrated by a 3D Shepp-Logan head phantom study. Comparison studies with our previously developed KL domain PWLS sinogram smoothing algorithm indicate that the KL+2D-PWLS algorithm shows better performance on in-plane noise-resolution trade-off while the 3D-PLWS shows better performance on z-axis noise-resolution trade-off. Receiver operating characteristic (ROC) studies by using channelized Hotelling observer (CHO) shows that 3D-PWLS and KL+2DPWLS algorithms have similar performance on detectability in low-contrast environment.

Building on crossvalidation for increasing the quality of geostatistical modeling

USGS Publications Warehouse

Olea, R.A.

2012-01-01

The random function is a mathematical model commonly used in the assessment of uncertainty associated with a spatially correlated attribute that has been partially sampled. There are multiple algorithms for modeling such random functions, all sharing the requirement of specifying various parameters that have critical influence on the results. The importance of finding ways to compare the methods and setting parameters to obtain results that better model uncertainty has increased as these algorithms have grown in number and complexity. Crossvalidation has been used in spatial statistics, mostly in kriging, for the analysis of mean square errors. An appeal of this approach is its ability to work with the same empirical sample available for running the algorithms. This paper goes beyond checking estimates by formulating a function sensitive to conditional bias. Under ideal conditions, such function turns into a straight line, which can be used as a reference for preparing measures of performance. Applied to kriging, deviations from the ideal line provide sensitivity to the semivariogram lacking in crossvalidation of kriging errors and are more sensitive to conditional bias than analyses of errors. In terms of stochastic simulation, in addition to finding better parameters, the deviations allow comparison of the realizations resulting from the applications of different methods. Examples show improvements of about 30% in the deviations and approximately 10% in the square root of mean square errors between reasonable starting modelling and the solutions according to the new criteria. ?? 2011 US Government.

Modeling Photo-multiplier Gain and Regenerating Pulse Height Data for Application Development

NASA Astrophysics Data System (ADS)

Aspinall, Michael D.; Jones, Ashley R.

2018-01-01

Systems that adopt organic scintillation detector arrays often require a calibration process prior to the intended measurement campaign to correct for significant performance variances between detectors within the array. These differences exist because of low tolerances associated with photo-multiplier tube technology and environmental influences. Differences in detector response can be corrected for by adjusting the supplied photo-multiplier tube voltage to control its gain and the effect that this has on the pulse height spectra from a gamma-only calibration source with a defined photo-peak. Automated methods that analyze these spectra and adjust the photo-multiplier tube bias accordingly are emerging for hardware that integrate acquisition electronics and high voltage control. However, development of such algorithms require access to the hardware, multiple detectors and calibration source for prolonged periods, all with associated constraints and risks. In this work, we report on a software function and related models developed to rescale and regenerate pulse height data acquired from a single scintillation detector. Such a function could be used to generate significant and varied pulse height data that can be used to integration-test algorithms that are capable of automatically response matching multiple detectors using pulse height spectra analysis. Furthermore, a function of this sort removes the dependence on multiple detectors, digital analyzers and calibration source. Results show a good match between the real and regenerated pulse height data. The function has also been used successfully to develop auto-calibration algorithms.

StralSV: assessment of sequence variability within similar 3D structures and application to polio RNA-dependent RNA polymerase

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zemla, A; Lang, D; Kostova, T

2010-11-29

Most of the currently used methods for protein function prediction rely on sequence-based comparisons between a query protein and those for which a functional annotation is provided. A serious limitation of sequence similarity-based approaches for identifying residue conservation among proteins is the low confidence in assigning residue-residue correspondences among proteins when the level of sequence identity between the compared proteins is poor. Multiple sequence alignment methods are more satisfactory - still, they cannot provide reliable results at low levels of sequence identity. Our goal in the current work was to develop an algorithm that could overcome these difficulties and facilitatemore » the identification of structurally (and possibly functionally) relevant residue-residue correspondences between compared protein structures. Here we present StralSV, a new algorithm for detecting closely related structure fragments and quantifying residue frequency from tight local structure alignments. We apply StralSV in a study of the RNA-dependent RNA polymerase of poliovirus and demonstrate that the algorithm can be used to determine regions of the protein that are relatively unique or that shared structural similarity with structures that are distantly related. By quantifying residue frequencies among many residue-residue pairs extracted from local alignments, one can infer potential structural or functional importance of specific residues that are determined to be highly conserved or that deviate from a consensus. We further demonstrate that considerable detailed structural and phylogenetic information can be derived from StralSV analyses. StralSV is a new structure-based algorithm for identifying and aligning structure fragments that have similarity to a reference protein. StralSV analysis can be used to quantify residue-residue correspondences and identify residues that may be of particular structural or functional importance, as well as unusual or unexpected residues at a given sequence position.« less

Query-Adaptive Reciprocal Hash Tables for Nearest Neighbor Search.

PubMed

Liu, Xianglong; Deng, Cheng; Lang, Bo; Tao, Dacheng; Li, Xuelong

2016-02-01

Recent years have witnessed the success of binary hashing techniques in approximate nearest neighbor search. In practice, multiple hash tables are usually built using hashing to cover more desired results in the hit buckets of each table. However, rare work studies the unified approach to constructing multiple informative hash tables using any type of hashing algorithms. Meanwhile, for multiple table search, it also lacks of a generic query-adaptive and fine-grained ranking scheme that can alleviate the binary quantization loss suffered in the standard hashing techniques. To solve the above problems, in this paper, we first regard the table construction as a selection problem over a set of candidate hash functions. With the graph representation of the function set, we propose an efficient solution that sequentially applies normalized dominant set to finding the most informative and independent hash functions for each table. To further reduce the redundancy between tables, we explore the reciprocal hash tables in a boosting manner, where the hash function graph is updated with high weights emphasized on the misclassified neighbor pairs of previous hash tables. To refine the ranking of the retrieved buckets within a certain Hamming radius from the query, we propose a query-adaptive bitwise weighting scheme to enable fine-grained bucket ranking in each hash table, exploiting the discriminative power of its hash functions and their complement for nearest neighbor search. Moreover, we integrate such scheme into the multiple table search using a fast, yet reciprocal table lookup algorithm within the adaptive weighted Hamming radius. In this paper, both the construction method and the query-adaptive search method are general and compatible with different types of hashing algorithms using different feature spaces and/or parameter settings. Our extensive experiments on several large-scale benchmarks demonstrate that the proposed techniques can significantly outperform both the naive construction methods and the state-of-the-art hashing algorithms.

StralSV: assessment of sequence variability within similar 3D structures and application to polio RNA-dependent RNA polymerase.

PubMed

Zemla, Adam T; Lang, Dorothy M; Kostova, Tanya; Andino, Raul; Ecale Zhou, Carol L

2011-06-02

Most of the currently used methods for protein function prediction rely on sequence-based comparisons between a query protein and those for which a functional annotation is provided. A serious limitation of sequence similarity-based approaches for identifying residue conservation among proteins is the low confidence in assigning residue-residue correspondences among proteins when the level of sequence identity between the compared proteins is poor. Multiple sequence alignment methods are more satisfactory--still, they cannot provide reliable results at low levels of sequence identity. Our goal in the current work was to develop an algorithm that could help overcome these difficulties by facilitating the identification of structurally (and possibly functionally) relevant residue-residue correspondences between compared protein structures. Here we present StralSV (structure-alignment sequence variability), a new algorithm for detecting closely related structure fragments and quantifying residue frequency from tight local structure alignments. We apply StralSV in a study of the RNA-dependent RNA polymerase of poliovirus, and we demonstrate that the algorithm can be used to determine regions of the protein that are relatively unique, or that share structural similarity with proteins that would be considered distantly related. By quantifying residue frequencies among many residue-residue pairs extracted from local structural alignments, one can infer potential structural or functional importance of specific residues that are determined to be highly conserved or that deviate from a consensus. We further demonstrate that considerable detailed structural and phylogenetic information can be derived from StralSV analyses. StralSV is a new structure-based algorithm for identifying and aligning structure fragments that have similarity to a reference protein. StralSV analysis can be used to quantify residue-residue correspondences and identify residues that may be of particular structural or functional importance, as well as unusual or unexpected residues at a given sequence position. StralSV is provided as a web service at http://proteinmodel.org/AS2TS/STRALSV/.

Observations on Student Misconceptions--A Case Study of the Build-Heap Algorithm

ERIC Educational Resources Information Center

Seppala, Otto; Malmi, Lauri; Korhonen, Ari

2006-01-01

Data structures and algorithms are core issues in computer programming. However, learning them is challenging for most students and many of them have various types of misconceptions on how algorithms work. In this study, we discuss the problem of identifying misconceptions on the principles of how algorithms work. Our context is algorithm…

Algorithms for accelerated convergence of adaptive PCA.

PubMed

Chatterjee, C; Kang, Z; Roychowdhury, V P

2000-01-01

We derive and discuss new adaptive algorithms for principal component analysis (PCA) that are shown to converge faster than the traditional PCA algorithms due to Oja, Sanger, and Xu. It is well known that traditional PCA algorithms that are derived by using gradient descent on an objective function are slow to converge. Furthermore, the convergence of these algorithms depends on appropriate choices of the gain sequences. Since online applications demand faster convergence and an automatic selection of gains, we present new adaptive algorithms to solve these problems. We first present an unconstrained objective function, which can be minimized to obtain the principal components. We derive adaptive algorithms from this objective function by using: 1) gradient descent; 2) steepest descent; 3) conjugate direction; and 4) Newton-Raphson methods. Although gradient descent produces Xu's LMSER algorithm, the steepest descent, conjugate direction, and Newton-Raphson methods produce new adaptive algorithms for PCA. We also provide a discussion on the landscape of the objective function, and present a global convergence proof of the adaptive gradient descent PCA algorithm using stochastic approximation theory. Extensive experiments with stationary and nonstationary multidimensional Gaussian sequences show faster convergence of the new algorithms over the traditional gradient descent methods.We also compare the steepest descent adaptive algorithm with state-of-the-art methods on stationary and nonstationary sequences.

An algorithm to identify functional groups in organic molecules.

PubMed

Ertl, Peter

2017-06-07

The concept of functional groups forms a basis of organic chemistry, medicinal chemistry, toxicity assessment, spectroscopy and also chemical nomenclature. All current software systems to identify functional groups are based on a predefined list of substructures. We are not aware of any program that can identify all functional groups in a molecule automatically. The algorithm presented in this article is an attempt to solve this scientific challenge. An algorithm to identify functional groups in a molecule based on iterative marching through its atoms is described. The procedure is illustrated by extracting functional groups from the bioactive portion of the ChEMBL database, resulting in identification of 3080 unique functional groups. A new algorithm to identify all functional groups in organic molecules is presented. The algorithm is relatively simple and full details with examples are provided, therefore implementation in any cheminformatics toolkit should be relatively easy. The new method allows the analysis of functional groups in large chemical databases in a way that was not possible using previous approaches. Graphical abstract .

UWB Tracking Software Development

NASA Technical Reports Server (NTRS)

Gross, Julia; Arndt, Dickey; Ngo, Phong; Phan, Chau; Dusl, John; Ni, Jianjun; Rafford, Melinda

2006-01-01

An Ultra-Wideband (UWB) two-cluster Angle of Arrival (AOA) tracking prototype system is currently being developed and tested at NASA Johnson Space Center for space exploration applications. This talk discusses the software development efforts for this UWB two-cluster AOA tracking system. The role the software plays in this system is to take waveform data from two UWB radio receivers as an input, feed this input into an AOA tracking algorithm, and generate the target position as an output. The architecture of the software (Input/Output Interface and Algorithm Core) will be introduced in this talk. The development of this software has three phases. In Phase I, the software is mostly Matlab driven and calls C++ socket functions to provide the communication links to the radios. This is beneficial in the early stage when it is necessary to frequently test changes in the algorithm. Phase II of the development is to have the software mostly C++ driven and call a Matlab function for the AOA tracking algorithm. This is beneficial in order to send the tracking results to other systems and also to improve the tracking update rate of the system. The third phase is part of future work and is to have the software completely C++ driven with a graphics user interface. This software design enables the fine resolution tracking of the UWB two-cluster AOA tracking system.

Novel Semi-Parametric Algorithm for Interference-Immune Tunable Absorption Spectroscopy Gas Sensing

PubMed Central

Michelucci, Umberto; Venturini, Francesca

2017-01-01

One of the most common limits to gas sensor performance is the presence of unwanted interference fringes arising, for example, from multiple reflections between surfaces in the optical path. Additionally, since the amplitude and the frequency of these interferences depend on the distance and alignment of the optical elements, they are affected by temperature changes and mechanical disturbances, giving rise to a drift of the signal. In this work, we present a novel semi-parametric algorithm that allows the extraction of a signal, like the spectroscopic absorption line of a gas molecule, from a background containing arbitrary disturbances, without having to make any assumption on the functional form of these disturbances. The algorithm is applied first to simulated data and then to oxygen absorption measurements in the presence of strong fringes.To the best of the authors’ knowledge, the algorithm enables an unprecedented accuracy particularly if the fringes have a free spectral range and amplitude comparable to those of the signal to be detected. The described method presents the advantage of being based purely on post processing, and to be of extremely straightforward implementation if the functional form of the Fourier transform of the signal is known. Therefore, it has the potential to enable interference-immune absorption spectroscopy. Finally, its relevance goes beyond absorption spectroscopy for gas sensing, since it can be applied to any kind of spectroscopic data. PMID:28991161

Multi-Objectivising Combinatorial Optimisation Problems by Means of Elementary Landscape Decompositions.

PubMed

Ceberio, Josu; Calvo, Borja; Mendiburu, Alexander; Lozano, Jose A

2018-02-15

In the last decade, many works in combinatorial optimisation have shown that, due to the advances in multi-objective optimisation, the algorithms from this field could be used for solving single-objective problems as well. In this sense, a number of papers have proposed multi-objectivising single-objective problems in order to use multi-objective algorithms in their optimisation. In this article, we follow up this idea by presenting a methodology for multi-objectivising combinatorial optimisation problems based on elementary landscape decompositions of their objective function. Under this framework, each of the elementary landscapes obtained from the decomposition is considered as an independent objective function to optimise. In order to illustrate this general methodology, we consider four problems from different domains: the quadratic assignment problem and the linear ordering problem (permutation domain), the 0-1 unconstrained quadratic optimisation problem (binary domain), and the frequency assignment problem (integer domain). We implemented two widely known multi-objective algorithms, NSGA-II and SPEA2, and compared their performance with that of a single-objective GA. The experiments conducted on a large benchmark of instances of the four problems show that the multi-objective algorithms clearly outperform the single-objective approaches. Furthermore, a discussion on the results suggests that the multi-objective space generated by this decomposition enhances the exploration ability, thus permitting NSGA-II and SPEA2 to obtain better results in the majority of the tested instances.

An iterative ensemble quasi-linear data assimilation approach for integrated reservoir monitoring

NASA Astrophysics Data System (ADS)

Li, J. Y.; Kitanidis, P. K.

2013-12-01

Reservoir forecasting and management are increasingly relying on an integrated reservoir monitoring approach, which involves data assimilation to calibrate the complex process of multi-phase flow and transport in the porous medium. The numbers of unknowns and measurements arising in such joint inversion problems are usually very large. The ensemble Kalman filter and other ensemble-based techniques are popular because they circumvent the computational barriers of computing Jacobian matrices and covariance matrices explicitly and allow nonlinear error propagation. These algorithms are very useful but their performance is not well understood and it is not clear how many realizations are needed for satisfactory results. In this presentation we introduce an iterative ensemble quasi-linear data assimilation approach for integrated reservoir monitoring. It is intended for problems for which the posterior or conditional probability density function is not too different from a Gaussian, despite nonlinearity in the state transition and observation equations. The algorithm generates realizations that have the potential to adequately represent the conditional probability density function (pdf). Theoretical analysis sheds light on the conditions under which this algorithm should work well and explains why some applications require very few realizations while others require many. This algorithm is compared with the classical ensemble Kalman filter (Evensen, 2003) and with Gu and Oliver's (2007) iterative ensemble Kalman filter on a synthetic problem of monitoring a reservoir using wellbore pressure and flux data.

Hyperopt: a Python library for model selection and hyperparameter optimization

NASA Astrophysics Data System (ADS)

Bergstra, James; Komer, Brent; Eliasmith, Chris; Yamins, Dan; Cox, David D.

2015-01-01

Sequential model-based optimization (also known as Bayesian optimization) is one of the most efficient methods (per function evaluation) of function minimization. This efficiency makes it appropriate for optimizing the hyperparameters of machine learning algorithms that are slow to train. The Hyperopt library provides algorithms and parallelization infrastructure for performing hyperparameter optimization (model selection) in Python. This paper presents an introductory tutorial on the usage of the Hyperopt library, including the description of search spaces, minimization (in serial and parallel), and the analysis of the results collected in the course of minimization. This paper also gives an overview of Hyperopt-Sklearn, a software project that provides automatic algorithm configuration of the Scikit-learn machine learning library. Following Auto-Weka, we take the view that the choice of classifier and even the choice of preprocessing module can be taken together to represent a single large hyperparameter optimization problem. We use Hyperopt to define a search space that encompasses many standard components (e.g. SVM, RF, KNN, PCA, TFIDF) and common patterns of composing them together. We demonstrate, using search algorithms in Hyperopt and standard benchmarking data sets (MNIST, 20-newsgroups, convex shapes), that searching this space is practical and effective. In particular, we improve on best-known scores for the model space for both MNIST and convex shapes. The paper closes with some discussion of ongoing and future work.

Explicit symplectic algorithms based on generating functions for charged particle dynamics.

PubMed

Zhang, Ruili; Qin, Hong; Tang, Yifa; Liu, Jian; He, Yang; Xiao, Jianyuan

2016-07-01

Dynamics of a charged particle in the canonical coordinates is a Hamiltonian system, and the well-known symplectic algorithm has been regarded as the de facto method for numerical integration of Hamiltonian systems due to its long-term accuracy and fidelity. For long-term simulations with high efficiency, explicit symplectic algorithms are desirable. However, it is generally believed that explicit symplectic algorithms are only available for sum-separable Hamiltonians, and this restriction limits the application of explicit symplectic algorithms to charged particle dynamics. To overcome this difficulty, we combine the familiar sum-split method and a generating function method to construct second- and third-order explicit symplectic algorithms for dynamics of charged particle. The generating function method is designed to generate explicit symplectic algorithms for product-separable Hamiltonian with form of H(x,p)=p_{i}f(x) or H(x,p)=x_{i}g(p). Applied to the simulations of charged particle dynamics, the explicit symplectic algorithms based on generating functions demonstrate superiorities in conservation and efficiency.

Explicit symplectic algorithms based on generating functions for charged particle dynamics

NASA Astrophysics Data System (ADS)

Zhang, Ruili; Qin, Hong; Tang, Yifa; Liu, Jian; He, Yang; Xiao, Jianyuan

2016-07-01

Dynamics of a charged particle in the canonical coordinates is a Hamiltonian system, and the well-known symplectic algorithm has been regarded as the de facto method for numerical integration of Hamiltonian systems due to its long-term accuracy and fidelity. For long-term simulations with high efficiency, explicit symplectic algorithms are desirable. However, it is generally believed that explicit symplectic algorithms are only available for sum-separable Hamiltonians, and this restriction limits the application of explicit symplectic algorithms to charged particle dynamics. To overcome this difficulty, we combine the familiar sum-split method and a generating function method to construct second- and third-order explicit symplectic algorithms for dynamics of charged particle. The generating function method is designed to generate explicit symplectic algorithms for product-separable Hamiltonian with form of H (x ,p ) =pif (x ) or H (x ,p ) =xig (p ) . Applied to the simulations of charged particle dynamics, the explicit symplectic algorithms based on generating functions demonstrate superiorities in conservation and efficiency.

A real-time MTFC algorithm of space remote-sensing camera based on FPGA

NASA Astrophysics Data System (ADS)

Zhao, Liting; Huang, Gang; Lin, Zhe

2018-01-01

A real-time MTFC algorithm of space remote-sensing camera based on FPGA was designed. The algorithm can provide real-time image processing to enhance image clarity when the remote-sensing camera running on-orbit. The image restoration algorithm adopted modular design. The MTF measurement calculation module on-orbit had the function of calculating the edge extension function, line extension function, ESF difference operation, normalization MTF and MTFC parameters. The MTFC image filtering and noise suppression had the function of filtering algorithm and effectively suppressing the noise. The algorithm used System Generator to design the image processing algorithms to simplify the design structure of system and the process redesign. The image gray gradient dot sharpness edge contrast and median-high frequency were enhanced. The image SNR after recovery reduced less than 1 dB compared to the original image. The image restoration system can be widely used in various fields.

Squish: Near-Optimal Compression for Archival of Relational Datasets

PubMed Central

Gao, Yihan; Parameswaran, Aditya

2017-01-01

Relational datasets are being generated at an alarmingly rapid rate across organizations and industries. Compressing these datasets could significantly reduce storage and archival costs. Traditional compression algorithms, e.g., gzip, are suboptimal for compressing relational datasets since they ignore the table structure and relationships between attributes. We study compression algorithms that leverage the relational structure to compress datasets to a much greater extent. We develop Squish, a system that uses a combination of Bayesian Networks and Arithmetic Coding to capture multiple kinds of dependencies among attributes and achieve near-entropy compression rate. Squish also supports user-defined attributes: users can instantiate new data types by simply implementing five functions for a new class interface. We prove the asymptotic optimality of our compression algorithm and conduct experiments to show the effectiveness of our system: Squish achieves a reduction of over 50% in storage size relative to systems developed in prior work on a variety of real datasets. PMID:28180028

Dark Energy Camera for Blanco

DOE Office of Scientific and Technical Information (OSTI.GOV)

Binder, Gary A.; /Caltech /SLAC

2010-08-25

In order to make accurate measurements of dark energy, a system is needed to monitor the focus and alignment of the Dark Energy Camera (DECam) to be located on the Blanco 4m Telescope for the upcoming Dark Energy Survey. One new approach under development is to fit out-of-focus star images to a point spread function from which information about the focus and tilt of the camera can be obtained. As a first test of a new algorithm using this idea, simulated star images produced from a model of DECam in the optics software Zemax were fitted. Then, real images frommore » the Mosaic II imager currently installed on the Blanco telescope were used to investigate the algorithm's capabilities. A number of problems with the algorithm were found, and more work is needed to understand its limitations and improve its capabilities so it can reliably predict camera alignment and focus.« less

The motion of a vortex on a closed surface of constant negative curvature.

PubMed

Ragazzo, C Grotta

2017-10-01

The purpose of this work is to present an algorithm to determine the motion of a single hydrodynamic vortex on a closed surface of constant curvature and of genus greater than one. The algorithm is based on a relation between the Laplace-Beltrami Green function and the heat kernel. The algorithm is used to compute the motion of a vortex on the Bolza surface. This is the first determination of the orbits of a vortex on a closed surface of genus greater than one. The numerical results show that all the 46 vortex equilibria can be explicitly computed using the symmetries of the Bolza surface. Some of these equilibria allow for the construction of the first two examples of infinite vortex crystals on the hyperbolic disc. The following theorem is proved: 'a Weierstrass point of a hyperellitic surface of constant curvature is always a vortex equilibrium'.

Development and experimentation of LQR/APF guidance and control for autonomous proximity maneuvers of multiple spacecraft

NASA Astrophysics Data System (ADS)

Bevilacqua, R.; Lehmann, T.; Romano, M.

2011-04-01

This work introduces a novel control algorithm for close proximity multiple spacecraft autonomous maneuvers, based on hybrid linear quadratic regulator/artificial potential function (LQR/APF), for applications including autonomous docking, on-orbit assembly and spacecraft servicing. Both theoretical developments and experimental validation of the proposed approach are presented. Fuel consumption is sub-optimized in real-time through re-computation of the LQR at each sample time, while performing collision avoidance through the APF and a high level decisional logic. The underlying LQR/APF controller is integrated with a customized wall-following technique and a decisional logic, overcoming problems such as local minima. The algorithm is experimentally tested on a four spacecraft simulators test bed at the Spacecraft Robotics Laboratory of the Naval Postgraduate School. The metrics to evaluate the control algorithm are: autonomy of the system in making decisions, successful completion of the maneuver, required time, and propellant consumption.

Automatic geospatial information Web service composition based on ontology interface matching

NASA Astrophysics Data System (ADS)

Xu, Xianbin; Wu, Qunyong; Wang, Qinmin

2008-10-01

With Web services technology the functions of WebGIS can be presented as a kind of geospatial information service, and helped to overcome the limitation of the information-isolated situation in geospatial information sharing field. Thus Geospatial Information Web service composition, which conglomerates outsourced services working in tandem to offer value-added service, plays the key role in fully taking advantage of geospatial information services. This paper proposes an automatic geospatial information web service composition algorithm that employed the ontology dictionary WordNet to analyze semantic distances among the interfaces. Through making matching between input/output parameters and the semantic meaning of pairs of service interfaces, a geospatial information web service chain can be created from a number of candidate services. A practice of the algorithm is also proposed and the result of it shows the feasibility of this algorithm and the great promise in the emerging demand for geospatial information web service composition.

Fast beampattern evaluation by polynomial rooting

NASA Astrophysics Data System (ADS)

Häcker, P.; Uhlich, S.; Yang, B.

2011-07-01

Current automotive radar systems measure the distance, the relative velocity and the direction of objects in their environment. This information enables the car to support the driver. The direction estimation capabilities of a sensor array depend on its beampattern. To find the array configuration leading to the best angle estimation by a global optimization algorithm, a huge amount of beampatterns have to be calculated to detect their maxima. In this paper, a novel algorithm is proposed to find all maxima of an array's beampattern fast and reliably, leading to accelerated array optimizations. The algorithm works for arrays having the sensors on a uniformly spaced grid. We use a general version of the gcd (greatest common divisor) function in order to write the problem as a polynomial. We differentiate and root the polynomial to get the extrema of the beampattern. In addition, we show a method to reduce the computational burden even more by decreasing the order of the polynomial.

Model-based spectral estimation of Doppler signals using parallel genetic algorithms.

PubMed

Solano González, J; Rodríguez Vázquez, K; García Nocetti, D F

2000-05-01

Conventional spectral analysis methods use a fast Fourier transform (FFT) on consecutive or overlapping windowed data segments. For Doppler ultrasound signals, this approach suffers from an inadequate frequency resolution due to the time segment duration and the non-stationarity characteristics of the signals. Parametric or model-based estimators can give significant improvements in the time-frequency resolution at the expense of a higher computational complexity. This work describes an approach which implements in real-time a parametric spectral estimator method using genetic algorithms (GAs) in order to find the optimum set of parameters for the adaptive filter that minimises the error function. The aim is to reduce the computational complexity of the conventional algorithm by using the simplicity associated to GAs and exploiting its parallel characteristics. This will allow the implementation of higher order filters, increasing the spectrum resolution, and opening a greater scope for using more complex methods.

Hardware Design of the Energy Efficient Fall Detection Device

NASA Astrophysics Data System (ADS)

Skorodumovs, A.; Avots, E.; Hofmanis, J.; Korāts, G.

2016-04-01

Health issues for elderly people may lead to different injuries obtained during simple activities of daily living. Potentially the most dangerous are unintentional falls that may be critical or even lethal to some patients due to the heavy injury risk. In the project "Wireless Sensor Systems in Telecare Application for Elderly People", we have developed a robust fall detection algorithm for a wearable wireless sensor. To optimise the algorithm for hardware performance and test it in field, we have designed an accelerometer based wireless fall detector. Our main considerations were: a) functionality - so that the algorithm can be applied to the chosen hardware, and b) power efficiency - so that it can run for a very long time. We have picked and tested the parts, built a prototype, optimised the firmware for lowest consumption, tested the performance and measured the consumption parameters. In this paper, we discuss our design choices and present the results of our work.

The algorithms for rational spline interpolation of surfaces

NASA Technical Reports Server (NTRS)

Schiess, J. R.

1986-01-01

Two algorithms for interpolating surfaces with spline functions containing tension parameters are discussed. Both algorithms are based on the tensor products of univariate rational spline functions. The simpler algorithm uses a single tension parameter for the entire surface. This algorithm is generalized to use separate tension parameters for each rectangular subregion. The new algorithm allows for local control of tension on the interpolating surface. Both algorithms are illustrated and the results are compared with the results of bicubic spline and bilinear interpolation of terrain elevation data.

Quantitative fluorescence microscopy and image deconvolution.

PubMed

Swedlow, Jason R

2013-01-01

Quantitative imaging and image deconvolution have become standard techniques for the modern cell biologist because they can form the basis of an increasing number of assays for molecular function in a cellular context. There are two major types of deconvolution approaches--deblurring and restoration algorithms. Deblurring algorithms remove blur but treat a series of optical sections as individual two-dimensional entities and therefore sometimes mishandle blurred light. Restoration algorithms determine an object that, when convolved with the point-spread function of the microscope, could produce the image data. The advantages and disadvantages of these methods are discussed in this chapter. Image deconvolution in fluorescence microscopy has usually been applied to high-resolution imaging to improve contrast and thus detect small, dim objects that might otherwise be obscured. Their proper use demands some consideration of the imaging hardware, the acquisition process, fundamental aspects of photon detection, and image processing. This can prove daunting for some cell biologists, but the power of these techniques has been proven many times in the works cited in the chapter and elsewhere. Their usage is now well defined, so they can be incorporated into the capabilities of most laboratories. A major application of fluorescence microscopy is the quantitative measurement of the localization, dynamics, and interactions of cellular factors. The introduction of green fluorescent protein and its spectral variants has led to a significant increase in the use of fluorescence microscopy as a quantitative assay system. For quantitative imaging assays, it is critical to consider the nature of the image-acquisition system and to validate its response to known standards. Any image-processing algorithms used before quantitative analysis should preserve the relative signal levels in different parts of the image. A very common image-processing algorithm, image deconvolution, is used to remove blurred signal from an image. There are two major types of deconvolution approaches, deblurring and restoration algorithms. Deblurring algorithms remove blur, but treat a series of optical sections as individual two-dimensional entities, and therefore sometimes mishandle blurred light. Restoration algorithms determine an object that, when convolved with the point-spread function of the microscope, could produce the image data. The advantages and disadvantages of these methods are discussed. Copyright © 1998 Elsevier Inc. All rights reserved.

Support the Design of Improved IUE NEWSIPS High Dispersion Extraction Algorithms: Improved IUE High Dispersion Extraction Algorithms

NASA Technical Reports Server (NTRS)

Lawton, Pat

2004-01-01

The objective of this work was to support the design of improved IUE NEWSIPS high dispersion extraction algorithms. The purpose of this work was to evaluate use of the Linearized Image (LIHI) file versus the Re-Sampled Image (SIHI) file, evaluate various extraction, and design algorithms for evaluation of IUE High Dispersion spectra. It was concluded the use of the Re-Sampled Image (SIHI) file was acceptable. Since the Gaussian profile worked well for the core and the Lorentzian profile worked well for the wings, the Voigt profile was chosen for use in the extraction algorithm. It was found that the gamma and sigma parameters varied significantly across the detector, so gamma and sigma masks for the SWP detector were developed. Extraction code was written.

Phase Retrieval from Modulus Using Homeomorphic Signal Processing and the Complex Cepstrum: An Algorithm for Lightning Protection Systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Clark, G A

2004-06-08

In general, the Phase Retrieval from Modulus problem is very difficult. In this report, we solve the difficult, but somewhat more tractable case in which we constrain the solution to a minimum phase reconstruction. We exploit the real-and imaginary part sufficiency properties of the Fourier and Hilbert Transforms of causal sequences to develop an algorithm for reconstructing spectral phase given only spectral modulus. The algorithm uses homeomorphic signal processing methods with the complex cepstrum. The formal problem of interest is: Given measurements of only the modulus {vert_bar}H(k){vert_bar} (no phase) of the Discrete Fourier Transform (DFT) of a real, finite-length, stable,more » causal time domain signal h(n), compute a minimum phase reconstruction {cflx h}(n) of the signal. Then compute the phase of {cflx h}(n) using a DFT, and exploit the result as an estimate of the phase of h(n). The development of the algorithm is quite involved, but the final algorithm and its implementation are very simple. This work was motivated by a Phase Retrieval from Modulus Problem that arose in LLNL Defense Sciences Engineering Division (DSED) projects in lightning protection for buildings. The measurements are limited to modulus-only spectra from a spectrum analyzer. However, it is desired to perform system identification on the building to compute impulse responses and transfer functions that describe the amount of lightning energy that will be transferred from the outside of the building to the inside. This calculation requires knowledge of the entire signals (both modulus and phase). The algorithm and software described in this report are proposed as an approach to phase retrieval that can be used for programmatic needs. This report presents a brief tutorial description of the mathematical problem and the derivation of the phase retrieval algorithm. The efficacy of the theory is demonstrated using simulated signals that meet the assumptions of the algorithm. We see that for the noiseless case, the reconstructions are extremely accurate. When moderate to heavy simulated white Gaussian noise was added, the algorithm performance remained reasonably robust, especially in the low frequency part of the spectrum, which is the part of most interest for lightning protection. Limitations of the algorithm include the following: (1) It does not account for noise in the given spectral modulus. Fortunately, the lightning protection signals of interest generally have a reasonably high signal-to-noise ratio (SNR). (2) The DFT length N must be even and larger than the length of the nonzero part of the measured signals. These constraints are simple to meet in practice. (3) Regardless of the properties of the actual signal h(n), the phase retrieval results are constrained to have the minimum phase property. In most problems of practical interest, these assumptions are very reasonable and probably valid. They are reasonable assumptions for Lightning Protection applications. Proposed future work includes (a) Evaluating the efficacy of the algorithm with real Lightning Protection signals from programmatic applications, (b) Performing a more rigorous analysis of noise effects, (c) Using the algorithm along with advanced system identification algorithms to estimate impulse responses and transfer functions, (d) Developing algorithms to deal with measured partial (truncated) spectral moduli, and (e) R & D of phase retrieval algorithms that specifically deal with general (not necessarily minimum phase) signals, and noisy spectral moduli.« less

Identification of significant intrinsic mode functions for the diagnosis of induction motor fault.

PubMed

Cho, Sangjin; Shahriar, Md Rifat; Chong, Uipil

2014-08-01

For the analysis of non-stationary signals generated by a non-linear process like fault of an induction motor, empirical mode decomposition (EMD) is the best choice as it decomposes the signal into its natural oscillatory modes known as intrinsic mode functions (IMFs). However, some of these oscillatory modes obtained from a fault signal are not significant as they do not bear any fault signature and can cause misclassification of the fault instance. To solve this issue, a novel IMF selection algorithm is proposed in this work.

Time-Domain Receiver Function Deconvolution using Genetic Algorithm

NASA Astrophysics Data System (ADS)

Moreira, L. P.

2017-12-01

Receiver Functions (RF) are well know method for crust modelling using passive seismological signals. Many different techniques were developed to calculate the RF traces, applying the deconvolution calculation to radial and vertical seismogram components. A popular method used a spectral division of both components, which requires human intervention to apply the Water Level procedure to avoid instabilities from division by small numbers. One of most used method is an iterative procedure to estimate the RF peaks and applying the convolution with vertical component seismogram, comparing the result with the radial component. This method is suitable for automatic processing, however several RF traces are invalid due to peak estimation failure.In this work it is proposed a deconvolution algorithm using Genetic Algorithm (GA) to estimate the RF peaks. This method is entirely processed in the time domain, avoiding the time-to-frequency calculations (and vice-versa), and totally suitable for automatic processing. Estimated peaks can be used to generate RF traces in a seismogram format for visualization. The RF trace quality is similar for high magnitude events, although there are less failures for RF calculation of smaller events, increasing the overall performance for high number of events per station.

A two-component Matched Interface and Boundary (MIB) regularization for charge singularity in implicit solvation

NASA Astrophysics Data System (ADS)

Geng, Weihua; Zhao, Shan

2017-12-01

We present a new Matched Interface and Boundary (MIB) regularization method for treating charge singularity in solvated biomolecules whose electrostatics are described by the Poisson-Boltzmann (PB) equation. In a regularization method, by decomposing the potential function into two or three components, the singular component can be analytically represented by the Green's function, while other components possess a higher regularity. Our new regularization combines the efficiency of two-component schemes with the accuracy of the three-component schemes. Based on this regularization, a new MIB finite difference algorithm is developed for solving both linear and nonlinear PB equations, where the nonlinearity is handled by using the inexact-Newton's method. Compared with the existing MIB PB solver based on a three-component regularization, the present algorithm is simpler to implement by circumventing the work to solve a boundary value Poisson equation inside the molecular interface and to compute related interface jump conditions numerically. Moreover, the new MIB algorithm becomes computationally less expensive, while maintains the same second order accuracy. This is numerically verified by calculating the electrostatic potential and solvation energy on the Kirkwood sphere on which the analytical solutions are available and on a series of proteins with various sizes.

Design of Neural Networks for Fast Convergence and Accuracy: Dynamics and Control

NASA Technical Reports Server (NTRS)

Maghami, Peiman G.; Sparks, Dean W., Jr.

1997-01-01

A procedure for the design and training of artificial neural networks, used for rapid and efficient controls and dynamics design and analysis for flexible space systems, has been developed. Artificial neural networks are employed, such that once properly trained, they provide a means of evaluating the impact of design changes rapidly. Specifically, two-layer feedforward neural networks are designed to approximate the functional relationship between the component/spacecraft design changes and measures of its performance or nonlinear dynamics of the system/components. A training algorithm, based on statistical sampling theory, is presented, which guarantees that the trained networks provide a designer-specified degree of accuracy in mapping the functional relationship. Within each iteration of this statistical-based algorithm, a sequential design algorithm is used for the design and training of the feedforward network to provide rapid convergence to the network goals. Here, at each sequence a new network is trained to minimize the error of previous network. The proposed method should work for applications wherein an arbitrary large source of training data can be generated. Two numerical examples are performed on a spacecraft application in order to demonstrate the feasibility of the proposed approach.

Design of neural networks for fast convergence and accuracy: dynamics and control.

PubMed

Maghami, P G; Sparks, D R

2000-01-01

A procedure for the design and training of artificial neural networks, used for rapid and efficient controls and dynamics design and analysis for flexible space systems, has been developed. Artificial neural networks are employed, such that once properly trained, they provide a means of evaluating the impact of design changes rapidly. Specifically, two-layer feedforward neural networks are designed to approximate the functional relationship between the component/spacecraft design changes and measures of its performance or nonlinear dynamics of the system/components. A training algorithm, based on statistical sampling theory, is presented, which guarantees that the trained networks provide a designer-specified degree of accuracy in mapping the functional relationship. Within each iteration of this statistical-based algorithm, a sequential design algorithm is used for the design and training of the feedforward network to provide rapid convergence to the network goals. Here, at each sequence a new network is trained to minimize the error of previous network. The proposed method should work for applications wherein an arbitrary large source of training data can be generated. Two numerical examples are performed on a spacecraft application in order to demonstrate the feasibility of the proposed approach.

Variability in Dopamine Genes Dissociates Model-Based and Model-Free Reinforcement Learning

PubMed Central

Bath, Kevin G.; Daw, Nathaniel D.; Frank, Michael J.

2016-01-01

Considerable evidence suggests that multiple learning systems can drive behavior. Choice can proceed reflexively from previous actions and their associated outcomes, as captured by “model-free” learning algorithms, or flexibly from prospective consideration of outcomes that might occur, as captured by “model-based” learning algorithms. However, differential contributions of dopamine to these systems are poorly understood. Dopamine is widely thought to support model-free learning by modulating plasticity in striatum. Model-based learning may also be affected by these striatal effects, or by other dopaminergic effects elsewhere, notably on prefrontal working memory function. Indeed, prominent demonstrations linking striatal dopamine to putatively model-free learning did not rule out model-based effects, whereas other studies have reported dopaminergic modulation of verifiably model-based learning, but without distinguishing a prefrontal versus striatal locus. To clarify the relationships between dopamine, neural systems, and learning strategies, we combine a genetic association approach in humans with two well-studied reinforcement learning tasks: one isolating model-based from model-free behavior and the other sensitive to key aspects of striatal plasticity. Prefrontal function was indexed by a polymorphism in the COMT gene, differences of which reflect dopamine levels in the prefrontal cortex. This polymorphism has been associated with differences in prefrontal activity and working memory. Striatal function was indexed by a gene coding for DARPP-32, which is densely expressed in the striatum where it is necessary for synaptic plasticity. We found evidence for our hypothesis that variations in prefrontal dopamine relate to model-based learning, whereas variations in striatal dopamine function relate to model-free learning. SIGNIFICANCE STATEMENT Decisions can stem reflexively from their previously associated outcomes or flexibly from deliberative consideration of potential choice outcomes. Research implicates a dopamine-dependent striatal learning mechanism in the former type of choice. Although recent work has indicated that dopamine is also involved in flexible, goal-directed decision-making, it remains unclear whether it also contributes via striatum or via the dopamine-dependent working memory function of prefrontal cortex. We examined genetic indices of dopamine function in these regions and their relation to the two choice strategies. We found that striatal dopamine function related most clearly to the reflexive strategy, as previously shown, and that prefrontal dopamine related most clearly to the flexible strategy. These findings suggest that dissociable brain regions support dissociable choice strategies. PMID:26818509

O2 A Band Studies for Cloud Detection and Algorithm Improvement

NASA Technical Reports Server (NTRS)

Chance, K. V.

1996-01-01

Detection of cloud parameters from space-based spectrometers can employ the vibrational bands of O2 in the (sup b1)Sigma(sub +)(sub g) yields X(sub 3) Sigma(sup -)(sub g) spin-forbidden electronic transition manifold, particularly the Delta nu = 0 A band. The GOME instrument uses the A band in the Initial Cloud Fitting Algorithm (ICFA). The work reported here consists of making substantial improvements in the line-by-line spectral database for the A band, testing whether an additional correction to the line shape function is necessary in order to correctly model the atmospheric transmission in this band, and calculating prototype cloud and ground template spectra for comparison with satellite measurements.

Navier-Stokes Dynamics by a Discrete Boltzmann Model

NASA Technical Reports Server (NTRS)

Rubinstein, Robet

2010-01-01

This work investigates the possibility of particle-based algorithms for the Navier-Stokes equations and higher order continuum approximations of the Boltzmann equation; such algorithms would generalize the well-known Pullin scheme for the Euler equations. One such method is proposed in the context of a discrete velocity model of the Boltzmann equation. Preliminary results on shock structure are consistent with the expectation that the shock should be much broader than the near discontinuity predicted by the Pullin scheme, yet narrower than the prediction of the Boltzmann equation. We discuss the extension of this essentially deterministic method to a stochastic particle method that, like DSMC, samples the distribution function rather than resolving it completely.

Algorithms for synthesizing management solutions based on OLAP-technologies

NASA Astrophysics Data System (ADS)

Pishchukhin, A. M.; Akhmedyanova, G. F.

2018-05-01

OLAP technologies are a convenient means of analyzing large amounts of information. An attempt was made in their work to improve the synthesis of optimal management decisions. The developed algorithms allow forecasting the needs and accepted management decisions on the main types of the enterprise resources. Their advantage is the efficiency, based on the simplicity of quadratic functions and differential equations of only the first order. At the same time, the optimal redistribution of resources between different types of products from the assortment of the enterprise is carried out, and the optimal allocation of allocated resources in time. The proposed solutions can be placed on additional specially entered coordinates of the hypercube representing the data warehouse.

Algorithms and Libraries

NASA Technical Reports Server (NTRS)

Dongarra, Jack

1998-01-01

This exploratory study initiated our inquiry into algorithms and applications that would benefit by latency tolerant approach to algorithm building, including the construction of new algorithms where appropriate. In a multithreaded execution, when a processor reaches a point where remote memory access is necessary, the request is sent out on the network and a context--switch occurs to a new thread of computation. This effectively masks a long and unpredictable latency due to remote loads, thereby providing tolerance to remote access latency. We began to develop standards to profile various algorithm and application parameters, such as the degree of parallelism, granularity, precision, instruction set mix, interprocessor communication, latency etc. These tools will continue to develop and evolve as the Information Power Grid environment matures. To provide a richer context for this research, the project also focused on issues of fault-tolerance and computation migration of numerical algorithms and software. During the initial phase we tried to increase our understanding of the bottlenecks in single processor performance. Our work began by developing an approach for the automatic generation and optimization of numerical software for processors with deep memory hierarchies and pipelined functional units. Based on the results we achieved in this study we are planning to study other architectures of interest, including development of cost models, and developing code generators appropriate to these architectures.

Rapid prototyping of update algorithm of discrete Fourier transform for real-time signal processing

NASA Astrophysics Data System (ADS)

Kakad, Yogendra P.; Sherlock, Barry G.; Chatapuram, Krishnan V.; Bishop, Stephen

2001-10-01

An algorithm is developed in the companion paper, to update the existing DFT to represent the new data series that results when a new signal point is received. Updating the DFT in this way uses less computation than directly evaluating the DFT using the FFT algorithm, This reduces the computational order by a factor of log2 N. The algorithm is able to work in the presence of data window function, for use with rectangular window, the split triangular, Hanning, Hamming, and Blackman windows. In this paper, a hardware implementation of this algorithm, using FPGA technology, is outlined. Unlike traditional fully customized VLSI circuits, FPGAs represent a technical break through in the corresponding industry. The FPGA implements thousands of gates of logic in a single IC chip and it can be programmed by users at their site in a few seconds or less depending on the type of device used. The risk is low and the development time is short. The advantages have made FPGAs very popular for rapid prototyping of algorithms in the area of digital communication, digital signal processing, and image processing. Our paper addresses the related issues of implementation using hardware descriptive language in the development of the design and the subsequent downloading on the programmable hardware chip.

Cuckoo Search Algorithm Based on Repeat-Cycle Asymptotic Self-Learning and Self-Evolving Disturbance for Function Optimization

PubMed Central

Wang, Jie-sheng; Li, Shu-xia; Song, Jiang-di

2015-01-01

In order to improve convergence velocity and optimization accuracy of the cuckoo search (CS) algorithm for solving the function optimization problems, a new improved cuckoo search algorithm based on the repeat-cycle asymptotic self-learning and self-evolving disturbance (RC-SSCS) is proposed. A disturbance operation is added into the algorithm by constructing a disturbance factor to make a more careful and thorough search near the bird's nests location. In order to select a reasonable repeat-cycled disturbance number, a further study on the choice of disturbance times is made. Finally, six typical test functions are adopted to carry out simulation experiments, meanwhile, compare algorithms of this paper with two typical swarm intelligence algorithms particle swarm optimization (PSO) algorithm and artificial bee colony (ABC) algorithm. The results show that the improved cuckoo search algorithm has better convergence velocity and optimization accuracy. PMID:26366164

Soft learning vector quantization and clustering algorithms based on ordered weighted aggregation operators.

PubMed

Karayiannis, N B

2000-01-01

This paper presents the development and investigates the properties of ordered weighted learning vector quantization (LVQ) and clustering algorithms. These algorithms are developed by using gradient descent to minimize reformulation functions based on aggregation operators. An axiomatic approach provides conditions for selecting aggregation operators that lead to admissible reformulation functions. Minimization of admissible reformulation functions based on ordered weighted aggregation operators produces a family of soft LVQ and clustering algorithms, which includes fuzzy LVQ and clustering algorithms as special cases. The proposed LVQ and clustering algorithms are used to perform segmentation of magnetic resonance (MR) images of the brain. The diagnostic value of the segmented MR images provides the basis for evaluating a variety of ordered weighted LVQ and clustering algorithms.

Directional Unfolded Source Term (DUST) for Compton Cameras.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mitchell, Dean J.; Horne, Steven M.; O'Brien, Sean

2018-03-01

A Directional Unfolded Source Term (DUST) algorithm was developed to enable improved spectral analysis capabilities using data collected by Compton cameras. Achieving this objective required modification of the detector response function in the Gamma Detector Response and Analysis Software (GADRAS). Experimental data that were collected in support of this work include measurements of calibration sources at a range of separation distances and cylindrical depleted uranium castings.

Data Association Algorithms for Tracking Satellites

DTIC Science & Technology

2013-03-27

validation of the new tools. The description provided here includes the mathematical back ground and description of the models implemented, as well as a...simulation development. This work includes the addition of higher-fidelity models in CU-TurboProp and validation of the new tools. The description...ode45(), used in Ananke, and (3) provide the necessary inputs to the bidirectional reflectance distribution function ( BRDF ) model provided by Pacific

A novel swarm intelligence algorithm for finding DNA motifs.

PubMed

Lei, Chengwei; Ruan, Jianhua

2009-01-01

Discovering DNA motifs from co-expressed or co-regulated genes is an important step towards deciphering complex gene regulatory networks and understanding gene functions. Despite significant improvement in the last decade, it still remains one of the most challenging problems in computational molecular biology. In this work, we propose a novel motif finding algorithm that finds consensus patterns using a population-based stochastic optimisation technique called Particle Swarm Optimisation (PSO), which has been shown to be effective in optimising difficult multidimensional problems in continuous domains. We propose to use a word dissimilarity graph to remap the neighborhood structure of the solution space of DNA motifs, and propose a modification of the naive PSO algorithm to accommodate discrete variables. In order to improve efficiency, we also propose several strategies for escaping from local optima and for automatically determining the termination criteria. Experimental results on simulated challenge problems show that our method is both more efficient and more accurate than several existing algorithms. Applications to several sets of real promoter sequences also show that our approach is able to detect known transcription factor binding sites, and outperforms two of the most popular existing algorithms.

Evaluation of several state-of-charge algorithms

NASA Astrophysics Data System (ADS)

Espinosa, J. M.; Martin, M. E.; Burke, A. F.

1988-09-01

One of the important needs in marketing an electric vehicle is a device which reliably indicates battery state-of-charge for all types of driving. The purpose of the state-of-charge indicator is analogous to a gas gauge in an internal combustion engine powered vehicle. Many different approaches have been tried to accurately predict battery state-of-charge. This report evaluates several of these approaches. Four different algorithms were implemented into software on an IBM PC and tested using a battery test database for ALCO 2200 lead-acid batteries generated at the INEL. The database was obtained under controlled conditions which compare with the battery response in real EV use. Each algorithm is described in detail as to theory and operational functionality. Also discussed is the hardware and data requirements particular to implementing the individual algorithms. The algorithms were evaluated for accuracy using constant power, stepped power, and simulated vehicle (SFUDS79) discharge profiles. Attempts were made to explain the cause of differences between the predicted and actual state-of-charge and to provide possible remedies to correct them. Recommendations for future work on battery state-of-charge indicators are presented that utilize the hardware and software now in place in the INEL Battery Laboratory.

Transcriptional network inference from functional similarity and expression data: a global supervised approach.

PubMed

Ambroise, Jérôme; Robert, Annie; Macq, Benoit; Gala, Jean-Luc

2012-01-06

An important challenge in system biology is the inference of biological networks from postgenomic data. Among these biological networks, a gene transcriptional regulatory network focuses on interactions existing between transcription factors (TFs) and and their corresponding target genes. A large number of reverse engineering algorithms were proposed to infer such networks from gene expression profiles, but most current methods have relatively low predictive performances. In this paper, we introduce the novel TNIFSED method (Transcriptional Network Inference from Functional Similarity and Expression Data), that infers a transcriptional network from the integration of correlations and partial correlations of gene expression profiles and gene functional similarities through a supervised classifier. In the current work, TNIFSED was applied to predict the transcriptional network in Escherichia coli and in Saccharomyces cerevisiae, using datasets of 445 and 170 affymetrix arrays, respectively. Using the area under the curve of the receiver operating characteristics and the F-measure as indicators, we showed the predictive performance of TNIFSED to be better than unsupervised state-of-the-art methods. TNIFSED performed slightly worse than the supervised SIRENE algorithm for the target genes identification of the TF having a wide range of yet identified target genes but better for TF having only few identified target genes. Our results indicate that TNIFSED is complementary to the SIRENE algorithm, and particularly suitable to discover target genes of "orphan" TFs.

Experimental validation of improved 3D SBP positioning algorithm in PET applications using UW Phase II Board

NASA Astrophysics Data System (ADS)

Jorge, L. S.; Bonifacio, D. A. B.; DeWitt, Don; Miyaoka, R. S.

2016-12-01

Continuous scintillator-based detectors have been considered as a competitive and cheaper approach than highly pixelated discrete crystal positron emission tomography (PET) detectors, despite the need for algorithms to estimate 3D gamma interaction position. In this work, we report on the implementation of a positioning algorithm to estimate the 3D interaction position in a continuous crystal PET detector using a Field Programmable Gate Array (FPGA). The evaluated method is the Statistics-Based Processing (SBP) technique that requires light response function and event position characterization. An algorithm has been implemented using the Verilog language and evaluated using a data acquisition board that contains an Altera Stratix III FPGA. The 3D SBP algorithm was previously successfully implemented on a Stratix II FPGA using simulated data and a different module design. In this work, improvements were made to the FPGA coding of the 3D positioning algorithm, reducing the total memory usage to around 34%. Further the algorithm was evaluated using experimental data from a continuous miniature crystal element (cMiCE) detector module. Using our new implementation, average FWHM (Full Width at Half Maximum) for the whole block is 1.71±0.01 mm, 1.70±0.01 mm and 1.632±0.005 mm for x, y and z directions, respectively. Using a pipelined architecture, the FPGA is able to process 245,000 events per second for interactions inside of the central area of the detector that represents 64% of the total block area. The weighted average of the event rate by regional area (corner, border and central regions) is about 198,000 events per second. This event rate is greater than the maximum expected coincidence rate for any given detector module in future PET systems using the cMiCE detector design.

Efficient algorithms for probing the RNA mutation landscape.

PubMed

Waldispühl, Jérôme; Devadas, Srinivas; Berger, Bonnie; Clote, Peter

2008-08-08

The diversity and importance of the role played by RNAs in the regulation and development of the cell are now well-known and well-documented. This broad range of functions is achieved through specific structures that have been (presumably) optimized through evolution. State-of-the-art methods, such as McCaskill's algorithm, use a statistical mechanics framework based on the computation of the partition function over the canonical ensemble of all possible secondary structures on a given sequence. Although secondary structure predictions from thermodynamics-based algorithms are not as accurate as methods employing comparative genomics, the former methods are the only available tools to investigate novel RNAs, such as the many RNAs of unknown function recently reported by the ENCODE consortium. In this paper, we generalize the McCaskill partition function algorithm to sum over the grand canonical ensemble of all secondary structures of all mutants of the given sequence. Specifically, our new program, RNAmutants, simultaneously computes for each integer k the minimum free energy structure MFE(k) and the partition function Z(k) over all secondary structures of all k-point mutants, even allowing the user to specify certain positions required not to mutate and certain positions required to base-pair or remain unpaired. This technically important extension allows us to study the resilience of an RNA molecule to pointwise mutations. By computing the mutation profile of a sequence, a novel graphical representation of the mutational tendency of nucleotide positions, we analyze the deleterious nature of mutating specific nucleotide positions or groups of positions. We have successfully applied RNAmutants to investigate deleterious mutations (mutations that radically modify the secondary structure) in the Hepatitis C virus cis-acting replication element and to evaluate the evolutionary pressure applied on different regions of the HIV trans-activation response element. In particular, we show qualitative agreement between published Hepatitis C and HIV experimental mutagenesis studies and our analysis of deleterious mutations using RNAmutants. Our work also predicts other deleterious mutations, which could be verified experimentally. Finally, we provide evidence that the 3' UTR of the GB RNA virus C has been optimized to preserve evolutionarily conserved stem regions from a deleterious effect of pointwise mutations. We hope that there will be long-term potential applications of RNAmutants in de novo RNA design and drug design against RNA viruses. This work also suggests potential applications for large-scale exploration of the RNA sequence-structure network. Binary distributions are available at http://RNAmutants.csail.mit.edu/.

On-line node fault injection training algorithm for MLP networks: objective function and convergence analysis.

PubMed

Sum, John Pui-Fai; Leung, Chi-Sing; Ho, Kevin I-J

2012-02-01

Improving fault tolerance of a neural network has been studied for more than two decades. Various training algorithms have been proposed in sequel. The on-line node fault injection-based algorithm is one of these algorithms, in which hidden nodes randomly output zeros during training. While the idea is simple, theoretical analyses on this algorithm are far from complete. This paper presents its objective function and the convergence proof. We consider three cases for multilayer perceptrons (MLPs). They are: (1) MLPs with single linear output node; (2) MLPs with multiple linear output nodes; and (3) MLPs with single sigmoid output node. For the convergence proof, we show that the algorithm converges with probability one. For the objective function, we show that the corresponding objective functions of cases (1) and (2) are of the same form. They both consist of a mean square errors term, a regularizer term, and a weight decay term. For case (3), the objective function is slight different from that of cases (1) and (2). With the objective functions derived, we can compare the similarities and differences among various algorithms and various cases.

Newton Algorithms for Analytic Rotation: An Implicit Function Approach

ERIC Educational Resources Information Center

Boik, Robert J.

2008-01-01

In this paper implicit function-based parameterizations for orthogonal and oblique rotation matrices are proposed. The parameterizations are used to construct Newton algorithms for minimizing differentiable rotation criteria applied to "m" factors and "p" variables. The speed of the new algorithms is compared to that of existing algorithms and to…

[Algorithms based on medico-administrative data in the field of endocrine, nutritional and metabolic diseases, especially diabetes].

PubMed

Fosse-Edorh, S; Rigou, A; Morin, S; Fezeu, L; Mandereau-Bruno, L; Fagot-Campagna, A

2017-10-01

Medico-administrative databases represent a very interesting source of information in the field of endocrine, nutritional and metabolic diseases. The objective of this article is to describe the early works of the Redsiam working group in this field. Algorithms developed in France in the field of diabetes, the treatment of dyslipidemia, precocious puberty, and bariatric surgery based on the National Inter-schema Information System on Health Insurance (SNIIRAM) data were identified and described. Three algorithms for identifying people with diabetes are available in France. These algorithms are based either on full insurance coverage for diabetes or on claims of diabetes treatments, or on the combination of these two methods associated with hospitalizations related to diabetes. Each of these algorithms has a different purpose, and the choice should depend on the goal of the study. Algorithms for identifying people treated for dyslipidemia or precocious puberty or who underwent bariatric surgery are also available. Early work from the Redsiam working group in the field of endocrine, nutritional and metabolic diseases produced an inventory of existing algorithms in France, linked with their goals, together with a presentation of their limitations and advantages, providing useful information for the scientific community. This work will continue with discussions about algorithms on the incidence of diabetes in children, thyroidectomy for thyroid nodules, hypothyroidism, hypoparathyroidism, and amyloidosis. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

Genecentric: a package to uncover graph-theoretic structure in high-throughput epistasis data.

PubMed

Gallant, Andrew; Leiserson, Mark D M; Kachalov, Maxim; Cowen, Lenore J; Hescott, Benjamin J

2013-01-18

New technology has resulted in high-throughput screens for pairwise genetic interactions in yeast and other model organisms. For each pair in a collection of non-essential genes, an epistasis score is obtained, representing how much sicker (or healthier) the double-knockout organism will be compared to what would be expected from the sickness of the component single knockouts. Recent algorithmic work has identified graph-theoretic patterns in this data that can indicate functional modules, and even sets of genes that may occur in compensatory pathways, such as a BPM-type schema first introduced by Kelley and Ideker. However, to date, any algorithms for finding such patterns in the data were implemented internally, with no software being made publically available. Genecentric is a new package that implements a parallelized version of the Leiserson et al. algorithm (J Comput Biol 18:1399-1409, 2011) for generating generalized BPMs from high-throughput genetic interaction data. Given a matrix of weighted epistasis values for a set of double knock-outs, Genecentric returns a list of generalized BPMs that may represent compensatory pathways. Genecentric also has an extension, GenecentricGO, to query FuncAssociate (Bioinformatics 25:3043-3044, 2009) to retrieve GO enrichment statistics on generated BPMs. Python is the only dependency, and our web site provides working examples and documentation. We find that Genecentric can be used to find coherent functional and perhaps compensatory gene sets from high throughput genetic interaction data. Genecentric is made freely available for download under the GPLv2 from http://bcb.cs.tufts.edu/genecentric.

Genecentric: a package to uncover graph-theoretic structure in high-throughput epistasis data

PubMed Central

2013-01-01

Background New technology has resulted in high-throughput screens for pairwise genetic interactions in yeast and other model organisms. For each pair in a collection of non-essential genes, an epistasis score is obtained, representing how much sicker (or healthier) the double-knockout organism will be compared to what would be expected from the sickness of the component single knockouts. Recent algorithmic work has identified graph-theoretic patterns in this data that can indicate functional modules, and even sets of genes that may occur in compensatory pathways, such as a BPM-type schema first introduced by Kelley and Ideker. However, to date, any algorithms for finding such patterns in the data were implemented internally, with no software being made publically available. Results Genecentric is a new package that implements a parallelized version of the Leiserson et al. algorithm (J Comput Biol 18:1399-1409, 2011) for generating generalized BPMs from high-throughput genetic interaction data. Given a matrix of weighted epistasis values for a set of double knock-outs, Genecentric returns a list of generalized BPMs that may represent compensatory pathways. Genecentric also has an extension, GenecentricGO, to query FuncAssociate (Bioinformatics 25:3043-3044, 2009) to retrieve GO enrichment statistics on generated BPMs. Python is the only dependency, and our web site provides working examples and documentation. Conclusion We find that Genecentric can be used to find coherent functional and perhaps compensatory gene sets from high throughput genetic interaction data. Genecentric is made freely available for download under the GPLv2 from http://bcb.cs.tufts.edu/genecentric. PMID:23331614

Hybrid fuzzy cluster ensemble framework for tumor clustering from biomolecular data.

PubMed

Yu, Zhiwen; Chen, Hantao; You, Jane; Han, Guoqiang; Li, Le

2013-01-01

Cancer class discovery using biomolecular data is one of the most important tasks for cancer diagnosis and treatment. Tumor clustering from gene expression data provides a new way to perform cancer class discovery. Most of the existing research works adopt single-clustering algorithms to perform tumor clustering is from biomolecular data that lack robustness, stability, and accuracy. To further improve the performance of tumor clustering from biomolecular data, we introduce the fuzzy theory into the cluster ensemble framework for tumor clustering from biomolecular data, and propose four kinds of hybrid fuzzy cluster ensemble frameworks (HFCEF), named as HFCEF-I, HFCEF-II, HFCEF-III, and HFCEF-IV, respectively, to identify samples that belong to different types of cancers. The difference between HFCEF-I and HFCEF-II is that they adopt different ensemble generator approaches to generate a set of fuzzy matrices in the ensemble. Specifically, HFCEF-I applies the affinity propagation algorithm (AP) to perform clustering on the sample dimension and generates a set of fuzzy matrices in the ensemble based on the fuzzy membership function and base samples selected by AP. HFCEF-II adopts AP to perform clustering on the attribute dimension, generates a set of subspaces, and obtains a set of fuzzy matrices in the ensemble by performing fuzzy c-means on subspaces. Compared with HFCEF-I and HFCEF-II, HFCEF-III and HFCEF-IV consider the characteristics of HFCEF-I and HFCEF-II. HFCEF-III combines HFCEF-I and HFCEF-II in a serial way, while HFCEF-IV integrates HFCEF-I and HFCEF-II in a concurrent way. HFCEFs adopt suitable consensus functions, such as the fuzzy c-means algorithm or the normalized cut algorithm (Ncut), to summarize generated fuzzy matrices, and obtain the final results. The experiments on real data sets from UCI machine learning repository and cancer gene expression profiles illustrate that 1) the proposed hybrid fuzzy cluster ensemble frameworks work well on real data sets, especially biomolecular data, and 2) the proposed approaches are able to provide more robust, stable, and accurate results when compared with the state-of-the-art single clustering algorithms and traditional cluster ensemble approaches.

Preconditioned alternating projection algorithms for maximum a posteriori ECT reconstruction

NASA Astrophysics Data System (ADS)

Krol, Andrzej; Li, Si; Shen, Lixin; Xu, Yuesheng

2012-11-01

We propose a preconditioned alternating projection algorithm (PAPA) for solving the maximum a posteriori (MAP) emission computed tomography (ECT) reconstruction problem. Specifically, we formulate the reconstruction problem as a constrained convex optimization problem with the total variation (TV) regularization. We then characterize the solution of the constrained convex optimization problem and show that it satisfies a system of fixed-point equations defined in terms of two proximity operators raised from the convex functions that define the TV-norm and the constraint involved in the problem. The characterization (of the solution) via the proximity operators that define two projection operators naturally leads to an alternating projection algorithm for finding the solution. For efficient numerical computation, we introduce to the alternating projection algorithm a preconditioning matrix (the EM-preconditioner) for the dense system matrix involved in the optimization problem. We prove theoretically convergence of the PAPA. In numerical experiments, performance of our algorithms, with an appropriately selected preconditioning matrix, is compared with performance of the conventional MAP expectation-maximization (MAP-EM) algorithm with TV regularizer (EM-TV) and that of the recently developed nested EM-TV algorithm for ECT reconstruction. Based on the numerical experiments performed in this work, we observe that the alternating projection algorithm with the EM-preconditioner outperforms significantly the EM-TV in all aspects including the convergence speed, the noise in the reconstructed images and the image quality. It also outperforms the nested EM-TV in the convergence speed while providing comparable image quality.

False alarm reduction by the And-ing of multiple multivariate Gaussian classifiers

NASA Astrophysics Data System (ADS)

Dobeck, Gerald J.; Cobb, J. Tory

2003-09-01

The high-resolution sonar is one of the principal sensors used by the Navy to detect and classify sea mines in minehunting operations. For such sonar systems, substantial effort has been devoted to the development of automated detection and classification (D/C) algorithms. These have been spurred by several factors including (1) aids for operators to reduce work overload, (2) more optimal use of all available data, and (3) the introduction of unmanned minehunting systems. The environments where sea mines are typically laid (harbor areas, shipping lanes, and the littorals) give rise to many false alarms caused by natural, biologic, and man-made clutter. The objective of the automated D/C algorithms is to eliminate most of these false alarms while still maintaining a very high probability of mine detection and classification (PdPc). In recent years, the benefits of fusing the outputs of multiple D/C algorithms have been studied. We refer to this as Algorithm Fusion. The results have been remarkable, including reliable robustness to new environments. This paper describes a method for training several multivariate Gaussian classifiers such that their And-ing dramatically reduces false alarms while maintaining a high probability of classification. This training approach is referred to as the Focused- Training method. This work extends our 2001-2002 work where the Focused-Training method was used with three other types of classifiers: the Attractor-based K-Nearest Neighbor Neural Network (a type of radial-basis, probabilistic neural network), the Optimal Discrimination Filter Classifier (based linear discrimination theory), and the Quadratic Penalty Function Support Vector Machine (QPFSVM). Although our experience has been gained in the area of sea mine detection and classification, the principles described herein are general and can be applied to a wide range of pattern recognition and automatic target recognition (ATR) problems.

Discrete-Time Deterministic $Q$ -Learning: A Novel Convergence Analysis.

PubMed

Wei, Qinglai; Lewis, Frank L; Sun, Qiuye; Yan, Pengfei; Song, Ruizhuo

2017-05-01

In this paper, a novel discrete-time deterministic Q -learning algorithm is developed. In each iteration of the developed Q -learning algorithm, the iterative Q function is updated for all the state and control spaces, instead of updating for a single state and a single control in traditional Q -learning algorithm. A new convergence criterion is established to guarantee that the iterative Q function converges to the optimum, where the convergence criterion of the learning rates for traditional Q -learning algorithms is simplified. During the convergence analysis, the upper and lower bounds of the iterative Q function are analyzed to obtain the convergence criterion, instead of analyzing the iterative Q function itself. For convenience of analysis, the convergence properties for undiscounted case of the deterministic Q -learning algorithm are first developed. Then, considering the discounted factor, the convergence criterion for the discounted case is established. Neural networks are used to approximate the iterative Q function and compute the iterative control law, respectively, for facilitating the implementation of the deterministic Q -learning algorithm. Finally, simulation results and comparisons are given to illustrate the performance of the developed algorithm.

Cache Locality Optimization for Recursive Programs

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lifflander, Jonathan; Krishnamoorthy, Sriram

We present an approach to optimize the cache locality for recursive programs by dynamically splicing--recursively interleaving--the execution of distinct function invocations. By utilizing data effect annotations, we identify concurrency and data reuse opportunities across function invocations and interleave them to reduce reuse distance. We present algorithms that efficiently track effects in recursive programs, detect interference and dependencies, and interleave execution of function invocations using user-level (non-kernel) lightweight threads. To enable multi-core execution, a program is parallelized using a nested fork/join programming model. Our cache optimization strategy is designed to work in the context of a random work stealing scheduler. Wemore » present an implementation using the MIT Cilk framework that demonstrates significant improvements in sequential and parallel performance, competitive with a state-of-the-art compile-time optimizer for loop programs and a domain- specific optimizer for stencil programs.« less

A false-alarm aware methodology to develop robust and efficient multi-scale infrared small target detection algorithm

NASA Astrophysics Data System (ADS)

Moradi, Saed; Moallem, Payman; Sabahi, Mohamad Farzan

2018-03-01

False alarm rate and detection rate are still two contradictory metrics for infrared small target detection in an infrared search and track system (IRST), despite the development of new detection algorithms. In certain circumstances, not detecting true targets is more tolerable than detecting false items as true targets. Hence, considering background clutter and detector noise as the sources of the false alarm in an IRST system, in this paper, a false alarm aware methodology is presented to reduce false alarm rate while the detection rate remains undegraded. To this end, advantages and disadvantages of each detection algorithm are investigated and the sources of the false alarms are determined. Two target detection algorithms having independent false alarm sources are chosen in a way that the disadvantages of the one algorithm can be compensated by the advantages of the other one. In this work, multi-scale average absolute gray difference (AAGD) and Laplacian of point spread function (LoPSF) are utilized as the cornerstones of the desired algorithm of the proposed methodology. After presenting a conceptual model for the desired algorithm, it is implemented through the most straightforward mechanism. The desired algorithm effectively suppresses background clutter and eliminates detector noise. Also, since the input images are processed through just four different scales, the desired algorithm has good capability for real-time implementation. Simulation results in term of signal to clutter ratio and background suppression factor on real and simulated images prove the effectiveness and the performance of the proposed methodology. Since the desired algorithm was developed based on independent false alarm sources, our proposed methodology is expandable to any pair of detection algorithms which have different false alarm sources.

Real-time state estimation in a flight simulator using fNIRS.

PubMed

Gateau, Thibault; Durantin, Gautier; Lancelot, Francois; Scannella, Sebastien; Dehais, Frederic

2015-01-01

Working memory is a key executive function for flying an aircraft. This function is particularly critical when pilots have to recall series of air traffic control instructions. However, working memory limitations may jeopardize flight safety. Since the functional near-infrared spectroscopy (fNIRS) method seems promising for assessing working memory load, our objective is to implement an on-line fNIRS-based inference system that integrates two complementary estimators. The first estimator is a real-time state estimation MACD-based algorithm dedicated to identifying the pilot's instantaneous mental state (not-on-task vs. on-task). It does not require a calibration process to perform its estimation. The second estimator is an on-line SVM-based classifier that is able to discriminate task difficulty (low working memory load vs. high working memory load). These two estimators were tested with 19 pilots who were placed in a realistic flight simulator and were asked to recall air traffic control instructions. We found that the estimated pilot's mental state matched significantly better than chance with the pilot's real state (62% global accuracy, 58% specificity, and 72% sensitivity). The second estimator, dedicated to assessing single trial working memory loads, led to 80% classification accuracy, 72% specificity, and 89% sensitivity. These two estimators establish reusable blocks for further fNIRS-based passive brain computer interface development.

An Overview of the JPSS Ground Project Algorithm Integration Process

NASA Astrophysics Data System (ADS)

Vicente, G. A.; Williams, R.; Dorman, T. J.; Williamson, R. C.; Shaw, F. J.; Thomas, W. M.; Hung, L.; Griffin, A.; Meade, P.; Steadley, R. S.; Cember, R. P.

2015-12-01

The smooth transition, implementation and operationalization of scientific software's from the National Oceanic and Atmospheric Administration (NOAA) development teams to the Join Polar Satellite System (JPSS) Ground Segment requires a variety of experiences and expertise. This task has been accomplished by a dedicated group of scientist and engineers working in close collaboration with the NOAA Satellite and Information Services (NESDIS) Center for Satellite Applications and Research (STAR) science teams for the JPSS/Suomi-NPOES Preparatory Project (S-NPP) Advanced Technology Microwave Sounder (ATMS), Cross-track Infrared Sounder (CrIS), Visible Infrared Imaging Radiometer Suite (VIIRS) and Ozone Mapping and Profiler Suite (OMPS) instruments. The presentation purpose is to describe the JPSS project process for algorithm implementation from the very early delivering stages by the science teams to the full operationalization into the Interface Processing Segment (IDPS), the processing system that provides Environmental Data Records (EDR's) to NOAA. Special focus is given to the NASA Data Products Engineering and Services (DPES) Algorithm Integration Team (AIT) functional and regression test activities. In the functional testing phase, the AIT uses one or a few specific chunks of data (granules) selected by the NOAA STAR Calibration and Validation (cal/val) Teams to demonstrate that a small change in the code performs properly and does not disrupt the rest of the algorithm chain. In the regression testing phase, the modified code is placed into to the Government Resources for Algorithm Verification, Integration, Test and Evaluation (GRAVITE) Algorithm Development Area (ADA), a simulated and smaller version of the operational IDPS. Baseline files are swapped out, not edited and the whole code package runs in one full orbit of Science Data Records (SDR's) using Calibration Look Up Tables (Cal LUT's) for the time of the orbit. The purpose of the regression test is to identify unintended outcomes. Overall the presentation provides a general and easy to follow overview of the JPSS Algorithm Change Process (ACP) and is intended to facility the audience understanding of a very extensive and complex process.

Introduction to multivariate discrimination

NASA Astrophysics Data System (ADS)

Kégl, Balázs

2013-07-01

Multivariate discrimination or classification is one of the best-studied problem in machine learning, with a plethora of well-tested and well-performing algorithms. There are also several good general textbooks [1-9] on the subject written to an average engineering, computer science, or statistics graduate student; most of them are also accessible for an average physics student with some background on computer science and statistics. Hence, instead of writing a generic introduction, we concentrate here on relating the subject to a practitioner experimental physicist. After a short introduction on the basic setup (Section 1) we delve into the practical issues of complexity regularization, model selection, and hyperparameter optimization (Section 2), since it is this step that makes high-complexity non-parametric fitting so different from low-dimensional parametric fitting. To emphasize that this issue is not restricted to classification, we illustrate the concept on a low-dimensional but non-parametric regression example (Section 2.1). Section 3 describes the common algorithmic-statistical formal framework that unifies the main families of multivariate classification algorithms. We explain here the large-margin principle that partly explains why these algorithms work. Section 4 is devoted to the description of the three main (families of) classification algorithms, neural networks, the support vector machine, and AdaBoost. We do not go into the algorithmic details; the goal is to give an overview on the form of the functions these methods learn and on the objective functions they optimize. Besides their technical description, we also make an attempt to put these algorithm into a socio-historical context. We then briefly describe some rather heterogeneous applications to illustrate the pattern recognition pipeline and to show how widespread the use of these methods is (Section 5). We conclude the chapter with three essentially open research problems that are either relevant to or even motivated by certain unorthodox applications of multivariate discrimination in experimental physics.

Time-domain parameter identification of aeroelastic loads by forced-vibration method for response of flexible structures subject to transient wind

NASA Astrophysics Data System (ADS)

Cao, Bochao

Slender structures representing civil, mechanical and aerospace systems such as long-span bridges, high-rise buildings, stay cables, power-line cables, high light mast poles, crane-booms and aircraft wings could experience vortex-induced and buffeting excitations below their design wind speeds and divergent self-excited oscillations (flutter) beyond a critical wind speed because these are flexible. Traditional linear aerodynamic theories that are routinely applied for their response prediction are not valid in the galloping, or near-flutter regime, where large-amplitude vibrations could occur and during non-stationary and transient wind excitations that occur, for example, during hurricanes, thunderstorms and gust fronts. The linear aerodynamic load formulation for lift, drag and moment are expressed in terms of aerodynamic functions in frequency domain that are valid for straight-line winds which are stationary or weakly-stationary. Application of the frequency domain formulation is restricted from use in the nonlinear and transient domain because these are valid for linear models and stationary wind. The time-domain aerodynamic force formulations are suitable for finite element modeling, feedback-dependent structural control mechanism, fatigue-life prediction, and above all modeling of transient structural behavior during non-stationary wind phenomena. This has motivated the developing of time-domain models of aerodynamic loads that are in parallel to the existing frequency-dependent models. Parameters defining these time-domain models can be now extracted from wind tunnel tests, for example, the Rational Function Coefficients defining the self-excited wind loads can be extracted using section model tests using the free vibration technique. However, the free vibration method has some limitations because it is difficult to apply at high wind speeds, in turbulent wind environment, or on unstable cross sections with negative aerodynamic damping. In the current research, new algorithms were developed based on forced vibration technique for direct extraction of the Rational Functions. The first of the two algorithms developed uses the two angular phase lag values between the measured vertical or torsional displacement and the measured aerodynamic lift and moment produced on the section model subject to forced vibration to identify the Rational Functions. This algorithm uses two separate one-degree-of-freedom tests (vertical or torsional) to identify all the four Rational Functions or corresponding Rational Function Coefficients for a two degrees-of-freedom (DOF) vertical-torsional vibration model. It was applied to a streamlined section model and the results compared well with those obtained from earlier free vibration experiment. The second algorithm that was developed is based on direct least squares method. It uses all the data points of displacements and aerodynamic lift and moment instead of phase lag values for more accurate estimates. This algorithm can be used for one-, two- and three-degree-of-freedom motions. A two-degree-of-freedom forced vibration system was developed and the algorithm was shown to work well for both streamlined and bluff section models. The uniqueness of the second algorithms lies in the fact that it requires testing the model at only two wind speeds for extraction of all four Rational Functions. The Rational Function Coefficients that were extracted for a streamlined section model using the two-DOF Least Squares algorithm were validated in a separate wind tunnel by testing a larger scaled model subject to straight-line, gusty and boundary-layer wind.

A Self Adaptive Differential Evolution Algorithm for Global Optimization

NASA Astrophysics Data System (ADS)

Kumar, Pravesh; Pant, Millie

This paper presents a new Differential Evolution algorithm based on hybridization of adaptive control parameters and trigonometric mutation. First we propose a self adaptive DE named ADE where choice of control parameter F and Cr is not fixed at some constant value but is taken iteratively. The proposed algorithm is further modified by applying trigonometric mutation in it and the corresponding algorithm is named as ATDE. The performance of ATDE is evaluated on the set of 8 benchmark functions and the results are compared with the classical DE algorithm in terms of average fitness function value, number of function evaluations, convergence time and success rate. The numerical result shows the competence of the proposed algorithm.

ibex: An open infrastructure software platform to facilitate collaborative work in radiomics

PubMed Central

Zhang, Lifei; Fried, David V.; Fave, Xenia J.; Hunter, Luke A.; Court, Laurence E.

2015-01-01

Purpose: Radiomics, which is the high-throughput extraction and analysis of quantitative image features, has been shown to have considerable potential to quantify the tumor phenotype. However, at present, a lack of software infrastructure has impeded the development of radiomics and its applications. Therefore, the authors developed the imaging biomarker explorer (ibex), an open infrastructure software platform that flexibly supports common radiomics workflow tasks such as multimodality image data import and review, development of feature extraction algorithms, model validation, and consistent data sharing among multiple institutions. Methods: The ibex software package was developed using the matlab and c/c++ programming languages. The software architecture deploys the modern model-view-controller, unit testing, and function handle programming concepts to isolate each quantitative imaging analysis task, to validate if their relevant data and algorithms are fit for use, and to plug in new modules. On one hand, ibex is self-contained and ready to use: it has implemented common data importers, common image filters, and common feature extraction algorithms. On the other hand, ibex provides an integrated development environment on top of matlab and c/c++, so users are not limited to its built-in functions. In the ibex developer studio, users can plug in, debug, and test new algorithms, extending ibex’s functionality. ibex also supports quality assurance for data and feature algorithms: image data, regions of interest, and feature algorithm-related data can be reviewed, validated, and/or modified. More importantly, two key elements in collaborative workflows, the consistency of data sharing and the reproducibility of calculation result, are embedded in the ibex workflow: image data, feature algorithms, and model validation including newly developed ones from different users can be easily and consistently shared so that results can be more easily reproduced between institutions. Results: Researchers with a variety of technical skill levels, including radiation oncologists, physicists, and computer scientists, have found the ibex software to be intuitive, powerful, and easy to use. ibex can be run at any computer with the windows operating system and 1GB RAM. The authors fully validated the implementation of all importers, preprocessing algorithms, and feature extraction algorithms. Windows version 1.0 beta of stand-alone ibex and ibex’s source code can be downloaded. Conclusions: The authors successfully implemented ibex, an open infrastructure software platform that streamlines common radiomics workflow tasks. Its transparency, flexibility, and portability can greatly accelerate the pace of radiomics research and pave the way toward successful clinical translation. PMID:25735289

IBEX: an open infrastructure software platform to facilitate collaborative work in radiomics.

PubMed

Zhang, Lifei; Fried, David V; Fave, Xenia J; Hunter, Luke A; Yang, Jinzhong; Court, Laurence E

2015-03-01

Radiomics, which is the high-throughput extraction and analysis of quantitative image features, has been shown to have considerable potential to quantify the tumor phenotype. However, at present, a lack of software infrastructure has impeded the development of radiomics and its applications. Therefore, the authors developed the imaging biomarker explorer (IBEX), an open infrastructure software platform that flexibly supports common radiomics workflow tasks such as multimodality image data import and review, development of feature extraction algorithms, model validation, and consistent data sharing among multiple institutions. The IBEX software package was developed using the MATLAB and c/c++ programming languages. The software architecture deploys the modern model-view-controller, unit testing, and function handle programming concepts to isolate each quantitative imaging analysis task, to validate if their relevant data and algorithms are fit for use, and to plug in new modules. On one hand, IBEX is self-contained and ready to use: it has implemented common data importers, common image filters, and common feature extraction algorithms. On the other hand, IBEX provides an integrated development environment on top of MATLAB and c/c++, so users are not limited to its built-in functions. In the IBEX developer studio, users can plug in, debug, and test new algorithms, extending IBEX's functionality. IBEX also supports quality assurance for data and feature algorithms: image data, regions of interest, and feature algorithm-related data can be reviewed, validated, and/or modified. More importantly, two key elements in collaborative workflows, the consistency of data sharing and the reproducibility of calculation result, are embedded in the IBEX workflow: image data, feature algorithms, and model validation including newly developed ones from different users can be easily and consistently shared so that results can be more easily reproduced between institutions. Researchers with a variety of technical skill levels, including radiation oncologists, physicists, and computer scientists, have found the IBEX software to be intuitive, powerful, and easy to use. IBEX can be run at any computer with the windows operating system and 1GB RAM. The authors fully validated the implementation of all importers, preprocessing algorithms, and feature extraction algorithms. Windows version 1.0 beta of stand-alone IBEX and IBEX's source code can be downloaded. The authors successfully implemented IBEX, an open infrastructure software platform that streamlines common radiomics workflow tasks. Its transparency, flexibility, and portability can greatly accelerate the pace of radiomics research and pave the way toward successful clinical translation.

Design requirements and development of an airborne descent path definition algorithm for time navigation

NASA Technical Reports Server (NTRS)

Izumi, K. H.; Thompson, J. L.; Groce, J. L.; Schwab, R. W.

1986-01-01

The design requirements for a 4D path definition algorithm are described. These requirements were developed for the NASA ATOPS as an extension of the Local Flow Management/Profile Descent algorithm. They specify the processing flow, functional and data architectures, and system input requirements, and recommended the addition of a broad path revision (reinitialization) function capability. The document also summarizes algorithm design enhancements and the implementation status of the algorithm on an in-house PDP-11/70 computer. Finally, the requirements for the pilot-computer interfaces, the lateral path processor, and guidance and steering function are described.

Securing mobile ad hoc networks using danger theory-based artificial immune algorithm.

PubMed

Abdelhaq, Maha; Alsaqour, Raed; Abdelhaq, Shawkat

2015-01-01

A mobile ad hoc network (MANET) is a set of mobile, decentralized, and self-organizing nodes that are used in special cases, such as in the military. MANET properties render the environment of this network vulnerable to different types of attacks, including black hole, wormhole and flooding-based attacks. Flooding-based attacks are one of the most dangerous attacks that aim to consume all network resources and thus paralyze the functionality of the whole network. Therefore, the objective of this paper is to investigate the capability of a danger theory-based artificial immune algorithm called the mobile dendritic cell algorithm (MDCA) to detect flooding-based attacks in MANETs. The MDCA applies the dendritic cell algorithm (DCA) to secure the MANET with additional improvements. The MDCA is tested and validated using Qualnet v7.1 simulation tool. This work also introduces a new simulation module for a flooding attack called the resource consumption attack (RCA) using Qualnet v7.1. The results highlight the high efficiency of the MDCA in detecting RCAs in MANETs.

Securing Mobile Ad Hoc Networks Using Danger Theory-Based Artificial Immune Algorithm

PubMed Central

2015-01-01

A mobile ad hoc network (MANET) is a set of mobile, decentralized, and self-organizing nodes that are used in special cases, such as in the military. MANET properties render the environment of this network vulnerable to different types of attacks, including black hole, wormhole and flooding-based attacks. Flooding-based attacks are one of the most dangerous attacks that aim to consume all network resources and thus paralyze the functionality of the whole network. Therefore, the objective of this paper is to investigate the capability of a danger theory-based artificial immune algorithm called the mobile dendritic cell algorithm (MDCA) to detect flooding-based attacks in MANETs. The MDCA applies the dendritic cell algorithm (DCA) to secure the MANET with additional improvements. The MDCA is tested and validated using Qualnet v7.1 simulation tool. This work also introduces a new simulation module for a flooding attack called the resource consumption attack (RCA) using Qualnet v7.1. The results highlight the high efficiency of the MDCA in detecting RCAs in MANETs. PMID:25946001

Two-voice fundamental frequency estimation

NASA Astrophysics Data System (ADS)

de Cheveigné, Alain

2002-05-01

An algorithm is presented that estimates the fundamental frequencies of two concurrent voices or instruments. The algorithm models each voice as a periodic function of time, and jointly estimates both periods by cancellation according to a previously proposed method [de Cheveigné and Kawahara, Speech Commun. 27, 175-185 (1999)]. The new algorithm improves on the old in several respects; it allows an unrestricted search range, effectively avoids harmonic and subharmonic errors, is more accurate (it uses two-dimensional parabolic interpolation), and is computationally less costly. It remains subject to unavoidable errors when periods are in certain simple ratios and the task is inherently ambiguous. The algorithm is evaluated on a small database including speech, singing voice, and instrumental sounds. It can be extended in several ways; to decide the number of voices, to handle amplitude variations, and to estimate more than two voices (at the expense of increased processing cost and decreased reliability). It makes no use of instrument models, learned or otherwise, although it could usefully be combined with such models. [Work supported by the Cognitique programme of the French Ministry of Research and Technology.

Deploying swarm intelligence in medical imaging identifying metastasis, micro-calcifications and brain image segmentation.

PubMed

al-Rifaie, Mohammad Majid; Aber, Ahmed; Hemanth, Duraiswamy Jude

2015-12-01

This study proposes an umbrella deployment of swarm intelligence algorithm, such as stochastic diffusion search for medical imaging applications. After summarising the results of some previous works which shows how the algorithm assists in the identification of metastasis in bone scans and microcalcifications on mammographs, for the first time, the use of the algorithm in assessing the CT images of the aorta is demonstrated along with its performance in detecting the nasogastric tube in chest X-ray. The swarm intelligence algorithm presented in this study is adapted to address these particular tasks and its functionality is investigated by running the swarms on sample CT images and X-rays whose status have been determined by senior radiologists. In addition, a hybrid swarm intelligence-learning vector quantisation (LVQ) approach is proposed in the context of magnetic resonance (MR) brain image segmentation. The particle swarm optimisation is used to train the LVQ which eliminates the iteration-dependent nature of LVQ. The proposed methodology is used to detect the tumour regions in the abnormal MR brain images.

Inverse determination of the penalty parameter in penalized weighted least-squares algorithm for noise reduction of low-dose CBCT

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Jing; Guan, Huaiqun; Solberg, Timothy

2011-07-15

Purpose: A statistical projection restoration algorithm based on the penalized weighted least-squares (PWLS) criterion can substantially improve the image quality of low-dose CBCT images. The performance of PWLS is largely dependent on the choice of the penalty parameter. Previously, the penalty parameter was chosen empirically by trial and error. In this work, the authors developed an inverse technique to calculate the penalty parameter in PWLS for noise suppression of low-dose CBCT in image guided radiotherapy (IGRT). Methods: In IGRT, a daily CBCT is acquired for the same patient during a treatment course. In this work, the authors acquired the CBCTmore » with a high-mAs protocol for the first session and then a lower mAs protocol for the subsequent sessions. The high-mAs projections served as the goal (ideal) toward, which the low-mAs projections were to be smoothed by minimizing the PWLS objective function. The penalty parameter was determined through an inverse calculation of the derivative of the objective function incorporating both the high and low-mAs projections. Then the parameter obtained can be used for PWLS to smooth the noise in low-dose projections. CBCT projections for a CatPhan 600 and an anthropomorphic head phantom, as well as for a brain patient, were used to evaluate the performance of the proposed technique. Results: The penalty parameter in PWLS was obtained for each CBCT projection using the proposed strategy. The noise in the low-dose CBCT images reconstructed from the smoothed projections was greatly suppressed. Image quality in PWLS-processed low-dose CBCT was comparable to its corresponding high-dose CBCT. Conclusions: A technique was proposed to estimate the penalty parameter for PWLS algorithm. It provides an objective and efficient way to obtain the penalty parameter for image restoration algorithms that require predefined smoothing parameters.« less

GeneRIF indexing: sentence selection based on machine learning.

PubMed

Jimeno-Yepes, Antonio J; Sticco, J Caitlin; Mork, James G; Aronson, Alan R

2013-05-31

A Gene Reference Into Function (GeneRIF) describes novel functionality of genes. GeneRIFs are available from the National Center for Biotechnology Information (NCBI) Gene database. GeneRIF indexing is performed manually, and the intention of our work is to provide methods to support creating the GeneRIF entries. The creation of GeneRIF entries involves the identification of the genes mentioned in MEDLINE®; citations and the sentences describing a novel function. We have compared several learning algorithms and several features extracted or derived from MEDLINE sentences to determine if a sentence should be selected for GeneRIF indexing. Features are derived from the sentences or using mechanisms to augment the information provided by them: assigning a discourse label using a previously trained model, for example. We show that machine learning approaches with specific feature combinations achieve results close to one of the annotators. We have evaluated different feature sets and learning algorithms. In particular, Naïve Bayes achieves better performance with a selection of features similar to one used in related work, which considers the location of the sentence, the discourse of the sentence and the functional terminology in it. The current performance is at a level similar to human annotation and it shows that machine learning can be used to automate the task of sentence selection for GeneRIF annotation. The current experiments are limited to the human species. We would like to see how the methodology can be extended to other species, specifically the normalization of gene mentions in other species.

Functional Validation and Comparison Framework for EIT Lung Imaging

PubMed Central

Meybohm, Patrick; Weiler, Norbert; Frerichs, Inéz; Adler, Andy

2014-01-01

Introduction Electrical impedance tomography (EIT) is an emerging clinical tool for monitoring ventilation distribution in mechanically ventilated patients, for which many image reconstruction algorithms have been suggested. We propose an experimental framework to assess such algorithms with respect to their ability to correctly represent well-defined physiological changes. We defined a set of clinically relevant ventilation conditions and induced them experimentally in 8 pigs by controlling three ventilator settings (tidal volume, positive end-expiratory pressure and the fraction of inspired oxygen). In this way, large and discrete shifts in global and regional lung air content were elicited. Methods We use the framework to compare twelve 2D EIT reconstruction algorithms, including backprojection (the original and still most frequently used algorithm), GREIT (a more recent consensus algorithm for lung imaging), truncated singular value decomposition (TSVD), several variants of the one-step Gauss-Newton approach and two iterative algorithms. We consider the effects of using a 3D finite element model, assuming non-uniform background conductivity, noise modeling, reconstructing for electrode movement, total variation (TV) reconstruction, robust error norms, smoothing priors, and using difference vs. normalized difference data. Results and Conclusions Our results indicate that, while variation in appearance of images reconstructed from the same data is not negligible, clinically relevant parameters do not vary considerably among the advanced algorithms. Among the analysed algorithms, several advanced algorithms perform well, while some others are significantly worse. Given its vintage and ad-hoc formulation backprojection works surprisingly well, supporting the validity of previous studies in lung EIT. PMID:25110887

Fractal Landscape Algorithms for Environmental Simulations

NASA Astrophysics Data System (ADS)

Mao, H.; Moran, S.

2014-12-01

Natural science and geographical research are now able to take advantage of environmental simulations that more accurately test experimental hypotheses, resulting in deeper understanding. Experiments affected by the natural environment can benefit from 3D landscape simulations capable of simulating a variety of terrains and environmental phenomena. Such simulations can employ random terrain generation algorithms that dynamically simulate environments to test specific models against a variety of factors. Through the use of noise functions such as Perlin noise, Simplex noise, and diamond square algorithms, computers can generate simulations that model a variety of landscapes and ecosystems. This study shows how these algorithms work together to create realistic landscapes. By seeding values into the diamond square algorithm, one can control the shape of landscape. Perlin noise and Simplex noise are also used to simulate moisture and temperature. The smooth gradient created by coherent noise allows more realistic landscapes to be simulated. Terrain generation algorithms can be used in environmental studies and physics simulations. Potential studies that would benefit from simulations include the geophysical impact of flash floods or drought on a particular region and regional impacts on low lying area due to global warming and rising sea levels. Furthermore, terrain generation algorithms also serve as aesthetic tools to display landscapes (Google Earth), and simulate planetary landscapes. Hence, it can be used as a tool to assist science education. Algorithms used to generate these natural phenomena provide scientists a different approach in analyzing our world. The random algorithms used in terrain generation not only contribute to the generating the terrains themselves, but are also capable of simulating weather patterns.

Experimental evaluation of leaky least-mean-square algorithms for active noise reduction in communication headsets.

PubMed

Cartes, David A; Ray, Laura R; Collier, Robert D

2002-04-01

An adaptive leaky normalized least-mean-square (NLMS) algorithm has been developed to optimize stability and performance of active noise cancellation systems. The research addresses LMS filter performance issues related to insufficient excitation, nonstationary noise fields, and time-varying signal-to-noise ratio. The adaptive leaky NLMS algorithm is based on a Lyapunov tuning approach in which three candidate algorithms, each of which is a function of the instantaneous measured reference input, measurement noise variance, and filter length, are shown to provide varying degrees of tradeoff between stability and noise reduction performance. Each algorithm is evaluated experimentally for reduction of low frequency noise in communication headsets, and stability and noise reduction performance are compared with that of traditional NLMS and fixed-leakage NLMS algorithms. Acoustic measurements are made in a specially designed acoustic test cell which is based on the original work of Ryan et al. ["Enclosure for low frequency assessment of active noise reducing circumaural headsets and hearing protection," Can. Acoust. 21, 19-20 (1993)] and which provides a highly controlled and uniform acoustic environment. The stability and performance of the active noise reduction system, including a prototype communication headset, are investigated for a variety of noise sources ranging from stationary tonal noise to highly nonstationary measured F-16 aircraft noise over a 20 dB dynamic range. Results demonstrate significant improvements in stability of Lyapunov-tuned LMS algorithms over traditional leaky or nonleaky normalized algorithms, while providing noise reduction performance equivalent to that of the NLMS algorithm for idealized noise fields.

A Modified Kriging Method to Interpolate the Soil Moisture Measured by Wireless Sensor Network with the Aid of Remote Sensing Images

NASA Astrophysics Data System (ADS)

Zhang, J.; Liu, Q.; Li, X.; Niu, H.; Cai, E.

2015-12-01

In recent years, wireless sensor network (WSN) emerges to collect Earth observation data at relatively low cost and light labor load, while its observations are still point-data. To learn the spatial distribution of a land surface parameter, interpolating the point data is necessary. Taking soil moisture (SM) for example, its spatial distribution is critical information for agriculture management, hydrological and ecological researches. This study developed a method to interpolate the WSN-measured SM to acquire the spatial distribution in a 5km*5km study area, located in the middle reaches of HEIHE River, western China. As SM is related to many factors such as topology, soil type, vegetation and etc., even the WSN observation grid is not dense enough to reflect the SM distribution pattern. Our idea is to revise the traditional Kriging algorithm, introducing spectral variables, i.e., vegetation index (VI) and abledo, from satellite imagery as supplementary information to aid the interpolation. Thus, the new Extended-Kriging algorithm operates on the spatial & spectral combined space. To run the algorithm, first we need to estimate the SM variance function, which is also extended to the combined space. As the number of WSN samples in the study area is not enough to gather robust statistics, we have to assume that the SM variance function is invariant over time. So, the variance function is estimated from a SM map, derived from the airborne CASI/TASI images acquired in July 10, 2012, and then applied to interpolate WSN data in that season. Data analysis indicates that the new algorithm can provide more details to the variation of land SM. Then, the Leave-one-out cross-validation is adopted to estimate the interpolation accuracy. Although a reasonable accuracy can be achieved, the result is not yet satisfactory. Besides improving the algorithm, the uncertainties in WSN measurements may also need to be controlled in our further work.

A wavelet based method for automatic detection of slow eye movements: a pilot study.

PubMed

Magosso, Elisa; Provini, Federica; Montagna, Pasquale; Ursino, Mauro

2006-11-01

Electro-oculographic (EOG) activity during the wake-sleep transition is characterized by the appearance of slow eye movements (SEM). The present work describes an algorithm for the automatic localisation of SEM events from EOG recordings. The algorithm is based on a wavelet multiresolution analysis of the difference between right and left EOG tracings, and includes three main steps: (i) wavelet decomposition down to 10 detail levels (i.e., 10 scales), using Daubechies order 4 wavelet; (ii) computation of energy in 0.5s time steps at any level of decomposition; (iii) construction of a non-linear discriminant function expressing the relative energy of high-scale details to both high- and low-scale details. The main assumption is that the value of the discriminant function increases above a given threshold during SEM episodes due to energy redistribution toward higher scales. Ten EOG recordings from ten male patients with obstructive sleep apnea syndrome were used. All tracings included a period from pre-sleep wakefulness to stage 2 sleep. Two experts inspected the tracings separately to score SEMs. A reference set of SEM (gold standard) were obtained by joint examination by both experts. Parameters of the discriminant function were assigned on three tracings (design set) to minimize the disagreement between the system classification and classification by the two experts; the algorithm was then tested on the remaining seven tracings (test set). Results show that the agreement between the algorithm and the gold standard was 80.44+/-4.09%, the sensitivity of the algorithm was 67.2+/-7.37% and the selectivity 83.93+/-8.65%. However, most errors were not caused by an inability of the system to detect intervals with SEM activity against NON-SEM intervals, but were due to a different localisation of the beginning and end of some SEM episodes. The proposed method may be a valuable tool for computerized EOG analysis.

Clinical evaluation of semi-automatic open-source algorithmic software segmentation of the mandibular bone: Practical feasibility and assessment of a new course of action.

PubMed

Wallner, Jürgen; Hochegger, Kerstin; Chen, Xiaojun; Mischak, Irene; Reinbacher, Knut; Pau, Mauro; Zrnc, Tomislav; Schwenzer-Zimmerer, Katja; Zemann, Wolfgang; Schmalstieg, Dieter; Egger, Jan

2018-01-01

Computer assisted technologies based on algorithmic software segmentation are an increasing topic of interest in complex surgical cases. However-due to functional instability, time consuming software processes, personnel resources or licensed-based financial costs many segmentation processes are often outsourced from clinical centers to third parties and the industry. Therefore, the aim of this trial was to assess the practical feasibility of an easy available, functional stable and licensed-free segmentation approach to be used in the clinical practice. In this retrospective, randomized, controlled trail the accuracy and accordance of the open-source based segmentation algorithm GrowCut was assessed through the comparison to the manually generated ground truth of the same anatomy using 10 CT lower jaw data-sets from the clinical routine. Assessment parameters were the segmentation time, the volume, the voxel number, the Dice Score and the Hausdorff distance. Overall semi-automatic GrowCut segmentation times were about one minute. Mean Dice Score values of over 85% and Hausdorff Distances below 33.5 voxel could be achieved between the algorithmic GrowCut-based segmentations and the manual generated ground truth schemes. Statistical differences between the assessment parameters were not significant (p<0.05) and correlation coefficients were close to the value one (r > 0.94) for any of the comparison made between the two groups. Complete functional stable and time saving segmentations with high accuracy and high positive correlation could be performed by the presented interactive open-source based approach. In the cranio-maxillofacial complex the used method could represent an algorithmic alternative for image-based segmentation in the clinical practice for e.g. surgical treatment planning or visualization of postoperative results and offers several advantages. Due to an open-source basis the used method could be further developed by other groups or specialists. Systematic comparisons to other segmentation approaches or with a greater data amount are areas of future works.

A traveling salesman approach for predicting protein functions.

PubMed

Johnson, Olin; Liu, Jing

2006-10-12

Protein-protein interaction information can be used to predict unknown protein functions and to help study biological pathways. Here we present a new approach utilizing the classic Traveling Salesman Problem to study the protein-protein interactions and to predict protein functions in budding yeast Saccharomyces cerevisiae. We apply the global optimization tool from combinatorial optimization algorithms to cluster the yeast proteins based on the global protein interaction information. We then use this clustering information to help us predict protein functions. We use our algorithm together with the direct neighbor algorithm 1 on characterized proteins and compare the prediction accuracy of the two methods. We show our algorithm can produce better predictions than the direct neighbor algorithm, which only considers the immediate neighbors of the query protein. Our method is a promising one to be used as a general tool to predict functions of uncharacterized proteins and a successful sample of using computer science knowledge and algorithms to study biological problems.

A traveling salesman approach for predicting protein functions

PubMed Central

Johnson, Olin; Liu, Jing

2006-01-01

Background Protein-protein interaction information can be used to predict unknown protein functions and to help study biological pathways. Results Here we present a new approach utilizing the classic Traveling Salesman Problem to study the protein-protein interactions and to predict protein functions in budding yeast Saccharomyces cerevisiae. We apply the global optimization tool from combinatorial optimization algorithms to cluster the yeast proteins based on the global protein interaction information. We then use this clustering information to help us predict protein functions. We use our algorithm together with the direct neighbor algorithm [1] on characterized proteins and compare the prediction accuracy of the two methods. We show our algorithm can produce better predictions than the direct neighbor algorithm, which only considers the immediate neighbors of the query protein. Conclusion Our method is a promising one to be used as a general tool to predict functions of uncharacterized proteins and a successful sample of using computer science knowledge and algorithms to study biological problems. PMID:17147783

Families of Graph Algorithms: SSSP Case Study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kanewala Appuhamilage, Thejaka Amila Jay; Zalewski, Marcin J.; Lumsdaine, Andrew

2017-08-28

Single-Source Shortest Paths (SSSP) is a well-studied graph problem. Examples of SSSP algorithms include the original Dijkstra’s algorithm and the parallel Δ-stepping and KLA-SSSP algorithms. In this paper, we use a novel Abstract Graph Machine (AGM) model to show that all these algorithms share a common logic and differ from one another by the order in which they perform work. We use the AGM model to thoroughly analyze the family of algorithms that arises from the common logic. We start with the basic algorithm without any ordering (Chaotic), and then we derive the existing and new algorithms by methodically exploringmore » semantic and spatial ordering of work. Our experimental results show that new derived algorithms show better performance than the existing distributed memory parallel algorithms, especially at higher scales.« less

A study on the performance comparison of metaheuristic algorithms on the learning of neural networks

NASA Astrophysics Data System (ADS)

Lai, Kee Huong; Zainuddin, Zarita; Ong, Pauline

2017-08-01

The learning or training process of neural networks entails the task of finding the most optimal set of parameters, which includes translation vectors, dilation parameter, synaptic weights, and bias terms. Apart from the traditional gradient descent-based methods, metaheuristic methods can also be used for this learning purpose. Since the inception of genetic algorithm half a century ago, the last decade witnessed the explosion of a variety of novel metaheuristic algorithms, such as harmony search algorithm, bat algorithm, and whale optimization algorithm. Despite the proof of the no free lunch theorem in the discipline of optimization, a survey in the literature of machine learning gives contrasting results. Some researchers report that certain metaheuristic algorithms are superior to the others, whereas some others argue that different metaheuristic algorithms give comparable performance. As such, this paper aims to investigate if a certain metaheuristic algorithm will outperform the other algorithms. In this work, three metaheuristic algorithms, namely genetic algorithms, particle swarm optimization, and harmony search algorithm are considered. The algorithms are incorporated in the learning of neural networks and their classification results on the benchmark UCI machine learning data sets are compared. It is found that all three metaheuristic algorithms give similar and comparable performance, as captured in the average overall classification accuracy. The results corroborate the findings reported in the works done by previous researchers. Several recommendations are given, which include the need of statistical analysis to verify the results and further theoretical works to support the obtained empirical results.

Roadmap of Advanced GNC and Image Processing Algorithms for Fully Autonomous MSR-Like Rendezvous Missions

NASA Astrophysics Data System (ADS)

Strippoli, L. S.; Gonzalez-Arjona, D. G.

2018-04-01

GMV extensively worked in many activities aimed at developing, validating, and verifying up to TRL-6 advanced GNC and IP algorithms for Mars Sample Return rendezvous working under different ESA contracts on the development of advanced algorithms for VBN sensor.

Implementation of digital image encryption algorithm using logistic function and DNA encoding

NASA Astrophysics Data System (ADS)

Suryadi, MT; Satria, Yudi; Fauzi, Muhammad

2018-03-01

Cryptography is a method to secure information that might be in form of digital image. Based on past research, in order to increase security level of chaos based encryption algorithm and DNA based encryption algorithm, encryption algorithm using logistic function and DNA encoding was proposed. Digital image encryption algorithm using logistic function and DNA encoding use DNA encoding to scramble the pixel values into DNA base and scramble it in DNA addition, DNA complement, and XOR operation. The logistic function in this algorithm used as random number generator needed in DNA complement and XOR operation. The result of the test show that the PSNR values of cipher images are 7.98-7.99 bits, the entropy values are close to 8, the histogram of cipher images are uniformly distributed and the correlation coefficient of cipher images are near 0. Thus, the cipher image can be decrypted perfectly and the encryption algorithm has good resistance to entropy attack and statistical attack.

Retooling Laser Speckle Contrast Analysis Algorithm to Enhance Non-Invasive High Resolution Laser Speckle Functional Imaging of Cutaneous Microcirculation

NASA Astrophysics Data System (ADS)

Gnyawali, Surya C.; Blum, Kevin; Pal, Durba; Ghatak, Subhadip; Khanna, Savita; Roy, Sashwati; Sen, Chandan K.

2017-01-01

Cutaneous microvasculopathy complicates wound healing. Functional assessment of gated individual dermal microvessels is therefore of outstanding interest. Functional performance of laser speckle contrast imaging (LSCI) systems is compromised by motion artefacts. To address such weakness, post-processing of stacked images is reported. We report the first post-processing of binary raw data from a high-resolution LSCI camera. Sharp images of low-flowing microvessels were enabled by introducing inverse variance in conjunction with speckle contrast in Matlab-based program code. Extended moving window averaging enhanced signal-to-noise ratio. Functional quantitative study of blood flow kinetics was performed on single gated microvessels using a free hand tool. Based on detection of flow in low-flow microvessels, a new sharp contrast image was derived. Thus, this work presents the first distinct image with quantitative microperfusion data from gated human foot microvasculature. This versatile platform is applicable to study a wide range of tissue systems including fine vascular network in murine brain without craniotomy as well as that in the murine dorsal skin. Importantly, the algorithm reported herein is hardware agnostic and is capable of post-processing binary raw data from any camera source to improve the sensitivity of functional flow data above and beyond standard limits of the optical system.

Retooling Laser Speckle Contrast Analysis Algorithm to Enhance Non-Invasive High Resolution Laser Speckle Functional Imaging of Cutaneous Microcirculation

PubMed Central

Gnyawali, Surya C.; Blum, Kevin; Pal, Durba; Ghatak, Subhadip; Khanna, Savita; Roy, Sashwati; Sen, Chandan K.

2017-01-01

Cutaneous microvasculopathy complicates wound healing. Functional assessment of gated individual dermal microvessels is therefore of outstanding interest. Functional performance of laser speckle contrast imaging (LSCI) systems is compromised by motion artefacts. To address such weakness, post-processing of stacked images is reported. We report the first post-processing of binary raw data from a high-resolution LSCI camera. Sharp images of low-flowing microvessels were enabled by introducing inverse variance in conjunction with speckle contrast in Matlab-based program code. Extended moving window averaging enhanced signal-to-noise ratio. Functional quantitative study of blood flow kinetics was performed on single gated microvessels using a free hand tool. Based on detection of flow in low-flow microvessels, a new sharp contrast image was derived. Thus, this work presents the first distinct image with quantitative microperfusion data from gated human foot microvasculature. This versatile platform is applicable to study a wide range of tissue systems including fine vascular network in murine brain without craniotomy as well as that in the murine dorsal skin. Importantly, the algorithm reported herein is hardware agnostic and is capable of post-processing binary raw data from any camera source to improve the sensitivity of functional flow data above and beyond standard limits of the optical system. PMID:28106129

Genetic Algorithm for Initial Orbit Determination with Too Short Arc (Continued)

NASA Astrophysics Data System (ADS)

Li, X. R.; Wang, X.

2016-03-01

When using the genetic algorithm to solve the problem of too-short-arc (TSA) determination, due to the difference of computing processes between the genetic algorithm and classical method, the methods for outliers editing are no longer applicable. In the genetic algorithm, the robust estimation is acquired by means of using different loss functions in the fitness function, then the outlier problem of TSAs is solved. Compared with the classical method, the application of loss functions in the genetic algorithm is greatly simplified. Through the comparison of results of different loss functions, it is clear that the methods of least median square and least trimmed square can greatly improve the robustness of TSAs, and have a high breakdown point.

Learning Time-Varying Coverage Functions

PubMed Central

Du, Nan; Liang, Yingyu; Balcan, Maria-Florina; Song, Le

2015-01-01

Coverage functions are an important class of discrete functions that capture the law of diminishing returns arising naturally from applications in social network analysis, machine learning, and algorithmic game theory. In this paper, we propose a new problem of learning time-varying coverage functions, and develop a novel parametrization of these functions using random features. Based on the connection between time-varying coverage functions and counting processes, we also propose an efficient parameter learning algorithm based on likelihood maximization, and provide a sample complexity analysis. We applied our algorithm to the influence function estimation problem in information diffusion in social networks, and show that with few assumptions about the diffusion processes, our algorithm is able to estimate influence significantly more accurately than existing approaches on both synthetic and real world data. PMID:25960624

Learning Time-Varying Coverage Functions.

PubMed

Du, Nan; Liang, Yingyu; Balcan, Maria-Florina; Song, Le

2014-12-08

Coverage functions are an important class of discrete functions that capture the law of diminishing returns arising naturally from applications in social network analysis, machine learning, and algorithmic game theory. In this paper, we propose a new problem of learning time-varying coverage functions, and develop a novel parametrization of these functions using random features. Based on the connection between time-varying coverage functions and counting processes, we also propose an efficient parameter learning algorithm based on likelihood maximization, and provide a sample complexity analysis. We applied our algorithm to the influence function estimation problem in information diffusion in social networks, and show that with few assumptions about the diffusion processes, our algorithm is able to estimate influence significantly more accurately than existing approaches on both synthetic and real world data.

An Evaluation of the Sniffer Global Optimization Algorithm Using Standard Test Functions

NASA Astrophysics Data System (ADS)

Butler, Roger A. R.; Slaminka, Edward E.

1992-03-01

The performance of Sniffer—a new global optimization algorithm—is compared with that of Simulated Annealing. Using the number of function evaluations as a measure of efficiency, the new algorithm is shown to be significantly better at finding the global minimum of seven standard test functions. Several of the test functions used have many local minima and very steep walls surrounding the global minimum. Such functions are intended to thwart global minimization algorithms.

Comparison of cyclic correlation algorithm implemented in matlab and python

NASA Astrophysics Data System (ADS)

Carr, Richard; Whitney, James

Simulation is a necessary step for all engineering projects. Simulation gives the engineers an approximation of how their devices will perform under different circumstances, without hav-ing to build, or before building a physical prototype. This is especially true for space bound devices, i.e., space communication systems, where the impact of system malfunction or failure is several orders of magnitude over that of terrestrial applications. Therefore having a reliable simulation tool is key in developing these devices and systems. Math Works Matrix Laboratory (MATLAB) is a matrix based software used by scientists and engineers to solve problems and perform complex simulations. MATLAB has a number of applications in a wide variety of fields which include communications, signal processing, image processing, mathematics, eco-nomics and physics. Because of its many uses MATLAB has become the preferred software for many engineers; it is also very expensive, especially for students and startups. One alternative to MATLAB is Python. The Python is a powerful, easy to use, open source programming environment that can be used to perform many of the same functions as MATLAB. Python programming environment has been steadily gaining popularity in niche programming circles. While there are not as many function included in the software as MATLAB, there are many open source functions that have been developed that are available to be downloaded for free. This paper illustrates how Python can implement the cyclic correlation algorithm and com-pares the results to the cyclic correlation algorithm implemented in the MATLAB environment. Some of the characteristics to be compared are the accuracy and precision of the results, and the length of the programs. The paper will demonstrate that Python is capable of performing simulations of complex algorithms such cyclic correlation.

Feasibility of a Smartphone-Based Exercise Program for Office Workers With Neck Pain: An Individualized Approach Using a Self-Classification Algorithm.

PubMed

Lee, Minyoung; Lee, Sang Heon; Kim, TaeYeong; Yoo, Hyun-Joon; Kim, Sung Hoon; Suh, Dong-Won; Son, Jaebum; Yoon, BumChul

2017-01-01

To explore the feasibility of a newly developed smartphone-based exercise program with an embedded self-classification algorithm for office workers with neck pain, by examining its effect on the pain intensity, functional disability, quality of life, fear avoidance, and cervical range of motion (ROM). Single-group, repeated-measures design. The laboratory and participants' home and work environments. Offices workers with neck pain (N=23; mean age ± SD, 28.13±2.97y; 13 men). Participants were classified as having 1 of 4 types of neck pain through a self-classification algorithm implemented as a smartphone application, and conducted corresponding exercise programs for 10 to 12min/d, 3d/wk, for 8 weeks. The visual analog scale (VAS), Neck Disability Index (NDI), Medical Outcomes Study 36-Item Short-Form Health Survey (SF-36), Fear-Avoidance Beliefs Questionnaire (FABQ), and cervical ROM were measured at baseline and postintervention. The VAS (P<.001) and NDI score (P<.001) indicated significant improvements in pain intensity and functional disability. Quality of life showed significant improvements in the physical functioning (P=.007), bodily pain (P=.018), general health (P=.022), vitality (P=.046), and physical component scores (P=.002) of the SF-36. The FABQ, cervical ROM, and mental component score of the SF-36 showed no significant improvements. The smartphone-based exercise program with an embedded self-classification algorithm improves the pain intensity and perceived physical health of office workers with neck pain, although not enough to affect their mental and emotional states. Copyright © 2016 American Congress of Rehabilitation Medicine. Published by Elsevier Inc. All rights reserved.

Speed and convergence properties of gradient algorithms for optimization of IMRT.

PubMed

Zhang, Xiaodong; Liu, Helen; Wang, Xiaochun; Dong, Lei; Wu, Qiuwen; Mohan, Radhe

2004-05-01

Gradient algorithms are the most commonly employed search methods in the routine optimization of IMRT plans. It is well known that local minima can exist for dose-volume-based and biology-based objective functions. The purpose of this paper is to compare the relative speed of different gradient algorithms, to investigate the strategies for accelerating the optimization process, to assess the validity of these strategies, and to study the convergence properties of these algorithms for dose-volume and biological objective functions. With these aims in mind, we implemented Newton's, conjugate gradient (CG), and the steepest decent (SD) algorithms for dose-volume- and EUD-based objective functions. Our implementation of Newton's algorithm approximates the second derivative matrix (Hessian) by its diagonal. The standard SD algorithm and the CG algorithm with "line minimization" were also implemented. In addition, we investigated the use of a variation of the CG algorithm, called the "scaled conjugate gradient" (SCG) algorithm. To accelerate the optimization process, we investigated the validity of the use of a "hybrid optimization" strategy, in which approximations to calculated dose distributions are used during most of the iterations. Published studies have indicated that getting trapped in local minima is not a significant problem. To investigate this issue further, we first obtained, by trial and error, and starting with uniform intensity distributions, the parameters of the dose-volume- or EUD-based objective functions which produced IMRT plans that satisfied the clinical requirements. Using the resulting optimized intensity distributions as the initial guess, we investigated the possibility of getting trapped in a local minimum. For most of the results presented, we used a lung cancer case. To illustrate the generality of our methods, the results for a prostate case are also presented. For both dose-volume and EUD based objective functions, Newton's method far outperforms other algorithms in terms of speed. The SCG algorithm, which avoids expensive "line minimization," can speed up the standard CG algorithm by at least a factor of 2. For the same initial conditions, all algorithms converge essentially to the same plan. However, we demonstrate that for any of the algorithms studied, starting with previously optimized intensity distributions as the initial guess but for different objective function parameters, the solution frequently gets trapped in local minima. We found that the initial intensity distribution obtained from IMRT optimization utilizing objective function parameters, which favor a specific anatomic structure, would lead to a local minimum corresponding to that structure. Our results indicate that from among the gradient algorithms tested, Newton's method appears to be the fastest by far. Different gradient algorithms have the same convergence properties for dose-volume- and EUD-based objective functions. The hybrid dose calculation strategy is valid and can significantly accelerate the optimization process. The degree of acceleration achieved depends on the type of optimization problem being addressed (e.g., IMRT optimization, intensity modulated beam configuration optimization, or objective function parameter optimization). Under special conditions, gradient algorithms will get trapped in local minima, and reoptimization, starting with the results of previous optimization, will lead to solutions that are generally not significantly different from the local minimum.

Quantum algorithms on Walsh transform and Hamming distance for Boolean functions

NASA Astrophysics Data System (ADS)

Xie, Zhengwei; Qiu, Daowen; Cai, Guangya

2018-06-01

Walsh spectrum or Walsh transform is an alternative description of Boolean functions. In this paper, we explore quantum algorithms to approximate the absolute value of Walsh transform W_f at a single point z0 (i.e., |W_f(z0)|) for n-variable Boolean functions with probability at least 8/π 2 using the number of O(1/|W_f(z_{0)|ɛ }) queries, promised that the accuracy is ɛ , while the best known classical algorithm requires O(2n) queries. The Hamming distance between Boolean functions is used to study the linearity testing and other important problems. We take advantage of Walsh transform to calculate the Hamming distance between two n-variable Boolean functions f and g using O(1) queries in some cases. Then, we exploit another quantum algorithm which converts computing Hamming distance between two Boolean functions to quantum amplitude estimation (i.e., approximate counting). If Ham(f,g)=t≠0, we can approximately compute Ham( f, g) with probability at least 2/3 by combining our algorithm and {Approx-Count(f,ɛ ) algorithm} using the expected number of Θ( √{N/(\\lfloor ɛ t\\rfloor +1)}+√{t(N-t)}/\\lfloor ɛ t\\rfloor +1) queries, promised that the accuracy is ɛ . Moreover, our algorithm is optimal, while the exact query complexity for the above problem is Θ(N) and the query complexity with the accuracy ɛ is O(1/ɛ 2N/(t+1)) in classical algorithm, where N=2n. Finally, we present three exact quantum query algorithms for two promise problems on Hamming distance using O(1) queries, while any classical deterministic algorithm solving the problem uses Ω(2n) queries.

Advanced time integration algorithms for dislocation dynamics simulations of work hardening

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sills, Ryan B.; Aghaei, Amin; Cai, Wei

Efficient time integration is a necessity for dislocation dynamics simulations of work hardening to achieve experimentally relevant strains. In this work, an efficient time integration scheme using a high order explicit method with time step subcycling and a newly-developed collision detection algorithm are evaluated. First, time integrator performance is examined for an annihilating Frank–Read source, showing the effects of dislocation line collision. The integrator with subcycling is found to significantly out-perform other integration schemes. The performance of the time integration and collision detection algorithms is then tested in a work hardening simulation. The new algorithms show a 100-fold speed-up relativemore » to traditional schemes. As a result, subcycling is shown to improve efficiency significantly while maintaining an accurate solution, and the new collision algorithm allows an arbitrarily large time step size without missing collisions.« less

Advanced time integration algorithms for dislocation dynamics simulations of work hardening

DOE PAGES

Sills, Ryan B.; Aghaei, Amin; Cai, Wei

2016-04-25

Efficient time integration is a necessity for dislocation dynamics simulations of work hardening to achieve experimentally relevant strains. In this work, an efficient time integration scheme using a high order explicit method with time step subcycling and a newly-developed collision detection algorithm are evaluated. First, time integrator performance is examined for an annihilating Frank–Read source, showing the effects of dislocation line collision. The integrator with subcycling is found to significantly out-perform other integration schemes. The performance of the time integration and collision detection algorithms is then tested in a work hardening simulation. The new algorithms show a 100-fold speed-up relativemore » to traditional schemes. As a result, subcycling is shown to improve efficiency significantly while maintaining an accurate solution, and the new collision algorithm allows an arbitrarily large time step size without missing collisions.« less

A three-way parallel ICA approach to analyze links among genetics, brain structure and brain function.

PubMed

Vergara, Victor M; Ulloa, Alvaro; Calhoun, Vince D; Boutte, David; Chen, Jiayu; Liu, Jingyu

2014-09-01

Multi-modal data analysis techniques, such as the Parallel Independent Component Analysis (pICA), are essential in neuroscience, medical imaging and genetic studies. The pICA algorithm allows the simultaneous decomposition of up to two data modalities achieving better performance than separate ICA decompositions and enabling the discovery of links between modalities. However, advances in data acquisition techniques facilitate the collection of more than two data modalities from each subject. Examples of commonly measured modalities include genetic information, structural magnetic resonance imaging (MRI) and functional MRI. In order to take full advantage of the available data, this work extends the pICA approach to incorporate three modalities in one comprehensive analysis. Simulations demonstrate the three-way pICA performance in identifying pairwise links between modalities and estimating independent components which more closely resemble the true sources than components found by pICA or separate ICA analyses. In addition, the three-way pICA algorithm is applied to real experimental data obtained from a study that investigate genetic effects on alcohol dependence. Considered data modalities include functional MRI (contrast images during alcohol exposure paradigm), gray matter concentration images from structural MRI and genetic single nucleotide polymorphism (SNP). The three-way pICA approach identified links between a SNP component (pointing to brain function and mental disorder associated genes, including BDNF, GRIN2B and NRG1), a functional component related to increased activation in the precuneus area, and a gray matter component comprising part of the default mode network and the caudate. Although such findings need further verification, the simulation and in-vivo results validate the three-way pICA algorithm presented here as a useful tool in biomedical data fusion applications. Copyright © 2014 Elsevier Inc. All rights reserved.

Location of coating defects and assessment of level of cathodic protection on underground pipelines using AC impedance, deterministic and non-deterministic models

NASA Astrophysics Data System (ADS)

Castaneda-Lopez, Homero

A methodology for detecting and locating defects or discontinuities on the outside covering of coated metal underground pipelines subjected to cathodic protection has been addressed. On the basis of wide range AC impedance signals for various frequencies applied to a steel-coated pipeline system and by measuring its corresponding transfer function under several laboratory simulation scenarios, a physical laboratory setup of an underground cathodic-protected, coated pipeline was built. This model included different variables and elements that exist under real conditions, such as soil resistivity, soil chemical composition, defect (holiday) location in the pipeline covering, defect area and geometry, and level of cathodic protection. The AC impedance data obtained under different working conditions were used to fit an electrical transmission line model. This model was then used as a tool to fit the impedance signal for different experimental conditions and to establish trends in the impedance behavior without the necessity of further experimental work. However, due to the chaotic nature of the transfer function response of this system under several conditions, it is believed that non-deterministic models based on pattern recognition algorithms are suitable for field condition analysis. A non-deterministic approach was used for experimental analysis by applying an artificial neural network (ANN) algorithm based on classification analysis capable of studying the pipeline system and differentiating the variables that can change impedance conditions. These variables include level of cathodic protection, location of discontinuities (holidays), and severity of corrosion. This work demonstrated a proof-of-concept for a well-known technique and a novel algorithm capable of classifying impedance data for experimental results to predict the exact location of the active holidays and defects on the buried pipelines. Laboratory findings from this procedure are promising, and efforts to develop it for field conditions should continue.

A Fast Algorithm for the Convolution of Functions with Compact Support Using Fourier Extensions

DOE PAGES

Xu, Kuan; Austin, Anthony P.; Wei, Ke

2017-12-21

In this paper, we present a new algorithm for computing the convolution of two compactly supported functions. The algorithm approximates the functions to be convolved using Fourier extensions and then uses the fast Fourier transform to efficiently compute Fourier extension approximations to the pieces of the result. Finally, the complexity of the algorithm is O(N(log N) 2), where N is the number of degrees of freedom used in each of the Fourier extensions.

A Fast Algorithm for the Convolution of Functions with Compact Support Using Fourier Extensions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xu, Kuan; Austin, Anthony P.; Wei, Ke

In this paper, we present a new algorithm for computing the convolution of two compactly supported functions. The algorithm approximates the functions to be convolved using Fourier extensions and then uses the fast Fourier transform to efficiently compute Fourier extension approximations to the pieces of the result. Finally, the complexity of the algorithm is O(N(log N) 2), where N is the number of degrees of freedom used in each of the Fourier extensions.

Rheological Models in the Time-Domain Modeling of Seismic Motion

NASA Astrophysics Data System (ADS)

Moczo, P.; Kristek, J.

2004-12-01

The time-domain stress-strain relation in a viscoelastic medium has a form of the convolutory integral which is numerically intractable. This was the reason for the oversimplified models of attenuation in the time-domain seismic wave propagation and earthquake motion modeling. In their pioneering work, Day and Minster (1984) showed the way how to convert the integral into numerically tractable differential form in the case of a general viscoelastic modulus. In response to the work by Day and Minster, Emmerich and Korn (1987) suggested using the rheology of their generalized Maxwell body (GMB) while Carcione et al. (1988) suggested using the generalized Zener body (GZB). The viscoelastic moduli of both rheological models have a form of the rational function and thus the differential form of the stress-strain relation is rather easy to obtain. After the papers by Emmerich and Korn and Carcione et al. numerical modelers decided either for the GMB or GZB rheology and developed 'non-communicating' algorithms. In the many following papers the authors using the GMB never commented the GZB rheology and the corresponding algorithms, and the authors using the GZB never related their methods to the GMB rheology and algorithms. We analyze and compare both rheologies and the corresponding incorporations of the realistic attenuation into the time-domain computations. We then focus on the most recent staggered-grid finite-difference modeling, mainly on accounting for the material heterogeneity in the viscoelastic media, and the computational efficiency of the finite-difference algorithms.

Watershed modeling at the Savannah River Site.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vache, Kellie

2015-04-29

The overall goal of the work was the development of a watershed scale model of hydrological function for application to the US Department of Energy’s (DOE) Savannah River Site (SRS). The primary outcomes is a grid based hydrological modeling system that captures near surface runoff as well as groundwater recharge and contributions of groundwater to streams. The model includes a physically-based algorithm to capture both evaporation and transpiration from forestland.

Algorithms for Adaptation in Aerial Surveillance

DTIC Science & Technology

2002-03-01

In the brain small local structures can involve inhibition whereas more distant functional areas are less likely to have inhibition. This appeals to...and 2. retains a more conventional programming model [than the PDP approach]. The former is achieved by appealing to well understood ideas from...1980s. The statistical techniques used in our implementation of these ideas (GRAVA) are appealing to us for three reasons: 91 5.2. PRIOR WORK 1. GRAVA

Generalized Entropies and Legendre Duality

DTIC Science & Technology

2012-04-22

region because of their one-to-one functional relationship. The standard algorithm using projection of a polyhedron [29, 6] commonly works well to...coordinate system is chosen to realize the corresponding Voronoi diagrams. In this coordinate system with one extra complementary coordinate the polyhedron is...dually flat. Using this property, α-Voronoi diagrams on Rn+1+ is discussed in [31]. While both of the above methods require computation of the polyhedrons

Assessment of Data Fusion Algorithms for Earth Observation Change Detection Processes

PubMed Central

Molina, Iñigo; Martinez, Estibaliz; Morillo, Carmen; Velasco, Jesus; Jara, Alvaro

2016-01-01

In this work a parametric multi-sensor Bayesian data fusion approach and a Support Vector Machine (SVM) are used for a Change Detection problem. For this purpose two sets of SPOT5-PAN images have been used, which are in turn used for Change Detection Indices (CDIs) calculation. For minimizing radiometric differences, a methodology based on zonal “invariant features” is suggested. The choice of one or the other CDI for a change detection process is a subjective task as each CDI is probably more or less sensitive to certain types of changes. Likewise, this idea might be employed to create and improve a “change map”, which can be accomplished by means of the CDI’s informational content. For this purpose, information metrics such as the Shannon Entropy and “Specific Information” have been used to weight the changes and no-changes categories contained in a certain CDI and thus introduced in the Bayesian information fusion algorithm. Furthermore, the parameters of the probability density functions (pdf’s) that best fit the involved categories have also been estimated. Conversely, these considerations are not necessary for mapping procedures based on the discriminant functions of a SVM. This work has confirmed the capabilities of probabilistic information fusion procedure under these circumstances. PMID:27706048

Fast decision algorithms in low-power embedded processors for quality-of-service based connectivity of mobile sensors in heterogeneous wireless sensor networks.

PubMed

Jaraíz-Simón, María D; Gómez-Pulido, Juan A; Vega-Rodríguez, Miguel A; Sánchez-Pérez, Juan M

2012-01-01

When a mobile wireless sensor is moving along heterogeneous wireless sensor networks, it can be under the coverage of more than one network many times. In these situations, the Vertical Handoff process can happen, where the mobile sensor decides to change its connection from a network to the best network among the available ones according to their quality of service characteristics. A fitness function is used for the handoff decision, being desirable to minimize it. This is an optimization problem which consists of the adjustment of a set of weights for the quality of service. Solving this problem efficiently is relevant to heterogeneous wireless sensor networks in many advanced applications. Numerous works can be found in the literature dealing with the vertical handoff decision, although they all suffer from the same shortfall: a non-comparable efficiency. Therefore, the aim of this work is twofold: first, to develop a fast decision algorithm that explores the entire space of possible combinations of weights, searching that one that minimizes the fitness function; and second, to design and implement a system on chip architecture based on reconfigurable hardware and embedded processors to achieve several goals necessary for competitive mobile terminals: good performance, low power consumption, low economic cost, and small area integration.

Toward the identification of molecular cogs.

PubMed

Dziubiński, Maciej; Lesyng, Bogdan

2016-04-05

Computer simulations of molecular systems allow determination of microscopic interactions between individual atoms or groups of atoms, as well as studies of intramolecular motions. Nevertheless, description of structural transformations at the mezoscopic level and identification of causal relations associated with these transformations is very difficult. Structural and functional properties are related to free energy changes. Therefore, to better understand structural and functional properties of molecular systems, it is required to deepen our knowledge of free energy contributions arising from molecular subsystems in the course of structural transformations. The method presented in this work quantifies the energetic contribution of each pair of atoms to the total free energy change along a given collective variable. Next, with the help of a genetic clustering algorithm, the method proposes a division of the system into two groups of atoms referred to as molecular cogs. Atoms which cooperate to push the system forward along a collective variable are referred to as forward cogs, and those which work in the opposite direction as reverse cogs. The procedure was tested on several small molecules for which the genetic clustering algorithm successfully found optimal partitionings into molecular cogs. The primary result of the method is a plot depicting the energetic contributions of the identified molecular cogs to the total Potential of Mean Force (PMF) change. Case-studies presented in this work should help better understand the implications of our approach, and were intended to pave the way to a future, publicly available implementation. © 2015 Wiley Periodicals, Inc.

Selecting materialized views using random algorithm

NASA Astrophysics Data System (ADS)

Zhou, Lijuan; Hao, Zhongxiao; Liu, Chi

2007-04-01

The data warehouse is a repository of information collected from multiple possibly heterogeneous autonomous distributed databases. The information stored at the data warehouse is in form of views referred to as materialized views. The selection of the materialized views is one of the most important decisions in designing a data warehouse. Materialized views are stored in the data warehouse for the purpose of efficiently implementing on-line analytical processing queries. The first issue for the user to consider is query response time. So in this paper, we develop algorithms to select a set of views to materialize in data warehouse in order to minimize the total view maintenance cost under the constraint of a given query response time. We call it query_cost view_ selection problem. First, cost graph and cost model of query_cost view_ selection problem are presented. Second, the methods for selecting materialized views by using random algorithms are presented. The genetic algorithm is applied to the materialized views selection problem. But with the development of genetic process, the legal solution produced become more and more difficult, so a lot of solutions are eliminated and producing time of the solutions is lengthened in genetic algorithm. Therefore, improved algorithm has been presented in this paper, which is the combination of simulated annealing algorithm and genetic algorithm for the purpose of solving the query cost view selection problem. Finally, in order to test the function and efficiency of our algorithms experiment simulation is adopted. The experiments show that the given methods can provide near-optimal solutions in limited time and works better in practical cases. Randomized algorithms will become invaluable tools for data warehouse evolution.

Investigating the performance of neural network backpropagation algorithms for TEC estimations using South African GPS data

NASA Astrophysics Data System (ADS)

Habarulema, J. B.; McKinnell, L.-A.

2012-05-01

In this work, results obtained by investigating the application of different neural network backpropagation training algorithms are presented. This was done to assess the performance accuracy of each training algorithm in total electron content (TEC) estimations using identical datasets in models development and verification processes. Investigated training algorithms are standard backpropagation (SBP), backpropagation with weight delay (BPWD), backpropagation with momentum (BPM) term, backpropagation with chunkwise weight update (BPC) and backpropagation for batch (BPB) training. These five algorithms are inbuilt functions within the Stuttgart Neural Network Simulator (SNNS) and the main objective was to find out the training algorithm that generates the minimum error between the TEC derived from Global Positioning System (GPS) observations and the modelled TEC data. Another investigated algorithm is the MatLab based Levenberg-Marquardt backpropagation (L-MBP), which achieves convergence after the least number of iterations during training. In this paper, neural network (NN) models were developed using hourly TEC data (for 8 years: 2000-2007) derived from GPS observations over a receiver station located at Sutherland (SUTH) (32.38° S, 20.81° E), South Africa. Verification of the NN models for all algorithms considered was performed on both "seen" and "unseen" data. Hourly TEC values over SUTH for 2003 formed the "seen" dataset. The "unseen" dataset consisted of hourly TEC data for 2002 and 2008 over Cape Town (CPTN) (33.95° S, 18.47° E) and SUTH, respectively. The models' verification showed that all algorithms investigated provide comparable results statistically, but differ significantly in terms of time required to achieve convergence during input-output data training/learning. This paper therefore provides a guide to neural network users for choosing appropriate algorithms based on the availability of computation capabilities used for research.

Gaussian diffusion sinogram inpainting for X-ray CT metal artifact reduction.

PubMed

Peng, Chengtao; Qiu, Bensheng; Li, Ming; Guan, Yihui; Zhang, Cheng; Wu, Zhongyi; Zheng, Jian

2017-01-05

Metal objects implanted in the bodies of patients usually generate severe streaking artifacts in reconstructed images of X-ray computed tomography, which degrade the image quality and affect the diagnosis of disease. Therefore, it is essential to reduce these artifacts to meet the clinical demands. In this work, we propose a Gaussian diffusion sinogram inpainting metal artifact reduction algorithm based on prior images to reduce these artifacts for fan-beam computed tomography reconstruction. In this algorithm, prior information that originated from a tissue-classified prior image is used for the inpainting of metal-corrupted projections, and it is incorporated into a Gaussian diffusion function. The prior knowledge is particularly designed to locate the diffusion position and improve the sparsity of the subtraction sinogram, which is obtained by subtracting the prior sinogram of the metal regions from the original sinogram. The sinogram inpainting algorithm is implemented through an approach of diffusing prior energy and is then solved by gradient descent. The performance of the proposed metal artifact reduction algorithm is compared with two conventional metal artifact reduction algorithms, namely the interpolation metal artifact reduction algorithm and normalized metal artifact reduction algorithm. The experimental datasets used included both simulated and clinical datasets. By evaluating the results subjectively, the proposed metal artifact reduction algorithm causes fewer secondary artifacts than the two conventional metal artifact reduction algorithms, which lead to severe secondary artifacts resulting from impertinent interpolation and normalization. Additionally, the objective evaluation shows the proposed approach has the smallest normalized mean absolute deviation and the highest signal-to-noise ratio, indicating that the proposed method has produced the image with the best quality. No matter for the simulated datasets or the clinical datasets, the proposed algorithm has reduced the metal artifacts apparently.

Methods Development for Spectral Simplification of Room-Temperature Rotational Spectra

NASA Astrophysics Data System (ADS)

Kent, Erin B.; Shipman, Steven

2014-06-01

Room-temperature rotational spectra are dense and difficult to assign, and so we have been working to develop methods to accelerate this process. We have tested two different methods with our waveguide-based spectrometer, which operates from 8.7 to 26.5 GHz. The first method, based on previous work by Medvedev and De Lucia, was used to estimate lower state energies of transitions by performing relative intensity measurements at a range of temperatures between -20 and +50 °C. The second method employed hundreds of microwave-microwave double resonance measurements to determine level connectivity between rotational transitions. The relative intensity measurements were not particularly successful in this frequency range (the reasons for this will be discussed), but the information gleaned from the double-resonance measurements can be incorporated into other spectral search algorithms (such as autofit or genetic algorithm approaches) via scoring or penalty functions to help with the spectral assignment process. I.R. Medvedev, F.C. De Lucia, Astrophys. J. 656, 621-628 (2007).

PyBoolNet: a python package for the generation, analysis and visualization of boolean networks.

PubMed

Klarner, Hannes; Streck, Adam; Siebert, Heike

2017-03-01

The goal of this project is to provide a simple interface to working with Boolean networks. Emphasis is put on easy access to a large number of common tasks including the generation and manipulation of networks, attractor and basin computation, model checking and trap space computation, execution of established graph algorithms as well as graph drawing and layouts. P y B ool N et is a Python package for working with Boolean networks that supports simple access to model checking via N u SMV, standard graph algorithms via N etwork X and visualization via dot . In addition, state of the art attractor computation exploiting P otassco ASP is implemented. The package is function-based and uses only native Python and N etwork X data types. https://github.com/hklarner/PyBoolNet. hannes.klarner@fu-berlin.de. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Modal Identification of Tsing MA Bridge by Using Improved Eigensystem Realization Algorithm

NASA Astrophysics Data System (ADS)

QIN, Q.; LI, H. B.; QIAN, L. Z.; LAU, C.-K.

2001-10-01

This paper presents the results of research work on modal identification of Tsing Ma bridge ambient testing data by using an improved eigensystem realization algorithm. The testing was carried out before the bridge was open to traffic and after the completion of surfacing. Without traffic load, ambient excitations were much less intensive, and the bridge responses to such ambient excitation were also less intensive. Consequently, the bridge responses were significantly influenced by the random movement of heavy construction vehicles on the deck. To cut off noises in the testing data and make the ambient signals more stationary, the Chebyshev digital filter was used instead of the digital filter with a Hanning window. Random decrement (RD) functions were built to convert the ambient responses to free vibrations. An improved eigensystem realization algorithm was employed to improve the accuracy and the efficiency of modal identification. It uses cross-correlation functions ofRD functions to form the Hankel matrix instead of RD functions themselves and uses eigenvalue decomposition instead of singular value decomposition. The data for response accelerations were acquired group by group because of limited number of high-quality accelerometers and channels of data loggers available. The modes were identified group by group and then assembled by using response accelerations acquired at reference points to form modes of the complete bridge. Seventy-nine modes of the Tsing Ma bridge were identified, including five complex modes formed in accordance with unevenly distributed damping in the bridge. The identified modes in time domain were then compared with those identified in frequency domain and finite element analytical results.

PID controller tuning using metaheuristic optimization algorithms for benchmark problems

NASA Astrophysics Data System (ADS)

Gholap, Vishal; Naik Dessai, Chaitali; Bagyaveereswaran, V.

2017-11-01

This paper contributes to find the optimal PID controller parameters using particle swarm optimization (PSO), Genetic Algorithm (GA) and Simulated Annealing (SA) algorithm. The algorithms were developed through simulation of chemical process and electrical system and the PID controller is tuned. Here, two different fitness functions such as Integral Time Absolute Error and Time domain Specifications were chosen and applied on PSO, GA and SA while tuning the controller. The proposed Algorithms are implemented on two benchmark problems of coupled tank system and DC motor. Finally, comparative study has been done with different algorithms based on best cost, number of iterations and different objective functions. The closed loop process response for each set of tuned parameters is plotted for each system with each fitness function.

Hybrid artificial bee colony algorithm for parameter optimization of five-parameter bidirectional reflectance distribution function model.

PubMed

Wang, Qianqian; Zhao, Jing; Gong, Yong; Hao, Qun; Peng, Zhong

2017-11-20

A hybrid artificial bee colony (ABC) algorithm inspired by the best-so-far solution and bacterial chemotaxis was introduced to optimize the parameters of the five-parameter bidirectional reflectance distribution function (BRDF) model. To verify the performance of the hybrid ABC algorithm, we measured BRDF of three kinds of samples and simulated the undetermined parameters of the five-parameter BRDF model using the hybrid ABC algorithm and the genetic algorithm, respectively. The experimental results demonstrate that the hybrid ABC algorithm outperforms the genetic algorithm in convergence speed, accuracy, and time efficiency under the same conditions.

Symbolic integration of a class of algebraic functions. [by an algorithmic approach

NASA Technical Reports Server (NTRS)

Ng, E. W.

1974-01-01

An algorithm is presented for the symbolic integration of a class of algebraic functions. This class consists of functions made up of rational expressions of an integration variable x and square roots of polynomials, trigonometric and hyperbolic functions of x. The algorithm is shown to consist of the following components:(1) the reduction of input integrands to conical form; (2) intermediate internal representations of integrals; (3) classification of outputs; and (4) reduction and simplification of outputs to well-known functions.

Particle swarm optimizer for weighting factor selection in intensity-modulated radiation therapy optimization algorithms.

PubMed

Yang, Jie; Zhang, Pengcheng; Zhang, Liyuan; Shu, Huazhong; Li, Baosheng; Gui, Zhiguo

2017-01-01

In inverse treatment planning of intensity-modulated radiation therapy (IMRT), the objective function is typically the sum of the weighted sub-scores, where the weights indicate the importance of the sub-scores. To obtain a high-quality treatment plan, the planner manually adjusts the objective weights using a trial-and-error procedure until an acceptable plan is reached. In this work, a new particle swarm optimization (PSO) method which can adjust the weighting factors automatically was investigated to overcome the requirement of manual adjustment, thereby reducing the workload of the human planner and contributing to the development of a fully automated planning process. The proposed optimization method consists of three steps. (i) First, a swarm of weighting factors (i.e., particles) is initialized randomly in the search space, where each particle corresponds to a global objective function. (ii) Then, a plan optimization solver is employed to obtain the optimal solution for each particle, and the values of the evaluation functions used to determine the particle's location and the population global location for the PSO are calculated based on these results. (iii) Next, the weighting factors are updated based on the particle's location and the population global location. Step (ii) is performed alternately with step (iii) until the termination condition is reached. In this method, the evaluation function is a combination of several key points on the dose volume histograms. Furthermore, a perturbation strategy - the crossover and mutation operator hybrid approach - is employed to enhance the population diversity, and two arguments are applied to the evaluation function to improve the flexibility of the algorithm. In this study, the proposed method was used to develop IMRT treatment plans involving five unequally spaced 6MV photon beams for 10 prostate cancer cases. The proposed optimization algorithm yielded high-quality plans for all of the cases, without human planner intervention. A comparison of the results with the optimized solution obtained using a similar optimization model but with human planner intervention revealed that the proposed algorithm produced optimized plans superior to that developed using the manual plan. The proposed algorithm can generate admissible solutions within reasonable computational times and can be used to develop fully automated IMRT treatment planning methods, thus reducing human planners' workloads during iterative processes. Copyright © 2017 Associazione Italiana di Fisica Medica. Published by Elsevier Ltd. All rights reserved.

Optimisation of Fabric Reinforced Polymer Composites Using a Variant of Genetic Algorithm

NASA Astrophysics Data System (ADS)

Axinte, Andrei; Taranu, Nicolae; Bejan, Liliana; Hudisteanu, Iuliana

2017-12-01

Fabric reinforced polymeric composites are high performance materials with a rather complex fabric geometry. Therefore, modelling this type of material is a cumbersome task, especially when an efficient use is targeted. One of the most important issue of its design process is the optimisation of the individual laminae and of the laminated structure as a whole. In order to do that, a parametric model of the material has been defined, emphasising the many geometric variables needed to be correlated in the complex process of optimisation. The input parameters involved in this work, include: widths or heights of the tows and the laminate stacking sequence, which are discrete variables, while the gaps between adjacent tows and the height of the neat matrix are continuous variables. This work is one of the first attempts of using a Genetic Algorithm ( GA) to optimise the geometrical parameters of satin reinforced multi-layer composites. Given the mixed type of the input parameters involved, an original software called SOMGA (Satin Optimisation with a Modified Genetic Algorithm) has been conceived and utilised in this work. The main goal is to find the best possible solution to the problem of designing a composite material which is able to withstand to a given set of external, in-plane, loads. The optimisation process has been performed using a fitness function which can analyse and compare mechanical behaviour of different fabric reinforced composites, the results being correlated with the ultimate strains, which demonstrate the efficiency of the composite structure.

Genetic algorithm based fuzzy control of spacecraft autonomous rendezvous

NASA Technical Reports Server (NTRS)

Karr, C. L.; Freeman, L. M.; Meredith, D. L.

1990-01-01

The U.S. Bureau of Mines is currently investigating ways to combine the control capabilities of fuzzy logic with the learning capabilities of genetic algorithms. Fuzzy logic allows for the uncertainty inherent in most control problems to be incorporated into conventional expert systems. Although fuzzy logic based expert systems have been used successfully for controlling a number of physical systems, the selection of acceptable fuzzy membership functions has generally been a subjective decision. High performance fuzzy membership functions for a fuzzy logic controller that manipulates a mathematical model simulating the autonomous rendezvous of spacecraft are learned using a genetic algorithm, a search technique based on the mechanics of natural genetics. The membership functions learned by the genetic algorithm provide for a more efficient fuzzy logic controller than membership functions selected by the authors for the rendezvous problem. Thus, genetic algorithms are potentially an effective and structured approach for learning fuzzy membership functions.

Discriminating Phytoplankton Functional Types (PFTs) in the Coastal Ocean Using the Inversion Algorithm Phydotax and Airborne Imaging Spectrometer Data

NASA Technical Reports Server (NTRS)

Palacios, Sherry L.; Schafer, Chris; Broughton, Jennifer; Guild, Liane S.; Kudela, Raphael M.

2013-01-01

There is a need in the Biological Oceanography community to discriminate among phytoplankton groups within the bulk chlorophyll pool to understand energy flow through ecosystems, to track the fate of carbon in the ocean, and to detect and monitor-for harmful algal blooms (HABs). The ocean color community has responded to this demand with the development of phytoplankton functional type (PFT) discrimination algorithms. These PFT algorithms fall into one of three categories depending on the science application: size-based, biogeochemical function, and taxonomy. The new PFT algorithm Phytoplankton Detection with Optics (PHYDOTax) is an inversion algorithm that discriminates taxon-specific biomass to differentiate among six taxa found in the California Current System: diatoms, dinoflagellates, haptophytes, chlorophytes, cryptophytes, and cyanophytes. PHYDOTax was developed and validated in Monterey Bay, CA for the high resolution imaging spectrometer, Spectroscopic Aerial Mapping System with On-board Navigation (SAMSON - 3.5 nm resolution). PHYDOTax exploits the high spectral resolution of an imaging spectrometer and the improved spatial resolution that airborne data provides for coastal areas. The objective of this study was to apply PHYDOTax to a relatively lower resolution imaging spectrometer to test the algorithm's sensitivity to atmospheric correction, to evaluate capability with other sensors, and to determine if down-sampling spectral resolution would degrade its ability to discriminate among phytoplankton taxa. This study is a part of the larger Hyperspectral Infrared Imager (HyspIRI) airborne simulation campaign which is collecting Airborne Visible/Infrared Imaging Spectrometer (AVIRIS) imagery aboard NASA's ER-2 aircraft during three seasons in each of two years over terrestrial and marine targets in California. Our aquatic component seeks to develop and test algorithms to retrieve water quality properties (e.g. HABs and river plumes) in both marine and in-land water bodies. Results presented are from the 10 April 2013 overflight of the Monterey Bay region and focus primarily on the first objective - sensitivity to atmospheric correction. On-going and future work will continue to evaluate if PHYDOTax can be applied to historical (SeaWiFS and MERIS), existing (MODIS, VIIRS, and HICO), and future (PACE, GEO-CAPE, and HyspIRI) satellite sensors. Demonstration of cross-platform continuity may aid in calibration and validation efforts of these sensors.

Estimating the size of the solution space of metabolic networks

PubMed Central

Braunstein, Alfredo; Mulet, Roberto; Pagnani, Andrea

2008-01-01

Background Cellular metabolism is one of the most investigated system of biological interactions. While the topological nature of individual reactions and pathways in the network is quite well understood there is still a lack of comprehension regarding the global functional behavior of the system. In the last few years flux-balance analysis (FBA) has been the most successful and widely used technique for studying metabolism at system level. This method strongly relies on the hypothesis that the organism maximizes an objective function. However only under very specific biological conditions (e.g. maximization of biomass for E. coli in reach nutrient medium) the cell seems to obey such optimization law. A more refined analysis not assuming extremization remains an elusive task for large metabolic systems due to algorithmic limitations. Results In this work we propose a novel algorithmic strategy that provides an efficient characterization of the whole set of stable fluxes compatible with the metabolic constraints. Using a technique derived from the fields of statistical physics and information theory we designed a message-passing algorithm to estimate the size of the affine space containing all possible steady-state flux distributions of metabolic networks. The algorithm, based on the well known Bethe approximation, can be used to approximately compute the volume of a non full-dimensional convex polytope in high dimensions. We first compare the accuracy of the predictions with an exact algorithm on small random metabolic networks. We also verify that the predictions of the algorithm match closely those of Monte Carlo based methods in the case of the Red Blood Cell metabolic network. Then we test the effect of gene knock-outs on the size of the solution space in the case of E. coli central metabolism. Finally we analyze the statistical properties of the average fluxes of the reactions in the E. coli metabolic network. Conclusion We propose a novel efficient distributed algorithmic strategy to estimate the size and shape of the affine space of a non full-dimensional convex polytope in high dimensions. The method is shown to obtain, quantitatively and qualitatively compatible results with the ones of standard algorithms (where this comparison is possible) being still efficient on the analysis of large biological systems, where exact deterministic methods experience an explosion in algorithmic time. The algorithm we propose can be considered as an alternative to Monte Carlo sampling methods. PMID:18489757

Automatic mission planning algorithms for aerial collection of imaging-specific tasks

NASA Astrophysics Data System (ADS)

Sponagle, Paul; Salvaggio, Carl

2017-05-01

The rapid advancement and availability of small unmanned aircraft systems (sUAS) has led to many novel exploitation tasks utilizing that utilize this unique aerial imagery data. Collection of this unique data requires novel flight planning to accomplish the task at hand. This work describes novel flight planning to better support structure-from-motion missions to minimize occlusions, autonomous and periodic overflight of reflectance calibration panels to permit more efficient and accurate data collection under varying illumination conditions, and the collection of imagery data to study optical properties such as the bidirectional reflectance distribution function without disturbing the target in sensitive or remote areas of interest. These novel mission planning algorithms will provide scientists with additional tools to meet their future data collection needs.

Information filtering on coupled social networks.

PubMed

Nie, Da-Cheng; Zhang, Zi-Ke; Zhou, Jun-Lin; Fu, Yan; Zhang, Kui

2014-01-01

In this paper, based on the coupled social networks (CSN), we propose a hybrid algorithm to nonlinearly integrate both social and behavior information of online users. Filtering algorithm, based on the coupled social networks, considers the effects of both social similarity and personalized preference. Experimental results based on two real datasets, Epinions and Friendfeed, show that the hybrid pattern can not only provide more accurate recommendations, but also enlarge the recommendation coverage while adopting global metric. Further empirical analyses demonstrate that the mutual reinforcement and rich-club phenomenon can also be found in coupled social networks where the identical individuals occupy the core position of the online system. This work may shed some light on the in-depth understanding of the structure and function of coupled social networks.

Study of the Z{sub 3} symmetry in QCD at finite temperature and chemical potential using a worm algorithm

DOE Office of Scientific and Technical Information (OSTI.GOV)

Krein, Gastao; Leme, Rafael R.; Woitek, Marcio

Traditional Monte Carlo simulations of QCD in the presence of a baryon chemical potential are plagued by the complex phase problem and new numerical approaches are necessary for studying the phase diagram of the theory. In this work we consider a Z{sub 3} Polyakov loop model for the deconfining phase transition in QCD and discuss how a flux representation of the model in terms of dimer and monomer variable solves the complex action problem. We present results of numerical simulations using a worm algorithm for the specific heat and two-point correlation function of Polyakov loops. Evidences of a first ordermore » deconfinement phase transition are discussed.« less

A surrogate accelerated multicanonical Monte Carlo method for uncertainty quantification

NASA Astrophysics Data System (ADS)

Wu, Keyi; Li, Jinglai

2016-09-01

In this work we consider a class of uncertainty quantification problems where the system performance or reliability is characterized by a scalar parameter y. The performance parameter y is random due to the presence of various sources of uncertainty in the system, and our goal is to estimate the probability density function (PDF) of y. We propose to use the multicanonical Monte Carlo (MMC) method, a special type of adaptive importance sampling algorithms, to compute the PDF of interest. Moreover, we develop an adaptive algorithm to construct local Gaussian process surrogates to further accelerate the MMC iterations. With numerical examples we demonstrate that the proposed method can achieve several orders of magnitudes of speedup over the standard Monte Carlo methods.

A Robust Method for Ego-Motion Estimation in Urban Environment Using Stereo Camera.

PubMed

Ci, Wenyan; Huang, Yingping

2016-10-17

Visual odometry estimates the ego-motion of an agent (e.g., vehicle and robot) using image information and is a key component for autonomous vehicles and robotics. This paper proposes a robust and precise method for estimating the 6-DoF ego-motion, using a stereo rig with optical flow analysis. An objective function fitted with a set of feature points is created by establishing the mathematical relationship between optical flow, depth and camera ego-motion parameters through the camera's 3-dimensional motion and planar imaging model. Accordingly, the six motion parameters are computed by minimizing the objective function, using the iterative Levenberg-Marquard method. One of key points for visual odometry is that the feature points selected for the computation should contain inliers as much as possible. In this work, the feature points and their optical flows are initially detected by using the Kanade-Lucas-Tomasi (KLT) algorithm. A circle matching is followed to remove the outliers caused by the mismatching of the KLT algorithm. A space position constraint is imposed to filter out the moving points from the point set detected by the KLT algorithm. The Random Sample Consensus (RANSAC) algorithm is employed to further refine the feature point set, i.e., to eliminate the effects of outliers. The remaining points are tracked to estimate the ego-motion parameters in the subsequent frames. The approach presented here is tested on real traffic videos and the results prove the robustness and precision of the method.

A Robust Method for Ego-Motion Estimation in Urban Environment Using Stereo Camera

PubMed Central

Ci, Wenyan; Huang, Yingping

2016-01-01

Visual odometry estimates the ego-motion of an agent (e.g., vehicle and robot) using image information and is a key component for autonomous vehicles and robotics. This paper proposes a robust and precise method for estimating the 6-DoF ego-motion, using a stereo rig with optical flow analysis. An objective function fitted with a set of feature points is created by establishing the mathematical relationship between optical flow, depth and camera ego-motion parameters through the camera’s 3-dimensional motion and planar imaging model. Accordingly, the six motion parameters are computed by minimizing the objective function, using the iterative Levenberg–Marquard method. One of key points for visual odometry is that the feature points selected for the computation should contain inliers as much as possible. In this work, the feature points and their optical flows are initially detected by using the Kanade–Lucas–Tomasi (KLT) algorithm. A circle matching is followed to remove the outliers caused by the mismatching of the KLT algorithm. A space position constraint is imposed to filter out the moving points from the point set detected by the KLT algorithm. The Random Sample Consensus (RANSAC) algorithm is employed to further refine the feature point set, i.e., to eliminate the effects of outliers. The remaining points are tracked to estimate the ego-motion parameters in the subsequent frames. The approach presented here is tested on real traffic videos and the results prove the robustness and precision of the method. PMID:27763508

Implementation of Real-Time Feedback Flow Control Algorithms on a Canonical Testbed

NASA Technical Reports Server (NTRS)

Tian, Ye; Song, Qi; Cattafesta, Louis

2005-01-01

This report summarizes the activities on "Implementation of Real-Time Feedback Flow Control Algorithms on a Canonical Testbed." The work summarized consists primarily of two parts. The first part summarizes our previous work and the extensions to adaptive ID and control algorithms. The second part concentrates on the validation of adaptive algorithms by applying them to a vibration beam test bed. Extensions to flow control problems are discussed.

Frequency Response Function Based Damage Identification for Aerospace Structures

NASA Astrophysics Data System (ADS)

Oliver, Joseph Acton

Structural health monitoring technologies continue to be pursued for aerospace structures in the interests of increased safety and, when combined with health prognosis, efficiency in life-cycle management. The current dissertation develops and validates damage identification technology as a critical component for structural health monitoring of aerospace structures and, in particular, composite unmanned aerial vehicles. The primary innovation is a statistical least-squares damage identification algorithm based in concepts of parameter estimation and model update. The algorithm uses frequency response function based residual force vectors derived from distributed vibration measurements to update a structural finite element model through statistically weighted least-squares minimization producing location and quantification of the damage, estimation uncertainty, and an updated model. Advantages compared to other approaches include robust applicability to systems which are heavily damped, large, and noisy, with a relatively low number of distributed measurement points compared to the number of analytical degrees-of-freedom of an associated analytical structural model (e.g., modal finite element model). Motivation, research objectives, and a dissertation summary are discussed in Chapter 1 followed by a literature review in Chapter 2. Chapter 3 gives background theory and the damage identification algorithm derivation followed by a study of fundamental algorithm behavior on a two degree-of-freedom mass-spring system with generalized damping. Chapter 4 investigates the impact of noise then successfully proves the algorithm against competing methods using an analytical eight degree-of-freedom mass-spring system with non-proportional structural damping. Chapter 5 extends use of the algorithm to finite element models, including solutions for numerical issues, approaches for modeling damping approximately in reduced coordinates, and analytical validation using a composite sandwich plate model. Chapter 6 presents the final extension to experimental systems-including methods for initial baseline correlation and data reduction-and validates the algorithm on an experimental composite plate with impact damage. The final chapter deviates from development and validation of the primary algorithm to discuss development of an experimental scaled-wing test bed as part of a collaborative effort for developing structural health monitoring and prognosis technology. The dissertation concludes with an overview of technical conclusions and recommendations for future work.

Genetic Algorithm for Initial Orbit Determination with Too Short Arc (Continued)

NASA Astrophysics Data System (ADS)

Li, Xin-ran; Wang, Xin

2017-04-01

When the genetic algorithm is used to solve the problem of too short-arc (TSA) orbit determination, due to the difference of computing process between the genetic algorithm and the classical method, the original method for outlier deletion is no longer applicable. In the genetic algorithm, the robust estimation is realized by introducing different loss functions for the fitness function, then the outlier problem of the TSA orbit determination is solved. Compared with the classical method, the genetic algorithm is greatly simplified by introducing in different loss functions. Through the comparison on the calculations of multiple loss functions, it is found that the least median square (LMS) estimation and least trimmed square (LTS) estimation can greatly improve the robustness of the TSA orbit determination, and have a high breakdown point.

Parametric Bayesian priors and better choice of negative examples improve protein function prediction.

PubMed

Youngs, Noah; Penfold-Brown, Duncan; Drew, Kevin; Shasha, Dennis; Bonneau, Richard

2013-05-01

Computational biologists have demonstrated the utility of using machine learning methods to predict protein function from an integration of multiple genome-wide data types. Yet, even the best performing function prediction algorithms rely on heuristics for important components of the algorithm, such as choosing negative examples (proteins without a given function) or determining key parameters. The improper choice of negative examples, in particular, can hamper the accuracy of protein function prediction. We present a novel approach for choosing negative examples, using a parameterizable Bayesian prior computed from all observed annotation data, which also generates priors used during function prediction. We incorporate this new method into the GeneMANIA function prediction algorithm and demonstrate improved accuracy of our algorithm over current top-performing function prediction methods on the yeast and mouse proteomes across all metrics tested. Code and Data are available at: http://bonneaulab.bio.nyu.edu/funcprop.html

Value Iteration Adaptive Dynamic Programming for Optimal Control of Discrete-Time Nonlinear Systems.

PubMed

Wei, Qinglai; Liu, Derong; Lin, Hanquan

2016-03-01

In this paper, a value iteration adaptive dynamic programming (ADP) algorithm is developed to solve infinite horizon undiscounted optimal control problems for discrete-time nonlinear systems. The present value iteration ADP algorithm permits an arbitrary positive semi-definite function to initialize the algorithm. A novel convergence analysis is developed to guarantee that the iterative value function converges to the optimal performance index function. Initialized by different initial functions, it is proven that the iterative value function will be monotonically nonincreasing, monotonically nondecreasing, or nonmonotonic and will converge to the optimum. In this paper, for the first time, the admissibility properties of the iterative control laws are developed for value iteration algorithms. It is emphasized that new termination criteria are established to guarantee the effectiveness of the iterative control laws. Neural networks are used to approximate the iterative value function and compute the iterative control law, respectively, for facilitating the implementation of the iterative ADP algorithm. Finally, two simulation examples are given to illustrate the performance of the present method.

Denni Algorithm An Enhanced Of SMS (Scan, Move and Sort) Algorithm

NASA Astrophysics Data System (ADS)

Aprilsyah Lubis, Denni; Salim Sitompul, Opim; Marwan; Tulus; Andri Budiman, M.

2017-12-01

Sorting has been a profound area for the algorithmic researchers, and many resources are invested to suggest a more working sorting algorithm. For this purpose many existing sorting algorithms were observed in terms of the efficiency of the algorithmic complexity. Efficient sorting is important to optimize the use of other algorithms that require sorted lists to work correctly. Sorting has been considered as a fundamental problem in the study of algorithms that due to many reasons namely, the necessary to sort information is inherent in many applications, algorithms often use sorting as a key subroutine, in algorithm design there are many essential techniques represented in the body of sorting algorithms, and many engineering issues come to the fore when implementing sorting algorithms., Many algorithms are very well known for sorting the unordered lists, and one of the well-known algorithms that make the process of sorting to be more economical and efficient is SMS (Scan, Move and Sort) algorithm, an enhancement of Quicksort invented Rami Mansi in 2010. This paper presents a new sorting algorithm called Denni-algorithm. The Denni algorithm is considered as an enhancement on the SMS algorithm in average, and worst cases. The Denni algorithm is compared with the SMS algorithm and the results were promising.

A General Event Location Algorithm with Applications to Eclipse and Station Line-of-Sight

NASA Technical Reports Server (NTRS)

Parker, Joel J. K.; Hughes, Steven P.

2011-01-01

A general-purpose algorithm for the detection and location of orbital events is developed. The proposed algorithm reduces the problem to a global root-finding problem by mapping events of interest (such as eclipses, station access events, etc.) to continuous, differentiable event functions. A stepping algorithm and a bracketing algorithm are used to detect and locate the roots. Examples of event functions and the stepping/bracketing algorithms are discussed, along with results indicating performance and accuracy in comparison to commercial tools across a variety of trajectories.

A General Event Location Algorithm with Applications to Eclispe and Station Line-of-Sight

NASA Technical Reports Server (NTRS)

Parker, Joel J. K.; Hughes, Steven P.

2011-01-01

A general-purpose algorithm for the detection and location of orbital events is developed. The proposed algorithm reduces the problem to a global root-finding problem by mapping events of interest (such as eclipses, station access events, etc.) to continuous, differentiable event functions. A stepping algorithm and a bracketing algorithm are used to detect and locate the roots. Examples of event functions and the stepping/bracketing algorithms are discussed, along with results indicating performance and accuracy in comparison to commercial tools across a variety of trajectories.

Modeling of diatomic molecule using the Morse potential and the Verlet algorithm

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fidiani, Elok

Performing molecular modeling usually uses special software for Molecular Dynamics (MD) such as: GROMACS, NAMD, JMOL etc. Molecular dynamics is a computational method to calculate the time dependent behavior of a molecular system. In this work, MATLAB was used as numerical method for a simple modeling of some diatomic molecules: HCl, H{sub 2} and O{sub 2}. MATLAB is a matrix based numerical software, in order to do numerical analysis, all the functions and equations describing properties of atoms and molecules must be developed manually in MATLAB. In this work, a Morse potential was generated to describe the bond interaction betweenmore » the two atoms. In order to analyze the simultaneous motion of molecules, the Verlet Algorithm derived from Newton’s Equations of Motion (classical mechanics) was operated. Both the Morse potential and the Verlet algorithm were integrated using MATLAB to derive physical properties and the trajectory of the molecules. The data computed by MATLAB is always in the form of a matrix. To visualize it, Visualized Molecular Dynamics (VMD) was performed. Such method is useful for development and testing some types of interaction on a molecular scale. Besides, this can be very helpful for describing some basic principles of molecular interaction for educational purposes.« less

Comparison of polynomial approximations and artificial neural nets for response surfaces in engineering optimization

NASA Technical Reports Server (NTRS)

Carpenter, William C.

1991-01-01

Engineering optimization problems involve minimizing some function subject to constraints. In areas such as aircraft optimization, the constraint equations may be from numerous disciplines such as transfer of information between these disciplines and the optimization algorithm. They are also suited to problems which may require numerous re-optimizations such as in multi-objective function optimization or to problems where the design space contains numerous local minima, thus requiring repeated optimizations from different initial designs. Their use has been limited, however, by the fact that development of response surfaces randomly selected or preselected points in the design space. Thus, they have been thought to be inefficient compared to algorithms to the optimum solution. A development has taken place in the last several years which may effect the desirability of using response surfaces. It may be possible that artificial neural nets are more efficient in developing response surfaces than polynomial approximations which have been used in the past. This development is the concern of the work.

Fractional Poisson-Nernst-Planck Model for Ion Channels I: Basic Formulations and Algorithms.

PubMed

Chen, Duan

2017-11-01

In this work, we propose a fractional Poisson-Nernst-Planck model to describe ion permeation in gated ion channels. Due to the intrinsic conformational changes, crowdedness in narrow channel pores, binding and trapping introduced by functioning units of channel proteins, ionic transport in the channel exhibits a power-law-like anomalous diffusion dynamics. We start from continuous-time random walk model for a single ion and use a long-tailed density distribution function for the particle jump waiting time, to derive the fractional Fokker-Planck equation. Then, it is generalized to the macroscopic fractional Poisson-Nernst-Planck model for ionic concentrations. Necessary computational algorithms are designed to implement numerical simulations for the proposed model, and the dynamics of gating current is investigated. Numerical simulations show that the fractional PNP model provides a more qualitatively reasonable match to the profile of gating currents from experimental observations. Meanwhile, the proposed model motivates new challenges in terms of mathematical modeling and computations.

Trace of totally positive algebraic integers and integer transfinite diameter

NASA Astrophysics Data System (ADS)

Flammang, V.

2009-06-01

Explicit auxiliary functions can be used in the ``Schur-Siegel- Smyth trace problem''. In the previous works, these functions were constructed only with polynomials having all their roots positive. Here, we use several polynomials with complex roots, which are found with Wu's algorithm, and we improve the known lower bounds for the absolute trace of totally positive algebraic integers. This improvement has a consequence for the search of Salem numbers that have a negative trace. The same method also gives a small improvement of the upper bound for the integer transfinite diameter of [0,1].

Firefly Mating Algorithm for Continuous Optimization Problems

PubMed Central

Ritthipakdee, Amarita; Premasathian, Nol; Jitkongchuen, Duangjai

2017-01-01

This paper proposes a swarm intelligence algorithm, called firefly mating algorithm (FMA), for solving continuous optimization problems. FMA uses genetic algorithm as the core of the algorithm. The main feature of the algorithm is a novel mating pair selection method which is inspired by the following 2 mating behaviors of fireflies in nature: (i) the mutual attraction between males and females causes them to mate and (ii) fireflies of both sexes are of the multiple-mating type, mating with multiple opposite sex partners. A female continues mating until her spermatheca becomes full, and, in the same vein, a male can provide sperms for several females until his sperm reservoir is depleted. This new feature enhances the global convergence capability of the algorithm. The performance of FMA was tested with 20 benchmark functions (sixteen 30-dimensional functions and four 2-dimensional ones) against FA, ALC-PSO, COA, MCPSO, LWGSODE, MPSODDS, DFOA, SHPSOS, LSA, MPDPGA, DE, and GABC algorithms. The experimental results showed that the success rates of our proposed algorithm with these functions were higher than those of other algorithms and the proposed algorithm also required fewer numbers of iterations to reach the global optima. PMID:28808442

Firefly Mating Algorithm for Continuous Optimization Problems.

PubMed

Ritthipakdee, Amarita; Thammano, Arit; Premasathian, Nol; Jitkongchuen, Duangjai

2017-01-01

This paper proposes a swarm intelligence algorithm, called firefly mating algorithm (FMA), for solving continuous optimization problems. FMA uses genetic algorithm as the core of the algorithm. The main feature of the algorithm is a novel mating pair selection method which is inspired by the following 2 mating behaviors of fireflies in nature: (i) the mutual attraction between males and females causes them to mate and (ii) fireflies of both sexes are of the multiple-mating type, mating with multiple opposite sex partners. A female continues mating until her spermatheca becomes full, and, in the same vein, a male can provide sperms for several females until his sperm reservoir is depleted. This new feature enhances the global convergence capability of the algorithm. The performance of FMA was tested with 20 benchmark functions (sixteen 30-dimensional functions and four 2-dimensional ones) against FA, ALC-PSO, COA, MCPSO, LWGSODE, MPSODDS, DFOA, SHPSOS, LSA, MPDPGA, DE, and GABC algorithms. The experimental results showed that the success rates of our proposed algorithm with these functions were higher than those of other algorithms and the proposed algorithm also required fewer numbers of iterations to reach the global optima.

Stochastic weighted particle methods for population balance equations with coagulation, fragmentation and spatial inhomogeneity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lee, Kok Foong; Patterson, Robert I.A.; Wagner, Wolfgang

2015-12-15

Graphical abstract: -- Highlights: •Problems concerning multi-compartment population balance equations are studied. •A class of fragmentation weight transfer functions is presented. •Three stochastic weighted algorithms are compared against the direct simulation algorithm. •The numerical errors of the stochastic solutions are assessed as a function of fragmentation rate. •The algorithms are applied to a multi-dimensional granulation model. -- Abstract: This paper introduces stochastic weighted particle algorithms for the solution of multi-compartment population balance equations. In particular, it presents a class of fragmentation weight transfer functions which are constructed such that the number of computational particles stays constant during fragmentation events. Themore » weight transfer functions are constructed based on systems of weighted computational particles and each of it leads to a stochastic particle algorithm for the numerical treatment of population balance equations. Besides fragmentation, the algorithms also consider physical processes such as coagulation and the exchange of mass with the surroundings. The numerical properties of the algorithms are compared to the direct simulation algorithm and an existing method for the fragmentation of weighted particles. It is found that the new algorithms show better numerical performance over the two existing methods especially for systems with significant amount of large particles and high fragmentation rates.« less

A model-based 3D phase unwrapping algorithm using Gegenbauer polynomials.

PubMed

Langley, Jason; Zhao, Qun

2009-09-07

The application of a two-dimensional (2D) phase unwrapping algorithm to a three-dimensional (3D) phase map may result in an unwrapped phase map that is discontinuous in the direction normal to the unwrapped plane. This work investigates the problem of phase unwrapping for 3D phase maps. The phase map is modeled as a product of three one-dimensional Gegenbauer polynomials. The orthogonality of Gegenbauer polynomials and their derivatives on the interval [-1, 1] are exploited to calculate the expansion coefficients. The algorithm was implemented using two well-known Gegenbauer polynomials: Chebyshev polynomials of the first kind and Legendre polynomials. Both implementations of the phase unwrapping algorithm were tested on 3D datasets acquired from a magnetic resonance imaging (MRI) scanner. The first dataset was acquired from a homogeneous spherical phantom. The second dataset was acquired using the same spherical phantom but magnetic field inhomogeneities were introduced by an external coil placed adjacent to the phantom, which provided an additional burden to the phase unwrapping algorithm. Then Gaussian noise was added to generate a low signal-to-noise ratio dataset. The third dataset was acquired from the brain of a human volunteer. The results showed that Chebyshev implementation and the Legendre implementation of the phase unwrapping algorithm give similar results on the 3D datasets. Both implementations of the phase unwrapping algorithm compare well to PRELUDE 3D, 3D phase unwrapping software well recognized for functional MRI.

Using advanced computer vision algorithms on small mobile robots

NASA Astrophysics Data System (ADS)

Kogut, G.; Birchmore, F.; Biagtan Pacis, E.; Everett, H. R.

2006-05-01

The Technology Transfer project employs a spiral development process to enhance the functionality and autonomy of mobile robot systems in the Joint Robotics Program (JRP) Robotic Systems Pool by converging existing component technologies onto a transition platform for optimization. An example of this approach is the implementation of advanced computer vision algorithms on small mobile robots. We demonstrate the implementation and testing of the following two algorithms useful on mobile robots: 1) object classification using a boosted Cascade of classifiers trained with the Adaboost training algorithm, and 2) human presence detection from a moving platform. Object classification is performed with an Adaboost training system developed at the University of California, San Diego (UCSD) Computer Vision Lab. This classification algorithm has been used to successfully detect the license plates of automobiles in motion in real-time. While working towards a solution to increase the robustness of this system to perform generic object recognition, this paper demonstrates an extension to this application by detecting soda cans in a cluttered indoor environment. The human presence detection from a moving platform system uses a data fusion algorithm which combines results from a scanning laser and a thermal imager. The system is able to detect the presence of humans while both the humans and the robot are moving simultaneously. In both systems, the two aforementioned algorithms were implemented on embedded hardware and optimized for use in real-time. Test results are shown for a variety of environments.

Application of firefly algorithm to the dynamic model updating problem

NASA Astrophysics Data System (ADS)

Shabbir, Faisal; Omenzetter, Piotr

2015-04-01

Model updating can be considered as a branch of optimization problems in which calibration of the finite element (FE) model is undertaken by comparing the modal properties of the actual structure with these of the FE predictions. The attainment of a global solution in a multi dimensional search space is a challenging problem. The nature-inspired algorithms have gained increasing attention in the previous decade for solving such complex optimization problems. This study applies the novel Firefly Algorithm (FA), a global optimization search technique, to a dynamic model updating problem. This is to the authors' best knowledge the first time FA is applied to model updating. The working of FA is inspired by the flashing characteristics of fireflies. Each firefly represents a randomly generated solution which is assigned brightness according to the value of the objective function. The physical structure under consideration is a full scale cable stayed pedestrian bridge with composite bridge deck. Data from dynamic testing of the bridge was used to correlate and update the initial model by using FA. The algorithm aimed at minimizing the difference between the natural frequencies and mode shapes of the structure. The performance of the algorithm is analyzed in finding the optimal solution in a multi dimensional search space. The paper concludes with an investigation of the efficacy of the algorithm in obtaining a reference finite element model which correctly represents the as-built original structure.

featsel: A framework for benchmarking of feature selection algorithms and cost functions

NASA Astrophysics Data System (ADS)

Reis, Marcelo S.; Estrela, Gustavo; Ferreira, Carlos Eduardo; Barrera, Junior

In this paper, we introduce featsel, a framework for benchmarking of feature selection algorithms and cost functions. This framework allows the user to deal with the search space as a Boolean lattice and has its core coded in C++ for computational efficiency purposes. Moreover, featsel includes Perl scripts to add new algorithms and/or cost functions, generate random instances, plot graphs and organize results into tables. Besides, this framework already comes with dozens of algorithms and cost functions for benchmarking experiments. We also provide illustrative examples, in which featsel outperforms the popular Weka workbench in feature selection procedures on data sets from the UCI Machine Learning Repository.

A Class of Manifold Regularized Multiplicative Update Algorithms for Image Clustering.

PubMed

Yang, Shangming; Yi, Zhang; He, Xiaofei; Li, Xuelong

2015-12-01

Multiplicative update algorithms are important tools for information retrieval, image processing, and pattern recognition. However, when the graph regularization is added to the cost function, different classes of sample data may be mapped to the same subspace, which leads to the increase of data clustering error rate. In this paper, an improved nonnegative matrix factorization (NMF) cost function is introduced. Based on the cost function, a class of novel graph regularized NMF algorithms is developed, which results in a class of extended multiplicative update algorithms with manifold structure regularization. Analysis shows that in the learning, the proposed algorithms can efficiently minimize the rank of the data representation matrix. Theoretical results presented in this paper are confirmed by simulations. For different initializations and data sets, variation curves of cost functions and decomposition data are presented to show the convergence features of the proposed update rules. Basis images, reconstructed images, and clustering results are utilized to present the efficiency of the new algorithms. Last, the clustering accuracies of different algorithms are also investigated, which shows that the proposed algorithms can achieve state-of-the-art performance in applications of image clustering.

Semi-supervised spectral algorithms for community detection in complex networks based on equivalence of clustering methods

NASA Astrophysics Data System (ADS)

Ma, Xiaoke; Wang, Bingbo; Yu, Liang

2018-01-01

Community detection is fundamental for revealing the structure-functionality relationship in complex networks, which involves two issues-the quantitative function for community as well as algorithms to discover communities. Despite significant research on either of them, few attempt has been made to establish the connection between the two issues. To attack this problem, a generalized quantification function is proposed for community in weighted networks, which provides a framework that unifies several well-known measures. Then, we prove that the trace optimization of the proposed measure is equivalent with the objective functions of algorithms such as nonnegative matrix factorization, kernel K-means as well as spectral clustering. It serves as the theoretical foundation for designing algorithms for community detection. On the second issue, a semi-supervised spectral clustering algorithm is developed by exploring the equivalence relation via combining the nonnegative matrix factorization and spectral clustering. Different from the traditional semi-supervised algorithms, the partial supervision is integrated into the objective of the spectral algorithm. Finally, through extensive experiments on both artificial and real world networks, we demonstrate that the proposed method improves the accuracy of the traditional spectral algorithms in community detection.

Evaluation of methods to produce an image library for automatic patient model localization for dose mapping during fluoroscopically guided procedures

NASA Astrophysics Data System (ADS)

Kilian-Meneghin, Josh; Xiong, Z.; Rudin, S.; Oines, A.; Bednarek, D. R.

2017-03-01

The purpose of this work is to evaluate methods for producing a library of 2D-radiographic images to be correlated to clinical images obtained during a fluoroscopically-guided procedure for automated patient-model localization. The localization algorithm will be used to improve the accuracy of the skin-dose map superimposed on the 3D patient- model of the real-time Dose-Tracking-System (DTS). For the library, 2D images were generated from CT datasets of the SK-150 anthropomorphic phantom using two methods: Schmid's 3D-visualization tool and Plastimatch's digitally-reconstructed-radiograph (DRR) code. Those images, as well as a standard 2D-radiographic image, were correlated to a 2D-fluoroscopic image of a phantom, which represented the clinical-fluoroscopic image, using the Corr2 function in Matlab. The Corr2 function takes two images and outputs the relative correlation between them, which is fed into the localization algorithm. Higher correlation means better alignment of the 3D patient-model with the patient image. In this instance, it was determined that the localization algorithm will succeed when Corr2 returns a correlation of at least 50%. The 3D-visualization tool images returned 55-80% correlation relative to the fluoroscopic-image, which was comparable to the correlation for the radiograph. The DRR images returned 61-90% correlation, again comparable to the radiograph. Both methods prove to be sufficient for the localization algorithm and can be produced quickly; however, the DRR method produces more accurate grey-levels. Using the DRR code, a library at varying angles can be produced for the localization algorithm.

Tsunami detection by high-frequency radar in British Columbia: performance assessment of the time-correlation algorithm for synthetic and real events

NASA Astrophysics Data System (ADS)

Guérin, Charles-Antoine; Grilli, Stéphan T.; Moran, Patrick; Grilli, Annette R.; Insua, Tania L.

2018-05-01

The authors recently proposed a new method for detecting tsunamis using high-frequency (HF) radar observations, referred to as "time-correlation algorithm" (TCA; Grilli et al. Pure Appl Geophys 173(12):3895-3934, 2016a, 174(1): 3003-3028, 2017). Unlike standard algorithms that detect surface current patterns, the TCA is based on analyzing space-time correlations of radar signal time series in pairs of radar cells, which does not require inverting radial surface currents. This was done by calculating a contrast function, which quantifies the change in pattern of the mean correlation between pairs of neighboring cells upon tsunami arrival, with respect to a reference correlation computed in the recent past. In earlier work, the TCA was successfully validated based on realistic numerical simulations of both the radar signal and tsunami wave trains. Here, this algorithm is adapted to apply to actual data from a HF radar installed in Tofino, BC, for three test cases: (1) a simulated far-field tsunami generated in the Semidi Subduction Zone in the Aleutian Arc; (2) a simulated near-field tsunami from a submarine mass failure on the continental slope off of Tofino; and (3) an event believed to be a meteotsunami, which occurred on October 14th, 2016, off of the Pacific West Coast and was measured by the radar. In the first two cases, the synthetic tsunami signal is superimposed onto the radar signal by way of a current memory term; in the third case, the tsunami signature is present within the radar data. In light of these test cases, we develop a detection methodology based on the TCA, using a correlation contrast function, and show that in all three cases the algorithm is able to trigger a timely early warning.

A Review of Function Allocation and En Route Separation Assurance

NASA Technical Reports Server (NTRS)

Lewis, Timothy A.; Aweiss, Arwa S.; Guerreiro, Nelson M.; Daiker, Ronald J.

2016-01-01

Today's air traffic control system has reached a limit to the number of aircraft that can be safely managed at the same time. This air traffic capacity bottleneck is a critical problem along the path to modernization for air transportation. The design of the next separation assurance system to address this problem is a cornerstone of air traffic management research today. This report reviews recent work by NASA and others in the areas of function allocation and en route separation assurance. This includes: separation assurance algorithms and technology prototypes; concepts of operations and designs for advanced separation assurance systems; and specific investigations into air-ground and human-automation function allocation.

Density functional theory for field emission from carbon nano-structures.

PubMed

Li, Zhibing

2015-12-01

Electron field emission is understood as a quantum mechanical many-body problem in which an electronic quasi-particle of the emitter is converted into an electron in vacuum. Fundamental concepts of field emission, such as the field enhancement factor, work-function, edge barrier and emission current density, will be investigated, using carbon nanotubes and graphene as examples. A multi-scale algorithm basing on density functional theory is introduced. We will argue that such a first principle approach is necessary and appropriate for field emission of nano-structures, not only for a more accurate quantitative description, but, more importantly, for deeper insight into field emission. Copyright © 2015 The Author. Published by Elsevier B.V. All rights reserved.

Maximum-likelihood soft-decision decoding of block codes using the A* algorithm

NASA Technical Reports Server (NTRS)

Ekroot, L.; Dolinar, S.

1994-01-01

The A* algorithm finds the path in a finite depth binary tree that optimizes a function. Here, it is applied to maximum-likelihood soft-decision decoding of block codes where the function optimized over the codewords is the likelihood function of the received sequence given each codeword. The algorithm considers codewords one bit at a time, making use of the most reliable received symbols first and pursuing only the partially expanded codewords that might be maximally likely. A version of the A* algorithm for maximum-likelihood decoding of block codes has been implemented for block codes up to 64 bits in length. The efficiency of this algorithm makes simulations of codes up to length 64 feasible. This article details the implementation currently in use, compares the decoding complexity with that of exhaustive search and Viterbi decoding algorithms, and presents performance curves obtained with this implementation of the A* algorithm for several codes.

Dementia diagnoses from clinical and neuropsychological data compared: the Cache County study.

PubMed

Tschanz, J T; Welsh-Bohmer, K A; Skoog, I; West, N; Norton, M C; Wyse, B W; Nickles, R; Breitner, J C

2000-03-28

To validate a neuropsychological algorithm for dementia diagnosis. We developed a neuropsychological algorithm in a sample of 1,023 elderly residents of Cache County, UT. We compared algorithmic and clinical dementia diagnoses both based on DSM-III-R criteria. The algorithm diagnosed dementia when there was impairment in memory and at least one other cognitive domain. We also tested a variant of the algorithm that incorporated functional measures that were based on structured informant reports. Of 1,023 participants, 87% could be classified by the basic algorithm, 94% when functional measures were considered. There was good concordance between basic psychometric and clinical diagnoses (79% agreement, kappa = 0.57). This improved after incorporating functional measures (90% agreement, kappa = 0.76). Neuropsychological algorithms may reasonably classify individuals on dementia status across a range of severity levels and ages and may provide a useful adjunct to clinical diagnoses in population studies.

A parallel approach of COFFEE objective function to multiple sequence alignment

NASA Astrophysics Data System (ADS)

Zafalon, G. F. D.; Visotaky, J. M. V.; Amorim, A. R.; Valêncio, C. R.; Neves, L. A.; de Souza, R. C. G.; Machado, J. M.

2015-09-01

The computational tools to assist genomic analyzes show even more necessary due to fast increasing of data amount available. With high computational costs of deterministic algorithms for sequence alignments, many works concentrate their efforts in the development of heuristic approaches to multiple sequence alignments. However, the selection of an approach, which offers solutions with good biological significance and feasible execution time, is a great challenge. Thus, this work aims to show the parallelization of the processing steps of MSA-GA tool using multithread paradigm in the execution of COFFEE objective function. The standard objective function implemented in the tool is the Weighted Sum of Pairs (WSP), which produces some distortions in the final alignments when sequences sets with low similarity are aligned. Then, in studies previously performed we implemented the COFFEE objective function in the tool to smooth these distortions. Although the nature of COFFEE objective function implies in the increasing of execution time, this approach presents points, which can be executed in parallel. With the improvements implemented in this work, we can verify the execution time of new approach is 24% faster than the sequential approach with COFFEE. Moreover, the COFFEE multithreaded approach is more efficient than WSP, because besides it is slightly fast, its biological results are better.

Performance analysis of a dual-tree algorithm for computing spatial distance histograms

PubMed Central

Chen, Shaoping; Tu, Yi-Cheng; Xia, Yuni

2011-01-01

Many scientific and engineering fields produce large volume of spatiotemporal data. The storage, retrieval, and analysis of such data impose great challenges to database systems design. Analysis of scientific spatiotemporal data often involves computing functions of all point-to-point interactions. One such analytics, the Spatial Distance Histogram (SDH), is of vital importance to scientific discovery. Recently, algorithms for efficient SDH processing in large-scale scientific databases have been proposed. These algorithms adopt a recursive tree-traversing strategy to process point-to-point distances in the visited tree nodes in batches, thus require less time when compared to the brute-force approach where all pairwise distances have to be computed. Despite the promising experimental results, the complexity of such algorithms has not been thoroughly studied. In this paper, we present an analysis of such algorithms based on a geometric modeling approach. The main technique is to transform the analysis of point counts into a problem of quantifying the area of regions where pairwise distances can be processed in batches by the algorithm. From the analysis, we conclude that the number of pairwise distances that are left to be processed decreases exponentially with more levels of the tree visited. This leads to the proof of a time complexity lower than the quadratic time needed for a brute-force algorithm and builds the foundation for a constant-time approximate algorithm. Our model is also general in that it works for a wide range of point spatial distributions, histogram types, and space-partitioning options in building the tree. PMID:21804753

A globally convergent Lagrange and barrier function iterative algorithm for the traveling salesman problem.

PubMed

Dang, C; Xu, L

2001-03-01

In this paper a globally convergent Lagrange and barrier function iterative algorithm is proposed for approximating a solution of the traveling salesman problem. The algorithm employs an entropy-type barrier function to deal with nonnegativity constraints and Lagrange multipliers to handle linear equality constraints, and attempts to produce a solution of high quality by generating a minimum point of a barrier problem for a sequence of descending values of the barrier parameter. For any given value of the barrier parameter, the algorithm searches for a minimum point of the barrier problem in a feasible descent direction, which has a desired property that the nonnegativity constraints are always satisfied automatically if the step length is a number between zero and one. At each iteration the feasible descent direction is found by updating Lagrange multipliers with a globally convergent iterative procedure. For any given value of the barrier parameter, the algorithm converges to a stationary point of the barrier problem without any condition on the objective function. Theoretical and numerical results show that the algorithm seems more effective and efficient than the softassign algorithm.

A Double-function Digital Watermarking Algorithm Based on Chaotic System and LWT

NASA Astrophysics Data System (ADS)

Yuxia, Zhao; Jingbo, Fan

A double- function digital watermarking technology is studied and a double-function digital watermarking algorithm of colored image is presented based on chaotic system and the lifting wavelet transformation (LWT).The algorithm has realized the double aims of the copyright protection and the integrity authentication of image content. Making use of feature of human visual system (HVS), the watermark image is embedded into the color image's low frequency component and middle frequency components by different means. The algorithm has great security by using two kinds chaotic mappings and Arnold to scramble the watermark image at the same time. The algorithm has good efficiency by using LWT. The emulation experiment indicates the algorithm has great efficiency and security, and the effect of concealing is really good.

Resting-state functional magnetic resonance imaging in hepatic encephalopathy: current status and perspectives.

PubMed

Zhang, Long Jiang; Wu, Shengyong; Ren, Jiaqian; Lu, Guang Ming

2014-09-01

Hepatic encephalopathy (HE) is a neuropsychiatric syndrome which develops in patients with severe liver diseases and/or portal-systemic shunting. Minimal HE, the earliest manifestation of HE, has drawn increasing attention in the last decade. Minimal HE is associated with a series of brain functional changes, such as attention, working memory, and so on. Blood oxygen level dependent (BOLD) functional MRI (fMRI), especially resting-state fMRI has been used to explore the brain functional changes of HE, yielding important insights for understanding pathophysiological mechanisms and functional reorganization of HE. This paper briefly reviews the principles of BOLD fMRI, potential applications of resting-state fMRI with advanced post-processing algorithms such as regional homogeneity, amplitude of low frequency fluctuation, functional connectivity and future research perspective in this field.

Dynamic Reconstruction Algorithm of Three-Dimensional Temperature Field Measurement by Acoustic Tomography

PubMed Central

Li, Yanqiu; Liu, Shi; Inaki, Schlaberg H.

2017-01-01

Accuracy and speed of algorithms play an important role in the reconstruction of temperature field measurements by acoustic tomography. Existing algorithms are based on static models which only consider the measurement information. A dynamic model of three-dimensional temperature reconstruction by acoustic tomography is established in this paper. A dynamic algorithm is proposed considering both acoustic measurement information and the dynamic evolution information of the temperature field. An objective function is built which fuses measurement information and the space constraint of the temperature field with its dynamic evolution information. Robust estimation is used to extend the objective function. The method combines a tunneling algorithm and a local minimization technique to solve the objective function. Numerical simulations show that the image quality and noise immunity of the dynamic reconstruction algorithm are better when compared with static algorithms such as least square method, algebraic reconstruction technique and standard Tikhonov regularization algorithms. An effective method is provided for temperature field reconstruction by acoustic tomography. PMID:28895930

Evaluation of a new charge algorithm for a lead-acid battery with gelled electrolyte using a 96V gel cell IV as a test battery

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nowak, D.K.

1989-10-01

This document has reported a summary of test results obtained utilizing the new UAH charge algorithm for Lead-Acid batteries with gelled electrolyte. The battery performance data for a 96V Phase IV Gel/Cell battery pack was tested in a Jet Industries Electrica vehicle. It was shown that the new charge concept is sound although there can be problems with batteries that are highly imbalanced and where excessive electronic noise is experienced on the electronic signal feed-back line that carries the voltage sensor signals from the battery. Additional work is needed to add intelligence to the charge algorithm in terms of amore » better ability to extract the beginning of gas development from the voltage spread function. This can probably be accomplished by scanning the voltages more often and including that data into the function analysis by adding software filters. The Phase IV Gel/Cell battery performance was found to be about 20% lower than that of the Phase III Gel/Cell battery. Problems with cell valve leakage were encountered in the Phase IV Gel/Cell that pose a threat to battery life although so far no battery module has been lost. 2 refs., 13 figs., 4 tabs.« less

Semiautomatic tumor segmentation with multimodal images in a conditional random field framework.

PubMed

Hu, Yu-Chi; Grossberg, Michael; Mageras, Gikas

2016-04-01

Volumetric medical images of a single subject can be acquired using different imaging modalities, such as computed tomography, magnetic resonance imaging (MRI), and positron emission tomography. In this work, we present a semiautomatic segmentation algorithm that can leverage the synergies between different image modalities while integrating interactive human guidance. The algorithm provides a statistical segmentation framework partly automating the segmentation task while still maintaining critical human oversight. The statistical models presented are trained interactively using simple brush strokes to indicate tumor and nontumor tissues and using intermediate results within a patient's image study. To accomplish the segmentation, we construct the energy function in the conditional random field (CRF) framework. For each slice, the energy function is set using the estimated probabilities from both user brush stroke data and prior approved segmented slices within a patient study. The progressive segmentation is obtained using a graph-cut-based minimization. Although no similar semiautomated algorithm is currently available, we evaluated our method with an MRI data set from Medical Image Computing and Computer Assisted Intervention Society multimodal brain segmentation challenge (BRATS 2012 and 2013) against a similar fully automatic method based on CRF and a semiautomatic method based on grow-cut, and our method shows superior performance.

Interpolation on the manifold of K component GMMs.

PubMed

Kim, Hyunwoo J; Adluru, Nagesh; Banerjee, Monami; Vemuri, Baba C; Singh, Vikas

2015-12-01

Probability density functions (PDFs) are fundamental objects in mathematics with numerous applications in computer vision, machine learning and medical imaging. The feasibility of basic operations such as computing the distance between two PDFs and estimating a mean of a set of PDFs is a direct function of the representation we choose to work with. In this paper, we study the Gaussian mixture model (GMM) representation of the PDFs motivated by its numerous attractive features. (1) GMMs are arguably more interpretable than, say, square root parameterizations (2) the model complexity can be explicitly controlled by the number of components and (3) they are already widely used in many applications. The main contributions of this paper are numerical algorithms to enable basic operations on such objects that strictly respect their underlying geometry. For instance, when operating with a set of K component GMMs, a first order expectation is that the result of simple operations like interpolation and averaging should provide an object that is also a K component GMM. The literature provides very little guidance on enforcing such requirements systematically. It turns out that these tasks are important internal modules for analysis and processing of a field of ensemble average propagators (EAPs), common in diffusion weighted magnetic resonance imaging. We provide proof of principle experiments showing how the proposed algorithms for interpolation can facilitate statistical analysis of such data, essential to many neuroimaging studies. Separately, we also derive interesting connections of our algorithm with functional spaces of Gaussians, that may be of independent interest.

Towards the automatization of the Foucault knife-edge quantitative test

NASA Astrophysics Data System (ADS)

Rodríguez, G.; Villa, J.; Martínez, G.; de la Rosa, I.; Ivanov, R.

2017-08-01

Given the increasing necessity of simple, economical and reliable methods and instruments for performing quality tests of optical surfaces such as mirrors and lenses, in the recent years we resumed the study of the long forgotten Foucault knife-edge test from the point of view of the physical optics, ultimately achieving a closed mathematical expression that directly relates the knife-edge position along the displacement paraxial axis with the observable irradiance pattern, which later allowed us to propose a quantitative methodology for estimating the wavefront error of an aspherical mirror with precision akin to interferometry. In this work, we present a further improved digital image processing algorithm in which the sigmoidal cost-function for calculating the transient slope-point of each associated intensity-illumination profile is replaced for a simplified version of it, thus making the whole process of estimating the wavefront gradient remarkably more stable and efficient, at the same time, the Fourier based algorithm employed for gradient integration has been replaced as well for a regularized quadratic cost-function that allows a considerably easier introduction of the region of interest (ROI) of the function, which solved by means of a linear gradient conjugate method largely increases the overall accuracy and efficiency of the algorithm. This revised approach of our methodology can be easily implemented and handled by most single-board microcontrollers in the market, hence enabling the implementation of a full-integrated automatized test apparatus, opening a realistic path for even the proposal of a stand-alone optical mirror analyzer prototype.

Theoretical and experimental study of a new algorithm for factoring numbers

NASA Astrophysics Data System (ADS)

Tamma, Vincenzo

The security of codes, for example in credit card and government information, relies on the fact that the factorization of a large integer N is a rather costly process on a classical digital computer. Such a security is endangered by Shor's algorithm which employs entangled quantum systems to find, with a polynomial number of resources, the period of a function which is connected with the factors of N. We can surely expect a possible future realization of such a method for large numbers, but so far the period of Shor's function has been only computed for the number 15. Inspired by Shor's idea, our work aims to methods of factorization based on the periodicity measurement of a given continuous periodic "factoring function" which is physically implementable using an analogue computer. In particular, we have focused on both the theoretical and the experimental analysis of Gauss sums with continuous arguments leading to a new factorization algorithm. The procedure allows, for the first time, to factor several numbers by measuring the periodicity of Gauss sums performing first-order "factoring" interfer ence processes. We experimentally implemented this idea by exploiting polychromatic optical interference in the visible range with a multi-path interferometer, and achieved the factorization of seven digit numbers. The physical principle behind this "factoring" interference procedure can be potentially exploited also on entangled systems, as multi-photon entangled states, in order to achieve a polynomial scaling in the number of resources.

Evaluation of an Area-Based matching algorithm with advanced shape models

NASA Astrophysics Data System (ADS)

Re, C.; Roncella, R.; Forlani, G.; Cremonese, G.; Naletto, G.

2014-04-01

Nowadays, the scientific institutions involved in planetary mapping are working on new strategies to produce accurate high resolution DTMs from space images at planetary scale, usually dealing with extremely large data volumes. From a methodological point of view, despite the introduction of a series of new algorithms for image matching (e.g. the Semi Global Matching) that yield superior results (especially because they produce usually smooth and continuous surfaces) with lower processing times, the preference in this field still goes to well established area-based matching techniques. Many efforts are consequently directed to improve each phase of the photogrammetric process, from image pre-processing to DTM interpolation. In this context, the Dense Matcher software (DM) developed at the University of Parma has been recently optimized to cope with very high resolution images provided by the most recent missions (LROC NAC and HiRISE) focusing the efforts mainly to the improvement of the correlation phase and the process automation. Important changes have been made to the correlation algorithm, still maintaining its high performance in terms of precision and accuracy, by implementing an advanced version of the Least Squares Matching (LSM) algorithm. In particular, an iterative algorithm has been developed to adapt the geometric transformation in image resampling using different shape functions as originally proposed by other authors in different applications.

The Separatrix Algorithm for Synthesis and Analysis of Stochastic Simulations with Applications in Disease Modeling

PubMed Central

Klein, Daniel J.; Baym, Michael; Eckhoff, Philip

2014-01-01

Decision makers in epidemiology and other disciplines are faced with the daunting challenge of designing interventions that will be successful with high probability and robust against a multitude of uncertainties. To facilitate the decision making process in the context of a goal-oriented objective (e.g., eradicate polio by ), stochastic models can be used to map the probability of achieving the goal as a function of parameters. Each run of a stochastic model can be viewed as a Bernoulli trial in which “success” is returned if and only if the goal is achieved in simulation. However, each run can take a significant amount of time to complete, and many replicates are required to characterize each point in parameter space, so specialized algorithms are required to locate desirable interventions. To address this need, we present the Separatrix Algorithm, which strategically locates parameter combinations that are expected to achieve the goal with a user-specified probability of success (e.g. 95%). Technically, the algorithm iteratively combines density-corrected binary kernel regression with a novel information-gathering experiment design to produce results that are asymptotically correct and work well in practice. The Separatrix Algorithm is demonstrated on several test problems, and on a detailed individual-based simulation of malaria. PMID:25078087

Intelligent agents: adaptation of autonomous bimodal microsystems

NASA Astrophysics Data System (ADS)

Smith, Patrice; Terry, Theodore B.

2014-03-01

Autonomous bimodal microsystems exhibiting survivability behaviors and characteristics are able to adapt dynamically in any given environment. Equipped with a background blending exoskeleton it will have the capability to stealthily detect and observe a self-chosen viewing area while exercising some measurable form of selfpreservation by either flying or crawling away from a potential adversary. The robotic agent in this capacity activates a walk-fly algorithm, which uses a built in multi-sensor processing and navigation subsystem or algorithm for visual guidance and best walk-fly path trajectory to evade capture or annihilation. The research detailed in this paper describes the theoretical walk-fly algorithm, which broadens the scope of spatial and temporal learning, locomotion, and navigational performances based on optical flow signals necessary for flight dynamics and walking stabilities. By observing a fly's travel and avoidance behaviors; and, understanding the reverse bioengineering research efforts of others, we were able to conceptualize an algorithm, which works in conjunction with decisionmaking functions, sensory processing, and sensorimotor integration. Our findings suggest that this highly complex decentralized algorithm promotes inflight or terrain travel mobile stability which is highly suitable for nonaggressive micro platforms supporting search and rescue (SAR), and chemical and explosive detection (CED) purposes; a necessity in turbulent, non-violent structured or unstructured environments.

Real-time trajectory optimization on parallel processors

NASA Technical Reports Server (NTRS)

Psiaki, Mark L.

1993-01-01

A parallel algorithm has been developed for rapidly solving trajectory optimization problems. The goal of the work has been to develop an algorithm that is suitable to do real-time, on-line optimal guidance through repeated solution of a trajectory optimization problem. The algorithm has been developed on an INTEL iPSC/860 message passing parallel processor. It uses a zero-order-hold discretization of a continuous-time problem and solves the resulting nonlinear programming problem using a custom-designed augmented Lagrangian nonlinear programming algorithm. The algorithm achieves parallelism of function, derivative, and search direction calculations through the principle of domain decomposition applied along the time axis. It has been encoded and tested on 3 example problems, the Goddard problem, the acceleration-limited, planar minimum-time to the origin problem, and a National Aerospace Plane minimum-fuel ascent guidance problem. Execution times as fast as 118 sec of wall clock time have been achieved for a 128-stage Goddard problem solved on 32 processors. A 32-stage minimum-time problem has been solved in 151 sec on 32 processors. A 32-stage National Aerospace Plane problem required 2 hours when solved on 32 processors. A speed-up factor of 7.2 has been achieved by using 32-nodes instead of 1-node to solve a 64-stage Goddard problem.

An efficient algorithm for function optimization: modified stem cells algorithm

NASA Astrophysics Data System (ADS)

Taherdangkoo, Mohammad; Paziresh, Mahsa; Yazdi, Mehran; Bagheri, Mohammad Hadi

2013-03-01

In this paper, we propose an optimization algorithm based on the intelligent behavior of stem cell swarms in reproduction and self-organization. Optimization algorithms, such as the Genetic Algorithm (GA), Particle Swarm Optimization (PSO) algorithm, Ant Colony Optimization (ACO) algorithm and Artificial Bee Colony (ABC) algorithm, can give solutions to linear and non-linear problems near to the optimum for many applications; however, in some case, they can suffer from becoming trapped in local optima. The Stem Cells Algorithm (SCA) is an optimization algorithm inspired by the natural behavior of stem cells in evolving themselves into new and improved cells. The SCA avoids the local optima problem successfully. In this paper, we have made small changes in the implementation of this algorithm to obtain improved performance over previous versions. Using a series of benchmark functions, we assess the performance of the proposed algorithm and compare it with that of the other aforementioned optimization algorithms. The obtained results prove the superiority of the Modified Stem Cells Algorithm (MSCA).

Kidney-inspired algorithm for optimization problems

NASA Astrophysics Data System (ADS)

Jaddi, Najmeh Sadat; Alvankarian, Jafar; Abdullah, Salwani

2017-01-01

In this paper, a population-based algorithm inspired by the kidney process in the human body is proposed. In this algorithm the solutions are filtered in a rate that is calculated based on the mean of objective functions of all solutions in the current population of each iteration. The filtered solutions as the better solutions are moved to filtered blood and the rest are transferred to waste representing the worse solutions. This is a simulation of the glomerular filtration process in the kidney. The waste solutions are reconsidered in the iterations if after applying a defined movement operator they satisfy the filtration rate, otherwise it is expelled from the waste solutions, simulating the reabsorption and excretion functions of the kidney. In addition, a solution assigned as better solution is secreted if it is not better than the worst solutions simulating the secreting process of blood in the kidney. After placement of all the solutions in the population, the best of them is ranked, the waste and filtered blood are merged to become a new population and the filtration rate is updated. Filtration provides the required exploitation while generating a new solution and reabsorption gives the necessary exploration for the algorithm. The algorithm is assessed by applying it on eight well-known benchmark test functions and compares the results with other algorithms in the literature. The performance of the proposed algorithm is better on seven out of eight test functions when it is compared with the most recent researches in literature. The proposed kidney-inspired algorithm is able to find the global optimum with less function evaluations on six out of eight test functions. A statistical analysis further confirms the ability of this algorithm to produce good-quality results.

Motion compensation for fully 4D PET reconstruction using PET superset data

NASA Astrophysics Data System (ADS)

Verhaeghe, J.; Gravel, P.; Mio, R.; Fukasawa, R.; Rosa-Neto, P.; Soucy, J.-P.; Thompson, C. J.; Reader, A. J.

2010-07-01

Fully 4D PET image reconstruction is receiving increasing research interest due to its ability to significantly reduce spatiotemporal noise in dynamic PET imaging. However, thus far in the literature, the important issue of correcting for subject head motion has not been considered. Specifically, as a direct consequence of using temporally extensive basis functions, a single instance of movement propagates to impair the reconstruction of multiple time frames, even if no further movement occurs in those frames. Existing 3D motion compensation strategies have not yet been adapted to 4D reconstruction, and as such the benefits of 4D algorithms have not yet been reaped in a clinical setting where head movement undoubtedly occurs. This work addresses this need, developing a motion compensation method suitable for fully 4D reconstruction methods which exploits an optical tracking system to measure the head motion along with PET superset data to store the motion compensated data. List-mode events are histogrammed as PET superset data according to the measured motion, and a specially devised normalization scheme for motion compensated reconstruction from the superset data is required. This work proceeds to propose the corresponding time-dependent normalization modifications which are required for a major class of fully 4D image reconstruction algorithms (those which use linear combinations of temporal basis functions). Using realistically simulated as well as real high-resolution PET data from the HRRT, we demonstrate both the detrimental impact of subject head motion in fully 4D PET reconstruction and the efficacy of our proposed modifications to 4D algorithms. Benefits are shown both for the individual PET image frames as well as for parametric images of tracer uptake and volume of distribution for 18F-FDG obtained from Patlak analysis.

On the elimination of the electronic structure bottleneck in on the fly nonadiabatic dynamics for small to moderate sized (10-15 atom) molecules using fit diabatic representations based solely on ab initio electronic structure data: The photodissociation of phenol

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhu, Xiaolei, E-mail: virtualzx@gmail.com; Yarkony, David R., E-mail: yarkony@jhu.edu

2016-01-14

In this work, we demonstrate that for moderate sized systems, here a system with 13 atoms, global coupled potential energy surfaces defined for several electronic states over a wide energy range and for distinct regions of nuclear coordinate space characterized by distinct electron configurations, can be constructed with precise energetics and an excellent description of non-adiabatic interactions in all regions. This is accomplished using a recently reported algorithm for constructing quasi-diabatic representations, H{sup d}, of adiabatic electronic states coupled by conical intersections. In this work, the algorithm is used to construct an H{sup d} to describe the photodissociation of phenolmore » from its first and second excited electronic states. The representation treats all 33 internal degrees of freedom in an even handed manner. The ab initio adiabatic electronic structure data used to construct the fit are obtained exclusively from multireference configuration interaction with single and double excitation wave functions comprised of 88 × 10{sup 6} configuration state functions, at geometries determined by quasi-classical trajectories. Since the algorithm uses energy gradients and derivative couplings in addition to electronic energies to construct H{sup d}, data at only 7379 nuclear configurations are required to construct a representation, which describes all nuclear configurations involved in H atom photodissociation to produce the phenoxyl radical in its ground or first excited electronic state, with a mean unsigned energy error of 202.9 cm{sup −1} for electronic energies <60 000 cm{sup −1}.« less

Motion compensation for fully 4D PET reconstruction using PET superset data.

PubMed

Verhaeghe, J; Gravel, P; Mio, R; Fukasawa, R; Rosa-Neto, P; Soucy, J-P; Thompson, C J; Reader, A J

2010-07-21

Fully 4D PET image reconstruction is receiving increasing research interest due to its ability to significantly reduce spatiotemporal noise in dynamic PET imaging. However, thus far in the literature, the important issue of correcting for subject head motion has not been considered. Specifically, as a direct consequence of using temporally extensive basis functions, a single instance of movement propagates to impair the reconstruction of multiple time frames, even if no further movement occurs in those frames. Existing 3D motion compensation strategies have not yet been adapted to 4D reconstruction, and as such the benefits of 4D algorithms have not yet been reaped in a clinical setting where head movement undoubtedly occurs. This work addresses this need, developing a motion compensation method suitable for fully 4D reconstruction methods which exploits an optical tracking system to measure the head motion along with PET superset data to store the motion compensated data. List-mode events are histogrammed as PET superset data according to the measured motion, and a specially devised normalization scheme for motion compensated reconstruction from the superset data is required. This work proceeds to propose the corresponding time-dependent normalization modifications which are required for a major class of fully 4D image reconstruction algorithms (those which use linear combinations of temporal basis functions). Using realistically simulated as well as real high-resolution PET data from the HRRT, we demonstrate both the detrimental impact of subject head motion in fully 4D PET reconstruction and the efficacy of our proposed modifications to 4D algorithms. Benefits are shown both for the individual PET image frames as well as for parametric images of tracer uptake and volume of distribution for (18)F-FDG obtained from Patlak analysis.

Brain-Inspired Constructive Learning Algorithms with Evolutionally Additive Nonlinear Neurons

NASA Astrophysics Data System (ADS)

Fang, Le-Heng; Lin, Wei; Luo, Qiang

In this article, inspired partially by the physiological evidence of brain’s growth and development, we developed a new type of constructive learning algorithm with evolutionally additive nonlinear neurons. The new algorithms have remarkable ability in effective regression and accurate classification. In particular, the algorithms are able to sustain a certain reduction of the loss function when the dynamics of the trained network are bogged down in the vicinity of the local minima. The algorithm augments the neural network by adding only a few connections as well as neurons whose activation functions are nonlinear, nonmonotonic, and self-adapted to the dynamics of the loss functions. Indeed, we analytically demonstrate the reduction dynamics of the algorithm for different problems, and further modify the algorithms so as to obtain an improved generalization capability for the augmented neural networks. Finally, through comparing with the classical algorithm and architecture for neural network construction, we show that our constructive learning algorithms as well as their modified versions have better performances, such as faster training speed and smaller network size, on several representative benchmark datasets including the MNIST dataset for handwriting digits.

Improved algorithm for calculating the Chandrasekhar function

NASA Astrophysics Data System (ADS)

Jablonski, A.

2013-02-01

Theoretical models of electron transport in condensed matter require an effective source of the Chandrasekhar H(x,omega) function. A code providing the H(x,omega) function has to be both accurate and very fast. The current revision of the code published earlier [A. Jablonski, Comput. Phys. Commun. 183 (2012) 1773] decreased the running time, averaged over different pairs of arguments x and omega, by a factor of more than 20. The decrease of the running time in the range of small values of the argument x, less than 0.05, is even more pronounced, reaching a factor of 30. The accuracy of the current code is not affected, and is typically better than 12 decimal places. New version program summaryProgram title: CHANDRAS_v2 Catalogue identifier: AEMC_v2_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEMC_v2_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC license, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 976 No. of bytes in distributed program, including test data, etc.: 11416 Distribution format: tar.gz Programming language: Fortran 90 Computer: Any computer with a Fortran 90 compiler Operating system: Windows 7, Windows XP, Unix/Linux RAM: 0.7 MB Classification: 2.4, 7.2 Catalogue identifier of previous version: AEMC_v1_0 Journal reference of previous version: Comput. Phys. Commun. 183 (2012) 1773 Does the new version supersede the old program: Yes Nature of problem: An attempt has been made to develop a subroutine that calculates the Chandrasekhar function with high accuracy, of at least 10 decimal places. Simultaneously, this subroutine should be very fast. Both requirements stem from the theory of electron transport in condensed matter. Solution method: Two algorithms were developed, each based on a different integral representation of the Chandrasekhar function. The final algorithm is edited by mixing these two algorithms by selecting ranges of the argument omega in which the performance is the fastest. Reasons for the new version: Some of the theoretical models describing electron transport in condensed matter need a source of the Chandrasekhar H function values with an accuracy of at least 10 decimal places. Additionally, calculations of this function should be as fast as possible since frequent calls to a subroutine providing this function are made (e.g., numerical evaluation of a double integral with a complicated integrand containing the H function). Both conditions were satisfied in the algorithm previously published [1]. However, it has been found that a proper selection of the quadrature in an integral representation of the Chandrasekhar function may considerably decrease the running time. By suitable selection of the number of abscissas in Gauss-Legendre quadrature, the execution time was decreased by a factor of more than 20. Simultaneously, the accuracy of results has not been affected. Summary of revisions: (1) As in previous work [1], two integral representations of the Chandrasekhar function, H(x,omega), were considered: the expression published by Dudarev and Whelan [2] and the expression published by Davidović et al. [3]. The algorithms implementing these representations were designated A and B, respectively. All integrals in these implementations were previously calculated using Romberg quadrature. It has been found, however, that the use of Gauss-Legendre quadrature considerably improved the performance of both algorithms. Two conditions have to be satisfied. (i) The number of abscissas, N, has to be rather large, and (ii) the abscissas and corresponding weights should be determined with accuracy as high as possible. The abscissas and weights are available for N=16, 20, 24, 32, 40, 48, 64, 80, and 96 with accuracy of 20 decimal places [4], and all these values were introduced into a new procedure GAUSS replacing procedure ROMBERG. Due to the fact that the implemented tables are rather extensive, they were recalculated using the Rybicki algorithm (Ref. [5], pp. 183-184) and rechecked. No errors or misprints were found. (2) In the integral representation of the H function derived by Davidović et al. [3], the positive root ν0 of the so-called dispersion function needs to be calculated with accuracy of at least 10 decimal places (see. Ref [6], pp. 61-64 and Ref. [1], Eqs. (5) and (29)). For small values of the argument omega and values of omega close to unity, the nonlinear equation in one unknown, ν0, can be solved analytically. New simple analytical expressions were derived here that can be efficiently used in calculations of the root. (3) The above modifications of the code considerably decreased the time of calculation of both algorithms A and B. The results are summarized in Fig. 1. The time of calculations is in fact the CPU time in microseconds for a computer equipped with an Inter Xeon processor (3.46 GHz) using Lahey-Fujitsu Fortran v. 7.2. Time of calculations of the H(x,omega) function averaged over different pairs of arguments x and omega. (a) 400 pairs uniformly distributed in the ranges 0<=x<=0.05 and 0<=omega<=1; (b) 400 pairs uniformly distributed in the ranges 0.05<=x<=1 and 0<=omega<=1. The shortest execution time averaged over values of the argument x exceeding 0.05 has been observed for algorithm B and Gauss-Legendre quadrature with the number of abscissas equal to 64 (23.2 μs). As compared with Romberg quadrature, the execution time was shortened by a factor of 22.5. For small x values, below 0.05, both algorithms A and B are considerably faster if Gauss-Legendre quadrature is used. For N=64, the average time of execution of algorithm B is decreased with respect to Romberg quadrature by a factor close to 30. However, in that range of argument x, algorithm A exhibits much faster performance. Furthermore, the average execution time of algorithm A, equal to about 100 μs, is practically independent of the number of abscissas N. (4) For Romberg quadrature, to optimize the performance, the mixed algorithm C was proposed in which algorithm A is used for argument x smaller than or equal to x0=0.4, while algorithm B is used for x larger than 0.4 [1]. For Gauss-Legendre quadrature, the limit x0 was found to depend on the number of abscissas N. For each value of N considered, the time of calculations of the H function was determined for pairs of arguments uniformly distributed in the ranges 0<=x<=0.05 and 0<=omega<=1, and for pairs of arguments uniformly distributed in the ranges 0.05<=x<=1 and 0<=omega<=1. As shown in Fig. 2 for N=64, algorithm A is faster than algorithm B for x smaller than or equal to 0.0225. Comparison of the running times of algorithms A and B. Open circles: algorithm B is faster than the algorithm A; full circles: algorithm A is faster than algorithm B. Thus, the value of x0=0.0225 is proposed for the mixed algorithm C when Gauss-Legendere quadrature with N=64 is used. Similar computer experiments performed for other values of N are summarized below. L N0 1 16 0.25 2 20 0.15 3 24 0.10 4 32 0.050 5 40 0.030 6 48 0.045 7 64 0.0225-Recommended 8 80 0.0125 9 96 0.020 The flag L is one of the input parameters for the subroutine GAUSS. In the programs implementing algorithms A, B, and C (CHANDRA, CHANDRB, and CHANDRC), Gauss-Legendre quadrature with N=64 is currently set. As follows from Fig. 1, algorithm B (and consequently algorithm C) is the fastest in that case. It is still possible to change the number of abscissas; the flag L then has to be modified in lines 165, 169, 185, 189, and 304 of program CHANDRAS_v2, and the value of x0 in line 111 has to be adjusted according to the table above. (5) The above modifications of the code did not affect the accuracy of the calculated Chandrasekhar function, as compared to the original code [1]. For the pairs of arguments shown in Fig. 2, the accuracy of the H function, calculated from algorithms A and B, reached at least 12 decimal digits; however, in the majority of cases, the accuracy is equal to 13 decimal digits. Restrictions: Two input parameters for the Chandrasekhar function, x and omega, are restricted to the ranges 0<=x<=1 and 0<=omega<=1, which is sufficient in numerous applications. Running time: between 15 and 100 μs for one pair of arguments of the Chandrasekhar function.

Quantum Chemistry on Quantum Computers: A Polynomial-Time Quantum Algorithm for Constructing the Wave Functions of Open-Shell Molecules.

PubMed

Sugisaki, Kenji; Yamamoto, Satoru; Nakazawa, Shigeaki; Toyota, Kazuo; Sato, Kazunobu; Shiomi, Daisuke; Takui, Takeji

2016-08-18

Quantum computers are capable to efficiently perform full configuration interaction (FCI) calculations of atoms and molecules by using the quantum phase estimation (QPE) algorithm. Because the success probability of the QPE depends on the overlap between approximate and exact wave functions, efficient methods to prepare accurate initial guess wave functions enough to have sufficiently large overlap with the exact ones are highly desired. Here, we propose a quantum algorithm to construct the wave function consisting of one configuration state function, which is suitable for the initial guess wave function in QPE-based FCI calculations of open-shell molecules, based on the addition theorem of angular momentum. The proposed quantum algorithm enables us to prepare the wave function consisting of an exponential number of Slater determinants only by a polynomial number of quantum operations.

Techniques for shuttle trajectory optimization

NASA Technical Reports Server (NTRS)

Edge, E. R.; Shieh, C. J.; Powers, W. F.

1973-01-01

The application of recently developed function-space Davidon-type techniques to the shuttle ascent trajectory optimization problem is discussed along with an investigation of the recently developed PRAXIS algorithm for parameter optimization. At the outset of this analysis, the major deficiency of the function-space algorithms was their potential storage problems. Since most previous analyses of the methods were with relatively low-dimension problems, no storage problems were encountered. However, in shuttle trajectory optimization, storage is a problem, and this problem was handled efficiently. Topics discussed include: the shuttle ascent model and the development of the particular optimization equations; the function-space algorithms; the operation of the algorithm and typical simulations; variable final-time problem considerations; and a modification of Powell's algorithm.

Unsupervised classification of multivariate geostatistical data: Two algorithms

NASA Astrophysics Data System (ADS)

Romary, Thomas; Ors, Fabien; Rivoirard, Jacques; Deraisme, Jacques

2015-12-01

With the increasing development of remote sensing platforms and the evolution of sampling facilities in mining and oil industry, spatial datasets are becoming increasingly large, inform a growing number of variables and cover wider and wider areas. Therefore, it is often necessary to split the domain of study to account for radically different behaviors of the natural phenomenon over the domain and to simplify the subsequent modeling step. The definition of these areas can be seen as a problem of unsupervised classification, or clustering, where we try to divide the domain into homogeneous domains with respect to the values taken by the variables in hand. The application of classical clustering methods, designed for independent observations, does not ensure the spatial coherence of the resulting classes. Image segmentation methods, based on e.g. Markov random fields, are not adapted to irregularly sampled data. Other existing approaches, based on mixtures of Gaussian random functions estimated via the expectation-maximization algorithm, are limited to reasonable sample sizes and a small number of variables. In this work, we propose two algorithms based on adaptations of classical algorithms to multivariate geostatistical data. Both algorithms are model free and can handle large volumes of multivariate, irregularly spaced data. The first one proceeds by agglomerative hierarchical clustering. The spatial coherence is ensured by a proximity condition imposed for two clusters to merge. This proximity condition relies on a graph organizing the data in the coordinates space. The hierarchical algorithm can then be seen as a graph-partitioning algorithm. Following this interpretation, a spatial version of the spectral clustering algorithm is also proposed. The performances of both algorithms are assessed on toy examples and a mining dataset.

Automatic identification of epileptic seizures from EEG signals using linear programming boosting.

PubMed

Hassan, Ahnaf Rashik; Subasi, Abdulhamit

2016-11-01

Computerized epileptic seizure detection is essential for expediting epilepsy diagnosis and research and for assisting medical professionals. Moreover, the implementation of an epilepsy monitoring device that has low power and is portable requires a reliable and successful seizure detection scheme. In this work, the problem of automated epilepsy seizure detection using singe-channel EEG signals has been addressed. At first, segments of EEG signals are decomposed using a newly proposed signal processing scheme, namely complete ensemble empirical mode decomposition with adaptive noise (CEEMDAN). Six spectral moments are extracted from the CEEMDAN mode functions and train and test matrices are formed afterward. These matrices are fed into the classifier to identify epileptic seizures from EEG signal segments. In this work, we implement an ensemble learning based machine learning algorithm, namely linear programming boosting (LPBoost) to perform classification. The efficacy of spectral features in the CEEMDAN domain is validated by graphical and statistical analyses. The performance of CEEMDAN is compared to those of its predecessors to further inspect its suitability. The effectiveness and the appropriateness of LPBoost are demonstrated as opposed to the commonly used classification models. Resubstitution and 10 fold cross-validation error analyses confirm the superior algorithm performance of the proposed scheme. The algorithmic performance of our epilepsy seizure identification scheme is also evaluated against state-of-the-art works in the literature. Experimental outcomes manifest that the proposed seizure detection scheme performs better than the existing works in terms of accuracy, sensitivity, specificity, and Cohen's Kappa coefficient. It can be anticipated that owing to its use of only one channel of EEG signal, the proposed method will be suitable for device implementation, eliminate the onus of clinicians for analyzing a large bulk of data manually, and expedite epilepsy diagnosis. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Forecasting Nonlinear Chaotic Time Series with Function Expression Method Based on an Improved Genetic-Simulated Annealing Algorithm

PubMed Central

Wang, Jun; Zhou, Bi-hua; Zhou, Shu-dao; Sheng, Zheng

2015-01-01

The paper proposes a novel function expression method to forecast chaotic time series, using an improved genetic-simulated annealing (IGSA) algorithm to establish the optimum function expression that describes the behavior of time series. In order to deal with the weakness associated with the genetic algorithm, the proposed algorithm incorporates the simulated annealing operation which has the strong local search ability into the genetic algorithm to enhance the performance of optimization; besides, the fitness function and genetic operators are also improved. Finally, the method is applied to the chaotic time series of Quadratic and Rossler maps for validation. The effect of noise in the chaotic time series is also studied numerically. The numerical results verify that the method can forecast chaotic time series with high precision and effectiveness, and the forecasting precision with certain noise is also satisfactory. It can be concluded that the IGSA algorithm is energy-efficient and superior. PMID:26000011

Forecasting nonlinear chaotic time series with function expression method based on an improved genetic-simulated annealing algorithm.

PubMed

Wang, Jun; Zhou, Bi-hua; Zhou, Shu-dao; Sheng, Zheng

2015-01-01

The paper proposes a novel function expression method to forecast chaotic time series, using an improved genetic-simulated annealing (IGSA) algorithm to establish the optimum function expression that describes the behavior of time series. In order to deal with the weakness associated with the genetic algorithm, the proposed algorithm incorporates the simulated annealing operation which has the strong local search ability into the genetic algorithm to enhance the performance of optimization; besides, the fitness function and genetic operators are also improved. Finally, the method is applied to the chaotic time series of Quadratic and Rossler maps for validation. The effect of noise in the chaotic time series is also studied numerically. The numerical results verify that the method can forecast chaotic time series with high precision and effectiveness, and the forecasting precision with certain noise is also satisfactory. It can be concluded that the IGSA algorithm is energy-efficient and superior.

A quasi-Newton approach to optimization problems with probability density constraints. [problem solving in mathematical programming

NASA Technical Reports Server (NTRS)

Tapia, R. A.; Vanrooy, D. L.

1976-01-01

A quasi-Newton method is presented for minimizing a nonlinear function while constraining the variables to be nonnegative and sum to one. The nonnegativity constraints were eliminated by working with the squares of the variables and the resulting problem was solved using Tapia's general theory of quasi-Newton methods for constrained optimization. A user's guide for a computer program implementing this algorithm is provided.

Foundations for a syntatic pattern recognition system for genomic DNA sequences

DOE Office of Scientific and Technical Information (OSTI.GOV)

Searles, D.B.

1993-03-01

The goal of the proposed work is the creation of a software system that will perform sophisticated pattern recognition and related functions at a level of abstraction and with expressive power beyond current general-purpose pattern-matching systems for biological sequences; and with a more uniform language, environment, and graphical user interface, and with greater flexibility, extensibility, embeddability, and ability to incorporate other algorithms, than current special-purpose analytic software.

Sparse Representations for Limited Data Tomography (PREPRINT)

DTIC Science & Technology

2007-11-01

predefined (such as wavelets ) or learned (e.g., by the K-SVD algorithm [8]), as in this work. Due to its highly effectiveness for tasks such as image...from den- tal data produced by the Focus intraoral X-ray source and the Sigma intraoral sensor (Instrumentarium Dental ; courtesy of Maaria Rantala...proposed method (right column). a functional, encouraging a sparse representation of the im- age patches while keeping the data constraints provided by

Real-Time State Estimation in a Flight Simulator Using fNIRS

PubMed Central

Gateau, Thibault; Durantin, Gautier; Lancelot, Francois; Scannella, Sebastien; Dehais, Frederic

2015-01-01

Working memory is a key executive function for flying an aircraft. This function is particularly critical when pilots have to recall series of air traffic control instructions. However, working memory limitations may jeopardize flight safety. Since the functional near-infrared spectroscopy (fNIRS) method seems promising for assessing working memory load, our objective is to implement an on-line fNIRS-based inference system that integrates two complementary estimators. The first estimator is a real-time state estimation MACD-based algorithm dedicated to identifying the pilot’s instantaneous mental state (not-on-task vs. on-task). It does not require a calibration process to perform its estimation. The second estimator is an on-line SVM-based classifier that is able to discriminate task difficulty (low working memory load vs. high working memory load). These two estimators were tested with 19 pilots who were placed in a realistic flight simulator and were asked to recall air traffic control instructions. We found that the estimated pilot’s mental state matched significantly better than chance with the pilot’s real state (62% global accuracy, 58% specificity, and 72% sensitivity). The second estimator, dedicated to assessing single trial working memory loads, led to 80% classification accuracy, 72% specificity, and 89% sensitivity. These two estimators establish reusable blocks for further fNIRS-based passive brain computer interface development. PMID:25816347

Dynamic Inertia Weight Binary Bat Algorithm with Neighborhood Search

PubMed Central

2017-01-01

Binary bat algorithm (BBA) is a binary version of the bat algorithm (BA). It has been proven that BBA is competitive compared to other binary heuristic algorithms. Since the update processes of velocity in the algorithm are consistent with BA, in some cases, this algorithm also faces the premature convergence problem. This paper proposes an improved binary bat algorithm (IBBA) to solve this problem. To evaluate the performance of IBBA, standard benchmark functions and zero-one knapsack problems have been employed. The numeric results obtained by benchmark functions experiment prove that the proposed approach greatly outperforms the original BBA and binary particle swarm optimization (BPSO). Compared with several other heuristic algorithms on zero-one knapsack problems, it also verifies that the proposed algorithm is more able to avoid local minima. PMID:28634487

Dynamic Inertia Weight Binary Bat Algorithm with Neighborhood Search.

PubMed

Huang, Xingwang; Zeng, Xuewen; Han, Rui

2017-01-01

Binary bat algorithm (BBA) is a binary version of the bat algorithm (BA). It has been proven that BBA is competitive compared to other binary heuristic algorithms. Since the update processes of velocity in the algorithm are consistent with BA, in some cases, this algorithm also faces the premature convergence problem. This paper proposes an improved binary bat algorithm (IBBA) to solve this problem. To evaluate the performance of IBBA, standard benchmark functions and zero-one knapsack problems have been employed. The numeric results obtained by benchmark functions experiment prove that the proposed approach greatly outperforms the original BBA and binary particle swarm optimization (BPSO). Compared with several other heuristic algorithms on zero-one knapsack problems, it also verifies that the proposed algorithm is more able to avoid local minima.

A new algorithm for construction of coarse-grained sites of large biomolecules.

PubMed

Li, Min; Zhang, John Z H; Xia, Fei

2016-04-05

The development of coarse-grained (CG) models for large biomolecules remains a challenge in multiscale simulations, including a rigorous definition of CG representations for them. In this work, we proposed a new stepwise optimization imposed with the boundary-constraint (SOBC) algorithm to construct the CG sites of large biomolecules, based on the s cheme of essential dynamics CG. By means of SOBC, we can rigorously derive the CG representations of biomolecules with less computational cost. The SOBC is particularly efficient for the CG definition of large systems with thousands of residues. The resulted CG sites can be parameterized as a CG model using the normal mode analysis based fluctuation matching method. Through normal mode analysis, the obtained modes of CG model can accurately reflect the functionally related slow motions of biomolecules. The SOBC algorithm can be used for the construction of CG sites of large biomolecules such as F-actin and for the study of mechanical properties of biomaterials. © 2015 Wiley Periodicals, Inc.

Automated parameterization of intermolecular pair potentials using global optimization techniques

NASA Astrophysics Data System (ADS)

Krämer, Andreas; Hülsmann, Marco; Köddermann, Thorsten; Reith, Dirk

2014-12-01

In this work, different global optimization techniques are assessed for the automated development of molecular force fields, as used in molecular dynamics and Monte Carlo simulations. The quest of finding suitable force field parameters is treated as a mathematical minimization problem. Intricate problem characteristics such as extremely costly and even abortive simulations, noisy simulation results, and especially multiple local minima naturally lead to the use of sophisticated global optimization algorithms. Five diverse algorithms (pure random search, recursive random search, CMA-ES, differential evolution, and taboo search) are compared to our own tailor-made solution named CoSMoS. CoSMoS is an automated workflow. It models the parameters' influence on the simulation observables to detect a globally optimal set of parameters. It is shown how and why this approach is superior to other algorithms. Applied to suitable test functions and simulations for phosgene, CoSMoS effectively reduces the number of required simulations and real time for the optimization task.

Comparison of artificial intelligence classifiers for SIP attack data

NASA Astrophysics Data System (ADS)

Safarik, Jakub; Slachta, Jiri

2016-05-01

Honeypot application is a source of valuable data about attacks on the network. We run several SIP honeypots in various computer networks, which are separated geographically and logically. Each honeypot runs on public IP address and uses standard SIP PBX ports. All information gathered via honeypot is periodically sent to the centralized server. This server classifies all attack data by neural network algorithm. The paper describes optimizations of a neural network classifier, which lower the classification error. The article contains the comparison of two neural network algorithm used for the classification of validation data. The first is the original implementation of the neural network described in recent work; the second neural network uses further optimizations like input normalization or cross-entropy cost function. We also use other implementations of neural networks and machine learning classification algorithms. The comparison test their capabilities on validation data to find the optimal classifier. The article result shows promise for further development of an accurate SIP attack classification engine.

A Shadowing Problem in the Detection of Overlapping Communities: Lifting the Resolution Limit through a Cascading Procedure

PubMed Central

Young, Jean-Gabriel; Allard, Antoine; Hébert-Dufresne, Laurent; Dubé, Louis J.

2015-01-01

Community detection is the process of assigning nodes and links in significant communities (e.g. clusters, function modules) and its development has led to a better understanding of complex networks. When applied to sizable networks, we argue that most detection algorithms correctly identify prominent communities, but fail to do so across multiple scales. As a result, a significant fraction of the network is left uncharted. We show that this problem stems from larger or denser communities overshadowing smaller or sparser ones, and that this effect accounts for most of the undetected communities and unassigned links. We propose a generic cascading approach to community detection that circumvents the problem. Using real and artificial network datasets with three widely used community detection algorithms, we show how a simple cascading procedure allows for the detection of the missing communities. This work highlights a new detection limit of community structure, and we hope that our approach can inspire better community detection algorithms. PMID:26461919

Forward and inverse uncertainty quantification using multilevel Monte Carlo algorithms for an elliptic non-local equation

DOE PAGES

Jasra, Ajay; Law, Kody J. H.; Zhou, Yan

2016-01-01

Our paper considers uncertainty quantification for an elliptic nonlocal equation. In particular, it is assumed that the parameters which define the kernel in the nonlocal operator are uncertain and a priori distributed according to a probability measure. It is shown that the induced probability measure on some quantities of interest arising from functionals of the solution to the equation with random inputs is well-defined,s as is the posterior distribution on parameters given observations. As the elliptic nonlocal equation cannot be solved approximate posteriors are constructed. The multilevel Monte Carlo (MLMC) and multilevel sequential Monte Carlo (MLSMC) sampling algorithms are usedmore » for a priori and a posteriori estimation, respectively, of quantities of interest. Furthermore, these algorithms reduce the amount of work to estimate posterior expectations, for a given level of error, relative to Monte Carlo and i.i.d. sampling from the posterior at a given level of approximation of the solution of the elliptic nonlocal equation.« less