Science.gov

Sample records for distributed clustering algorithm

  1. Fuzzy-Logic Based Distributed Energy-Efficient Clustering Algorithm for Wireless Sensor Networks

    PubMed Central

    Zhang, Ying; Wang, Jun; Han, Dezhi; Wu, Huafeng; Zhou, Rundong

    2017-01-01

    Due to the high-energy efficiency and scalability, the clustering routing algorithm has been widely used in wireless sensor networks (WSNs). In order to gather information more efficiently, each sensor node transmits data to its Cluster Head (CH) to which it belongs, by multi-hop communication. However, the multi-hop communication in the cluster brings the problem of excessive energy consumption of the relay nodes which are closer to the CH. These nodes’ energy will be consumed more quickly than the farther nodes, which brings the negative influence on load balance for the whole networks. Therefore, we propose an energy-efficient distributed clustering algorithm based on fuzzy approach with non-uniform distribution (EEDCF). During CHs’ election, we take nodes’ energies, nodes’ degree and neighbor nodes’ residual energies into consideration as the input parameters. In addition, we take advantage of Takagi, Sugeno and Kang (TSK) fuzzy model instead of traditional method as our inference system to guarantee the quantitative analysis more reasonable. In our scheme, each sensor node calculates the probability of being as CH with the help of fuzzy inference system in a distributed way. The experimental results indicate EEDCF algorithm is better than some current representative methods in aspects of data transmission, energy consumption and lifetime of networks. PMID:28671641

  2. Fuzzy-Logic Based Distributed Energy-Efficient Clustering Algorithm for Wireless Sensor Networks.

    PubMed

    Zhang, Ying; Wang, Jun; Han, Dezhi; Wu, Huafeng; Zhou, Rundong

    2017-07-03

    Due to the high-energy efficiency and scalability, the clustering routing algorithm has been widely used in wireless sensor networks (WSNs). In order to gather information more efficiently, each sensor node transmits data to its Cluster Head (CH) to which it belongs, by multi-hop communication. However, the multi-hop communication in the cluster brings the problem of excessive energy consumption of the relay nodes which are closer to the CH. These nodes' energy will be consumed more quickly than the farther nodes, which brings the negative influence on load balance for the whole networks. Therefore, we propose an energy-efficient distributed clustering algorithm based on fuzzy approach with non-uniform distribution (EEDCF). During CHs' election, we take nodes' energies, nodes' degree and neighbor nodes' residual energies into consideration as the input parameters. In addition, we take advantage of Takagi, Sugeno and Kang (TSK) fuzzy model instead of traditional method as our inference system to guarantee the quantitative analysis more reasonable. In our scheme, each sensor node calculates the probability of being as CH with the help of fuzzy inference system in a distributed way. The experimental results indicate EEDCF algorithm is better than some current representative methods in aspects of data transmission, energy consumption and lifetime of networks.

  3. Clustering algorithm studies

    NASA Astrophysics Data System (ADS)

    Graf, Norman A.

    2001-07-01

    An object-oriented framework for undertaking clustering algorithm studies has been developed. We present here the definitions for the abstract Cells and Clusters as well as the interface for the algorithm. We intend to use this framework to investigate the interplay between various clustering algorithms and the resulting jet reconstruction efficiency and energy resolutions to assist in the design of the calorimeter detector.

  4. Basic cluster compression algorithm

    NASA Technical Reports Server (NTRS)

    Hilbert, E. E.; Lee, J.

    1980-01-01

    Feature extraction and data compression of LANDSAT data is accomplished by BCCA program which reduces costs associated with transmitting, storing, distributing, and interpreting multispectral image data. Algorithm uses spatially local clustering to extract features from image data to describe spectral characteristics of data set. Approach requires only simple repetitive computations, and parallel processing can be used for very high data rates. Program is written in FORTRAN IV for batch execution and has been implemented on SEL 32/55.

  5. Ultrametric Hierarchical Clustering Algorithms.

    ERIC Educational Resources Information Center

    Milligan, Glenn W.

    1979-01-01

    Johnson has shown that the single linkage and complete linkage hierarchical clustering algorithms induce a metric on the data known as the ultrametric. Johnson's proof is extended to four other common clustering algorithms. Two additional methods also produce hierarchical structures which can violate the ultrametric inequality. (Author/CTM)

  6. Parallel Wolff Cluster Algorithms

    NASA Astrophysics Data System (ADS)

    Bae, S.; Ko, S. H.; Coddington, P. D.

    The Wolff single-cluster algorithm is the most efficient method known for Monte Carlo simulation of many spin models. Due to the irregular size, shape and position of the Wolff clusters, this method does not easily lend itself to efficient parallel implementation, so that simulations using this method have thus far been confined to workstations and vector machines. Here we present two parallel implementations of this algorithm, and show that one gives fairly good performance on a MIMD parallel computer.

  7. A Novel Energy-Aware Distributed Clustering Algorithm for Heterogeneous Wireless Sensor Networks in the Mobile Environment.

    PubMed

    Gao, Ying; Wkram, Chris Hadri; Duan, Jiajie; Chou, Jarong

    2015-12-10

    In order to prolong the network lifetime, energy-efficient protocols adapted to the features of wireless sensor networks should be used. This paper explores in depth the nature of heterogeneous wireless sensor networks, and finally proposes an algorithm to address the problem of finding an effective pathway for heterogeneous clustering energy. The proposed algorithm implements cluster head selection according to the degree of energy attenuation during the network's running and the degree of candidate nodes' effective coverage on the whole network, so as to obtain an even energy consumption over the whole network for the situation with high degree of coverage. Simulation results show that the proposed clustering protocol has better adaptability to heterogeneous environments than existing clustering algorithms in prolonging the network lifetime.

  8. A Novel Energy-Aware Distributed Clustering Algorithm for Heterogeneous Wireless Sensor Networks in the Mobile Environment

    PubMed Central

    Gao, Ying; Wkram, Chris Hadri; Duan, Jiajie; Chou, Jarong

    2015-01-01

    In order to prolong the network lifetime, energy-efficient protocols adapted to the features of wireless sensor networks should be used. This paper explores in depth the nature of heterogeneous wireless sensor networks, and finally proposes an algorithm to address the problem of finding an effective pathway for heterogeneous clustering energy. The proposed algorithm implements cluster head selection according to the degree of energy attenuation during the network’s running and the degree of candidate nodes’ effective coverage on the whole network, so as to obtain an even energy consumption over the whole network for the situation with high degree of coverage. Simulation results show that the proposed clustering protocol has better adaptability to heterogeneous environments than existing clustering algorithms in prolonging the network lifetime. PMID:26690440

  9. Multimodal Estimation of Distribution Algorithms.

    PubMed

    Yang, Qiang; Chen, Wei-Neng; Li, Yun; Chen, C L Philip; Xu, Xiang-Min; Zhang, Jun

    2016-02-15

    Taking the advantage of estimation of distribution algorithms (EDAs) in preserving high diversity, this paper proposes a multimodal EDA. Integrated with clustering strategies for crowding and speciation, two versions of this algorithm are developed, which operate at the niche level. Then these two algorithms are equipped with three distinctive techniques: 1) a dynamic cluster sizing strategy; 2) an alternative utilization of Gaussian and Cauchy distributions to generate offspring; and 3) an adaptive local search. The dynamic cluster sizing affords a potential balance between exploration and exploitation and reduces the sensitivity to the cluster size in the niching methods. Taking advantages of Gaussian and Cauchy distributions, we generate the offspring at the niche level through alternatively using these two distributions. Such utilization can also potentially offer a balance between exploration and exploitation. Further, solution accuracy is enhanced through a new local search scheme probabilistically conducted around seeds of niches with probabilities determined self-adaptively according to fitness values of these seeds. Extensive experiments conducted on 20 benchmark multimodal problems confirm that both algorithms can achieve competitive performance compared with several state-of-the-art multimodal algorithms, which is supported by nonparametric tests. Especially, the proposed algorithms are very promising for complex problems with many local optima.

  10. Energy Aware Clustering Algorithms for Wireless Sensor Networks

    NASA Astrophysics Data System (ADS)

    Rakhshan, Noushin; Rafsanjani, Marjan Kuchaki; Liu, Chenglian

    2011-09-01

    The sensor nodes deployed in wireless sensor networks (WSNs) are extremely power constrained, so maximizing the lifetime of the entire networks is mainly considered in the design. In wireless sensor networks, hierarchical network structures have the advantage of providing scalable and energy efficient solutions. In this paper, we investigate different clustering algorithms for WSNs and also compare these clustering algorithms based on metrics such as clustering distribution, cluster's load balancing, Cluster Head's (CH) selection strategy, CH's role rotation, node mobility, clusters overlapping, intra-cluster communications, reliability, security and location awareness.

  11. Overlapping clusters for distributed computation.

    SciTech Connect

    Mirrokni, Vahab; Andersen, Reid; Gleich, David F.

    2010-11-01

    Scalable, distributed algorithms must address communication problems. We investigate overlapping clusters, or vertex partitions that intersect, for graph computations. This setup stores more of the graph than required but then affords the ease of implementation of vertex partitioned algorithms. Our hope is that this technique allows us to reduce communication in a computation on a distributed graph. The motivation above draws on recent work in communication avoiding algorithms. Mohiyuddin et al. (SC09) design a matrix-powers kernel that gives rise to an overlapping partition. Fritzsche et al. (CSC2009) develop an overlapping clustering for a Schwarz method. Both techniques extend an initial partitioning with overlap. Our procedure generates overlap directly. Indeed, Schwarz methods are commonly used to capitalize on overlap. Elsewhere, overlapping communities (Ahn et al, Nature 2009; Mishra et al. WAW2007) are now a popular model of structure in social networks. These have long been studied in statistics (Cole and Wishart, CompJ 1970). We present two types of results: (i) an estimated swapping probability {rho}{infinity}; and (ii) the communication volume of a parallel PageRank solution (link-following {alpha} = 0.85) using an additive Schwarz method. The volume ratio is the amount of extra storage for the overlap (2 means we store the graph twice). Below, as the ratio increases, the swapping probability and PageRank communication volume decreases.

  12. Cluster compression algorithm: A joint clustering/data compression concept

    NASA Technical Reports Server (NTRS)

    Hilbert, E. E.

    1977-01-01

    The Cluster Compression Algorithm (CCA), which was developed to reduce costs associated with transmitting, storing, distributing, and interpreting LANDSAT multispectral image data is described. The CCA is a preprocessing algorithm that uses feature extraction and data compression to more efficiently represent the information in the image data. The format of the preprocessed data enables simply a look-up table decoding and direct use of the extracted features to reduce user computation for either image reconstruction, or computer interpretation of the image data. Basically, the CCA uses spatially local clustering to extract features from the image data to describe spectral characteristics of the data set. In addition, the features may be used to form a sequence of scalar numbers that define each picture element in terms of the cluster features. This sequence, called the feature map, is then efficiently represented by using source encoding concepts. Various forms of the CCA are defined and experimental results are presented to show trade-offs and characteristics of the various implementations. Examples are provided that demonstrate the application of the cluster compression concept to multi-spectral images from LANDSAT and other sources.

  13. Introduction to Cluster Monte Carlo Algorithms

    NASA Astrophysics Data System (ADS)

    Luijten, E.

    This chapter provides an introduction to cluster Monte Carlo algorithms for classical statistical-mechanical systems. A brief review of the conventional Metropolis algorithm is given, followed by a detailed discussion of the lattice cluster algorithm developed by Swendsen and Wang and the single-cluster variant introduced by Wolff. For continuum systems, the geometric cluster algorithm of Dress and Krauth is described. It is shown how their geometric approach can be generalized to incorporate particle interactions beyond hardcore repulsions, thus forging a connection between the lattice and continuum approaches. Several illustrative examples are discussed.

  14. Examining distributional characteristics of clusters.

    PubMed

    von Eye, A

    2010-01-01

    Standard cluster analysis creates clusters based on the criterion that their members be closer to each other than to members of other clusters. In this article, it is proposed to examine empirical clusters that result from standard clustering, with the goal of assessing whether they contradict distributional assumptions. Four models are proposed. The models consider two data generation processes, the Poisson and the multinormal, as well as two convex shapes of cluster hulls, the spherical and the ellipsoidal. Based on the model, the probability of being in a cluster of a given location, size, and shape is estimated. This probability is compared with the observed proportion of cases. The observed proportion can turn out to be larger, as large, or smaller than expected. Examples are given using simulated and empirical data. The simulation showed that the size of a cluster, the data generation process, and the true distribution of data have the strongest effect on the results obtained with the proposed method. The empirical examples discuss distributional characteristics of cross-sectional and longitudinal clusters of aggressive behavior in adolescents. The examples show that clustering methods do not always yield clusters that contradict distributional assumptions. Some clusters contain even fewer cases than expected.

  15. Algorithms for Finding Substructure in Galaxy Clusters

    NASA Astrophysics Data System (ADS)

    Delworth, Natalie; Wilcots, Eric M.

    2017-01-01

    In order to better understand the role of environment in determining the properties of galaxies, we present statistical approaches to identifying substructure in galaxy clusters and groups. A subgroup is composed of a set of galaxies within a galaxy cluster that share similar attributes. To create subgroups from galaxies in a cluster, we explored several different clustering algorithms: Agglomerative Hierarchical Clustering, Spectral Clustering, and K-Means Clustering. We evaluate the strengths and weaknesses of these algorithms by applying them both to data from the Antlia Cluster, as well as to output from simulated galaxy clusters. We also examined how subgroups and the properties of the galaxies in those subgroups changed over time through analysis of data from simulations that extend over a long time scale. We synthesize these results to provide a perspective on how these analyses contribute to our understanding of galactic evolution.

  16. A novel spatial clustering algorithm based on Delaunay triangulation

    NASA Astrophysics Data System (ADS)

    Yang, Xiankun; Cui, Weihong

    2008-12-01

    Exploratory data analysis is increasingly more necessary as larger spatial data is managed in electro-magnetic media. Spatial clustering is one of the very important spatial data mining techniques. So far, a lot of spatial clustering algorithms have been proposed. In this paper we propose a robust spatial clustering algorithm named SCABDT (Spatial Clustering Algorithm Based on Delaunay Triangulation). SCABDT demonstrates important advantages over the previous works. First, it discovers even arbitrary shape of cluster distribution. Second, in order to execute SCABDT, we do not need to know any priori nature of distribution. Third, like DBSCAN, Experiments show that SCABDT does not require so much CPU processing time. Finally it handles efficiently outliers.

  17. Single-Pass Clustering Algorithm Based on Storm

    NASA Astrophysics Data System (ADS)

    Fang, LI; Longlong, DAI; Zhiying, JIANG; Shunzi, LI

    2017-02-01

    The dramatically increasing volume of data makes the computational complexity of traditional clustering algorithm rise rapidly accordingly, which leads to the longer time. So as to improve the efficiency of the stream data clustering, a distributed real-time clustering algorithm (S-Single-Pass) based on the classic Single-Pass [1] algorithm and Storm [2] computation framework was designed in this paper. By employing this kind of method in the Topic Detection and Tracking (TDT) [3], the real-time performance of topic detection arises effectively. The proposed method splits the clustering process into two parts: one part is to form clusters for the multi-thread parallel clustering, the other part is to merge the generated clusters in the previous process and update the global clusters. Through the experimental results, the conclusion can be drawn that the proposed method have the nearly same clustering accuracy as the traditional Single-Pass algorithm and the clustering accuracy remains steady, computing rate increases linearly when increasing the number of cluster machines and nodes (processing threads).

  18. Online clustering algorithms for radar emitter classification.

    PubMed

    Liu, Jun; Lee, Jim P Y; Senior; Li, Lingjie; Luo, Zhi-Quan; Wong, K Max

    2005-08-01

    Radar emitter classification is a special application of data clustering for classifying unknown radar emitters from received radar pulse samples. The main challenges of this task are the high dimensionality of radar pulse samples, small sample group size, and closely located radar pulse clusters. In this paper, two new online clustering algorithms are developed for radar emitter classification: One is model-based using the Minimum Description Length (MDL) criterion and the other is based on competitive learning. Computational complexity is analyzed for each algorithm and then compared. Simulation results show the superior performance of the model-based algorithm over competitive learning in terms of better classification accuracy, flexibility, and stability.

  19. Distributed Minimum Hop Algorithms

    DTIC Science & Technology

    1982-01-01

    acknowledgement), node d starts iteration i+1, and otherwise the algorithm terminates. A detailed description of the algorithm is given in pidgin algol...precise behavior of the algorithm under these circumstances is described by the pidgin algol program in the appendix which is executed by each node. The...l) < N!(2) for each neighbor j, and thus by induction,J -1 N!(2-1) < n-i + (Z-1) + N!(Z-1), completing the proof. Algorithm Dl in Pidgin Algol It is

  20. A Geometric Clustering Algorithm with Applications to Structural Data

    PubMed Central

    Xu, Shutan; Zou, Shuxue

    2015-01-01

    Abstract An important feature of structural data, especially those from structural determination and protein-ligand docking programs, is that their distribution could be mostly uniform. Traditional clustering algorithms developed specifically for nonuniformly distributed data may not be adequate for their classification. Here we present a geometric partitional algorithm that could be applied to both uniformly and nonuniformly distributed data. The algorithm is a top-down approach that recursively selects the outliers as the seeds to form new clusters until all the structures within a cluster satisfy a classification criterion. The algorithm has been evaluated on a diverse set of real structural data and six sets of test data. The results show that it is superior to the previous algorithms for the clustering of structural data and is similar to or better than them for the classification of the test data. The algorithm should be especially useful for the identification of the best but minor clusters and for speeding up an iterative process widely used in NMR structure determination. PMID:25517067

  1. A geometric clustering algorithm with applications to structural data.

    PubMed

    Xu, Shutan; Zou, Shuxue; Wang, Lincong

    2015-05-01

    An important feature of structural data, especially those from structural determination and protein-ligand docking programs, is that their distribution could be mostly uniform. Traditional clustering algorithms developed specifically for nonuniformly distributed data may not be adequate for their classification. Here we present a geometric partitional algorithm that could be applied to both uniformly and nonuniformly distributed data. The algorithm is a top-down approach that recursively selects the outliers as the seeds to form new clusters until all the structures within a cluster satisfy a classification criterion. The algorithm has been evaluated on a diverse set of real structural data and six sets of test data. The results show that it is superior to the previous algorithms for the clustering of structural data and is similar to or better than them for the classification of the test data. The algorithm should be especially useful for the identification of the best but minor clusters and for speeding up an iterative process widely used in NMR structure determination.

  2. A scheduling algorithm based on Clara clustering

    NASA Astrophysics Data System (ADS)

    Kuang, Ling; Zhang, Lichen

    2017-08-01

    Task scheduling is a key issue in cloud computing. A new algorithm for queuing task scheduling based on Clara clustering and SJF cloud computing is proposed to introduce the Clara clustering for the shortcomings of SJF algorithm load imbalance. The Clara clustering method prepares the task clustering based on the task execution time and the waiting time of the task, and then divides the task into three groups according to the reference point obtained by the clustering. Based on the number of tasks per group in the proportion of the total number of tasks assigned to the implementation of the quota. Each queue team will perform task scheduling based on these quotas and SJF. The simulation results show that the algorithm has good load balancing and system performance.

  3. Algorithm Calculates Cumulative Poisson Distribution

    NASA Technical Reports Server (NTRS)

    Bowerman, Paul N.; Nolty, Robert C.; Scheuer, Ernest M.

    1992-01-01

    Algorithm calculates accurate values of cumulative Poisson distribution under conditions where other algorithms fail because numbers are so small (underflow) or so large (overflow) that computer cannot process them. Factors inserted temporarily to prevent underflow and overflow. Implemented in CUMPOIS computer program described in "Cumulative Poisson Distribution Program" (NPO-17714).

  4. Self-organization and clustering algorithms

    NASA Technical Reports Server (NTRS)

    Bezdek, James C.

    1991-01-01

    Kohonen's feature maps approach to clustering is often likened to the k or c-means clustering algorithms. Here, the author identifies some similarities and differences between the hard and fuzzy c-Means (HCM/FCM) or ISODATA algorithms and Kohonen's self-organizing approach. The author concludes that some differences are significant, but at the same time there may be some important unknown relationships between the two methodologies. Several avenues of research are proposed.

  5. Quantum AdaBoost algorithm via cluster state

    NASA Astrophysics Data System (ADS)

    Li, Yuan

    2017-03-01

    The principle and theory of quantum computation are investigated by researchers for many years, and further applied to improve the efficiency of classical machine learning algorithms. Based on physical mechanism, a quantum version of AdaBoost (Adaptive Boosting) training algorithm is proposed in this paper, of which purpose is to construct a strong classifier. In the proposed scheme with cluster state in quantum mechanism is to realize the weak learning algorithm, and then update the corresponding weight of examples. As a result, a final classifier can be obtained by combining efficiently weak hypothesis based on measuring cluster state to reweight the distribution of examples.

  6. Research on retailer data clustering algorithm based on Spark

    NASA Astrophysics Data System (ADS)

    Huang, Qiuman; Zhou, Feng

    2017-03-01

    Big data analysis is a hot topic in the IT field now. Spark is a high-reliability and high-performance distributed parallel computing framework for big data sets. K-means algorithm is one of the classical partition methods in clustering algorithm. In this paper, we study the k-means clustering algorithm on Spark. Firstly, the principle of the algorithm is analyzed, and then the clustering analysis is carried out on the supermarket customers through the experiment to find out the different shopping patterns. At the same time, this paper proposes the parallelization of k-means algorithm and the distributed computing framework of Spark, and gives the concrete design scheme and implementation scheme. This paper uses the two-year sales data of a supermarket to validate the proposed clustering algorithm and achieve the goal of subdividing customers, and then analyze the clustering results to help enterprises to take different marketing strategies for different customer groups to improve sales performance.

  7. Optimal Hops-Based Adaptive Clustering Algorithm

    NASA Astrophysics Data System (ADS)

    Xuan, Xin; Chen, Jian; Zhen, Shanshan; Kuo, Yonghong

    This paper proposes an optimal hops-based adaptive clustering algorithm (OHACA). The algorithm sets an energy selection threshold before the cluster forms so that the nodes with less energy are more likely to go to sleep immediately. In setup phase, OHACA introduces an adaptive mechanism to adjust cluster head and load balance. And the optimal distance theory is applied to discover the practical optimal routing path to minimize the total energy for transmission. Simulation results show that OHACA prolongs the life of network, improves utilizing rate and transmits more data because of energy balance.

  8. Asynchronous Distributed Flow Control Algorithms.

    DTIC Science & Technology

    1984-10-01

    SCHEDULE IS. DISTRIBUTION STATEMENT (of this Report) Approved for public release; distribution unlimited. I?. DISTRIBUTION STATEMENT (of the abstract...model for asynchronous computation developed by Bertsekas [14] to get some results relating to general-asynchronous distributed algo- rithms with update...to get some results relating to general asynchronous distributed algorithms with update protocols. These results are used to give an alternate proof of

  9. An algorithm for spatial heirarchy clustering

    NASA Technical Reports Server (NTRS)

    Dejesusparada, N. (Principal Investigator); Velasco, F. R. D.

    1981-01-01

    A method for utilizing both spectral and spatial redundancy in compacting and preclassifying images is presented. In multispectral satellite images, a high correlation exists between neighboring image points which tend to occupy dense and restricted regions of the feature space. The image is divided into windows of the same size where the clustering is made. The classes obtained in several neighboring windows are clustered, and then again successively clustered until only one region corresponding to the whole image is obtained. By employing this algorithm only a few points are considered in each clustering, thus reducing computational effort. The method is illustrated as applied to LANDSAT images.

  10. Cluster hybrid Monte Carlo simulation algorithms.

    PubMed

    Plascak, J A; Ferrenberg, Alan M; Landau, D P

    2002-06-01

    We show that addition of Metropolis single spin flips to the Wolff cluster-flipping Monte Carlo procedure leads to a dramatic increase in performance for the spin-1/2 Ising model. We also show that adding Wolff cluster flipping to the Metropolis or heat bath algorithms in systems where just cluster flipping is not immediately obvious (such as the spin-3/2 Ising model) can substantially reduce the statistical errors of the simulations. A further advantage of these methods is that systematic errors introduced by the use of imperfect random-number generation may be largely healed by hybridizing single spin flips with cluster flipping.

  11. Cluster hybrid Monte Carlo simulation algorithms

    NASA Astrophysics Data System (ADS)

    Plascak, J. A.; Ferrenberg, Alan M.; Landau, D. P.

    2002-06-01

    We show that addition of Metropolis single spin flips to the Wolff cluster-flipping Monte Carlo procedure leads to a dramatic increase in performance for the spin-1/2 Ising model. We also show that adding Wolff cluster flipping to the Metropolis or heat bath algorithms in systems where just cluster flipping is not immediately obvious (such as the spin-3/2 Ising model) can substantially reduce the statistical errors of the simulations. A further advantage of these methods is that systematic errors introduced by the use of imperfect random-number generation may be largely healed by hybridizing single spin flips with cluster flipping.

  12. Coupled cluster algorithms for networks of shared memory parallel processors

    NASA Astrophysics Data System (ADS)

    Bentz, Jonathan L.; Olson, Ryan M.; Gordon, Mark S.; Schmidt, Michael W.; Kendall, Ricky A.

    2007-05-01

    As the popularity of using SMP systems as the building blocks for high performance supercomputers increases, so too increases the need for applications that can utilize the multiple levels of parallelism available in clusters of SMPs. This paper presents a dual-layer distributed algorithm, using both shared-memory and distributed-memory techniques to parallelize a very important algorithm (often called the "gold standard") used in computational chemistry, the single and double excitation coupled cluster method with perturbative triples, i.e. CCSD(T). The algorithm is presented within the framework of the GAMESS [M.W. Schmidt, K.K. Baldridge, J.A. Boatz, S.T. Elbert, M.S. Gordon, J.J. Jensen, S. Koseki, N. Matsunaga, K.A. Nguyen, S. Su, T.L. Windus, M. Dupuis, J.A. Montgomery, General atomic and molecular electronic structure system, J. Comput. Chem. 14 (1993) 1347-1363]. (General Atomic and Molecular Electronic Structure System) program suite and the Distributed Data Interface [M.W. Schmidt, G.D. Fletcher, B.M. Bode, M.S. Gordon, The distributed data interface in GAMESS, Comput. Phys. Comm. 128 (2000) 190]. (DDI), however, the essential features of the algorithm (data distribution, load-balancing and communication overhead) can be applied to more general computational problems. Timing and performance data for our dual-level algorithm is presented on several large-scale clusters of SMPs.

  13. On scaling properties of cluster distributions in Ising models

    NASA Astrophysics Data System (ADS)

    Ruge, C.; Wagner, F.

    1992-01-01

    Scaling relations of cluster distributions for the Wolff algorithm are derived. We found them to be well satisfied for the Ising model in d=3 dimensions. Using scaling and a parametrization of the cluster distribution, we determine the critical exponent β/ν=0.516(6) with moderate effort in computing time.

  14. Parallel Clustering Algorithms for Structured AMR

    SciTech Connect

    Gunney, B T; Wissink, A M; Hysom, D A

    2005-10-26

    We compare several different parallel implementation approaches for the clustering operations performed during adaptive gridding operations in patch-based structured adaptive mesh refinement (SAMR) applications. Specifically, we target the clustering algorithm of Berger and Rigoutsos (BR91), which is commonly used in many SAMR applications. The baseline for comparison is a simplistic parallel extension of the original algorithm that works well for up to O(10{sup 2}) processors. Our goal is a clustering algorithm for machines of up to O(10{sup 5}) processors, such as the 64K-processor IBM BlueGene/Light system. We first present an algorithm that avoids the unneeded communications of the simplistic approach to improve the clustering speed by up to an order of magnitude. We then present a new task-parallel implementation to further reduce communication wait time, adding another order of magnitude of improvement. The new algorithms also exhibit more favorable scaling behavior for our test problems. Performance is evaluated on a number of large scale parallel computer systems, including a 16K-processor BlueGene/Light system.

  15. Cluster Algorithm Special Purpose Processor

    NASA Astrophysics Data System (ADS)

    Talapov, A. L.; Shchur, L. N.; Andreichenko, V. B.; Dotsenko, Vl. S.

    We describe a Special Purpose Processor, realizing the Wolff algorithm in hardware, which is fast enough to study the critical behaviour of 2D Ising-like systems containing more than one million spins. The processor has been checked to produce correct results for a pure Ising model and for Ising model with random bonds. Its data also agree with the Nishimori exact results for spin glass. Only minor changes of the SPP design are necessary to increase the dimensionality and to take into account more complex systems such as Potts models.

  16. Performance Comparison Of Evolutionary Algorithms For Image Clustering

    NASA Astrophysics Data System (ADS)

    Civicioglu, P.; Atasever, U. H.; Ozkan, C.; Besdok, E.; Karkinli, A. E.; Kesikoglu, A.

    2014-09-01

    Evolutionary computation tools are able to process real valued numerical sets in order to extract suboptimal solution of designed problem. Data clustering algorithms have been intensively used for image segmentation in remote sensing applications. Despite of wide usage of evolutionary algorithms on data clustering, their clustering performances have been scarcely studied by using clustering validation indexes. In this paper, the recently proposed evolutionary algorithms (i.e., Artificial Bee Colony Algorithm (ABC), Gravitational Search Algorithm (GSA), Cuckoo Search Algorithm (CS), Adaptive Differential Evolution Algorithm (JADE), Differential Search Algorithm (DSA) and Backtracking Search Optimization Algorithm (BSA)) and some classical image clustering techniques (i.e., k-means, fcm, som networks) have been used to cluster images and their performances have been compared by using four clustering validation indexes. Experimental test results exposed that evolutionary algorithms give more reliable cluster-centers than classical clustering techniques, but their convergence time is quite long.

  17. A hierarchical clustering algorithm for MIMD architecture.

    PubMed

    Du, Zhihua; Lin, Feng

    2004-12-01

    Hierarchical clustering is the most often used method for grouping similar patterns of gene expression data. A fundamental problem with existing implementations of this clustering method is the inability to handle large data sets within a reasonable time and memory resources. We propose a parallelized algorithm of hierarchical clustering to solve this problem. Our implementation on a multiple instruction multiple data (MIMD) architecture shows considerable reduction in computational time and inter-node communication overhead, especially for large data sets. We use the standard message passing library, message passing interface (MPI) for any MIMD systems.

  18. Spectral clustering algorithms for ultrasound image segmentation.

    PubMed

    Archip, Neculai; Rohling, Robert; Cooperberg, Peter; Tahmasebpour, Hamid; Warfield, Simon K

    2005-01-01

    Image segmentation algorithms derived from spectral clustering analysis rely on the eigenvectors of the Laplacian of a weighted graph obtained from the image. The NCut criterion was previously used for image segmentation in supervised manner. We derive a new strategy for unsupervised image segmentation. This article describes an initial investigation to determine the suitability of such segmentation techniques for ultrasound images. The extension of the NCut technique to the unsupervised clustering is first described. The novel segmentation algorithm is then performed on simulated ultrasound images. Tests are also performed on abdominal and fetal images with the segmentation results compared to manual segmentation. Comparisons with the classical NCut algorithm are also presented. Finally, segmentation results on other types of medical images are shown.

  19. Genetic algorithm optimization of atomic clusters

    SciTech Connect

    Morris, J.R.; Deaven, D.M.; Ho, K.M.; Wang, C.Z.; Pan, B.C.; Wacker, J.G.; Turner, D.E. |

    1996-12-31

    The authors have been using genetic algorithms to study the structures of atomic clusters and related problems. This is a problem where local minima are easy to locate, but barriers between the many minima are large, and the number of minima prohibit a systematic search. They use a novel mating algorithm that preserves some of the geometrical relationship between atoms, in order to ensure that the resultant structures are likely to inherit the best features of the parent clusters. Using this approach, they have been able to find lower energy structures than had been previously obtained. Most recently, they have been able to turn around the building block idea, using optimized structures from the GA to learn about systematic structural trends. They believe that an effective GA can help provide such heuristic information, and (conversely) that such information can be introduced back into the algorithm to assist in the search process.

  20. Noise-enhanced clustering and competitive learning algorithms.

    PubMed

    Osoba, Osonde; Kosko, Bart

    2013-01-01

    Noise can provably speed up convergence in many centroid-based clustering algorithms. This includes the popular k-means clustering algorithm. The clustering noise benefit follows from the general noise benefit for the expectation-maximization algorithm because many clustering algorithms are special cases of the expectation-maximization algorithm. Simulations show that noise also speeds up convergence in stochastic unsupervised competitive learning, supervised competitive learning, and differential competitive learning.

  1. Morphology of open clusters NGC 1857 and Czernik 20 using clustering algorithms

    NASA Astrophysics Data System (ADS)

    Bhattacharya, S.; Mahulkar, V.; Pandaokar, S.; Singh, P. K.

    2017-01-01

    The morphology and cluster membership of the Galactic open clusters-Czernik 20 and NGC 1857 were analyzed using two different clustering algorithms. We present the maiden use of density-based spatial clustering of applications with noise (DBSCAN) to determine open cluster morphology from spatial distribution. The region of analysis has also been spatially classified using a statistical membership determination algorithm. We utilized near infrared (NIR) data for a suitably large region around the clusters from the United Kingdom Infrared Deep Sky Survey Galactic Plane Survey star catalogue database, and also from the Two Micron All Sky Survey star catalogue database. The densest regions of the cluster morphologies (1 for Czernik 20 and 2 for NGC 1857) thus identified were analyzed with a K-band extinction map and color-magnitude diagrams (CMDs). To address significant discrepancy in known distance and reddening parameters, we carried out field decontamination of these CMDs and subsequent isochrone fitting of the cleaned CMDs to obtain reliable distance and reddening parameters for the clusters (Czernik 20: D = 2900 pc; E(J- K) = 0 . 33; NGC 1857: D = 2400 pc; E(J- K) =0.18-0.19). The isochrones were also used to convert the luminosity functions for the densest regions of Czernik 20 and NGC 1857 into mass function, to derive their slopes. Additionally, a previously unknown over-density consistent with that of a star cluster is identified in the region of analysis.

  2. Chaotic map clustering algorithm for EEG analysis

    NASA Astrophysics Data System (ADS)

    Bellotti, R.; De Carlo, F.; Stramaglia, S.

    2004-03-01

    The non-parametric chaotic map clustering algorithm has been applied to the analysis of electroencephalographic signals, in order to recognize the Huntington's disease, one of the most dangerous pathologies of the central nervous system. The performance of the method has been compared with those obtained through parametric algorithms, as K-means and deterministic annealing, and supervised multi-layer perceptron. While supervised neural networks need a training phase, performed by means of data tagged by the genetic test, and the parametric methods require a prior choice of the number of classes to find, the chaotic map clustering gives a natural evidence of the pathological class, without any training or supervision, thus providing a new efficient methodology for the recognition of patterns affected by the Huntington's disease.

  3. Dynamic exponents for potts model cluster algorithms

    NASA Astrophysics Data System (ADS)

    Coddington, Paul D.; Baillie, Clive F.

    We have studied the Swendsen-Wang and Wolff cluster update algorithms for the Ising model in 2, 3 and 4 dimensions. The data indicate simple relations between the specific heat and the Wolff autocorrelations, and between the magnetization and the Swendsen-Wang autocorrelations. This implies that the dynamic critical exponents are related to the static exponents of the Ising model. We also investigate the possibility of similar relationships for the Q-state Potts model.

  4. First Cluster Algorithm Special Purpose Processor

    NASA Astrophysics Data System (ADS)

    Talapov, A. L.; Andreichenko, V. B.; Dotsenko S., Vi.; Shchur, L. N.

    We describe the architecture of the special purpose processor built to realize in hardware cluster Wolff algorithm, which is not hampered by a critical slowing down. The processor simulates two-dimensional Ising-like spin systems. With minor changes the same very effective architecture, which can be defined as a Memory Machine, can be used to study phase transitions in a wide range of models in two or three dimensions.

  5. Dimensionality Reduction Particle Swarm Algorithm for High Dimensional Clustering

    SciTech Connect

    Cui, Xiaohui; ST Charles, Jesse Lee; Potok, Thomas E; Beaver, Justin M

    2008-01-01

    The Particle Swarm Optimization (PSO) clustering algorithm can generate more compact clustering results than the traditional K-means clustering algorithm. However, when clustering high dimensional datasets, the PSO clustering algorithm is notoriously slow because its computation cost increases exponentially with the size of the dataset dimension. Dimensionality reduction techniques offer solutions that both significantly improve the computation time, and yield reasonably accurate clustering results in high dimensional data analysis. In this paper, we introduce research that combines different dimensionality reduction techniques with the PSO clustering algorithm in order to reduce the complexity of high dimensional datasets and speed up the PSO clustering process. We report significant improvements in total runtime. Moreover, the clustering accuracy of the dimensionality reduction PSO clustering algorithm is comparable to the one that uses full dimension space.

  6. A Distributed Flocking Approach for Information Stream Clustering Analysis

    SciTech Connect

    Cui, Xiaohui; Potok, Thomas E

    2006-01-01

    Intelligence analysts are currently overwhelmed with the amount of information streams generated everyday. There is a lack of comprehensive tool that can real-time analyze the information streams. Document clustering analysis plays an important role in improving the accuracy of information retrieval. However, most clustering technologies can only be applied for analyzing the static document collection because they normally require a large amount of computation resource and long time to get accurate result. It is very difficult to cluster a dynamic changed text information streams on an individual computer. Our early research has resulted in a dynamic reactive flock clustering algorithm which can continually refine the clustering result and quickly react to the change of document contents. This character makes the algorithm suitable for cluster analyzing dynamic changed document information, such as text information stream. Because of the decentralized character of this algorithm, a distributed approach is a very natural way to increase the clustering speed of the algorithm. In this paper, we present a distributed multi-agent flocking approach for the text information stream clustering and discuss the decentralized architectures and communication schemes for load balance and status information synchronization in this approach.

  7. Evaluation of Hierarchical Clustering Algorithms for Document Datasets

    DTIC Science & Technology

    2002-06-03

    new class of agglomerative algorithms, in which we introduced intermediate clusters obtained by partitional clustering algorithms to constrain the space ...of the corresponding clusters. The various clustering algorithms that are described in this paper use the vector- space model [26] to represent each...document. In this model, each document d is considered to be a vector in the term- space . In particular, we employed the t f id f term weighting model

  8. Improved Ant Colony Clustering Algorithm and Its Performance Study.

    PubMed

    Gao, Wei

    2016-01-01

    Clustering analysis is used in many disciplines and applications; it is an important tool that descriptively identifies homogeneous groups of objects based on attribute values. The ant colony clustering algorithm is a swarm-intelligent method used for clustering problems that is inspired by the behavior of ant colonies that cluster their corpses and sort their larvae. A new abstraction ant colony clustering algorithm using a data combination mechanism is proposed to improve the computational efficiency and accuracy of the ant colony clustering algorithm. The abstraction ant colony clustering algorithm is used to cluster benchmark problems, and its performance is compared with the ant colony clustering algorithm and other methods used in existing literature. Based on similar computational difficulties and complexities, the results show that the abstraction ant colony clustering algorithm produces results that are not only more accurate but also more efficiently determined than the ant colony clustering algorithm and the other methods. Thus, the abstraction ant colony clustering algorithm can be used for efficient multivariate data clustering.

  9. Improved Ant Colony Clustering Algorithm and Its Performance Study

    PubMed Central

    Gao, Wei

    2016-01-01

    Clustering analysis is used in many disciplines and applications; it is an important tool that descriptively identifies homogeneous groups of objects based on attribute values. The ant colony clustering algorithm is a swarm-intelligent method used for clustering problems that is inspired by the behavior of ant colonies that cluster their corpses and sort their larvae. A new abstraction ant colony clustering algorithm using a data combination mechanism is proposed to improve the computational efficiency and accuracy of the ant colony clustering algorithm. The abstraction ant colony clustering algorithm is used to cluster benchmark problems, and its performance is compared with the ant colony clustering algorithm and other methods used in existing literature. Based on similar computational difficulties and complexities, the results show that the abstraction ant colony clustering algorithm produces results that are not only more accurate but also more efficiently determined than the ant colony clustering algorithm and the other methods. Thus, the abstraction ant colony clustering algorithm can be used for efficient multivariate data clustering. PMID:26839533

  10. Cross-Clustering: A Partial Clustering Algorithm with Automatic Estimation of the Number of Clusters

    PubMed Central

    Tellaroli, Paola; Bazzi, Marco; Donato, Michele; Brazzale, Alessandra R.; Drăghici, Sorin

    2016-01-01

    Four of the most common limitations of the many available clustering methods are: i) the lack of a proper strategy to deal with outliers; ii) the need for a good a priori estimate of the number of clusters to obtain reasonable results; iii) the lack of a method able to detect when partitioning of a specific data set is not appropriate; and iv) the dependence of the result on the initialization. Here we propose Cross-clustering (CC), a partial clustering algorithm that overcomes these four limitations by combining the principles of two well established hierarchical clustering algorithms: Ward’s minimum variance and Complete-linkage. We validated CC by comparing it with a number of existing clustering methods, including Ward’s and Complete-linkage. We show on both simulated and real datasets, that CC performs better than the other methods in terms of: the identification of the correct number of clusters, the identification of outliers, and the determination of real cluster memberships. We used CC to cluster samples in order to identify disease subtypes, and on gene profiles, in order to determine groups of genes with the same behavior. Results obtained on a non-biological dataset show that the method is general enough to be successfully used in such diverse applications. The algorithm has been implemented in the statistical language R and is freely available from the CRAN contributed packages repository. PMID:27015427

  11. Parallelization of Edge Detection Algorithm using MPI on Beowulf Cluster

    NASA Astrophysics Data System (ADS)

    Haron, Nazleeni; Amir, Ruzaini; Aziz, Izzatdin A.; Jung, Low Tan; Shukri, Siti Rohkmah

    In this paper, we present the design of parallel Sobel edge detection algorithm using Foster's methodology. The parallel algorithm is implemented using MPI message passing library and master/slave algorithm. Every processor performs the same sequential algorithm but on different part of the image. Experimental results conducted on Beowulf cluster are presented to demonstrate the performance of the parallel algorithm.

  12. Applying fuzzy clustering optimization algorithm to extracting traffic spatial pattern

    NASA Astrophysics Data System (ADS)

    Hu, Chunchun; Shi, Wenzhong; Meng, Lingkui; Liu, Min

    2009-10-01

    Traditional analytical methods for traffic information can't meet to need of intelligent traffic system. Mining value-add information can deal with more traffic problems. The paper exploits a new clustering optimization algorithm to extract useful spatial clustered pattern for predicting long-term traffic flow from macroscopic view. Considering the sensitivity of initial parameters and easy falling into local extreme in FCM algorithm, the new algorithm applies Particle Swarm Optimization method, which can discovery the globe optimal result, to the FCM algorithm. And the algorithm exploits the union of the clustering validity index and objective function of the FCM algorithm as the fitness function of the PSO algorithm. The experimental result indicates that it is effective and efficient. For fuzzy clustering of road traffic data, it can produce useful spatial clustered pattern. And the clustered centers represent the locations which have heavy traffic flow. Moreover, the parameters of the patterns can provide intelligent traffic system with assistant decision support.

  13. A hybrid monkey search algorithm for clustering analysis.

    PubMed

    Chen, Xin; Zhou, Yongquan; Luo, Qifang

    2014-01-01

    Clustering is a popular data analysis and data mining technique. The k-means clustering algorithm is one of the most commonly used methods. However, it highly depends on the initial solution and is easy to fall into local optimum solution. In view of the disadvantages of the k-means method, this paper proposed a hybrid monkey algorithm based on search operator of artificial bee colony algorithm for clustering analysis and experiment on synthetic and real life datasets to show that the algorithm has a good performance than that of the basic monkey algorithm for clustering analysis.

  14. a Distributed Polygon Retrieval Algorithm Using Mapreduce

    NASA Astrophysics Data System (ADS)

    Guo, Q.; Palanisamy, B.; Karimi, H. A.

    2015-07-01

    The burst of large-scale spatial terrain data due to the proliferation of data acquisition devices like 3D laser scanners poses challenges to spatial data analysis and computation. Among many spatial analyses and computations, polygon retrieval is a fundamental operation which is often performed under real-time constraints. However, existing sequential algorithms fail to meet this demand for larger sizes of terrain data. Motivated by the MapReduce programming model, a well-adopted large-scale parallel data processing technique, we present a MapReduce-based polygon retrieval algorithm designed with the objective of reducing the IO and CPU loads of spatial data processing. By indexing the data based on a quad-tree approach, a significant amount of unneeded data is filtered in the filtering stage and it reduces the IO overhead. The indexed data also facilitates querying the relationship between the terrain data and query area in shorter time. The results of the experiments performed in our Hadoop cluster demonstrate that our algorithm performs significantly better than the existing distributed algorithms.

  15. The Georgi algorithms of jet clustering

    NASA Astrophysics Data System (ADS)

    Ge, Shao-Feng

    2015-05-01

    We reveal the direct link between the jet clustering algorithms recently proposed by Howard Georgi and parton shower kinematics, providing firm foundation from the theoretical side. The kinematics of this class of elegant algorithms is explored systematically for partons with arbitrary masses and the jet function is generalized to J {/β ( n)} with a jet function index n in order to achieve more degrees of freedom. Based on three basic requirements that, the result of jet clustering is process-independent and hence logically consistent, for softer subjets the inclusion cone is larger to conform with the fact that parton shower tends to emit softer partons at earlier stage with larger opening angle, and that the cone size cannot be too large in order to avoid mixing up neighbor jets, we derive constraints on the jet function parameter β and index n which are closely related to cone size cutoff. Finally, we discuss how jet function values can be made invariant under Lorentz boost.

  16. Multiscale mutation clustering algorithm identifies pan-cancer mutational clusters associated with pathway-level changes in gene expression.

    PubMed

    Poole, William; Leinonen, Kalle; Shmulevich, Ilya; Knijnenburg, Theo A; Bernard, Brady

    2017-02-01

    Cancer researchers have long recognized that somatic mutations are not uniformly distributed within genes. However, most approaches for identifying cancer mutations focus on either the entire-gene or single amino-acid level. We have bridged these two methodologies with a multiscale mutation clustering algorithm that identifies variable length mutation clusters in cancer genes. We ran our algorithm on 539 genes using the combined mutation data in 23 cancer types from The Cancer Genome Atlas (TCGA) and identified 1295 mutation clusters. The resulting mutation clusters cover a wide range of scales and often overlap with many kinds of protein features including structured domains, phosphorylation sites, and known single nucleotide variants. We statistically associated these multiscale clusters with gene expression and drug response data to illuminate the functional and clinical consequences of mutations in our clusters. Interestingly, we find multiple clusters within individual genes that have differential functional associations: these include PTEN, FUBP1, and CDH1. This methodology has potential implications in identifying protein regions for drug targets, understanding the biological underpinnings of cancer, and personalizing cancer treatments. Toward this end, we have made the mutation clusters and the clustering algorithm available to the public. Clusters and pathway associations can be interactively browsed at m2c.systemsbiology.net. The multiscale mutation clustering algorithm is available at https://github.com/IlyaLab/M2C.

  17. Multiscale mutation clustering algorithm identifies pan-cancer mutational clusters associated with pathway-level changes in gene expression

    PubMed Central

    Poole, William; Leinonen, Kalle; Shmulevich, Ilya

    2017-01-01

    Cancer researchers have long recognized that somatic mutations are not uniformly distributed within genes. However, most approaches for identifying cancer mutations focus on either the entire-gene or single amino-acid level. We have bridged these two methodologies with a multiscale mutation clustering algorithm that identifies variable length mutation clusters in cancer genes. We ran our algorithm on 539 genes using the combined mutation data in 23 cancer types from The Cancer Genome Atlas (TCGA) and identified 1295 mutation clusters. The resulting mutation clusters cover a wide range of scales and often overlap with many kinds of protein features including structured domains, phosphorylation sites, and known single nucleotide variants. We statistically associated these multiscale clusters with gene expression and drug response data to illuminate the functional and clinical consequences of mutations in our clusters. Interestingly, we find multiple clusters within individual genes that have differential functional associations: these include PTEN, FUBP1, and CDH1. This methodology has potential implications in identifying protein regions for drug targets, understanding the biological underpinnings of cancer, and personalizing cancer treatments. Toward this end, we have made the mutation clusters and the clustering algorithm available to the public. Clusters and pathway associations can be interactively browsed at m2c.systemsbiology.net. The multiscale mutation clustering algorithm is available at https://github.com/IlyaLab/M2C. PMID:28170390

  18. Clustering algorithm for determining community structure in large networks

    NASA Astrophysics Data System (ADS)

    Pujol, Josep M.; Béjar, Javier; Delgado, Jordi

    2006-07-01

    We propose an algorithm to find the community structure in complex networks based on the combination of spectral analysis and modularity optimization. The clustering produced by our algorithm is as accurate as the best algorithms on the literature of modularity optimization; however, the main asset of the algorithm is its efficiency. The best match for our algorithm is Newman’s fast algorithm, which is the reference algorithm for clustering in large networks due to its efficiency. When both algorithms are compared, our algorithm outperforms the fast algorithm both in efficiency and accuracy of the clustering, in terms of modularity. Thus, the results suggest that the proposed algorithm is a good choice to analyze the community structure of medium and large networks in the range of tens and hundreds of thousand vertices.

  19. Clustering algorithm based on grid and density for data stream

    NASA Astrophysics Data System (ADS)

    Wang, Lang; Li, Haiqing

    2017-05-01

    Data stream clustering analysis can extract useful information in real time from massive data, and have been widely applied in many fields. The traditional grid-based data stream clustering algorithm is not precise and the processing of the grid cell boundary points is crude. On the other side, the density-based clustering algorithm is inefficient and is not easy for the discovery of arbitrary shape cluster problem. Thus, this paper proposes a kind of clustering algorithm based on both grid and density for data stream. This algorithm method processes the boundary points by segmenting the data space and using data points to deal with the influence coefficient of the adjacent grid elements, in order to improve the efficiency and accuracy of the algorithm. The experimental results prove this algorithmic method to an accurate, quick, feasible way to identify clusters.

  20. Space complexity of estimation of distribution algorithms.

    PubMed

    Gao, Yong; Culberson, Joseph

    2005-01-01

    In this paper, we investigate the space complexity of the Estimation of Distribution Algorithms (EDAs), a class of sampling-based variants of the genetic algorithm. By analyzing the nature of EDAs, we identify criteria that characterize the space complexity of two typical implementation schemes of EDAs, the factorized distribution algorithm and Bayesian network-based algorithms. Using random additive functions as the prototype, we prove that the space complexity of the factorized distribution algorithm and Bayesian network-based algorithms is exponential in the problem size even if the optimization problem has a very sparse interaction structure.

  1. Identifying multiple influential spreaders by a heuristic clustering algorithm

    NASA Astrophysics Data System (ADS)

    Bao, Zhong-Kui; Liu, Jian-Guo; Zhang, Hai-Feng

    2017-03-01

    The problem of influence maximization in social networks has attracted much attention. However, traditional centrality indices are suitable for the case where a single spreader is chosen as the spreading source. Many times, spreading process is initiated by simultaneously choosing multiple nodes as the spreading sources. In this situation, choosing the top ranked nodes as multiple spreaders is not an optimal strategy, since the chosen nodes are not sufficiently scattered in networks. Therefore, one ideal situation for multiple spreaders case is that the spreaders themselves are not only influential but also they are dispersively distributed in networks, but it is difficult to meet the two conditions together. In this paper, we propose a heuristic clustering (HC) algorithm based on the similarity index to classify nodes into different clusters, and finally the center nodes in clusters are chosen as the multiple spreaders. HC algorithm not only ensures that the multiple spreaders are dispersively distributed in networks but also avoids the selected nodes to be very "negligible". Compared with the traditional methods, our experimental results on synthetic and real networks indicate that the performance of HC method on influence maximization is more significant.

  2. MM Algorithms for Some Discrete Multivariate Distributions.

    PubMed

    Zhou, Hua; Lange, Kenneth

    2010-09-01

    The MM (minorization-maximization) principle is a versatile tool for constructing optimization algorithms. Every EM algorithm is an MM algorithm but not vice versa. This article derives MM algorithms for maximum likelihood estimation with discrete multivariate distributions such as the Dirichlet-multinomial and Connor-Mosimann distributions, the Neerchal-Morel distribution, the negative-multinomial distribution, certain distributions on partitions, and zero-truncated and zero-inflated distributions. These MM algorithms increase the likelihood at each iteration and reliably converge to the maximum from well-chosen initial values. Because they involve no matrix inversion, the algorithms are especially pertinent to high-dimensional problems. To illustrate the performance of the MM algorithms, we compare them to Newton's method on data used to classify handwritten digits.

  3. Multi-Parent Clustering Algorithms from Stochastic Grammar Data Models

    NASA Technical Reports Server (NTRS)

    Mjoisness, Eric; Castano, Rebecca; Gray, Alexander

    1999-01-01

    We introduce a statistical data model and an associated optimization-based clustering algorithm which allows data vectors to belong to zero, one or several "parent" clusters. For each data vector the algorithm makes a discrete decision among these alternatives. Thus, a recursive version of this algorithm would place data clusters in a Directed Acyclic Graph rather than a tree. We test the algorithm with synthetic data generated according to the statistical data model. We also illustrate the algorithm using real data from large-scale gene expression assays.

  4. Application of hybrid clustering using parallel k-means algorithm and DIANA algorithm

    NASA Astrophysics Data System (ADS)

    Umam, Khoirul; Bustamam, Alhadi; Lestari, Dian

    2017-03-01

    DNA is one of the carrier of genetic information of living organisms. Encoding, sequencing, and clustering DNA sequences has become the key jobs and routine in the world of molecular biology, in particular on bioinformatics application. There are two type of clustering, hierarchical clustering and partitioning clustering. In this paper, we combined two type clustering i.e. K-Means (partitioning clustering) and DIANA (hierarchical clustering), therefore it called Hybrid clustering. Application of hybrid clustering using Parallel K-Means algorithm and DIANA algorithm used to clustering DNA sequences of Human Papillomavirus (HPV). The clustering process is started with Collecting DNA sequences of HPV are obtained from NCBI (National Centre for Biotechnology Information), then performing characteristics extraction of DNA sequences. The characteristics extraction result is store in a matrix form, then normalize this matrix using Min-Max normalization and calculate genetic distance using Euclidian Distance. Furthermore, the hybrid clustering is applied by using implementation of Parallel K-Means algorithm and DIANA algorithm. The aim of using Hybrid Clustering is to obtain better clusters result. For validating the resulted clusters, to get optimum number of clusters, we use Davies-Bouldin Index (DBI). In this study, the result of implementation of Parallel K-Means clustering is data clustered become 5 clusters with minimal IDB value is 0.8741, and Hybrid Clustering clustered data become 13 sub-clusters with minimal IDB values = 0.8216, 0.6845, 0.3331, 0.1994 and 0.3952. The IDB value of hybrid clustering less than IBD value of Parallel K-Means clustering only that perform at 1ts stage. Its means clustering using Hybrid Clustering have the better result to clustered DNA sequence of HPV than perform parallel K-Means Clustering only.

  5. Efficient approximation of the cluster size distribution in binary condensation

    NASA Astrophysics Data System (ADS)

    van Putten, Dennis S.; Sidin, Ryan S. R.; Hagmeijer, Rob

    2010-05-01

    We propose a computationally efficient method for the calculation of the binary cluster size distribution. This method is based on the phase path analysis algorithm, which was originally derived for single-component condensation. We extend this method by constructing the binary general dynamic equation, which introduces clusters at a point in two component n1,n2-space. The location of this source point is determined by the Gibbs free energy of formation and the impingement rates of the two constituents. The resulting model describes the binary cluster size distribution along a line in n1,n2-space. The solution of the binary general dynamic equation is compared with the solution of formally exact binary Becker-Döring equations for a typical nucleation pulse experiment. The results show good agreement for the cluster composition and size and the integral properties of the size distribution.

  6. A Flocking Based algorithm for Document Clustering Analysis

    SciTech Connect

    Cui, Xiaohui; Gao, Jinzhu; Potok, Thomas E

    2006-01-01

    Social animals or insects in nature often exhibit a form of emergent collective behavior known as flocking. In this paper, we present a novel Flocking based approach for document clustering analysis. Our Flocking clustering algorithm uses stochastic and heuristic principles discovered from observing bird flocks or fish schools. Unlike other partition clustering algorithm such as K-means, the Flocking based algorithm does not require initial partitional seeds. The algorithm generates a clustering of a given set of data through the embedding of the high-dimensional data items on a two-dimensional grid for easy clustering result retrieval and visualization. Inspired by the self-organized behavior of bird flocks, we represent each document object with a flock boid. The simple local rules followed by each flock boid result in the entire document flock generating complex global behaviors, which eventually result in a clustering of the documents. We evaluate the efficiency of our algorithm with both a synthetic dataset and a real document collection that includes 100 news articles collected from the Internet. Our results show that the Flocking clustering algorithm achieves better performance compared to the K- means and the Ant clustering algorithm for real document clustering.

  7. A Comparative Study of Protein Sequence Clustering Algorithms

    NASA Astrophysics Data System (ADS)

    Eldin, A. Sharaf; Abdelgaber, S.; Soliman, T.; Kassim, S.; Abdo, A.

    In this paper, we survey four clustering techniques and discuss their advantages and drawbacks. A review of eight different protein sequence clustering algorithms has been accomplished. Moreover, a comparison between the algorithms on the basis of some factors has been presented.

  8. Privacy Preservation in Distributed Subgradient Optimization Algorithms.

    PubMed

    Lou, Youcheng; Yu, Lean; Wang, Shouyang; Yi, Peng

    2017-07-31

    In this paper, some privacy-preserving features for distributed subgradient optimization algorithms are considered. Most of the existing distributed algorithms focus mainly on the algorithm design and convergence analysis, but not the protection of agents' privacy. Privacy is becoming an increasingly important issue in applications involving sensitive information. In this paper, we first show that the distributed subgradient synchronous homogeneous-stepsize algorithm is not privacy preserving in the sense that the malicious agent can asymptotically discover other agents' subgradients by transmitting untrue estimates to its neighbors. Then a distributed subgradient asynchronous heterogeneous-stepsize projection algorithm is proposed and accordingly its convergence and optimality is established. In contrast to the synchronous homogeneous-stepsize algorithm, in the new algorithm agents make their optimization updates asynchronously with heterogeneous stepsizes. The introduced two mechanisms of projection operation and asynchronous heterogeneous-stepsize optimization can guarantee that agents' privacy can be effectively protected.

  9. An algorithm on distributed mining association rules

    NASA Astrophysics Data System (ADS)

    Xu, Fan

    2005-12-01

    With the rapid development of the Internet/Intranet, distributed databases have become a broadly used environment in various areas. It is a critical task to mine association rules in distributed databases. The algorithms of distributed mining association rules can be divided into two classes. One is a DD algorithm, and another is a CD algorithm. A DD algorithm focuses on data partition optimization so as to enhance the efficiency. A CD algorithm, on the other hand, considers a setting where the data is arbitrarily partitioned horizontally among the parties to begin with, and focuses on parallelizing the communication. A DD algorithm is not always applicable, however, at the time the data is generated, it is often already partitioned. In many cases, it cannot be gathered and repartitioned for reasons of security and secrecy, cost transmission, or sheer efficiency. A CD algorithm may be a more appealing solution for systems which are naturally distributed over large expenses, such as stock exchange and credit card systems. An FDM algorithm provides enhancement to CD algorithm. However, CD and FDM algorithms are both based on net-structure and executing in non-shareable resources. In practical applications, however, distributed databases often are star-structured. This paper proposes an algorithm based on star-structure networks, which are more practical in application, have lower maintenance costs and which are more practical in the construction of the networks. In addition, the algorithm provides high efficiency in communication and good extension in parallel computation.

  10. Textural defect detect using a revised ant colony clustering algorithm

    NASA Astrophysics Data System (ADS)

    Zou, Chao; Xiao, Li; Wang, Bingwen

    2007-11-01

    We propose a totally novel method based on a revised ant colony clustering algorithm (ACCA) to explore the topic of textural defect detection. In this algorithm, our efforts are mainly made on the definition of local irregularity measurement and the implementation of the revised ACCA. The local irregular measurement defined evaluates the local textural inconsistency of each pixel against their mini-environment. In our revised ACCA, the behaviors of each ant are divided into two steps: release pheromone and act. The quantity of pheromone released is proportional to the irregularity measurement; the actions of the ants to act next are chosen independently of each other in a stochastic way according to some evaluated heuristic knowledge. The independency of ants implies the inherent parallel computation architecture of this algorithm. We apply the proposed method in some typical textural images with defects. From the series of pheromone distribution map (PDM), it can be clearly seen that the pheromone distribution approaches the textual defects gradually. By some post-processing, the final distribution of pheromone can demonstrate the shape and area of the defects well.

  11. Android Malware Classification Using K-Means Clustering Algorithm

    NASA Astrophysics Data System (ADS)

    Hamid, Isredza Rahmi A.; Syafiqah Khalid, Nur; Azma Abdullah, Nurul; Rahman, Nurul Hidayah Ab; Chai Wen, Chuah

    2017-08-01

    Malware was designed to gain access or damage a computer system without user notice. Besides, attacker exploits malware to commit crime or fraud. This paper proposed Android malware classification approach based on K-Means clustering algorithm. We evaluate the proposed model in terms of accuracy using machine learning algorithms. Two datasets were selected to demonstrate the practicing of K-Means clustering algorithms that are Virus Total and Malgenome dataset. We classify the Android malware into three clusters which are ransomware, scareware and goodware. Nine features were considered for each types of dataset such as Lock Detected, Text Detected, Text Score, Encryption Detected, Threat, Porn, Law, Copyright and Moneypak. We used IBM SPSS Statistic software for data classification and WEKA tools to evaluate the built cluster. The proposed K-Means clustering algorithm shows promising result with high accuracy when tested using Random Forest algorithm.

  12. New SIMD Algorithms for Cluster Labeling on Parallel Computers

    NASA Astrophysics Data System (ADS)

    Apostolakis, John; Coddington, Paul; Marinari, Enzo

    Cluster algorithms are non-local Monte Carlo update schemes which can greatly increase the efficiency of computer simulations of spin models of magnets. The major computational task in these algorithms is connected component labeling, to identify clusters of connected sites on a lattice. We have devised some new SIMD component labeling algorithms, and implemented them on the Connection Machine. We investigate their performance when applied to the cluster update of the two-dimensional Ising spin model. These algorithms could also be applied to other problems which use connected component labeling, such as percolation and image analysis.

  13. Distributed sensor data compression algorithm

    NASA Astrophysics Data System (ADS)

    Ambrose, Barry; Lin, Freddie

    2006-04-01

    Theoretically it is possible for two sensors to reliably send data at rates smaller than the sum of the necessary data rates for sending the data independently, essentially taking advantage of the correlation of sensor readings to reduce the data rate. In 2001, Caltech researchers Michelle Effros and Qian Zhao developed new techniques for data compression code design for correlated sensor data, which were published in a paper at the 2001 Data Compression Conference (DCC 2001). These techniques take advantage of correlations between two or more closely positioned sensors in a distributed sensor network. Given two signals, X and Y, the X signal is sent using standard data compression. The goal is to design a partition tree for the Y signal. The Y signal is sent using a code based on the partition tree. At the receiving end, if ambiguity arises when using the partition tree to decode the Y signal, the X signal is used to resolve the ambiguity. We have extended this work to increase the efficiency of the code search algorithms. Our results have shown that development of a highly integrated sensor network protocol that takes advantage of a correlation in sensor readings can result in 20-30% sensor data transport cost savings. In contrast, the best possible compression using state-of-the-art compression techniques that did not take into account the correlation of the incoming data signals achieved only 9-10% compression at most. This work was sponsored by MDA, but has very widespread applicability to ad hoc sensor networks, hyperspectral imaging sensors and vehicle health monitoring sensors for space applications.

  14. A practical comparison of two K-Means clustering algorithms.

    PubMed

    Wilkin, Gregory A; Huang, Xiuzhen

    2008-05-28

    Data clustering is a powerful technique for identifying data with similar characteristics, such as genes with similar expression patterns. However, not all implementations of clustering algorithms yield the same performance or the same clusters. In this paper, we study two implementations of a general method for data clustering: k-means clustering. Our experimentation compares the running times and distance efficiency of Lloyd's K-means Clustering and the Progressive Greedy K-means Clustering. Based on our implementation, not just in processing time, but also in terms of mean squared-difference (MSD), Lloyd's K-means Clustering algorithm is more efficient. This analysis was performed using both a gene expression level sample and on randomly-generated datasets in three-dimensional space. However, other circumstances may dictate a different choice in some situations.

  15. Clustering algorithms for Stokes space modulation format recognition.

    PubMed

    Boada, Ricard; Borkowski, Robert; Monroy, Idelfonso Tafur

    2015-06-15

    Stokes space modulation format recognition (Stokes MFR) is a blind method enabling digital coherent receivers to infer modulation format information directly from a received polarization-division-multiplexed signal. A crucial part of the Stokes MFR is a clustering algorithm, which largely influences the performance of the detection process, particularly at low signal-to-noise ratios. This paper reports on an extensive study of six different clustering algorithms: k-means, expectation maximization, density-based DBSCAN and OPTICS, spectral clustering and maximum likelihood clustering, used for discriminating between dual polarization: BPSK, QPSK, 8-PSK, 8-QAM, and 16-QAM. We determine essential performance metrics for each clustering algorithm and modulation format under test: minimum required signal-to-noise ratio, detection accuracy and algorithm complexity.

  16. A highly efficient multi-core algorithm for clustering extremely large datasets

    PubMed Central

    2010-01-01

    Background In recent years, the demand for computational power in computational biology has increased due to rapidly growing data sets from microarray and other high-throughput technologies. This demand is likely to increase. Standard algorithms for analyzing data, such as cluster algorithms, need to be parallelized for fast processing. Unfortunately, most approaches for parallelizing algorithms largely rely on network communication protocols connecting and requiring multiple computers. One answer to this problem is to utilize the intrinsic capabilities in current multi-core hardware to distribute the tasks among the different cores of one computer. Results We introduce a multi-core parallelization of the k-means and k-modes cluster algorithms based on the design principles of transactional memory for clustering gene expression microarray type data and categorial SNP data. Our new shared memory parallel algorithms show to be highly efficient. We demonstrate their computational power and show their utility in cluster stability and sensitivity analysis employing repeated runs with slightly changed parameters. Computation speed of our Java based algorithm was increased by a factor of 10 for large data sets while preserving computational accuracy compared to single-core implementations and a recently published network based parallelization. Conclusions Most desktop computers and even notebooks provide at least dual-core processors. Our multi-core algorithms show that using modern algorithmic concepts, parallelization makes it possible to perform even such laborious tasks as cluster sensitivity and cluster number estimation on the laboratory computer. PMID:20370922

  17. A biased random-key genetic algorithm for data clustering.

    PubMed

    Festa, P

    2013-09-01

    Cluster analysis aims at finding subsets (clusters) of a given set of entities, which are homogeneous and/or well separated. Starting from the 1990s, cluster analysis has been applied to several domains with numerous applications. It has emerged as one of the most exciting interdisciplinary fields, having benefited from concepts and theoretical results obtained by different scientific research communities, including genetics, biology, biochemistry, mathematics, and computer science. The last decade has brought several new algorithms, which are able to solve larger sized and real-world instances. We will give an overview of the main types of clustering and criteria for homogeneity or separation. Solution techniques are discussed, with special emphasis on the combinatorial optimization perspective, with the goal of providing conceptual insights and literature references to the broad community of clustering practitioners. A new biased random-key genetic algorithm is also described and compared with several efficient hybrid GRASP algorithms recently proposed to cluster biological data.

  18. Adaptive link selection algorithms for distributed estimation

    NASA Astrophysics Data System (ADS)

    Xu, Songcen; de Lamare, Rodrigo C.; Poor, H. Vincent

    2015-12-01

    This paper presents adaptive link selection algorithms for distributed estimation and considers their application to wireless sensor networks and smart grids. In particular, exhaustive search-based least mean squares (LMS) / recursive least squares (RLS) link selection algorithms and sparsity-inspired LMS / RLS link selection algorithms that can exploit the topology of networks with poor-quality links are considered. The proposed link selection algorithms are then analyzed in terms of their stability, steady-state, and tracking performance and computational complexity. In comparison with the existing centralized or distributed estimation strategies, the key features of the proposed algorithms are as follows: (1) more accurate estimates and faster convergence speed can be obtained and (2) the network is equipped with the ability of link selection that can circumvent link failures and improve the estimation performance. The performance of the proposed algorithms for distributed estimation is illustrated via simulations in applications of wireless sensor networks and smart grids.

  19. Modification of MSDR algorithm and ITS implementation on graph clustering

    NASA Astrophysics Data System (ADS)

    Prastiwi, D.; Sugeng, K. A.; Siswantining, T.

    2017-07-01

    Maximum Standard Deviation Reduction (MSDR) is a graph clustering algorithm to minimize the distance variation within a cluster. In this paper we propose a modified MSDR by replacing one technical step in MSDR which uses polynomial regression, with a new and simpler step. This leads to our new algorithm called Modified MSDR (MMSDR). We implement the new algorithm to separate a domestic flight network of an Indonesian airline into two large clusters. Further analysis allows us to discover a weak link in the network, which should be improved by adding more flights.

  20. Using k-means++ algorithm for researchers clustering

    NASA Astrophysics Data System (ADS)

    Rukmi, Alvida Mustika; Iqbal, Ikhwan Muhammad

    2017-08-01

    The Clustering of researchers based on publications is one of identifying community of researchers in a research environment. The researchers will know the relationships with other researchers regarding the similarity of topics and disciplines of publications based on the research community. The clustering will perform the extraction and analysis of the concept, topic detection and clustering of researchers. The attributes of data that can be obtained through the publications and characteristics of researchers on social networks that have been formed on the relations among researchers. The extraction and analysis of document, has two stages: extraction of keywords using keyphrase automatic rapid extraction (RAKE), and extraction concept of using latent semantic analysis (LSA). Clustering concept use k-means ++ algorithm. The last process, clustering of researchers is formed by feature extraction of social networking analysis,also use the k-means ++ algorithm. Applications for clustering researchers will be presented in the table containing information on researchers in each of these clusters.

  1. A fuzzy co-clustering algorithm for biomedical data

    PubMed Central

    Liu, Zhizhong; Chao, Hao

    2017-01-01

    Fuzzy co-clustering extends co-clustering by assigning membership functions to both the objects and the features, and is helpful to improve clustering accurarcy of biomedical data. In this paper, we introduce a new fuzzy co-clustering algorithm based on information bottleneck named ibFCC. The ibFCC formulates an objective function which includes a distance function that employs information bottleneck theory to measure the distance between feature data point and the feature cluster centroid. Many experiments were conducted on five biomedical datasets, and the ibFCC was compared with such prominent fuzzy (co-)clustering algorithms as FCM, FCCM, RFCC and FCCI. Experimental results showed that ibFCC could yield high quality clusters and was better than all these methods in terms of accuracy. PMID:28445496

  2. The Enhanced Hoshen-Kopelman Algorithm for Cluster Analysis

    NASA Astrophysics Data System (ADS)

    Hoshen, Joseph

    1997-08-01

    In 1976 Hoshen and Kopelman(J. Hoshen and R. Kopelman, Phys. Rev. B, 14, 3438 (1976).) introduced a breakthrough algorithm, known today as the Hoshen-Kopelman algorithm, for cluster analysis. This algorithm revolutionized Monte Carlo cluster calculations in percolation theory as it enables analysis of very large lattices containing 10^11 or more sites. Initially the HK algorithm primary use was in the domain of pure and basic sciences. Later it began finding applications in diverse fields of technology and applied sciences. Example of such applications are two and three dimensional image analysis, composite material modeling, polymers, remote sensing, brain modeling and food processing. While the original HK algorithm provides only cluster size data for only one class of sites, the Enhanced HK (EHK) algorithm, presented in this paper, enables calculations of cluster spatial moments -- characteristics of cluster shapes -- for multiple classes of sites. These enhancements preserve the time and space complexities of the original HK algorithm, such that very large lattices could be still analyzed simultaneously in a single pass through the lattice for cluster sizes, classes and shapes.

  3. A fuzzy clustering algorithm to detect planar and quadric shapes

    NASA Technical Reports Server (NTRS)

    Krishnapuram, Raghu; Frigui, Hichem; Nasraoui, Olfa

    1992-01-01

    In this paper, we introduce a new fuzzy clustering algorithm to detect an unknown number of planar and quadric shapes in noisy data. The proposed algorithm is computationally and implementationally simple, and it overcomes many of the drawbacks of the existing algorithms that have been proposed for similar tasks. Since the clustering is performed in the original image space, and since no features need to be computed, this approach is particularly suited for sparse data. The algorithm may also be used in pattern recognition applications.

  4. A robust fuzzy local information C-Means clustering algorithm.

    PubMed

    Krinidis, Stelios; Chatzis, Vassilios

    2010-05-01

    This paper presents a variation of fuzzy c-means (FCM) algorithm that provides image clustering. The proposed algorithm incorporates the local spatial information and gray level information in a novel fuzzy way. The new algorithm is called fuzzy local information C-Means (FLICM). FLICM can overcome the disadvantages of the known fuzzy c-means algorithms and at the same time enhances the clustering performance. The major characteristic of FLICM is the use of a fuzzy local (both spatial and gray level) similarity measure, aiming to guarantee noise insensitiveness and image detail preservation. Furthermore, the proposed algorithm is fully free of the empirically adjusted parameters (a, ¿(g), ¿(s), etc.) incorporated into all other fuzzy c-means algorithms proposed in the literature. Experiments performed on synthetic and real-world images show that FLICM algorithm is effective and efficient, providing robustness to noisy images.

  5. Learning factorizations in estimation of distribution algorithms using affinity propagation.

    PubMed

    Santana, Roberto; Larrañaga, Pedro; Lozano, José A

    2010-01-01

    Estimation of distribution algorithms (EDAs) that use marginal product model factorizations have been widely applied to a broad range of mainly binary optimization problems. In this paper, we introduce the affinity propagation EDA (AffEDA) which learns a marginal product model by clustering a matrix of mutual information learned from the data using a very efficient message-passing algorithm known as affinity propagation. The introduced algorithm is tested on a set of binary and nonbinary decomposable functions and using a hard combinatorial class of problem known as the HP protein model. The results show that the algorithm is a very efficient alternative to other EDAs that use marginal product model factorizations such as the extended compact genetic algorithm (ECGA) and improves the quality of the results achieved by ECGA when the cardinality of the variables is increased.

  6. CLAG: an unsupervised non hierarchical clustering algorithm handling biological data

    PubMed Central

    2012-01-01

    Background Searching for similarities in a set of biological data is intrinsically difficult due to possible data points that should not be clustered, or that should group within several clusters. Under these hypotheses, hierarchical agglomerative clustering is not appropriate. Moreover, if the dataset is not known enough, like often is the case, supervised classification is not appropriate either. Results CLAG (for CLusters AGgregation) is an unsupervised non hierarchical clustering algorithm designed to cluster a large variety of biological data and to provide a clustered matrix and numerical values indicating cluster strength. CLAG clusterizes correlation matrices for residues in protein families, gene-expression and miRNA data related to various cancer types, sets of species described by multidimensional vectors of characters, binary matrices. It does not ask to all data points to cluster and it converges yielding the same result at each run. Its simplicity and speed allows it to run on reasonably large datasets. Conclusions CLAG can be used to investigate the cluster structure present in biological datasets and to identify its underlying graph. It showed to be more informative and accurate than several known clustering methods, as hierarchical agglomerative clustering, k-means, fuzzy c-means, model-based clustering, affinity propagation clustering, and not to suffer of the convergence problem proper to this latter. PMID:23216858

  7. Efficient Cluster Algorithm for Spin Glasses in Any Space Dimension

    NASA Astrophysics Data System (ADS)

    Zhu, Zheng; Ochoa, Andrew J.; Katzgraber, Helmut G.

    2015-08-01

    Spin systems with frustration and disorder are notoriously difficult to study, both analytically and numerically. While the simulation of ferromagnetic statistical mechanical models benefits greatly from cluster algorithms, these accelerated dynamics methods remain elusive for generic spin-glass-like systems. Here, we present a cluster algorithm for Ising spin glasses that works in any space dimension and speeds up thermalization by at least one order of magnitude at temperatures where thermalization is typically difficult. Our isoenergetic cluster moves are based on the Houdayer cluster algorithm for two-dimensional spin glasses and lead to a speedup over conventional state-of-the-art methods that increases with the system size. We illustrate the benefits of the isoenergetic cluster moves in two and three space dimensions, as well as the nonplanar chimera topology found in the D-Wave Inc. quantum annealing machine.

  8. Ultrafast clustering algorithms for metagenomic sequence analysis

    PubMed Central

    Fu, Limin; Niu, Beifang; Wu, Sitao; Wooley, John

    2012-01-01

    The rapid advances of high-throughput sequencing technologies dramatically prompted metagenomic studies of microbial communities that exist at various environments. Fundamental questions in metagenomics include the identities, composition and dynamics of microbial populations and their functions and interactions. However, the massive quantity and the comprehensive complexity of these sequence data pose tremendous challenges in data analysis. These challenges include but are not limited to ever-increasing computational demand, biased sequence sampling, sequence errors, sequence artifacts and novel sequences. Sequence clustering methods can directly answer many of the fundamental questions by grouping similar sequences into families. In addition, clustering analysis also addresses the challenges in metagenomics. Thus, a large redundant data set can be represented with a small non-redundant set, where each cluster can be represented by a single entry or a consensus. Artifacts can be rapidly detected through clustering. Errors can be identified, filtered or corrected by using consensus from sequences within clusters. PMID:22772836

  9. A Fast Implementation of the ISODATA Clustering Algorithm

    NASA Technical Reports Server (NTRS)

    Memarsadeghi, Nargess; Mount, David M.; Netanyahu, Nathan S.; LeMoigne, Jacqueline

    2005-01-01

    Clustering is central to many image processing and remote sensing applications. ISODATA is one of the most popular and widely used clustering methods in geoscience applications, but it can run slowly, particularly with large data sets. We present a more efficient approach to ISODATA clustering, which achieves better running times by storing the points in a kd-tree and through a modification of the way in which the algorithm estimates the dispersion of each cluster. We also present an approximate version of the algorithm which allows the user to further improve the running time, at the expense of lower fidelity in computing the nearest cluster center to each point. We provide both theoretical and empirical justification that our modified approach produces clusterings that are very similar to those produced by the standard ISODATA approach. We also provide empirical studies on both synthetic data and remotely sensed Landsat and MODIS images that show that our approach has significantly lower running times.

  10. Implementing Agglomerative Hierarchic Clustering Algorithms for Use in Document Retrieval.

    ERIC Educational Resources Information Center

    Voorhees, Ellen M.

    1986-01-01

    Describes a computerized information retrieval system that uses three agglomerative hierarchic clustering algorithms--single link, complete link, and group average link--and explains their implementations. It is noted that these implementations have been used to cluster a collection of 12,000 documents. (LRW)

  11. Clustering Molecular Dynamics Trajectories: 1. Characterizing the Performance of Different Clustering Algorithms.

    PubMed

    Shao, Jianyin; Tanner, Stephen W; Thompson, Nephi; Cheatham, Thomas E

    2007-11-01

    Molecular dynamics simulation methods produce trajectories of atomic positions (and optionally velocities and energies) as a function of time and provide a representation of the sampling of a given molecule's energetically accessible conformational ensemble. As simulations on the 10-100 ns time scale become routine, with sampled configurations stored on the picosecond time scale, such trajectories contain large amounts of data. Data-mining techniques, like clustering, provide one means to group and make sense of the information in the trajectory. In this work, several clustering algorithms were implemented, compared, and utilized to understand MD trajectory data. The development of the algorithms into a freely available C code library, and their application to a simple test example of random (or systematically placed) points in a 2D plane (where the pairwise metric is the distance between points) provide a means to understand the relative performance. Eleven different clustering algorithms were developed, ranging from top-down splitting (hierarchical) and bottom-up aggregating (including single-linkage edge joining, centroid-linkage, average-linkage, complete-linkage, centripetal, and centripetal-complete) to various refinement (means, Bayesian, and self-organizing maps) and tree (COBWEB) algorithms. Systematic testing in the context of MD simulation of various DNA systems (including DNA single strands and the interaction of a minor groove binding drug DB226 with a DNA hairpin) allows a more direct assessment of the relative merits of the distinct clustering algorithms. Additionally, means to assess the relative performance and differences between the algorithms, to dynamically select the initial cluster count, and to achieve faster data mining by "sieved clustering" were evaluated. Overall, it was found that there is no one perfect "one size fits all" algorithm for clustering MD trajectories and that the results strongly depend on the choice of atoms for the

  12. Efficient Record Linkage Algorithms Using Complete Linkage Clustering.

    PubMed

    Mamun, Abdullah-Al; Aseltine, Robert; Rajasekaran, Sanguthevar

    2016-01-01

    Data from different agencies share data of the same individuals. Linking these datasets to identify all the records belonging to the same individuals is a crucial and challenging problem, especially given the large volumes of data. A large number of available algorithms for record linkage are prone to either time inefficiency or low-accuracy in finding matches and non-matches among the records. In this paper we propose efficient as well as reliable sequential and parallel algorithms for the record linkage problem employing hierarchical clustering methods. We employ complete linkage hierarchical clustering algorithms to address this problem. In addition to hierarchical clustering, we also use two other techniques: elimination of duplicate records and blocking. Our algorithms use sorting as a sub-routine to identify identical copies of records. We have tested our algorithms on datasets with millions of synthetic records. Experimental results show that our algorithms achieve nearly 100% accuracy. Parallel implementations achieve almost linear speedups. Time complexities of these algorithms do not exceed those of previous best-known algorithms. Our proposed algorithms outperform previous best-known algorithms in terms of accuracy consuming reasonable run times.

  13. Efficient Record Linkage Algorithms Using Complete Linkage Clustering

    PubMed Central

    Mamun, Abdullah-Al; Aseltine, Robert; Rajasekaran, Sanguthevar

    2016-01-01

    Data from different agencies share data of the same individuals. Linking these datasets to identify all the records belonging to the same individuals is a crucial and challenging problem, especially given the large volumes of data. A large number of available algorithms for record linkage are prone to either time inefficiency or low-accuracy in finding matches and non-matches among the records. In this paper we propose efficient as well as reliable sequential and parallel algorithms for the record linkage problem employing hierarchical clustering methods. We employ complete linkage hierarchical clustering algorithms to address this problem. In addition to hierarchical clustering, we also use two other techniques: elimination of duplicate records and blocking. Our algorithms use sorting as a sub-routine to identify identical copies of records. We have tested our algorithms on datasets with millions of synthetic records. Experimental results show that our algorithms achieve nearly 100% accuracy. Parallel implementations achieve almost linear speedups. Time complexities of these algorithms do not exceed those of previous best-known algorithms. Our proposed algorithms outperform previous best-known algorithms in terms of accuracy consuming reasonable run times. PMID:27124604

  14. Clustering of Hadronic Showers with a Structural Algorithm

    SciTech Connect

    Charles, M.J.; /SLAC

    2005-12-13

    The internal structure of hadronic showers can be resolved in a high-granularity calorimeter. This structure is described in terms of simple components and an algorithm for reconstruction of hadronic clusters using these components is presented. Results from applying this algorithm to simulated hadronic Z-pole events in the SiD concept are discussed.

  15. Critical dynamics of cluster algorithms in the dilute Ising model

    NASA Astrophysics Data System (ADS)

    Hennecke, M.; Heyken, U.

    1993-08-01

    Autocorrelation times for thermodynamic quantities at T C are calculated from Monte Carlo simulations of the site-diluted simple cubic Ising model, using the Swendsen-Wang and Wolff cluster algorithms. Our results show that for these algorithms the autocorrelation times decrease when reducing the concentration of magnetic sites from 100% down to 40%. This is of crucial importance when estimating static properties of the model, since the variances of these estimators increase with autocorrelation time. The dynamical critical exponents are calculated for both algorithms, observing pronounced finite-size effects in the energy autocorrelation data for the algorithm of Wolff. We conclude that, when applied to the dilute Ising model, cluster algorithms become even more effective than local algorithms, for which increasing autocorrelation times are expected.

  16. CCL: an algorithm for the efficient comparison of clusters

    PubMed Central

    Hundt, R.; Schön, J. C.; Neelamraju, S.; Zagorac, J.; Jansen, M.

    2013-01-01

    The systematic comparison of the atomic structure of solids and clusters has become an important task in crystallography, chemistry, physics and materials science, in particular in the context of structure prediction and structure determination of nanomaterials. In this work, an efficient and robust algorithm for the comparison of cluster structures is presented, which is based on the mapping of the point patterns of the two clusters onto each other. This algorithm has been implemented as the module CCL in the structure visualization and analysis program KPLOT. PMID:23682193

  17. Learning theory of distributed spectral algorithms

    NASA Astrophysics Data System (ADS)

    Guo, Zheng-Chu; Lin, Shao-Bo; Zhou, Ding-Xuan

    2017-07-01

    Spectral algorithms have been widely used and studied in learning theory and inverse problems. This paper is concerned with distributed spectral algorithms, for handling big data, based on a divide-and-conquer approach. We present a learning theory for these distributed kernel-based learning algorithms in a regression framework including nice error bounds and optimal minimax learning rates achieved by means of a novel integral operator approach and a second order decomposition of inverse operators. Our quantitative estimates are given in terms of regularity of the regression function, effective dimension of the reproducing kernel Hilbert space, and qualification of the filter function of the spectral algorithm. They do not need any eigenfunction or noise conditions and are better than the existing results even for the classical family of spectral algorithms.

  18. A Distributed Agent Implementation of Multiple Species Flocking Model for Document Partitioning Clustering

    SciTech Connect

    Cui, Xiaohui; Potok, Thomas E

    2006-01-01

    The Flocking model, first proposed by Craig Reynolds, is one of the first bio-inspired computational collective behavior models that has many popular applications, such as animation. Our early research has resulted in a flock clustering algorithm that can achieve better performance than the Kmeans or the Ant clustering algorithms for data clustering. This algorithm generates a clustering of a given set of data through the embedding of the highdimensional data items on a two-dimensional grid for efficient clustering result retrieval and visualization. In this paper, we propose a bio-inspired clustering model, the Multiple Species Flocking clustering model (MSF), and present a distributed multi-agent MSF approach for document clustering.

  19. Mass Distribution in Galaxy Cluster Cores

    NASA Astrophysics Data System (ADS)

    Hogan, M. T.; McNamara, B. R.; Pulido, F.; Nulsen, P. E. J.; Russell, H. R.; Vantyghem, A. N.; Edge, A. C.; Main, R. A.

    2017-03-01

    Many processes within galaxy clusters, such as those believed to govern the onset of thermally unstable cooling and active galactic nucleus feedback, are dependent upon local dynamical timescales. However, accurate mapping of the mass distribution within individual clusters is challenging, particularly toward cluster centers where the total mass budget has substantial radially dependent contributions from the stellar (M *), gas (M gas), and dark matter (M DM) components. In this paper we use a small sample of galaxy clusters with deep Chandra observations and good ancillary tracers of their gravitating mass at both large and small radii to develop a method for determining mass profiles that span a wide radial range and extend down into the central galaxy. We also consider potential observational pitfalls in understanding cooling in hot cluster atmospheres, and find tentative evidence for a relationship between the radial extent of cooling X-ray gas and nebular Hα emission in cool-core clusters. At large radii the entropy profiles of our clusters agree with the baseline power law of K ∝ r 1.1 expected from gravity alone. At smaller radii our entropy profiles become shallower but continue with a power law of the form K ∝ r 0.67 down to our resolution limit. Among this small sample of cool-core clusters we therefore find no support for the existence of a central flat “entropy floor.”

  20. Efficient cluster algorithm for CP(N-1) models

    NASA Astrophysics Data System (ADS)

    Beard, B. B.; Pepe, M.; Riederer, S.; Wiese, U.-J.

    2006-11-01

    Despite several attempts, no efficient cluster algorithm has been constructed for CP(N-1) models in the standard Wilson formulation of lattice field theory. In fact, there is a no-go theorem that prevents the construction of an efficient Wolff-type embedding algorithm. In this paper, we construct an efficient cluster algorithm for ferromagnetic SU(N)-symmetric quantum spin systems. Such systems provide a regularization for CP(N-1) models in the framework of D-theory. We present detailed studies of the autocorrelations and find a dynamical critical exponent that is consistent with z=0.

  1. Measuring Constraint-Set Utility for Partitional Clustering Algorithms

    NASA Technical Reports Server (NTRS)

    Davidson, Ian; Wagstaff, Kiri L.; Basu, Sugato

    2006-01-01

    Clustering with constraints is an active area of machine learning and data mining research. Previous empirical work has convincingly shown that adding constraints to clustering improves the performance of a variety of algorithms. However, in most of these experiments, results are averaged over different randomly chosen constraint sets from a given set of labels, thereby masking interesting properties of individual sets. We demonstrate that constraint sets vary significantly in how useful they are for constrained clustering; some constraint sets can actually decrease algorithm performance. We create two quantitative measures, informativeness and coherence, that can be used to identify useful constraint sets. We show that these measures can also help explain differences in performance for four particular constrained clustering algorithms.

  2. Measuring Constraint-Set Utility for Partitional Clustering Algorithms

    NASA Technical Reports Server (NTRS)

    Davidson, Ian; Wagstaff, Kiri L.; Basu, Sugato

    2006-01-01

    Clustering with constraints is an active area of machine learning and data mining research. Previous empirical work has convincingly shown that adding constraints to clustering improves the performance of a variety of algorithms. However, in most of these experiments, results are averaged over different randomly chosen constraint sets from a given set of labels, thereby masking interesting properties of individual sets. We demonstrate that constraint sets vary significantly in how useful they are for constrained clustering; some constraint sets can actually decrease algorithm performance. We create two quantitative measures, informativeness and coherence, that can be used to identify useful constraint sets. We show that these measures can also help explain differences in performance for four particular constrained clustering algorithms.

  3. Digital News Graph Clustering using Chinese Whispers Algorithm

    NASA Astrophysics Data System (ADS)

    Pratama, M. F. E.; Kemas, R. S. W.; Anisa, H.

    2017-01-01

    As the exponential growth of news creation on the internet, the amount of digital news has reached out billion numbers. Digital news is naturally linked each other but it needs to be grouped so that user can easily classify the news that they read. Graph is the most suitable data model to represent digital news since its can describing relation in easy and flexible manner. Thus, to overcome grouping problems, in this paper we using Chinese Whispers Algorithm as the graph clustering approach. We choose Chinese Whisper Algorithm based on consideration that the algorithm is able to make clusters from a big graph data with a relatively fast process [8], that appropriate with the characteristics of digital news. In this research, we examine the graph quality by comparing intra and inter-cluster weights of every node. This scenario gives us a quite high result that 95% of nodes have intra-cluster weight higher than its inter-cluster weight. We also investigate the graph accuracy by comparing the cluster results with expert judgement. As the result, the average accuracy of digital news graph clustering using Chinese Whisper algorithm is 80%.

  4. Symmetric nonnegative matrix factorization: algorithms and applications to probabilistic clustering.

    PubMed

    He, Zhaoshui; Xie, Shengli; Zdunek, Rafal; Zhou, Guoxu; Cichocki, Andrzej

    2011-12-01

    Nonnegative matrix factorization (NMF) is an unsupervised learning method useful in various applications including image processing and semantic analysis of documents. This paper focuses on symmetric NMF (SNMF), which is a special case of NMF decomposition. Three parallel multiplicative update algorithms using level 3 basic linear algebra subprograms directly are developed for this problem. First, by minimizing the Euclidean distance, a multiplicative update algorithm is proposed, and its convergence under mild conditions is proved. Based on it, we further propose another two fast parallel methods: α-SNMF and β -SNMF algorithms. All of them are easy to implement. These algorithms are applied to probabilistic clustering. We demonstrate their effectiveness for facial image clustering, document categorization, and pattern clustering in gene expression.

  5. An improved algorithm for clustering gene expression data.

    PubMed

    Bandyopadhyay, Sanghamitra; Mukhopadhyay, Anirban; Maulik, Ujjwal

    2007-11-01

    Recent advancements in microarray technology allows simultaneous monitoring of the expression levels of a large number of genes over different time points. Clustering is an important tool for analyzing such microarray data, typical properties of which are its inherent uncertainty, noise and imprecision. In this article, a two-stage clustering algorithm, which employs a recently proposed variable string length genetic scheme and a multiobjective genetic clustering algorithm, is proposed. It is based on the novel concept of points having significant membership to multiple classes. An iterated version of the well-known Fuzzy C-Means is also utilized for clustering. The significant superiority of the proposed two-stage clustering algorithm as compared to the average linkage method, Self Organizing Map (SOM) and a recently developed weighted Chinese restaurant-based clustering method (CRC), widely used methods for clustering gene expression data, is established on a variety of artificial and publicly available real life data sets. The biological relevance of the clustering solutions are also analyzed.

  6. Advanced algorithms for distributed fusion

    NASA Astrophysics Data System (ADS)

    Gelfand, A.; Smith, C.; Colony, M.; Bowman, C.; Pei, R.; Huynh, T.; Brown, C.

    2008-03-01

    The US Military has been undergoing a radical transition from a traditional "platform-centric" force to one capable of performing in a "Network-Centric" environment. This transformation will place all of the data needed to efficiently meet tactical and strategic goals at the warfighter's fingertips. With access to this information, the challenge of fusing data from across the batttlespace into an operational picture for real-time Situational Awareness emerges. In such an environment, centralized fusion approaches will have limited application due to the constraints of real-time communications networks and computational resources. To overcome these limitations, we are developing a formalized architecture for fusion and track adjudication that allows the distribution of fusion processes over a dynamically created and managed information network. This network will support the incorporation and utilization of low level tracking information within the Army Distributed Common Ground System (DCGS-A) or Future Combat System (FCS). The framework is based on Bowman's Dual Node Network (DNN) architecture that utilizes a distributed network of interlaced fusion and track adjudication nodes to build and maintain a globally consistent picture across all assets.

  7. Learning the Distribution Preserving Semantic Subspace for Clustering.

    PubMed

    Tian, Jinyu; Zhang, Taiping; Qin, Anyong; Shang, Zhaowei; Tang, Yuan Yan

    2017-09-04

    This work proposes a new clustering method for images called Distribution Preserving Indexing (DPI). It aims to find a lower-dimensional semantic space approximating the original image space in the sense of preserving the distribution of the data. In the theory, the intrinsic structure of the data clusters can be described by the distribution of the data effectively. Therefore, the cluster structure of the data in a lower-dimensional semantic space derived by DPI becomes clear. Unlike these distance based clustering methods which reveal the intrinsic Euclidean structure of data, our method attempts to discover the intrinsic cluster structure of the data space that actually is the union of some sub-manifolds. Moreover, we propose a revised Kernel Density Estimator for the case of high-dimensional data, which is a crucial step in DPI. Also, we provide a theoretical analysis of the bound of our method. Finally, the extensive experiments compared with other algorithms, on COIL20, CBCL, and MNIST demonstrate the effectiveness of our proposed approach.

  8. Sampling Within k-Means Algorithm to Cluster Large Datasets

    SciTech Connect

    Bejarano, Jeremy; Bose, Koushiki; Brannan, Tyler; Thomas, Anita; Adragni, Kofi; Neerchal, Nagaraj; Ostrouchov, George

    2011-08-01

    Due to current data collection technology, our ability to gather data has surpassed our ability to analyze it. In particular, k-means, one of the simplest and fastest clustering algorithms, is ill-equipped to handle extremely large datasets on even the most powerful machines. Our new algorithm uses a sample from a dataset to decrease runtime by reducing the amount of data analyzed. We perform a simulation study to compare our sampling based k-means to the standard k-means algorithm by analyzing both the speed and accuracy of the two methods. Results show that our algorithm is significantly more efficient than the existing algorithm with comparable accuracy. Further work on this project might include a more comprehensive study both on more varied test datasets as well as on real weather datasets. This is especially important considering that this preliminary study was performed on rather tame datasets. Also, these datasets should analyze the performance of the algorithm on varied values of k. Lastly, this paper showed that the algorithm was accurate for relatively low sample sizes. We would like to analyze this further to see how accurate the algorithm is for even lower sample sizes. We could find the lowest sample sizes, by manipulating width and confidence level, for which the algorithm would be acceptably accurate. In order for our algorithm to be a success, it needs to meet two benchmarks: match the accuracy of the standard k-means algorithm and significantly reduce runtime. Both goals are accomplished for all six datasets analyzed. However, on datasets of three and four dimension, as the data becomes more difficult to cluster, both algorithms fail to obtain the correct classifications on some trials. Nevertheless, our algorithm consistently matches the performance of the standard algorithm while becoming remarkably more efficient with time. Therefore, we conclude that analysts can use our algorithm, expecting accurate results in considerably less time.

  9. A modified hyperplane clustering algorithm allows for efficient and accurate clustering of extremely large datasets.

    PubMed

    Sharma, Ashok; Podolsky, Robert; Zhao, Jieping; McIndoe, Richard A

    2009-05-01

    As the number of publically available microarray experiments increases, the ability to analyze extremely large datasets across multiple experiments becomes critical. There is a requirement to develop algorithms which are fast and can cluster extremely large datasets without affecting the cluster quality. Clustering is an unsupervised exploratory technique applied to microarray data to find similar data structures or expression patterns. Because of the high input/output costs involved and large distance matrices calculated, most of the algomerative clustering algorithms fail on large datasets (30,000 + genes/200 + arrays). In this article, we propose a new two-stage algorithm which partitions the high-dimensional space associated with microarray data using hyperplanes. The first stage is based on the Balanced Iterative Reducing and Clustering using Hierarchies algorithm with the second stage being a conventional k-means clustering technique. This algorithm has been implemented in a software tool (HPCluster) designed to cluster gene expression data. We compared the clustering results using the two-stage hyperplane algorithm with the conventional k-means algorithm from other available programs. Because, the first stage traverses the data in a single scan, the performance and speed increases substantially. The data reduction accomplished in the first stage of the algorithm reduces the memory requirements allowing us to cluster 44,460 genes without failure and significantly decreases the time to complete when compared with popular k-means programs. The software was written in C# (.NET 1.1). The program is freely available and can be downloaded from http://www.amdcc.org/bioinformatics/bioinformatics.aspx. Supplementary data are available at Bioinformatics online.

  10. A Genetic Algorithm That Exchanges Neighboring Centers for Fuzzy c-Means Clustering

    ERIC Educational Resources Information Center

    Chahine, Firas Safwan

    2012-01-01

    Clustering algorithms are widely used in pattern recognition and data mining applications. Due to their computational efficiency, partitional clustering algorithms are better suited for applications with large datasets than hierarchical clustering algorithms. K-means is among the most popular partitional clustering algorithm, but has a major…

  11. A Genetic Algorithm That Exchanges Neighboring Centers for Fuzzy c-Means Clustering

    ERIC Educational Resources Information Center

    Chahine, Firas Safwan

    2012-01-01

    Clustering algorithms are widely used in pattern recognition and data mining applications. Due to their computational efficiency, partitional clustering algorithms are better suited for applications with large datasets than hierarchical clustering algorithms. K-means is among the most popular partitional clustering algorithm, but has a major…

  12. CACONET: Ant Colony Optimization (ACO) Based Clustering Algorithm for VANET

    PubMed Central

    Bajwa, Khalid Bashir; Khan, Salabat; Chaudary, Nadeem Majeed; Akram, Adeel

    2016-01-01

    A vehicular ad hoc network (VANET) is a wirelessly connected network of vehicular nodes. A number of techniques, such as message ferrying, data aggregation, and vehicular node clustering aim to improve communication efficiency in VANETs. Cluster heads (CHs), selected in the process of clustering, manage inter-cluster and intra-cluster communication. The lifetime of clusters and number of CHs determines the efficiency of network. In this paper a Clustering algorithm based on Ant Colony Optimization (ACO) for VANETs (CACONET) is proposed. CACONET forms optimized clusters for robust communication. CACONET is compared empirically with state-of-the-art baseline techniques like Multi-Objective Particle Swarm Optimization (MOPSO) and Comprehensive Learning Particle Swarm Optimization (CLPSO). Experiments varying the grid size of the network, the transmission range of nodes, and number of nodes in the network were performed to evaluate the comparative effectiveness of these algorithms. For optimized clustering, the parameters considered are the transmission range, direction and speed of the nodes. The results indicate that CACONET significantly outperforms MOPSO and CLPSO. PMID:27149517

  13. CACONET: Ant Colony Optimization (ACO) Based Clustering Algorithm for VANET.

    PubMed

    Aadil, Farhan; Bajwa, Khalid Bashir; Khan, Salabat; Chaudary, Nadeem Majeed; Akram, Adeel

    2016-01-01

    A vehicular ad hoc network (VANET) is a wirelessly connected network of vehicular nodes. A number of techniques, such as message ferrying, data aggregation, and vehicular node clustering aim to improve communication efficiency in VANETs. Cluster heads (CHs), selected in the process of clustering, manage inter-cluster and intra-cluster communication. The lifetime of clusters and number of CHs determines the efficiency of network. In this paper a Clustering algorithm based on Ant Colony Optimization (ACO) for VANETs (CACONET) is proposed. CACONET forms optimized clusters for robust communication. CACONET is compared empirically with state-of-the-art baseline techniques like Multi-Objective Particle Swarm Optimization (MOPSO) and Comprehensive Learning Particle Swarm Optimization (CLPSO). Experiments varying the grid size of the network, the transmission range of nodes, and number of nodes in the network were performed to evaluate the comparative effectiveness of these algorithms. For optimized clustering, the parameters considered are the transmission range, direction and speed of the nodes. The results indicate that CACONET significantly outperforms MOPSO and CLPSO.

  14. Parallel and Distributed Computing Combinatorial Algorithms

    DTIC Science & Technology

    1993-10-01

    FUPNDKC %2,•, PARALLEL AND DISTRIBUTED COMPUTING COMBINATORIAL ALGORITHMS 6. AUTHOR(S) 2304/DS F49620-92-J-0125 DR. LEIGHTON 7 PERFORMING ORGANIZATION NAME...on several problems involving parallel and distributed computing and combinatorial optimization. This research is reported in the numerous papers that...network decom- position. In Proceedings of the Eleventh Annual ACM Symposium on Principles of Distributed Computing , August 1992. [15] B. Awerbuch, B

  15. Exact and heuristic algorithms for weighted cluster editing.

    PubMed

    Rahmann, Sven; Wittkop, Tobias; Baumbach, Jan; Martin, Marcel; Truss, Anke; Böcker, Sebastian

    2007-01-01

    Clustering objects according to given similarity or distance values is a ubiquitous problem in computational biology with diverse applications, e.g., in defining families of orthologous genes, or in the analysis of microarray experiments. While there exists a plenitude of methods, many of them produce clusterings that can be further improved. "Cleaning up" initial clusterings can be formalized as projecting a graph on the space of transitive graphs; it is also known as the cluster editing or cluster partitioning problem in the literature. In contrast to previous work on cluster editing, we allow arbitrary weights on the similarity graph. To solve the so-defined weighted transitive graph projection problem, we present (1) the first exact fixed-parameter algorithm, (2) a polynomial-time greedy algorithm that returns the optimal result on a well-defined subset of "close-to-transitive" graphs and works heuristically on other graphs, and (3) a fast heuristic that uses ideas similar to those from the Fruchterman-Reingold graph layout algorithm. We compare quality and running times of these algorithms on both artificial graphs and protein similarity graphs derived from the 66 organisms of the COG dataset.

  16. Distributed controller clustering in software defined networks.

    PubMed

    Abdelaziz, Ahmed; Fong, Ang Tan; Gani, Abdullah; Garba, Usman; Khan, Suleman; Akhunzada, Adnan; Talebian, Hamid; Choo, Kim-Kwang Raymond

    2017-01-01

    Software Defined Networking (SDN) is an emerging promising paradigm for network management because of its centralized network intelligence. However, the centralized control architecture of the software-defined networks (SDNs) brings novel challenges of reliability, scalability, fault tolerance and interoperability. In this paper, we proposed a novel clustered distributed controller architecture in the real setting of SDNs. The distributed cluster implementation comprises of multiple popular SDN controllers. The proposed mechanism is evaluated using a real world network topology running on top of an emulated SDN environment. The result shows that the proposed distributed controller clustering mechanism is able to significantly reduce the average latency from 8.1% to 1.6%, the packet loss from 5.22% to 4.15%, compared to distributed controller without clustering running on HP Virtual Application Network (VAN) SDN and Open Network Operating System (ONOS) controllers respectively. Moreover, proposed method also shows reasonable CPU utilization results. Furthermore, the proposed mechanism makes possible to handle unexpected load fluctuations while maintaining a continuous network operation, even when there is a controller failure. The paper is a potential contribution stepping towards addressing the issues of reliability, scalability, fault tolerance, and inter-operability.

  17. Distributed controller clustering in software defined networks

    PubMed Central

    Gani, Abdullah; Akhunzada, Adnan; Talebian, Hamid; Choo, Kim-Kwang Raymond

    2017-01-01

    Software Defined Networking (SDN) is an emerging promising paradigm for network management because of its centralized network intelligence. However, the centralized control architecture of the software-defined networks (SDNs) brings novel challenges of reliability, scalability, fault tolerance and interoperability. In this paper, we proposed a novel clustered distributed controller architecture in the real setting of SDNs. The distributed cluster implementation comprises of multiple popular SDN controllers. The proposed mechanism is evaluated using a real world network topology running on top of an emulated SDN environment. The result shows that the proposed distributed controller clustering mechanism is able to significantly reduce the average latency from 8.1% to 1.6%, the packet loss from 5.22% to 4.15%, compared to distributed controller without clustering running on HP Virtual Application Network (VAN) SDN and Open Network Operating System (ONOS) controllers respectively. Moreover, proposed method also shows reasonable CPU utilization results. Furthermore, the proposed mechanism makes possible to handle unexpected load fluctuations while maintaining a continuous network operation, even when there is a controller failure. The paper is a potential contribution stepping towards addressing the issues of reliability, scalability, fault tolerance, and inter-operability. PMID:28384312

  18. Distributed k-Means Algorithm and Fuzzy c-Means Algorithm for Sensor Networks Based on Multiagent Consensus Theory.

    PubMed

    Qin, Jiahu; Fu, Weiming; Gao, Huijun; Zheng, Wei Xing

    2016-03-03

    This paper is concerned with developing a distributed k-means algorithm and a distributed fuzzy c-means algorithm for wireless sensor networks (WSNs) where each node is equipped with sensors. The underlying topology of the WSN is supposed to be strongly connected. The consensus algorithm in multiagent consensus theory is utilized to exchange the measurement information of the sensors in WSN. To obtain a faster convergence speed as well as a higher possibility of having the global optimum, a distributed k-means++ algorithm is first proposed to find the initial centroids before executing the distributed k-means algorithm and the distributed fuzzy c-means algorithm. The proposed distributed k-means algorithm is capable of partitioning the data observed by the nodes into measure-dependent groups which have small in-group and large out-group distances, while the proposed distributed fuzzy c-means algorithm is capable of partitioning the data observed by the nodes into different measure-dependent groups with degrees of membership values ranging from 0 to 1. Simulation results show that the proposed distributed algorithms can achieve almost the same results as that given by the centralized clustering algorithms.

  19. A Community Detection Algorithm Based on Topology Potential and Spectral Clustering

    PubMed Central

    Wang, Zhixiao; Chen, Zhaotong; Zhao, Ya; Chen, Shaoda

    2014-01-01

    Community detection is of great value for complex networks in understanding their inherent law and predicting their behavior. Spectral clustering algorithms have been successfully applied in community detection. This kind of methods has two inadequacies: one is that the input matrixes they used cannot provide sufficient structural information for community detection and the other is that they cannot necessarily derive the proper community number from the ladder distribution of eigenvector elements. In order to solve these problems, this paper puts forward a novel community detection algorithm based on topology potential and spectral clustering. The new algorithm constructs the normalized Laplacian matrix with nodes' topology potential, which contains rich structural information of the network. In addition, the new algorithm can automatically get the optimal community number from the local maximum potential nodes. Experiments results showed that the new algorithm gave excellent performance on artificial networks and real world networks and outperforms other community detection methods. PMID:25147846

  20. Cluster Recognition Algorithms for Battlefield Simulation.

    DTIC Science & Technology

    1996-01-01

    j,s’ 1 4 acJ y • 4 1 I A, r 22403 ( 23268 •s 0.. 233700 b "Ilk 0 *3 5* % ** % ,i• .3 0. •,. 3 4%4 ;4 26 " 24564 - N.. 24996 Figure A-65. Initial...22153 22403 22657 4 I 22909 23161 23413 23665 23917 Figure A-142. Circular clustering from data set 45. 170 p 424 27-21 427PO � � 142858

  1. Critical slowing down of cluster algorithms for Ising models coupled to 2-d gravity

    NASA Astrophysics Data System (ADS)

    Bowick, Mark; Falcioni, Marco; Harris, Geoffrey; Marinari, Enzo

    1994-02-01

    We simulate single and multiple Ising models coupled to 2-d gravity using both the Swendsen-Wang and Wolff algorithms to update the spins. We study the integrated autocorrelation time and find that there is considerable critical slowing down, particularly in the magnetization. We argue that this is primarily due to the local nature of the dynamical triangulation algorithm and to the generation of a distribution of baby universes which inhibits cluster growth.

  2. Characterising superclusters with the galaxy cluster distribution

    NASA Astrophysics Data System (ADS)

    Chon, Gayoung; Böhringer, Hans; Collins, Chris A.; Krause, Martin

    2014-07-01

    Superclusters are the largest observed matter density structures in the Universe. Recently, we presented the first supercluster catalogue constructed with a well-defined selection function based on the X-ray flux-limited cluster survey, REFLEX II. To construct the sample we proposed a concept to find large objects with a minimum overdensity such that it can be expected that most of their mass will collapse in the future. The main goal is to provide support for our concept here by using simulation that we can, on the basis of our observational sample of X-ray clusters, construct a supercluster sample defined by a certain minimum overdensity. On this sample we also test how superclusters trace the underlying dark matter distribution. Our results confirm that an overdensity in the number of clusters is tightly correlated with an overdensity of the dark matter distribution. This enables us to define superclusters within which most of the mass will collapse in the future. We also obtain first-order mass estimates of superclusters on the basis of the properties of the member clusters. We also show that in this context the ratio of the cluster number density and dark matter mass density is consistent with the theoretically expected cluster bias. Our previous work provided evidence that superclusters are a special environment in which the density structures of the dark matter grow differently from those in the field, as characterised by the X-ray luminosity function. Here we confirm for the first time that this originates from a top-heavy mass function at high statistical significance that is provided by a Kolmogorov-Smirnov test. We also find in close agreement with observations that the superclusters only occupy a small volume of a few per cent, but contain more than half of the clusters in the present-day Universe.

  3. Functional clustering algorithm for the analysis of dynamic network data

    NASA Astrophysics Data System (ADS)

    Feldt, S.; Waddell, J.; Hetrick, V. L.; Berke, J. D.; Żochowski, M.

    2009-05-01

    We formulate a technique for the detection of functional clusters in discrete event data. The advantage of this algorithm is that no prior knowledge of the number of functional groups is needed, as our procedure progressively combines data traces and derives the optimal clustering cutoff in a simple and intuitive manner through the use of surrogate data sets. In order to demonstrate the power of this algorithm to detect changes in network dynamics and connectivity, we apply it to both simulated neural spike train data and real neural data obtained from the mouse hippocampus during exploration and slow-wave sleep. Using the simulated data, we show that our algorithm performs better than existing methods. In the experimental data, we observe state-dependent clustering patterns consistent with known neurophysiological processes involved in memory consolidation.

  4. Development of clustering algorithms for Compressed Baryonic Matter experiment

    NASA Astrophysics Data System (ADS)

    Kozlov, G. E.; Ivanov, V. V.; Lebedev, A. A.; Vassiliev, Yu. O.

    2015-05-01

    A clustering problem for the coordinate detectors in the Compressed Baryonic Matter (CBM) experiment is discussed. Because of the high interaction rate and huge datasets to be dealt with, clustering algorithms are required to be fast and efficient and capable of processing events with high track multiplicity. At present there are two different approaches to the problem. In the first one each fired pad bears information about its charge, while in the second one a pad can or cannot be fired, thus rendering the separation of overlapping clusters a difficult task. To deal with the latter, two different clustering algorithms were developed, integrated into the CBMROOT software environment, and tested with various types of simulated events. Both of them are found to be highly efficient and accurate.

  5. Analysis of Network Clustering Algorithms and Cluster Quality Metrics at Scale

    PubMed Central

    Kobourov, Stephen; Gallant, Mike; Börner, Katy

    2016-01-01

    Overview Notions of community quality underlie the clustering of networks. While studies surrounding network clustering are increasingly common, a precise understanding of the realtionship between different cluster quality metrics is unknown. In this paper, we examine the relationship between stand-alone cluster quality metrics and information recovery metrics through a rigorous analysis of four widely-used network clustering algorithms—Louvain, Infomap, label propagation, and smart local moving. We consider the stand-alone quality metrics of modularity, conductance, and coverage, and we consider the information recovery metrics of adjusted Rand score, normalized mutual information, and a variant of normalized mutual information used in previous work. Our study includes both synthetic graphs and empirical data sets of sizes varying from 1,000 to 1,000,000 nodes. Cluster Quality Metrics We find significant differences among the results of the different cluster quality metrics. For example, clustering algorithms can return a value of 0.4 out of 1 on modularity but score 0 out of 1 on information recovery. We find conductance, though imperfect, to be the stand-alone quality metric that best indicates performance on the information recovery metrics. Additionally, our study shows that the variant of normalized mutual information used in previous work cannot be assumed to differ only slightly from traditional normalized mutual information. Network Clustering Algorithms Smart local moving is the overall best performing algorithm in our study, but discrepancies between cluster evaluation metrics prevent us from declaring it an absolutely superior algorithm. Interestingly, Louvain performed better than Infomap in nearly all the tests in our study, contradicting the results of previous work in which Infomap was superior to Louvain. We find that although label propagation performs poorly when clusters are less clearly defined, it scales efficiently and accurately to large

  6. NCUBE - A clustering algorithm based on a discretized data space

    NASA Technical Reports Server (NTRS)

    Eigen, D. J.; Northouse, R. A.

    1974-01-01

    Cluster analysis involves the unsupervised grouping of data. The process provides an automatic procedure for generating known training samples for pattern classification. NCUBE, the clustering algorithm presented, is based upon the concept of imposing a gridwork on the data space. The NCUBE computer implementation of this concept provides an easily derived form of piecewise linear discrimination. This piecewise linear discrimination permits the separation of some types of data groups that are not linearly separable.

  7. Particle flow reconstruction based on the directed tree clustering algorithm

    SciTech Connect

    Chakraborty, D.; Lima, J. G. R.; McIntosh, R.; Zutshi, V.

    2006-10-27

    We present the status of particle flow algorithm development at Northern Illinois University. A key element in our approach is the calorimeter-based directed tree clustering algorithm. We have attempted to identify and tackle the essential challenges and analyze the effect of several different approaches to the reconstruction of jet energies and the Z-boson mass. A number of possibilities have been studied, such as analog vs. digital energy measurement, hit density-based clustering and the use of single or multiple energy thresholds. We plan to use this PFA-based reconstruction to compare some of the proposed detector technologies and geometries.

  8. Atmospheric Ion Clusters: Properties and Size Distributions

    NASA Astrophysics Data System (ADS)

    D'Auria, R.; Turco, R. P.

    2002-12-01

    Ions are continuously generated in the atmosphere by the action of galactic cosmic radiation. Measured charge concentrations are of the order of 103 ~ {cm-3} throughout the troposphere, increasing to about 5 x 103 ~ {cm-3} in the lower stratosphere [Cole and Pierce, 1965; Paltridge, 1965, 1966]. The lifetimes of these ions are sufficient to allow substantial clustering with common trace constituents in air, including water, nitric and sulfuric acids, ammonia, and a variety of organic compounds [e.g., D'Auria and Turco, 2001 and references cited therein]. The populations of the resulting charged molecular clusters represent a pre-nucleation phase of particle formation, and in this regard comprise a key segment of the over-all nucleation size spectrum [e.g., Castleman and Tang, 1972]. It has been suggested that these clusters may catalyze certain heterogeneous reactions, and given their characteristic crystal-like structures may act as freezing nuclei for supercooled droplets. To investigate these possibilities, basic information on cluster thermodynamic properties and chemical kinetics is needed. Here, we present new results for several relevant atmospheric ion cluster families. In particular, predictions based on quantum mechanical simulations of cluster structure, and related thermodynamic parameters, are compared against laboratory data. We also describe a hybrid approach for modeling cluster sequences that combines laboratory measurements and quantum predictions with the classical liquid droplet (Thomson) model to treat a wider range of cluster sizes. Calculations of cluster mass distributions based on this hybrid model are illustrated, and the advantages and limitations of such an analysis are summarized. References: Castelman, A. W., Jr., and I. N. Tang, Role of small clusters in nucleation about ions, J. Chem. Phys., 57, 3629-3638, 1972. Cole, R. K., and E. T. Pierce, Electrification in the Earth's atmosphere for altitudes between 0 and 100 kilometers, J

  9. A Sensor Network Data Compression Algorithm Based on Suboptimal Clustering and Virtual Landmark Routing Within Clusters

    PubMed Central

    Jiang, Peng; Li, Shengqiang

    2010-01-01

    A kind of data compression algorithm for sensor networks based on suboptimal clustering and virtual landmark routing within clusters is proposed in this paper. Firstly, temporal redundancy existing in data obtained by the same node in sequential instants can be eliminated. Then sensor networks nodes will be clustered. Virtual node landmarks in clusters can be established based on cluster heads. Routing in clusters can be realized by combining a greedy algorithm and a flooding algorithm. Thirdly, a global structure tree based on cluster heads will be established. During the course of data transmissions from nodes to cluster heads and from cluster heads to sink, the spatial redundancy existing in the data will be eliminated. Only part of the raw data needs to be transmitted from nodes to sink, and all raw data can be recovered in the sink based on a compression code and part of the raw data. Consequently, node energy can be saved, largely because transmission of redundant data can be avoided. As a result the overall performance of the sensor network can obviously be improved. PMID:22163396

  10. Segmentation of retinal blood vessels using a novel clustering algorithm (RACAL) with a partial supervision strategy.

    PubMed

    Salem, Sameh A; Salem, Nancy M; Nandi, Asoke K

    2007-03-01

    In this paper, segmentation of blood vessels from colour retinal images using a novel clustering algorithm with a partial supervision strategy is proposed. The proposed clustering algorithm, which is a RAdius based Clustering ALgorithm (RACAL), uses a distance based principle to map the distributions of the data by utilising the premise that clusters are determined by a distance parameter, without having to specify the number of clusters. Additionally, the proposed clustering algorithm is enhanced with a partial supervision strategy and it is demonstrated that it is able to segment blood vessels of small diameters and low contrasts. Results are compared with those from the KNN classifier and show that the proposed RACAL performs better than the KNN in case of abnormal images as it succeeds in segmenting small and low contrast blood vessels, while it achieves comparable results for normal images. For automation process, RACAL can be used as a classifier and results show that it performs better than the KNN classifier in both normal and abnormal images.

  11. The Effect of Document Ordering in Rocchio's Clustering Algorithm

    ERIC Educational Resources Information Center

    Cody, Roger

    1973-01-01

    Presented is an empirical confirmation of clustering behavior that has been proposed as a conjecture in the literature; namely, that document ordering is more significant in an algorithm using a full document space search, rather than a search of just unclustered documents, each time a density test is performed. (4 references) (Author)

  12. Clustered Self Organising Migrating Algorithm for the Quadratic Assignment Problem

    NASA Astrophysics Data System (ADS)

    Davendra, Donald; Zelinka, Ivan; Senkerik, Roman

    2009-08-01

    An approach of population dynamics and clustering for permutative problems is presented in this paper. Diversity indicators are created from solution ordering and its mapping is shown as an advantage for population control in metaheuristics. Self Organising Migrating Algorithm (SOMA) is modified using this approach and vetted with the Quadratic Assignment Problem (QAP). Extensive experimentation is conducted on benchmark problems in this area.

  13. A modified K-means algorithm for circular invariant clustering.

    PubMed

    Charalampidis, Dimitrios

    2005-12-01

    Several important pattern recognition applications are based on feature vector extraction and vector clustering. Directional patterns are commonly represented by rotation-variant vectors Fd formed from features uniformly extracted in M directions. It is often desirable that pattern recognition algorithms are invariant under pattern rotation. This paper introduces a distance measure and a K-means-based algorithm, namely, Circular K-means (CK-means) to cluster vectors containing directional information, such as Fd, in a circular-shift invariant manner. A circular shift of Fd corresponds to pattern rotation, thus, the algorithm is rotation invariant. An efficient Fourier domain representation of the proposed measure is presented to reduce computational complexity. A split and merge approach (SMCK-means), suited to the proposed CK-means technique, is proposed to reduce the possibility of converging at local minima and to estimate the correct number of clusters. Experiments performed for textural images illustrate the superior performance of the proposed algorithm for clustering directional vectors Fd, compared to the alternative approach that uses the original K-means and rotation-invariant feature vectors transformed from Fd.

  14. Analysis of Network Clustering Algorithms and Cluster Quality Metrics at Scale.

    PubMed

    Emmons, Scott; Kobourov, Stephen; Gallant, Mike; Börner, Katy

    2016-01-01

    Notions of community quality underlie the clustering of networks. While studies surrounding network clustering are increasingly common, a precise understanding of the realtionship between different cluster quality metrics is unknown. In this paper, we examine the relationship between stand-alone cluster quality metrics and information recovery metrics through a rigorous analysis of four widely-used network clustering algorithms-Louvain, Infomap, label propagation, and smart local moving. We consider the stand-alone quality metrics of modularity, conductance, and coverage, and we consider the information recovery metrics of adjusted Rand score, normalized mutual information, and a variant of normalized mutual information used in previous work. Our study includes both synthetic graphs and empirical data sets of sizes varying from 1,000 to 1,000,000 nodes. We find significant differences among the results of the different cluster quality metrics. For example, clustering algorithms can return a value of 0.4 out of 1 on modularity but score 0 out of 1 on information recovery. We find conductance, though imperfect, to be the stand-alone quality metric that best indicates performance on the information recovery metrics. Additionally, our study shows that the variant of normalized mutual information used in previous work cannot be assumed to differ only slightly from traditional normalized mutual information. Smart local moving is the overall best performing algorithm in our study, but discrepancies between cluster evaluation metrics prevent us from declaring it an absolutely superior algorithm. Interestingly, Louvain performed better than Infomap in nearly all the tests in our study, contradicting the results of previous work in which Infomap was superior to Louvain. We find that although label propagation performs poorly when clusters are less clearly defined, it scales efficiently and accurately to large graphs with well-defined clusters.

  15. Estimation of distribution algorithms with Kikuchi approximations.

    PubMed

    Santana, Roberto

    2005-01-01

    The question of finding feasible ways for estimating probability distributions is one of the main challenges for Estimation of Distribution Algorithms (EDAs). To estimate the distribution of the selected solutions, EDAs use factorizations constructed according to graphical models. The class of factorizations that can be obtained from these probability models is highly constrained. Expanding the class of factorizations that could be employed for probability approximation is a necessary step for the conception of more robust EDAs. In this paper we introduce a method for learning a more general class of probability factorizations. The method combines a reformulation of a probability approximation procedure known in statistical physics as the Kikuchi approximation of energy, with a novel approach for finding graph decompositions. We present the Markov Network Estimation of Distribution Algorithm (MN-EDA), an EDA that uses Kikuchi approximations to estimate the distribution, and Gibbs Sampling (GS) to generate new points. A systematic empirical evaluation of MN-EDA is done in comparison with different Bayesian network based EDAs. From our experiments we conclude that the algorithm can outperform other EDAs that use traditional methods of probability approximation in the optimization of functions with strong interactions among their variables.

  16. The C4 clustering algorithm: Clusters of galaxies in the Sloan Digital Sky Survey

    SciTech Connect

    Miller, Christopher J.; Nichol, Robert; Reichart, Dan; Wechsler, Risa H.; Evrard, August; Annis, James; McKay, Timothy; Bahcall, Neta; Bernardi, Mariangela; Boehringer, Hans; Connolly, Andrew; Goto, Tomo; Kniazev, Alexie; Lamb, Donald; Postman, Marc; Schneider, Donald; Sheth, Ravi; Voges, Wolfgang; /Cerro-Tololo InterAmerican Obs. /Portsmouth U., ICG /North Carolina U. /Chicago U., Astron. Astrophys. Ctr. /Chicago U., EFI /Michigan U. /Fermilab /Princeton U. Observ. /Garching, Max Planck Inst., MPE /Pittsburgh U. /Tokyo U., ICRR /Baltimore, Space Telescope Sci. /Penn State U. /Chicago U. /Stavropol, Astrophys. Observ. /Heidelberg, Max Planck Inst. Astron. /INI, SAO

    2005-03-01

    We present the ''C4 Cluster Catalog'', a new sample of 748 clusters of galaxies identified in the spectroscopic sample of the Second Data Release (DR2) of the Sloan Digital Sky Survey (SDSS). The C4 cluster-finding algorithm identifies clusters as overdensities in a seven-dimensional position and color space, thus minimizing projection effects that have plagued previous optical cluster selection. The present C4 catalog covers {approx}2600 square degrees of sky and ranges in redshift from z = 0.02 to z = 0.17. The mean cluster membership is 36 galaxies (with redshifts) brighter than r = 17.7, but the catalog includes a range of systems, from groups containing 10 members to massive clusters with over 200 cluster members with redshifts. The catalog provides a large number of measured cluster properties including sky location, mean redshift, galaxy membership, summed r-band optical luminosity (L{sub r}), velocity dispersion, as well as quantitative measures of substructure and the surrounding large-scale environment. We use new, multi-color mock SDSS galaxy catalogs, empirically constructed from the {Lambda}CDM Hubble Volume (HV) Sky Survey output, to investigate the sensitivity of the C4 catalog to the various algorithm parameters (detection threshold, choice of passbands and search aperture), as well as to quantify the purity and completeness of the C4 cluster catalog. These mock catalogs indicate that the C4 catalog is {approx_equal}90% complete and 95% pure above M{sub 200} = 1 x 10{sup 14} h{sup -1}M{sub {circle_dot}} and within 0.03 {le} z {le} 0.12. Using the SDSS DR2 data, we show that the C4 algorithm finds 98% of X-ray identified clusters and 90% of Abell clusters within 0.03 {le} z {le} 0.12. Using the mock galaxy catalogs and the full HV dark matter simulations, we show that the L{sub r} of a cluster is a more robust estimator of the halo mass (M{sub 200}) than the galaxy line-of-sight velocity dispersion or the richness of the cluster. However, if we

  17. Generalized chemical distance distribution in all-sided critical percolation clusters

    NASA Astrophysics Data System (ADS)

    Katunin, Andrzej

    2016-12-01

    The algorithm of evaluation of chemical distance distribution in 2D and 3D critical percolation clusters is presented in the following study. The algorithm is enriched by numerous examples of 2D and 3D critical percolation clusters related to the currently investigated problem of electrical percolation in a mixture of conducting/dielectric polymers. The introduced measure of the chemical distance distribution can be a useful tool for characterization of percolation clusters, and in problems of percolation theory and graphs theory in general.

  18. Analysis and Implementation of Graph Clustering for Digital News Using Star Clustering Algorithm

    NASA Astrophysics Data System (ADS)

    Ahdi, A. B.; SW, K. R.; Herdiani, A.

    2017-01-01

    Since Web 2.0 notion emerged and is used extensively by many services in the Internet, we see an unprecedented proliferation of digital news. Those digital news is very rich in term of content and link to other news/sources but lack of category information. This make the user could not easily identify or grouping all the news that they read into set of groups. Naturally, digital news are linked data because every digital new has relation/connection with other digital news/resources. The most appropriate model for linked data is graph model. Graph model is suitable for this purpose due its flexibility in describing relation and its easy-to-understand visualization. To handle the grouping issue, we use graph clustering approach. There are many graph clustering algorithm available, such as MST Clustering, Chameleon, Makarov Clustering and Star Clustering. From all of these options, we choose Star Clustering because this algorithm is more easy-to-understand, more accurate, efficient and guarantee the quality of clusters results. In this research, we investigate the accuracy of the cluster results by comparing it with expert judgement. We got quite high accuracy level, which is 80.98% and for the cluster quality, we got promising result which is 62.87%.

  19. K-region-based Clustering Algorithm for Image Segmentation

    NASA Astrophysics Data System (ADS)

    Kumar, R.; Arthanariee, A. M.

    2013-12-01

    In this paper, authors have proposed K-region-based clustering algorithm which is based on performing the clustering techniques in K number of regions of given image of size N × N. The K and N are power of 2 and K < N. The authors have divided the given image into 4 regions, 16 regions, 64 regions, 256 regions, 1024 regions, 4096 regions and 16384 regions based on the value of K. Authors have grouped the adjacent pixels of similar intensity value into same cluster in each region. The clusters of similar values in each adjacent region are grouped together to form the bigger clusters. The authors have obtained the different segmented images based on the K number of regions. These segmented images are useful for image understanding. The authors have been taken four parameters: Probabilistic rand index, variation of information, global consistency error and boundary displacement error. These parameters have used to evaluate and analyze the performance of the K-region-based clustering algorithm.

  20. A Likelihood-Based SLIC Superpixel Algorithm for SAR Images Using Generalized Gamma Distribution

    PubMed Central

    Zou, Huanxin; Qin, Xianxiang; Zhou, Shilin; Ji, Kefeng

    2016-01-01

    The simple linear iterative clustering (SLIC) method is a recently proposed popular superpixel algorithm. However, this method may generate bad superpixels for synthetic aperture radar (SAR) images due to effects of speckle and the large dynamic range of pixel intensity. In this paper, an improved SLIC algorithm for SAR images is proposed. This algorithm exploits the likelihood information of SAR image pixel clusters. Specifically, a local clustering scheme combining intensity similarity with spatial proximity is proposed. Additionally, for post-processing, a local edge-evolving scheme that combines spatial context and likelihood information is introduced as an alternative to the connected components algorithm. To estimate the likelihood information of SAR image clusters, we incorporated a generalized gamma distribution (GГD). Finally, the superiority of the proposed algorithm was validated using both simulated and real-world SAR images. PMID:27438840

  1. A Likelihood-Based SLIC Superpixel Algorithm for SAR Images Using Generalized Gamma Distribution.

    PubMed

    Zou, Huanxin; Qin, Xianxiang; Zhou, Shilin; Ji, Kefeng

    2016-07-18

    The simple linear iterative clustering (SLIC) method is a recently proposed popular superpixel algorithm. However, this method may generate bad superpixels for synthetic aperture radar (SAR) images due to effects of speckle and the large dynamic range of pixel intensity. In this paper, an improved SLIC algorithm for SAR images is proposed. This algorithm exploits the likelihood information of SAR image pixel clusters. Specifically, a local clustering scheme combining intensity similarity with spatial proximity is proposed. Additionally, for post-processing, a local edge-evolving scheme that combines spatial context and likelihood information is introduced as an alternative to the connected components algorithm. To estimate the likelihood information of SAR image clusters, we incorporated a generalized gamma distribution (GГD). Finally, the superiority of the proposed algorithm was validated using both simulated and real-world SAR images.

  2. Clustering algorithm evaluation and the development of a replacement for procedure 1. [for crop inventories

    NASA Technical Reports Server (NTRS)

    Lennington, R. K.; Johnson, J. K.

    1979-01-01

    An efficient procedure which clusters data using a completely unsupervised clustering algorithm and then uses labeled pixels to label the resulting clusters or perform a stratified estimate using the clusters as strata is developed. Three clustering algorithms, CLASSY, AMOEBA, and ISOCLS, are compared for efficiency. Three stratified estimation schemes and three labeling schemes are also considered and compared.

  3. LYDIAN: An Extensible Educational Animation Environment for Distributed Algorithms

    ERIC Educational Resources Information Center

    Koldehofe, Boris; Papatriantafilou, Marina; Tsigas, Philippas

    2006-01-01

    LYDIAN is an environment to support the teaching and learning of distributed algorithms. It provides a collection of distributed algorithms as well as continuous animations. Users can combine algorithms and animations with arbitrary network structures defining the interconnection and behavior of the distributed algorithm. Further, it facilitates…

  4. The Geometric Cluster Algorithm: Rejection-Free Monte Carlo Simulation of Complex Fluids

    NASA Astrophysics Data System (ADS)

    Luijten, Erik

    2005-03-01

    The study of complex fluids is an area of intense research activity, in which exciting and counter-intuitive behavior continue to be uncovered. Ironically, one of the very factors responsible for such interesting properties, namely the presence of multiple relevant time and length scales, often greatly complicates accurate theoretical calculations and computer simulations that could explain the observations. We have recently developed a new Monte Carlo simulation methodootnotetextJ. Liu and E. Luijten, Phys. Rev. Lett.92, 035504 (2004); see also Physics Today, March 2004, pp. 25--27. that overcomes this problem for several classes of complex fluids. Our approach can accelerate simulations by orders of magnitude by introducing nonlocal, collective moves of the constituents. Strikingly, these cluster Monte Carlo moves are proposed in such a manner that the algorithm is rejection-free. The identification of the clusters is based upon geometric symmetries and can be considered as the off-latice generalization of the widely-used Swendsen--Wang and Wolff algorithms for lattice spin models. While phrased originally for complex fluids that are governed by the Boltzmann distribution, the geometric cluster algorithm can be used to efficiently sample configurations from an arbitrary underlying distribution function and may thus be applied in a variety of other areas. In addition, I will briefly discuss various extensions of the original algorithm, including methods to influence the size of the clusters that are generated and ways to introduce density fluctuations.

  5. Large Data Visualization on Distributed Memory Mulit-GPU Clusters

    SciTech Connect

    Childs, Henry R.

    2010-03-01

    Data sets of immense size are regularly generated on large scale computing resources. Even among more traditional methods for acquisition of volume data, such as MRI and CT scanners, data which is too large to be effectively visualization on standard workstations is now commonplace. One solution to this problem is to employ a 'visualization cluster,' a small to medium scale cluster dedicated to performing visualization and analysis of massive data sets generated on larger scale supercomputers. These clusters are designed to fit a different need than traditional supercomputers, and therefore their design mandates different hardware choices, such as increased memory, and more recently, graphics processing units (GPUs). While there has been much previous work on distributed memory visualization as well as GPU visualization, there is a relative dearth of algorithms which effectively use GPUs at a large scale in a distributed memory environment. In this work, we study a common visualization technique in a GPU-accelerated, distributed memory setting, and present performance characteristics when scaling to extremely large data sets.

  6. Improved Gravitation Field Algorithm and Its Application in Hierarchical Clustering

    PubMed Central

    Zheng, Ming; Sun, Ying; Liu, Gui-xia; Zhou, You; Zhou, Chun-guang

    2012-01-01

    Background Gravitation field algorithm (GFA) is a new optimization algorithm which is based on an imitation of natural phenomena. GFA can do well both for searching global minimum and multi-minima in computational biology. But GFA needs to be improved for increasing efficiency, and modified for applying to some discrete data problems in system biology. Method An improved GFA called IGFA was proposed in this paper. Two parts were improved in IGFA. The first one is the rule of random division, which is a reasonable strategy and makes running time shorter. The other one is rotation factor, which can improve the accuracy of IGFA. And to apply IGFA to the hierarchical clustering, the initial part and the movement operator were modified. Results Two kinds of experiments were used to test IGFA. And IGFA was applied to hierarchical clustering. The global minimum experiment was used with IGFA, GFA, GA (genetic algorithm) and SA (simulated annealing). Multi-minima experiment was used with IGFA and GFA. The two experiments results were compared with each other and proved the efficiency of IGFA. IGFA is better than GFA both in accuracy and running time. For the hierarchical clustering, IGFA is used to optimize the smallest distance of genes pairs, and the results were compared with GA and SA, singular-linkage clustering, UPGMA. The efficiency of IGFA is proved. PMID:23173043

  7. A comparison of clustering algorithms in article recommendation system

    NASA Astrophysics Data System (ADS)

    Tantanasiriwong, Supaporn

    2011-12-01

    Recommendation system is considered a tool that can be used to recommend researchers about resources that are suitable for their research of interest by using content-based filtering. In this paper, clustering algorithm as an unsupervised learning is introduced for grouping objects based on their feature selection and similarities. The information of publication in Science Cited Index is used to be dataset for clustering as a feature extraction in terms of dimensionality reduction of these articles by comparing Latent Dirichlet Allocation (LDA), Principal Component Analysis (PCA), and K-Mean to determine the best algorithm. In my experiment, the selected database consists of 2625 documents extraction extracted from SCI corpus from 2001 to 2009. Clustering into ranks as 50,100,200,250 is used to consider and using F-Measure evaluate among them in three algorithms. The result of this paper showed that LDA technique given the accuracy up to 95.5% which is the highest effective than any other clustering technique.

  8. A comparison of clustering algorithms in article recommendation system

    NASA Astrophysics Data System (ADS)

    Tantanasiriwong, Supaporn

    2012-01-01

    Recommendation system is considered a tool that can be used to recommend researchers about resources that are suitable for their research of interest by using content-based filtering. In this paper, clustering algorithm as an unsupervised learning is introduced for grouping objects based on their feature selection and similarities. The information of publication in Science Cited Index is used to be dataset for clustering as a feature extraction in terms of dimensionality reduction of these articles by comparing Latent Dirichlet Allocation (LDA), Principal Component Analysis (PCA), and K-Mean to determine the best algorithm. In my experiment, the selected database consists of 2625 documents extraction extracted from SCI corpus from 2001 to 2009. Clustering into ranks as 50,100,200,250 is used to consider and using F-Measure evaluate among them in three algorithms. The result of this paper showed that LDA technique given the accuracy up to 95.5% which is the highest effective than any other clustering technique.

  9. Improved gravitation field algorithm and its application in hierarchical clustering.

    PubMed

    Zheng, Ming; Sun, Ying; Liu, Gui-Xia; Zhou, You; Zhou, Chun-Guang

    2012-01-01

    Gravitation field algorithm (GFA) is a new optimization algorithm which is based on an imitation of natural phenomena. GFA can do well both for searching global minimum and multi-minima in computational biology. But GFA needs to be improved for increasing efficiency, and modified for applying to some discrete data problems in system biology. An improved GFA called IGFA was proposed in this paper. Two parts were improved in IGFA. The first one is the rule of random division, which is a reasonable strategy and makes running time shorter. The other one is rotation factor, which can improve the accuracy of IGFA. And to apply IGFA to the hierarchical clustering, the initial part and the movement operator were modified. Two kinds of experiments were used to test IGFA. And IGFA was applied to hierarchical clustering. The global minimum experiment was used with IGFA, GFA, GA (genetic algorithm) and SA (simulated annealing). Multi-minima experiment was used with IGFA and GFA. The two experiments results were compared with each other and proved the efficiency of IGFA. IGFA is better than GFA both in accuracy and running time. For the hierarchical clustering, IGFA is used to optimize the smallest distance of genes pairs, and the results were compared with GA and SA, singular-linkage clustering, UPGMA. The efficiency of IGFA is proved.

  10. Adaptive k-means algorithm for overlapped graph clustering.

    PubMed

    Bello-Orgaz, Gema; Menéndez, Héctor D; Camacho, David

    2012-10-01

    The graph clustering problem has become highly relevant due to the growing interest of several research communities in social networks and their possible applications. Overlapped graph clustering algorithms try to find subsets of nodes that can belong to different clusters. In social network-based applications it is quite usual for a node of the network to belong to different groups, or communities, in the graph. Therefore, algorithms trying to discover, or analyze, the behavior of these networks needed to handle this feature, detecting and identifying the overlapped nodes. This paper shows a soft clustering approach based on a genetic algorithm where a new encoding is designed to achieve two main goals: first, the automatic adaptation of the number of communities that can be detected and second, the definition of several fitness functions that guide the searching process using some measures extracted from graph theory. Finally, our approach has been experimentally tested using the Eurovision contest dataset, a well-known social-based data network, to show how overlapped communities can be found using our method.

  11. Irreversible Growth Algorithm for Branched Polymers (Lattice Animals), and Their Relation to Colloidal Cluster-Cluster Aggregates

    NASA Astrophysics Data System (ADS)

    Ball, R. C.; Lee, J. R.

    1996-03-01

    We prove that a new, irreversible growth algorithm, Non-Deletion Reaction-Limited Cluster-cluster Aggregation (NDRLCA), produces equilibrium Branched Polymers, expected to exhibit Lattice Animal statistics [1]. We implement NDRLCA, off-lattice, as a computer simulation for embedding dimension d=2 and 3, obtaining values for critical exponents, fractal dimension D and cluster mass distribution exponent tau: d=2, D≈ 1.53± 0.05, tau = 1.09± 0.06; d=3, D=1.96± 0.04, tau =1.50± 0.04 in good agreement with theoretical LA values. The simulation results do not support recent suggestions [2] that BPs may be in the same universality class as percolation. We also obtain values for a model-dependent critical “fugacity”, z_c and investigate the finite-size effects of our simulation, quantifying notions of “inbreeding” that occur in this algorithm. Finally we use an extension of the NDRLCA proof to show that standard Reaction-Limited Cluster-cluster Aggregation is very unlikely to be in the same universality class as Branched Polymers/Lattice Animals unless the backnone dimension for the latter is considerably less than the published value.

  12. Pruning Neural Networks with Distribution Estimation Algorithms

    SciTech Connect

    Cantu-Paz, E

    2003-01-15

    This paper describes the application of four evolutionary algorithms to the pruning of neural networks used in classification problems. Besides of a simple genetic algorithm (GA), the paper considers three distribution estimation algorithms (DEAs): a compact GA, an extended compact GA, and the Bayesian Optimization Algorithm. The objective is to determine if the DEAs present advantages over the simple GA in terms of accuracy or speed in this problem. The experiments used a feed forward neural network trained with standard back propagation and public-domain and artificial data sets. The pruned networks seemed to have better or equal accuracy than the original fully-connected networks. Only in a few cases, pruning resulted in less accurate networks. We found few differences in the accuracy of the networks pruned by the four EAs, but found important differences in the execution time. The results suggest that a simple GA with a small population might be the best algorithm for pruning networks on the data sets we tested.

  13. GEANT4 distributed computing for compact clusters

    NASA Astrophysics Data System (ADS)

    Harrawood, Brian P.; Agasthya, Greeshma A.; Lakshmanan, Manu N.; Raterman, Gretchen; Kapadia, Anuj J.

    2014-11-01

    A new technique for distribution of GEANT4 processes is introduced to simplify running a simulation in a parallel environment such as a tightly coupled computer cluster. Using a new C++ class derived from the GEANT4 toolkit, multiple runs forming a single simulation are managed across a local network of computers with a simple inter-node communication protocol. The class is integrated with the GEANT4 toolkit and is designed to scale from a single symmetric multiprocessing (SMP) machine to compact clusters ranging in size from tens to thousands of nodes. User designed 'work tickets' are distributed to clients using a client-server work flow model to specify the parameters for each individual run of the simulation. The new g4DistributedRunManager class was developed and well tested in the course of our Neutron Stimulated Emission Computed Tomography (NSECT) experiments. It will be useful for anyone running GEANT4 for large discrete data sets such as covering a range of angles in computed tomography, calculating dose delivery with multiple fractions or simply speeding the through-put of a single model.

  14. clusterMaker: a multi-algorithm clustering plugin for Cytoscape

    PubMed Central

    2011-01-01

    Background In the post-genomic era, the rapid increase in high-throughput data calls for computational tools capable of integrating data of diverse types and facilitating recognition of biologically meaningful patterns within them. For example, protein-protein interaction data sets have been clustered to identify stable complexes, but scientists lack easily accessible tools to facilitate combined analyses of multiple data sets from different types of experiments. Here we present clusterMaker, a Cytoscape plugin that implements several clustering algorithms and provides network, dendrogram, and heat map views of the results. The Cytoscape network is linked to all of the other views, so that a selection in one is immediately reflected in the others. clusterMaker is the first Cytoscape plugin to implement such a wide variety of clustering algorithms and visualizations, including the only implementations of hierarchical clustering, dendrogram plus heat map visualization (tree view), k-means, k-medoid, SCPS, AutoSOME, and native (Java) MCL. Results Results are presented in the form of three scenarios of use: analysis of protein expression data using a recently published mouse interactome and a mouse microarray data set of nearly one hundred diverse cell/tissue types; the identification of protein complexes in the yeast Saccharomyces cerevisiae; and the cluster analysis of the vicinal oxygen chelate (VOC) enzyme superfamily. For scenario one, we explore functionally enriched mouse interactomes specific to particular cellular phenotypes and apply fuzzy clustering. For scenario two, we explore the prefoldin complex in detail using both physical and genetic interaction clusters. For scenario three, we explore the possible annotation of a protein as a methylmalonyl-CoA epimerase within the VOC superfamily. Cytoscape session files for all three scenarios are provided in the Additional Files section. Conclusions The Cytoscape plugin clusterMaker provides a number of clustering

  15. clusterMaker: a multi-algorithm clustering plugin for Cytoscape.

    PubMed

    Morris, John H; Apeltsin, Leonard; Newman, Aaron M; Baumbach, Jan; Wittkop, Tobias; Su, Gang; Bader, Gary D; Ferrin, Thomas E

    2011-11-09

    In the post-genomic era, the rapid increase in high-throughput data calls for computational tools capable of integrating data of diverse types and facilitating recognition of biologically meaningful patterns within them. For example, protein-protein interaction data sets have been clustered to identify stable complexes, but scientists lack easily accessible tools to facilitate combined analyses of multiple data sets from different types of experiments. Here we present clusterMaker, a Cytoscape plugin that implements several clustering algorithms and provides network, dendrogram, and heat map views of the results. The Cytoscape network is linked to all of the other views, so that a selection in one is immediately reflected in the others. clusterMaker is the first Cytoscape plugin to implement such a wide variety of clustering algorithms and visualizations, including the only implementations of hierarchical clustering, dendrogram plus heat map visualization (tree view), k-means, k-medoid, SCPS, AutoSOME, and native (Java) MCL. Results are presented in the form of three scenarios of use: analysis of protein expression data using a recently published mouse interactome and a mouse microarray data set of nearly one hundred diverse cell/tissue types; the identification of protein complexes in the yeast Saccharomyces cerevisiae; and the cluster analysis of the vicinal oxygen chelate (VOC) enzyme superfamily. For scenario one, we explore functionally enriched mouse interactomes specific to particular cellular phenotypes and apply fuzzy clustering. For scenario two, we explore the prefoldin complex in detail using both physical and genetic interaction clusters. For scenario three, we explore the possible annotation of a protein as a methylmalonyl-CoA epimerase within the VOC superfamily. Cytoscape session files for all three scenarios are provided in the Additional Files section. The Cytoscape plugin clusterMaker provides a number of clustering algorithms and visualizations

  16. BMI optimization by using parallel UNDX real-coded genetic algorithm with Beowulf cluster

    NASA Astrophysics Data System (ADS)

    Handa, Masaya; Kawanishi, Michihiro; Kanki, Hiroshi

    2007-12-01

    This paper deals with the global optimization algorithm of the Bilinear Matrix Inequalities (BMIs) based on the Unimodal Normal Distribution Crossover (UNDX) GA. First, analyzing the structure of the BMIs, the existence of the typical difficult structures is confirmed. Then, in order to improve the performance of algorithm, based on results of the problem structures analysis and consideration of BMIs characteristic properties, we proposed the algorithm using primary search direction with relaxed Linear Matrix Inequality (LMI) convex estimation. Moreover, in these algorithms, we propose two types of evaluation methods for GA individuals based on LMI calculation considering BMI characteristic properties more. In addition, in order to reduce computational time, we proposed parallelization of RCGA algorithm, Master-Worker paradigm with cluster computing technique.

  17. Mapping cultivable land from satellite imagery with clustering algorithms

    NASA Astrophysics Data System (ADS)

    Arango, R. B.; Campos, A. M.; Combarro, E. F.; Canas, E. R.; Díaz, I.

    2016-07-01

    Open data satellite imagery provides valuable data for the planning and decision-making processes related with environmental domains. Specifically, agriculture uses remote sensing in a wide range of services, ranging from monitoring the health of the crops to forecasting the spread of crop diseases. In particular, this paper focuses on a methodology for the automatic delimitation of cultivable land by means of machine learning algorithms and satellite data. The method uses a partition clustering algorithm called Partitioning Around Medoids and considers the quality of the clusters obtained for each satellite band in order to evaluate which one better identifies cultivable land. The proposed method was tested with vineyards using as input the spectral and thermal bands of the Landsat 8 satellite. The experimental results show the great potential of this method for cultivable land monitoring from remote-sensed multispectral imagery.

  18. Advanced defect detection algorithm using clustering in ultrasonic NDE

    NASA Astrophysics Data System (ADS)

    Gongzhang, Rui; Gachagan, Anthony

    2016-02-01

    A range of materials used in industry exhibit scattering properties which limits ultrasonic NDE. Many algorithms have been proposed to enhance defect detection ability, such as the well-known Split Spectrum Processing (SSP) technique. Scattering noise usually cannot be fully removed and the remaining noise can be easily confused with real feature signals, hence becoming artefacts during the image interpretation stage. This paper presents an advanced algorithm to further reduce the influence of artefacts remaining in A-scan data after processing using a conventional defect detection algorithm. The raw A-scan data can be acquired from either traditional single transducer or phased array configurations. The proposed algorithm uses the concept of unsupervised machine learning to cluster segmental defect signals from pre-processed A-scans into different classes. The distinction and similarity between each class and the ensemble of randomly selected noise segments can be observed by applying a classification algorithm. Each class will then be labelled as `legitimate reflector' or `artefacts' based on this observation and the expected probability of defection (PoD) and probability of false alarm (PFA) determined. To facilitate data collection and validate the proposed algorithm, a 5MHz linear array transducer is used to collect A-scans from both austenitic steel and Inconel samples. Each pulse-echo A-scan is pre-processed using SSP and the subsequent application of the proposed clustering algorithm has provided an additional reduction to PFA while maintaining PoD for both samples compared with SSP results alone.

  19. Synchronous Firefly Algorithm for Cluster Head Selection in WSN

    PubMed Central

    Baskaran, Madhusudhanan; Sadagopan, Chitra

    2015-01-01

    Wireless Sensor Network (WSN) consists of small low-cost, low-power multifunctional nodes interconnected to efficiently aggregate and transmit data to sink. Cluster-based approaches use some nodes as Cluster Heads (CHs) and organize WSNs efficiently for aggregation of data and energy saving. A CH conveys information gathered by cluster nodes and aggregates/compresses data before transmitting it to a sink. However, this additional responsibility of the node results in a higher energy drain leading to uneven network degradation. Low Energy Adaptive Clustering Hierarchy (LEACH) offsets this by probabilistically rotating cluster heads role among nodes with energy above a set threshold. CH selection in WSN is NP-Hard as optimal data aggregation with efficient energy savings cannot be solved in polynomial time. In this work, a modified firefly heuristic, synchronous firefly algorithm, is proposed to improve the network performance. Extensive simulation shows the proposed technique to perform well compared to LEACH and energy-efficient hierarchical clustering. Simulations show the effectiveness of the proposed method in decreasing the packet loss ratio by an average of 9.63% and improving the energy efficiency of the network when compared to LEACH and EEHC. PMID:26495431

  20. ICANP2: Isoenergetic cluster algorithm for NP-complete Problems

    NASA Astrophysics Data System (ADS)

    Zhu, Zheng; Fang, Chao; Katzgraber, Helmut G.

    NP-complete optimization problems with Boolean variables are of fundamental importance in computer science, mathematics and physics. Most notably, the minimization of general spin-glass-like Hamiltonians remains a difficult numerical task. There has been a great interest in designing efficient heuristics to solve these computationally difficult problems. Inspired by the rejection-free isoenergetic cluster algorithm developed for Ising spin glasses, we present a generalized cluster update that can be applied to different NP-complete optimization problems with Boolean variables. The cluster updates allow for a wide-spread sampling of phase space, thus speeding up optimization. By carefully tuning the pseudo-temperature (needed to randomize the configurations) of the problem, we show that the method can efficiently tackle problems on topologies with a large site-percolation threshold. We illustrate the ICANP2 heuristic on paradigmatic optimization problems, such as the satisfiability problem and the vertex cover problem.

  1. An improved clustering algorithm based on reverse learning in intelligent transportation

    NASA Astrophysics Data System (ADS)

    Qiu, Guoqing; Kou, Qianqian; Niu, Ting

    2017-05-01

    With the development of artificial intelligence and data mining technology, big data has gradually entered people's field of vision. In the process of dealing with large data, clustering is an important processing method. By introducing the reverse learning method in the clustering process of PAM clustering algorithm, to further improve the limitations of one-time clustering in unsupervised clustering learning, and increase the diversity of clustering clusters, so as to improve the quality of clustering. The algorithm analysis and experimental results show that the algorithm is feasible.

  2. Genetic weighted k-means algorithm for clustering large-scale gene expression data.

    PubMed

    Wu, Fang-Xiang

    2008-05-28

    The traditional (unweighted) k-means is one of the most popular clustering methods for analyzing gene expression data. However, it suffers three major shortcomings. It is sensitive to initial partitions, its result is prone to the local minima, and it is only applicable to data with spherical-shape clusters. The last shortcoming means that we must assume that gene expression data at the different conditions follow the independent distribution with the same variances. Nevertheless, this assumption is not true in practice. In this paper, we propose a genetic weighted K-means algorithm (denoted by GWKMA), which solves the first two problems and partially remedies the third one. GWKMA is a hybridization of a genetic algorithm (GA) and a weighted K-means algorithm (WKMA). In GWKMA, each individual is encoded by a partitioning table which uniquely determines a clustering, and three genetic operators (selection, crossover, mutation) and a WKM operator derived from WKMA are employed. The superiority of the GWKMA over the k-means is illustrated on a synthetic and two real-life gene expression datasets. The proposed algorithm has general application to clustering large-scale biological data such as gene expression data and peptide mass spectral data.

  3. NIC-based Reduction Algorithms for Large-scale Clusters

    SciTech Connect

    Petrini, F; Moody, A T; Fernandez, J; Frachtenberg, E; Panda, D K

    2004-07-30

    Efficient algorithms for reduction operations across a group of processes are crucial for good performance in many large-scale, parallel scientific applications. While previous algorithms limit processing to the host CPU, we utilize the programmable processors and local memory available on modern cluster network interface cards (NICs) to explore a new dimension in the design of reduction algorithms. In this paper, we present the benefits and challenges, design issues and solutions, analytical models, and experimental evaluations of a family of NIC-based reduction algorithms. Performance and scalability evaluations were conducted on the ASCI Linux Cluster (ALC), a 960-node, 1920-processor machine at Lawrence Livermore National Laboratory, which uses the Quadrics QsNet interconnect. We find NIC-based reductions on modern interconnects to be more efficient than host-based implementations in both scalability and consistency. In particular, at large-scale--1812 processes--NIC-based reductions of small integer and floating-point arrays provided respective speedups of 121% and 39% over the host-based, production-level MPI implementation.

  4. A cluster analysis on road traffic accidents using genetic algorithms

    NASA Astrophysics Data System (ADS)

    Saharan, Sabariah; Baragona, Roberto

    2017-04-01

    The analysis of traffic road accidents is increasingly important because of the accidents cost and public road safety. The availability or large data sets makes the study of factors that affect the frequency and severity accidents are viable. However, the data are often highly unbalanced and overlapped. We deal with the data set of the road traffic accidents recorded in Christchurch, New Zealand, from 2000-2009 with a total of 26440 accidents. The data is in a binary set and there are 50 factors road traffic accidents with four level of severity. We used genetic algorithm for the analysis because we are in the presence of a large unbalanced data set and standard clustering like k-means algorithm may not be suitable for the task. The genetic algorithm based on clustering for unknown K, (GCUK) has been used to identify the factors associated with accidents of different levels of severity. The results provided us with an interesting insight into the relationship between factors and accidents severity level and suggest that the two main factors that contributes to fatal accidents are "Speed greater than 60 km h" and "Did not see other people until it was too late". A comparison with the k-means algorithm and the independent component analysis is performed to validate the results.

  5. New sampling distributions for evolution algorithms

    NASA Astrophysics Data System (ADS)

    Sweeney, Francis Dermot

    Evolution algorithms are stochastic optimization methods based on evolutionary principles. They have long been used in optimization, and are gaining in popularity. They are particularly useful in high dimensional problems, or in problems where gradient methods fails. Evolution strategies, a class of evolutionary algorithms, are stochastic searches which evolve by mutation. This work proposes a new mutation distribution for use in single objective optimization. Up to now, cost function information obtained by mutations that do not improve fitness has been discarded. In many problems, particularly when cost function calls are expensive, it is desirable to use all available information to guide the search. The new method in this work patches Gaussians of different variances together to create a sampling distribution which delivers mutations designed to direct the search away from regions where low values of fitness have been observed. Analytic results for this new method are derived on idealized problems. The method is compared with existing methods on a range of test problems, and its overall performance attributes are assessed. A new method for multiobjective optimization is also developed. Genetic Algorithms introduce innovation into their populations by a process of bit mutation. This small scale mutation is often insufficient to successfully direct the search, unless the initial population is of sufficient quality. The new method proposed here, termed Rank Biased Sampling, uses the population to create new members, which are resampled across the entire search space from a distribution designed to favor regions which are inadequately represented by the current population. Again, this method is compared to existing methods on some standard test problems. These new optimization methods are then applied to some real-world problems of engineering interest. The optimization routines developed in this work performed well on these applications, and provide good

  6. Algorithms for distributed and mobile sensing

    NASA Astrophysics Data System (ADS)

    Isler, Ibrahim Volkan

    Sensing remote, complex and large environments is an important task that arises in diverse applications including planetary exploration, monitoring forest fires and the surveillance of large factories. Currently, automation of such sensing tasks in complex environments is achieved either by deploying many stationary sensors to the environment, or by mounting a sensor on a mobile device and using the device to sense the environment. The Eighties and Nineties witnessed tremendous advances in both distributed and mobile sensing technologies. To take advantage of these technologies, it is crucial to design algorithms to perform sensing tasks in an autonomous fashion. In this dissertation, we study four fundamental sensing problems that arise in sensing complex environments with distributed and mobile systems. For mobile sensing systems we study exploration and pursuit-evasion problems. In the exploration problem, the goal is to design a strategy for a mobile robot so that the robot sees every point in an unknown environment as quickly as possible. In the pursuit-evasion problem, the goal is to design a strategy for a pursuer to capture an adversarial evader. For distributed sensing systems we study placement and assignment problems. In the placement problem, the goal is to place sensors to an environment so that every point in the environment is in the range of at least one sensor. The assignment problem deals with the issue of assigning targets to sensors in a network, so that overall error in estimating the position of the targets is minimized. We present algorithms to perform these sensing tasks in an efficient fashion. Performance guarantees of the algorithms are mathematically proven and evaluated by simulations.

  7. Algorithm-dependent fault tolerance for distributed computing

    SciTech Connect

    P. D. Hough; M. e. Goldsby; E. J. Walsh

    2000-02-01

    Large-scale distributed systems assembled from commodity parts, like CPlant, have become common tools in the distributed computing world. Because of their size and diversity of parts, these systems are prone to failures. Applications that are being run on these systems have not been equipped to efficiently deal with failures, nor is there vendor support for fault tolerance. Thus, when a failure occurs, the application crashes. While most programmers make use of checkpoints to allow for restarting of their applications, this is cumbersome and incurs substantial overhead. In many cases, there are more efficient and more elegant ways in which to address failures. The goal of this project is to develop a software architecture for the detection of and recovery from faults in a cluster computing environment. The detection phase relies on the latest techniques developed in the fault tolerance community. Recovery is being addressed in an application-dependent manner, thus allowing the programmer to take advantage of algorithmic characteristics to reduce the overhead of fault tolerance. This architecture will allow large-scale applications to be more robust in high-performance computing environments that are comprised of clusters of commodity computers such as CPlant and SMP clusters.

  8. Clustering Algorithms: Their Application to Gene Expression Data

    PubMed Central

    Oyelade, Jelili; Isewon, Itunuoluwa; Oladipupo, Funke; Aromolaran, Olufemi; Uwoghiren, Efosa; Ameh, Faridah; Achas, Moses; Adebiyi, Ezekiel

    2016-01-01

    Gene expression data hide vital information required to understand the biological process that takes place in a particular organism in relation to its environment. Deciphering the hidden patterns in gene expression data proffers a prodigious preference to strengthen the understanding of functional genomics. The complexity of biological networks and the volume of genes present increase the challenges of comprehending and interpretation of the resulting mass of data, which consists of millions of measurements; these data also inhibit vagueness, imprecision, and noise. Therefore, the use of clustering techniques is a first step toward addressing these challenges, which is essential in the data mining process to reveal natural structures and identify interesting patterns in the underlying data. The clustering of gene expression data has been proven to be useful in making known the natural structure inherent in gene expression data, understanding gene functions, cellular processes, and subtypes of cells, mining useful information from noisy data, and understanding gene regulation. The other benefit of clustering gene expression data is the identification of homology, which is very important in vaccine design. This review examines the various clustering algorithms applicable to the gene expression data in order to discover and provide useful knowledge of the appropriate clustering technique that will guarantee stability and high degree of accuracy in its analysis procedure. PMID:27932867

  9. Finding reproducible cluster partitions for the k-means algorithm.

    PubMed

    Lisboa, Paulo J G; Etchells, Terence A; Jarman, Ian H; Chambers, Simon J

    2013-01-01

    K-means clustering is widely used for exploratory data analysis. While its dependence on initialisation is well-known, it is common practice to assume that the partition with lowest sum-of-squares (SSQ) total i.e. within cluster variance, is both reproducible under repeated initialisations and also the closest that k-means can provide to true structure, when applied to synthetic data. We show that this is generally the case for small numbers of clusters, but for values of k that are still of theoretical and practical interest, similar values of SSQ can correspond to markedly different cluster partitions. This paper extends stability measures previously presented in the context of finding optimal values of cluster number, into a component of a 2-d map of the local minima found by the k-means algorithm, from which not only can values of k be identified for further analysis but, more importantly, it is made clear whether the best SSQ is a suitable solution or whether obtaining a consistently good partition requires further application of the stability index. The proposed method is illustrated by application to five synthetic datasets replicating a real world breast cancer dataset with varying data density, and a large bioinformatics dataset.

  10. Finding reproducible cluster partitions for the k-means algorithm

    PubMed Central

    2013-01-01

    K-means clustering is widely used for exploratory data analysis. While its dependence on initialisation is well-known, it is common practice to assume that the partition with lowest sum-of-squares (SSQ) total i.e. within cluster variance, is both reproducible under repeated initialisations and also the closest that k-means can provide to true structure, when applied to synthetic data. We show that this is generally the case for small numbers of clusters, but for values of k that are still of theoretical and practical interest, similar values of SSQ can correspond to markedly different cluster partitions. This paper extends stability measures previously presented in the context of finding optimal values of cluster number, into a component of a 2-d map of the local minima found by the k-means algorithm, from which not only can values of k be identified for further analysis but, more importantly, it is made clear whether the best SSQ is a suitable solution or whether obtaining a consistently good partition requires further application of the stability index. The proposed method is illustrated by application to five synthetic datasets replicating a real world breast cancer dataset with varying data density, and a large bioinformatics dataset. PMID:23369085

  11. Optical Cluster-Finding with an Adaptive Matched-Filter Technique: Algorithm and Comparison with Simulations

    SciTech Connect

    Dong, Feng; Pierpaoli, Elena; Gunn, James E.; Wechsler, Risa H.

    2007-10-29

    We present a modified adaptive matched filter algorithm designed to identify clusters of galaxies in wide-field imaging surveys such as the Sloan Digital Sky Survey. The cluster-finding technique is fully adaptive to imaging surveys with spectroscopic coverage, multicolor photometric redshifts, no redshift information at all, and any combination of these within one survey. It works with high efficiency in multi-band imaging surveys where photometric redshifts can be estimated with well-understood error distributions. Tests of the algorithm on realistic mock SDSS catalogs suggest that the detected sample is {approx} 85% complete and over 90% pure for clusters with masses above 1.0 x 10{sup 14}h{sup -1} M and redshifts up to z = 0.45. The errors of estimated cluster redshifts from maximum likelihood method are shown to be small (typically less that 0.01) over the whole redshift range with photometric redshift errors typical of those found in the Sloan survey. Inside the spherical radius corresponding to a galaxy overdensity of {Delta} = 200, we find the derived cluster richness {Lambda}{sub 200} a roughly linear indicator of its virial mass M{sub 200}, which well recovers the relation between total luminosity and cluster mass of the input simulation.

  12. Oscillator clustering in a resource distribution chain.

    PubMed

    Postnov, Dmitry E; Sosnovtseva, Olga V; Mosekilde, Erik

    2005-03-01

    The paper investigates the special clustering phenomena that one can observe in systems of nonlinear oscillators that are coupled via a shared flow of primary resources (or a common power supply). This type of coupling, which appears to be quite frequent in nature, implies that one can no longer separate the inherent dynamics of the individual oscillator from the properties of the coupling network. Illustrated by examples from microbiological population dynamics, renal physiology, and electronic oscillator theory, we show how competition for primary resources in a resource distribution chain leads to a number of new generic phenomena, including partial synchronization, sliding of the synchronization region with the resource supply, and coupling-induced inhomogeneity.

  13. Performance Analysis of Apriori Algorithm with Different Data Structures on Hadoop Cluster

    NASA Astrophysics Data System (ADS)

    Singh, Sudhakar; Garg, Rakhi; Mishra, P. K.

    2015-10-01

    Mining frequent itemsets from massive datasets is always being a most important problem of data mining. Apriori is the most popular and simplest algorithm for frequent itemset mining. To enhance the efficiency and scalability of Apriori, a number of algorithms have been proposed addressing the design of efficient data structures, minimizing database scan and parallel and distributed processing. MapReduce is the emerging parallel and distributed technology to process big datasets on Hadoop Cluster. To mine big datasets it is essential to re-design the data mining algorithm on this new paradigm. In this paper, we implement three variations of Apriori algorithm using data structures hash tree, trie and hash table trie i.e. trie with hash technique on MapReduce paradigm. We emphasize and investigate the significance of these three data structures for Apriori algorithm on Hadoop cluster, which has not been given attention yet. Experiments are carried out on both real life and synthetic datasets which shows that hash table trie data structures performs far better than trie and hash tree in terms of execution time. Moreover the performance in case of hash tree becomes worst.

  14. Mammographic images segmentation based on chaotic map clustering algorithm

    PubMed Central

    2014-01-01

    Background This work investigates the applicability of a novel clustering approach to the segmentation of mammographic digital images. The chaotic map clustering algorithm is used to group together similar subsets of image pixels resulting in a medically meaningful partition of the mammography. Methods The image is divided into pixels subsets characterized by a set of conveniently chosen features and each of the corresponding points in the feature space is associated to a map. A mutual coupling strength between the maps depending on the associated distance between feature space points is subsequently introduced. On the system of maps, the simulated evolution through chaotic dynamics leads to its natural partitioning, which corresponds to a particular segmentation scheme of the initial mammographic image. Results The system provides a high recognition rate for small mass lesions (about 94% correctly segmented inside the breast) and the reproduction of the shape of regions with denser micro-calcifications in about 2/3 of the cases, while being less effective on identification of larger mass lesions. Conclusions We can summarize our analysis by asserting that due to the particularities of the mammographic images, the chaotic map clustering algorithm should not be used as the sole method of segmentation. It is rather the joint use of this method along with other segmentation techniques that could be successfully used for increasing the segmentation performance and for providing extra information for the subsequent analysis stages such as the classification of the segmented ROI. PMID:24666766

  15. Mammographic images segmentation based on chaotic map clustering algorithm.

    PubMed

    Iacomi, Marius; Cascio, Donato; Fauci, Francesco; Raso, Giuseppe

    2014-03-25

    This work investigates the applicability of a novel clustering approach to the segmentation of mammographic digital images. The chaotic map clustering algorithm is used to group together similar subsets of image pixels resulting in a medically meaningful partition of the mammography. The image is divided into pixels subsets characterized by a set of conveniently chosen features and each of the corresponding points in the feature space is associated to a map. A mutual coupling strength between the maps depending on the associated distance between feature space points is subsequently introduced. On the system of maps, the simulated evolution through chaotic dynamics leads to its natural partitioning, which corresponds to a particular segmentation scheme of the initial mammographic image. The system provides a high recognition rate for small mass lesions (about 94% correctly segmented inside the breast) and the reproduction of the shape of regions with denser micro-calcifications in about 2/3 of the cases, while being less effective on identification of larger mass lesions. We can summarize our analysis by asserting that due to the particularities of the mammographic images, the chaotic map clustering algorithm should not be used as the sole method of segmentation. It is rather the joint use of this method along with other segmentation techniques that could be successfully used for increasing the segmentation performance and for providing extra information for the subsequent analysis stages such as the classification of the segmented ROI.

  16. Scalable clustering algorithms for continuous environmental flow cytometry.

    PubMed

    Hyrkas, Jeremy; Clayton, Sophie; Ribalet, Francois; Halperin, Daniel; Armbrust, E Virginia; Howe, Bill

    2016-02-01

    Recent technological innovations in flow cytometry now allow oceanographers to collect high-frequency flow cytometry data from particles in aquatic environments on a scale far surpassing conventional flow cytometers. The SeaFlow cytometer continuously profiles microbial phytoplankton populations across thousands of kilometers of the surface ocean. The data streams produced by instruments such as SeaFlow challenge the traditional sample-by-sample approach in cytometric analysis and highlight the need for scalable clustering algorithms to extract population information from these large-scale, high-frequency flow cytometers. We explore how available algorithms commonly used for medical applications perform at classification of such a large-scale, environmental flow cytometry data. We apply large-scale Gaussian mixture models to massive datasets using Hadoop. This approach outperforms current state-of-the-art cytometry classification algorithms in accuracy and can be coupled with manual or automatic partitioning of data into homogeneous sections for further classification gains. We propose the Gaussian mixture model with partitioning approach for classification of large-scale, high-frequency flow cytometry data. Source code available for download at https://github.com/jhyrkas/seaflow_cluster, implemented in Java for use with Hadoop. hyrkas@cs.washington.edu Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  17. Gravitation field algorithm and its application in gene cluster

    PubMed Central

    2010-01-01

    Background Searching optima is one of the most challenging tasks in clustering genes from available experimental data or given functions. SA, GA, PSO and other similar efficient global optimization methods are used by biotechnologists. All these algorithms are based on the imitation of natural phenomena. Results This paper proposes a novel searching optimization algorithm called Gravitation Field Algorithm (GFA) which is derived from the famous astronomy theory Solar Nebular Disk Model (SNDM) of planetary formation. GFA simulates the Gravitation field and outperforms GA and SA in some multimodal functions optimization problem. And GFA also can be used in the forms of unimodal functions. GFA clusters the dataset well from the Gene Expression Omnibus. Conclusions The mathematical proof demonstrates that GFA could be convergent in the global optimum by probability 1 in three conditions for one independent variable mass functions. In addition to these results, the fundamental optimization concept in this paper is used to analyze how SA and GA affect the global search and the inherent defects in SA and GA. Some results and source code (in Matlab) are publicly available at http://ccst.jlu.edu.cn/CSBG/GFA. PMID:20854683

  18. Gravitation field algorithm and its application in gene cluster.

    PubMed

    Zheng, Ming; Liu, Gui-Xia; Zhou, Chun-Guang; Liang, Yan-Chun; Wang, Yan

    2010-09-20

    Searching optima is one of the most challenging tasks in clustering genes from available experimental data or given functions. SA, GA, PSO and other similar efficient global optimization methods are used by biotechnologists. All these algorithms are based on the imitation of natural phenomena. This paper proposes a novel searching optimization algorithm called Gravitation Field Algorithm (GFA) which is derived from the famous astronomy theory Solar Nebular Disk Model (SNDM) of planetary formation. GFA simulates the Gravitation field and outperforms GA and SA in some multimodal functions optimization problem. And GFA also can be used in the forms of unimodal functions. GFA clusters the dataset well from the Gene Expression Omnibus. The mathematical proof demonstrates that GFA could be convergent in the global optimum by probability 1 in three conditions for one independent variable mass functions. In addition to these results, the fundamental optimization concept in this paper is used to analyze how SA and GA affect the global search and the inherent defects in SA and GA. Some results and source code (in Matlab) are publicly available at http://ccst.jlu.edu.cn/CSBG/GFA.

  19. HPC-CLUST: distributed hierarchical clustering for large sets of nucleotide sequences.

    PubMed

    Matias Rodrigues, João F; von Mering, Christian

    2014-01-15

    Nucleotide sequence data are being produced at an ever increasing rate. Clustering such sequences by similarity is often an essential first step in their analysis-intended to reduce redundancy, define gene families or suggest taxonomic units. Exact clustering algorithms, such as hierarchical clustering, scale relatively poorly in terms of run time and memory usage, yet they are desirable because heuristic shortcuts taken during clustering might have unintended consequences in later analysis steps. Here we present HPC-CLUST, a highly optimized software pipeline that can cluster large numbers of pre-aligned DNA sequences by running on distributed computing hardware. It allocates both memory and computing resources efficiently, and can process more than a million sequences in a few hours on a small cluster. Source code and binaries are freely available at http://meringlab.org/software/hpc-clust/; the pipeline is implemented in Cþþ and uses the Message Passing Interface (MPI) standard for distributed computing.

  20. Combined Mapping of Multiple clUsteriNg ALgorithms (COMMUNAL): A Robust Method for Selection of Cluster Number, K.

    PubMed

    Sweeney, Timothy E; Chen, Albert C; Gevaert, Olivier

    2015-11-19

    In order to discover new subsets (clusters) of a data set, researchers often use algorithms that perform unsupervised clustering, namely, the algorithmic separation of a dataset into some number of distinct clusters. Deciding whether a particular separation (or number of clusters, K) is correct is a sort of 'dark art', with multiple techniques available for assessing the validity of unsupervised clustering algorithms. Here, we present a new technique for unsupervised clustering that uses multiple clustering algorithms, multiple validity metrics, and progressively bigger subsets of the data to produce an intuitive 3D map of cluster stability that can help determine the optimal number of clusters in a data set, a technique we call COmbined Mapping of Multiple clUsteriNg ALgorithms (COMMUNAL). COMMUNAL locally optimizes algorithms and validity measures for the data being used. We show its application to simulated data with a known K, and then apply this technique to several well-known cancer gene expression datasets, showing that COMMUNAL provides new insights into clustering behavior and stability in all tested cases. COMMUNAL is shown to be a useful tool for determining K in complex biological datasets, and is freely available as a package for R.

  1. HST Imaging of the Globular Clusters in the Formax Cluster: Color and Luminosity Distributions

    NASA Technical Reports Server (NTRS)

    Grillmair, C. J.; Forbes, D. A.; Brodie, J.; Elson, R.

    1998-01-01

    We examine the luminosity and B - I color distribution of globular clusters for three early-type galaxies in the Fornax cluster using imaging data from the Wide Field/Planetary Camera 2 on the Hubble Space Telescope.

  2. A new detection algorithm for microcalcification clusters in mammographic screening

    NASA Astrophysics Data System (ADS)

    Xie, Weiying; Ma, Yide; Li, Yunsong

    2015-05-01

    A novel approach for microcalcification clusters detection is proposed. At the first time, we make a short analysis of mammographic images with microcalcification lesions to confirm these lesions have much greater gray values than normal regions. After summarizing the specific feature of microcalcification clusters in mammographic screening, we make more focus on preprocessing step including eliminating the background, image enhancement and eliminating the pectoral muscle. In detail, Chan-Vese Model is used for eliminating background. Then, we do the application of combining morphology method and edge detection method. After the AND operation and Sobel filter, we use Hough Transform, it can be seen that the result have outperformed for eliminating the pectoral muscle which is approximately the gray of microcalcification. Additionally, the enhancement step is achieved by morphology. We make effort on mammographic image preprocessing to achieve lower computational complexity. As well known, it is difficult to robustly achieve mammograms analysis due to low contrast between normal and lesion tissues, there are also much noise in such images. After a serious preprocessing algorithm, a method based on blob detection is performed to microcalcification clusters according their specific features. The proposed algorithm has employed Laplace operator to improve Difference of Gaussians (DoG) function in terms of low contrast images. A preliminary evaluation of the proposed method performs on a known public database namely MIAS, rather than synthetic images. The comparison experiments and Cohen's kappa coefficients all demonstrate that our proposed approach can potentially obtain better microcalcification clusters detection results in terms of accuracy, sensitivity and specificity.

  3. Classification of posture maintenance data with fuzzy clustering algorithms

    NASA Technical Reports Server (NTRS)

    Bezdek, James C.

    1992-01-01

    Sensory inputs from the visual, vestibular, and proprioreceptive systems are integrated by the central nervous system to maintain postural equilibrium. Sustained exposure to microgravity causes neurosensory adaptation during spaceflight, which results in decreased postural stability until readaptation occurs upon return to the terrestrial environment. Data which simulate sensory inputs under various sensory organization test (SOT) conditions were collected in conjunction with Johnson Space Center postural control studies using a tilt-translation device (TTD). The University of West Florida applied the fuzzy c-meams (FCM) clustering algorithms to this data with a view towards identifying various states and stages of subjects experiencing such changes. Feature analysis, time step analysis, pooling data, response of the subjects, and the algorithms used are discussed.

  4. Graphical representations and cluster algorithms I. Discrete spin systems

    NASA Astrophysics Data System (ADS)

    Chayes, L.; Machta, J.

    1997-02-01

    Graphical representations similar to the FK representation are developed for a variety of spin-systems. In several cases, it is established that these representations have (FKG) monotonicity properties which enables characterization theorems for the uniqueness phase and the low-temperature phase of the spin system. Certain systems with intermediate phases and/or first-order transitions are also described in terms of the percolation properties of the representations. In all cases, these representations lead, in a natural fashion, to Swendsen-Wang-type algorithms. Hence, at least in the above-mentioned instances, these algorithms realize the program described by Kandel and Domany, Phys. Rev. B 43 (1991) 8539-8548. All of the algorithms are shown to satisfy a Li-Sokal bound which (at least for systems with a divergent specific heat) implies critical slowing down. However, the representations also give rise to invaded cluster algorithms which may allow for the rapid simulation of some of these systems at their transition points.

  5. Dynamic and static properties of the invaded cluster algorithm

    NASA Astrophysics Data System (ADS)

    Moriarty, K.; Machta, J.; Chayes, L. Y.

    1999-02-01

    Simulations of the two-dimensional Ising and three-state Potts models at their critical points are performed using the invaded cluster (IC) algorithm. It is argued that observables measured on a sublattice of size l should exhibit a crossover to Swendsen-Wang (SW) behavior for l sufficiently less than the lattice size L, and a scaling form is proposed to describe the crossover phenomenon. It is found that the energy autocorrelation time τɛ(l,L) for an l×l sublattice attains a maximum in the crossover region, and a dynamic exponent zIC for the IC algorithm is defined according to τɛ,max~LzIC. Simulation results for the three-state model yield zIC=0.346+/-0.002, which is smaller than values of the dynamic exponent found for the SW and Wolff algorithms and also less than the Li-Sokal bound. The results are less conclusive for the Ising model, but it appears that zIC<0.21 and possibly that τɛ,max~ln L so that zIC=0-similar to previous results for the SW and Wolff algorithms.

  6. The Hierarchical Distribution of Young Stellar Clusters in Nearby Galaxies

    NASA Astrophysics Data System (ADS)

    Grasha, Kathryn; Calzetti, Daniela

    2017-01-01

    We investigate the spatial distributions of young stellar clusters in six nearby galaxies to trace the large scale hierarchical star-forming structures. The six galaxies are drawn from the Legacy ExtraGalactic UV Survey (LEGUS). We quantify the strength of the clustering among stellar clusters as a function of spatial scale and age to establish the survival timescale of the substructures. We separate the clusters into different classes, compact (bound) clusters and associations (unbound), and compare the clustering among them. We find that younger star clusters are more strongly clustered over small spatial scales and that the clustering disappears rapidly for ages as young as a few tens of Myr, consistent with clusters slowly losing the fractal dimension inherited at birth from their natal molecular clouds.

  7. A clustering method of Chinese medicine prescriptions based on modified firefly algorithm.

    PubMed

    Yuan, Feng; Liu, Hong; Chen, Shou-Qiang; Xu, Liang

    2016-12-01

    This paper is aimed to study the clustering method for Chinese medicine (CM) medical cases. The traditional K-means clustering algorithm had shortcomings such as dependence of results on the selection of initial value, trapping in local optimum when processing prescriptions form CM medical cases. Therefore, a new clustering method based on the collaboration of firefly algorithm and simulated annealing algorithm was proposed. This algorithm dynamically determined the iteration of firefly algorithm and simulates sampling of annealing algorithm by fitness changes, and increased the diversity of swarm through expansion of the scope of the sudden jump, thereby effectively avoiding premature problem. The results from confirmatory experiments for CM medical cases suggested that, comparing with traditional K-means clustering algorithms, this method was greatly improved in the individual diversity and the obtained clustering results, the computing results from this method had a certain reference value for cluster analysis on CM prescriptions.

  8. Ternary alloy material prediction using genetic algorithm and cluster expansion

    SciTech Connect

    Chen, Chong

    2015-12-01

    This thesis summarizes our study on the crystal structures prediction of Fe-V-Si system using genetic algorithm and cluster expansion. Our goal is to explore and look for new stable compounds. We started from the current ten known experimental phases, and calculated formation energies of those compounds using density functional theory (DFT) package, namely, VASP. The convex hull was generated based on the DFT calculations of the experimental known phases. Then we did random search on some metal rich (Fe and V) compositions and found that the lowest energy structures were body centered cube (bcc) underlying lattice, under which we did our computational systematic searches using genetic algorithm and cluster expansion. Among hundreds of the searched compositions, thirteen were selected and DFT formation energies were obtained by VASP. The stability checking of those thirteen compounds was done in reference to the experimental convex hull. We found that the composition, 24-8-16, i.e., Fe3VSi2 is a new stable phase and it can be very inspiring to the future experiments.

  9. Thermodynamic Casimir effect in films: the exchange cluster algorithm.

    PubMed

    Hasenbusch, Martin

    2015-02-01

    We study the thermodynamic Casimir force for films with various types of boundary conditions and the bulk universality class of the three-dimensional Ising model. To this end, we perform Monte Carlo simulations of the improved Blume-Capel model on the simple cubic lattice. In particular, we employ the exchange or geometric cluster cluster algorithm [Heringa and Blöte, Phys. Rev. E 57, 4976 (1998)]. In a previous work, we demonstrated that this algorithm allows us to compute the thermodynamic Casimir force for the plate-sphere geometry efficiently. It turns out that also for the film geometry a substantial reduction of the statistical error can achieved. Concerning physics, we focus on (O,O) boundary conditions, where O denotes the ordinary surface transition. These are implemented by free boundary conditions on both sides of the film. Films with such boundary conditions undergo a phase transition in the universality class of the two-dimensional Ising model. We determine the inverse transition temperature for a large range of thicknesses L(0) of the film and study the scaling of this temperature with L(0). In the neighborhood of the transition, the thermodynamic Casimir force is affected by finite size effects, where finite size refers to a finite transversal extension L of the film. We demonstrate that these finite size effects can be computed by using the universal finite size scaling function of the free energy of the two-dimensional Ising model.

  10. Classification of posture maintenance data with fuzzy clustering algorithms

    NASA Technical Reports Server (NTRS)

    Bezdek, James C.

    1991-01-01

    Sensory inputs from the visual, vestibular, and proprioreceptive systems are integrated by the central nervous system to maintain postural equilibrium. Sustained exposure to microgravity causes neurosensory adaptation during spaceflight, which results in decreased postural stability until readaptation occurs upon return to the terrestrial environment. Data which simulate sensory inputs under various conditions were collected in conjunction with JSC postural control studies using a Tilt-Translation Device (TTD). The University of West Florida proposed applying the Fuzzy C-Means Clustering (FCM) Algorithms to this data with a view towards identifying various states and stages. Data supplied by NASA/JSC were submitted to the FCM algorithms in an attempt to identify and characterize cluster substructure in a mixed ensemble of pre- and post-adaptational TTD data. Following several unsuccessful trials with FCM using a full 11 dimensional data set, a set of two channels (features) were found to enable FCM to separate pre- from post-adaptational TTD data. The main conclusions are that: (1) FCM seems able to separate pre- from post-TTD subject no. 2 on the one trial that was used, but only in certain subintervals of time; and (2) Channels 2 (right rear transducer force) and 8 (hip sway bar) contain better discrimination information than other supersets and combinations of the data that were tried so far.

  11. jClustering, an open framework for the development of 4D clustering algorithms.

    PubMed

    Mateos-Pérez, José María; García-Villalba, Carmen; Pascau, Javier; Desco, Manuel; Vaquero, Juan J

    2013-01-01

    We present jClustering, an open framework for the design of clustering algorithms in dynamic medical imaging. We developed this tool because of the difficulty involved in manually segmenting dynamic PET images and the lack of availability of source code for published segmentation algorithms. Providing an easily extensible open tool encourages publication of source code to facilitate the process of comparing algorithms and provide interested third parties with the opportunity to review code. The internal structure of the framework allows an external developer to implement new algorithms easily and quickly, focusing only on the particulars of the method being implemented and not on image data handling and preprocessing. This tool has been coded in Java and is presented as an ImageJ plugin in order to take advantage of all the functionalities offered by this imaging analysis platform. Both binary packages and source code have been published, the latter under a free software license (GNU General Public License) to allow modification if necessary.

  12. jClustering, an Open Framework for the Development of 4D Clustering Algorithms

    PubMed Central

    Mateos-Pérez, José María; García-Villalba, Carmen; Pascau, Javier; Desco, Manuel; Vaquero, Juan J.

    2013-01-01

    We present jClustering, an open framework for the design of clustering algorithms in dynamic medical imaging. We developed this tool because of the difficulty involved in manually segmenting dynamic PET images and the lack of availability of source code for published segmentation algorithms. Providing an easily extensible open tool encourages publication of source code to facilitate the process of comparing algorithms and provide interested third parties with the opportunity to review code. The internal structure of the framework allows an external developer to implement new algorithms easily and quickly, focusing only on the particulars of the method being implemented and not on image data handling and preprocessing. This tool has been coded in Java and is presented as an ImageJ plugin in order to take advantage of all the functionalities offered by this imaging analysis platform. Both binary packages and source code have been published, the latter under a free software license (GNU General Public License) to allow modification if necessary. PMID:23990913

  13. GPU-based cluster-labeling algorithm without the use of conventional iteration: Application to the Swendsen-Wang multi-cluster spin flip algorithm

    NASA Astrophysics Data System (ADS)

    Komura, Yukihiro

    2015-09-01

    Cluster-labeling algorithms that use a single GPU can be roughly divided into direct and two-stage approaches. To date, both types use an iterative method to compare the labels of nearest-neighbor sites. In this paper, I present a GPU-based cluster-labeling algorithm that does not use conventional iteration. The proposed method is applicable to both direct algorithms and two-stage approaches. Under the proposed approach, only one comparison with the nearest-neighbor site is needed for a two-dimensional (2D) system, and just two comparisons are needed for three-dimensional (3D) systems. As an application of the new cluster-labeling algorithm, I consider the Swendsen-Wang (SW) multi-cluster spin flip algorithm. The performance of the proposed method is compared with that of other cluster-labeling algorithms for the SW multi-cluster spin flip problem using the 2D and 3D Ising models. As a result, the computation time of the new algorithm is shown to be 40% faster than that of the previous algorithm for the 2D Ising model, and 20% faster than that of the previous algorithm for the 3D Ising model at the critical temperature.

  14. A comparison of queueing, cluster and distributed computing systems

    NASA Technical Reports Server (NTRS)

    Kaplan, Joseph A.; Nelson, Michael L.

    1993-01-01

    Using workstation clusters for distributed computing has become popular with the proliferation of inexpensive, powerful workstations. Workstation clusters offer both a cost effective alternative to batch processing and an easy entry into parallel computing. However, a number of workstations on a network does not constitute a cluster. Cluster management software is necessary to harness the collective computing power. A variety of cluster management and queuing systems are compared: Distributed Queueing Systems (DQS), Condor, Load Leveler, Load Balancer, Load Sharing Facility (LSF - formerly Utopia), Distributed Job Manager (DJM), Computing in Distributed Networked Environments (CODINE), and NQS/Exec. The systems differ in their design philosophy and implementation. Based on published reports on the different systems and conversations with the system's developers and vendors, a comparison of the systems are made on the integral issues of clustered computing.

  15. The application of mixed recommendation algorithm with user clustering in the microblog advertisements promotion

    NASA Astrophysics Data System (ADS)

    Gong, Lina; Xu, Tao; Zhang, Wei; Li, Xuhong; Wang, Xia; Pan, Wenwen

    2017-03-01

    The traditional microblog recommendation algorithm has the problems of low efficiency and modest effect in the era of big data. In the aim of solving these issues, this paper proposed a mixed recommendation algorithm with user clustering. This paper first introduced the situation of microblog marketing industry. Then, this paper elaborates the user interest modeling process and detailed advertisement recommendation methods. Finally, this paper compared the mixed recommendation algorithm with the traditional classification algorithm and mixed recommendation algorithm without user clustering. The results show that the mixed recommendation algorithm with user clustering has good accuracy and recall rate in the microblog advertisements promotion.

  16. Node Self-Deployment Algorithm Based on an Uneven Cluster with Radius Adjusting for Underwater Sensor Networks.

    PubMed

    Jiang, Peng; Xu, Yiming; Wu, Feng

    2016-01-14

    Existing move-restricted node self-deployment algorithms are based on a fixed node communication radius, evaluate the performance based on network coverage or the connectivity rate and do not consider the number of nodes near the sink node and the energy consumption distribution of the network topology, thereby degrading network reliability and the energy consumption balance. Therefore, we propose a distributed underwater node self-deployment algorithm. First, each node begins the uneven clustering based on the distance on the water surface. Each cluster head node selects its next-hop node to synchronously construct a connected path to the sink node. Second, the cluster head node adjusts its depth while maintaining the layout formed by the uneven clustering and then adjusts the positions of in-cluster nodes. The algorithm originally considers the network reliability and energy consumption balance during node deployment and considers the coverage redundancy rate of all positions that a node may reach during the node position adjustment. Simulation results show, compared to the connected dominating set (CDS) based depth computation algorithm, that the proposed algorithm can increase the number of the nodes near the sink node and improve network reliability while guaranteeing the network connectivity rate. Moreover, it can balance energy consumption during network operation, further improve network coverage rate and reduce energy consumption.

  17. Node Self-Deployment Algorithm Based on an Uneven Cluster with Radius Adjusting for Underwater Sensor Networks

    PubMed Central

    Jiang, Peng; Xu, Yiming; Wu, Feng

    2016-01-01

    Existing move-restricted node self-deployment algorithms are based on a fixed node communication radius, evaluate the performance based on network coverage or the connectivity rate and do not consider the number of nodes near the sink node and the energy consumption distribution of the network topology, thereby degrading network reliability and the energy consumption balance. Therefore, we propose a distributed underwater node self-deployment algorithm. First, each node begins the uneven clustering based on the distance on the water surface. Each cluster head node selects its next-hop node to synchronously construct a connected path to the sink node. Second, the cluster head node adjusts its depth while maintaining the layout formed by the uneven clustering and then adjusts the positions of in-cluster nodes. The algorithm originally considers the network reliability and energy consumption balance during node deployment and considers the coverage redundancy rate of all positions that a node may reach during the node position adjustment. Simulation results show, compared to the connected dominating set (CDS) based depth computation algorithm, that the proposed algorithm can increase the number of the nodes near the sink node and improve network reliability while guaranteeing the network connectivity rate. Moreover, it can balance energy consumption during network operation, further improve network coverage rate and reduce energy consumption. PMID:26784193

  18. CTDGFinder: A Novel Homology-Based Algorithm for Identifying Closely Spaced Clusters of Tandemly Duplicated Genes.

    PubMed

    Ortiz, Juan F; Rokas, Antonis

    2017-01-01

    Closely spaced clusters of tandemly duplicated genes (CTDGs) contribute to the diversity of many phenotypes, including chemosensation, snake venom, and animal body plans. CTDGs have traditionally been identified subjectively as genomic neighborhoods containing several gene duplicates in close proximity; however, CTDGs are often highly variable with respect to gene number, intergenic distance, and synteny. This lack of formal definition hampers the study of CTDG evolutionary dynamics and the discovery of novel CTDGs in the exponentially growing body of genomic data. To address this gap, we developed a novel homology-based algorithm, CTDGFinder, which formalizes and automates the identification of CTDGs by examining the physical distribution of individual members of families of duplicated genes across chromosomes. Application of CTDGFinder accurately identified CTDGs for many well-known gene clusters (e.g., Hox and beta-globin gene clusters) in the human, mouse and 20 other mammalian genomes. Differences between previously annotated gene clusters and our inferred CTDGs were due to the exclusion of nonhomologs that have historically been considered parts of specific gene clusters, the inclusion or absence of genes between the CTDGs and their corresponding gene clusters, and the splitting of certain gene clusters into distinct CTDGs. Examination of human genes showing tissue-specific enhancement of their expression by CTDGFinder identified members of several well-known gene clusters (e.g., cytochrome P450s and olfactory receptors) and revealed that they were unequally distributed across tissues. By formalizing and automating CTDG identification, CTDGFinder will facilitate understanding of CTDG evolutionary dynamics, their functional implications, and how they are associated with phenotypic diversity. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e

  19. ClusterControl: a web interface for distributing and monitoring bioinformatics applications on a Linux cluster.

    PubMed

    Stocker, Gernot; Rieder, Dietmar; Trajanoski, Zlatko

    2004-03-22

    ClusterControl is a web interface to simplify distributing and monitoring bioinformatics applications on Linux cluster systems. We have developed a modular concept that enables integration of command line oriented program into the application framework of ClusterControl. The systems facilitate integration of different applications accessed through one interface and executed on a distributed cluster system. The package is based on freely available technologies like Apache as web server, PHP as server-side scripting language and OpenPBS as queuing system and is available free of charge for academic and non-profit institutions. http://genome.tugraz.at/Software/ClusterControl

  20. GX-Means: A model-based divide and merge algorithm for geospatial image clustering

    SciTech Connect

    Vatsavai, Raju; Symons, Christopher T; Chandola, Varun; Jun, Goo

    2011-01-01

    One of the practical issues in clustering is the specification of the appropriate number of clusters, which is not obvious when analyzing geospatial datasets, partly because they are huge (both in size and spatial extent) and high dimensional. In this paper we present a computationally efficient model-based split and merge clustering algorithm that incrementally finds model parameters and the number of clusters. Additionally, we attempt to provide insights into this problem and other data mining challenges that are encountered when clustering geospatial data. The basic algorithm we present is similar to the G-means and X-means algorithms; however, our proposed approach avoids certain limitations of these well-known clustering algorithms that are pertinent when dealing with geospatial data. We compare the performance of our approach with the G-means and X-means algorithms. Experimental evaluation on simulated data and on multispectral and hyperspectral remotely sensed image data demonstrates the effectiveness of our algorithm.

  1. Moving Target Tracking through Distributed Clustering in Directional Sensor Networks

    PubMed Central

    Enayet, Asma; Razzaque, Md. Abdur; Hassan, Mohammad Mehedi; Almogren, Ahmad; Alamri, Atif

    2014-01-01

    The problem of moving target tracking in directional sensor networks (DSNs) introduces new research challenges, including optimal selection of sensing and communication sectors of the directional sensor nodes, determination of the precise location of the target and an energy-efficient data collection mechanism. Existing solutions allow individual sensor nodes to detect the target's location through collaboration among neighboring nodes, where most of the sensors are activated and communicate with the sink. Therefore, they incur much overhead, loss of energy and reduced target tracking accuracy. In this paper, we have proposed a clustering algorithm, where distributed cluster heads coordinate their member nodes in optimizing the active sensing and communication directions of the nodes, precisely determining the target location by aggregating reported sensing data from multiple nodes and transferring the resultant location information to the sink. Thus, the proposed target tracking mechanism minimizes the sensing redundancy and maximizes the number of sleeping nodes in the network. We have also investigated the dynamic approach of activating sleeping nodes on-demand so that the moving target tracking accuracy can be enhanced while maximizing the network lifetime. We have carried out our extensive simulations in ns-3, and the results show that the proposed mechanism achieves higher performance compared to the state-of-the-art works. PMID:25529205

  2. Moving target tracking through distributed clustering in directional sensor networks.

    PubMed

    Enayet, Asma; Razzaque, Md Abdur; Hassan, Mohammad Mehedi; Almogren, Ahmad; Alamri, Atif

    2014-12-18

    The problem of moving target tracking in directional sensor networks (DSNs) introduces new research challenges, including optimal selection of sensing and communication sectors of the directional sensor nodes, determination of the precise location of the target and an energy-efficient data collection mechanism. Existing solutions allow individual sensor nodes to detect the target's location through collaboration among neighboring nodes, where most of the sensors are activated and communicate with the sink. Therefore, they incur much overhead, loss of energy and reduced target tracking accuracy. In this paper, we have proposed a clustering algorithm, where distributed cluster heads coordinate their member nodes in optimizing the active sensing and communication directions of the nodes, precisely determining the target location by aggregating reported sensing data from multiple nodes and transferring the resultant location information to the sink. Thus, the proposed target tracking mechanism minimizes the sensing redundancy and maximizes the number of sleeping nodes in the network. We have also investigated the dynamic approach of activating sleeping nodes on-demand so that the moving target tracking accuracy can be enhanced while maximizing the network lifetime. We have carried out our extensive simulations in ns-3, and the results show that the proposed mechanism achieves higher performance compared to the state-of-the-art works.

  3. Comparing simulated and experimental molecular cluster distributions.

    PubMed

    Olenius, Tinja; Schobesberger, Siegfried; Kupiainen-Määttä, Oona; Franchin, Alessandro; Junninen, Heikki; Ortega, Ismael K; Kurtén, Theo; Loukonen, Ville; Worsnop, Douglas R; Kulmala, Markku; Vehkamäki, Hanna

    2013-01-01

    Formation of secondary atmospheric aerosol particles starts with gas phase molecules forming small molecular clusters. High-resolution mass spectrometry enables the detection and chemical characterization of electrically charged clusters from the molecular scale upward, whereas the experimental detection of electrically neutral clusters, especially as a chemical composition measurement, down to 1 nm in diameter and beyond still remains challenging. In this work we simulated a set of both electrically neutral and charged small molecular clusters, consisting of sulfuric acid and ammonia molecules, with a dynamic collision and evaporation model. Collision frequencies between the clusters were calculated according to classical kinetics, and evaporation rates were derived from first principles quantum chemical calculations with no fitting parameters. We found a good agreement between the modeled steady-state concentrations of negative cluster ions and experimental results measured with the state-of-the-art Atmospheric Pressure interface Time-Of-Flight mass spectrometer (APi-TOF) in the CLOUD chamber experiments at CERN. The model can be used to interpret experimental results and give information on neutral clusters that cannot be directly measured.

  4. Evaluation of particle clustering algorithms in the prediction of brownout dust clouds

    NASA Astrophysics Data System (ADS)

    Govindarajan, Bharath Madapusi

    2011-07-01

    A study of three Lagrangian particle clustering methods has been conducted with application to the problem of predicting brownout dust clouds that develop when rotorcraft land over surfaces covered with loose sediment. A significant impediment in performing such particle modeling simulations is the extremely large number of particles needed to obtain dust clouds of acceptable fidelity. Computing the motion of each and every individual sediment particle in a dust cloud (which can reach into tens of billions per cubic meter) is computationally prohibitive. The reported work involved the development of computationally efficient clustering algorithms that can be applied to the simulation of dilute gas-particle suspensions at low Reynolds numbers of the relative particle motion. The Gaussian distribution, k-means and Osiptsov's clustering methods were studied in detail to highlight the nuances of each method for a prototypical flow field that mimics the highly unsteady, two-phase vortical particle flow obtained when rotorcraft encounter brownout conditions. It is shown that although clustering algorithms can be problem dependent and have bounds of applicability, they offer the potential to significantly reduce computational costs while retaining the overall accuracy of a brownout dust cloud solution.

  5. ASTErIsM: application of topometric clustering algorithms in automatic galaxy detection and classification

    NASA Astrophysics Data System (ADS)

    Tramacere, A.; Paraficz, D.; Dubath, P.; Kneib, J.-P.; Courbin, F.

    2016-12-01

    We present a study on galaxy detection and shape classification using topometric clustering algorithms. We first use the DBSCAN algorithm to extract, from CCD frames, groups of adjacent pixels with significant fluxes and we then apply the DENCLUE algorithm to separate the contributions of overlapping sources. The DENCLUE separation is based on the localization of pattern of local maxima, through an iterative algorithm, which associates each pixel to the closest local maximum. Our main classification goal is to take apart elliptical from spiral galaxies. We introduce new sets of features derived from the computation of geometrical invariant moments of the pixel group shape and from the statistics of the spatial distribution of the DENCLUE local maxima patterns. Ellipticals are characterized by a single group of local maxima, related to the galaxy core, while spiral galaxies have additional groups related to segments of spiral arms. We use two different supervised ensemble classification algorithms: Random Forest and Gradient Boosting. Using a sample of ≃24 000 galaxies taken from the Galaxy Zoo 2 main sample with spectroscopic redshifts, and we test our classification against the Galaxy Zoo 2 catalogue. We find that features extracted from our pipeline give, on average, an accuracy of ≃93 per cent, when testing on a test set with a size of 20 per cent of our full data set, with features deriving from the angular distribution of density attractor ranking at the top of the discrimination power.

  6. Clustering Algorithm for Unsupervised Monaural Musical Sound Separation Based on Non-negative Matrix Factorization

    NASA Astrophysics Data System (ADS)

    Park, Sang Ha; Lee, Seokjin; Sung, Koeng-Mo

    Non-negative matrix factorization (NMF) is widely used for monaural musical sound source separation because of its efficiency and good performance. However, an additional clustering process is required because the musical sound mixture is separated into more signals than the number of musical tracks during NMF separation. In the conventional method, manual clustering or training-based clustering is performed with an additional learning process. Recently, a clustering algorithm based on the mel-frequency cepstrum coefficient (MFCC) was proposed for unsupervised clustering. However, MFCC clustering supplies limited information for clustering. In this paper, we propose various timbre features for unsupervised clustering and a clustering algorithm with these features. Simulation experiments are carried out using various musical sound mixtures. The results indicate that the proposed method improves clustering performance, as compared to conventional MFCC-based clustering.

  7. a New Online Distributed Process Fault Detection and Isolation Approach Using Potential Clustering Technique

    NASA Astrophysics Data System (ADS)

    Bahrampour, Soheil; Moshiri, Behzad; Salahshoor, Karim

    2009-08-01

    Most of process fault monitoring systems suffer from offline computations and confronting with novel faults that limit their applicabilities. This paper presents a new online fault detection and isolation (FDI) algorithm based on distributed online clustering approach. In the proposed approach, clustering algorithm is used for online detection of a new trend of time series data which indicates faulty condition. On the other hand, distributed technique is used to decompose the overall monitoring task into a series of local monitoring sub-tasks so as to locally track and capture the process faults. This algorithm not only solves the problem of online FDI, but also can handle novel faults. The diagnostic performances of the proposed FDI approach is evaluated on the Tennessee Eastman process plant as a large-scale benchmark problem.

  8. Are judgments a form of data clustering? Reexamining contrast effects with the k-means algorithm.

    PubMed

    Boillaud, Eric; Molina, Guylaine

    2015-04-01

    A number of theories have been proposed to explain in precise mathematical terms how statistical parameters and sequential properties of stimulus distributions affect category ratings. Various contextual factors such as the mean, the midrange, and the median of the stimuli; the stimulus range; the percentile rank of each stimulus; and the order of appearance have been assumed to influence judgmental contrast. A data clustering reinterpretation of judgmental relativity is offered wherein the influence of the initial choice of centroids on judgmental contrast involves 2 combined frequency and consistency tendencies. Accounts of the k-means algorithm are provided, showing good agreement with effects observed on multiple distribution shapes and with a variety of interaction effects relating to the number of stimuli, the number of response categories, and the method of skewing. Experiment 1 demonstrates that centroid initialization accounts for contrast effects obtained with stretched distributions. Experiment 2 demonstrates that the iterative convergence inherent to the k-means algorithm accounts for the contrast reduction observed across repeated blocks of trials. The concept of within-cluster variance minimization is discussed, as is the applicability of a backward k-means calculation method for inferring, from empirical data, the values of the centroids that would serve as a representation of the judgmental context. (c) 2015 APA, all rights reserved.

  9. Poster - Thur Eve - 37: Improved clustering MLC leaf-sequencing algorithm for step-and-shoot IMRT.

    PubMed

    Jing, J; Lin, H; Chow, J

    2012-07-01

    This study examines how to reduce the complexity of fluence map generated using an improved clustering leaf-sequencing method, and evaluates such method in step-and-shoot intensity-modulated radiotherapy (IMRT). Based on the current equal-space grouping algorithm for multileaf collimator (MLC) leaf sequence, we proposed an improved K-means grouping algorithm which can replace the stratification routine in the program of existing leaf sequence. The improved algorithm can be thought of as a gradient descent procedure, which begins at starting cluster centroids, and iteratively updates these centroids to decrease the objective function. The K-means always converge to a local minimum depending on the starting cluster centroids. The K-means algorithm continuously updates cluster centroids until the local minimum is reached. We compare the leaf-sequencing results in term of numerical values from the improved K-means and equal-space grouping algorithm. A representative 1D intensity map from a clinical treatment plan was investigated and optimized by the K-means and equal-space grouping algorithm. It was found that the K-means algorithm decreased the dose square error from 53.67 to 35.27. Moreover, the normalized square differences of the equal-space and K-means algorithm are equal to 2881 and 1244, respectively. The results demonstrated an improvement in accuracy achievable by allowing the fluence map to be defined in an optimal way rather than using the pre-defined criteria. Therefore, the K-means leaf-sequencing algorithm can better simulate the distributions of the input fluence data compared to the traditional grouping algorithm in step-and-shoot IMRT. © 2012 American Association of Physicists in Medicine.

  10. A new concept of wildland-urban interface based on city clustering algorithm

    NASA Astrophysics Data System (ADS)

    Kanevski, M.; Champendal, A.; Vega Orozco, C.; Tonini, M.; Conedera, M.

    2012-04-01

    Wildland-Urban-Interface (WUI) is a widely used term in the context of wild and forest fires to indicate areas where human infrastructures interact with wildland/forest areas. Many complex problems are associated to the WUI; but the most relevant ones are those related to forest fire hazard and management in dense populated areas where fire regime is dominated by anthropogenic-induced ignition fires. This coexistence enhances both anthropogenic-ignition sources and flammable fuels. Furthermore, the growing trend of the WUI and global change effects may even worsening the situation in the near future. Therefore, many studies are dedicated to the WUI problem, focusing on refinement of its definition, development of mapping methods, implementation of measures into specific fire management plans and the validation of the proposed approaches. The present study introduces a new concept of WUI based on city clustering algorithm (CCA) introduced in Rosenfeld et al., 2008. CCA was proposed as an automatic tool for studying the definition of cities and their distribution. The algorithm uses demographic data - either on a regular or non-regular grid in space - where a city (urban zone) is detected as a cluster of connected populated cells with maximal size. In the present study the CCA is proposed as a tool to develop a new concept of population dynamic analysis crucial to define and to localise WUI. The real case study is based on demographic/census data - organised in a regular grid with a resolution of 100 m and the forest fire ignition points database from canton Ticino, Switzerland. By changing spatial scales of demographic cells the relationships between urban zones (demographic clusters) and forest fire events were statistically analyzed. Corresponding scaling laws were used to understand the interaction between urban zones and forest fires. The first results are good and indicate that the method can be applied to define WUI in an innovative way. Keywords: forest fires

  11. The new image segmentation algorithm using adaptive evolutionary programming and fuzzy c-means clustering

    NASA Astrophysics Data System (ADS)

    Liu, Fang

    2011-06-01

    Image segmentation remains one of the major challenges in image analysis and computer vision. Fuzzy clustering, as a soft segmentation method, has been widely studied and successfully applied in mage clustering and segmentation. The fuzzy c-means (FCM) algorithm is the most popular method used in mage segmentation. However, most clustering algorithms such as the k-means and the FCM clustering algorithms search for the final clusters values based on the predetermined initial centers. The FCM clustering algorithms does not consider the space information of pixels and is sensitive to noise. In the paper, presents a new fuzzy c-means (FCM) algorithm with adaptive evolutionary programming that provides image clustering. The features of this algorithm are: 1) firstly, it need not predetermined initial centers. Evolutionary programming will help FCM search for better center and escape bad centers at local minima. Secondly, the spatial distance and the Euclidean distance is also considered in the FCM clustering. So this algorithm is more robust to the noises. Thirdly, the adaptive evolutionary programming is proposed. The mutation rule is adaptively changed with learning the useful knowledge in the evolving process. Experiment results shows that the new image segmentation algorithm is effective. It is providing robustness to noisy images.

  12. User-Based Document Clustering by Redescribing Subject Descriptions with a Genetic Algorithm.

    ERIC Educational Resources Information Center

    Gordon, Michael D.

    1991-01-01

    Discussion of clustering of documents and queries in information retrieval systems focuses on the use of a genetic algorithm to adapt subject descriptions so that documents become more effective in matching relevant queries. Various types of clustering are explained, and simulation experiments used to test the genetic algorithm are described. (27…

  13. Contributions to "k"-Means Clustering and Regression via Classification Algorithms

    ERIC Educational Resources Information Center

    Salman, Raied

    2012-01-01

    The dissertation deals with clustering algorithms and transforming regression problems into classification problems. The main contributions of the dissertation are twofold; first, to improve (speed up) the clustering algorithms and second, to develop a strict learning environment for solving regression problems as classification tasks by using…

  14. Contributions to "k"-Means Clustering and Regression via Classification Algorithms

    ERIC Educational Resources Information Center

    Salman, Raied

    2012-01-01

    The dissertation deals with clustering algorithms and transforming regression problems into classification problems. The main contributions of the dissertation are twofold; first, to improve (speed up) the clustering algorithms and second, to develop a strict learning environment for solving regression problems as classification tasks by using…

  15. User-Based Document Clustering by Redescribing Subject Descriptions with a Genetic Algorithm.

    ERIC Educational Resources Information Center

    Gordon, Michael D.

    1991-01-01

    Discussion of clustering of documents and queries in information retrieval systems focuses on the use of a genetic algorithm to adapt subject descriptions so that documents become more effective in matching relevant queries. Various types of clustering are explained, and simulation experiments used to test the genetic algorithm are described. (27…

  16. A Cluster Algorithm for the 2-D SU(3) × SU(3) Chiral Model

    NASA Astrophysics Data System (ADS)

    Ji, Da-ren; Zhang, Jian-bo

    1996-07-01

    To extend the cluster algorithm to SU(N) × SU(N) chiral models, a variant version of Wolff's cluster algorithm is proposed and tested for the 2-dimensional SU(3) × SU(3) chiral model. The results show that the new method can reduce the critical slowing down in SU(3) × SU(3) chiral model.

  17. Security clustering algorithm based on reputation in hierarchical peer-to-peer network

    NASA Astrophysics Data System (ADS)

    Chen, Mei; Luo, Xin; Wu, Guowen; Tan, Yang; Kita, Kenji

    2013-03-01

    For the security problems of the hierarchical P2P network (HPN), the paper presents a security clustering algorithm based on reputation (CABR). In the algorithm, we take the reputation mechanism for ensuring the security of transaction and use cluster for managing the reputation mechanism. In order to improve security, reduce cost of network brought by management of reputation and enhance stability of cluster, we select reputation, the historical average online time, and the network bandwidth as the basic factors of the comprehensive performance of node. Simulation results showed that the proposed algorithm improved the security, reduced the network overhead, and enhanced stability of cluster.

  18. MEASURING THE MASS DISTRIBUTION IN GALAXY CLUSTERS

    SciTech Connect

    Geller, Margaret J.; Diaferio, Antonaldo; Rines, Kenneth J.; Serra, Ana Laura E-mail: diaferio@ph.unito.it E-mail: serra@to.infn.it

    2013-02-10

    Cluster mass profiles are tests of models of structure formation. Only two current observational methods of determining the mass profile, gravitational lensing, and the caustic technique are independent of the assumption of dynamical equilibrium. Both techniques enable the determination of the extended mass profile at radii beyond the virial radius. For 19 clusters, we compare the mass profile based on the caustic technique with weak lensing measurements taken from the literature. This comparison offers a test of systematic issues in both techniques. Around the virial radius, the two methods of mass estimation agree to within {approx}30%, consistent with the expected errors in the individual techniques. At small radii, the caustic technique overestimates the mass as expected from numerical simulations. The ratio between the lensing profile and the caustic mass profile at these radii suggests that the weak lensing profiles are a good representation of the true mass profile. At radii larger than the virial radius, the extrapolated Navarro, Frenk and White fit to the lensing mass profile exceeds the caustic mass profile. Contamination of the lensing profile by unrelated structures within the lensing kernel may be an issue in some cases; we highlight the clusters MS0906+11 and A750, superposed along the line of sight, to illustrate the potential seriousness of contamination of the weak lensing signal by these unrelated structures.

  19. The kinetic evolution and velocity distribution of gravitational galaxy clustering

    NASA Astrophysics Data System (ADS)

    Saslaw, William C.; Chitre, S. M.; Itoh, Makoto; Inagaki, Shogo

    1990-12-01

    The spatial statistical distribution function for quasi-equilibrium gravitational clustering in an expanding universe is derived from more general assumptions than before, without needing an earlier Ansatz. Then, it is shown how this statistical distribution is related to the kinetic development of the BBGKY hierarchy and how to obtain an analytic descriptioin for the time evolution of an initial Poisson distribution. From general principles, an analytic velocity distribution function for quasi-equilibrium gravitational clustering is also derived. It has no free parameters. Comparison with N-body experiments shows excellent agreement.

  20. Logistics distribution centers location problem and algorithm under fuzzy environment

    NASA Astrophysics Data System (ADS)

    Yang, Lixing; Ji, Xiaoyu; Gao, Ziyou; Li, Keping

    2007-11-01

    Distribution centers location problem is concerned with how to select distribution centers from the potential set so that the total relevant cost is minimized. This paper mainly investigates this problem under fuzzy environment. Consequentially, chance-constrained programming model for the problem is designed and some properties of the model are investigated. Tabu search algorithm, genetic algorithm and fuzzy simulation algorithm are integrated to seek the approximate best solution of the model. A numerical example is also given to show the application of the algorithm.

  1. A multi-level spatial clustering algorithm for detection of disease outbreaks.

    PubMed

    Que, Jialan; Tsui, Fu-Chiang

    2008-11-06

    In this paper, we proposed a Multi-level Spatial Clustering (MSC) algorithm for rapid detection of emerging disease outbreaks prospectively. We used the semi-synthetic data for algorithm evaluation. We applied BARD algorithm [1] to generate outbreak counts for simulation of aerosol release of Anthrax. We compared MSC with two spatial clustering algorithms: Kulldorff's spatial scan statistic [2] and Bayesian spatial scan statistic [3]. The evaluation results showed that the areas under ROC had no significant difference among the three algorithms, so did the areas under AMOC. MSC demonstrated significant computational efficiency (100 + times faster) and higher PPV. However, MSC showed 2-6 hours delay on average for outbreak detection when the false alarm rate was lower than 1 false alarm per 4 weeks. We concluded that the MSC algorithm is computationally efficient and it is able to provide more precise and compact clusters in a timely manner while keeping high detection accuracy (cluster sensitivity) and low false alarm rates.

  2. LMC clusters - Age calibration and age distribution revisited

    NASA Technical Reports Server (NTRS)

    Elson, Rebecca A.; Fall, S. Michael

    1988-01-01

    The empirical age relation for star clusters in the Large Magellanic Cloud presented by Elson and Fall (1985) are reexamined using ages based only on main-sequence turnoffs. The present sample includes 57 clusters, 24 of which have color-magnitude diagrams published since 1985. The new calibration is very similar to that found previously, and the scatter in the relation corresponds to uncertainties of about a factor of 2 in age. The age distribution derived from the new calibration does not differ significantly from that derived in earlier work. It is compared with age distributions estimated by other authors for different samples of clusters, and the results are discussed.

  3. Signature extension through the application of cluster matching algorithms to determine appropriate signature transformations

    NASA Technical Reports Server (NTRS)

    Lambeck, P. F.; Rice, D. P.

    1976-01-01

    Signature extension is intended to increase the space-time range over which a set of training statistics can be used to classify data without significant loss of recognition accuracy. A first cluster matching algorithm MASC (Multiplicative and Additive Signature Correction) was developed at the Environmental Research Institute of Michigan to test the concept of using associations between training and recognition area cluster statistics to define an average signature transformation. A more recent signature extension module CROP-A (Cluster Regression Ordered on Principal Axis) has shown evidence of making significant associations between training and recognition area cluster statistics, with the clusters to be matched being selected automatically by the algorithm.

  4. A Self-Adaptive Fuzzy c-Means Algorithm for Determining the Optimal Number of Clusters

    PubMed Central

    Wang, Zhihao; Yi, Jing

    2016-01-01

    For the shortcoming of fuzzy c-means algorithm (FCM) needing to know the number of clusters in advance, this paper proposed a new self-adaptive method to determine the optimal number of clusters. Firstly, a density-based algorithm was put forward. The algorithm, according to the characteristics of the dataset, automatically determined the possible maximum number of clusters instead of using the empirical rule n and obtained the optimal initial cluster centroids, improving the limitation of FCM that randomly selected cluster centroids lead the convergence result to the local minimum. Secondly, this paper, by introducing a penalty function, proposed a new fuzzy clustering validity index based on fuzzy compactness and separation, which ensured that when the number of clusters verged on that of objects in the dataset, the value of clustering validity index did not monotonically decrease and was close to zero, so that the optimal number of clusters lost robustness and decision function. Then, based on these studies, a self-adaptive FCM algorithm was put forward to estimate the optimal number of clusters by the iterative trial-and-error process. At last, experiments were done on the UCI, KDD Cup 1999, and synthetic datasets, which showed that the method not only effectively determined the optimal number of clusters, but also reduced the iteration of FCM with the stable clustering result. PMID:28042291

  5. A Self-Adaptive Fuzzy c-Means Algorithm for Determining the Optimal Number of Clusters.

    PubMed

    Ren, Min; Liu, Peiyu; Wang, Zhihao; Yi, Jing

    2016-01-01

    For the shortcoming of fuzzy c-means algorithm (FCM) needing to know the number of clusters in advance, this paper proposed a new self-adaptive method to determine the optimal number of clusters. Firstly, a density-based algorithm was put forward. The algorithm, according to the characteristics of the dataset, automatically determined the possible maximum number of clusters instead of using the empirical rule [Formula: see text] and obtained the optimal initial cluster centroids, improving the limitation of FCM that randomly selected cluster centroids lead the convergence result to the local minimum. Secondly, this paper, by introducing a penalty function, proposed a new fuzzy clustering validity index based on fuzzy compactness and separation, which ensured that when the number of clusters verged on that of objects in the dataset, the value of clustering validity index did not monotonically decrease and was close to zero, so that the optimal number of clusters lost robustness and decision function. Then, based on these studies, a self-adaptive FCM algorithm was put forward to estimate the optimal number of clusters by the iterative trial-and-error process. At last, experiments were done on the UCI, KDD Cup 1999, and synthetic datasets, which showed that the method not only effectively determined the optimal number of clusters, but also reduced the iteration of FCM with the stable clustering result.

  6. The global kernel k-means algorithm for clustering in feature space.

    PubMed

    Tzortzis, Grigorios F; Likas, Aristidis C

    2009-07-01

    Kernel k-means is an extension of the standard k -means clustering algorithm that identifies nonlinearly separable clusters. In order to overcome the cluster initialization problem associated with this method, we propose the global kernel k-means algorithm, a deterministic and incremental approach to kernel-based clustering. Our method adds one cluster at each stage, through a global search procedure consisting of several executions of kernel k-means from suitable initializations. This algorithm does not depend on cluster initialization, identifies nonlinearly separable clusters, and, due to its incremental nature and search procedure, locates near-optimal solutions avoiding poor local minima. Furthermore, two modifications are developed to reduce the computational cost that do not significantly affect the solution quality. The proposed methods are extended to handle weighted data points, which enables their application to graph partitioning. We experiment with several data sets and the proposed approach compares favorably to kernel k -means with random restarts.

  7. The distribution of early- and late-type galaxies in the Coma cluster

    NASA Technical Reports Server (NTRS)

    Doi, M.; Fukugita, M.; Okamura, S.; Turner, E. L.

    1995-01-01

    The spatial distribution and the morohology-density relation of Coma cluster galaxies are studied using a new homogeneous photmetric sample of 450 galaxies down to B = 16.0 mag with quantitative morphology classification. The sample covers a wide area (10 deg X 10 deg), extending well beyond the Coma cluster. Morphological classifications into early- (E+SO) and late-(S) type galaxies are made by an automated algorithm using simple photometric parameters, with which the misclassification rate is expected to be approximately 10% with respect to early and late types given in the Third Reference Catalogue of Bright Galaxies. The flattened distribution of Coma cluster galaxies, as noted in previous studies, is most conspicuously seen if the early-type galaxies are selected. Early-type galaxies are distributed in a thick filament extended from the NE to the WSW direction that delineates a part of large-scale structure. Spiral galaxies show a distribution with a modest density gradient toward the cluster center; at least bright spiral galaxies are present close to the center of the Coma cluster. We also examine the morphology-density relation for the Coma cluster including its surrounding regions.

  8. The distribution of early- and late-type galaxies in the Coma cluster

    NASA Technical Reports Server (NTRS)

    Doi, M.; Fukugita, M.; Okamura, S.; Turner, E. L.

    1995-01-01

    The spatial distribution and the morohology-density relation of Coma cluster galaxies are studied using a new homogeneous photmetric sample of 450 galaxies down to B = 16.0 mag with quantitative morphology classification. The sample covers a wide area (10 deg X 10 deg), extending well beyond the Coma cluster. Morphological classifications into early- (E+SO) and late-(S) type galaxies are made by an automated algorithm using simple photometric parameters, with which the misclassification rate is expected to be approximately 10% with respect to early and late types given in the Third Reference Catalogue of Bright Galaxies. The flattened distribution of Coma cluster galaxies, as noted in previous studies, is most conspicuously seen if the early-type galaxies are selected. Early-type galaxies are distributed in a thick filament extended from the NE to the WSW direction that delineates a part of large-scale structure. Spiral galaxies show a distribution with a modest density gradient toward the cluster center; at least bright spiral galaxies are present close to the center of the Coma cluster. We also examine the morphology-density relation for the Coma cluster including its surrounding regions.

  9. Gravitational lensing by clusters of galaxies - Constraining the mass distribution

    NASA Technical Reports Server (NTRS)

    Miralda-Escude, Jordi

    1991-01-01

    The possibility of placing constraints on the mass distribution of a cluster of galaxies by analyzing the cluster's gravitational lensing effect on the images of more distant galaxies is investigated theoretically in the limit of weak distortion. The steps in the proposed analysis are examined in detail, and it is concluded that detectable distortion can be produced by clusters with line-of-sight velocity dispersions of over 500 km/sec. Hence it should be possible to determine (1) the cluster center position (with accuracy equal to the mean separation of the background galaxies), (2) the cluster-potential quadrupole moment (to within about 20 percent of the total potential if velocity dispersion is 1000 km/sec), and (3) the power law for the outer-cluster density profile (if enough background galaxies in the surrounding region are observed).

  10. Using Clustering Algorithms to Identify Brown Dwarf Characteristics

    NASA Astrophysics Data System (ADS)

    Choban, Caleb

    2016-06-01

    Brown dwarfs are stars that are not massive enough to sustain core hydrogen fusion, and thus fade and cool over time. The molecular composition of brown dwarf atmospheres can be determined by observing absorption features in their infrared spectrum, which can be quantified using spectral indices. Comparing these indices to one another, we can determine what kind of brown dwarf it is, and if it is young or metal-poor. We explored a new method for identifying these subgroups through the expectation-maximization machine learning clustering algorithm, which provides a quantitative and statistical way of identifying index pairs which separate rare populations. We specifically quantified two statistics, completeness and concentration, to identify the best index pairs. Starting with a training set, we defined selection regions for young, metal-poor and binary brown dwarfs, and tested these on a large sample of L dwarfs. We present the results of this analysis, and demonstrate that new objects in these classes can be found through these methods.

  11. Parallelization of the Wolff single-cluster algorithm

    NASA Astrophysics Data System (ADS)

    Kaupužs, J.; Rimšāns, J.; Melnik, R. V. N.

    2010-02-01

    A parallel [open multiprocessing (OpenMP)] implementation of the Wolff single-cluster algorithm has been developed and tested for the three-dimensional (3D) Ising model. The developed procedure is generalizable to other lattice spin models and its effectiveness depends on the specific application at hand. The applicability of the developed methodology is discussed in the context of the applications, where a sophisticated shuffling scheme is used to generate pseudorandom numbers of high quality, and an iterative method is applied to find the critical temperature of the 3D Ising model with a great accuracy. For the lattice with linear size L=1024 , we have reached the speedup about 1.79 times on two processors and about 2.67 times on four processors, as compared to the serial code. According to our estimation, the speedup about three times on four processors is reachable for the O(n) models with n≥2 . Furthermore, the application of the developed OpenMP code allows us to simulate larger lattices due to greater operative (shared) memory available.

  12. Parallelization of the Wolff single-cluster algorithm.

    PubMed

    Kaupuzs, J; Rimsāns, J; Melnik, R V N

    2010-02-01

    A parallel [open multiprocessing (OpenMP)] implementation of the Wolff single-cluster algorithm has been developed and tested for the three-dimensional (3D) Ising model. The developed procedure is generalizable to other lattice spin models and its effectiveness depends on the specific application at hand. The applicability of the developed methodology is discussed in the context of the applications, where a sophisticated shuffling scheme is used to generate pseudorandom numbers of high quality, and an iterative method is applied to find the critical temperature of the 3D Ising model with a great accuracy. For the lattice with linear size L=1024, we have reached the speedup about 1.79 times on two processors and about 2.67 times on four processors, as compared to the serial code. According to our estimation, the speedup about three times on four processors is reachable for the O(n) models with n> or =2. Furthermore, the application of the developed OpenMP code allows us to simulate larger lattices due to greater operative (shared) memory available.

  13. Comparison and evaluation of network clustering algorithms applied to genetic interaction networks.

    PubMed

    Hou, Lin; Wang, Lin; Berg, Arthur; Qian, Minping; Zhu, Yunping; Li, Fangting; Deng, Minghua

    2012-01-01

    The goal of network clustering algorithms detect dense clusters in a network, and provide a first step towards the understanding of large scale biological networks. With numerous recent advances in biotechnologies, large-scale genetic interactions are widely available, but there is a limited understanding of which clustering algorithms may be most effective. In order to address this problem, we conducted a systematic study to compare and evaluate six clustering algorithms in analyzing genetic interaction networks, and investigated influencing factors in choosing algorithms. The algorithms considered in this comparison include hierarchical clustering, topological overlap matrix, bi-clustering, Markov clustering, Bayesian discriminant analysis based community detection, and variational Bayes approach to modularity. Both experimentally identified and synthetically constructed networks were used in this comparison. The accuracy of the algorithms is measured by the Jaccard index in comparing predicted gene modules with benchmark gene sets. The results suggest that the choice differs according to the network topology and evaluation criteria. Hierarchical clustering showed to be best at predicting protein complexes; Bayesian discriminant analysis based community detection proved best under epistatic miniarray profile (EMAP) datasets; the variational Bayes approach to modularity was noticeably better than the other algorithms in the genome-scale networks.

  14. Multi-stage filtering for improving confidence level and determining dominant clusters in clustering algorithms of gene expression data.

    PubMed

    Kasim, Shahreen; Deris, Safaai; Othman, Razib M

    2013-09-01

    A drastic improvement in the analysis of gene expression has lead to new discoveries in bioinformatics research. In order to analyse the gene expression data, fuzzy clustering algorithms are widely used. However, the resulting analyses from these specific types of algorithms may lead to confusion in hypotheses with regard to the suggestion of dominant function for genes of interest. Besides that, the current fuzzy clustering algorithms do not conduct a thorough analysis of genes with low membership values. Therefore, we present a novel computational framework called the "multi-stage filtering-Clustering Functional Annotation" (msf-CluFA) for clustering gene expression data. The framework consists of four components: fuzzy c-means clustering (msf-CluFA-0), achieving dominant cluster (msf-CluFA-1), improving confidence level (msf-CluFA-2) and combination of msf-CluFA-0, msf-CluFA-1 and msf-CluFA-2 (msf-CluFA-3). By employing double filtering in msf-CluFA-1 and apriori algorithms in msf-CluFA-2, our new framework is capable of determining the dominant clusters and improving the confidence level of genes with lower membership values by means of which the unknown genes can be predicted. Copyright © 2013 Elsevier Ltd. All rights reserved.

  15. Automatic Regionalization Algorithm for Distributed State Estimation in Power Systems: Preprint

    SciTech Connect

    Wang, Dexin; Yang, Liuqing; Florita, Anthony; Alam, S.M. Shafiul; Elgindy, Tarek; Hodge, Bri-Mathias

    2016-08-01

    The deregulation of the power system and the incorporation of generation from renewable energy sources recessitates faster state estimation in the smart grid. Distributed state estimation (DSE) has become a promising and scalable solution to this urgent demand. In this paper, we investigate the regionalization algorithms for the power system, a necessary step before distributed state estimation can be performed. To the best of the authors' knowledge, this is the first investigation on automatic regionalization (AR). We propose three spectral clustering based AR algorithms. Simulations show that our proposed algorithms outperform the two investigated manual regionalization cases. With the help of AR algorithms, we also show how the number of regions impacts the accuracy and convergence speed of the DSE and conclude that the number of regions needs to be chosen carefully to improve the convergence speed of DSEs.

  16. Damage cluster distributions in numerical concrete at the mesoscale.

    PubMed

    Yılmaz, Okan; Derlet, Peter Michael; Molinari, Jean-François

    2017-04-01

    We investigate the size distribution of damage clusters in concrete under uniaxial tension loading conditions. Using the finite-element method, the concrete is modeled at the mesoscale by a random distribution of elastic spherical aggregates within an elastic mortar paste. The propagation and coalescence of damage zones are then simulated by means of dynamically inserted cohesive elements. Dynamic failure analysis shows that the size distribution of damage clusters follows a power law when a system-spanning cluster is first observed, with an exponent close to that of percolation theory. This is found for a range of selected mesostructural parameters, material defects, and applied strain rates. In all cases, the system-spanning cluster occurs prior to the onset of local decohesion, a regime of crack nucleation and propagation, and eventual material failure. The resulting fully damaged crack surfaces after failure are found to be only weakly correlated with the percolated damage region structures.

  17. Damage cluster distributions in numerical concrete at the mesoscale

    NASA Astrophysics Data System (ADS)

    Yılmaz, Okan; Derlet, Peter Michael; Molinari, Jean-François

    2017-04-01

    We investigate the size distribution of damage clusters in concrete under uniaxial tension loading conditions. Using the finite-element method, the concrete is modeled at the mesoscale by a random distribution of elastic spherical aggregates within an elastic mortar paste. The propagation and coalescence of damage zones are then simulated by means of dynamically inserted cohesive elements. Dynamic failure analysis shows that the size distribution of damage clusters follows a power law when a system-spanning cluster is first observed, with an exponent close to that of percolation theory. This is found for a range of selected mesostructural parameters, material defects, and applied strain rates. In all cases, the system-spanning cluster occurs prior to the onset of local decohesion, a regime of crack nucleation and propagation, and eventual material failure. The resulting fully damaged crack surfaces after failure are found to be only weakly correlated with the percolated damage region structures.

  18. A fast partitioning algorithm using adaptive Mahalanobis clustering with application to seismic zoning

    NASA Astrophysics Data System (ADS)

    Morales-Esteban, Antonio; Martínez-Álvarez, Francisco; Scitovski, Sanja; Scitovski, Rudolf

    2014-12-01

    In this paper we construct an efficient adaptive Mahalanobis k-means algorithm. In addition, we propose a new efficient algorithm to search for a globally optimal partition obtained by using the adoptive Mahalanobis distance-like function. The algorithm is a generalization of the previously proposed incremental algorithm (Scitovski and Scitovski, 2013). It successively finds optimal partitions with k = 2 , 3 , … clusters. Therefore, it can also be used for the estimation of the most appropriate number of clusters in a partition by using various validity indexes. The algorithm has been applied to the seismic catalogues of Croatia and the Iberian Peninsula. Both regions are characterized by a moderate seismic activity. One of the main advantages of the algorithm is its ability to discover not only circular but also elliptical shapes, whose geometry fits the faults better. Three seismogenic zonings are proposed for Croatia and two for the Iberian Peninsula and adjacent areas, according to the clusters discovered by the algorithm.

  19. Distribution-based fuzzy clustering of electrical resistivity tomography images for interface detection

    NASA Astrophysics Data System (ADS)

    Ward, W. O. C.; Wilkinson, P. B.; Chambers, J. E.; Oxby, L. S.; Bai, L.

    2014-04-01

    A novel method for the effective identification of bedrock subsurface elevation from electrical resistivity tomography images is described. Identifying subsurface boundaries in the topographic data can be difficult due to smoothness constraints used in inversion, so a statistical population-based approach is used that extends previous work in calculating isoresistivity surfaces. The analysis framework involves a procedure for guiding a clustering approach based on the fuzzy c-means algorithm. An approximation of resistivity distributions, found using kernel density estimation, was utilized as a means of guiding the cluster centroids used to classify data. A fuzzy method was chosen over hard clustering due to uncertainty in hard edges in the topography data, and a measure of clustering uncertainty was identified based on the reciprocal of cluster membership. The algorithm was validated using a direct comparison of known observed bedrock depths at two 3-D survey sites, using real-time GPS information of exposed bedrock by quarrying on one site, and borehole logs at the other. Results show similarly accurate detection as a leading isosurface estimation method, and the proposed algorithm requires significantly less user input and prior site knowledge. Furthermore, the method is effectively dimension-independent and will scale to data of increased spatial dimensions without a significant effect on the runtime. A discussion on the results by automated versus supervised analysis is also presented.

  20. Optimization of composite structures by estimation of distribution algorithms

    NASA Astrophysics Data System (ADS)

    Grosset, Laurent

    The design of high performance composite laminates, such as those used in aerospace structures, leads to complex combinatorial optimization problems that cannot be addressed by conventional methods. These problems are typically solved by stochastic algorithms, such as evolutionary algorithms. This dissertation proposes a new evolutionary algorithm for composite laminate optimization, named Double-Distribution Optimization Algorithm (DDOA). DDOA belongs to the family of estimation of distributions algorithms (EDA) that build a statistical model of promising regions of the design space based on sets of good points, and use it to guide the search. A generic framework for introducing statistical variable dependencies by making use of the physics of the problem is proposed. The algorithm uses two distributions simultaneously: the marginal distributions of the design variables, complemented by the distribution of auxiliary variables. The combination of the two generates complex distributions at a low computational cost. The dissertation demonstrates the efficiency of DDOA for several laminate optimization problems where the design variables are the fiber angles and the auxiliary variables are the lamination parameters. The results show that its reliability in finding the optima is greater than that of a simple EDA and of a standard genetic algorithm, and that its advantage increases with the problem dimension. A continuous version of the algorithm is presented and applied to a constrained quadratic problem. Finally, a modification of the algorithm incorporating probabilistic and directional search mechanisms is proposed. The algorithm exhibits a faster convergence to the optimum and opens the way for a unified framework for stochastic and directional optimization.

  1. Software Model Checking for Verifying Distributed Algorithms

    DTIC Science & Technology

    2014-10-28

    Verification procedure is an intelligent exhaustive search of the state space of the design Model Checking 6 Verifying Synchronous Distributed App...Distributed App Sagar Chaki, June 11, 2014 © 2014 Carnegie Mellon University Tool Usage Project webpage (http://mcda.googlecode.com) • Tutorial

  2. Clustering performance comparison using K-means and expectation maximization algorithms.

    PubMed

    Jung, Yong Gyu; Kang, Min Soo; Heo, Jun

    2014-11-14

    Clustering is an important means of data mining based on separating data categories by similar features. Unlike the classification algorithm, clustering belongs to the unsupervised type of algorithms. Two representatives of the clustering algorithms are the K-means and the expectation maximization (EM) algorithm. Linear regression analysis was extended to the category-type dependent variable, while logistic regression was achieved using a linear combination of independent variables. To predict the possibility of occurrence of an event, a statistical approach is used. However, the classification of all data by means of logistic regression analysis cannot guarantee the accuracy of the results. In this paper, the logistic regression analysis is applied to EM clusters and the K-means clustering method for quality assessment of red wine, and a method is proposed for ensuring the accuracy of the classification results.

  3. A Novel Artificial Immune Algorithm for Spatial Clustering with Obstacle Constraint and Its Applications

    PubMed Central

    Sun, Liping; Luo, Yonglong; Ding, Xintao; Zhang, Ji

    2014-01-01

    An important component of a spatial clustering algorithm is the distance measure between sample points in object space. In this paper, the traditional Euclidean distance measure is replaced with innovative obstacle distance measure for spatial clustering under obstacle constraints. Firstly, we present a path searching algorithm to approximate the obstacle distance between two points for dealing with obstacles and facilitators. Taking obstacle distance as similarity metric, we subsequently propose the artificial immune clustering with obstacle entity (AICOE) algorithm for clustering spatial point data in the presence of obstacles and facilitators. Finally, the paper presents a comparative analysis of AICOE algorithm and the classical clustering algorithms. Our clustering model based on artificial immune system is also applied to the case of public facility location problem in order to establish the practical applicability of our approach. By using the clone selection principle and updating the cluster centers based on the elite antibodies, the AICOE algorithm is able to achieve the global optimum and better clustering effect. PMID:25435862

  4. Implementation of spectral clustering on microarray data of carcinoma using k-means algorithm

    NASA Astrophysics Data System (ADS)

    Frisca, Bustamam, Alhadi; Siswantining, Titin

    2017-03-01

    Clustering is one of data analysis methods that aims to classify data which have similar characteristics in the same group. Spectral clustering is one of the most popular modern clustering algorithms. As an effective clustering technique, spectral clustering method emerged from the concepts of spectral graph theory. Spectral clustering method needs partitioning algorithm. There are some partitioning methods including PAM, SOM, Fuzzy c-means, and k-means. Based on the research that has been done by Capital and Choudhury in 2013, when using Euclidian distance k-means algorithm provide better accuracy than PAM algorithm. So in this paper we use k-means as our partition algorithm. The major advantage of spectral clustering is in reducing data dimension, especially in this case to reduce the dimension of large microarray dataset. Microarray data is a small-sized chip made of a glass plate containing thousands and even tens of thousands kinds of genes in the DNA fragments derived from doubling cDNA. Application of microarray data is widely used to detect cancer, for the example is carcinoma, in which cancer cells express the abnormalities in his genes. The purpose of this research is to classify the data that have high similarity in the same group and the data that have low similarity in the others. In this research, Carcinoma microarray data using 7457 genes. The result of partitioning using k-means algorithm is two clusters.

  5. A novel artificial immune algorithm for spatial clustering with obstacle constraint and its applications.

    PubMed

    Sun, Liping; Luo, Yonglong; Ding, Xintao; Zhang, Ji

    2014-01-01

    An important component of a spatial clustering algorithm is the distance measure between sample points in object space. In this paper, the traditional Euclidean distance measure is replaced with innovative obstacle distance measure for spatial clustering under obstacle constraints. Firstly, we present a path searching algorithm to approximate the obstacle distance between two points for dealing with obstacles and facilitators. Taking obstacle distance as similarity metric, we subsequently propose the artificial immune clustering with obstacle entity (AICOE) algorithm for clustering spatial point data in the presence of obstacles and facilitators. Finally, the paper presents a comparative analysis of AICOE algorithm and the classical clustering algorithms. Our clustering model based on artificial immune system is also applied to the case of public facility location problem in order to establish the practical applicability of our approach. By using the clone selection principle and updating the cluster centers based on the elite antibodies, the AICOE algorithm is able to achieve the global optimum and better clustering effect.

  6. Divisive Correlation Clustering Algorithm (DCCA) for grouping of genes: detecting varying patterns in expression profiles.

    PubMed

    Bhattacharya, Anindya; De, Rajat K

    2008-06-01

    Cluster analysis (of gene-expression data) is a useful tool for identifying biologically relevant groups of genes that show similar expression patterns under multiple experimental conditions. Various methods have been proposed for clustering gene-expression data. However most of these algorithms have several shortcomings for gene-expression data clustering. In the present article, we focus on several shortcomings of conventional clustering algorithms and propose a new one that is able to produce better clustering solution than that produced by some others. We present the Divisive Correlation Clustering Algorithm (DCCA) that is suitable for finding a group of genes having similar pattern of variation in their expression values. To detect clusters with high correlation and biological significance, we use the correlation clustering concept introduced by Bansal et al. Our proposed algorithm DCCA produces a clustering solution without taking number of clusters to be created as an input. DCCA uses the correlation matrix in such a way that all genes in a cluster have highest average correlation with genes in that cluster. To test the performance of the DCCA, we have applied DCCA and some well-known conventional methods to an artificial dataset, and nine gene-expression datasets, and compared the performance of the algorithms. The clustering results of the DCCA are found to be more significantly relevant to the biological annotations than those of the other methods. All these facts show the superiority of the DCCA over some others for the clustering of gene-expression data. The software has been developed using C and Visual Basic languages, and can be executed on the Microsoft Windows platforms. The software may be downloaded as a zip file from http://www.isical.ac.in/~rajat. Then it needs to be installed. Two word files (included in the zip file) need to be consulted before installation and execution of the software.

  7. C-element: a new clustering algorithm to find high quality functional modules in PPI networks.

    PubMed

    Ghasemi, Mahdieh; Rahgozar, Maseud; Bidkhori, Gholamreza; Masoudi-Nejad, Ali

    2013-01-01

    Graph clustering algorithms are widely used in the analysis of biological networks. Extracting functional modules in protein-protein interaction (PPI) networks is one such use. Most clustering algorithms whose focuses are on finding functional modules try either to find a clique like sub networks or to grow clusters starting from vertices with high degrees as seeds. These algorithms do not make any difference between a biological network and any other networks. In the current research, we present a new procedure to find functional modules in PPI networks. Our main idea is to model a biological concept and to use this concept for finding good functional modules in PPI networks. In order to evaluate the quality of the obtained clusters, we compared the results of our algorithm with those of some other widely used clustering algorithms on three high throughput PPI networks from Sacchromyces Cerevisiae, Homo sapiens and Caenorhabditis elegans as well as on some tissue specific networks. Gene Ontology (GO) analyses were used to compare the results of different algorithms. Each algorithm's result was then compared with GO-term derived functional modules. We also analyzed the effect of using tissue specific networks on the quality of the obtained clusters. The experimental results indicate that the new algorithm outperforms most of the others, and this improvement is more significant when tissue specific networks are used.

  8. 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.

  9. The efficiency of star formation in clustered and distributed regions

    NASA Astrophysics Data System (ADS)

    Bonnell, Ian A.; Smith, Rowan J.; Clark, Paul C.; Bate, Matthew R.

    2011-02-01

    We investigate the formation of both clustered and distributed populations of young stars in a single molecular cloud. We present a numerical simulation of a 104 M⊙ elongated, turbulent, molecular cloud and the formation of over 2500 stars. The stars form both in stellar clusters and in a distributed mode, which is determined by the local gravitational binding of the cloud. A density gradient along the major axis of the cloud produces bound regions that form stellar clusters and unbound regions that form a more distributed population. The initial mass function (IMF) also depends on the local gravitational binding of the cloud with bound regions forming full IMFs whereas in the unbound, distributed regions the stellar masses cluster around the local Jeans mass and lack both the high-mass and the low-mass stars. The overall efficiency of star formation is ≈ 15 per cent in the cloud when the calculation is terminated, but varies from less than 1 per cent in the regions of distributed star formation to ≈ 40 per cent in regions containing large stellar clusters. Considering that large-scale surveys are likely to catch clouds at all evolutionary stages, estimates of the (time-averaged) star formation efficiency (SFE) for the giant molecular cloud reported here is only ≈ 4 per cent. This would lead to the erroneous conclusion of slow star formation when in fact it is occurring on a dynamical time-scale.

  10. A Special Local Clustering Algorithm for Identifying the Genes Associated With Alzheimer’s Disease

    PubMed Central

    Pang, Chao-Yang; Hu, Wei; Hu, Ben-Qiong; Shi, Ying; Vanderburg, Charles R.; Rogers, Jack T.

    2010-01-01

    Clustering is the grouping of similar objects into a class. Local clustering feature refers to the phenomenon whereby one group of data is separated from another, and the data from these different groups are clustered locally. A compact class is defined as one cluster in which all similar elements cluster tightly within the cluster. Herein, the essence of the local clustering feature, revealed by mathematical manipulation, results in a novel clustering algorithm termed as the special local clustering (SLC) algorithm that was used to process gene microarray data related to Alzheimer’s disease (AD). SLC algorithm was able to group together genes with similar expression patterns and identify significantly varied gene expression values as isolated points. If a gene belongs to a compact class in control data and appears as an isolated point in incipient, moderate and/or severe AD gene microarray data, this gene is possibly associated with AD. Application of a clustering algorithm in disease-associated gene identification such as in AD is rarely reported. PMID:20089478

  11. Towards Enhancement of Performance of K-Means Clustering Using Nature-Inspired Optimization Algorithms

    PubMed Central

    Deb, Suash; Yang, Xin-She

    2014-01-01

    Traditional K-means clustering algorithms have the drawback of getting stuck at local optima that depend on the random values of initial centroids. Optimization algorithms have their advantages in guiding iterative computation to search for global optima while avoiding local optima. The algorithms help speed up the clustering process by converging into a global optimum early with multiple search agents in action. Inspired by nature, some contemporary optimization algorithms which include Ant, Bat, Cuckoo, Firefly, and Wolf search algorithms mimic the swarming behavior allowing them to cooperatively steer towards an optimal objective within a reasonable time. It is known that these so-called nature-inspired optimization algorithms have their own characteristics as well as pros and cons in different applications. When these algorithms are combined with K-means clustering mechanism for the sake of enhancing its clustering quality by avoiding local optima and finding global optima, the new hybrids are anticipated to produce unprecedented performance. In this paper, we report the results of our evaluation experiments on the integration of nature-inspired optimization methods into K-means algorithms. In addition to the standard evaluation metrics in evaluating clustering quality, the extended K-means algorithms that are empowered by nature-inspired optimization methods are applied on image segmentation as a case study of application scenario. PMID:25202730

  12. Towards enhancement of performance of K-means clustering using nature-inspired optimization algorithms.

    PubMed

    Fong, Simon; Deb, Suash; Yang, Xin-She; Zhuang, Yan

    2014-01-01

    Traditional K-means clustering algorithms have the drawback of getting stuck at local optima that depend on the random values of initial centroids. Optimization algorithms have their advantages in guiding iterative computation to search for global optima while avoiding local optima. The algorithms help speed up the clustering process by converging into a global optimum early with multiple search agents in action. Inspired by nature, some contemporary optimization algorithms which include Ant, Bat, Cuckoo, Firefly, and Wolf search algorithms mimic the swarming behavior allowing them to cooperatively steer towards an optimal objective within a reasonable time. It is known that these so-called nature-inspired optimization algorithms have their own characteristics as well as pros and cons in different applications. When these algorithms are combined with K-means clustering mechanism for the sake of enhancing its clustering quality by avoiding local optima and finding global optima, the new hybrids are anticipated to produce unprecedented performance. In this paper, we report the results of our evaluation experiments on the integration of nature-inspired optimization methods into K-means algorithms. In addition to the standard evaluation metrics in evaluating clustering quality, the extended K-means algorithms that are empowered by nature-inspired optimization methods are applied on image segmentation as a case study of application scenario.

  13. Block clustering based on difference of convex functions (DC) programming and DC algorithms.

    PubMed

    Le, Hoai Minh; Le Thi, Hoai An; Dinh, Tao Pham; Huynh, Van Ngai

    2013-10-01

    We investigate difference of convex functions (DC) programming and the DC algorithm (DCA) to solve the block clustering problem in the continuous framework, which traditionally requires solving a hard combinatorial optimization problem. DC reformulation techniques and exact penalty in DC programming are developed to build an appropriate equivalent DC program of the block clustering problem. They lead to an elegant and explicit DCA scheme for the resulting DC program. Computational experiments show the robustness and efficiency of the proposed algorithm and its superiority over standard algorithms such as two-mode K-means, two-mode fuzzy clustering, and block classification EM.

  14. A distributed scheduling algorithm for heterogeneous real-time systems

    NASA Technical Reports Server (NTRS)

    Zeineldine, Osman; El-Toweissy, Mohamed; Mukkamala, Ravi

    1991-01-01

    Much of the previous work on load balancing and scheduling in distributed environments was concerned with homogeneous systems and homogeneous loads. Several of the results indicated that random policies are as effective as other more complex load allocation policies. The effects of heterogeneity on scheduling algorithms for hard real time systems is examined. A distributed scheduler specifically to handle heterogeneities in both nodes and node traffic is proposed. The performance of the algorithm is measured in terms of the percentage of jobs discarded. While a random task allocation is very sensitive to heterogeneities, the algorithm is shown to be robust to such non-uniformities in system components and load.

  15. A fast distributed algorithm for mining association rules

    SciTech Connect

    Cheung, D.W.; Fu, A.W.; Ng, V.T.

    1996-12-31

    With the existence of many large transaction databases, the huge amounts of data, the high scalability of distributed systems, and the easy partition and distribution of a centralized database, it is important to investigate efficient methods for distributed mining of association rules. This study discloses some interesting relationships between locally large and globally large itemsets and proposes an interesting distributed association rule mining algorithm, FDM (Fast Distributed Mining of association rules), which generates a small number of candidate sets and substantially reduces the number of messages to be passed at mining association rules. Our performance study shows that FDM has a superior performance over the direct application of a typical sequential algorithm Further performance enhancement leads to a few variations of the algorithm.

  16. Ab initio study on (CO2)n clusters via electrostatics- and molecular tailoring-based algorithm

    NASA Astrophysics Data System (ADS)

    Jovan Jose, K. V.; Gadre, Shridhar R.

    An algorithm based on molecular electrostatic potential (MESP) and molecular tailoring approach (MTA) for building energetically favorable molecular clusters is presented. This algorithm is tested on prototype (CO2)n clusters with n = 13, 20, and 25 to explore their structure, energetics, and properties. The most stable clusters in this series are seen to show more number of triangular motifs. Many-body energy decomposition analysis performed on the most stable clusters reveals that the 2-body is the major contributor (>96%) to the total interaction energy. Vibrational frequencies and molecular electrostatic potentials are also evaluated for these large clusters through MTA. The MTA-based MESPs of these clusters show a remarkably good agreement with the corresponding actual ones. The most intense MTA-based normal mode frequencies are in fair agreement with the actual ones for smaller clusters. These calculated asymmetric stretching frequencies are blue-shifted with reference to the CO2 monomer.

  17. A Novel Method to Predict Genomic Islands Based on Mean Shift Clustering Algorithm

    PubMed Central

    de Brito, Daniel M.; Maracaja-Coutinho, Vinicius; de Farias, Savio T.; Batista, Leonardo V.; do Rêgo, Thaís G.

    2016-01-01

    Genomic Islands (GIs) are regions of bacterial genomes that are acquired from other organisms by the phenomenon of horizontal transfer. These regions are often responsible for many important acquired adaptations of the bacteria, with great impact on their evolution and behavior. Nevertheless, these adaptations are usually associated with pathogenicity, antibiotic resistance, degradation and metabolism. Identification of such regions is of medical and industrial interest. For this reason, different approaches for genomic islands prediction have been proposed. However, none of them are capable of predicting precisely the complete repertory of GIs in a genome. The difficulties arise due to the changes in performance of different algorithms in the face of the variety of nucleotide distribution in different species. In this paper, we present a novel method to predict GIs that is built upon mean shift clustering algorithm. It does not require any information regarding the number of clusters, and the bandwidth parameter is automatically calculated based on a heuristic approach. The method was implemented in a new user-friendly tool named MSGIP—Mean Shift Genomic Island Predictor. Genomes of bacteria with GIs discussed in other papers were used to evaluate the proposed method. The application of this tool revealed the same GIs predicted by other methods and also different novel unpredicted islands. A detailed investigation of the different features related to typical GI elements inserted in these new regions confirmed its effectiveness. Stand-alone and user-friendly versions for this new methodology are available at http://msgip.integrativebioinformatics.me. PMID:26731657

  18. Hierarchical trie packet classification algorithm based on expectation-maximization clustering

    PubMed Central

    Bi, Xia-an; Zhao, Junxia

    2017-01-01

    With the development of computer network bandwidth, packet classification algorithms which are able to deal with large-scale rule sets are in urgent need. Among the existing algorithms, researches on packet classification algorithms based on hierarchical trie have become an important packet classification research branch because of their widely practical use. Although hierarchical trie is beneficial to save large storage space, it has several shortcomings such as the existence of backtracking and empty nodes. This paper proposes a new packet classification algorithm, Hierarchical Trie Algorithm Based on Expectation-Maximization Clustering (HTEMC). Firstly, this paper uses the formalization method to deal with the packet classification problem by means of mapping the rules and data packets into a two-dimensional space. Secondly, this paper uses expectation-maximization algorithm to cluster the rules based on their aggregate characteristics, and thereby diversified clusters are formed. Thirdly, this paper proposes a hierarchical trie based on the results of expectation-maximization clustering. Finally, this paper respectively conducts simulation experiments and real-environment experiments to compare the performances of our algorithm with other typical algorithms, and analyzes the results of the experiments. The hierarchical trie structure in our algorithm not only adopts trie path compression to eliminate backtracking, but also solves the problem of low efficiency of trie updates, which greatly improves the performance of the algorithm. PMID:28704476

  19. Hierarchical trie packet classification algorithm based on expectation-maximization clustering.

    PubMed

    Bi, Xia-An; Zhao, Junxia

    2017-01-01

    With the development of computer network bandwidth, packet classification algorithms which are able to deal with large-scale rule sets are in urgent need. Among the existing algorithms, researches on packet classification algorithms based on hierarchical trie have become an important packet classification research branch because of their widely practical use. Although hierarchical trie is beneficial to save large storage space, it has several shortcomings such as the existence of backtracking and empty nodes. This paper proposes a new packet classification algorithm, Hierarchical Trie Algorithm Based on Expectation-Maximization Clustering (HTEMC). Firstly, this paper uses the formalization method to deal with the packet classification problem by means of mapping the rules and data packets into a two-dimensional space. Secondly, this paper uses expectation-maximization algorithm to cluster the rules based on their aggregate characteristics, and thereby diversified clusters are formed. Thirdly, this paper proposes a hierarchical trie based on the results of expectation-maximization clustering. Finally, this paper respectively conducts simulation experiments and real-environment experiments to compare the performances of our algorithm with other typical algorithms, and analyzes the results of the experiments. The hierarchical trie structure in our algorithm not only adopts trie path compression to eliminate backtracking, but also solves the problem of low efficiency of trie updates, which greatly improves the performance of the algorithm.

  20. Clustering dynamic textures with the hierarchical em algorithm for modeling video.

    PubMed

    Mumtaz, Adeel; Coviello, Emanuele; Lanckriet, Gert R G; Chan, Antoni B

    2013-07-01

    Dynamic texture (DT) is a probabilistic generative model, defined over space and time, that represents a video as the output of a linear dynamical system (LDS). The DT model has been applied to a wide variety of computer vision problems, such as motion segmentation, motion classification, and video registration. In this paper, we derive a new algorithm for clustering DT models that is based on the hierarchical EM algorithm. The proposed clustering algorithm is capable of both clustering DTs and learning novel DT cluster centers that are representative of the cluster members in a manner that is consistent with the underlying generative probabilistic model of the DT. We also derive an efficient recursive algorithm for sensitivity analysis of the discrete-time Kalman smoothing filter, which is used as the basis for computing expectations in the E-step of the HEM algorithm. Finally, we demonstrate the efficacy of the clustering algorithm on several applications in motion analysis, including hierarchical motion clustering, semantic motion annotation, and learning bag-of-systems (BoS) codebooks for dynamic texture recognition.

  1. A High-Efficiency Uneven Cluster Deployment Algorithm Based on Network Layered for Event Coverage in UWSNs

    PubMed Central

    Yu, Shanen; Liu, Shuai; Jiang, Peng

    2016-01-01

    Most existing deployment algorithms for event coverage in underwater wireless sensor networks (UWSNs) usually do not consider that network communication has non-uniform characteristics on three-dimensional underwater environments. Such deployment algorithms ignore that the nodes are distributed at different depths and have different probabilities for data acquisition, thereby leading to imbalances in the overall network energy consumption, decreasing the network performance, and resulting in poor and unreliable late network operation. Therefore, in this study, we proposed an uneven cluster deployment algorithm based network layered for event coverage. First, according to the energy consumption requirement of the communication load at different depths of the underwater network, we obtained the expected value of deployment nodes and the distribution density of each layer network after theoretical analysis and deduction. Afterward, the network is divided into multilayers based on uneven clusters, and the heterogeneous communication radius of nodes can improve the network connectivity rate. The recovery strategy is used to balance the energy consumption of nodes in the cluster and can efficiently reconstruct the network topology, which ensures that the network has a high network coverage and connectivity rate in a long period of data acquisition. Simulation results show that the proposed algorithm improves network reliability and prolongs network lifetime by significantly reducing the blind movement of overall network nodes while maintaining a high network coverage and connectivity rate. PMID:27973448

  2. Novel density-based and hierarchical density-based clustering algorithms for uncertain data.

    PubMed

    Zhang, Xianchao; Liu, Han; Zhang, Xiaotong

    2017-09-01

    Uncertain data has posed a great challenge to traditional clustering algorithms. Recently, several algorithms have been proposed for clustering uncertain data, and among them density-based techniques seem promising for handling data uncertainty. However, some issues like losing uncertain information, high time complexity and nonadaptive threshold have not been addressed well in the previous density-based algorithm FDBSCAN and hierarchical density-based algorithm FOPTICS. In this paper, we firstly propose a novel density-based algorithm PDBSCAN, which improves the previous FDBSCAN from the following aspects: (1) it employs a more accurate method to compute the probability that the distance between two uncertain objects is less than or equal to a boundary value, instead of the sampling-based method in FDBSCAN; (2) it introduces new definitions of probability neighborhood, support degree, core object probability, direct reachability probability, thus reducing the complexity and solving the issue of nonadaptive threshold (for core object judgement) in FDBSCAN. Then, we modify the algorithm PDBSCAN to an improved version (PDBSCANi), by using a better cluster assignment strategy to ensure that every object will be assigned to the most appropriate cluster, thus solving the issue of nonadaptive threshold (for direct density reachability judgement) in FDBSCAN. Furthermore, as PDBSCAN and PDBSCANi have difficulties for clustering uncertain data with non-uniform cluster density, we propose a novel hierarchical density-based algorithm POPTICS by extending the definitions of PDBSCAN, adding new definitions of fuzzy core distance and fuzzy reachability distance, and employing a new clustering framework. POPTICS can reveal the cluster structures of the datasets with different local densities in different regions better than PDBSCAN and PDBSCANi, and it addresses the issues in FOPTICS. Experimental results demonstrate the superiority of our proposed algorithms over the existing

  3. `Inter-Arrival Time' Inspired Algorithm and its Application in Clustering and Molecular Phylogeny

    NASA Astrophysics Data System (ADS)

    Kolekar, Pandurang S.; Kale, Mohan M.; Kulkarni-Kale, Urmila

    2010-10-01

    Bioinformatics, being multidisciplinary field, involves applications of various methods from allied areas of Science for data mining using computational approaches. Clustering and molecular phylogeny is one of the key areas in Bioinformatics, which help in study of classification and evolution of organisms. Molecular phylogeny algorithms can be divided into distance based and character based methods. But most of these methods are dependent on pre-alignment of sequences and become computationally intensive with increase in size of data and hence demand alternative efficient approaches. `Inter arrival time distribution' (IATD) is a popular concept in the theory of stochastic system modeling but its potential in molecular data analysis has not been fully explored. The present study reports application of IATD in Bioinformatics for clustering and molecular phylogeny. The proposed method provides IATDs of nucleotides in genomic sequences. The distance function based on statistical parameters of IATDs is proposed and distance matrix thus obtained is used for the purpose of clustering and molecular phylogeny. The method is applied on a dataset of 3' non-coding region sequences (NCR) of Dengue virus type 3 (DENV-3), subtype III, reported in 2008. The phylogram thus obtained revealed the geographical distribution of DENV-3 isolates. Sri Lankan DENV-3 isolates were further observed to be clustered in two sub-clades corresponding to pre and post Dengue hemorrhagic fever emergence groups. These results are consistent with those reported earlier, which are obtained using pre-aligned sequence data as an input. These findings encourage applications of the IATD based method in molecular phylogenetic analysis in particular and data mining in general.

  4. Complex Network Clustering by a Multi-objective Evolutionary Algorithm Based on Decomposition and Membrane Structure

    NASA Astrophysics Data System (ADS)

    Ju, Ying; Zhang, Songming; Ding, Ningxiang; Zeng, Xiangxiang; Zhang, Xingyi

    2016-09-01

    The field of complex network clustering is gaining considerable attention in recent years. In this study, a multi-objective evolutionary algorithm based on membranes is proposed to solve the network clustering problem. Population are divided into different membrane structures on average. The evolutionary algorithm is carried out in the membrane structures. The population are eliminated by the vector of membranes. In the proposed method, two evaluation objectives termed as Kernel J-means and Ratio Cut are to be minimized. Extensive experimental studies comparison with state-of-the-art algorithms proves that the proposed algorithm is effective and promising.

  5. Complex Network Clustering by a Multi-objective Evolutionary Algorithm Based on Decomposition and Membrane Structure

    PubMed Central

    Ju, Ying; Zhang, Songming; Ding, Ningxiang; Zeng, Xiangxiang; Zhang, Xingyi

    2016-01-01

    The field of complex network clustering is gaining considerable attention in recent years. In this study, a multi-objective evolutionary algorithm based on membranes is proposed to solve the network clustering problem. Population are divided into different membrane structures on average. The evolutionary algorithm is carried out in the membrane structures. The population are eliminated by the vector of membranes. In the proposed method, two evaluation objectives termed as Kernel J-means and Ratio Cut are to be minimized. Extensive experimental studies comparison with state-of-the-art algorithms proves that the proposed algorithm is effective and promising. PMID:27670156

  6. The age distribution of stellar clusters in M83

    NASA Astrophysics Data System (ADS)

    Silva-Villa, E.; Adamo, A.; Bastian, N.; Fouesneau, M.; Zackrisson, E.

    2014-05-01

    In order to empirically determine the time-scale and environmental dependence of stellar cluster disruption, we have undertaken an analysis of the unprecedented multipointing (seven), multiwavelength (U, B, V, Hα, and I) Hubble Space Telescope imaging survey of the nearby, face-on spiral galaxy M83. The images are used to locate stellar clusters and stellar associations throughout the galaxy. Estimation of cluster properties (age, mass, and extinction) was done through a comparison of their spectral energy distributions with simple stellar population models. We constructed the largest catalogue of stellar clusters and associations in this galaxy to-date, with ˜1800 sources with masses above ˜5000 M⊙ and ages younger than ˜300 Myr. In this Letter, we focus on the age distribution of the resulting clusters and associations. In particular, we explicitly test whether the age distributions are related with the ambient environment. Our results are in excellent agreement with previous studies of age distributions in the centre of the galaxy, which gives us confidence to expand out to search for similarities or differences in the other fields which sample different environments. We find that the age distribution of the clusters inside M83 varies strongly as a function of position within the galaxy, indicating a strong correlation with the galactic environment. If the age distributions are approximated as a power law of the form {d N/dt}∝ t^{ζ }, we find ζ values between 0 and -0.62 (ζ ˜ -0.40 for the whole galaxy), in good agreement with previous results and theoretical predictions. L101

  7. The distribution of ejected brown dwarfs in clusters

    NASA Astrophysics Data System (ADS)

    Goodwin, S. P.; Hubber, D. A.; Moraux, E.; Whitworth, A. P.

    2005-12-01

    We examine the spatial distribution of brown dwarfs produced by the decay of small-N stellar systems as expected from the embryo ejection scenario. We model a cluster of several hundred stars grouped into 'cores' of a few stars/brown dwarfs. These cores decay, preferentially ejecting their lowest-mass members. Brown dwarfs are found to have a wider spatial distribution than stars, however once the effects of limited survey areas and unresolved binaries are taken into account it can be difficult to distinguish between clusters with many or no ejections. A large difference between the distributions probably indicates that ejections have occurred, however similar distributions sometimes arise even with ejections. Thus the spatial distribution of brown dwarfs is not necessarily a good discriminator between ejection and non-ejection scenarios.

  8. An artificial immune system algorithm approach for reconfiguring distribution network

    NASA Astrophysics Data System (ADS)

    Syahputra, Ramadoni; Soesanti, Indah

    2017-08-01

    This paper proposes an artificial immune system (AIS) algorithm approach for reconfiguring distribution network with the presence distributed generators (DG). The distribution network with high-performance is a network that has a low power loss, better voltage profile, and loading balance among feeders. The task for improving the performance of the distribution network is optimization of network configuration. The optimization has become a necessary study with the presence of DG in entire networks. In this work, optimization of network configuration is based on an AIS algorithm. The methodology has been tested in a model of 33 bus IEEE radial distribution networks with and without DG integration. The results have been showed that the optimal configuration of the distribution network is able to reduce power loss and to improve the voltage profile of the distribution network significantly.

  9. A novel harmony search-K means hybrid algorithm for clustering gene expression data.

    PubMed

    Nazeer, Ka Abdul; Sebastian, Mp; Kumar, Sd Madhu

    2013-01-01

    Recent progress in bioinformatics research has led to the accumulation of huge quantities of biological data at various data sources. The DNA microarray technology makes it possible to simultaneously analyze large number of genes across different samples. Clustering of microarray data can reveal the hidden gene expression patterns from large quantities of expression data that in turn offers tremendous possibilities in functional genomics, comparative genomics, disease diagnosis and drug development. The k- ¬means clustering algorithm is widely used for many practical applications. But the original k-¬means algorithm has several drawbacks. It is computationally expensive and generates locally optimal solutions based on the random choice of the initial centroids. Several methods have been proposed in the literature for improving the performance of the k-¬means algorithm. A meta-heuristic optimization algorithm named harmony search helps find out near-global optimal solutions by searching the entire solution space. Low clustering accuracy of the existing algorithms limits their use in many crucial applications of life sciences. In this paper we propose a novel Harmony Search-K means Hybrid (HSKH) algorithm for clustering the gene expression data. Experimental results show that the proposed algorithm produces clusters with better accuracy in comparison with the existing algorithms.

  10. Performance Assessment of the Optical Transient Detector and Lightning Imaging Sensor. Part 2; Clustering Algorithm

    NASA Technical Reports Server (NTRS)

    Mach, Douglas M.; Christian, Hugh J.; Blakeslee, Richard; Boccippio, Dennis J.; Goodman, Steve J.; Boeck, William

    2006-01-01

    We describe the clustering algorithm used by the Lightning Imaging Sensor (LIS) and the Optical Transient Detector (OTD) for combining the lightning pulse data into events, groups, flashes, and areas. Events are single pixels that exceed the LIS/OTD background level during a single frame (2 ms). Groups are clusters of events that occur within the same frame and in adjacent pixels. Flashes are clusters of groups that occur within 330 ms and either 5.5 km (for LIS) or 16.5 km (for OTD) of each other. Areas are clusters of flashes that occur within 16.5 km of each other. Many investigators are utilizing the LIS/OTD flash data; therefore, we test how variations in the algorithms for the event group and group-flash clustering affect the flash count for a subset of the LIS data. We divided the subset into areas with low (1-3), medium (4-15), high (16-63), and very high (64+) flashes to see how changes in the clustering parameters affect the flash rates in these different sizes of areas. We found that as long as the cluster parameters are within about a factor of two of the current values, the flash counts do not change by more than about 20%. Therefore, the flash clustering algorithm used by the LIS and OTD sensors create flash rates that are relatively insensitive to reasonable variations in the clustering algorithms.

  11. The distribution of saturated clusters in wetted granular materials

    NASA Astrophysics Data System (ADS)

    Li, Shuoqi; Hanaor, Dorian; Gan, Yixiang

    2017-06-01

    The hydro-mechanical behaviour of partially saturated granular materials is greatly influenced by the spatial and temporal distribution of liquid within the media. The aim of this paper is to characterise the distribution of saturated clusters in granular materials using an optical imaging method under different water drainage conditions. A saturated cluster is formed when a liquid phase fully occupies the pore space between solid grains in a localized region. The samples considered here were prepared by vibrating mono-sized glass beads to form closely packed assemblies in a rectangular container. A range of drainage conditions were applied to the specimen by tilting the container and employing different flow rates, and the liquid pressure was recorded at different positions in the experimental cell. The formation of saturated clusters during the liquid withdrawal processes is governed by three competing mechanisms arising from viscous, capillary, and gravitational forces. When the flow rate is sufficiently large and the gravity component is sufficiently small, the viscous force tends to destabilize the liquid front leading to the formation of narrow fingers of saturated material. As the water channels along these liquid fingers break, saturated clusters are formed inside the specimen. Subsequently, a spatial and temporal distribution of saturated clusters can be observed. We investigated the resulting saturated cluster distribution as a function of flow rate and gravity to achieve a fundamental understanding of the formation and evolution of such clusters in partially saturated granular materials. This study serves as a bridge between pore-scale behavior and the overall hydro-mechanical characteristics in partially saturated soils.

  12. A Novel Artificial Bee Colony Based Clustering Algorithm for Categorical Data

    PubMed Central

    2015-01-01

    Data with categorical attributes are ubiquitous in the real world. However, existing partitional clustering algorithms for categorical data are prone to fall into local optima. To address this issue, in this paper we propose a novel clustering algorithm, ABC-K-Modes (Artificial Bee Colony clustering based on K-Modes), based on the traditional k-modes clustering algorithm and the artificial bee colony approach. In our approach, we first introduce a one-step k-modes procedure, and then integrate this procedure with the artificial bee colony approach to deal with categorical data. In the search process performed by scout bees, we adopt the multi-source search inspired by the idea of batch processing to accelerate the convergence of ABC-K-Modes. The performance of ABC-K-Modes is evaluated by a series of experiments in comparison with that of the other popular algorithms for categorical data. PMID:25993469

  13. A Novel Automatic Detection System for ECG Arrhythmias Using Maximum Margin Clustering with Immune Evolutionary Algorithm

    PubMed Central

    Zhu, Bohui; Ding, Yongsheng; Hao, Kuangrong

    2013-01-01

    This paper presents a novel maximum margin clustering method with immune evolution (IEMMC) for automatic diagnosis of electrocardiogram (ECG) arrhythmias. This diagnostic system consists of signal processing, feature extraction, and the IEMMC algorithm for clustering of ECG arrhythmias. First, raw ECG signal is processed by an adaptive ECG filter based on wavelet transforms, and waveform of the ECG signal is detected; then, features are extracted from ECG signal to cluster different types of arrhythmias by the IEMMC algorithm. Three types of performance evaluation indicators are used to assess the effect of the IEMMC method for ECG arrhythmias, such as sensitivity, specificity, and accuracy. Compared with K-means and iterSVR algorithms, the IEMMC algorithm reflects better performance not only in clustering result but also in terms of global search ability and convergence ability, which proves its effectiveness for the detection of ECG arrhythmias. PMID:23690875

  14. Estimating the abundance of clustered animal population by using adaptive cluster sampling and negative binomial distribution

    NASA Astrophysics Data System (ADS)

    Bo, Yizhou; Shifa, Naima

    2013-09-01

    An estimator for finding the abundance of a rare, clustered and mobile population has been introduced. This model is based on adaptive cluster sampling (ACS) to identify the location of the population and negative binomial distribution to estimate the total in each site. To identify the location of the population we consider both sampling with replacement (WR) and sampling without replacement (WOR). Some mathematical properties of the model are also developed.

  15. Parallel matrix transpose algorithms on distributed memory concurrent computers

    SciTech Connect

    Choi, J.; Walker, D.W.; Dongarra, J.J. |

    1993-10-01

    This paper describes parallel matrix transpose algorithms on distributed memory concurrent processors. It is assumed that the matrix is distributed over a P x Q processor template with a block scattered data distribution. P, Q, and the block size can be arbitrary, so the algorithms have wide applicability. The communication schemes of the algorithms are determined by the greatest common divisor (GCD) of P and Q. If P and Q are relatively prime, the matrix transpose algorithm involves complete exchange communication. If P and Q are not relatively prime, processors are divided into GCD groups and the communication operations are overlapped for different groups of processors. Processors transpose GCD wrapped diagonal blocks simultaneously, and the matrix can be transposed with LCM/GCD steps, where LCM is the least common multiple of P and Q. The algorithms make use of non-blocking, point-to-point communication between processors. The use of nonblocking communication allows a processor to overlap the messages that it sends to different processors, thereby avoiding unnecessary synchronization. Combined with the matrix multiplication routine, C = A{center_dot}B, the algorithms are used to compute parallel multiplications of transposed matrices, C = A{sup T}{center_dot}B{sup T}, in the PUMMA package. Details of the parallel implementation of the algorithms are given, and results are presented for runs on the Intel Touchstone Delta computer.

  16. A Local Scalable Distributed Expectation Maximization Algorithm for Large Peer-to-Peer Networks

    NASA Technical Reports Server (NTRS)

    Bhaduri, Kanishka; Srivastava, Ashok N.

    2009-01-01

    This paper offers a local distributed algorithm for expectation maximization in large peer-to-peer environments. The algorithm can be used for a variety of well-known data mining tasks in a distributed environment such as clustering, anomaly detection, target tracking to name a few. This technology is crucial for many emerging peer-to-peer applications for bioinformatics, astronomy, social networking, sensor networks and web mining. Centralizing all or some of the data for building global models is impractical in such peer-to-peer environments because of the large number of data sources, the asynchronous nature of the peer-to-peer networks, and dynamic nature of the data/network. The distributed algorithm we have developed in this paper is provably-correct i.e. it converges to the same result compared to a similar centralized algorithm and can automatically adapt to changes to the data and the network. We show that the communication overhead of the algorithm is very low due to its local nature. This monitoring algorithm is then used as a feedback loop to sample data from the network and rebuild the model when it is outdated. We present thorough experimental results to verify our theoretical claims.

  17. Optimization of self-interstitial clusters in 3C-SiC with genetic algorithm

    NASA Astrophysics Data System (ADS)

    Ko, Hyunseok; Kaczmarowski, Amy; Szlufarska, Izabela; Morgan, Dane

    2017-08-01

    Under irradiation, SiC develops damage commonly referred to as black spot defects, which are speculated to be self-interstitial atom clusters. To understand the evolution of these defect clusters and their impacts (e.g., through radiation induced swelling) on the performance of SiC in nuclear applications, it is important to identify the cluster composition, structure, and shape. In this work the genetic algorithm code StructOpt was utilized to identify groundstate cluster structures in 3C-SiC. The genetic algorithm was used to explore clusters of up to ∼30 interstitials of C-only, Si-only, and Si-C mixtures embedded in the SiC lattice. We performed the structure search using Hamiltonians from both density functional theory and empirical potentials. The thermodynamic stability of clusters was investigated in terms of their composition (with a focus on Si-only, C-only, and stoichiometric) and shape (spherical vs. planar), as a function of the cluster size (n). Our results suggest that large Si-only clusters are likely unstable, and clusters are predominantly C-only for n ≤ 10 and stoichiometric for n > 10. The results imply that there is an evolution of the shape of the most stable clusters, where small clusters are stable in more spherical geometries while larger clusters are stable in more planar configurations. We also provide an estimated energy vs. size relationship, E(n), for use in future analysis.

  18. Hyperspectral image clustering method based on artificial bee colony algorithm and Markov random fields

    NASA Astrophysics Data System (ADS)

    Sun, Xu; Yang, Lina; Gao, Lianru; Zhang, Bing; Li, Shanshan; Li, Jun

    2015-01-01

    Center-oriented hyperspectral image clustering methods have been widely applied to hyperspectral remote sensing image processing; however, the drawbacks are obvious, including the over-simplicity of computing models and underutilized spatial information. In recent years, some studies have been conducted trying to improve this situation. We introduce the artificial bee colony (ABC) and Markov random field (MRF) algorithms to propose an ABC-MRF-cluster model to solve the problems mentioned above. In this model, a typical ABC algorithm framework is adopted in which cluster centers and iteration conditional model algorithm's results are considered as feasible solutions and objective functions separately, and MRF is modified to be capable of dealing with the clustering problem. Finally, four datasets and two indices are used to show that the application of ABC-cluster and ABC-MRF-cluster methods could help to obtain better image accuracy than conventional methods. Specifically, the ABC-cluster method is superior when used for a higher power of spectral discrimination, whereas the ABC-MRF-cluster method can provide better results when used for an adjusted random index. In experiments on simulated images with different signal-to-noise ratios, ABC-cluster and ABC-MRF-cluster showed good stability.

  19. Label propagation algorithm based on edge clustering coefficient for community detection in complex networks

    NASA Astrophysics Data System (ADS)

    Zhang, Xian-Kun; Tian, Xue; Li, Ya-Nan; Song, Chen

    2014-08-01

    The label propagation algorithm (LPA) is a graph-based semi-supervised learning algorithm, which can predict the information of unlabeled nodes by a few of labeled nodes. It is a community detection method in the field of complex networks. This algorithm is easy to implement with low complexity and the effect is remarkable. It is widely applied in various fields. However, the randomness of the label propagation leads to the poor robustness of the algorithm, and the classification result is unstable. This paper proposes a LPA based on edge clustering coefficient. The node in the network selects a neighbor node whose edge clustering coefficient is the highest to update the label of node rather than a random neighbor node, so that we can effectively restrain the random spread of the label. The experimental results show that the LPA based on edge clustering coefficient has made improvement in the stability and accuracy of the algorithm.

  20. Improved fuzzy clustering algorithms in segmentation of DC-enhanced breast MRI.

    PubMed

    Kannan, S R; Ramathilagam, S; Devi, Pandiyarajan; Sathya, A

    2012-02-01

    Segmentation of medical images is a difficult and challenging problem due to poor image contrast and artifacts that result in missing or diffuse organ/tissue boundaries. Many researchers have applied various techniques however fuzzy c-means (FCM) based algorithms is more effective compared to other methods. The objective of this work is to develop some robust fuzzy clustering segmentation systems for effective segmentation of DCE - breast MRI. This paper obtains the robust fuzzy clustering algorithms by incorporating kernel methods, penalty terms, tolerance of the neighborhood attraction, additional entropy term and fuzzy parameters. The initial centers are obtained using initialization algorithm to reduce the computation complexity and running time of proposed algorithms. Experimental works on breast images show that the proposed algorithms are effective to improve the similarity measurement, to handle large amount of noise, to have better results in dealing the data corrupted by noise, and other artifacts. The clustering results of proposed methods are validated using Silhouette Method.

  1. Methods for evaluating clustering algorithms for gene expression data using a reference set of functional classes.

    PubMed

    Datta, Susmita; Datta, Somnath

    2006-08-31

    A cluster analysis is the most commonly performed procedure (often regarded as a first step) on a set of gene expression profiles. In most cases, a post hoc analysis is done to see if the genes in the same clusters can be functionally correlated. While past successes of such analyses have often been reported in a number of microarray studies (most of which used the standard hierarchical clustering, UPGMA, with one minus the Pearson's correlation coefficient as a measure of dissimilarity), often times such groupings could be misleading. More importantly, a systematic evaluation of the entire set of clusters produced by such unsupervised procedures is necessary since they also contain genes that are seemingly unrelated or may have more than one common function. Here we quantify the performance of a given unsupervised clustering algorithm applied to a given microarray study in terms of its ability to produce biologically meaningful clusters using a reference set of functional classes. Such a reference set may come from prior biological knowledge specific to a microarray study or may be formed using the growing databases of gene ontologies (GO) for the annotated genes of the relevant species. In this paper, we introduce two performance measures for evaluating the results of a clustering algorithm in its ability to produce biologically meaningful clusters. The first measure is a biological homogeneity index (BHI). As the name suggests, it is a measure of how biologically homogeneous the clusters are. This can be used to quantify the performance of a given clustering algorithm such as UPGMA in grouping genes for a particular data set and also for comparing the performance of a number of competing clustering algorithms applied to the same data set. The second performance measure is called a biological stability index (BSI). For a given clustering algorithm and an expression data set, it measures the consistency of the clustering algorithm's ability to produce biologically

  2. An improved fuzzy c-means clustering algorithm based on shadowed sets and PSO.

    PubMed

    Zhang, Jian; Shen, Ling

    2014-01-01

    To organize the wide variety of data sets automatically and acquire accurate classification, this paper presents a modified fuzzy c-means algorithm (SP-FCM) based on particle swarm optimization (PSO) and shadowed sets to perform feature clustering. SP-FCM introduces the global search property of PSO to deal with the problem of premature convergence of conventional fuzzy clustering, utilizes vagueness balance property of shadowed sets to handle overlapping among clusters, and models uncertainty in class boundaries. This new method uses Xie-Beni index as cluster validity and automatically finds the optimal cluster number within a specific range with cluster partitions that provide compact and well-separated clusters. Experiments show that the proposed approach significantly improves the clustering effect.

  3. An Improved Fuzzy c-Means Clustering Algorithm Based on Shadowed Sets and PSO

    PubMed Central

    Zhang, Jian; Shen, Ling

    2014-01-01

    To organize the wide variety of data sets automatically and acquire accurate classification, this paper presents a modified fuzzy c-means algorithm (SP-FCM) based on particle swarm optimization (PSO) and shadowed sets to perform feature clustering. SP-FCM introduces the global search property of PSO to deal with the problem of premature convergence of conventional fuzzy clustering, utilizes vagueness balance property of shadowed sets to handle overlapping among clusters, and models uncertainty in class boundaries. This new method uses Xie-Beni index as cluster validity and automatically finds the optimal cluster number within a specific range with cluster partitions that provide compact and well-separated clusters. Experiments show that the proposed approach significantly improves the clustering effect. PMID:25477953

  4. Unsupervised Cryo-EM Data Clustering through Adaptively Constrained K-Means Algorithm.

    PubMed

    Xu, Yaofang; Wu, Jiayi; Yin, Chang-Cheng; Mao, Youdong

    2016-01-01

    In single-particle cryo-electron microscopy (cryo-EM), K-means clustering algorithm is widely used in unsupervised 2D classification of projection images of biological macromolecules. 3D ab initio reconstruction requires accurate unsupervised classification in order to separate molecular projections of distinct orientations. Due to background noise in single-particle images and uncertainty of molecular orientations, traditional K-means clustering algorithm may classify images into wrong classes and produce classes with a large variation in membership. Overcoming these limitations requires further development on clustering algorithms for cryo-EM data analysis. We propose a novel unsupervised data clustering method building upon the traditional K-means algorithm. By introducing an adaptive constraint term in the objective function, our algorithm not only avoids a large variation in class sizes but also produces more accurate data clustering. Applications of this approach to both simulated and experimental cryo-EM data demonstrate that our algorithm is a significantly improved alterative to the traditional K-means algorithm in single-particle cryo-EM analysis.

  5. Unsupervised Cryo-EM Data Clustering through Adaptively Constrained K-Means Algorithm

    PubMed Central

    Xu, Yaofang; Wu, Jiayi; Yin, Chang-Cheng; Mao, Youdong

    2016-01-01

    In single-particle cryo-electron microscopy (cryo-EM), K-means clustering algorithm is widely used in unsupervised 2D classification of projection images of biological macromolecules. 3D ab initio reconstruction requires accurate unsupervised classification in order to separate molecular projections of distinct orientations. Due to background noise in single-particle images and uncertainty of molecular orientations, traditional K-means clustering algorithm may classify images into wrong classes and produce classes with a large variation in membership. Overcoming these limitations requires further development on clustering algorithms for cryo-EM data analysis. We propose a novel unsupervised data clustering method building upon the traditional K-means algorithm. By introducing an adaptive constraint term in the objective function, our algorithm not only avoids a large variation in class sizes but also produces more accurate data clustering. Applications of this approach to both simulated and experimental cryo-EM data demonstrate that our algorithm is a significantly improved alterative to the traditional K-means algorithm in single-particle cryo-EM analysis. PMID:27959895

  6. A new clustering algorithm applicable to multispectral and polarimetric SAR images

    NASA Technical Reports Server (NTRS)

    Wong, Yiu-Fai; Posner, Edward C.

    1993-01-01

    We describe an application of a scale-space clustering algorithm to the classification of a multispectral and polarimetric SAR image of an agricultural site. After the initial polarimetric and radiometric calibration and noise cancellation, we extracted a 12-dimensional feature vector for each pixel from the scattering matrix. The clustering algorithm was able to partition a set of unlabeled feature vectors from 13 selected sites, each site corresponding to a distinct crop, into 13 clusters without any supervision. The cluster parameters were then used to classify the whole image. The classification map is much less noisy and more accurate than those obtained by hierarchical rules. Starting with every point as a cluster, the algorithm works by melting the system to produce a tree of clusters in the scale space. It can cluster data in any multidimensional space and is insensitive to variability in cluster densities, sizes and ellipsoidal shapes. This algorithm, more powerful than existing ones, may be useful for remote sensing for land use.

  7. A new clustering algorithm applicable to multispectral and polarimetric SAR images

    NASA Technical Reports Server (NTRS)

    Wong, Yiu-Fai; Posner, Edward C.

    1993-01-01

    We describe an application of a scale-space clustering algorithm to the classification of a multispectral and polarimetric SAR image of an agricultural site. After the initial polarimetric and radiometric calibration and noise cancellation, we extracted a 12-dimensional feature vector for each pixel from the scattering matrix. The clustering algorithm was able to partition a set of unlabeled feature vectors from 13 selected sites, each site corresponding to a distinct crop, into 13 clusters without any supervision. The cluster parameters were then used to classify the whole image. The classification map is much less noisy and more accurate than those obtained by hierarchical rules. Starting with every point as a cluster, the algorithm works by melting the system to produce a tree of clusters in the scale space. It can cluster data in any multidimensional space and is insensitive to variability in cluster densities, sizes and ellipsoidal shapes. This algorithm, more powerful than existing ones, may be useful for remote sensing for land use.

  8. Tidal Densities of Globular Clusters and the Galactic Mass Distribution

    NASA Astrophysics Data System (ADS)

    Lee, Hyung Mok

    1990-12-01

    The tidal radii of globular clusters reflect the tidal field of the Galaxy. The mass distribution of the Galaxy thus may be obtained if the tidal fields of clusters are well known. Although large amounts of uncertainties in the determination of tidal radii have been obstacles in utilizing this method, analysis of tidal density could give independent check for the Galactic mass distribution. Recent theoretical modeling of dynamical evolution including steady Galactic tidal field shows that the observationally determined tidal radii could be systematically larger by about a factor of 1.5 compared to the theoretical values. From the analysis of entire sample of 148 globular clusters and 7 dwarf spheroidal systems compiled by Webbink(1985), we find that such reduction from observed values would make the tidal density(the mean density within the tidal radius) distribution consistent with the flat rotation curve of our Galaxy out to large distances if the velocity distribution of clusters and dwarf spheroidals with respect to the Galactic center is isotropic.

  9. Illinois Occupational Skill Standards: Finishing and Distribution Cluster.

    ERIC Educational Resources Information Center

    Illinois Occupational Skill Standards and Credentialing Council, Carbondale.

    This document, which is intended as a guide for work force preparation program providers, details the Illinois occupational skill standards for programs preparing students for employment in occupations in the finishing and distribution cluster. The document begins with a brief overview of the Illinois perspective on occupational skill standards…

  10. A review of estimation of distribution algorithms in bioinformatics

    PubMed Central

    Armañanzas, Rubén; Inza, Iñaki; Santana, Roberto; Saeys, Yvan; Flores, Jose Luis; Lozano, Jose Antonio; Peer, Yves Van de; Blanco, Rosa; Robles, Víctor; Bielza, Concha; Larrañaga, Pedro

    2008-01-01

    Evolutionary search algorithms have become an essential asset in the algorithmic toolbox for solving high-dimensional optimization problems in across a broad range of bioinformatics problems. Genetic algorithms, the most well-known and representative evolutionary search technique, have been the subject of the major part of such applications. Estimation of distribution algorithms (EDAs) offer a novel evolutionary paradigm that constitutes a natural and attractive alternative to genetic algorithms. They make use of a probabilistic model, learnt from the promising solutions, to guide the search process. In this paper, we set out a basic taxonomy of EDA techniques, underlining the nature and complexity of the probabilistic model of each EDA variant. We review a set of innovative works that make use of EDA techniques to solve challenging bioinformatics problems, emphasizing the EDA paradigm's potential for further research in this domain. PMID:18822112

  11. An Efficient Document Clustering Algorithm and Its Application to a Document Browser.

    ERIC Educational Resources Information Center

    Tanaka, Hideki; Kumano, Tadashi; Uratani, Noriyoshi; Ehara, Terumasa

    1999-01-01

    Presents a document-clustering algorithm that uses a term frequency vector for each document in a Japanese collection to produce a hierarchy in the form of a document classification tree. Introduces an application of this algorithm to a Japanese-to-English translation-aid system. (Author/LRW)

  12. Impacts of Time Delays on Distributed Algorithms for Economic Dispatch

    SciTech Connect

    Yang, Tao; Wu, Di; Sun, Yannan; Lian, Jianming

    2015-07-26

    Economic dispatch problem (EDP) is an important problem in power systems. It can be formulated as an optimization problem with the objective to minimize the total generation cost subject to the power balance constraint and generator capacity limits. Recently, several consensus-based algorithms have been proposed to solve EDP in a distributed manner. However, impacts of communication time delays on these distributed algorithms are not fully understood, especially for the case where the communication network is directed, i.e., the information exchange is unidirectional. This paper investigates communication time delay effects on a distributed algorithm for directed communication networks. The algorithm has been tested by applying time delays to different types of information exchange. Several case studies are carried out to evaluate the effectiveness and performance of the algorithm in the presence of time delays in communication networks. It is found that time delay effects have negative effects on the convergence rate, and can even result in an incorrect converge value or fail the algorithm to converge.

  13. Distributed query plan generation using multiobjective genetic algorithm.

    PubMed

    Panicker, Shina; Kumar, T V Vijay

    2014-01-01

    A distributed query processing strategy, which is a key performance determinant in accessing distributed databases, aims to minimize the total query processing cost. One way to achieve this is by generating efficient distributed query plans that involve fewer sites for processing a query. In the case of distributed relational databases, the number of possible query plans increases exponentially with respect to the number of relations accessed by the query and the number of sites where these relations reside. Consequently, computing optimal distributed query plans becomes a complex problem. This distributed query plan generation (DQPG) problem has already been addressed using single objective genetic algorithm, where the objective is to minimize the total query processing cost comprising the local processing cost (LPC) and the site-to-site communication cost (CC). In this paper, this DQPG problem is formulated and solved as a biobjective optimization problem with the two objectives being minimize total LPC and minimize total CC. These objectives are simultaneously optimized using a multiobjective genetic algorithm NSGA-II. Experimental comparison of the proposed NSGA-II based DQPG algorithm with the single objective genetic algorithm shows that the former performs comparatively better and converges quickly towards optimal solutions for an observed crossover and mutation probability.

  14. GenClust: a genetic algorithm for clustering gene expression data.

    PubMed

    Di Gesú, Vito; Giancarlo, Raffaele; Lo Bosco, Giosué; Raimondi, Alessandra; Scaturro, Davide

    2005-12-07

    Clustering is a key step in the analysis of gene expression data, and in fact, many classical clustering algorithms are used, or more innovative ones have been designed and validated for the task. Despite the widespread use of artificial intelligence techniques in bioinformatics and, more generally, data analysis, there are very few clustering algorithms based on the genetic paradigm, yet that paradigm has great potential in finding good heuristic solutions to a difficult optimization problem such as clustering. GenClust is a new genetic algorithm for clustering gene expression data. It has two key features: (a) a novel coding of the search space that is simple, compact and easy to update; (b) it can be used naturally in conjunction with data driven internal validation methods. We have experimented with the FOM methodology, specifically conceived for validating clusters of gene expression data. The validity of GenClust has been assessed experimentally on real data sets, both with the use of validation measures and in comparison with other algorithms, i.e., Average Link, Cast, Click and K-means. Experiments show that none of the algorithms we have used is markedly superior to the others across data sets and validation measures; i.e., in many cases the observed differences between the worst and best performing algorithm may be statistically insignificant and they could be considered equivalent. However, there are cases in which an algorithm may be better than others and therefore worthwhile. In particular, experiments for GenClust show that, although simple in its data representation, it converges very rapidly to a local optimum and that its ability to identify meaningful clusters is comparable, and sometimes superior, to that of more sophisticated algorithms. In addition, it is well suited for use in conjunction with data driven internal validation measures and, in particular, the FOM methodology.

  15. GenClust: A genetic algorithm for clustering gene expression data

    PubMed Central

    Di Gesú, Vito; Giancarlo, Raffaele; Lo Bosco, Giosué; Raimondi, Alessandra; Scaturro, Davide

    2005-01-01

    Background Clustering is a key step in the analysis of gene expression data, and in fact, many classical clustering algorithms are used, or more innovative ones have been designed and validated for the task. Despite the widespread use of artificial intelligence techniques in bioinformatics and, more generally, data analysis, there are very few clustering algorithms based on the genetic paradigm, yet that paradigm has great potential in finding good heuristic solutions to a difficult optimization problem such as clustering. Results GenClust is a new genetic algorithm for clustering gene expression data. It has two key features: (a) a novel coding of the search space that is simple, compact and easy to update; (b) it can be used naturally in conjunction with data driven internal validation methods. We have experimented with the FOM methodology, specifically conceived for validating clusters of gene expression data. The validity of GenClust has been assessed experimentally on real data sets, both with the use of validation measures and in comparison with other algorithms, i.e., Average Link, Cast, Click and K-means. Conclusion Experiments show that none of the algorithms we have used is markedly superior to the others across data sets and validation measures; i.e., in many cases the observed differences between the worst and best performing algorithm may be statistically insignificant and they could be considered equivalent. However, there are cases in which an algorithm may be better than others and therefore worthwhile. In particular, experiments for GenClust show that, although simple in its data representation, it converges very rapidly to a local optimum and that its ability to identify meaningful clusters is comparable, and sometimes superior, to that of more sophisticated algorithms. In addition, it is well suited for use in conjunction with data driven internal validation measures and, in particular, the FOM methodology. PMID:16336639

  16. The loop-cluster algorithm for the case of the 6 vertex model

    NASA Astrophysics Data System (ADS)

    Evertz, Hans Gerd; Marcu, Mihai

    1993-03-01

    We present the loop algorithm, a new type of cluster algorithm that we recently introduced for the F model. Using the framework of Kandel and Domany, we show how to generalize the algorithm to the arrow flip symmetric 6 vertex model. We propose the principle of least possible freezing as the guide to choosing the values of free parameters in the algorithm. Finally, we briefly discuss the application of our algorithm to simulations of quantum spin systems. In particular, all necessary information is provided for the simulation of spin {1}/{2} Heisenberg and ¢x¢x z models.

  17. Mesh Algorithms for PDE with Sieve I: Mesh Distribution

    DOE PAGES

    Knepley, Matthew G.; Karpeev, Dmitry A.

    2009-01-01

    We have developed a new programming framework, called Sieve, to support parallel numerical partial differential equation(s) (PDE) algorithms operating over distributed meshes. We have also developed a reference implementation of Sieve in C++ as a library of generic algorithms operating on distributed containers conforming to the Sieve interface. Sieve makes instances of the incidence relation, or arrows, the conceptual first-class objects represented in the containers. Further, generic algorithms acting on this arrow container are systematically used to provide natural geometric operations on the topology and also, through duality, on the data. Finally, coverings and duality are used to encode notmore » only individual meshes, but all types of hierarchies underlying PDE data structures, including multigrid and mesh partitions. In order to demonstrate the usefulness of the framework, we show how the mesh partition data can be represented and manipulated using the same fundamental mechanisms used to represent meshes. We present the complete description of an algorithm to encode a mesh partition and then distribute a mesh, which is independent of the mesh dimension, element shape, or embedding. Moreover, data associated with the mesh can be similarly distributed with exactly the same algorithm. The use of a high level of abstraction within the Sieve leads to several benefits in terms of code reuse, simplicity, and extensibility. We discuss these benefits and compare our approach to other existing mesh libraries.« less

  18. Semi-supervised clustering algorithm for haplotype assembly problem based on MEC model.

    PubMed

    Xu, Xin-Shun; Li, Ying-Xin

    2012-01-01

    Haplotype assembly is to infer a pair of haplotypes from localized polymorphism data. In this paper, a semi-supervised clustering algorithm-SSK (semi-supervised K-means) is proposed for it, which, to our knowledge, is the first semi-supervised clustering method for it. In SSK, some positive information is firstly extracted. The information is then used to help k-means to cluster all SNP fragments into two sets from which two haplotypes can be reconstructed. The performance of SSK is tested on both real data and simulated data. The results show that it outperforms several state-of-the-art algorithms on minimum error correction (MEC) model.

  19. Clustering box office movie with Partition Around Medoids (PAM) Algorithm based on Text Mining of Indonesian subtitle

    NASA Astrophysics Data System (ADS)

    Alfarizy, A. D.; Indahwati; Sartono, B.

    2017-03-01

    Indonesia is the largest Hollywood movie industry target market in Southeast Asia in 2015. Hollywood movies distributed in Indonesia targeted people in all range of ages including children. Low awareness of guiding children while watching movies make them could watch any rated films even the unsuitable ones for their ages. Even after being translated into Bahasa and passed the censorship phase, words that uncomfortable for children to watch still exist. The purpose of this research is to cluster box office Hollywood movies based on Indonesian subtitle, revenue, IMDb user rating and genres as one of the reference for adults to choose right movies for their children to watch. Text mining is used to extract words from the subtitles and count the frequency for three group of words (bad words, sexual words and terror words), while Partition Around Medoids (PAM) Algorithm with Gower similarity coefficient as proximity matrix is used as clustering method. We clustered 624 movies from 2006 until first half of 2016 from IMDb. Cluster with highest silhouette coefficient value (0.36) is the one with 5 clusters. Animation, Adventure and Comedy movies with high revenue like in cluster 5 is recommended for children to watch, while Comedy movies with high revenue like in cluster 4 should be avoided to watch.

  20. CHRONICLE: A Two-Stage Density-Based Clustering Algorithm for Dynamic Networks

    NASA Astrophysics Data System (ADS)

    Kim, Min-Soo; Han, Jiawei

    Information networks, such as social networks and that extracted from bibliographic data, are changing dynamically over time. It is crucial to discover time-evolving communities in dynamic networks. In this paper, we study the problem of finding time-evolving communities such that each community freely forms, evolves, and dissolves for any time period. Although the previous t-partite graph based methods are quite effective for discovering such communities from large-scale dynamic networks, they have some weak points such as finding only stable clusters of single path type and not being scalable w.r.t. the time period. We propose CHRONICLE, an efficient clustering algorithm that discovers not only clusters of single path type but also clusters of path group type. In order to find clusters of both types and also control the dynamicity of clusters, CHRONICLE performs the two-stage density-based clustering, which performs the 2nd-stage density-based clustering for the t-partite graph constructed from the 1st-stage density-based clustering result for each timestamp network. For a given data set, CHRONICLE finds all clusters in a fixed time by using a fixed amount of memory, regardless of the number of clusters and the length of clusters. Experimental results using real data sets show that CHRONICLE finds a wider range of clusters in a shorter time with a much smaller amount of memory than the previous method.

  1. A clustering algorithm based on two distance functions for MEC model.

    PubMed

    Wang, Ying; Feng, Enmin; Wang, Ruisheng

    2007-04-01

    Haplotype reconstruction, based on aligned single nucleotide polymorphism (SNP) fragments, is to infer a pair of haplotypes from localized polymorphism data gathered through short genome fragment assembly. This paper first presents two distance functions, which are used to measure the difference degree and similarity degree between SNP fragments. Based on the two distance functions, a clustering algorithm is proposed in order to solve MEC model. The algorithm involves two sections. One is to determine the initial haplotype pair, the other concerns with inferring true haplotype pair by re-clustering. The comparison results prove that our algorithm utilizing two distance functions is effective and feasible.

  2. Empirical relations between static and dynamic exponents for Ising model cluster algorithms

    NASA Astrophysics Data System (ADS)

    Coddington, Paul D.; Baillie, Clive F.

    1992-02-01

    We have measured the autocorrelations for the Swendsen-Wang and the Wolff cluster update algorithms for the Ising model in two, three, and four dimensions. The data for the Wolff algorithm suggest that the autocorrelations are linearly related to the specific heat, in which case the dynamic critical exponent is zint,EW=α/ν. For the Swendsen-Wang algorithm, scaling the autocorrelations by the average maximum cluster size gives either a constant or a logarithm, which implies that zint,ESW=β/ν for the Ising model.

  3. A Hybrid Algorithm for Clustering of Time Series Data Based on Affinity Search Technique

    PubMed Central

    Aghabozorgi, Saeed; Ying Wah, Teh; Herawan, Tutut; Jalab, Hamid A.; Shaygan, Mohammad Amin; Jalali, Alireza

    2014-01-01

    Time series clustering is an important solution to various problems in numerous fields of research, including business, medical science, and finance. However, conventional clustering algorithms are not practical for time series data because they are essentially designed for static data. This impracticality results in poor clustering accuracy in several systems. In this paper, a new hybrid clustering algorithm is proposed based on the similarity in shape of time series data. Time series data are first grouped as subclusters based on similarity in time. The subclusters are then merged using the k-Medoids algorithm based on similarity in shape. This model has two contributions: (1) it is more accurate than other conventional and hybrid approaches and (2) it determines the similarity in shape among time series data with a low complexity. To evaluate the accuracy of the proposed model, the model is tested extensively using syntactic and real-world time series datasets. PMID:24982966

  4. An Enhanced PSO-Based Clustering Energy Optimization Algorithm for Wireless Sensor Network.

    PubMed

    Vimalarani, C; Subramanian, R; Sivanandam, S N

    2016-01-01

    Wireless Sensor Network (WSN) is a network which formed with a maximum number of sensor nodes which are positioned in an application environment to monitor the physical entities in a target area, for example, temperature monitoring environment, water level, monitoring pressure, and health care, and various military applications. Mostly sensor nodes are equipped with self-supported battery power through which they can perform adequate operations and communication among neighboring nodes. Maximizing the lifetime of the Wireless Sensor networks, energy conservation measures are essential for improving the performance of WSNs. This paper proposes an Enhanced PSO-Based Clustering Energy Optimization (EPSO-CEO) algorithm for Wireless Sensor Network in which clustering and clustering head selection are done by using Particle Swarm Optimization (PSO) algorithm with respect to minimizing the power consumption in WSN. The performance metrics are evaluated and results are compared with competitive clustering algorithm to validate the reduction in energy consumption.

  5. An improved clustering algorithm of tunnel monitoring data for cloud computing.

    PubMed

    Zhong, Luo; Tang, KunHao; Li, Lin; Yang, Guang; Ye, JingJing

    2014-01-01

    With the rapid development of urban construction, the number of urban tunnels is increasing and the data they produce become more and more complex. It results in the fact that the traditional clustering algorithm cannot handle the mass data of the tunnel. To solve this problem, an improved parallel clustering algorithm based on k-means has been proposed. It is a clustering algorithm using the MapReduce within cloud computing that deals with data. It not only has the advantage of being used to deal with mass data but also is more efficient. Moreover, it is able to compute the average dissimilarity degree of each cluster in order to clean the abnormal data.

  6. A New Collaborative Recommendation Approach Based on Users Clustering Using Artificial Bee Colony Algorithm

    PubMed Central

    Ju, Chunhua

    2013-01-01

    Although there are many good collaborative recommendation methods, it is still a challenge to increase the accuracy and diversity of these methods to fulfill users' preferences. In this paper, we propose a novel collaborative filtering recommendation approach based on K-means clustering algorithm. In the process of clustering, we use artificial bee colony (ABC) algorithm to overcome the local optimal problem caused by K-means. After that we adopt the modified cosine similarity to compute the similarity between users in the same clusters. Finally, we generate recommendation results for the corresponding target users. Detailed numerical analysis on a benchmark dataset MovieLens and a real-world dataset indicates that our new collaborative filtering approach based on users clustering algorithm outperforms many other recommendation methods. PMID:24381525

  7. An Improved Clustering Algorithm of Tunnel Monitoring Data for Cloud Computing

    PubMed Central

    Zhong, Luo; Tang, KunHao; Li, Lin; Yang, Guang; Ye, JingJing

    2014-01-01

    With the rapid development of urban construction, the number of urban tunnels is increasing and the data they produce become more and more complex. It results in the fact that the traditional clustering algorithm cannot handle the mass data of the tunnel. To solve this problem, an improved parallel clustering algorithm based on k-means has been proposed. It is a clustering algorithm using the MapReduce within cloud computing that deals with data. It not only has the advantage of being used to deal with mass data but also is more efficient. Moreover, it is able to compute the average dissimilarity degree of each cluster in order to clean the abnormal data. PMID:24982971

  8. GPU-based single-cluster algorithm for the simulation of the Ising model

    NASA Astrophysics Data System (ADS)

    Komura, Yukihiro; Okabe, Yutaka

    2012-02-01

    We present the GPU calculation with the common unified device architecture (CUDA) for the Wolff single-cluster algorithm of the Ising model. Proposing an algorithm for a quasi-block synchronization, we realize the Wolff single-cluster Monte Carlo simulation with CUDA. We perform parallel computations for the newly added spins in the growing cluster. As a result, the GPU calculation speed for the two-dimensional Ising model at the critical temperature with the linear size L = 4096 is 5.60 times as fast as the calculation speed on a current CPU core. For the three-dimensional Ising model with the linear size L = 256, the GPU calculation speed is 7.90 times as fast as the CPU calculation speed. The idea of quasi-block synchronization can be used not only in the cluster algorithm but also in many fields where the synchronization of all threads is required.

  9. A new collaborative recommendation approach based on users clustering using artificial bee colony algorithm.

    PubMed

    Ju, Chunhua; Xu, Chonghuan

    2013-01-01

    Although there are many good collaborative recommendation methods, it is still a challenge to increase the accuracy and diversity of these methods to fulfill users' preferences. In this paper, we propose a novel collaborative filtering recommendation approach based on K-means clustering algorithm. In the process of clustering, we use artificial bee colony (ABC) algorithm to overcome the local optimal problem caused by K-means. After that we adopt the modified cosine similarity to compute the similarity between users in the same clusters. Finally, we generate recommendation results for the corresponding target users. Detailed numerical analysis on a benchmark dataset MovieLens and a real-world dataset indicates that our new collaborative filtering approach based on users clustering algorithm outperforms many other recommendation methods.

  10. Learning assignment order of instances for the constrained K-means clustering algorithm.

    PubMed

    Hong, Yi; Kwong, Sam

    2009-04-01

    The sensitivity of the constrained K-means clustering algorithm (Cop-Kmeans) to the assignment order of instances is studied, and a novel assignment order learning method for Cop-Kmeans, termed as clustering Uncertainty-based Assignment order Learning Algorithm (UALA), is proposed in this paper. The main idea of UALA is to rank all instances in the data set according to their clustering uncertainties calculated by using the ensembles of multiple clustering algorithms. Experimental results on several real data sets with artificial instance-level constraints demonstrate that UALA can identify a good assignment order of instances for Cop-Kmeans. In addition, the effects of ensemble sizes on the performance of UALA are analyzed, and the generalization property of Cop-Kmeans is also studied.

  11. Functional Principal Component Analysis and Randomized Sparse Clustering Algorithm for Medical Image Analysis

    PubMed Central

    Lin, Nan; Jiang, Junhai; Guo, Shicheng; Xiong, Momiao

    2015-01-01

    Due to the advancement in sensor technology, the growing large medical image data have the ability to visualize the anatomical changes in biological tissues. As a consequence, the medical images have the potential to enhance the diagnosis of disease, the prediction of clinical outcomes and the characterization of disease progression. But in the meantime, the growing data dimensions pose great methodological and computational challenges for the representation and selection of features in image cluster analysis. To address these challenges, we first extend the functional principal component analysis (FPCA) from one dimension to two dimensions to fully capture the space variation of image the signals. The image signals contain a large number of redundant features which provide no additional information for clustering analysis. The widely used methods for removing the irrelevant features are sparse clustering algorithms using a lasso-type penalty to select the features. However, the accuracy of clustering using a lasso-type penalty depends on the selection of the penalty parameters and the threshold value. In practice, they are difficult to determine. Recently, randomized algorithms have received a great deal of attentions in big data analysis. This paper presents a randomized algorithm for accurate feature selection in image clustering analysis. The proposed method is applied to both the liver and kidney cancer histology image data from the TCGA database. The results demonstrate that the randomized feature selection method coupled with functional principal component analysis substantially outperforms the current sparse clustering algorithms in image cluster analysis. PMID:26196383

  12. Functional Principal Component Analysis and Randomized Sparse Clustering Algorithm for Medical Image Analysis.

    PubMed

    Lin, Nan; Jiang, Junhai; Guo, Shicheng; Xiong, Momiao

    2015-01-01

    Due to the advancement in sensor technology, the growing large medical image data have the ability to visualize the anatomical changes in biological tissues. As a consequence, the medical images have the potential to enhance the diagnosis of disease, the prediction of clinical outcomes and the characterization of disease progression. But in the meantime, the growing data dimensions pose great methodological and computational challenges for the representation and selection of features in image cluster analysis. To address these challenges, we first extend the functional principal component analysis (FPCA) from one dimension to two dimensions to fully capture the space variation of image the signals. The image signals contain a large number of redundant features which provide no additional information for clustering analysis. The widely used methods for removing the irrelevant features are sparse clustering algorithms using a lasso-type penalty to select the features. However, the accuracy of clustering using a lasso-type penalty depends on the selection of the penalty parameters and the threshold value. In practice, they are difficult to determine. Recently, randomized algorithms have received a great deal of attentions in big data analysis. This paper presents a randomized algorithm for accurate feature selection in image clustering analysis. The proposed method is applied to both the liver and kidney cancer histology image data from the TCGA database. The results demonstrate that the randomized feature selection method coupled with functional principal component analysis substantially outperforms the current sparse clustering algorithms in image cluster analysis.

  13. Knitting distributed cluster-state ladders with spin chains

    SciTech Connect

    Ronke, R.; D'Amico, I.; Spiller, T. P.

    2011-09-15

    Recently there has been much study on the application of spin chains to quantum state transfer and communication. Here we discuss the utilization of spin chains (set up for perfect quantum state transfer) for the knitting of distributed cluster-state structures, between spin qubits repeatedly injected and extracted at the ends of the chain. The cluster states emerge from the natural evolution of the system across different excitation number sectors. We discuss the decohering effects of errors in the injection and extraction process as well as the effects of fabrication and random errors.

  14. Geographical Distribution and Cluster Detection of Childhood Leukemia in the Metropolitan Area of Guadalajara, Mexico.

    PubMed

    Tlacuilo-Parra, Alberto; Garibaldi-Covarrubias, Roberto; Romo-Rubio, Hugo; Soto-Sumuano, Leonardo; Ruiz-Chávez, Carlos Fernando; Suárez-Arredondo, Mijail; Sánchez-Zubieta, Fernando; Gallegos-Castorena, Sergio

    2017-01-01

    Acute leukemia is the most common cancer in childhood. Analyzing the spatial distribution of acute leukemia may generate the identification of risk factors. To study the incidence rate of acute leukemia, its geographic distribution, and cluster detection in the metropolitan area of Guadalajara, Mexico. We included children under 15 years of age diagnosed with acute leukemia during the period 2010-2014 in the metropolitan area of Guadalajara. Each case was geo-referenced to street level to latitude and longitude coordinates using Quantum Geographic Information System (QGIS). Spatial clusters were found in the location of the acute leukemia cases applying the Density-Based Spatial Clustering of Applications with Noise (DBSCAN) algorithm with R statistical software. A total of 269 cases of leukemia were registered, 227 (84%) were acute lymphoblastic leukemia and 42 (16%) acute myeloblastic leukemia. The mean age was 6 ± 4 years. The mean incidence of acute leukemia was 6.44 cases/100,000 inhabitants: El Salto 10.12/100,000, Guadalajara 7.55/100,000, and Tlaquepaque 6.74/100,000. The DBSCAN found three clusters, all located within the municipality of Guadalajara. The incidence of acute leukemia in our population is higher than that in Canada and the USA. We found three spatial clusters of childhood acute lymphoblastic leukemia in the municipality of Guadalajara, suggesting the presence of local predisposing factors.

  15. Haplotype-based quantitative trait mapping using a clustering algorithm

    PubMed Central

    Li, Jing; Zhou, Yingyao; Elston, Robert C

    2006-01-01

    Background With the availability of large-scale, high-density single-nucleotide polymorphism (SNP) markers, substantial effort has been made in identifying disease-causing genes using linkage disequilibrium (LD) mapping by haplotype analysis of unrelated individuals. In addition to complex diseases, many continuously distributed quantitative traits are of primary clinical and health significance. However the development of association mapping methods using unrelated individuals for quantitative traits has received relatively less attention. Results We recently developed an association mapping method for complex diseases by mining the sharing of haplotype segments (i.e., phased genotype pairs) in affected individuals that are rarely present in normal individuals. In this paper, we extend our previous work to address the problem of quantitative trait mapping from unrelated individuals. The method is non-parametric in nature, and statistical significance can be obtained by a permutation test. It can also be incorporated into the one-way ANCOVA (analysis of covariance) framework so that other factors and covariates can be easily incorporated. The effectiveness of the approach is demonstrated by extensive experimental studies using both simulated and real data sets. The results show that our haplotype-based approach is more robust than two statistical methods based on single markers: a single SNP association test (SSA) and the Mann-Whitney U-test (MWU). The algorithm has been incorporated into our existing software package called HapMiner, which is available from our website at . Conclusion For QTL (quantitative trait loci) fine mapping, to identify QTNs (quantitative trait nucleotides) with realistic effects (the contribution of each QTN less than 10% of total variance of the trait), large samples sizes (≥ 500) are needed for all the methods. The overall performance of HapMiner is better than that of the other two methods. Its effectiveness further depends on other

  16. An algorithm for image clusters detection and identification based on color for an autonomous mobile robot

    SciTech Connect

    Uy, D.L.

    1996-02-01

    An algorithm for detection and identification of image clusters or {open_quotes}blobs{close_quotes} based on color information for an autonomous mobile robot is developed. The input image data are first processed using a crisp color fuszzyfier, a binary smoothing filter, and a median filter. The processed image data is then inputed to the image clusters detection and identification program. The program employed the concept of {open_quotes}elastic rectangle{close_quotes}that stretches in such a way that the whole blob is finally enclosed in a rectangle. A C-program is develop to test the algorithm. The algorithm is tested only on image data of 8x8 sizes with different number of blobs in them. The algorithm works very in detecting and identifying image clusters.

  17. 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.

  18. Improved K-means clustering algorithm for exploring local protein sequence motifs representing common structural property.

    PubMed

    Zhong, Wei; Altun, Gulsah; Harrison, Robert; Tai, Phang C; Pan, Yi

    2005-09-01

    Information about local protein sequence motifs is very important to the analysis of biologically significant conserved regions of protein sequences. These conserved regions can potentially determine the diverse conformation and activities of proteins. In this work, recurring sequence motifs of proteins are explored with an improved K-means clustering algorithm on a new dataset. The structural similarity of these recurring sequence clusters to produce sequence motifs is studied in order to evaluate the relationship between sequence motifs and their structures. To the best of our knowledge, the dataset used by our research is the most updated dataset among similar studies for sequence motifs. A new greedy initialization method for the K-means algorithm is proposed to improve traditional K-means clustering techniques. The new initialization method tries to choose suitable initial points, which are well separated and have the potential to form high-quality clusters. Our experiments indicate that the improved K-means algorithm satisfactorily increases the percentage of sequence segments belonging to clusters with high structural similarity. Careful comparison of sequence motifs obtained by the improved and traditional algorithms also suggests that the improved K-means clustering algorithm may discover some relatively weak and subtle sequence motifs, which are undetectable by the traditional K-means algorithms. Many biochemical tests reported in the literature show that these sequence motifs are biologically meaningful. Experimental results also indicate that the improved K-means algorithm generates more detailed sequence motifs representing common structures than previous research. Furthermore, these motifs are universally conserved sequence patterns across protein families, overcoming some weak points of other popular sequence motifs. The satisfactory result of the experiment suggests that this new K-means algorithm may be applied to other areas of bioinformatics

  19. A fast density-based clustering algorithm for real-time Internet of Things stream.

    PubMed

    Amini, Amineh; Saboohi, Hadi; Wah, Teh Ying; Herawan, Tutut

    2014-01-01

    Data streams are continuously generated over time from Internet of Things (IoT) devices. The faster all of this data is analyzed, its hidden trends and patterns discovered, and new strategies created, the faster action can be taken, creating greater value for organizations. Density-based method is a prominent class in clustering data streams. It has the ability to detect arbitrary shape clusters, to handle outlier, and it does not need the number of clusters in advance. Therefore, density-based clustering algorithm is a proper choice for clustering IoT streams. Recently, several density-based algorithms have been proposed for clustering data streams. However, density-based clustering in limited time is still a challenging issue. In this paper, we propose a density-based clustering algorithm for IoT streams. The method has fast processing time to be applicable in real-time application of IoT devices. Experimental results show that the proposed approach obtains high quality results with low computation time on real and synthetic datasets.

  20. A Fast Density-Based Clustering Algorithm for Real-Time Internet of Things Stream

    PubMed Central

    Ying Wah, Teh

    2014-01-01

    Data streams are continuously generated over time from Internet of Things (IoT) devices. The faster all of this data is analyzed, its hidden trends and patterns discovered, and new strategies created, the faster action can be taken, creating greater value for organizations. Density-based method is a prominent class in clustering data streams. It has the ability to detect arbitrary shape clusters, to handle outlier, and it does not need the number of clusters in advance. Therefore, density-based clustering algorithm is a proper choice for clustering IoT streams. Recently, several density-based algorithms have been proposed for clustering data streams. However, density-based clustering in limited time is still a challenging issue. In this paper, we propose a density-based clustering algorithm for IoT streams. The method has fast processing time to be applicable in real-time application of IoT devices. Experimental results show that the proposed approach obtains high quality results with low computation time on real and synthetic datasets. PMID:25110753

  1. Efficient cluster Monte Carlo algorithm for Ising spin glasses in more than two space dimensions

    NASA Astrophysics Data System (ADS)

    Ochoa, Andrew J.; Zhu, Zheng; Katzgraber, Helmut G.

    2015-03-01

    A cluster algorithm that speeds up slow dynamics in simulations of nonplanar Ising spin glasses away from criticality is urgently needed. In theory, the cluster algorithm proposed by Houdayer poses no advantage over local moves in systems with a percolation threshold below 50%, such as cubic lattices. However, we show that the frustration present in Ising spin glasses prevents the growth of system-spanning clusters at temperatures roughly below the characteristic energy scale J of the problem. Adding Houdayer cluster moves to simulations of Ising spin glasses for T ~ J produces a speedup that grows with the system size over conventional local moves. We show results for the nonplanar quasi-two-dimensional Chimera graph of the D-Wave Two quantum annealer, as well as conventional three-dimensional Ising spin glasses, where in both cases the addition of cluster moves speeds up thermalization visibly in the physically-interesting low temperature regime.

  2. Intelligent decision support algorithm for distribution system restoration.

    PubMed

    Singh, Reetu; Mehfuz, Shabana; Kumar, Parmod

    2016-01-01

    Distribution system is the means of revenue for electric utility. It needs to be restored at the earliest if any feeder or complete system is tripped out due to fault or any other cause. Further, uncertainty of the loads, result in variations in the distribution network's parameters. Thus, an intelligent algorithm incorporating hybrid fuzzy-grey relation, which can take into account the uncertainties and compare the sequences is discussed to analyse and restore the distribution system. The simulation studies are carried out to show the utility of the method by ranking the restoration plans for a typical distribution system. This algorithm also meets the smart grid requirements in terms of an automated restoration plan for the partial/full blackout of network.

  3. Generalized quantum counting algorithm for non-uniform amplitude distribution

    NASA Astrophysics Data System (ADS)

    Tan, Jianing; Ruan, Yue; Li, Xi; Chen, Hanwu

    2017-03-01

    We give generalized quantum counting algorithm to increase universality of quantum counting algorithm. Non-uniform initial amplitude distribution is possible due to the diversity of situations on counting problems or external noise in the amplitude initialization procedure. We give the reason why quantum counting algorithm is invalid on this situation. By modeling in three-dimensional space spanned by unmarked state, marked state and free state to the entire Hilbert space of n qubits, we find Grover iteration can be regarded as improper rotation in the space. This allows us to give formula to solve counting problem. Furthermore, we express initial amplitude distribution in the eigenvector basis of improper rotation matrix. This is necessary to obtain mathematical analysis of counting problem on various situations. Finally, we design four simulation experiments, the results of which show that compared with original quantum counting algorithm, generalized quantum counting algorithm wins great satisfaction from three aspects: (1) Whether initial amplitude distribution is uniform; (2) the diversity of situations on counting problems; and (3) whether phase estimation technique can get phase exactly.

  4. The distribution of dark matter in the A2256 cluster

    NASA Technical Reports Server (NTRS)

    Henry, J. Patrick; Briel, Ulrich G.; Nulsen, Paul E. J.

    1993-01-01

    Using spatially resolved X-ray spectroscopy, it was determined that the X-ray emitting gas in the rich cluster A2256 is nearly isothermal to a radius of at least 0.76/h Mpc, or about three core radii. These data can be used to measure the distribution of the dark matter in the cluster. It was found that the total mass interior to 0.76/h Mpc and 1.5/h Mpc is (0.5 +/- 0.1 and 1.0 +/- 0.5) x 10(exp 15)/h of the solar mass respectively where the errors encompass the full range allowed by all models used. Thus, the mass appropriate to the region where spectral information was obtained is well determined, but the uncertainties become large upon extrapolating beyond that region. It is shown that the galaxy orbits are midly anisotropic which may cause the beta discrepancy in this cluster.

  5. The distribution of dark matter in the A2256 cluster

    NASA Technical Reports Server (NTRS)

    Henry, J. Patrick; Briel, Ulrich G.; Nulsen, Paul E. J.

    1993-01-01

    Using spatially resolved X-ray spectroscopy, it was determined that the X-ray emitting gas in the rich cluster A2256 is nearly isothermal to a radius of at least 0.76/h Mpc, or about three core radii. These data can be used to measure the distribution of the dark matter in the cluster. It was found that the total mass interior to 0.76/h Mpc and 1.5/h Mpc is (0.5 +/- 0.1 and 1.0 +/- 0.5) x 10(exp 15)/h of the solar mass respectively where the errors encompass the full range allowed by all models used. Thus, the mass appropriate to the region where spectral information was obtained is well determined, but the uncertainties become large upon extrapolating beyond that region. It is shown that the galaxy orbits are midly anisotropic which may cause the beta discrepancy in this cluster.

  6. The Gas Distribution in the Outer Regions of Galaxy Clusters

    NASA Technical Reports Server (NTRS)

    Eckert, D.; Vazza, F.; Ettori, S.; Molendi, S.; Nagai, D.; Lau, E. T.; Roncarelli, M.; Rossetti, M.; Snowden, L.; Gastaldello, F.

    2012-01-01

    Aims. We present our analysis of a local (z = 0.04 - 0.2) sample of 31 galaxy clusters with the aim of measuring the density of the X-ray emitting gas in cluster outskirts. We compare our results with numerical simulations to set constraints on the azimuthal symmetry and gas clumping in the outer regions of galaxy clusters. Methods. We have exploited the large field-of-view and low instrumental background of ROSAT/PSPC to trace the density of the intracluster gas out to the virial radius, We stacked the density profiles to detect a signal beyond T200 and measured the typical density and scatter in cluster outskirts. We also computed the azimuthal scatter of the profiles with respect to the mean value to look for deviations from spherical symmetry. Finally, we compared our average density and scatter profiles with the results of numerical simulations. Results. As opposed to some recent Suzaku results, and confirming previous evidence from ROSAT and Chandra, we observe a steepening of the density profiles beyond approximately r(sub 500). Comparing our density profiles with simulations, we find that non-radiative runs predict density profiles that are too steep, whereas runs including additional physics and/ or treating gas clumping agree better with the observed gas distribution. We report high-confidence detection of a systematic difference between cool-core and non cool-core clusters beyond approximately 0.3r(sub 200), which we explain by a different distribution of the gas in the two classes. Beyond approximately r(sub 500), galaxy clusters deviate significantly from spherical symmetry, with only small differences between relaxed and disturbed systems. We find good agreement between the observed and predicted scatter profiles, but only when the 1% densest clumps are filtered out in the ENZO simulations. Conclusions. Comparing our results with numerical simulations, we find that non-radiative simulations fail to reproduce the gas distribution, even well outside

  7. The Gas Distribution in Galaxy Cluster Outer Regions

    NASA Technical Reports Server (NTRS)

    Eckert, D.; Vazza, F.; Ettori, S.; Molendi, S.; Nagai, D.; Laue, E. T.; Roncarelli, M.; Rossetti, M.; Snowden, S. L.; Gastaldello, F.

    2012-01-01

    Aims. We present the analysis of a local (z = 0.04 - 0.2) sample of 31 galaxy clusters with the aim of measuring the density of the X-ray emitting gas in cluster outskirts. We compare our results with numerical simulations to set constraints on the azimuthal symmetry and gas clumping in the outer regions of galaxy clusters. Methods. We exploit the large field-of-view and low instrumental background of ROSAT/PSPC to trace the density of the intracluster gas out to the virial radius. We perform a stacking of the density profiles to detect a signal beyond r200 and measure the typical density and scatter in cluster outskirts. We also compute the azimuthal scatter of the profiles with respect to the mean value to look for deviations from spherical symmetry. Finally, we compare our average density and scatter profiles with the results of numerical simulations. Results. As opposed to some recent Suzaku results, and confirming previous evidence from ROSAT and Chandra, we observe a steepening of the density profiles beyond approximately r(sub 500). Comparing our density profiles with simulations, we find that non-radiative runs predict too steep density profiles, whereas runs including additional physics and/or treating gas clumping are in better agreement with the observed gas distribution. We report for the first time the high-confidence detection of a systematic difference between cool-core and non-cool core clusters beyond 0.3r(sub 200), which we explain by a different distribution of the gas in the two classes. Beyond r(sub 500), galaxy clusters deviate significantly from spherical symmetry, with only little differences between relaxed and disturbed systems. We find good agreement between the observed and predicted scatter profiles, but only when the 1% densest clumps are filtered out in the simulations. Conclusions. Comparing our results with numerical simulations, we find that non-radiative simulations fail to reproduce the gas distribution, even well outside cluster

  8. Spatial event cluster detection using an approximate normal distribution.

    PubMed

    Torabi, Mahmoud; Rosychuk, Rhonda J

    2008-12-12

    In geographic surveillance of disease, areas with large numbers of disease cases are to be identified so that investigations of the causes of high disease rates can be pursued. Areas with high rates are called disease clusters and statistical cluster detection tests are used to identify geographic areas with higher disease rates than expected by chance alone. Typically cluster detection tests are applied to incident or prevalent cases of disease, but surveillance of disease-related events, where an individual may have multiple events, may also be of interest. Previously, a compound Poisson approach that detects clusters of events by testing individual areas that may be combined with their neighbours has been proposed. However, the relevant probabilities from the compound Poisson distribution are obtained from a recursion relation that can be cumbersome if the number of events are large or analyses by strata are performed. We propose a simpler approach that uses an approximate normal distribution. This method is very easy to implement and is applicable to situations where the population sizes are large and the population distribution by important strata may differ by area. We demonstrate the approach on pediatric self-inflicted injury presentations to emergency departments and compare the results for probabilities based on the recursion and the normal approach. We also implement a Monte Carlo simulation to study the performance of the proposed approach. In a self-inflicted injury data example, the normal approach identifies twelve out of thirteen of the same clusters as the compound Poisson approach, noting that the compound Poisson method detects twelve significant clusters in total. Through simulation studies, the normal approach well approximates the compound Poisson approach for a variety of different population sizes and case and event thresholds. A drawback of the compound Poisson approach is that the relevant probabilities must be determined through a

  9. The cluster distribution as a test of dark matter models - I. Clustering properties

    NASA Astrophysics Data System (ADS)

    Borgani, Stefano; Plionis, Manolis; Coles, Peter; Moscardini, Lauro

    1995-12-01

    We present extended simulations of the large-scale distribution of galaxy clusters in several dark matter models, using an optimized version of the truncated Zel'dovich approximation (TZA). In order to test the reliability of our simulations, we compare them with N-body-based cluster simulations. We find that the TZA provides a very accurate description of the cluster distribution as long as fluctuations on the cluster mass-scale are in the mildly non-linear regime (sigma_8<~1). The low computational cost of this simulation technique allows us to run a large ensemble of 50 realizations for each model, so we are able to quantify accurately the effects of cosmic variance. Six different dark matter models are studied in this work: standard CDM (SCDM), tilted CDM (TCDM) with primordial spectral index n=0.7, cold+hot DM (CHDM) with Omega_hot=0.3, low Hubble constant (h=0.3) CDM (LOWH), and two spatially flat low-density CDM models with Omega_0=0.2 and Omega_Lambda=0.8, having two different normalizations, sigma_8=0.8 (LambdaCDM_1) and sigma_8=1.3 (LambdaCDM_2). We compare the cluster simulations with an extended redshift sample of Abell/ACO clusters, using various statistical measures, such as the integral of the two-point correlation function, J_3, and the probability density function (pdf). We find that the models that best reproduce the clustering of the Abell/ACO cluster sample are the CHDM and the LambdaCDM_1 models. The LambdaCDM_2 model is too strongly clustered, and this clustering is probably overestimated in our simulations as a result of the large sigma_8-value of this model. All of the other models are ruled out at a high confidence level. The pdfs of all models are well approximated by a lognormal distribution, consistent with similar findings for Abell/ACO clusters. The low-order moments of all the pdfs are found to obey a variance-skewness relation of the form gamma~=S_3sigma^4, with S_3~=1.9, independent of the primordial spectral shape and consistent

  10. Distributed genetic algorithms for the floorplan design problem

    NASA Technical Reports Server (NTRS)

    Cohoon, James P.; Hegde, Shailesh U.; Martin, Worthy N.; Richards, Dana S.

    1991-01-01

    Designing a VLSI floorplan calls for arranging a given set of modules in the plane to minimize the weighted sum of area and wire-length measures. A method of solving the floorplan design problem using distributed genetic algorithms is presented. Distributed genetic algorithms, based on the paleontological theory of punctuated equilibria, offer a conceptual modification to the traditional genetic algorithms. Experimental results on several problem instances demonstrate the efficacy of this method and indicate the advantages of this method over other methods, such as simulated annealing. The method has performed better than the simulated annealing approach, both in terms of the average cost of the solutions found and the best-found solution, in almost all the problem instances tried.

  11. Distributed Encoding Algorithm for Source Localization in Sensor Networks

    NASA Astrophysics Data System (ADS)

    Kim, YoonHak; Ortega, Antonio

    2010-12-01

    We consider sensor-based distributed source localization applications, where sensors transmit quantized data to a fusion node, which then produces an estimate of the source location. For this application, the goal is to minimize the amount of information that the sensor nodes have to exchange in order to attain a certain source localization accuracy. We propose a distributed encoding algorithm that is applied after quantization and achieves significant rate savings by merging quantization bins. The bin-merging technique exploits the fact that certain combinations of quantization bins at each node cannot occur because the corresponding spatial regions have an empty intersection. We apply the algorithm to a system where an acoustic amplitude sensor model is employed at each node for source localization. Our experiments demonstrate significant rate savings (e.g., over 30%, 5 nodes, and 4 bits per node) when our novel bin-merging algorithms are used.

  12. Evaluating clustering methods within the Artificial Ecosystem Algorithm and their application to bike redistribution in London.

    PubMed

    Adham, Manal T; Bentley, Peter J

    2016-08-01

    This paper proposes and evaluates a solution to the truck redistribution problem prominent in London's Santander Cycle scheme. Due to the complexity of this NP-hard combinatorial optimisation problem, no efficient optimisation techniques are known to solve the problem exactly. This motivates our use of the heuristic Artificial Ecosystem Algorithm (AEA) to find good solutions in a reasonable amount of time. The AEA is designed to take advantage of highly distributed computer architectures and adapt to changing problems. In the AEA a problem is first decomposed into its relative sub-components; they then evolve solution building blocks that fit together to form a single optimal solution. Three variants of the AEA centred on evaluating clustering methods are presented: the baseline AEA, the community-based AEA which groups stations according to journey flows, and the Adaptive AEA which actively modifies clusters to cater for changes in demand. We applied these AEA variants to the redistribution problem prominent in bike share schemes (BSS). The AEA variants are empirically evaluated using historical data from Santander Cycles to validate the proposed approach and prove its potential effectiveness. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  13. The CLASSY clustering algorithm: Description, evaluation, and comparison with the iterative self-organizing clustering system (ISOCLS). [used for LACIE data

    NASA Technical Reports Server (NTRS)

    Lennington, R. K.; Malek, H.

    1978-01-01

    A clustering method, CLASSY, was developed, which alternates maximum likelihood iteration with a procedure for splitting, combining, and eliminating the resulting statistics. The method maximizes the fit of a mixture of normal distributions to the observed first through fourth central moments of the data and produces an estimate of the proportions, means, and covariances in this mixture. The mathematical model which is the basic for CLASSY and the actual operation of the algorithm is described. Data comparing the performances of CLASSY and ISOCLS on simulated and actual LACIE data are presented.

  14. An Efficient Distributed Compressed Sensing Algorithm for Decentralized Sensor Network.

    PubMed

    Liu, Jing; Huang, Kaiyu; Zhang, Guoxian

    2017-04-20

    We consider the joint sparsity Model 1 (JSM-1) in a decentralized scenario, where a number of sensors are connected through a network and there is no fusion center. A novel algorithm, named distributed compact sensing matrix pursuit (DCSMP), is proposed to exploit the computational and communication capabilities of the sensor nodes. In contrast to the conventional distributed compressed sensing algorithms adopting a random sensing matrix, the proposed algorithm focuses on the deterministic sensing matrices built directly on the real acquisition systems. The proposed DCSMP algorithm can be divided into two independent parts, the common and innovation support set estimation processes. The goal of the common support set estimation process is to obtain an estimated common support set by fusing the candidate support set information from an individual node and its neighboring nodes. In the following innovation support set estimation process, the measurement vector is projected into a subspace that is perpendicular to the subspace spanned by the columns indexed by the estimated common support set, to remove the impact of the estimated common support set. We can then search the innovation support set using an orthogonal matching pursuit (OMP) algorithm based on the projected measurement vector and projected sensing matrix. In the proposed DCSMP algorithm, the process of estimating the common component/support set is decoupled with that of estimating the innovation component/support set. Thus, the inaccurately estimated common support set will have no impact on estimating the innovation support set. It is proven that under the condition the estimated common support set contains the true common support set, the proposed algorithm can find the true innovation set correctly. Moreover, since the innovation support set estimation process is independent of the common support set estimation process, there is no requirement for the cardinality of both sets; thus, the proposed DCSMP

  15. An Efficient Distributed Compressed Sensing Algorithm for Decentralized Sensor Network

    PubMed Central

    Liu, Jing; Huang, Kaiyu; Zhang, Guoxian

    2017-01-01

    We consider the joint sparsity Model 1 (JSM-1) in a decentralized scenario, where a number of sensors are connected through a network and there is no fusion center. A novel algorithm, named distributed compact sensing matrix pursuit (DCSMP), is proposed to exploit the computational and communication capabilities of the sensor nodes. In contrast to the conventional distributed compressed sensing algorithms adopting a random sensing matrix, the proposed algorithm focuses on the deterministic sensing matrices built directly on the real acquisition systems. The proposed DCSMP algorithm can be divided into two independent parts, the common and innovation support set estimation processes. The goal of the common support set estimation process is to obtain an estimated common support set by fusing the candidate support set information from an individual node and its neighboring nodes. In the following innovation support set estimation process, the measurement vector is projected into a subspace that is perpendicular to the subspace spanned by the columns indexed by the estimated common support set, to remove the impact of the estimated common support set. We can then search the innovation support set using an orthogonal matching pursuit (OMP) algorithm based on the projected measurement vector and projected sensing matrix. In the proposed DCSMP algorithm, the process of estimating the common component/support set is decoupled with that of estimating the innovation component/support set. Thus, the inaccurately estimated common support set will have no impact on estimating the innovation support set. It is proven that under the condition the estimated common support set contains the true common support set, the proposed algorithm can find the true innovation set correctly. Moreover, since the innovation support set estimation process is independent of the common support set estimation process, there is no requirement for the cardinality of both sets; thus, the proposed DCSMP

  16. Comparing Different Fault Identification Algorithms in Distributed Power System

    NASA Astrophysics Data System (ADS)

    Alkaabi, Salim

    A power system is a huge complex system that delivers the electrical power from the generation units to the consumers. As the demand for electrical power increases, distributed power generation was introduced to the power system. Faults may occur in the power system at any time in different locations. These faults cause a huge damage to the system as they might lead to full failure of the power system. Using distributed generation in the power system made it even harder to identify the location of the faults in the system. The main objective of this work is to test the different fault location identification algorithms while tested on a power system with the different amount of power injected using distributed generators. As faults may lead the system to full failure, this is an important area for research. In this thesis different fault location identification algorithms have been tested and compared while the different amount of power is injected from distributed generators. The algorithms were tested on IEEE 34 node test feeder using MATLAB and the results were compared to find when these algorithms might fail and the reliability of these methods.

  17. CAMPAIGN: an open-source library of GPU-accelerated data clustering algorithms

    PubMed Central

    Kohlhoff, Kai J.; Sosnick, Marc H.; Hsu, William T.; Pande, Vijay S.; Altman, Russ B.

    2011-01-01

    Motivation: Data clustering techniques are an essential component of a good data analysis toolbox. Many current bioinformatics applications are inherently compute-intense and work with very large datasets. Sequential algorithms are inadequate for providing the necessary performance. For this reason, we have created Clustering Algorithms for Massively Parallel Architectures, Including GPU Nodes (CAMPAIGN), a central resource for data clustering algorithms and tools that are implemented specifically for execution on massively parallel processing architectures. Results: CAMPAIGN is a library of data clustering algorithms and tools, written in ‘C for CUDA’ for Nvidia GPUs. The library provides up to two orders of magnitude speed-up over respective CPU-based clustering algorithms and is intended as an open-source resource. New modules from the community will be accepted into the library and the layout of it is such that it can easily be extended to promising future platforms such as OpenCL. Availability: Releases of the CAMPAIGN library are freely available for download under the LGPL from https://simtk.org/home/campaign. Source code can also be obtained through anonymous subversion access as described on https://simtk.org/scm/?group_id=453. Contact: kjk33@cantab.net PMID:21712246

  18. Interlog protein network: an evolutionary benchmark of protein interaction networks for the evaluation of clustering algorithms.

    PubMed

    Jafari, Mohieddin; Mirzaie, Mehdi; Sadeghi, Mehdi

    2015-10-05

    In the field of network science, exploring principal and crucial modules or communities is critical in the deduction of relationships and organization of complex networks. This approach expands an arena, and thus allows further study of biological functions in the field of network biology. As the clustering algorithms that are currently employed in finding modules have innate uncertainties, external and internal validations are necessary. Sequence and network structure alignment, has been used to define the Interlog Protein Network (IPN). This network is an evolutionarily conserved network with communal nodes and less false-positive links. In the current study, the IPN is employed as an evolution-based benchmark in the validation of the module finding methods. The clustering results of five algorithms; Markov Clustering (MCL), Restricted Neighborhood Search Clustering (RNSC), Cartographic Representation (CR), Laplacian Dynamics (LD) and Genetic Algorithm; to find communities in Protein-Protein Interaction networks (GAPPI) are assessed by IPN in four distinct Protein-Protein Interaction Networks (PPINs). The MCL shows a more accurate algorithm based on this evolutionary benchmarking approach. Also, the biological relevance of proteins in the IPN modules generated by MCL is compatible with biological standard databases such as Gene Ontology, KEGG and Reactome. In this study, the IPN shows its potential for validation of clustering algorithms due to its biological logic and straightforward implementation.

  19. CAMPAIGN: an open-source library of GPU-accelerated data clustering algorithms.

    PubMed

    Kohlhoff, Kai J; Sosnick, Marc H; Hsu, William T; Pande, Vijay S; Altman, Russ B

    2011-08-15

    Data clustering techniques are an essential component of a good data analysis toolbox. Many current bioinformatics applications are inherently compute-intense and work with very large datasets. Sequential algorithms are inadequate for providing the necessary performance. For this reason, we have created Clustering Algorithms for Massively Parallel Architectures, Including GPU Nodes (CAMPAIGN), a central resource for data clustering algorithms and tools that are implemented specifically for execution on massively parallel processing architectures. CAMPAIGN is a library of data clustering algorithms and tools, written in 'C for CUDA' for Nvidia GPUs. The library provides up to two orders of magnitude speed-up over respective CPU-based clustering algorithms and is intended as an open-source resource. New modules from the community will be accepted into the library and the layout of it is such that it can easily be extended to promising future platforms such as OpenCL. Releases of the CAMPAIGN library are freely available for download under the LGPL from https://simtk.org/home/campaign. Source code can also be obtained through anonymous subversion access as described on https://simtk.org/scm/?group_id=453. kjk33@cantab.net.

  20. Distributed autonomous systems: resource management, planning, and control algorithms

    NASA Astrophysics Data System (ADS)

    Smith, James F., III; Nguyen, ThanhVu H.

    2005-05-01

    Distributed autonomous systems, i.e., systems that have separated distributed components, each of which, exhibit some degree of autonomy are increasingly providing solutions to naval and other DoD problems. Recently developed control, planning and resource allocation algorithms for two types of distributed autonomous systems will be discussed. The first distributed autonomous system (DAS) to be discussed consists of a collection of unmanned aerial vehicles (UAVs) that are under fuzzy logic control. The UAVs fly and conduct meteorological sampling in a coordinated fashion determined by their fuzzy logic controllers to determine the atmospheric index of refraction. Once in flight no human intervention is required. A fuzzy planning algorithm determines the optimal trajectory, sampling rate and pattern for the UAVs and an interferometer platform while taking into account risk, reliability, priority for sampling in certain regions, fuel limitations, mission cost, and related uncertainties. The real-time fuzzy control algorithm running on each UAV will give the UAV limited autonomy allowing it to change course immediately without consulting with any commander, request other UAVs to help it, alter its sampling pattern and rate when observing interesting phenomena, or to terminate the mission and return to base. The algorithms developed will be compared to a resource manager (RM) developed for another DAS problem related to electronic attack (EA). This RM is based on fuzzy logic and optimized by evolutionary algorithms. It allows a group of dissimilar platforms to use EA resources distributed throughout the group. For both DAS types significant theoretical and simulation results will be presented.

  1. A pairwise alignment algorithm which favors clusters of blocks.

    PubMed

    Nédélec, Elodie; Moncion, Thomas; Gassiat, Elisabeth; Bossard, Bruno; Duchateau-Nguyen, Guillemette; Denise, Alain; Termier, Michel

    2005-01-01

    Pairwise sequence alignments aim to decide whether two sequences are related and, if so, to exhibit their related domains. Recent works have pointed out that a significant number of true homologous sequences are missed when using classical comparison algorithms. This is the case when two homologous sequences share several little blocks of homology, too small to lead to a significant score. On the other hand, classical alignment algorithms, when detecting homologies, may fail to recognize all the significant biological signals. The aim of the paper is to give a solution to these two problems. We propose a new scoring method which tends to increase the score of an alignment when "blocks" are detected. This so-called Block-Scoring algorithm, which makes use of dynamic programming, is worth being used as a complementary tool to classical exact alignments methods. We validate our approach by applying it on a large set of biological data. Finally, we give a limit theorem for the score statistics of the algorithm.

  2. A Multi-level Spatial Clustering Algorithm for Detection of Disease Outbreaks

    PubMed Central

    Que, Jialan; Tsui, Fu-Chiang

    2008-01-01

    In this paper, we proposed a Multi-level Spatial Clustering (MSC) algorithm for rapid detection of emerging disease outbreaks prospectively. We used the semi-synthetic data for algorithm evaluation. We applied BARD algorithm[1] to generate outbreak counts for simulation of aerosol release of Anthrax. We compared MSC with two spatial clustering algorithms: Kulldorff’s spatial scan statistic[2] and Bayesian spatial scan statistic[3]. The evaluation results showed that the areas under ROC had no significant difference among the three algorithms, so did the areas under AMOC. MSC demonstrated significant computational effciency (100+ times faster) and higher PPV. However, MSC showed 2–6 hours delay on average for outbreak detection when the false alarm rate was lower than 1 false alarm per 4 weeks. We concluded that the MSC algorithm is computationally efficient and it is able to provide more precise and compact clusters in a timely manner while keeping high detection accuracy (cluster sensitivity) and low false alarm rates. PMID:18999304

  3. Accelerating Bayesian hierarchical clustering of time series data with a randomised algorithm.

    PubMed

    Darkins, Robert; Cooke, Emma J; Ghahramani, Zoubin; Kirk, Paul D W; Wild, David L; Savage, Richard S

    2013-01-01

    We live in an era of abundant data. This has necessitated the development of new and innovative statistical algorithms to get the most from experimental data. For example, faster algorithms make practical the analysis of larger genomic data sets, allowing us to extend the utility of cutting-edge statistical methods. We present a randomised algorithm that accelerates the clustering of time series data using the Bayesian Hierarchical Clustering (BHC) statistical method. BHC is a general method for clustering any discretely sampled time series data. In this paper we focus on a particular application to microarray gene expression data. We define and analyse the randomised algorithm, before presenting results on both synthetic and real biological data sets. We show that the randomised algorithm leads to substantial gains in speed with minimal loss in clustering quality. The randomised time series BHC algorithm is available as part of the R package BHC, which is available for download from Bioconductor (version 2.10 and above) via http://bioconductor.org/packages/2.10/bioc/html/BHC.html. We have also made available a set of R scripts which can be used to reproduce the analyses carried out in this paper. These are available from the following URL. https://sites.google.com/site/randomisedbhc/.

  4. A New-Fangled FES-k-Means Clustering Algorithm for Disease Discovery and Visual Analytics.

    PubMed

    Oyana, Tonny J

    2010-01-01

    The central purpose of this study is to further evaluate the quality of the performance of a new algorithm. The study provides additional evidence on this algorithm that was designed to increase the overall efficiency of the original k-means clustering technique-the Fast, Efficient, and Scalable k-means algorithm (FES-k-means). The FES-k-means algorithm uses a hybrid approach that comprises the k-d tree data structure that enhances the nearest neighbor query, the original k-means algorithm, and an adaptation rate proposed by Mashor. This algorithm was tested using two real datasets and one synthetic dataset. It was employed twice on all three datasets: once on data trained by the innovative MIL-SOM method and then on the actual untrained data in order to evaluate its competence. This two-step approach of data training prior to clustering provides a solid foundation for knowledge discovery and data mining, otherwise unclaimed by clustering methods alone. The benefits of this method are that it produces clusters similar to the original k-means method at a much faster rate as shown by runtime comparison data; and it provides efficient analysis of large geospatial data with implications for disease mechanism discovery. From a disease mechanism discovery perspective, it is hypothesized that the linear-like pattern of elevated blood lead levels discovered in the city of Chicago may be spatially linked to the city's water service lines.

  5. A New-Fangled FES-k-Means Clustering Algorithm for Disease Discovery and Visual Analytics

    PubMed Central

    2010-01-01

    The central purpose of this study is to further evaluate the quality of the performance of a new algorithm. The study provides additional evidence on this algorithm that was designed to increase the overall efficiency of the original k-means clustering technique—the Fast, Efficient, and Scalable k-means algorithm (FES-k-means). The FES-k-means algorithm uses a hybrid approach that comprises the k-d tree data structure that enhances the nearest neighbor query, the original k-means algorithm, and an adaptation rate proposed by Mashor. This algorithm was tested using two real datasets and one synthetic dataset. It was employed twice on all three datasets: once on data trained by the innovative MIL-SOM method and then on the actual untrained data in order to evaluate its competence. This two-step approach of data training prior to clustering provides a solid foundation for knowledge discovery and data mining, otherwise unclaimed by clustering methods alone. The benefits of this method are that it produces clusters similar to the original k-means method at a much faster rate as shown by runtime comparison data; and it provides efficient analysis of large geospatial data with implications for disease mechanism discovery. From a disease mechanism discovery perspective, it is hypothesized that the linear-like pattern of elevated blood lead levels discovered in the city of Chicago may be spatially linked to the city's water service lines. PMID:20689710

  6. A distributed Canny edge detector: algorithm and FPGA implementation.

    PubMed

    Xu, Qian; Varadarajan, Srenivas; Chakrabarti, Chaitali; Karam, Lina J

    2014-07-01

    The Canny edge detector is one of the most widely used edge detection algorithms due to its superior performance. Unfortunately, not only is it computationally more intensive as compared with other edge detection algorithms, but it also has a higher latency because it is based on frame-level statistics. In this paper, we propose a mechanism to implement the Canny algorithm at the block level without any loss in edge detection performance compared with the original frame-level Canny algorithm. Directly applying the original Canny algorithm at the block-level leads to excessive edges in smooth regions and to loss of significant edges in high-detailed regions since the original Canny computes the high and low thresholds based on the frame-level statistics. To solve this problem, we present a distributed Canny edge detection algorithm that adaptively computes the edge detection thresholds based on the block type and the local distribution of the gradients in the image block. In addition, the new algorithm uses a nonuniform gradient magnitude histogram to compute block-based hysteresis thresholds. The resulting block-based algorithm has a significantly reduced latency and can be easily integrated with other block-based image codecs. It is capable of supporting fast edge detection of images and videos with high resolutions, including full-HD since the latency is now a function of the block size instead of the frame size. In addition, quantitative conformance evaluations and subjective tests show that the edge detection performance of the proposed algorithm is better than the original frame-based algorithm, especially when noise is present in the images. Finally, this algorithm is implemented using a 32 computing engine architecture and is synthesized on the Xilinx Virtex-5 FPGA. The synthesized architecture takes only 0.721 ms (including the SRAM READ/WRITE time and the computation time) to detect edges of 512 × 512 images in the USC SIPI database when clocked at 100

  7. The next generation Virgo cluster survey. VIII. The spatial distribution of globular clusters in the Virgo cluster

    SciTech Connect

    Durrell, Patrick R.; Accetta, Katharine; Côté, Patrick; Blakeslee, John P.; Ferrarese, Laura; McConnachie, Alan; Gwyn, Stephen; Peng, Eric W.; Zhang, Hongxin; Mihos, J. Christopher; Puzia, Thomas H.; Jordán, Andrés; Lançon, Ariane; Liu, Chengze; Cuillandre, Jean-Charles; Boissier, Samuel; Boselli, Alessandro; Courteau, Stéphane; Duc, Pierre-Alain; and others

    2014-10-20

    We report on a large-scale study of the distribution of globular clusters (GCs) throughout the Virgo cluster, based on photometry from the Next Generation Virgo Cluster Survey (NGVS), a large imaging survey covering Virgo's primary subclusters (Virgo A = M87 and Virgo B = M49) out to their virial radii. Using the g{sub o}{sup ′}, (g' – i') {sub o} color-magnitude diagram of unresolved and marginally resolved sources within the NGVS, we have constructed two-dimensional maps of the (irregular) GC distribution over 100 deg{sup 2} to a depth of g{sub o}{sup ′} = 24. We present the clearest evidence to date showing the difference in concentration between red and blue GCs over the full extent of the cluster, where the red (more metal-rich) GCs are largely located around the massive early-type galaxies in Virgo, while the blue (metal-poor) GCs have a much more extended spatial distribution with significant populations still present beyond 83' (∼215 kpc) along the major axes of both M49 and M87. A comparison of our GC maps to the diffuse light in the outermost regions of M49 and M87 show remarkable agreement in the shape, ellipticity, and boxiness of both luminous systems. We also find evidence for spatial enhancements of GCs surrounding M87 that may be indicative of recent interactions or an ongoing merger history. We compare the GC map to that of the locations of Virgo galaxies and the X-ray intracluster gas, and find generally good agreement between these various baryonic structures. We calculate the Virgo cluster contains a total population of N {sub GC} = 67, 300 ± 14, 400, of which 35% are located in M87 and M49 alone. For the first time, we compute a cluster-wide specific frequency S {sub N,} {sub CL} = 2.8 ± 0.7, after correcting for Virgo's diffuse light. We also find a GC-to-baryonic mass fraction ε {sub b} = 5.7 ± 1.1 × 10{sup –4} and a GC-to-total cluster mass formation efficiency ε {sub t} = 2.9 ± 0.5 × 10{sup –5}, the latter values

  8. Globular Cluster Systems in Brightest Cluster Galaxies: Bimodal Metallicity Distributions and the Nature of the High-Luminosity Clusters

    NASA Astrophysics Data System (ADS)

    Harris, William E.; Whitmore, Bradley C.; Karakla, Diane; Okoń, Waldemar; Baum, William A.; Hanes, David A.; Kavelaars, J. J.

    2006-01-01

    We present new (B, I) photometry for the globular cluster systems in eight brightest cluster galaxies (BCGs), obtained with the ACS/WFC camera on the Hubble Space Telescope. In the very rich cluster systems that reside within these giant galaxies, we find that all have strongly bimodal color distributions that are clearly resolved by the metallicity-sensitive (B-I) index. Furthermore, the mean colors and internal color range of the blue subpopulation are remarkably similar from one galaxy to the next, to well within the +/-0.02-0.03 mag uncertainties in the foreground reddenings and photometric zero points. By contrast, the mean color and internal color range for the red subpopulation differ from one galaxy to the next by twice as much as the blue population. All the BCGs show population gradients, with much higher relative numbers of red clusters within 5 kpc of their centers, consistent with their having formed at later times than the blue, metal-poor population. A striking new feature of the color distributions emerging from our data is that for the brightest clusters (MI<-10.5) the color distribution becomes broad and less obviously bimodal. This effect was first noticed by Ostrov et al. and Dirsch et al. for the Fornax giant NGC 1399; our data suggest that it may be a characteristic of many BCGs and perhaps other large galaxies. Our data indicate that the blue (metal-poor) clusters brighter than MI~=-10 become progressively redder with increasing luminosity, following a mass/metallicity scaling relation Z~M0.55. A basically similar relation has been found for M87 by Strader et al. (2005). We argue that these GCS characteristics are consistent with a hierarchical-merging galaxy formation picture in which the metal-poor clusters formed in protogalactic clouds or dense starburst complexes with gas masses in the range 107-1010 Msolar, but where the more massive clusters on average formed in bigger clouds with deeper potential wells where more preenrichment could

  9. A Degree Distribution Optimization Algorithm for Image Transmission

    NASA Astrophysics Data System (ADS)

    Jiang, Wei; Yang, Junjie

    2016-09-01

    Luby Transform (LT) code is the first practical implementation of digital fountain code. The coding behavior of LT code is mainly decided by the degree distribution which determines the relationship between source data and codewords. Two degree distributions are suggested by Luby. They work well in typical situations but not optimally in case of finite encoding symbols. In this work, the degree distribution optimization algorithm is proposed to explore the potential of LT code. Firstly selection scheme of sparse degrees for LT codes is introduced. Then probability distribution is optimized according to the selected degrees. In image transmission, bit stream is sensitive to the channel noise and even a single bit error may cause the loss of synchronization between the encoder and the decoder. Therefore the proposed algorithm is designed for image transmission situation. Moreover, optimal class partition is studied for image transmission with unequal error protection. The experimental results are quite promising. Compared with LT code with robust soliton distribution, the proposed algorithm improves the final quality of recovered images obviously with the same overhead.

  10. Solvation Effects on Structure and Charge Distribution in Anionic Clusters

    NASA Astrophysics Data System (ADS)

    Weber, J. Mathias

    2015-03-01

    The interaction of ions with solvent molecules modifies the properties of both solvent and solute. Solvation generally stabilizes compact charge distributions compared to more diffuse ones. In the most extreme cases, solvation will alter the very composition of the ion itself. We use infrared photodissociation spectroscopy of mass-selected ions to probe how solvation affects the structures and charge distributions of metal-CO2 cluster anions. We gratefully acknowledge the National Science Foundation for funding through Grant CHE-0845618 (for graduate student support) and for instrumentation funding through Grant PHY-1125844.

  11. Fast Nonparametric Density-Based Clustering of Large Data Sets Using a Stochastic Approximation Mean-Shift Algorithm

    PubMed Central

    Baran, Andrea

    2016-01-01

    Mean-shift is an iterative procedure often used as a nonparametric clustering algorithm that defines clusters based on the modal regions of a density function. The algorithm is conceptually appealing and makes assumptions neither about the shape of the clusters nor about their number. However, with a complexity of O(n2) per iteration, it does not scale well to large data sets. We propose a novel algorithm which performs density-based clustering much quicker than mean-shift, yet delivering virtually identical results. This algorithm combines subsampling and a stochastic approximation procedure to achieve a potential complexity of O(n) at each step. Its convergence is established. Its performances are evaluated using simulations and applications to image segmentation, where the algorithm was tens or hundreds of times faster than mean-shift, yet causing negligible amounts of clustering errors. The algorithm can be combined with existing approaches to further accelerate clustering. PMID:28479847

  12. An efficient clustering algorithm for partitioning Y-short tandem repeats data

    PubMed Central

    2012-01-01

    Background Y-Short Tandem Repeats (Y-STR) data consist of many similar and almost similar objects. This characteristic of Y-STR data causes two problems with partitioning: non-unique centroids and local minima problems. As a result, the existing partitioning algorithms produce poor clustering results. Results Our new algorithm, called k-Approximate Modal Haplotypes (k-AMH), obtains the highest clustering accuracy scores for five out of six datasets, and produces an equal performance for the remaining dataset. Furthermore, clustering accuracy scores of 100% are achieved for two of the datasets. The k-AMH algorithm records the highest mean accuracy score of 0.93 overall, compared to that of other algorithms: k-Population (0.91), k-Modes-RVF (0.81), New Fuzzy k-Modes (0.80), k-Modes (0.76), k-Modes-Hybrid 1 (0.76), k-Modes-Hybrid 2 (0.75), Fuzzy k-Modes (0.74), and k-Modes-UAVM (0.70). Conclusions The partitioning performance of the k-AMH algorithm for Y-STR data is superior to that of other algorithms, owing to its ability to solve the non-unique centroids and local minima problems. Our algorithm is also efficient in terms of time complexity, which is recorded as O(km(n-k)) and considered to be linear. PMID:23039132

  13. [The multi-spectra classification algorithm based on K-means clustering and spectral angle cosine].

    PubMed

    Wei, Jun-xia; Xiangli, Bin; Gao, Xiao-hui; Duan, Xiao-feng

    2011-05-01

    The classification and de-aliasing methods with respect to multi-spectra and hyper-spectra have been widely studied in recent years. And both K-mean clustering algorithm and spectral similarity algorithm are familiar classification methods. The present paper improved the K-mean clustering algorithm by using spectral similarity match algorithm to perform a new spectral classification algorithm. Two spectra with the farthest distance first were chosen as reference spectra. The Euclidean distance method or spectral angle cosine method then were used to classify data cube on the basis of the two reference spectra, and delete the spectra which belongs to the two reference spectra. The rest data cube was used to perform new classification according to a third spectrum, which is the farthest distance or the biggest angle one corresponding to the two reference spectra. Multi-spectral data cube was applied in the experimental test. The results of K-mean clustering classification by ENVI, compared with simulation results of the improved K-mean algorithm and the spectral angle cosine method, demonstrated that the latter two classify two air bubbles explicitly and effectively, and the improved K-mean algorithm classifies backgrounds better, especially the Euclidean distance method can classify the backgrounds integrally.

  14. Longitudinally-invariant k⊥-clustering algorithms for hadron-hadron collisions

    NASA Astrophysics Data System (ADS)

    Catani, S.; Dokshitzer, Yu. L.; Seymour, M. H.; Webber, B. R.

    1993-09-01

    We propose a version of the QCD-motivated " k⊥" jet-clustering algorithm for hadron-hadron collisions which is invariant under boosts along the beam directions. This leads to improved factorization properties and closer correspondence to experimental practice at hadron colliders. We examine alternative definitions of the resolution variables and cluster recombination scheme, and show that the algorithm can be implemented efficiently on a computer to provide a full clustering history of each event. Using simulated data at √ S = 1.8 TeV, we study the effects of calorimeter segmentation, hadronization and the soft underlying event, and compare the results with those obtained using a conventional cone-type algorithm.

  15. Combining Evolutionary Algorithms with Clustering toward Rational Global Structure Optimization at the Atomic Scale.

    PubMed

    Jørgensen, Mathias S; Groves, Michael N; Hammer, Bjørk

    2017-03-14

    Predicting structures at the atomic scale is of great importance for understanding the properties of materials. Such predictions are infeasible without efficient global optimization techniques. Many current techniques produce a large amount of idle intermediate data before converging to the global minimum. If this information could be analyzed during optimization, many new possibilities emerge for more rational search algorithms. We combine an evolutionary algorithm (EA) and clustering, a machine-learning technique, to produce a rational algorithm for global structure optimization. Clustering the configuration space of intermediate structures into regions of geometrically similar structures enables the EA to suppress certain regions and favor others. For two test systems, an organic molecule and an oxide surface, the global minimum search proves significantly faster when favoring stable structures in unexplored regions. This clustering-enhanced EA is a step toward adaptive global optimization techniques that can act upon information in accumulated data.

  16. Tuning a Major Part of a Clustering Algorithm.

    DTIC Science & Technology

    1988-02-01

    with core points identified by the local density algorithm TOTAL MINORITES t-4.5* t.A4* Median 8 Ilb uHinge 10 20 Max 14 44 (Mean) 8.1 15.4 *Actual...2.7) curent* average-linkage" coniplete-linkage*** Median 25h 47h 35 u~linge 33 65 39 Max 73 97 56 (Mean) 29.7 51.1 36.0 *Actual total minorites

  17. Changes in tropical precipitation cluster size distributions under global warming

    NASA Astrophysics Data System (ADS)

    Neelin, J. D.; Quinn, K. M.

    2016-12-01

    The total amount of precipitation integrated across a tropical storm or other precipitation feature (contiguous clusters of precipitation exceeding a minimum rain rate) is a useful measure of the aggregate size of the disturbance. To establish baseline behavior in current climate, the probability distribution of cluster sizes from multiple satellite retrievals and National Center for Environmental Prediction (NCEP) reanalysis is compared to those from Coupled Model Intercomparison Project (CMIP5) models and the Geophysical Fluid Dynamics Laboratory high-resolution atmospheric model (HIRAM-360 and -180). With the caveat that a minimum rain rate threshold is important in the models (which tend to overproduce low rain rates), the models agree well with observations in leading properties. In particular, scale-free power law ranges in which the probability drops slowly with increasing cluster size are well modeled, followed by a rapid drop in probability of the largest clusters above a cutoff scale. Under the RCP 8.5 global warming scenario, the models indicate substantial increases in probability (up to an order of magnitude) of the largest clusters by the end of century. For models with continuous time series of high resolution output, there is substantial spread on when these probability increases for the largest precipitation clusters should be detectable, ranging from detectable within the observational period to statistically significant trends emerging only in the second half of the century. Examination of NCEP reanalysis and SSMI/SSMIS series of satellite retrievals from 1979 to present does not yield reliable evidence of trends at this time. The results suggest improvements in inter-satellite calibration of the SSMI/SSMIS retrievals could aid future detection.

  18. Clustering WHO-ART Terms Using Semantic Distance and Machine Learning Algorithms

    PubMed Central

    Iavindrasana, Jimison; Bousquet, Cedric; Degoulet, Patrice; Jaulent, Marie-Christine

    2006-01-01

    WHO-ART was developed by the WHO collaborating centre for international drug monitoring in order to code adverse drug reactions. We assume that computation of semantic distance between WHO-ART terms may be an efficient way to group related medical conditions in the WHO database in order to improve signal detection. Our objective was to develop a method for clustering WHO-ART terms according to some proximity of their meanings. Our material comprises 758 WHO-ART terms. A formal definition was acquired for each term as a list of elementary concepts belonging to SNOMED international axes and characterized by modifier terms in some cases. Clustering was implemented as a terminology service on a J2EE server. Two different unsupervised machine learning algorithms (KMeans, Pvclust) clustered WHO-ART terms according to a semantic distance operator previously described. Pvclust grouped 51% of WHO-ART terms. K-Means grouped 100% of WHO-ART terms but 25% clusters were heterogeneous with k = 180 clusters and 6% clusters were heterogeneous with k = 32 clusters. Clustering algorithms associated to semantic distance could suggest potential groupings of WHO-ART terms that need validation according to the user’s requirements. PMID:17238365

  19. Clustering WHO-ART terms using semantic distance and machine learning algorithms.

    PubMed

    Iavindrasana, Jimison; Bousquet, Cedric; Degoulet, Patrice; Jaulent, Marie-Christine

    2006-01-01

    WHO-ART was developed by the WHO collaborating centre for international drug monitoring in order to code adverse drug reactions. We assume that computation of semantic distance between WHO-ART terms may be an efficient way to group related medical conditions in the WHO database in order to improve signal detection. Our objective was to develop a method for clustering WHO-ART terms according to some proximity of their meanings. Our material comprises 758 WHO-ART terms. A formal definition was acquired for each term as a list of elementary concepts belonging to SNOMED international axes and characterized by modifier terms in some cases. Clustering was implemented as a terminology service on a J2EE server. Two different unsupervised machine learning algorithms (KMeans, Pvclust) clustered WHO-ART terms according to a semantic distance operator previously described. Pvclust grouped 51% of WHO-ART terms. K-Means grouped 100% of WHO-ART terms but 25% clusters were heterogeneous with k = 180 clusters and 6% clusters were heterogeneous with k = 32 clusters. Clustering algorithms associated to semantic distance could suggest potential groupings of WHO-ART terms that need validation according to the user's requirements.

  20. Improved evolutionary algorithm for the global optimization of clusters with competing attractive and repulsive interactions

    NASA Astrophysics Data System (ADS)

    Cruz, S. M. A.; Marques, J. M. C.; Pereira, F. B.

    2016-10-01

    We propose improvements to our evolutionary algorithm (EA) [J. M. C. Marques and F. B. Pereira, J. Mol. Liq. 210, 51 (2015)] in order to avoid dissociative solutions in the global optimization of clusters with competing attractive and repulsive interactions. The improved EA outperforms the original version of the method for charged colloidal clusters in the size range 3 ≤ N ≤ 25, which is a very stringent test for global optimization algorithms. While the Bernal spiral is the global minimum for clusters in the interval 13 ≤ N ≤ 18, the lowest-energy structure is a peculiar, so-called beaded-necklace, motif for 19 ≤ N ≤ 25. We have also applied the method for larger sizes and unusual quasi-linear and branched clusters arise as low-energy structures.

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

    PubMed Central

    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. PMID:26447713

  2. Spitzer IR Colors and ISM Distributions of Virgo Cluster Spirals

    NASA Astrophysics Data System (ADS)

    Kenney, Jeffrey D.; Wong, I.; Kenney, Z.; Murphy, E.; Helou, G.; Howell, J.

    2012-01-01

    IRAC infrared images of 44 spiral and peculiar galaxies from the Spitzer Survey of the Virgo Cluster help reveal the interactions which transform galaxies in clusters. We explore how the location of galaxies in the IR 3.6-8μm color-magnitude diagram is related to the spatial distributions of ISM/star formation, as traced by PAH emission in the 8μm band. Based on their 8μm/PAH radial distributions, we divide the galaxies into 4 groups: normal, truncated, truncated/compact, and anemic. Normal galaxies have relatively normal PAH distributions. They are the "bluest" galaxies, with the largest 8/3.6μm ratios. They are relatively unaffected by the cluster environment, and have probably never passed through the cluster core. Truncated galaxies have a relatively normal 8μm/PAH surface brightness in the inner disk, but are abruptly truncated with little or no emission in the outer disk. They have intermediate ("green") colors, while those which are more severely truncated are "redder". Most truncated galaxies have undisturbed stellar disks and many show direct evidence of active ram pressure stripping. Truncated/compact galaxies have high 8μm/PAH surface brightness in the very inner disk (central 1 kpc) but are abruptly truncated close to center with little or no emission in the outer disk. They have intermediate global colors, similar to the other truncated galaxies. While they have the most extreme ISM truncation, they have vigorous circumnuclear star formation. Most of these have disturbed stellar disks, and they are probably produced by a combination of gravitational interaction plus ram pressure stripping. Anemic galaxies have a low 8μm/PAH surface brightness even in the inner disk. These are the "reddest" galaxies, with the smallest 8/3.6μm ratios. The origin of the anemics seems to a combination of starvation, gravitational interactions, and long-ago ram pressure stripping.

  3. Cluster Monte Carlo distributions in fractal dimensions between two and three: Scaling properties and dynamical aspects for the Ising model

    NASA Astrophysics Data System (ADS)

    Monceau, Pascal; Hsiao, Pai-Yi

    2002-09-01

    We study the Wolff cluster size distributions obtained from Monte Carlo simulations of the Ising phase transition on Sierpinski fractals with Hausdorff dimensions Df between 2 and 3. These distributions are shown to be invariant when going from an iteration step of the fractal to the next under a scaling of the cluster sizes involving the exponent (β/ν)+(γ/ν). Moreover, the decay of the autocorrelation functions at the critical points enables us to calculate the Wolff dynamical critical exponents z for three different values of Df. The Wolff algorithm is more efficient in reducing the critical slowing down when Df is lowered.

  4. A Game Theory Algorithm for Intra-Cluster Data Aggregation in a Vehicular Ad Hoc Network.

    PubMed

    Chen, Yuzhong; Weng, Shining; Guo, Wenzhong; Xiong, Naixue

    2016-02-19

    Vehicular ad hoc networks (VANETs) have an important role in urban management and planning. The effective integration of vehicle information in VANETs is critical to traffic analysis, large-scale vehicle route planning and intelligent transportation scheduling. However, given the limitations in the precision of the output information of a single sensor and the difficulty of information sharing among various sensors in a highly dynamic VANET, effectively performing data aggregation in VANETs remains a challenge. Moreover, current studies have mainly focused on data aggregation in large-scale environments but have rarely discussed the issue of intra-cluster data aggregation in VANETs. In this study, we propose a multi-player game theory algorithm for intra-cluster data aggregation in VANETs by analyzing the competitive and cooperative relationships among sensor nodes. Several sensor-centric metrics are proposed to measure the data redundancy and stability of a cluster. We then study the utility function to achieve efficient intra-cluster data aggregation by considering both data redundancy and cluster stability. In particular, we prove the existence of a unique Nash equilibrium in the game model, and conduct extensive experiments to validate the proposed algorithm. Results demonstrate that the proposed algorithm has advantages over typical data aggregation algorithms in both accuracy and efficiency.

  5. A Game Theory Algorithm for Intra-Cluster Data Aggregation in a Vehicular Ad Hoc Network

    PubMed Central

    Chen, Yuzhong; Weng, Shining; Guo, Wenzhong; Xiong, Naixue

    2016-01-01

    Vehicular ad hoc networks (VANETs) have an important role in urban management and planning. The effective integration of vehicle information in VANETs is critical to traffic analysis, large-scale vehicle route planning and intelligent transportation scheduling. However, given the limitations in the precision of the output information of a single sensor and the difficulty of information sharing among various sensors in a highly dynamic VANET, effectively performing data aggregation in VANETs remains a challenge. Moreover, current studies have mainly focused on data aggregation in large-scale environments but have rarely discussed the issue of intra-cluster data aggregation in VANETs. In this study, we propose a multi-player game theory algorithm for intra-cluster data aggregation in VANETs by analyzing the competitive and cooperative relationships among sensor nodes. Several sensor-centric metrics are proposed to measure the data redundancy and stability of a cluster. We then study the utility function to achieve efficient intra-cluster data aggregation by considering both data redundancy and cluster stability. In particular, we prove the existence of a unique Nash equilibrium in the game model, and conduct extensive experiments to validate the proposed algorithm. Results demonstrate that the proposed algorithm has advantages over typical data aggregation algorithms in both accuracy and efficiency. PMID:26907272

  6. Nearest hyperplane distance neighbor clustering algorithm applied to gene co-expression analysis in Alzheimer's disease.

    PubMed

    Pasluosta, Cristian F; Dua, Prerna; Lukiw, Walter J

    2011-01-01

    Microarray analysis can contribute considerably to the understanding of biologically significant cellular mechanisms that yield novel information regarding co-regulated sets of gene patterns. Clustering is one of the most popular tools for analyzing DNA microarray data. In this paper, we present an unsupervised clustering algorithm based on the K-local hyperplane distance nearest-neighbor classifier (HKNN). We adapted the well-known nearest neighbor clustering algorithm for use with hyperplane distance. The result is a simple and computationally inexpensive unsupervised clustering algorithm that can be applied to high-dimensional data. It has been reported that the NFkB1 gene is progressively over-expressed in moderate-to-severe Alzheimer's disease (AD) cases, and that the NF-kB complex plays a key role in neuroinflammatory responses in AD pathogenesis. In this study, we apply the proposed clustering algorithm to identify co-expression patterns with the NFkB1 in gene expression data from hippocampal tissue samples. Finally, we validate our experiments with biomedical literature search.

  7. A Fusion Method of Gabor Wavelet Transform and Unsupervised Clustering Algorithms for Tissue Edge Detection

    PubMed Central

    Ergen, Burhan

    2014-01-01

    This paper proposes two edge detection methods for medical images by integrating the advantages of Gabor wavelet transform (GWT) and unsupervised clustering algorithms. The GWT is used to enhance the edge information in an image while suppressing noise. Following this, the k-means and Fuzzy c-means (FCM) clustering algorithms are used to convert a gray level image into a binary image. The proposed methods are tested using medical images obtained through Computed Tomography (CT) and Magnetic Resonance Imaging (MRI) devices, and a phantom image. The results prove that the proposed methods are successful for edge detection, even in noisy cases. PMID:24790590

  8. Study of item matching algorithm based on bipartite graph joint clustering for technology transaction platform

    NASA Astrophysics Data System (ADS)

    Zhu, Ming; Huang, Nana; Yan, Cairong

    2013-03-01

    For How to match supply items with demand items is the most important on technology transaction platform. A matching algorithm based on bipartite graph is proposed in this paper. Firstly, by abstracting characters the suppliers and demanders can be clustered into groups based on bipartite graph joint clustering method. Then, an incidence matrix between items in each group is built which is used to find the optimal matching relation. The simulate experiment results showed that the algorithm can return the item pairs of biggest transaction probability so as to make the Technology transaction platform efficient and profit.

  9. The Development of FPGA-Based Pseudo-Iterative Clustering Algorithms

    NASA Astrophysics Data System (ADS)

    Drueke, Elizabeth; Fisher, Wade; Plucinski, Pawel

    2016-03-01

    The Large Hadron Collider (LHC) in Geneva, Switzerland, is set to undergo major upgrades in 2025 in the form of the High-Luminosity Large Hadron Collider (HL-LHC). In particular, several hardware upgrades are proposed to the ATLAS detector, one of the two general purpose detectors. These hardware upgrades include, but are not limited to, a new hardware-level clustering algorithm, to be performed by a field programmable gate array, or FPGA. In this study, we develop that clustering algorithm and compare the output to a Python-implemented topoclustering algorithm developed at the University of Oregon. Here, we present the agreement between the FPGA output and expected output, with particular attention to the time required by the FPGA to complete the algorithm and other limitations set by the FPGA itself.

  10. Node Non-Uniform Deployment Based on Clustering Algorithm for Underwater Sensor Networks

    PubMed Central

    Jiang, Peng; Liu, Jun; Wu, Feng

    2015-01-01

    A node non-uniform deployment based on clustering algorithm for underwater sensor networks (UWSNs) is proposed in this study. This algorithm is proposed because optimizing network connectivity rate and network lifetime is difficult for the existing node non-uniform deployment algorithms under the premise of improving the network coverage rate for UWSNs. A high network connectivity rate is achieved by determining the heterogeneous communication ranges of nodes during node clustering. Moreover, the concept of aggregate contribution degree is defined, and the nodes with lower aggregate contribution degrees are used to substitute the dying nodes to decrease the total movement distance of nodes and prolong the network lifetime. Simulation results show that the proposed algorithm can achieve a better network coverage rate and network connectivity rate, as well as decrease the total movement distance of nodes and prolong the network lifetime. PMID:26633408

  11. Distributed-memory Parallel Algorithms for Matching and Coloring

    SciTech Connect

    Catalyurek, Umit; Dobrian, Florin; Gebremedhin, Assefaw H.; Halappanavar, Mahantesh; Pothen, Alex

    2011-05-31

    Graph matching and coloring constitute two fundamental classes of combinatorial problems having numerous established as well as emerging applications in computational science and engineering, high-performance computing, and informatics. We provide a snapshot of an on-going work on the design and implementation of new highly-scalable distributed-memory parallel algorithms for two prototypical problems from these classes, edge-weighted matching and distance-1 vertex coloring. Graph algorithms in general have low concurrency and poor data locality, making it challenging to achieve scalability on massively parallel machines. We overcome this challenge by employing a variety of techniques, including approximation, speculation and iteration, optimized communication, and randomization, in concert. We present preliminary results on weak and strong scalability studies conducted on an IBM Blue Gene/P machine employing up to tens of thousands of processors. The results show that the algorithms hold strong potential for computing at petascale.

  12. An Efficient Algorithm for Clustering of Large-Scale Mass Spectrometry Data.

    PubMed

    Saeed, Fahad; Pisitkun, Trairak; Knepper, Mark A; Hoffert, Jason D

    2012-10-04

    High-throughput spectrometers are capable of producing data sets containing thousands of spectra for a single biological sample. These data sets contain a substantial amount of redundancy from peptides that may get selected multiple times in a LC-MS/MS experiment. In this paper, we present an efficient algorithm, CAMS (Clustering Algorithm for Mass Spectra) for clustering mass spectrometry data which increases both the sensitivity and confidence of spectral assignment. CAMS utilizes a novel metric, called F-set, that allows accurate identification of the spectra that are similar. A graph theoretic framework is defined that allows the use of F-set metric efficiently for accurate cluster identifications. The accuracy of the algorithm is tested on real HCD and CID data sets with varying amounts of peptides. Our experiments show that the proposed algorithm is able to cluster spectra with very high accuracy in a reasonable amount of time for large spectral data sets. Thus, the algorithm is able to decrease the computational time by compressing the data sets while increasing the throughput of the data by interpreting low S/N spectra.

  13. Improving permafrost distribution modelling using feature selection algorithms

    NASA Astrophysics Data System (ADS)

    Deluigi, Nicola; Lambiel, Christophe; Kanevski, Mikhail

    2016-04-01

    The availability of an increasing number of spatial data on the occurrence of mountain permafrost allows the employment of machine learning (ML) classification algorithms for modelling the distribution of the phenomenon. One of the major problems when dealing with high-dimensional dataset is the number of input features (variables) involved. Application of ML classification algorithms to this large number of variables leads to the risk of overfitting, with the consequence of a poor generalization/prediction. For this reason, applying feature selection (FS) techniques helps simplifying the amount of factors required and improves the knowledge on adopted features and their relation with the studied phenomenon. Moreover, taking away irrelevant or redundant variables from the dataset effectively improves the quality of the ML prediction. This research deals with a comparative analysis of permafrost distribution models supported by FS variable importance assessment. The input dataset (dimension = 20-25, 10 m spatial resolution) was constructed using landcover maps, climate data and DEM derived variables (altitude, aspect, slope, terrain curvature, solar radiation, etc.). It was completed with permafrost evidences (geophysical and thermal data and rock glacier inventories) that serve as training permafrost data. Used FS algorithms informed about variables that appeared less statistically important for permafrost presence/absence. Three different algorithms were compared: Information Gain (IG), Correlation-based Feature Selection (CFS) and Random Forest (RF). IG is a filter technique that evaluates the worth of a predictor by measuring the information gain with respect to the permafrost presence/absence. Conversely, CFS is a wrapper technique that evaluates the worth of a subset of predictors by considering the individual predictive ability of each variable along with the degree of redundancy between them. Finally, RF is a ML algorithm that performs FS as part of its

  14. An Auto-Recognizing System for Dice Games Using a Modified Unsupervised Grey Clustering Algorithm.

    PubMed

    Huang, Kuo-Yi

    2008-02-21

    In this paper, a novel identification method based on a machine vision system is proposed to recognize the score of dice. The system employs image processing techniques, and the modified unsupervised grey clustering algorithm (MUGCA) to estimate the location of each die and identify the spot number accurately and effectively. The proposed algorithms are substituted for manual recognition. From the experimental results, it is found that this system is excellent due to its good capabilities which include flexibility, high speed, and high accuracy.

  15. Quantum cluster algorithm for frustrated Ising models in a transverse field

    NASA Astrophysics Data System (ADS)

    Biswas, Sounak; Rakala, Geet; Damle, Kedar

    2016-06-01

    Working within the stochastic series expansion framework, we introduce and characterize a plaquette-based quantum cluster algorithm for quantum Monte Carlo simulations of transverse field Ising models with frustrated Ising exchange interactions. As a demonstration of the capabilities of this algorithm, we show that a relatively small ferromagnetic next-nearest-neighbor coupling drives the transverse field Ising antiferromagnet on the triangular lattice from an antiferromagnetic three-sublattice ordered state at low temperature to a ferrimagnetic three-sublattice ordered state.

  16. A Distributed Geo-Routing Algorithm for Wireless Sensor Networks

    PubMed Central

    Joshi, Gyanendra Prasad; Kim, Sung Won

    2009-01-01

    Geographic wireless sensor networks use position information for greedy routing. Greedy routing works well in dense networks, whereas in sparse networks it may fail and require a recovery algorithm. Recovery algorithms help the packet to get out of the communication void. However, these algorithms are generally costly for resource constrained position-based wireless sensor networks (WSNs). In this paper, we propose a void avoidance algorithm (VAA), a novel idea based on upgrading virtual distance. VAA allows wireless sensor nodes to remove all stuck nodes by transforming the routing graph and forwarding packets using only greedy routing. In VAA, the stuck node upgrades distance unless it finds a next hop node that is closer to the destination than it is. VAA guarantees packet delivery if there is a topologically valid path. Further, it is completely distributed, immediately responds to node failure or topology changes and does not require planarization of the network. NS-2 is used to evaluate the performance and correctness of VAA and we compare its performance to other protocols. Simulations show our proposed algorithm consumes less energy, has an efficient path and substantially less control overheads. PMID:22408514

  17. A distributed geo-routing algorithm for wireless sensor networks.

    PubMed

    Joshi, Gyanendra Prasad; Kim, Sung Won

    2009-01-01

    Geographic wireless sensor networks use position information for greedy routing. Greedy routing works well in dense networks, whereas in sparse networks it may fail and require a recovery algorithm. Recovery algorithms help the packet to get out of the communication void. However, these algorithms are generally costly for resource constrained position-based wireless sensor networks (WSNs). In this paper, we propose a void avoidance algorithm (VAA), a novel idea based on upgrading virtual distance. VAA allows wireless sensor nodes to remove all stuck nodes by transforming the routing graph and forwarding packets using only greedy routing. In VAA, the stuck node upgrades distance unless it finds a next hop node that is closer to the destination than it is. VAA guarantees packet delivery if there is a topologically valid path. Further, it is completely distributed, immediately responds to node failure or topology changes and does not require planarization of the network. NS-2 is used to evaluate the performance and correctness of VAA and we compare its performance to other protocols. Simulations show our proposed algorithm consumes less energy, has an efficient path and substantially less control overheads.

  18. Experimental investigations of size distribution through large van der Waals cluster beam cross-section

    NASA Astrophysics Data System (ADS)

    Yang, Shenghong; Daineka, D. V.; Châtelet, M.

    2003-08-01

    Size distributions through large van der Waals cluster beam cross-section are studied with the pick-up technique. Based on our experimental results, we observed that the larger cluster is always concentrated in the center of the beam. From the center to the periphery, the cluster size gradually decreases. The size distributions through the beam cross-section depend on incoming cluster size and incoming cluster velocity. The larger the incoming cluster size or the faster the incoming cluster velocity, the flatter the size distributions through the beam cross-section are found. These experimental results are interpreted by the Mack focusing effect.

  19. Clustering and Candidate Motif Detection in Exosomal miRNAs by Application of Machine Learning Algorithms.

    PubMed

    Gaur, Pallavi; Chaturvedi, Anoop

    2017-07-22

    The clustering pattern and motifs give immense information about any biological data. An application of machine learning algorithms for clustering and candidate motif detection in miRNAs derived from exosomes is depicted in this paper. Recent progress in the field of exosome research and more particularly regarding exosomal miRNAs has led much bioinformatic-based research to come into existence. The information on clustering pattern and candidate motifs in miRNAs of exosomal origin would help in analyzing existing, as well as newly discovered miRNAs within exosomes. Along with obtaining clustering pattern and candidate motifs in exosomal miRNAs, this work also elaborates the usefulness of the machine learning algorithms that can be efficiently used and executed on various programming languages/platforms. Data were clustered and sequence candidate motifs were detected successfully. The results were compared and validated with some available web tools such as 'BLASTN' and 'MEME suite'. The machine learning algorithms for aforementioned objectives were applied successfully. This work elaborated utility of machine learning algorithms and language platforms to achieve the tasks of clustering and candidate motif detection in exosomal miRNAs. With the information on mentioned objectives, deeper insight would be gained for analyses of newly discovered miRNAs in exosomes which are considered to be circulating biomarkers. In addition, the execution of machine learning algorithms on various language platforms gives more flexibility to users to try multiple iterations according to their requirements. This approach can be applied to other biological data-mining tasks as well.

  20. An improved K-means clustering algorithm in agricultural image segmentation

    NASA Astrophysics Data System (ADS)

    Cheng, Huifeng; Peng, Hui; Liu, Shanmei

    Image segmentation is the first important step to image analysis and image processing. In this paper, according to color crops image characteristics, we firstly transform the color space of image from RGB to HIS, and then select proper initial clustering center and cluster number in application of mean-variance approach and rough set theory followed by clustering calculation in such a way as to automatically segment color component rapidly and extract target objects from background accurately, which provides a reliable basis for identification, analysis, follow-up calculation and process of crops images. Experimental results demonstrate that improved k-means clustering algorithm is able to reduce the computation amounts and enhance precision and accuracy of clustering.

  1. Evaluation of availability of cluster distributed disaster tolerant systems for control and information processing based on a cluster quorum

    NASA Astrophysics Data System (ADS)

    Tsarev, R. Yu; Gruzenkin, D. V.; Kovalev, I. V.; Prokopenko, A. V.; Knyazkov, A. N.

    2016-11-01

    Control and information processing systems, which often executes critical functions, must satisfy requirements not only of fault tolerance, but also of disaster tolerance. Cluster architecture is reasonable to be applied to provide disaster tolerance of these systems. In this case clusters are separate control and information processing centers united by means of communication channels. Thus, clusters are a single hardware resource interacting with each other to achieve system objectives. Remote cluster positioning allows ensuring system availability and disaster tolerance even in case of some units’ failures or a whole cluster crash. A technique for evaluation of availability of cluster distributed systems for control and information processing based on a cluster quorum is presented in the paper. This technique can be applied to different cluster distributed control and information processing systems, claimed to be based on the disaster tolerance principles. In the article we discuss a communications satellite system as an example of a cluster distributed disaster tolerant control and information processing system. Evaluation of availability of the communications satellite system is provided. Possible scenarios of communications satellite system cluster-based components failures were analyzed. The analysis made it possible to choose the best way to implement the cluster structure for a distributed control and information processing system.

  2. Approximation algorithm for the problem of partitioning a sequence into clusters

    NASA Astrophysics Data System (ADS)

    Kel'manov, A. V.; Mikhailova, L. V.; Khamidullin, S. A.; Khandeev, V. I.

    2017-08-01

    We consider the problem of partitioning a finite sequence of Euclidean points into a given number of clusters (subsequences) using the criterion of the minimal sum (over all clusters) of intercluster sums of squared distances from the elements of the clusters to their centers. It is assumed that the center of one of the desired clusters is at the origin, while the center of each of the other clusters is unknown and determined as the mean value over all elements in this cluster. Additionally, the partition obeys two structural constraints on the indices of sequence elements contained in the clusters with unknown centers: (1) the concatenation of the indices of elements in these clusters is an increasing sequence, and (2) the difference between an index and the preceding one is bounded above and below by prescribed constants. It is shown that this problem is strongly NP-hard. A 2-approximation algorithm is constructed that is polynomial-time for a fixed number of clusters.

  3. Cluster algorithms for frustrated two-dimensional Ising antiferromagnets via dual worm constructions

    NASA Astrophysics Data System (ADS)

    Rakala, Geet; Damle, Kedar

    2017-08-01

    We report on the development of two dual worm constructions that lead to cluster algorithms for efficient and ergodic Monte Carlo simulations of frustrated Ising models with arbitrary two-spin interactions that extend up to third-neighbors on the triangular lattice. One of these algorithms generalizes readily to other frustrated systems, such as Ising antiferromagnets on the Kagome lattice with further neighbor couplings. We characterize the performance of both these algorithms in a challenging regime with power-law correlations at finite wave vector.

  4. Experimental realization of the Deutsch-Jozsa algorithm with a six-qubit cluster state

    SciTech Connect

    Vallone, Giuseppe; Donati, Gaia; Bruno, Natalia; Chiuri, Andrea; Mataloni, Paolo

    2010-05-15

    We describe an experimental realization of the Deutsch-Jozsa quantum algorithm to evaluate the properties of a two-bit Boolean function in the framework of one-way quantum computation. For this purpose, a two-photon six-qubit cluster state was engineered. Its peculiar topological structure is the basis of the original measurement pattern allowing the algorithm realization. The good agreement of the experimental results with the theoretical predictions, obtained at {approx}1 kHz success rate, demonstrates the correct implementation of the algorithm.

  5. A Clustering Algorithm for Liver Lesion Segmentation of Diffusion-Weighted MR Images

    PubMed Central

    Jha, Abhinav K.; Rodríguez, Jeffrey J.; Stephen, Renu M.; Stopeck, Alison T.

    2010-01-01

    In diffusion-weighted magnetic resonance imaging, accurate segmentation of liver lesions in the diffusion-weighted images is required for computation of the apparent diffusion coefficient (ADC) of the lesion, the parameter that serves as an indicator of lesion response to therapy. However, the segmentation problem is challenging due to low SNR, fuzzy boundaries and speckle and motion artifacts. We propose a clustering algorithm that incorporates spatial information and a geometric constraint to solve this issue. We show that our algorithm provides improved accuracy compared to existing segmentation algorithms. PMID:21151837

  6. An Evaluation of Biosurveillance Grid—Dynamic Algorithm Distribution Across Multiple Computer Nodes

    PubMed Central

    Tsai, Ming-Chi; Tsui, Fu-Chiang; Wagner, Michael M.

    2007-01-01

    Performing fast data analysis to detect disease outbreaks plays a critical role in real-time biosurveillance. In this paper, we described and evaluated an Algorithm Distribution Manager Service (ADMS) based on grid technologies, which dynamically partition and distribute detection algorithms across multiple computers. We compared the execution time to perform the analysis on a single computer and on a grid network (3 computing nodes) with and without using dynamic algorithm distribution. We found that algorithms with long runtime completed approximately three times earlier in distributed environment than in a single computer while short runtime algorithms performed worse in distributed environment. A dynamic algorithm distribution approach also performed better than static algorithm distribution approach. This pilot study shows a great potential to reduce lengthy analysis time through dynamic algorithm partitioning and parallel processing, and provides the opportunity of distributing algorithms from a client to remote computers in a grid network. PMID:18693936

  7. An evaluation of biosurveillance grid--dynamic algorithm distribution across multiple computer nodes.

    PubMed

    Tsai, Ming-Chi; Tsui, Fu-Chiang; Wagner, Michael M

    2007-10-11

    Performing fast data analysis to detect disease outbreaks plays a critical role in real-time biosurveillance. In this paper, we described and evaluated an Algorithm Distribution Manager Service (ADMS) based on grid technologies, which dynamically partition and distribute detection algorithms across multiple computers. We compared the execution time to perform the analysis on a single computer and on a grid network (3 computing nodes) with and without using dynamic algorithm distribution. We found that algorithms with long runtime completed approximately three times earlier in distributed environment than in a single computer while short runtime algorithms performed worse in distributed environment. A dynamic algorithm distribution approach also performed better than static algorithm distribution approach. This pilot study shows a great potential to reduce lengthy analysis time through dynamic algorithm partitioning and parallel processing, and provides the opportunity of distributing algorithms from a client to remote computers in a grid network.

  8. Design of multiple sequence alignment algorithms on parallel, distributed memory supercomputers.

    PubMed

    Church, Philip C; Goscinski, Andrzej; Holt, Kathryn; Inouye, Michael; Ghoting, Amol; Makarychev, Konstantin; Reumann, Matthias

    2011-01-01

    The challenge of comparing two or more genomes that have undergone recombination and substantial amounts of segmental loss and gain has recently been addressed for small numbers of genomes. However, datasets of hundreds of genomes are now common and their sizes will only increase in the future. Multiple sequence alignment of hundreds of genomes remains an intractable problem due to quadratic increases in compute time and memory footprint. To date, most alignment algorithms are designed for commodity clusters without parallelism. Hence, we propose the design of a multiple sequence alignment algorithm on massively parallel, distributed memory supercomputers to enable research into comparative genomics on large data sets. Following the methodology of the sequential progressiveMauve algorithm, we design data structures including sequences and sorted k-mer lists on the IBM Blue Gene/P supercomputer (BG/P). Preliminary results show that we can reduce the memory footprint so that we can potentially align over 250 bacterial genomes on a single BG/P compute node. We verify our results on a dataset of E.coli, Shigella and S.pneumoniae genomes. Our implementation returns results matching those of the original algorithm but in 1/2 the time and with 1/4 the memory footprint for scaffold building. In this study, we have laid the basis for multiple sequence alignment of large-scale datasets on a massively parallel, distributed memory supercomputer, thus enabling comparison of hundreds instead of a few genome sequences within reasonable time.

  9. Solving the depth of the repeated texture areas based on the clustering algorithm

    NASA Astrophysics Data System (ADS)

    Xiong, Zhang; Zhang, Jun; Tian, Jinwen

    2015-12-01

    The reconstruction of the 3D scene in the monocular stereo vision needs to get the depth of the field scenic points in the picture scene. But there will inevitably be error matching in the process of image matching, especially when there are a large number of repeat texture areas in the images, there will be lots of error matches. At present, multiple baseline stereo imaging algorithm is commonly used to eliminate matching error for repeated texture areas. This algorithm can eliminate the ambiguity correspond to common repetition texture. But this algorithm has restrictions on the baseline, and has low speed. In this paper, we put forward an algorithm of calculating the depth of the matching points in the repeat texture areas based on the clustering algorithm. Firstly, we adopt Gauss Filter to preprocess the images. Secondly, we segment the repeated texture regions in the images into image blocks by using spectral clustering segmentation algorithm based on super pixel and tag the image blocks. Then, match the two images and solve the depth of the image. Finally, the depth of the image blocks takes the median in all depth values of calculating point in the bock. So the depth of repeated texture areas is got. The results of a lot of image experiments show that the effect of our algorithm for calculating the depth of repeated texture areas is very good.

  10. A multilevel gamma-clustering layout algorithm for visualization of biological networks.

    PubMed

    Hruz, Tomas; Wyss, Markus; Lucas, Christoph; Laule, Oliver; von Rohr, Peter; Zimmermann, Philip; Bleuler, Stefan

    2013-01-01

    Visualization of large complex networks has become an indispensable part of systems biology, where organisms need to be considered as one complex system. The visualization of the corresponding network is challenging due to the size and density of edges. In many cases, the use of standard visualization algorithms can lead to high running times and poorly readable visualizations due to many edge crossings. We suggest an approach that analyzes the structure of the graph first and then generates a new graph which contains specific semantic symbols for regular substructures like dense clusters. We propose a multilevel gamma-clustering layout visualization algorithm (MLGA) which proceeds in three subsequent steps: (i) a multilevel γ -clustering is used to identify the structure of the underlying network, (ii) the network is transformed to a tree, and (iii) finally, the resulting tree which shows the network structure is drawn using a variation of a force-directed algorithm. The algorithm has a potential to visualize very large networks because it uses modern clustering heuristics which are optimized for large graphs. Moreover, most of the edges are removed from the visual representation which allows keeping the overview over complex graphs with dense subgraphs.

  11. Scalable method for demonstrating the Deutsch-Jozsa and Bernstein-Vazirani algorithms using cluster states

    SciTech Connect

    Tame, M. S.; Kim, M. S.

    2010-09-15

    We show that fundamental versions of the Deutsch-Jozsa and Bernstein-Vazirani quantum algorithms can be performed using a small entangled cluster state resource of only six qubits. We then investigate the minimal resource states needed to demonstrate general n-qubit versions and a scalable method to produce them. For this purpose, we propose a versatile photonic on-chip setup.

  12. A genetic algorithm using hyper-quadtrees for low-dimensional K-means clustering.

    PubMed

    Laszlo, Michael; Mukherjee, Sumitra

    2006-04-01

    The k-means algorithm is widely used for clustering because of its computational efficiency. Given n points in d-dimensional space and the number of desired clusters k, k-means seeks a set of k cluster centers so as to minimize the sum of the squared Euclidean distance between each point and its nearest cluster center. However, the algorithm is very sensitive to the initial selection of centers and is likely to converge to partitions that are significantly inferior to the global optimum. We present a genetic algorithm (GA) for evolving centers in the k-means algorithm that simultaneously identifies good partitions for a range of values around a specified k. The set of centers is represented using a hyper-quadtree constructed on the data. This representation is exploited in our GA to generate an initial population of good centers and to support a novel crossover operation that selectively passes good subsets of neighboring centers from parents to offspring by swapping subtrees. Experimental results indicate that our GA finds the global optimum for data sets with known optima and finds good solutions for large simulated data sets.

  13. Cluster algorithm for two-dimensional U(1) lattice gauge theory

    NASA Astrophysics Data System (ADS)

    Sinclair, R.

    1992-03-01

    We use gauge fixing to rewrite the two-dimensional U(1) pure gauge model with Wilson action and periodic boundary conditions as a nonfrustrated XY model on a closed chain. The Wolff single-cluster algorithm is then applied, eliminating critical slowing down of topological modes and Polyakov loops.

  14. NEW MDS AND CLUSTERING BASED ALGORITHMS FOR PROTEIN MODEL QUALITY ASSESSMENT AND SELECTION.

    PubMed

    Wang, Qingguo; Shang, Charles; Xu, Dong; Shang, Yi

    2013-10-25

    In protein tertiary structure prediction, assessing the quality of predicted models is an essential task. Over the past years, many methods have been proposed for the protein model quality assessment (QA) and selection problem. Despite significant advances, the discerning power of current methods is still unsatisfactory. In this paper, we propose two new algorithms, CC-Select and MDS-QA, based on multidimensional scaling and k-means clustering. For the model selection problem, CC-Select combines consensus with clustering techniques to select the best models from a given pool. Given a set of predicted models, CC-Select first calculates a consensus score for each structure based on its average pairwise structural similarity to other models. Then, similar structures are grouped into clusters using multidimensional scaling and clustering algorithms. In each cluster, the one with the highest consensus score is selected as a candidate model. For the QA problem, MDS-QA combines single-model scoring functions with consensus to determine more accurate assessment score for every model in a given pool. Using extensive benchmark sets of a large collection of predicted models, we compare the two algorithms with existing state-of-the-art quality assessment methods and show significant improvement.

  15. An effective trust-based recommendation method using a novel graph clustering algorithm

    NASA Astrophysics Data System (ADS)

    Moradi, Parham; Ahmadian, Sajad; Akhlaghian, Fardin

    2015-10-01

    Recommender systems are programs that aim to provide personalized recommendations to users for specific items (e.g. music, books) in online sharing communities or on e-commerce sites. Collaborative filtering methods are important and widely accepted types of recommender systems that generate recommendations based on the ratings of like-minded users. On the other hand, these systems confront several inherent issues such as data sparsity and cold start problems, caused by fewer ratings against the unknowns that need to be predicted. Incorporating trust information into the collaborative filtering systems is an attractive approach to resolve these problems. In this paper, we present a model-based collaborative filtering method by applying a novel graph clustering algorithm and also considering trust statements. In the proposed method first of all, the problem space is represented as a graph and then a sparsest subgraph finding algorithm is applied on the graph to find the initial cluster centers. Then, the proposed graph clustering algorithm is performed to obtain the appropriate users/items clusters. Finally, the identified clusters are used as a set of neighbors to recommend unseen items to the current active user. Experimental results based on three real-world datasets demonstrate that the proposed method outperforms several state-of-the-art recommender system methods.

  16. Performance evaluation of simple linear iterative clustering algorithm on medical image processing.

    PubMed

    Cong, Jinyu; Wei, Benzheng; Yin, Yilong; Xi, Xiaoming; Zheng, Yuanjie

    2014-01-01

    Simple Linear Iterative Clustering (SLIC) algorithm is increasingly applied to different kinds of image processing because of its excellent perceptually meaningful characteristics. In order to better meet the needs of medical image processing and provide technical reference for SLIC on the application of medical image segmentation, two indicators of boundary accuracy and superpixel uniformity are introduced with other indicators to systematically analyze the performance of SLIC algorithm, compared with Normalized cuts and Turbopixels algorithm. The extensive experimental results show that SLIC is faster and less sensitive to the image type and the setting superpixel number than other similar algorithms such as Turbopixels and Normalized cuts algorithms. And it also has a great benefit to the boundary recall, the robustness of fuzzy boundary, the setting superpixel size and the segmentation performance on medical image segmentation.

  17. Unsupervised unstained cell detection by SIFT keypoint clustering and self-labeling algorithm.

    PubMed

    Muallal, Firas; Schöll, Simon; Sommerfeldt, Björn; Maier, Andreas; Steidl, Stefan; Buchholz, Rainer; Hornegger, Joachim

    2014-01-01

    We propose a novel unstained cell detection algorithm based on unsupervised learning. The algorithm utilizes the scale invariant feature transform (SIFT), a self-labeling algorithm, and two clustering steps in order to achieve high performance in terms of time and detection accuracy. Unstained cell imaging is dominated by phase contrast and bright field microscopy. Therefore, the algorithm was assessed on images acquired using these two modalities. Five cell lines having in total 37 images and 7250 cells were considered for the evaluation: CHO, L929, Sf21, HeLa, and Bovine cells. The obtained F-measures were between 85.1 and 89.5. Compared to the state-of-the-art, the algorithm achieves very close F-measure to the supervised approaches in much less time.

  18. Community detection in complex networks using density-based clustering algorithm and manifold learning

    NASA Astrophysics Data System (ADS)

    You, Tao; Cheng, Hui-Min; Ning, Yi-Zi; Shia, Ben-Chang; Zhang, Zhong-Yuan

    2016-12-01

    Like clustering analysis, community detection aims at assigning nodes in a network into different communities. Fdp is a recently proposed density-based clustering algorithm which does not need the number of clusters as prior input and the result is insensitive to its parameter. However, Fdp cannot be directly applied to community detection due to its inability to recognize the community centers in the network. To solve the problem, a new community detection method (named IsoFdp) is proposed in this paper. First, we use IsoMap technique to map the network data into a low dimensional manifold which can reveal diverse pair-wised similarity. Then Fdp is applied to detect the communities in the network. An improved partition density function is proposed to select the proper number of communities automatically. We test our method on both synthetic and real-world networks, and the results demonstrate the effectiveness of our algorithm over the state-of-the-art methods.

  19. Minimum mutual information based level set clustering algorithm for fast MRI tissue segmentation.

    PubMed

    Dai, Shuanglu; Man, Hong; Zhan, Shu

    2015-01-01

    Accurate and accelerated MRI tissue recognition is a crucial preprocessing for real-time 3d tissue modeling and medical diagnosis. This paper proposed an information de-correlated clustering algorithm implemented by variational level set method for fast tissue segmentation. The key idea is to design a local correlation term between original image and piecewise constant into the variational framework. The minimized correlation will then lead to de-correlated piecewise regions. Firstly, by introducing a continuous bounded variational domain describing the image, a probabilistic image restoration model is assumed to modify the distortion. Secondly, regional mutual information is introduced to measure the correlation between piecewise regions and original images. As a de-correlated description of the image, piecewise constants are finally solved by numerical approximation and level set evolution. The converged piecewise constants automatically clusters image domain into discriminative regions. The segmentation results show that our algorithm performs well in terms of time consuming, accuracy, convergence and clustering capability.

  20. Hybridization of evolutionary algorithms and local search by means of a clustering method.

    PubMed

    Martínez-Estudillo, Alfonso C; Hervás-Martínez, César; Martínez-Estudillo, Francisco J; García-Pedrajas, Nicolás

    2006-06-01

    This paper presents a hybrid evolutionary algorithm (EA) to solve nonlinear-regression problems. Although EAs have proven their ability to explore large search spaces, they are comparatively inefficient in fine tuning the solution. This drawback is usually avoided by means of local optimization algorithms that are applied to the individuals of the population. The algorithms that use local optimization procedures are usually called hybrid algorithms. On the other hand, it is well known that the clustering process enables the creation of groups (clusters) with mutually close points that hopefully correspond to relevant regions of attraction. Local-search procedures can then be started once in every such region. This paper proposes the combination of an EA, a clustering process, and a local-search procedure to the evolutionary design of product-units neural networks. In the methodology presented, only a few individuals are subject to local optimization. Moreover, the local optimization algorithm is only applied at specific stages of the evolutionary process. Our results show a favorable performance when the regression method proposed is compared to other standard methods.

  1. A Grouping Method of Distribution Substations Using Cluster Analysis

    NASA Astrophysics Data System (ADS)

    Ohtaka, Toshiya; Iwamoto, Shinichi

    Recently, it has been considered to group distribution substations together for evaluating the reinforcement planning of distribution systems. However, the grouping is carried out by the knowledge and experience of an expert who is in charge of distribution systems, and a subjective feeling of a human being causes ambiguous grouping at the moment. Therefore, a method for imitating the grouping by the expert has been desired in order to carry out a systematic grouping which has numerical corroboration. In this paper, we propose a grouping method of distribution substations using cluster analysis based on the interconnected power between the distribution substations. Moreover, we consider the geographical constraints such as rivers, roads, business office boundaries and branch boundaries, and also examine a method for adjusting the interconnected power. Simulations are carried out to verify the validity of the proposed method using an example system. From the simulation results, we can find that the imitation of the grouping by the expert becomes possible due to considering the geographical constraints and adjusting the interconnected power, and also the calculation time and iterations can be greatly reduced by introducing the local and tabu search methods.

  2. Performance Enhancement of Radial Distributed System with Distributed Generators by Reconfiguration Using Binary Firefly Algorithm

    NASA Astrophysics Data System (ADS)

    Rajalakshmi, N.; Padma Subramanian, D.; Thamizhavel, K.

    2015-03-01

    The extent of real power loss and voltage deviation associated with overloaded feeders in radial distribution system can be reduced by reconfiguration. Reconfiguration is normally achieved by changing the open/closed state of tie/sectionalizing switches. Finding optimal switch combination is a complicated problem as there are many switching combinations possible in a distribution system. Hence optimization techniques are finding greater importance in reducing the complexity of reconfiguration problem. This paper presents the application of firefly algorithm (FA) for optimal reconfiguration of radial distribution system with distributed generators (DG). The algorithm is tested on IEEE 33 bus system installed with DGs and the results are compared with binary genetic algorithm. It is found that binary FA is more effective than binary genetic algorithm in achieving real power loss reduction and improving voltage profile and hence enhancing the performance of radial distribution system. Results are found to be optimum when DGs are added to the test system, which proved the impact of DGs on distribution system.

  3. Calculation of the probability distribution of basic clusters involved in cluster-variation approximations to the Ising model

    NASA Astrophysics Data System (ADS)

    Vinograd, Victor L.; Saxena, Surendra K.; Putnis, Andrew

    1997-11-01

    The free energy of the Ising model in the cluster-variation method (CVM) is traditionally described as a function of many configuration variables (correlation functions) the number of which is equal to the number of all distinct subclusters of the chosen set of basic clusters. According to the present approach the description of the equilibrium distribution of basic clusters such as point, pair, triangle, square, hexagon, octagon, tetrahedron, cube, and octahedron requires no more than four basic variables corresponding to the four basic subclusters, namely, point, pair, triangle, and tetrahedron. The values of all other correlation functions can be found with the help of a set of irreversible transformations on basic clusters which equilibrate the cluster distributions with respect to the given distribution of their basic subclusters. The decrease in the number of cluster variables results in a significant simplification of formulation and minimization of the free-energy expressions used in the CVM.

  4. A Parallel Ghosting Algorithm for The Flexible Distributed Mesh Database

    DOE PAGES

    Mubarak, Misbah; Seol, Seegyoung; Lu, Qiukai; ...

    2013-01-01

    Critical to the scalability of parallel adaptive simulations are parallel control functions including load balancing, reduced inter-process communication and optimal data decomposition. In distributed meshes, many mesh-based applications frequently access neighborhood information for computational purposes which must be transmitted efficiently to avoid parallel performance degradation when the neighbors are on different processors. This article presents a parallel algorithm of creating and deleting data copies, referred to as ghost copies, which localize neighborhood data for computation purposes while minimizing inter-process communication. The key characteristics of the algorithm are: (1) It can create ghost copies of any permissible topological order inmore » a 1D, 2D or 3D mesh based on selected adjacencies. (2) It exploits neighborhood communication patterns during the ghost creation process thus eliminating all-to-all communication. (3) For applications that need neighbors of neighbors, the algorithm can create n number of ghost layers up to a point where the whole partitioned mesh can be ghosted. Strong and weak scaling results are presented for the IBM BG/P and Cray XE6 architectures up to a core count of 32,768 processors. The algorithm also leads to scalable results when used in a parallel super-convergent patch recovery error estimator, an application that frequently accesses neighborhood data to carry out computation.« less

  5. Whistler Waves Driven by Anisotropic Strahl Velocity Distributions: Cluster Observations

    NASA Technical Reports Server (NTRS)

    Vinas, A.F.; Gurgiolo, C.; Nieves-Chinchilla, T.; Gary, S. P.; Goldstein, M. L.

    2010-01-01

    Observed properties of the strahl using high resolution 3D electron velocity distribution data obtained from the Cluster/PEACE experiment are used to investigate its linear stability. An automated method to isolate the strahl is used to allow its moments to be computed independent of the solar wind core+halo. Results show that the strahl can have a high temperature anisotropy (T(perpindicular)/T(parallell) approximately > 2). This anisotropy is shown to be an important free energy source for the excitation of high frequency whistler waves. The analysis suggests that the resultant whistler waves are strong enough to regulate the electron velocity distributions in the solar wind through pitch-angle scattering

  6. CHIMERA: Clustering of Heterogeneous Disease Effects via Distribution Matching of Imaging Patterns.

    PubMed

    Dong, Aoyan; Honnorat, Nicolas; Gaonkar, Bilwaj; Davatzikos, Christos

    2016-02-01

    Many brain disorders and diseases exhibit heterogeneous symptoms and imaging characteristics. This heterogeneity is typically not captured by commonly adopted neuroimaging analyses that seek only a main imaging pattern when two groups need to be differentiated (e.g., patients and controls, or clinical progressors and non-progressors). We propose a novel probabilistic clustering approach, CHIMERA, modeling the pathological process by a combination of multiple regularized transformations from normal/control population to the patient population, thereby seeking to identify multiple imaging patterns that relate to disease effects and to better characterize disease heterogeneity. In our framework, normal and patient populations are considered as point distributions that are matched by a variant of the coherent point drift algorithm. We explain how the posterior probabilities produced during the MAP optimization of CHIMERA can be used for clustering the patients into groups and identifying disease subtypes. CHIMERA was first validated on a synthetic dataset and then on a clinical dataset mixing 317 control subjects and patients suffering from Alzheimer's Disease (AD) and Parkison's Disease (PD). CHIMERA produced better clustering results compared to two standard clustering approaches. We further analyzed 390 T1 MRI scans from Alzheimer's patients. We discovered two main and reproducible AD subtypes displaying significant differences in cognitive performance.

  7. Numerical convergence and interpretation of the fuzzy c-shells clustering algorithm.

    PubMed

    Bezdek, J C; Hathaway, R J

    1992-01-01

    R. N. Dave's (1990) version of fuzzy c-shells is an iterative clustering algorithm which requires the application of Newton's method or a similar general optimization technique at each half step in any sequence of iterates for minimizing the associated objective function. An important computational question concerns the accuracy of the solution required at each half step within the overall iteration. The general convergence theory for grouped coordination minimization is applied to this question to show that numerically exact solution of the half-step subproblems in Dave's algorithm is not necessary. One iteration of Newton's method in each coordinate minimization half step yields a sequence obtained using the fuzzy c-shells algorithm with numerically exact coordinate minimization at each half step. It is shown that fuzzy c-shells generates hyperspherical prototypes to the clusters it finds for certain special cases of the measure of dissimilarity used.

  8. Reexamining cluster radioactivity in trans-lead nuclei with consideration of specific density distributions in daughter nuclei and clusters

    NASA Astrophysics Data System (ADS)

    Qian, Yibin; Ren, Zhongzhou; Ni, Dongdong

    2016-08-01

    We further investigate the cluster emission from heavy nuclei beyond the lead region in the framework of the preformed cluster model. The refined cluster-core potential is constructed by the double-folding integral of the density distributions of the daughter nucleus and the emitted cluster, where the radius or the diffuseness parameter in the Fermi density distribution formula is determined according to the available experimental data on the charge radii and the neutron skin thickness. The Schrödinger equation of the cluster-daughter relative motion is then solved within the outgoing Coulomb wave-function boundary conditions to obtain the decay width. It is found that the present decay width of cluster emitters is clearly enhanced as compared to that in the previous case, which involved the fixed parametrization for the density distributions of daughter nuclei and clusters. Among the whole procedure, the nuclear deformation of clusters is also introduced into the calculations, and the degree of its influence on the final decay half-life is checked to some extent. Moreover, the effect from the bubble density distribution of clusters on the final decay width is carefully discussed by using the central depressed distribution.

  9. Analysis of an algorithm for distributed recognition and accountability

    SciTech Connect

    Ko, C.; Frincke, D.A.; Goan, T. Jr.; Heberlein, L.T.; Levitt, K.; Mukherjee, B.; Wee, C.

    1993-08-01

    Computer and network systems are available to attacks. Abandoning the existing huge infrastructure of possibly-insecure computer and network systems is impossible, and replacing them by totally secure systems may not be feasible or cost effective. A common element in many attacks is that a single user will often attempt to intrude upon multiple resources throughout a network. Detecting the attack can become significantly easier by compiling and integrating evidence of such intrusion attempts across the network rather than attempting to assess the situation from the vantage point of only a single host. To solve this problem, we suggest an approach for distributed recognition and accountability (DRA), which consists of algorithms which ``process,`` at a central location, distributed and asynchronous ``reports`` generated by computers (or a subset thereof) throughout the network. Our highest-priority objectives are to observe ways by which an individual moves around in a network of computers, including changing user names to possibly hide his/her true identity, and to associate all activities of multiple instance of the same individual to the same network-wide user. We present the DRA algorithm and a sketch of its proof under an initial set of simplifying albeit realistic assumptions. Later, we relax these assumptions to accommodate pragmatic aspects such as missing or delayed ``reports,`` clock slew, tampered ``reports,`` etc. We believe that such algorithms will have widespread applications in the future, particularly in intrusion-detection system.

  10. Classification of bioinformatics workflows using weighted versions of partitioning and hierarchical clustering algorithms.

    PubMed

    Lord, Etienne; Diallo, Abdoulaye Baniré; Makarenkov, Vladimir

    2015-03-03

    Workflows, or computational pipelines, consisting of collections of multiple linked tasks are becoming more and more popular in many scientific fields, including computational biology. For example, simulation studies, which are now a must for statistical validation of new bioinformatics methods and software, are frequently carried out using the available workflow platforms. Workflows are typically organized to minimize the total execution time and to maximize the efficiency of the included operations. Clustering algorithms can be applied either for regrouping similar workflows for their simultaneous execution on a server, or for dispatching some lengthy workflows to different servers, or for classifying the available workflows with a view to performing a specific keyword search. In this study, we consider four different workflow encoding and clustering schemes which are representative for bioinformatics projects. Some of them allow for clustering workflows with similar topological features, while the others regroup workflows according to their specific attributes (e.g. associated keywords) or execution time. The four types of workflow encoding examined in this study were compared using the weighted versions of k-means and k-medoids partitioning algorithms. The Calinski-Harabasz, Silhouette and logSS clustering indices were considered. Hierarchical classification methods, including the UPGMA, Neighbor Joining, Fitch and Kitsch algorithms, were also applied to classify bioinformatics workflows. Moreover, a novel pairwise measure of clustering solution stability, which can be computed in situations when a series of independent program runs is carried out, was introduced. Our findings based on the analysis of 220 real-life bioinformatics workflows suggest that the weighted clustering models based on keywords information or tasks execution times provide the most appropriate clustering solutions. Using datasets generated by the Armadillo and Taverna scientific workflow

  11. Estimation of Distribution Algorithms for Solving Reinforcement Learning Problems

    NASA Astrophysics Data System (ADS)

    Handa, Hisashi

    Estimation of Distribution Algorithms (EDAs) are a promising evolutionary computation method. Due to the use of probabilistic models, EDAs can outperform conventional evolutionary computation. In this paper, EDAs are extended to solve reinforcement learning problems which are a framework for autonomous agents. In the reinforcement learning problems, we have to find out better policy of agents such that it yields a large amount of reward for the agents in the future. In general, such policy can be represented by conditional probabilities of agents' actions, given the perceptual inputs. In order to estimate such a conditional probability distribution, Conditional Random Fields (CRFs) by Lafferty (2001) are introduced into EDAs. The reason why CRFs are adopted is that CRFs are able to learn conditional probabilistic distributions from a large amount of input-output data, i.e., episodes in the case of reinforcement learning problems. Computer simulations on Probabilistic Transition Problems and Perceptual Aliasing Maze Problems show the effectiveness of EDA-RL.

  12. BoCluSt: Bootstrap Clustering Stability Algorithm for Community Detection.

    PubMed

    Garcia, Carlos

    2016-01-01

    The identification of modules or communities in sets of related variables is a key step in the analysis and modeling of biological systems. Procedures for this identification are usually designed to allow fast analyses of very large datasets and may produce suboptimal results when these sets are of a small to moderate size. This article introduces BoCluSt, a new, somewhat more computationally intensive, community detection procedure that is based on combining a clustering algorithm with a measure of stability under bootstrap resampling. Both computer simulation and analyses of experimental data showed that BoCluSt can outperform current procedures in the identification of multiple modules in data sets with a moderate number of variables. In addition, the procedure provides users with a null distribution of results to evaluate the support for the existence of community structure in the data. BoCluSt takes individual measures for a set of variables as input, and may be a valuable and robust exploratory tool of network analysis, as it provides 1) an estimation of the best partition of variables into modules, 2) a measure of the support for the existence of modular structures, and 3) an overall description of the whole structure, which may reveal hierarchical modular situations, in which modules are composed of smaller sub-modules.

  13. A Parallel EM Algorithm for Model-Based Clustering Applied to the Exploration of Large Spatio-Temporal Data

    SciTech Connect

    Chen, Wei-Chen; Ostrouchov, George; Pugmire, Dave; Prabhat,; Wehner, Michael

    2013-01-01

    We develop a parallel EM algorithm for multivariate Gaussian mixture models and use it to perform model-based clustering of a large climate data set. Three variants of the EM algorithm are reformulated in parallel and a new variant that is faster is presented. All are implemented using the single program, multiple data (SPMD) programming model, which is able to take advantage of the combined collective memory of large distributed computer architectures to process larger data sets. Displays of the estimated mixture model rather than the data allow us to explore multivariate relationships in a way that scales to arbitrary size data. We study the performance of our methodology on simulated data and apply our methodology to a high resolution climate dataset produced by the community atmosphere model (CAM5). This article has supplementary material online.

  14. Distributed Minimal Residual (DMR) method for acceleration of iterative algorithms

    NASA Technical Reports Server (NTRS)

    Lee, Seungsoo; Dulikravich, George S.

    1991-01-01

    A new method for enhancing the convergence rate of iterative algorithms for the numerical integration of systems of partial differential equations was developed. It is termed the Distributed Minimal Residual (DMR) method and it is based on general Krylov subspace methods. The DMR method differs from the Krylov subspace methods by the fact that the iterative acceleration factors are different from equation to equation in the system. At the same time, the DMR method can be viewed as an incomplete Newton iteration method. The DMR method was applied to Euler equations of gas dynamics and incompressible Navier-Stokes equations. All numerical test cases were obtained using either explicit four stage Runge-Kutta or Euler implicit time integration. The formulation for the DMR method is general in nature and can be applied to explicit and implicit iterative algorithms for arbitrary systems of partial differential equations.

  15. High performance computational chemistry: Towards fully distributed parallel algorithms

    SciTech Connect

    Guest, M.F.; Apra, E.; Bernholdt, D.E.

    1994-07-01

    An account is given of work in progress within the High Performance Computational Chemistry Group (HPCC) at the Pacific Northwest Laboratory (PNL) to develop molecular modeling software applications for massively parallel processors (MPPs). A discussion of the issues in developing scalable parallel algorithms is presented, with a particular focus on the distribution, as opposed to the replication, of key data structures. Replication of large data structures limits the maximum calculation size by imposing a low ratio of processors to memory. Only applications that distribute both data and computation across processors are truly scalable. The use of shared data structures, which may be independently accessed by each process even in a distributed-memory environment, greatly simplifies development and provides a significant performance enhancement. In describing tools to support this programming paradigm, an outline is given of the implementation and performance of a highly efficient and scalable algorithm to perform quadratically convergent, self-consistent field calculations on molecular systems. A brief account is given of the development of corresponding MPP capabilities in the areas of periodic Hartree Fock, Moeller-Plesset perturbation theory (MP2), density functional theory, and molecular dynamics. Performance figures are presented using both the Intel Touchstone Delta and Kendall Square Research KSR-2 supercomputers.

  16. Sampling cluster stability for peer-to-peer based content distribution networks

    NASA Astrophysics Data System (ADS)

    Darlagiannis, Vasilios; Mauthe, Andreas; Steinmetz, Ralf

    2006-01-01

    Several types of Content Distribution Networks are being deployed over the Internet today, based on different architectures to meet their requirements (e.g., scalability, efficiency and resiliency). Peer-to-Peer (P2P) based Content Distribution Networks are promising approaches that have several advantages. Structured P2P networks, for instance, take a proactive approach and provide efficient routing mechanisms. Nevertheless, their maintenance can increase considerably in highly dynamic P2P environments. In order to address this issue, a two-tier architecture that combines a structured overlay network with a clustering mechanism is suggested in a hybrid scheme. In this paper, we examine several sampling algorithms utilized in the aforementioned hybrid network that collect local information in order to apply a selective join procedure. The algorithms are based mostly on random walks inside the overlay network. The aim of the selective join procedure is to provide a well balanced and stable overlay infrastructure that can easily overcome the unreliable behavior of the autonomous peers that constitute the network. The sampling algorithms are evaluated using simulation experiments where several properties related to the graph structure are revealed.

  17. A priori data-driven multi-clustered reservoir generation algorithm for echo state network.

    PubMed

    Li, Xiumin; Zhong, Ling; Xue, Fangzheng; Zhang, Anguo

    2015-01-01

    Echo state networks (ESNs) with multi-clustered reservoir topology perform better in reservoir computing and robustness than those with random reservoir topology. However, these ESNs have a complex reservoir topology, which leads to difficulties in reservoir generation. This study focuses on the reservoir generation problem when ESN is used in environments with sufficient priori data available. Accordingly, a priori data-driven multi-cluster reservoir generation algorithm is proposed. The priori data in the proposed algorithm are used to evaluate reservoirs by calculating the precision and standard deviation of ESNs. The reservoirs are produced using the clustering method; only the reservoir with a better evaluation performance takes the place of a previous one. The final reservoir is obtained when its evaluation score reaches the preset requirement. The prediction experiment results obtained using the Mackey-Glass chaotic time series show that the proposed reservoir generation algorithm provides ESNs with extra prediction precision and increases the structure complexity of the network. Further experiments also reveal the appropriate values of the number of clusters and time window size to obtain optimal performance. The information entropy of the reservoir reaches the maximum when ESN gains the greatest precision.

  18. Room Acoustical Simulation Algorithm Based on the Free Path Distribution

    NASA Astrophysics Data System (ADS)

    VORLÄNDER, M.

    2000-04-01

    A new algorithm is presented which provides estimates of impulse responses in rooms. It is applicable to arbitrary shaped rooms, thus including non-diffuse spaces like workrooms or offices. In the latter cases, for instance, sound propagation curves are of interest to be applied in noise control. In the case of concert halls and opera houses, the method enables very fast predictions of room acoustical criteria like reverberation time, strength or clarity. The method is based on a low-resolved ray tracing and recording of the free paths. Estimates of impulse responses are derived from evaluation of the free path distribution and of the free path transition probabilities.

  19. 3D Hail Size Distribution Interpolation/Extrapolation Algorithm

    NASA Technical Reports Server (NTRS)

    Lane, John

    2013-01-01

    Radar data can usually detect hail; however, it is difficult for present day radar to accurately discriminate between hail and rain. Local ground-based hail sensors are much better at detecting hail against a rain background, and when incorporated with radar data, provide a much better local picture of a severe rain or hail event. The previous disdrometer interpolation/ extrapolation algorithm described a method to interpolate horizontally between multiple ground sensors (a minimum of three) and extrapolate vertically. This work is a modification to that approach that generates a purely extrapolated 3D spatial distribution when using a single sensor.

  20. Cluster-Based Multipolling Sequencing Algorithm for Collecting RFID Data in Wireless LANs

    NASA Astrophysics Data System (ADS)

    Choi, Woo-Yong; Chatterjee, Mainak

    2015-03-01

    With the growing use of RFID (Radio Frequency Identification), it is becoming important to devise ways to read RFID tags in real time. Access points (APs) of IEEE 802.11-based wireless Local Area Networks (LANs) are being integrated with RFID networks that can efficiently collect real-time RFID data. Several schemes, such as multipolling methods based on the dynamic search algorithm and random sequencing, have been proposed. However, as the number of RFID readers associated with an AP increases, it becomes difficult for the dynamic search algorithm to derive the multipolling sequence in real time. Though multipolling methods can eliminate the polling overhead, we still need to enhance the performance of the multipolling methods based on random sequencing. To that extent, we propose a real-time cluster-based multipolling sequencing algorithm that drastically eliminates more than 90% of the polling overhead, particularly so when the dynamic search algorithm fails to derive the multipolling sequence in real time.

  1. An algorithm of discovering signatures from DNA databases on a computer cluster.

    PubMed

    Lee, Hsiao Ping; Sheu, Tzu-Fang

    2014-10-05

    Signatures are short sequences that are unique and not similar to any other sequence in a database that can be used as the basis to identify different species. Even though several signature discovery algorithms have been proposed in the past, these algorithms require the entirety of databases to be loaded in the memory, thus restricting the amount of data that they can process. It makes those algorithms unable to process databases with large amounts of data. Also, those algorithms use sequential models and have slower discovery speeds, meaning that the efficiency can be improved. In this research, we are debuting the utilization of a divide-and-conquer strategy in signature discovery and have proposed a parallel signature discovery algorithm on a computer cluster. The algorithm applies the divide-and-conquer strategy to solve the problem posed to the existing algorithms where they are unable to process large databases and uses a parallel computing mechanism to effectively improve the efficiency of signature discovery. Even when run with just the memory of regular personal computers, the algorithm can still process large databases such as the human whole-genome EST database which were previously unable to be processed by the existing algorithms. The algorithm proposed in this research is not limited by the amount of usable memory and can rapidly find signatures in large databases, making it useful in applications such as Next Generation Sequencing and other large database analysis and processing. The implementation of the proposed algorithm is available at http://www.cs.pu.edu.tw/~fang/DDCSDPrograms/DDCSD.htm.

  2. Density-based cluster algorithms for the identification of core sets

    NASA Astrophysics Data System (ADS)

    Lemke, Oliver; Keller, Bettina G.

    2016-10-01

    The core-set approach is a discretization method for Markov state models of complex molecular dynamics. Core sets are disjoint metastable regions in the conformational space, which need to be known prior to the construction of the core-set model. We propose to use density-based cluster algorithms to identify the cores. We compare three different density-based cluster algorithms: the CNN, the DBSCAN, and the Jarvis-Patrick algorithm. While the core-set models based on the CNN and DBSCAN clustering are well-converged, constructing core-set models based on the Jarvis-Patrick clustering cannot be recommended. In a well-converged core-set model, the number of core sets is up to an order of magnitude smaller than the number of states in a conventional Markov state model with comparable approximation error. Moreover, using the density-based clustering one can extend the core-set method to systems which are not strongly metastable. This is important for the practical application of the core-set method because most biologically interesting systems are only marginally metastable. The key point is to perform a hierarchical density-based clustering while monitoring the structure of the metric matrix which appears in the core-set method. We test this approach on a molecular-dynamics simulation of a highly flexible 14-residue peptide. The resulting core-set models have a high spatial resolution and can distinguish between conformationally similar yet chemically different structures, such as register-shifted hairpin structures.

  3. An adaptive enhancement algorithm for infrared video based on modified k-means clustering

    NASA Astrophysics Data System (ADS)

    Zhang, Linze; Wang, Jingqi; Wu, Wen

    2016-09-01

    In this paper, we have proposed a video enhancement algorithm to improve the output video of the infrared camera. Sometimes the video obtained by infrared camera is very dark since there is no clear target. In this case, infrared video should be divided into frame images by frame extraction, in order to carry out the image enhancement. For the first frame image, which can be divided into k sub images by using K-means clustering according to the gray interval it occupies before k sub images' histogram equalization according to the amount of information per sub image, we used a method to solve a problem that final cluster centers close to each other in some cases; and for the other frame images, their initial cluster centers can be determined by the final clustering centers of the previous ones, and the histogram equalization of each sub image will be carried out after image segmentation based on K-means clustering. The histogram equalization can make the gray value of the image to the whole gray level, and the gray level of each sub image is determined by the ratio of pixels to a frame image. Experimental results show that this algorithm can improve the contrast of infrared video where night target is not obvious which lead to a dim scene, and reduce the negative effect given by the overexposed pixels adaptively in a certain range.

  4. A brief summary on formalizing parallel tensor distributions redistributions and algorithm derivations.

    SciTech Connect

    Schatz, Martin D.; Kolda, Tamara G.; van de Geijn, Robert

    2015-09-01

    Large-scale datasets in computational chemistry typically require distributed-memory parallel methods to perform a special operation known as tensor contraction. Tensors are multidimensional arrays, and a tensor contraction is akin to matrix multiplication with special types of permutations. Creating an efficient algorithm and optimized im- plementation in this domain is complex, tedious, and error-prone. To address this, we develop a notation to express data distributions so that we can apply use automated methods to find optimized implementations for tensor contractions. We consider the spin-adapted coupled cluster singles and doubles method from computational chemistry and use our methodology to produce an efficient implementation. Experiments per- formed on the IBM Blue Gene/Q and Cray XC30 demonstrate impact both improved performance and reduced memory consumption.

  5. Combustion distribution control using the extremum seeking algorithm

    NASA Astrophysics Data System (ADS)

    Marjanovic, A.; Krstic, M.; Djurovic, Z.; Kvascev, G.; Papic, V.

    2014-12-01

    Quality regulation of the combustion process inside the furnace is the basis of high demands for increasing robustness, safety and efficiency of thermal power plants. The paper considers the possibility of spatial temperature distribution control inside the boiler, based on the correction of distribution of coal over the mills. Such control system ensures the maintenance of the flame focus away from the walls of the boiler, and thus preserves the equipment and reduces the possibility of ash slugging. At the same time, uniform heat dissipation over mills enhances the energy efficiency of the boiler, while reducing the pollution of the system. A constrained multivariable extremum seeking algorithm is proposed as a tool for combustion process optimization with the main objective of centralizing the flame in the furnace. Simulations are conducted on a model corresponding to the 350MW boiler of the Nikola Tesla Power Plant, in Obrenovac, Serbia.

  6. K-Means Re-Clustering-Algorithmic Options with Quantifiable Performance Comparisons

    SciTech Connect

    Meyer, A W; Paglieroni, D; Asteneh, C

    2002-12-17

    This paper presents various architectural options for implementing a K-Means Re-Clustering algorithm suitable for unsupervised segmentation of hyperspectral images. Performance metrics are developed based upon quantitative comparisons of convergence rates and segmentation quality. A methodology for making these comparisons is developed and used to establish K values that produce the best segmentations with minimal processing requirements. Convergence rates depend on the initial choice of cluster centers. Consequently, this same methodology may be used to evaluate the effectiveness of different initialization techniques.

  7. A genetic algorithmic approach to antenna null-steering using a cluster computer.

    NASA Astrophysics Data System (ADS)

    Recine, Greg; Cui, Hong-Liang

    2001-06-01

    We apply a genetic algorithm (GA) to the problem of electronically steering the maximums and nulls of an antenna array to desired positions (null toward enemy listener/jammer, max toward friendly listener/transmitter). The antenna pattern itself is computed using NEC2 which is called by the main GA program. Since a GA naturally lends itself to parallelization, this simulation was applied to our new twin 64-node cluster computers (Gemini). Design issues and uses of the Gemini cluster in our group are also discussed.

  8. Modelling galaxy clustering: halo occupation distribution versus subhalo matching.

    PubMed

    Guo, Hong; Zheng, Zheng; Behroozi, Peter S; Zehavi, Idit; Chuang, Chia-Hsun; Comparat, Johan; Favole, Ginevra; Gottloeber, Stefan; Klypin, Anatoly; Prada, Francisco; Rodríguez-Torres, Sergio A; Weinberg, David H; Yepes, Gustavo

    2016-07-01

    We model the luminosity-dependent projected and redshift-space two-point correlation functions (2PCFs) of the Sloan Digital Sky Survey (SDSS) Data Release 7 Main galaxy sample, using the halo occupation distribution (HOD) model and the subhalo abundance matching (SHAM) model and its extension. All the models are built on the same high-resolution N-body simulations. We find that the HOD model generally provides the best performance in reproducing the clustering measurements in both projected and redshift spaces. The SHAM model with the same halo-galaxy relation for central and satellite galaxies (or distinct haloes and subhaloes), when including scatters, has a best-fitting χ(2)/dof around 2-3. We therefore extend the SHAM model to the subhalo clustering and abundance matching (SCAM) by allowing the central and satellite galaxies to have different galaxy-halo relations. We infer the corresponding halo/subhalo parameters by jointly fitting the galaxy 2PCFs and abundances and consider subhaloes selected based on three properties, the mass Macc at the time of accretion, the maximum circular velocity Vacc at the time of accretion, and the peak maximum circular velocity Vpeak over the history of the subhaloes. The three subhalo models work well for luminous galaxy samples (with luminosity above L*). For low-luminosity samples, the Vacc model stands out in reproducing the data, with the Vpeak model slightly worse, while the Macc model fails to fit the data. We discuss the implications of the modelling results.

  9. MetaCluster 4.0: a novel binning algorithm for NGS reads and huge number of species.

    PubMed

    Wang, Yi; Leung, Henry C M; Yiu, S M; Chin, Francis Y L

    2012-02-01

    Next-generation sequencing (NGS) technologies allow the sequencing of microbial communities directly from the environment without prior culturing. The output of environmental DNA sequencing consists of many reads from genomes of different unknown species, making the clustering together reads from the same (or similar) species (also known as binning) a crucial step. The difficulties of the binning problem are due to the following four factors: (1) the lack of reference genomes; (2) uneven abundance ratio of species; (3) short NGS reads; and (4) a large number of species (can be more than a hundred). None of the existing binning tools can handle all four factors. No tools, including both AbundanceBin and MetaCluster 3.0, have demonstrated reasonable performance on a sample with more than 20 species. In this article, we introduce MetaCluster 4.0, an unsupervised binning algorithm that can accurately (with about 80% precision and sensitivity in all cases and at least 90% in some cases) and efficiently bin short reads with varying abundance ratios and is able to handle datasets with 100 species. The novelty of MetaCluster 4.0 stems from solving a few important problems: how to divide reads into groups by a probabilistic approach, how to estimate the 4-mer distribution of each group, how to estimate the number of species, and how to modify MetaCluster 3.0 to handle a large number of species. We show that Meta Cluster 4.0 is effective for both simulated and real datasets. Supplementary Material is available at www.liebertonline.com/cmb.

  10. What to Do When K-Means Clustering Fails: A Simple yet Principled Alternative Algorithm.

    PubMed

    Raykov, Yordan P; Boukouvalas, Alexis; Baig, Fahd; Little, Max A

    The K-means algorithm is one of the most popular clustering algorithms in current use as it is relatively fast yet simple to understand and deploy in practice. Nevertheless, its use entails certain restrictive assumptions about the data, the negative consequences of which are not always immediately apparent, as we demonstrate. While more flexible algorithms have been developed, their widespread use has been hindered by their computational and technical complexity. Motivated by these considerations, we present a flexible alternative to K-means that relaxes most of the assumptions, whilst remaining almost as fast and simple. This novel algorithm which we call MAP-DP (maximum a-posteriori Dirichlet process mixtures), is statistically rigorous as it is based on nonparametric Bayesian Dirichlet process mixture modeling. This approach allows us to overcome most of the limitations imposed by K-means. The number of clusters K is estimated from the data instead of being fixed a-priori as in K-means. In addition, while K-means is restricted to continuous data, the MAP-DP framework can be applied to many kinds of data, for example, binary, count or ordinal data. Also, it can efficiently separate outliers from the data. This additional flexibility does not incur a significant computational overhead compared to K-means with MAP-DP convergence typically achieved in the order of seconds for many practical problems. Finally, in contrast to K-means, since the algorithm is based on an underlying statistical model, the MAP-DP framework can deal with missing data and enables model testing such as cross validation in a principled way. We demonstrate the simplicity and effectiveness of this algorithm on the health informatics problem of clinical sub-typing in a cluster of diseases known as parkinsonism.

  11. What to Do When K-Means Clustering Fails: A Simple yet Principled Alternative Algorithm

    PubMed Central

    Baig, Fahd; Little, Max A.

    2016-01-01

    The K-means algorithm is one of the most popular clustering algorithms in current use as it is relatively fast yet simple to understand and deploy in practice. Nevertheless, its use entails certain restrictive assumptions about the data, the negative consequences of which are not always immediately apparent, as we demonstrate. While more flexible algorithms have been developed, their widespread use has been hindered by their computational and technical complexity. Motivated by these considerations, we present a flexible alternative to K-means that relaxes most of the assumptions, whilst remaining almost as fast and simple. This novel algorithm which we call MAP-DP (maximum a-posteriori Dirichlet process mixtures), is statistically rigorous as it is based on nonparametric Bayesian Dirichlet process mixture modeling. This approach allows us to overcome most of the limitations imposed by K-means. The number of clusters K is estimated from the data instead of being fixed a-priori as in K-means. In addition, while K-means is restricted to continuous data, the MAP-DP framework can be applied to many kinds of data, for example, binary, count or ordinal data. Also, it can efficiently separate outliers from the data. This additional flexibility does not incur a significant computational overhead compared to K-means with MAP-DP convergence typically achieved in the order of seconds for many practical problems. Finally, in contrast to K-means, since the algorithm is based on an underlying statistical model, the MAP-DP framework can deal with missing data and enables model testing such as cross validation in a principled way. We demonstrate the simplicity and effectiveness of this algorithm on the health informatics problem of clinical sub-typing in a cluster of diseases known as parkinsonism. PMID:27669525

  12. Climatological analyses of LMA data with an open-source lightning flash-clustering algorithm

    NASA Astrophysics Data System (ADS)

    Fuchs, Brody R.; Bruning, Eric C.; Rutledge, Steven A.; Carey, Lawrence D.; Krehbiel, Paul R.; Rison, William

    2016-07-01

    Approximately 63 million lightning flashes have been identified and analyzed from multiple years of Washington, D. C., northern Alabama, and northeast Colorado lightning mapping array (LMA) data using an open-source flash-clustering algorithm. LMA networks detect radiation produced by lightning breakdown processes, allowing for high-resolution mapping of lightning flashes. Similar to other existing clustering algorithms, the algorithm described herein groups lightning-produced radiation sources by space and time to estimate total flash counts and information about each detected flash. Various flash characteristics and their sensitivity to detection efficiency are investigated to elucidate biases in the algorithm, detail detection efficiencies of various LMAs, and guide future improvements. Furthermore, flash density values in each region are compared to corresponding satellite estimates. While total flash density values produced by the algorithm in Washington, D. C. ( 20 flashes km-2 yr-1), and Alabama ( 35 flashes km-2 yr-1) are within 50% of satellite estimates, LMA-based estimates are approximately a factor of 3 larger (50 flashes km-2 yr-1) than satellite estimates in northeast Colorado. Accordingly, estimates of the ratio of in-cloud to cloud-to-ground flashes near the LMA network ( 20) are approximately a factor of 3 larger than satellite estimates in Colorado. These large differences between estimates may be related to the distinct environment conducive to intense convection, low-altitude flashes, and unique charge structures in northeast Colorado.

  13. An Auto-Recognizing System for Dice Games Using a Modified Unsupervised Grey Clustering Algorithm

    PubMed Central

    Huang, Kuo-Yi

    2008-01-01

    In this paper, a novel identification method based on a machine vision system is proposed to recognize the score of dice. The system employs image processing techniques, and the modified unsupervised grey clustering algorithm (MUGCA) to estimate the location of each die and identify the spot number accurately and effectively. The proposed algorithms are substituted for manual recognition. From the experimental results, it is found that this system is excellent due to its good capabilities which include flexibility, high speed, and high accuracy. PMID:27879761

  14. Robustness of ‘cut and splice’ genetic algorithms in the structural optimization of atomic clusters

    NASA Astrophysics Data System (ADS)

    Froltsov, Vladimir A.; Reuter, Karsten

    2009-05-01

    We return to the geometry optimization problem of Lennard-Jones clusters to analyze the performance dependence of 'cut and splice' genetic algorithms (GAs) on the employed population size. We generally find that admixing twinning mutation moves leads to an improved robustness of the algorithm efficiency with respect to this a priori unknown technical parameter. The resulting very stable performance of the corresponding mutation + mating GA implementation over a wide range of population sizes is an important feature when addressing unknown systems with computationally involved first-principles based GA sampling.

  15. Distribution-based clustering: using ecology to refine the operational taxonomic unit.

    PubMed

    Preheim, Sarah P; Perrotta, Allison R; Martin-Platero, Antonio M; Gupta, Anika; Alm, Eric J

    2013-11-01

    16S rRNA sequencing, commonly used to survey microbial communities, begins by grouping individual reads into operational taxonomic units (OTUs). There are two major challenges in calling OTUs: identifying bacterial population boundaries and differentiating true diversity from sequencing errors. Current approaches to identifying taxonomic groups or eliminating sequencing errors rely on sequence data alone, but both of these activities could be informed by the distribution of sequences across samples. Here, we show that using the distribution of sequences across samples can help identify population boundaries even in noisy sequence data. The logic underlying our approach is that bacteria in different populations will often be highly correlated in their abundance across different samples. Conversely, 16S rRNA sequences derived from the same population, whether slightly different copies in the same organism, variation of the 16S rRNA gene within a population, or sequences generated randomly in error, will have the same underlying distribution across sampled environments. We present a simple OTU-calling algorithm (distribution-based clustering) that uses both genetic distance and the distribution of sequences across samples and demonstrate that it is more accurate than other methods at grouping reads into OTUs in a mock community. Distribution-based clustering also performs well on environmental samples: it is sensitive enough to differentiate between OTUs that differ by a single base pair yet predicts fewer overall OTUs than most other methods. The program can decrease the total number of OTUs with redundant information and improve the power of many downstream analyses to describe biologically relevant trends.

  16. Application of a clustering-based peak alignment algorithm to analyze various DNA fingerprinting data.

    PubMed

    Ishii, Satoshi; Kadota, Koji; Senoo, Keishi

    2009-09-01

    DNA fingerprinting analysis such as amplified ribosomal DNA restriction analysis (ARDRA), repetitive extragenic palindromic PCR (rep-PCR), ribosomal intergenic spacer analysis (RISA), and denaturing gradient gel electrophoresis (DGGE) are frequently used in various fields of microbiology. The major difficulty in DNA fingerprinting data analysis is the alignment of multiple peak sets. We report here an R program for a clustering-based peak alignment algorithm, and its application to analyze various DNA fingerprinting data, such as ARDRA, rep-PCR, RISA, and DGGE data. The results obtained by our clustering algorithm and by BioNumerics software showed high similarity. Since several R packages have been established to statistically analyze various biological data, the distance matrix obtained by our R program can be used for subsequent statistical analyses, some of which were not previously performed but are useful in DNA fingerprinting studies.

  17. [Automatic segmentation of clustered breast cancer cells based on modified watershed algorithm and concavity points searching].

    PubMed

    Tong, Zhen; Pu, Lixin; Dong, Fangjie

    2013-08-01

    As a common malignant tumor, breast cancer has seriously affected women's physical and psychological health even threatened their lives. Breast cancer has even begun to show a gradual trend of high incidence in some places in the world. As a kind of common pathological assist diagnosis technique, immunohistochemical technique plays an important role in the diagnosis of breast cancer. Usually, Pathologists isolate positive cells from the stained specimen which were processed by immunohistochemical technique and calculate the ratio of positive cells which is a core indicator of breast cancer in diagnosis. In this paper, we present a new algorithm which was based on modified watershed algorithm and concavity points searching to identify the positive cells and segment the clustered cells automatically, and then realize automatic counting. By comparison of the results of our experiments with those of other methods, our method can exactly segment the clustered cells without losing any geometrical cell features and give the exact number of separating cells.

  18. Sample size calculation for weighted rank tests comparing survival distributions under cluster randomization: a simulation method.

    PubMed

    Jung, Sin-Ho

    2007-01-01

    We propose a sample size calculation method for rank tests comparing two survival distributions under cluster randomization with possibly variable cluster sizes. Here, sample size refers to number of clusters. Our method is based on simulation procedure generating clustered exponential survival variables whose distribution is specified by the marginal hazard rate and the intracluster correlation coefficient. Sample size is calculated given significance level, power, marginal hazard rates (or median survival times) under the alternative hypothesis, intracluster correlation coefficient, accrual rate, follow-up period, and cluster size distribution.

  19. Selecting Random Distributed Elements for HIFU using Genetic Algorithm

    NASA Astrophysics Data System (ADS)

    Zhou, Yufeng

    2011-09-01

    As an effective and noninvasive therapeutic modality for tumor treatment, high-intensity focused ultrasound (HIFU) has attracted attention from both physicians and patients. New generations of HIFU systems with the ability to electrically steer the HIFU focus using phased array transducers have been under development. The presence of side and grating lobes may cause undesired thermal accumulation at the interface of the coupling medium (i.e. water) and skin, or in the intervening tissue. Although sparse randomly distributed piston elements could reduce the amplitude of grating lobes, there are theoretically no grating lobes with the use of concave elements in the new phased array HIFU. A new HIFU transmission strategy is proposed in this study, firing a number of but not all elements for a certain period and then changing to another group for the next firing sequence. The advantages are: 1) the asymmetric position of active elements may reduce the side lobes, and 2) each element has some resting time during the entire HIFU ablation (up to several hours for some clinical applications) so that the decreasing efficiency of the transducer due to thermal accumulation is minimized. Genetic algorithm was used for selecting randomly distributed elements in a HIFU array. Amplitudes of the first side lobes at the focal plane were used as the fitness value in the optimization. Overall, it is suggested that the proposed new strategy could reduce the side lobe and the consequent side-effects, and the genetic algorithm is effective in selecting those randomly distributed elements in a HIFU array.

  20. Detection of uterine MMG contractions using a multiple change point estimator and the K-means cluster algorithm.

    PubMed

    La Rosa, Patricio S; Nehorai, Arye; Eswaran, Hari; Lowery, Curtis L; Preissl, Hubert

    2008-02-01

    We propose a single channel two-stage time-segment discriminator of uterine magnetomyogram (MMG) contractions during pregnancy. We assume that the preprocessed signals are piecewise stationary having distribution in a common family with a fixed number of parameters. Therefore, at the first stage, we propose a model-based segmentation procedure, which detects multiple change-points in the parameters of a piecewise constant time-varying autoregressive model using a robust formulation of the Schwarz information criterion (SIC) and a binary search approach. In particular, we propose a test statistic that depends on the SIC, derive its asymptotic distribution, and obtain closed-form optimal detection thresholds in the sense of the Neyman-Pearson criterion; therefore, we control the probability of false alarm and maximize the probability of change-point detection in each stage of the binary search algorithm. We compute and evaluate the relative energy variation [root mean squares (RMS)] and the dominant frequency component [first order zero crossing (FOZC)] in discriminating between time segments with and without contractions. The former consistently detects a time segment with contractions. Thus, at the second stage, we apply a nonsupervised K-means cluster algorithm to classify the detected time segments using the RMS values. We apply our detection algorithm to real MMG records obtained from ten patients admitted to the hospital for contractions with gestational ages between 31 and 40 weeks. We evaluate the performance of our detection algorithm in computing the detection and false alarm rate, respectively, using as a reference the patients' feedback. We also analyze the fusion of the decision signals from all the sensors as in the parallel distributed detection approach.

  1. Kinetic energy distributions of sputtered neutral aluminum clusters: Al--Al[sub 6

    SciTech Connect

    Coon, S.R.; Calaway, W.F.; Pellin, M.J. ); Curlee, G.A. . Dept. of Physics); White, J.M. . Dept. of Chemistry and Biochemistry)

    1992-01-01

    Neutral aluminum clusters sputtered from polycrystalline aluminum were analyzed by laser postionization time-of-flight (TOF) mass spectrometry. The kinetic energy distributions of Al through Al[sub 6] were measured by a neutrals time-of-flight technique. The interpretation of laser postionization TOF data to extract velocity and energy distributions is presented. The aluminum cluster distributions are qualitatively similar to previous copper cluster distribution measurements from our laboratory. In contrast to the steep high energy tails predicted by the single- or multiple- collision models, the measured cluster distributions have high energy power law dependences in the range of E[sup [minus]3] to E[sup [minus]4.5]. Correlated collision models may explain the substantial abundance of energetic clusters that are observed in these experiments. Possible influences of cluster fragmentation on the distributions are discussed.

  2. Kinetic energy distributions of sputtered neutral aluminum clusters: Al--Al{sub 6}

    SciTech Connect

    Coon, S.R.; Calaway, W.F.; Pellin, M.J.; Curlee, G.A.; White, J.M.

    1992-12-01

    Neutral aluminum clusters sputtered from polycrystalline aluminum were analyzed by laser postionization time-of-flight (TOF) mass spectrometry. The kinetic energy distributions of Al through Al{sub 6} were measured by a neutrals time-of-flight technique. The interpretation of laser postionization TOF data to extract velocity and energy distributions is presented. The aluminum cluster distributions are qualitatively similar to previous copper cluster distribution measurements from our laboratory. In contrast to the steep high energy tails predicted by the single- or multiple- collision models, the measured cluster distributions have high energy power law dependences in the range of E{sup {minus}3} to E{sup {minus}4.5}. Correlated collision models may explain the substantial abundance of energetic clusters that are observed in these experiments. Possible influences of cluster fragmentation on the distributions are discussed.

  3. Double-layer evolutionary algorithm for distributed optimization of particle detection on the Grid

    NASA Astrophysics Data System (ADS)

    Padée, Adam; Kurek, Krzysztof; Zaremba, Krzysztof

    2013-08-01

    Reconstruction of particle tracks from information collected by position-sensitive detectors is an important procedure in HEP experiments. It is usually controlled by a set of numerical parameters which have to be manually optimized. This paper proposes an automatic approach to this task by utilizing evolutionary algorithm (EA) operating on both real-valued and binary representations. Because of computational complexity of the task a special distributed architecture of the algorithm is proposed, designed to be run in grid environment. It is two-level hierarchical hybrid utilizing asynchronous master-slave EA on the level of clusters and island model EA on the level of the grid. The technical aspects of usage of production grid infrastructure are covered, including communication protocols on both levels. The paper deals also with the problem of heterogeneity of the resources, presenting efficiency tests on a benchmark function. These tests confirm that even relatively small islands (clusters) can be beneficial to the optimization process when connected to the larger ones. Finally a real-life usage example is presented, which is an optimization of track reconstruction in Large Angle Spectrometer of NA-58 COMPASS experiment held at CERN, using a sample of Monte Carlo simulated data. The overall reconstruction efficiency gain, achieved by the proposed method, is more than 4%, compared to the manually optimized parameters.

  4. User Activity Recognition in Smart Homes Using Pattern Clustering Applied to Temporal ANN Algorithm

    PubMed Central

    Bourobou, Serge Thomas Mickala; Yoo, Younghwan

    2015-01-01

    This paper discusses the possibility of recognizing and predicting user activities in the IoT (Internet of Things) based smart environment. The activity recognition is usually done through two steps: activity pattern clustering and activity type decision. Although many related works have been suggested, they had some limited performance because they focused only on one part between the two steps. This paper tries to find the best combination of a pattern clustering method and an activity decision algorithm among various existing works. For the first step, in order to classify so varied and complex user activities, we use a relevant and efficient unsupervised learning method called the K-pattern clustering algorithm. In the second step, the training of smart environment for recognizing and predicting user activities inside his/her personal space is done by utilizing the artificial neural network based on the Allen’s temporal relations. The experimental results show that our combined method provides the higher recognition accuracy for various activities, as compared with other data mining classification algorithms. Furthermore, it is more appropriate for a dynamic environment like an IoT based smart home. PMID:26007738

  5. User Activity Recognition in Smart Homes Using Pattern Clustering Applied to Temporal ANN Algorithm.

    PubMed

    Bourobou, Serge Thomas Mickala; Yoo, Younghwan

    2015-05-21

    This paper discusses the possibility of recognizing and predicting user activities in the IoT (Internet of Things) based smart environment. The activity recognition is usually done through two steps: activity pattern clustering and activity type decision. Although many related works have been suggested, they had some limited performance because they focused only on one part between the two steps. This paper tries to find the best combination of a pattern clustering method and an activity decision algorithm among various existing works. For the first step, in order to classify so varied and complex user activities, we use a relevant and efficient unsupervised learning method called the K-pattern clustering algorithm. In the second step, the training of smart environment for recognizing and predicting user activities inside his/her personal space is done by utilizing the artificial neural network based on the Allen's temporal relations. The experimental results show that our combined method provides the higher recognition accuracy for various activities, as compared with other data mining classification algorithms. Furthermore, it is more appropriate for a dynamic environment like an IoT based smart home.

  6. Implementation of hybrid clustering based on partitioning around medoids algorithm and divisive analysis on human Papillomavirus DNA

    NASA Astrophysics Data System (ADS)

    Arimbi, Mentari Dian; Bustamam, Alhadi; Lestari, Dian

    2017-03-01

    Data clustering can be executed through partition or hierarchical method for many types of data including DNA sequences. Both clustering methods can be combined by processing partition algorithm in the first level and hierarchical in the second level, called hybrid clustering. In the partition phase some popular methods such as PAM, K-means, or Fuzzy c-means methods could be applied. In this study we selected partitioning around medoids (PAM) in our partition stage. Furthermore, following the partition algorithm, in hierarchical stage we applied divisive analysis algorithm (DIANA) in order to have more specific clusters and sub clusters structures. The number of main clusters is determined using Davies Bouldin Index (DBI) value. We choose the optimal number of clusters if the results minimize the DBI value. In this work, we conduct the clustering on 1252 HPV DNA sequences data from GenBank. The characteristic extraction is initially performed, followed by normalizing and genetic distance calculation using Euclidean distance. In our implementation, we used the hybrid PAM and DIANA using the R open source programming tool. In our results, we obtained 3 main clusters with average DBI value is 0.979, using PAM in the first stage. After executing DIANA in the second stage, we obtained 4 sub clusters for Cluster-1, 9 sub clusters for Cluster-2 and 2 sub clusters in Cluster-3, with the BDI value 0.972, 0.771, and 0.768 for each main cluster respectively. Since the second stage produce lower DBI value compare to the DBI value in the first stage, we conclude that this hybrid approach can improve the accuracy of our clustering results.

  7. A spectral clustering search algorithm for predicting shallow landslide size and location

    NASA Astrophysics Data System (ADS)

    Bellugi, Dino; Milledge, David G.; Dietrich, William E.; McKean, Jim A.; Perron, J. Taylor; Sudderth, Erik B.; Kazian, Brian

    2015-02-01

    The potential hazard and geomorphic significance of shallow landslides depend on their location and size. Commonly applied one-dimensional stability models do not include lateral resistances and cannot predict landslide size. Multidimensional models must be applied to specific geometries, which are not known a priori, and testing all possible geometries is computationally prohibitive. We present an efficient deterministic search algorithm based on spectral graph theory and couple it with a multidimensional stability model to predict discrete landslides in applications at scales broader than a single hillslope using gridded spatial data. The algorithm is general, assuming only that instability results when driving forces acting on a cluster of cells exceed the resisting forces on its margins and that clusters behave as rigid blocks with a failure plane at the soil-bedrock interface. This algorithm recovers predefined clusters of unstable cells of varying shape and size on a synthetic landscape, predicts the size, location, and shape of an observed shallow landslide using field-measured physical parameters, and is robust to modest changes in input parameters. The search algorithm identifies patches of potential instability within large areas of stable landscape. Within these patches will be many different combinations of cells with a Factor of Safety less than one, suggesting that subtle variations in local conditions (e.g., pore pressure and root strength) may determine the ultimate form and exact location at a specific site. Nonetheless, the tests presented here suggest that the search algorithm enables the prediction of shallow landslide size as well as location across landscapes.

  8. Klystron Cluster Scheme for ILC High Power RF Distribution

    SciTech Connect

    Nantista, Christopher; Adolphsen, Chris; /SLAC

    2009-07-06

    We present a concept for powering the main linacs of the International Linear Collider (ILC) by delivering high power RF from the surface via overmoded, low-loss waveguides at widely spaced intervals. The baseline design employs a two-tunnel layout, with klystrons and modulators evenly distributed along a service tunnel running parallel to the accelerator tunnel. This new idea eliminates the need for the service tunnel. It also brings most of the warm heat load to the surface, dramatically reducing the tunnel water cooling and HVAC requirements. In the envisioned configuration, groups of 70 klystrons and modulators are clustered in surface buildings every 2.5 km. Their outputs are combined into two half-meter diameter circular TE{sub 01} mode evacuated waveguides. These are directed via special bends through a deep shaft and along the tunnel, one upstream and one downstream. Each feeds approximately 1.25 km of linac with power tapped off in 10 MW portions at 38 m intervals. The power is extracted through a novel coaxial tap-off (CTO), after which the local distribution is as it would be from a klystron. The tap-off design is also employed in reverse for the initial combining.

  9. Comments on "A robust fuzzy local information C-means clustering algorithm".

    PubMed

    Celik, Turgay; Lee, Hwee Kuan

    2013-03-01

    In a recent paper, Krinidis and Chatzis proposed a variation of fuzzy c-means algorithm for image clustering. The local spatial and gray-level information are incorporated in a fuzzy way through an energy function. The local minimizers of the designed energy function to obtain the fuzzy membership of each pixel and cluster centers are proposed. In this paper, it is shown that the local minimizers of Krinidis and Chatzis to obtain the fuzzy membership and the cluster centers in an iterative manner are not exclusively solutions for true local minimizers of their designed energy function. Thus, the local minimizers of Krinidis and Chatzis do not converge to the correct local minima of the designed energy function not because of tackling to the local minima, but because of the design of energy function.

  10. Numerical linked-cluster algorithms. I. Spin systems on square, triangular, and kagomé lattices.

    PubMed

    Rigol, Marcos; Bryant, Tyler; Singh, Rajiv R P

    2007-06-01

    We discuss recently introduced numerical linked-cluster (NLC) algorithms that allow one to obtain temperature-dependent properties of quantum lattice models, in the thermodynamic limit, from exact diagonalization of finite clusters. We present studies of thermodynamic observables for spin models on square, triangular, and kagomé lattices. Results for several choices of clusters and extrapolations methods, that accelerate the convergence of NLCs, are presented. We also include a comparison of NLC results with those obtained from exact analytical expressions (where available), high-temperature expansions (HTE), exact diagonalization (ED) of finite periodic systems, and quantum Monte Carlo simulations. For many models and properties NLC results are substantially more accurate than HTE and ED.

  11. Joint inversion of multiple geophysical and petrophysical data using generalized fuzzy clustering algorithms

    NASA Astrophysics Data System (ADS)

    Sun, Jiajia; Li, Yaoguo

    2016-11-01

    Joint inversion that simultaneously inverts multiple geophysical data sets to recover a common Earth model is increasingly being applied to exploration problems. Petrophysical data can serve as an effective constraint to link different physical property models in such inversions. There are two challenges, among others, associated with the petrophysical approach to joint inversion. One is related to the multi-modality of petrophysical data because there often exist more than one relationship between different physical properties in a region of study. The other challenge arises from the fact that petrophysical relationships have different characteristics and can exhibit point, linear, quadratic, or exponential forms in a crossplot. The fuzzy c-means (FCM) clustering technique is effective in tackling the first challenge and has been applied successfully. We focus on the second challenge in this paper and develop a joint inversion method based on variations of the FCM clustering technique. To account for the specific shapes of petrophysical relationships, we introduce several different fuzzy clustering algorithms that are capable of handling different shapes of petrophysical relationships. We present two synthetic and one field data examples and demonstrate that, by choosing appropriate distance measures for the clustering component in the joint inversion algorithm, the proposed joint inversion method provides an effective means of handling common petrophysical situations we encounter in practice. The jointly inverted models have both enhanced structural similarity and increased petrophysical correlation, and better represent the subsurface in the spatial domain and the parameter domain of physical properties.

  12. Joint inversion of multiple geophysical and petrophysical data using generalized fuzzy clustering algorithms

    NASA Astrophysics Data System (ADS)

    Sun, Jiajia; Li, Yaoguo

    2017-02-01

    Joint inversion that simultaneously inverts multiple geophysical data sets to recover a common Earth model is increasingly being applied to exploration problems. Petrophysical data can serve as an effective constraint to link different physical property models in such inversions. There are two challenges, among others, associated with the petrophysical approach to joint inversion. One is related to the multimodality of petrophysical data because there often exist more than one relationship between different physical properties in a region of study. The other challenge arises from the fact that petrophysical relationships have different characteristics and can exhibit point, linear, quadratic, or exponential forms in a crossplot. The fuzzy c-means (FCM) clustering technique is effective in tackling the first challenge and has been applied successfully. We focus on the second challenge in this paper and develop a joint inversion method based on variations of the FCM clustering technique. To account for the specific shapes of petrophysical relationships, we introduce several different fuzzy clustering algorithms that are capable of handling different shapes of petrophysical relationships. We present two synthetic and one field data examples and demonstrate that, by choosing appropriate distance measures for the clustering component in the joint inversion algorithm, the proposed joint inversion method provides an effective means of handling common petrophysical situations we encounter in practice. The jointly inverted models have both enhanced structural similarity and increased petrophysical correlation, and better represent the subsurface in the spatial domain and the parameter domain of physical properties.

  13. Big Data GPU-Driven Parallel Processing Spatial and Spatio-Temporal Clustering Algorithms

    NASA Astrophysics Data System (ADS)

    Konstantaras, Antonios; Skounakis, Emmanouil; Kilty, James-Alexander; Frantzeskakis, Theofanis; Maravelakis, Emmanuel

    2016-04-01

    Advances in graphics processing units' technology towards encompassing parallel architectures [1], comprised of thousands of cores and multiples of parallel threads, provide the foundation in terms of hardware for the rapid processing of various parallel applications regarding seismic big data analysis. Seismic data are normally stored as collections of vectors in massive matrices, growing rapidly in size as wider areas are covered, denser recording networks are being established and decades of data are being compiled together [2]. Yet, many processes regarding seismic data analysis are performed on each seismic event independently or as distinct tiles [3] of specific grouped seismic events within a much larger data set. Such processes, independent of one another can be performed in parallel narrowing down processing times drastically [1,3]. This research work presents the development and implementation of three parallel processing algorithms using Cuda C [4] for the investigation of potentially distinct seismic regions [5,6] present in the vicinity of the southern Hellenic seismic arc. The algorithms, programmed and executed in parallel comparatively, are the: fuzzy k-means clustering with expert knowledge [7] in assigning overall clusters' number; density-based clustering [8]; and a selves-developed spatio-temporal clustering algorithm encompassing expert [9] and empirical knowledge [10] for the specific area under investigation. Indexing terms: GPU parallel programming, Cuda C, heterogeneous processing, distinct seismic regions, parallel clustering algorithms, spatio-temporal clustering References [1] Kirk, D. and Hwu, W.: 'Programming massively parallel processors - A hands-on approach', 2nd Edition, Morgan Kaufman Publisher, 2013 [2] Konstantaras, A., Valianatos, F., Varley, M.R. and Makris, J.P.: 'Soft-Computing Modelling of Seismicity in the Southern Hellenic Arc', Geoscience and Remote Sensing Letters, vol. 5 (3), pp. 323-327, 2008 [3] Papadakis, S. and

  14. Segmentation of dermatoscopic images by frequency domain filtering and k-means clustering algorithms.

    PubMed

    Rajab, Maher I

    2011-11-01

    Since the introduction of epiluminescence microscopy (ELM), image analysis tools have been extended to the field of dermatology, in an attempt to algorithmically reproduce clinical evaluation. Accurate image segmentation of skin lesions is one of the key steps for useful, early and non-invasive diagnosis of coetaneous melanomas. This paper proposes two image segmentation algorithms based on frequency domain processing and k-means clustering/fuzzy k-means clustering. The two methods are capable of segmenting and extracting the true border that reveals the global structure irregularity (indentations and protrusions), which may suggest excessive cell growth or regression of a melanoma. As a pre-processing step, Fourier low-pass filtering is applied to reduce the surrounding noise in a skin lesion image. A quantitative comparison of the techniques is enabled by the use of synthetic skin lesion images that model lesions covered with hair to which Gaussian noise is added. The proposed techniques are also compared with an established optimal-based thresholding skin-segmentation method. It is demonstrated that for lesions with a range of different border irregularity properties, the k-means clustering and fuzzy k-means clustering segmentation methods provide the best performance over a range of signal to noise ratios. The proposed segmentation techniques are also demonstrated to have similar performance when tested on real skin lesions representing high-resolution ELM images. This study suggests that the segmentation results obtained using a combination of low-pass frequency filtering and k-means or fuzzy k-means clustering are superior to the result that would be obtained by using k-means or fuzzy k-means clustering segmentation methods alone. © 2011 John Wiley & Sons A/S.

  15. A Smartphone Indoor Localization Algorithm Based on WLAN Location Fingerprinting with Feature Extraction and Clustering

    PubMed Central

    Luo, Junhai; Fu, Liang

    2017-01-01

    With the development of communication technology, the demand for location-based services is growing rapidly. This paper presents an algorithm for indoor localization based on Received Signal Strength (RSS), which is collected from Access Points (APs). The proposed localization algorithm contains the offline information acquisition phase and online positioning phase. Firstly, the AP selection algorithm is reviewed and improved based on the stability of signals to remove useless AP; secondly, Kernel Principal Component Analysis (KPCA) is analyzed and used to remove the data redundancy and maintain useful characteristics for nonlinear feature extraction; thirdly, the Affinity Propagation Clustering (APC) algorithm utilizes RSS values to classify data samples and narrow the positioning range. In the online positioning phase, the classified data will be matched with the testing data to determine the position area, and the Maximum Likelihood (ML) estimate will be employed for precise positioning. Eventually, the proposed algorithm is implemented in a real-world environment for performance evaluation. Experimental results demonstrate that the proposed algorithm improves the accuracy and computational complexity. PMID:28598358

  16. Commodity cluster and hardware-based massively parallel implementations of hyperspectral imaging algorithms

    NASA Astrophysics Data System (ADS)

    Plaza, Antonio; Chang, Chein-I.; Plaza, Javier; Valencia, David

    2006-05-01

    The incorporation of hyperspectral sensors aboard airborne/satellite platforms is currently producing a nearly continual stream of multidimensional image data, and this high data volume has soon introduced new processing challenges. The price paid for the wealth spatial and spectral information available from hyperspectral sensors is the enormous amounts of data that they generate. Several applications exist, however, where having the desired information calculated quickly enough for practical use is highly desirable. High computing performance of algorithm analysis is particularly important in homeland defense and security applications, in which swift decisions often involve detection of (sub-pixel) military targets (including hostile weaponry, camouflage, concealment, and decoys) or chemical/biological agents. In order to speed-up computational performance of hyperspectral imaging algorithms, this paper develops several fast parallel data processing techniques. Techniques include four classes of algorithms: (1) unsupervised classification, (2) spectral unmixing, and (3) automatic target recognition, and (4) onboard data compression. A massively parallel Beowulf cluster (Thunderhead) at NASA's Goddard Space Flight Center in Maryland is used to measure parallel performance of the proposed algorithms. In order to explore the viability of developing onboard, real-time hyperspectral data compression algorithms, a Xilinx Virtex-II field programmable gate array (FPGA) is also used in experiments. Our quantitative and comparative assessment of parallel techniques and strategies may help image analysts in selection of parallel hyperspectral algorithms for specific applications.

  17. Identification of metastable ultrasmall titanium oxide clusters using a hybrid optimization algorithm

    NASA Astrophysics Data System (ADS)

    Inclan, Eric; Geohegan, David; Yoon, Mina

    2015-03-01

    Nanostructured TiO2 materials have interesting properties that are highly relevant to energy and device applications. However, precise control of their morphologies and characterization are still a grand challenge in the field. Using a hybrid optimization algorithm we theoretically explored configuration spaces of energetically metastable TiO2 nanostructures. Our approach is to minimize the total energy of TiO2 clusters in order to identify the structural characteristics and energy landscape of plausible (TiO2)n (n = 1-100). The hybrid algorithm includes a modified differential evolution algorithm, a permutation operator to perform global optimization on a set of randomly generated structures, and then structure refinement using a BFGS Quasi-Newton algorithm. The results were compared against known physical structures and numerical results in the literature as well as our experimentally synthesized structures. Although the global minimum became more computationally expensive to locate with increasing number of TiO2 units, the optimizer successfully identified numerous plausible structures along a range of energies close to the global minimum energy structure for all clusters in the given range. This work is supported by the U.S. Department of Energy, Office of Science, Basic Energy Sciences, Materials Sciences and Engineering Division.

  18. The Spatial Distribution of the Young Stellar Clusters in the Star-forming Galaxy NGC 628

    NASA Astrophysics Data System (ADS)

    Grasha, K.; Calzetti, D.; Adamo, A.; Kim, H.; Elmegreen, B. G.; Gouliermis, D. A.; Aloisi, A.; Bright, S. N.; Christian, C.; Cignoni, M.; Dale, D. A.; Dobbs, C.; Elmegreen, D. M.; Fumagalli, M.; Gallagher, J. S., III; Grebel, E. K.; Johnson, K. E.; Lee, J. C.; Messa, M.; Smith, L. J.; Ryon, J. E.; Thilker, D.; Ubeda, L.; Wofford, A.

    2015-12-01

    We present a study of the spatial distribution of the stellar cluster populations in the star-forming galaxy NGC 628. Using Hubble Space Telescope broadband WFC3/UVIS UV and optical images from the Treasury Program LEGUS (Legacy ExtraGalactic UV Survey), we have identified 1392 potential young (≲ 100 Myr) stellar clusters within the galaxy using a combination of visual inspection and automatic selection. We investigate the clustering of these young stellar clusters and quantify the strength and change of clustering strength with scale using the two-point correlation function. We also investigate how image boundary conditions and dust lanes affect the observed clustering. The distribution of the clusters is well fit by a broken power law with negative exponent α. We recover a weighted mean index of α ∼ -0.8 for all spatial scales below the break at 3.″3 (158 pc at a distance of 9.9 Mpc) and an index of α ∼ -0.18 above 158 pc for the accumulation of all cluster types. The strength of the clustering increases with decreasing age and clusters older than 40 Myr lose their clustered structure very rapidly and tend to be randomly distributed in this galaxy, whereas the mass of the star cluster has little effect on the clustering strength. This is consistent with results from other studies that the morphological hierarchy in stellar clustering resembles the same hierarchy as the turbulent interstellar medium.

  19. INITIAL SIZE DISTRIBUTION OF THE GALACTIC GLOBULAR CLUSTER SYSTEM

    SciTech Connect

    Shin, Jihye; Kim, Sungsoo S.; Yoon, Suk-Jin; Kim, Juhan

    2013-01-10

    Despite the importance of their size evolution in understanding the dynamical evolution of globular clusters (GCs) of the Milky Way, studies that focus specifically on this issue are rare. Based on the advanced, realistic Fokker-Planck (FP) approach, we theoretically predict the initial size distribution (SD) of the Galactic GCs along with their initial mass function and radial distribution. Over one thousand FP calculations in a wide parameter space have pinpointed the best-fit initial conditions for the SD, mass function, and radial distribution. Our best-fit model shows that the initial SD of the Galactic GCs is of larger dispersion than today's SD, and that the typical projected half-light radius of the initial GCs is {approx}4.6 pc, which is 1.8 times larger than that of the present-day GCs ({approx}2.5 pc). Their large size signifies greater susceptibility to the Galactic tides: the total mass of destroyed GCs reaches 3-5 Multiplication-Sign 10{sup 8} M {sub Sun }, several times larger than previous estimates. Our result challenges a recent view that the Milky Way GCs were born compact on the sub-pc scale, and rather implies that (1) the initial GCs were generally larger than the typical size of the present-day GCs, (2) the initially large GCs mostly shrank and/or disrupted as a result of the galactic tides, and (3) the initially small GCs expanded by two-body relaxation, and later shrank by the galactic tides.

  20. Parallel OSEM Reconstruction Algorithm for Fully 3-D SPECT on a Beowulf Cluster.

    PubMed

    Rong, Zhou; Tianyu, Ma; Yongjie, Jin

    2005-01-01

    In order to improve the computation speed of ordered subset expectation maximization (OSEM) algorithm for fully 3-D single photon emission computed tomography (SPECT) reconstruction, an experimental beowulf-type cluster was built and several parallel reconstruction schemes were described. We implemented a single-program-multiple-data (SPMD) parallel 3-D OSEM reconstruction algorithm based on message passing interface (MPI) and tested it with combinations of different number of calculating processors and different size of voxel grid in reconstruction (64×64×64 and 128×128×128). Performance of parallelization was evaluated in terms of the speedup factor and parallel efficiency. This parallel implementation methodology is expected to be helpful to make fully 3-D OSEM algorithms more feasible in clinical SPECT studies.

  1. Fast Parabola Detection Using Estimation of Distribution Algorithms.

    PubMed

    Guerrero-Turrubiates, Jose de Jesus; Cruz-Aceves, Ivan; Ledesma, Sergio; Sierra-Hernandez, Juan Manuel; Velasco, Jonas; Avina-Cervantes, Juan Gabriel; Avila-Garcia, Maria Susana; Rostro-Gonzalez, Horacio; Rojas-Laguna, Roberto

    2017-01-01

    This paper presents a new method based on Estimation of Distribution Algorithms (EDAs) to detect parabolic shapes in synthetic and medical images. The method computes a virtual parabola using three random boundary pixels to calculate the constant values of the generic parabola equation. The resulting parabola is evaluated by matching it with the parabolic shape in the input image by using the Hadamard product as fitness function. This proposed method is evaluated in terms of computational time and compared with two implementations of the generalized Hough transform and RANSAC method for parabola detection. Experimental results show that the proposed method outperforms the comparative methods in terms of execution time about 93.61% on synthetic images and 89% on retinal fundus and human plantar arch images. In addition, experimental results have also shown that the proposed method can be highly suitable for different medical applications.

  2. A modified estimation distribution algorithm based on extreme elitism.

    PubMed

    Gao, Shujun; de Silva, Clarence W

    2016-12-01

    An existing estimation distribution algorithm (EDA) with univariate marginal Gaussian model was improved by designing and incorporating an extreme elitism selection method. This selection method highlighted the effect of a few top best solutions in the evolution and advanced EDA to form a primary evolution direction and obtain a fast convergence rate. Simultaneously, this selection can also keep the population diversity to make EDA avoid premature convergence. Then the modified EDA was tested by means of benchmark low-dimensional and high-dimensional optimization problems to illustrate the gains in using this extreme elitism selection. Besides, no-free-lunch theorem was implemented in the analysis of the effect of this new selection on EDAs.

  3. Fast Parabola Detection Using Estimation of Distribution Algorithms

    PubMed Central

    Sierra-Hernandez, Juan Manuel; Avila-Garcia, Maria Susana; Rojas-Laguna, Roberto

    2017-01-01

    This paper presents a new method based on Estimation of Distribution Algorithms (EDAs) to detect parabolic shapes in synthetic and medical images. The method computes a virtual parabola using three random boundary pixels to calculate the constant values of the generic parabola equation. The resulting parabola is evaluated by matching it with the parabolic shape in the input image by using the Hadamard product as fitness function. This proposed method is evaluated in terms of computational time and compared with two implementations of the generalized Hough transform and RANSAC method for parabola detection. Experimental results show that the proposed method outperforms the comparative methods in terms of execution time about 93.61% on synthetic images and 89% on retinal fundus and human plantar arch images. In addition, experimental results have also shown that the proposed method can be highly suitable for different medical applications. PMID:28321264

  4. A Novel Clustering Algorithm for Mobile Ad Hoc Networks Based on Determination of Virtual Links' Weight to Increase Network Stability

    PubMed Central

    Karimi, Abbas; Afsharfarnia, Abbas; Zarafshan, Faraneh; Al-Haddad, S. A. R.

    2014-01-01

    The stability of clusters is a serious issue in mobile ad hoc networks. Low stability of clusters may lead to rapid failure of clusters, high energy consumption for reclustering, and decrease in the overall network stability in mobile ad hoc network. In order to improve the stability of clusters, weight-based clustering algorithms are utilized. However, these algorithms only use limited features of the nodes. Thus, they decrease the weight accuracy in determining node's competency and lead to incorrect selection of cluster heads. A new weight-based algorithm presented in this paper not only determines node's weight using its own features, but also considers the direct effect of feature of adjacent nodes. It determines the weight of virtual links between nodes and the effect of the weights on determining node's final weight. By using this strategy, the highest weight is assigned to the best choices for being the cluster heads and the accuracy of nodes selection increases. The performance of new algorithm is analyzed by using computer simulation. The results show that produced clusters have longer lifetime and higher stability. Mathematical simulation shows that this algorithm has high availability in case of failure. PMID:25114965

  5. The cascaded moving k-means and fuzzy c-means clustering algorithms for unsupervised segmentation of malaria images

    NASA Astrophysics Data System (ADS)

    Abdul-Nasir, Aimi Salihah; Mashor, Mohd Yusoff; Halim, Nurul Hazwani Abd; Mohamed, Zeehaida

    2015-05-01

    Malaria is a life-threatening parasitic infectious disease that corresponds for nearly one million deaths each year. Due to the requirement of prompt and accurate diagnosis of malaria, the current study has proposed an unsupervised pixel segmentation based on clustering algorithm in order to obtain the fully segmented red blood cells (RBCs) infected with malaria parasites based on the thin blood smear images of P. vivax species. In order to obtain the segmented infected cell, the malaria images are first enhanced by using modified global contrast stretching technique. Then, an unsupervised segmentation technique based on clustering algorithm has been applied on the intensity component of malaria image in order to segment the infected cell from its blood cells background. In this study, cascaded moving k-means (MKM) and fuzzy c-means (FCM) clustering algorithms has been proposed for malaria slide image segmentation. After that, median filter algorithm has been applied to smooth the image as well as to remove any unwanted regions such as small background pixels from the image. Finally, seeded region growing area extraction algorithm has been applied in order to remove large unwanted regions that are still appeared on the image due to their size in which cannot be cleaned by using median filter. The effectiveness of the proposed cascaded MKM and FCM clustering algorithms has been analyzed qualitatively and quantitatively by comparing the proposed cascaded clustering algorithm with MKM and FCM clustering algorithms. Overall, the results indicate that segmentation using the proposed cascaded clustering algorithm has produced the best segmentation performances by achieving acceptable sensitivity as well as high specificity and accuracy values compared to the segmentation results provided by MKM and FCM algorithms.

  6. Constraints on the richness-mass relation and the optical-SZE positional offset distribution for SZE-selected clusters

    DOE PAGES

    Saro, A.

    2015-10-12

    In this study, we cross-match galaxy cluster candidates selected via their Sunyaev–Zel'dovich effect (SZE) signatures in 129.1 deg2 of the South Pole Telescope 2500d SPT-SZ survey with optically identified clusters selected from the Dark Energy Survey science verification data. We identify 25 clusters between 0.1 ≲ z ≲ 0.8 in the union of the SPT-SZ and redMaPPer (RM) samples. RM is an optical cluster finding algorithm that also returns a richness estimate for each cluster. We model the richness λ-mass relation with the following function 500> ∝ BλlnM500 + CλlnE(z) and use SPT-SZ cluster masses and RM richnesses λ tomore » constrain the parameters. We find Bλ = 1.14+0.21–0.18 and Cλ = 0.73+0.77–0.75. The associated scatter in mass at fixed richness is σlnM|λ = 0.18+0.08–0.05 at a characteristic richness λ = 70. We demonstrate that our model provides an adequate description of the matched sample, showing that the fraction of SPT-SZ-selected clusters with RM counterparts is consistent with expectations and that the fraction of RM-selected clusters with SPT-SZ counterparts is in mild tension with expectation. We model the optical-SZE cluster positional offset distribution with the sum of two Gaussians, showing that it is consistent with a dominant, centrally peaked population and a subdominant population characterized by larger offsets. We also cross-match the RM catalogue with SPT-SZ candidates below the official catalogue threshold significance ξ = 4.5, using the RM catalogue to provide optical confirmation and redshifts for 15 additional clusters with ξ ϵ [4, 4.5].« less

  7. Constraints on the richness-mass relation and the optical-SZE positional offset distribution for SZE-selected clusters

    NASA Astrophysics Data System (ADS)

    Saro, A.; Bocquet, S.; Rozo, E.; Benson, B. A.; Mohr, J.; Rykoff, E. S.; Soares-Santos, M.; Bleem, L.; Dodelson, S.; Melchior, P.; Sobreira, F.; Upadhyay, V.; Weller, J.; Abbott, T.; Abdalla, F. B.; Allam, S.; Armstrong, R.; Banerji, M.; Bauer, A. H.; Bayliss, M.; Benoit-Lévy, A.; Bernstein, G. M.; Bertin, E.; Brodwin, M.; Brooks, D.; Buckley-Geer, E.; Burke, D. L.; Carlstrom, J. E.; Capasso, R.; Capozzi, D.; Carnero Rosell, A.; Carrasco Kind, M.; Chiu, I.; Covarrubias, R.; Crawford, T. M.; Crocce, M.; D'Andrea, C. B.; da Costa, L. N.; DePoy, D. L.; Desai, S.; de Haan, T.; Diehl, H. T.; Dietrich, J. P.; Doel, P.; Cunha, C. E.; Eifler, T. F.; Evrard, A. E.; Fausti Neto, A.; Fernandez, E.; Flaugher, B.; Fosalba, P.; Frieman, J.; Gangkofner, C.; Gaztanaga, E.; Gerdes, D.; Gruen, D.; Gruendl, R. A.; Gupta, N.; Hennig, C.; Holzapfel, W. L.; Honscheid, K.; Jain, B.; James, D.; Kuehn, K.; Kuropatkin, N.; Lahav, O.; Li, T. S.; Lin, H.; Maia, M. A. G.; March, M.; Marshall, J. L.; Martini, Paul; McDonald, M.; Miller, C. J.; Miquel, R.; Nord, B.; Ogando, R.; Plazas, A. A.; Reichardt, C. L.; Romer, A. K.; Roodman, A.; Sako, M.; Sanchez, E.; Schubnell, M.; Sevilla, I.; Smith, R. C.; Stalder, B.; Stark, A. A.; Strazzullo, V.; Suchyta, E.; Swanson, M. E. C.; Tarle, G.; Thaler, J.; Thomas, D.; Tucker, D.; Vikram, V.; von der Linden, A.; Walker, A. R.; Wechsler, R. H.; Wester, W.; Zenteno, A.; Ziegler, K. E.

    2015-12-01

    We cross-match galaxy cluster candidates selected via their Sunyaev-Zel'dovich effect (SZE) signatures in 129.1 deg2 of the South Pole Telescope 2500d SPT-SZ survey with optically identified clusters selected from the Dark Energy Survey science verification data. We identify 25 clusters between 0.1 ≲ z ≲ 0.8 in the union of the SPT-SZ and redMaPPer (RM) samples. RM is an optical cluster finding algorithm that also returns a richness estimate for each cluster. We model the richness λ-mass relation with the following function ∝ Bλln M500 + Cλln E(z) and use SPT-SZ cluster masses and RM richnesses λ to constrain the parameters. We find B_λ = 1.14^{+0.21}_{-0.18} and C_λ =0.73^{+0.77}_{-0.75}. The associated scatter in mass at fixed richness is σ _{ln M|λ } = 0.18^{+0.08}_{-0.05} at a characteristic richness λ = 70. We demonstrate that our model provides an adequate description of the matched sample, showing that the fraction of SPT-SZ-selected clusters with RM counterparts is consistent with expectations and that the fraction of RM-selected clusters with SPT-SZ counterparts is in mild tension with expectation. We model the optical-SZE cluster positional offset distribution with the sum of two Gaussians, showing that it is consistent with a dominant, centrally peaked population and a subdominant population characterized by larger offsets. We also cross-match the RM catalogue with SPT-SZ candidates below the official catalogue threshold significance ξ = 4.5, using the RM catalogue to provide optical confirmation and redshifts for 15 additional clusters with ξ ∈ [4, 4.5].

  8. Galaxy clusters in visible light (I): catalogues, large-scale distribution, and general properties.

    NASA Astrophysics Data System (ADS)

    Bian, Yulin

    1995-12-01

    While the nature, behaviour, and evolution of galaxy clusters is a such wide research field, only some of their optical properties are underlined in the present review. The whole article is divided into two parts, of which this is the first one, contributed to cluster catalogues, large-scale distribution, and some general characteristics of galaxy clusters.

  9. Efficiently determining transform filter coefficients for image processing by applying distributed genetic algorithms

    NASA Astrophysics Data System (ADS)

    Gilligan, Martin; Lamont, Gary B.; Peterson, Michael R.

    2009-05-01

    An important aspect of contemporary military communications in the design of robust image transforms for defense surveillance applications. In particular, efficient yet effective transfer of critical image information is required for decision making. The generic use of wavelets to transform an image is a standard transform approach. However, the resulting bandwidth requirements can be quite high, suggesting that a different bandwidth-limited transform be developed. Thus, our specific use of genetic algorithms (GAs) attempts to replace standard wavelet filter coefficients with an optimized transform filter in order to retain or improve image quality for bandwidth-restricted surveillance applications. To find improved coefficients efficiently, we have developed a software engineered distributed design employing a genetic algorithm (GA) parallel island model on small and large computational clusters with multi-core nodes. The main objective is to determine whether running a distributed GA with multiple islands would either give statistically equivalent results quicker or obtain better results in the same amount of time. In order to compare computational performance with our previous serial results, we evaluate the obtained "optimal" wavelet coefficients on test images from both approaches which results in excellent comparative metric values.

  10. Cluster mass fraction and size distribution determined by fs-time-resolved measurements

    NASA Astrophysics Data System (ADS)

    Gao, Xiaohui; Wang, Xiaoming; Shim, Bonggu; Arefiev, Alexey; Tushentsov, Mikhail; Breizman, Boris; Downer, Mike

    2009-11-01

    Characterization of supersonic gas jets is important for accurate interpretation and control of laser-cluster experiments. While average size and total atomic density can be found by standard Rayleigh scatter and interferometry, cluster mass fraction and size distribution are usually difficult to measure. Here we determine the cluster fraction and the size distribution with fs-time-resolved refractive index and absorption measurements in cluster gas jets after ionization and heating by an intense pump pulse. The fs-time-resolved refractive index measured with frequency domain interferometer (FDI) shows different contributions from monomer plasma and cluster plasma in the time domain, enabling us to determine the cluster fraction. The fs-time-resolved absorption measured by a delayed probe shows the contribution from clusters of various sizes, allowing us to find the size distribution.

  11. A Hybrid Method for Image Segmentation Based on Artificial Fish Swarm Algorithm and Fuzzy c-Means Clustering.

    PubMed

    Ma, Li; Li, Yang; Fan, Suohai; Fan, Runzhu

    2015-01-01

    Image segmentation plays an important role in medical image processing. Fuzzy c-means (FCM) clustering is one of the popular clustering algorithms for medical image segmentation. However, FCM has the problems of depending on initial clustering centers, falling into local optimal solution easily, and sensitivity to noise disturbance. To solve these problems, this paper proposes a hybrid artificial fish swarm algorithm (HAFSA). The proposed algorithm combines artificial fish swarm algorithm (AFSA) with FCM whose advantages of global optimization searching and parallel computing ability of AFSA are utilized to find a superior result. Meanwhile, Metropolis criterion and noise reduction mechanism are introduced to AFSA for enhancing the convergence rate and antinoise ability. The artificial grid graph and Magnetic Resonance Imaging (MRI) are used in the experiments, and the experimental results show that the proposed algorithm has stronger antinoise ability and higher precision. A number of evaluation indicators also demonstrate that the effect of HAFSA is more excellent than FCM and suppressed FCM (SFCM).

  12. Application of Bron-Kerbosch algorithm in graph clustering using complement matrix

    NASA Astrophysics Data System (ADS)

    Antoro, S. C.; Sugeng, K. A.; Handari, B. D.

    2017-07-01

    Maximal clique enumeration is a graph clustering method for finding all vertices that have the most influence in a graph. The Bron-Kerbosch algorithm is one of the fastest algorithms to find all maximal cliques. Hence, this paper will focus on that algorithm to find all maximal cliques. Counting all maximal cliques of a graph usually uses an adjacency matrix of the graph to find all vertices in the graph that have the most influence. But, in this paper, a complement matrix of a graph will be used in counting all maximal cliques. This research uses a graph that represents a domestic flight route of one of the airlines in Indonesia. By using Bron-Kerbosch algorithm, all maximal cliques of the graph will be listed, so that it will come up with the vertices which are the most influential in this graph. The graph will be represented in complement matrix. The result of applying the Bron-Kerbosch algorithm with the complement matrix of graph will determine vertices that have the most influence in the graph. Besides that, by using a complement matrix, the result gives more information on the vertices which are only connected to the vertices that have the most influence.

  13. Text grouping in patent analysis using adaptive K-means clustering algorithm

    NASA Astrophysics Data System (ADS)

    Shanie, Tiara; Suprijadi, Jadi; Zulhanif

    2017-03-01

    Patents are one of the Intellectual Property. Analyzing patent is one requirement in knowing well the development of technology in each country and in the world now. This study uses the patent document coming from the Espacenet server about Green Tea. Patent documents related to the technology in the field of tea is still widespread, so it will be difficult for users to information retrieval (IR). Therefore, it is necessary efforts to categorize documents in a specific group of related terms contained therein. This study uses titles patent text data with the proposed Green Tea in Statistical Text Mining methods consists of two phases: data preparation and data analysis stage. The data preparation phase uses Text Mining methods and data analysis stage is done by statistics. Statistical analysis in this study using a cluster analysis algorithm, the Adaptive K-Means Clustering Algorithm. Results from this study showed that based on the maximum value Silhouette, generate 87 clusters associated fifteen terms therein that can be utilized in the process of information retrieval needs.

  14. Detection and clustering of features in aerial images by neuron network-based algorithm

    NASA Astrophysics Data System (ADS)

    Vozenilek, Vit

    2015-12-01

    The paper presents the algorithm for detection and clustering of feature in aerial photographs based on artificial neural networks. The presented approach is not focused on the detection of specific topographic features, but on the combination of general features analysis and their use for clustering and backward projection of clusters to aerial image. The basis of the algorithm is a calculation of the total error of the network and a change of weights of the network to minimize the error. A classic bipolar sigmoid was used for the activation function of the neurons and the basic method of backpropagation was used for learning. To verify that a set of features is able to represent the image content from the user's perspective, the web application was compiled (ASP.NET on the Microsoft .NET platform). The main achievements include the knowledge that man-made objects in aerial images can be successfully identified by detection of shapes and anomalies. It was also found that the appropriate combination of comprehensive features that describe the colors and selected shapes of individual areas can be useful for image analysis.

  15. Clustering of tethered satellite system simulation data by an adaptive neuro-fuzzy algorithm

    NASA Technical Reports Server (NTRS)

    Mitra, Sunanda; Pemmaraju, Surya

    1992-01-01

    Recent developments in neuro-fuzzy systems indicate that the concepts of adaptive pattern recognition, when used to identify appropriate control actions corresponding to clusters of patterns representing system states in dynamic nonlinear control systems, may result in innovative designs. A modular, unsupervised neural network architecture, in which fuzzy learning rules have been embedded is used for on-line identification of similar states. The architecture and control rules involved in Adaptive Fuzzy Leader Clustering (AFLC) allow this system to be incorporated in control systems for identification of system states corresponding to specific control actions. We have used this algorithm to cluster the simulation data of Tethered Satellite System (TSS) to estimate the range of delta voltages necessary to maintain the desired length rate of the tether. The AFLC algorithm is capable of on-line estimation of the appropriate control voltages from the corresponding length error and length rate error without a priori knowledge of their membership functions and familarity with the behavior of the Tethered Satellite System.

  16. A Network-Based Algorithm for Clustering Multivariate Repeated Measures Data

    NASA Technical Reports Server (NTRS)

    Koslovsky, Matthew; Arellano, John; Schaefer, Caroline; Feiveson, Alan; Young, Millennia; Lee, Stuart

    2017-01-01

    The National Aeronautics and Space Administration (NASA) Astronaut Corps is a unique occupational cohort for which vast amounts of measures data have been collected repeatedly in research or operational studies pre-, in-, and post-flight, as well as during multiple clinical care visits. In exploratory analyses aimed at generating hypotheses regarding physiological changes associated with spaceflight exposure, such as impaired vision, it is of interest to identify anomalies and trends across these expansive datasets. Multivariate clustering algorithms for repeated measures data may help parse the data to identify homogeneous groups of astronauts that have higher risks for a particular physiological change. However, available clustering methods may not be able to accommodate the complex data structures found in NASA data, since the methods often rely on strict model assumptions, require equally-spaced and balanced assessment times, cannot accommodate missing data or differing time scales across variables, and cannot process continuous and discrete data simultaneously. To fill this gap, we propose a network-based, multivariate clustering algorithm for repeated measures data that can be tailored to fit various research settings. Using simulated data, we demonstrate how our method can be used to identify patterns in complex data structures found in practice.

  17. Probability-changing cluster algorithm for two-dimensional XY and clock models

    NASA Astrophysics Data System (ADS)

    Tomita, Yusuke; Okabe, Yutaka

    2002-05-01

    We extend the newly proposed probability-changing cluster (PCC) Monte Carlo algorithm to the study of systems with the vector order parameter. Wolff's idea of the embedded cluster formalism is used for assigning clusters. The Kosterlitz-Thouless (KT) transitions for the two-dimensional (2D) XY and q-state clock models are studied by using the PCC algorithm. Combined with the finite-size scaling analysis based on the KT form of the correlation length, ξ~exp(c/(T/TKT-1)), we determine the KT transition temperature and the decay exponent η as TKT=0.8933(6) and η=0.243(4) for the 2D XY model. We investigate two transitions of the KT type for the 2D q-state clock models with q=6,8,12 and confirm the prediction of η=4/q2 at T1, the low-temperature critical point between the ordered and XY-like phases, systematically.

  18. Crowded Cluster Cores. Algorithms for Deblending in Dark Energy Survey Images

    DOE PAGES

    Zhang, Yuanyuan; McKay, Timothy A.; Bertin, Emmanuel; ...

    2015-10-26

    Deep optical images are often crowded with overlapping objects. We found that this is especially true in the cores of galaxy clusters, where images of dozens of galaxies may lie atop one another. Accurate measurements of cluster properties require deblending algorithms designed to automatically extract a list of individual objects and decide what fraction of the light in each pixel comes from each object. In this article, we introduce a new software tool called the Gradient And Interpolation based (GAIN) deblender. GAIN is used as a secondary deblender to improve the separation of overlapping objects in galaxy cluster cores inmore » Dark Energy Survey images. It uses image intensity gradients and an interpolation technique originally developed to correct flawed digital images. Our paper is dedicated to describing the algorithm of the GAIN deblender and its applications, but we additionally include modest tests of the software based on real Dark Energy Survey co-add images. GAIN helps to extract an unbiased photometry measurement for blended sources and improve detection completeness, while introducing few spurious detections. When applied to processed Dark Energy Survey data, GAIN serves as a useful quick fix when a high level of deblending is desired.« less

  19. Crowded Cluster Cores. Algorithms for Deblending in Dark Energy Survey Images

    SciTech Connect

    Zhang, Yuanyuan; McKay, Timothy A.; Bertin, Emmanuel; Jeltema, Tesla; Miller, Christopher J.; Rykoff, Eli; Song, Jeeseon

    2015-10-26

    Deep optical images are often crowded with overlapping objects. We found that this is especially true in the cores of galaxy clusters, where images of dozens of galaxies may lie atop one another. Accurate measurements of cluster properties require deblending algorithms designed to automatically extract a list of individual objects and decide what fraction of the light in each pixel comes from each object. In this article, we introduce a new software tool called the Gradient And Interpolation based (GAIN) deblender. GAIN is used as a secondary deblender to improve the separation of overlapping objects in galaxy cluster cores in Dark Energy Survey images. It uses image intensity gradients and an interpolation technique originally developed to correct flawed digital images. Our paper is dedicated to describing the algorithm of the GAIN deblender and its applications, but we additionally include modest tests of the software based on real Dark Energy Survey co-add images. GAIN helps to extract an unbiased photometry measurement for blended sources and improve detection completeness, while introducing few spurious detections. When applied to processed Dark Energy Survey data, GAIN serves as a useful quick fix when a high level of deblending is desired.

  20. BCRgt: a Bayesian cluster regression-based genotyping algorithm for the samples with copy number alterations

    PubMed Central

    2014-01-01

    Background Accurate genotype calling is a pre-requisite of a successful Genome-Wide Association Study (GWAS). Although most genotyping algorithms can achieve an accuracy rate greater than 99% for genotyping DNA samples without copy number alterations (CNAs), almost all of these algorithms are not designed for genotyping tumor samples that are known to have large regions of CNAs. Results This study aims to develop a statistical method that can accurately genotype tumor samples with CNAs. The proposed method adds a Bayesian layer to a cluster regression model and is termed a Bayesian Cluster Regression-based genotyping algorithm (BCRgt). We demonstrate that high concordance rates with HapMap calls can be achieved without using reference/training samples, when CNAs do not exist. By adding a training step, we have obtained higher genotyping concordance rates, without requiring large sample sizes. When CNAs exist in the samples, accuracy can be dramatically improved in regions with DNA copy loss and slightly improved in regions with copy number gain, comparing with the Bayesian Robust Linear Model with Mahalanobis distance classifier (BRLMM). Conclusions In conclusion, we have demonstrated that BCRgt can provide accurate genotyping calls for tumor samples with CNAs. PMID:24629125

  1. An improved scheduling algorithm for 3D cluster rendering with platform LSF

    NASA Astrophysics Data System (ADS)

    Xu, Wenli; Zhu, Yi; Zhang, Liping

    2013-10-01

    High-quality photorealistic rendering of 3D modeling needs powerful computing systems. On this demand highly efficient management of cluster resources develops fast to exert advantages. This paper is absorbed in the aim of how to improve the efficiency of 3D rendering tasks in cluster. It focuses research on a dynamic feedback load balance (DFLB) algorithm, the work principle of load sharing facility (LSF) and optimization of external scheduler plug-in. The algorithm can be applied into match and allocation phase of a scheduling cycle. Candidate hosts is prepared in sequence in match phase. And the scheduler makes allocation decisions for each job in allocation phase. With the dynamic mechanism, new weight is assigned to each candidate host for rearrangement. The most suitable one will be dispatched for rendering. A new plugin module of this algorithm has been designed and integrated into the internal scheduler. Simulation experiments demonstrate the ability of improved plugin module is superior to the default one for rendering tasks. It can help avoid load imbalance among servers, increase system throughput and improve system utilization.

  2. Modelling Paleoearthquake Slip Distributions using a Gentic Algorithm

    NASA Astrophysics Data System (ADS)

    Lindsay, Anthony; Simão, Nuno; McCloskey, John; Nalbant, Suleyman; Murphy, Shane; Bhloscaidh, Mairead Nic

    2013-04-01

    Along the Sunda trench, the annual growth rings of coral microatolls store long term records of tectonic deformation. Spread over large areas of an active megathrust fault, they offer the possibility of high resolution reconstructions of slip for a number of paleo-earthquakes. These data are complex with spatial and temporal variations in uncertainty. Rather than assuming that any one model will uniquely fit the data, Monte Carlo Slip Estimation (MCSE) modelling produces a catalogue of possible models for each event. From each earthquake's catalogue, a model is selected and a possible history of slip along the fault reconstructed. By generating multiple histories, then finding the average slip during each earthquake, a probabilistic history of slip along the fault can be generated and areas that may have a large slip deficit identified. However, the MCSE technique requires the production of many hundreds of billions of models to yield the few models that fit the observed coral data. In an attempt to accelerate this process, we have designed a Genetic Algorithm (GA). The GA uses evolutionary operators to recombine the information held by a population of possible slip models to produce a set of new models, based on how well they reproduce a set of coral deformation data. Repeated iterations of the algorithm produce populations of improved models, each generation better satisfying the coral data. Preliminary results have shown the GA to be capable of recovering synthetically generated slip distributions based their displacements of sets of corals faster than the MCSE technique. The results of the systematic testing of the GA technique and its performance using both synthetic and observed coral displacement data will be presented.

  3. Clustering Educational Digital Library Usage Data: A Comparison of Latent Class Analysis and K-Means Algorithms

    ERIC Educational Resources Information Center

    Xu, Beijie; Recker, Mimi; Qi, Xiaojun; Flann, Nicholas; Ye, Lei

    2013-01-01

    This article examines clustering as an educational data mining method. In particular, two clustering algorithms, the widely used K-means and the model-based Latent Class Analysis, are compared, using usage data from an educational digital library service, the Instructional Architect (IA.usu.edu). Using a multi-faceted approach and multiple data…

  4. Clustering Educational Digital Library Usage Data: A Comparison of Latent Class Analysis and K-Means Algorithms

    ERIC Educational Resources Information Center

    Xu, Beijie; Recker, Mimi; Qi, Xiaojun; Flann, Nicholas; Ye, Lei

    2013-01-01

    This article examines clustering as an educational data mining method. In particular, two clustering algorithms, the widely used K-means and the model-based Latent Class Analysis, are compared, using usage data from an educational digital library service, the Instructional Architect (IA.usu.edu). Using a multi-faceted approach and multiple data…

  5. Clusters and cycles in the cosmic ray age distributions of meteorites

    NASA Technical Reports Server (NTRS)

    Woodard, M. F.; Marti, K.

    1985-01-01

    Statistically significant clusters in the cosmic ray exposure age distributions of some groups of iron and stone meteorites were observed, suggesting epochs of enhanced collision and breakups. Fourier analyses of the age distributions of chondrites reveal no significant periods, nor does the same analysis when applied to iron meteorite clusters.

  6. Development of a Genetic Algorithm to Automate Clustering of a Dependency Structure Matrix

    NASA Technical Reports Server (NTRS)

    Rogers, James L.; Korte, John J.; Bilardo, Vincent J.

    2006-01-01

    Much technology assessment and organization design data exists in Microsoft Excel spreadsheets. Tools are needed to put this data into a form that can be used by design managers to make design decisions. One need is to cluster data that is highly coupled. Tools such as the Dependency Structure Matrix (DSM) and a Genetic Algorithm (GA) can be of great benefit. However, no tool currently combines the DSM and a GA to solve the clustering problem. This paper describes a new software tool that interfaces a GA written as an Excel macro with a DSM in spreadsheet format. The results of several test cases are included to demonstrate how well this new tool works.

  7. Clustering Haze Trajectory of Peatland Fires in Riau Province using K-Means Algorithm

    NASA Astrophysics Data System (ADS)

    Khairat, H.; Sukaesih Sitanggang, I.; E Nuryanto, D.

    2017-03-01

    Haze is one of the impacts caused by forest and land fires. In order to determine how far the movement of haze from forest and land fires including in peatland, this research aims to determine the haze trajectory patterns from peatland fires in Riau Province in 2015 using HYSPLIT model. Furthermore, the haze trajectory patterns were grouped using the K-Means algorithm. The results show that the trajectory consists of 4887 positions of haze that moves to the northeast and northwest. The clustering results using K-Means show that the largest cluster has 3702 positions of haze and these haze movements are located at the average of height of 23.554 m AGL. Those haze positions were located in Riau, North Sumatra, Malaysia, and Malacca Strait.

  8. Application of Fuzzy C-Means Clustering Algorithm Based on Particle Swarm Optimization in Computer Forensics

    NASA Astrophysics Data System (ADS)

    Wang, Deguang; Han, Baochang; Huang, Ming

    Computer forensics is the technology of applying computer technology to access, investigate and analysis the evidence of computer crime. It mainly include the process of determine and obtain digital evidence, analyze and take data, file and submit result. And the data analysis is the key link of computer forensics. As the complexity of real data and the characteristics of fuzzy, evidence analysis has been difficult to obtain the desired results. This paper applies fuzzy c-means clustering algorithm based on particle swarm optimization (FCMP) in computer forensics, and it can be more satisfactory results.

  9. Clustering Multiple Sclerosis Subgroups with Multifractal Methods and Self-Organizing Map Algorithm

    NASA Astrophysics Data System (ADS)

    Karaca, Yeliz; Cattani, Carlo

    Magnetic resonance imaging (MRI) is the most sensitive method to detect chronic nervous system diseases such as multiple sclerosis (MS). In this paper, Brownian motion Hölder regularity functions (polynomial, periodic (sine), exponential) for 2D image, such as multifractal methods were applied to MR brain images, aiming to easily identify distressed regions, in MS patients. With these regions, we have proposed an MS classification based on the multifractal method by using the Self-Organizing Map (SOM) algorithm. Thus, we obtained a cluster analysis by identifying pixels from distressed regions in MR images through multifractal methods and by diagnosing subgroups of MS patients through artificial neural networks.

  10. CLUSTAG & WCLUSTAG: Hierarchical Clustering Algorithms for Efficient Tag-SNP Selection

    NASA Astrophysics Data System (ADS)

    Ao, Sio-Iong

    More than 6 million single nucleotide polymorphisms (SNPs) in the human genome have been genotyped by the HapMap project. Although only a pro portion of these SNPs are functional, all can be considered as candidate markers for indirect association studies to detect disease-related genetic variants. The complete screening of a gene or a chromosomal region is nevertheless an expensive undertak ing for association studies. A key strategy for improving the efficiency of association studies is to select a subset of informative SNPs, called tag SNPs, for analysis. In the chapter, hierarchical clustering algorithms have been proposed for efficient tag SNP selection.

  11. Multispectral image classification of MRI data using an empirically-derived clustering algorithm

    SciTech Connect

    Horn, K.M.; Osbourn, G.C.; Bouchard, A.M.; Sanders, J.A. |

    1998-08-01

    Multispectral image analysis of magnetic resonance imaging (MRI) data has been performed using an empirically-derived clustering algorithm. This algorithm groups image pixels into distinct classes which exhibit similar response in the T{sub 2} 1st and 2nd-echo, and T{sub 1} (with ad without gadolinium) MRI images. The grouping is performed in an n-dimensional mathematical space; the n-dimensional volumes bounding each class define each specific tissue type. The classification results are rendered again in real-space by colored-coding each grouped class of pixels (associated with differing tissue types). This classification method is especially well suited for class volumes with complex boundary shapes, and is also expected to robustly detect abnormal tissue classes. The classification process is demonstrated using a three dimensional data set of MRI scans of a human brain tumor.

  12. Thermal and log-normal distributions of plasma in laser driven Coulomb explosions of deuterium clusters

    NASA Astrophysics Data System (ADS)

    Barbarino, M.; Warrens, M.; Bonasera, A.; Lattuada, D.; Bang, W.; Quevedo, H. J.; Consoli, F.; de Angelis, R.; Andreoli, P.; Kimura, S.; Dyer, G.; Bernstein, A. C.; Hagel, K.; Barbui, M.; Schmidt, K.; Gaul, E.; Donovan, M. E.; Natowitz, J. B.; Ditmire, T.

    2016-08-01

    In this work, we explore the possibility that the motion of the deuterium ions emitted from Coulomb cluster explosions is highly disordered enough to resemble thermalization. We analyze the process of nuclear fusion reactions driven by laser-cluster interactions in experiments conducted at the Texas Petawatt laser facility using a mixture of D2+3He and CD4+3He cluster targets. When clusters explode by Coulomb repulsion, the emission of the energetic ions is “nearly” isotropic. In the framework of cluster Coulomb explosions, we analyze the energy distributions of the ions using a Maxwell-Boltzmann (MB) distribution, a shifted MB distribution (sMB), and the energy distribution derived from a log-normal (LN) size distribution of clusters. We show that the first two distributions reproduce well the experimentally measured ion energy distributions and the number of fusions from d-d and d-3He reactions. The LN distribution is a good representation of the ion kinetic energy distribution well up to high momenta where the noise becomes dominant, but overestimates both the neutron and the proton yields. If the parameters of the LN distributions are chosen to reproduce the fusion yields correctly, the experimentally measured high energy ion spectrum is not well represented. We conclude that the ion kinetic energy distribution is highly disordered and practically not distinguishable from a thermalized one.

  13. Meanie3D - a mean-shift based, multivariate, multi-scale clustering and tracking algorithm

    NASA Astrophysics Data System (ADS)

    Simon, Jürgen-Lorenz; Malte, Diederich; Silke, Troemel

    2014-05-01

    Project OASE is the one of 5 work groups at the HErZ (Hans Ertel Centre for Weather Research), an ongoing effort by the German weather service (DWD) to further research at Universities concerning weather prediction. The goal of project OASE is to gain an object-based perspective on convective events by identifying them early in the onset of convective initiation and follow then through the entire lifecycle. The ability to follow objects in this fashion requires new ways of object definition and tracking, which incorporate all the available data sets of interest, such as Satellite imagery, weather Radar or lightning counts. The Meanie3D algorithm provides the necessary tool for this purpose. Core features of this new approach to clustering (object identification) and tracking are the ability to identify objects using the mean-shift algorithm applied to a multitude of variables (multivariate), as well as the ability to detect objects on various scales (multi-scale) using elements of Scale-Space theory. The algorithm works in 2D as well as 3D without modifications. It is an extension of a method well known from the field of computer vision and image processing, which has been tailored to serve the needs of the meteorological community. In spite of the special application to be demonstrated here (like convective initiation), the algorithm is easily tailored to provide clustering and tracking for a wide class of data sets and problems. In this talk, the demonstration is carried out on two of the OASE group's own composite sets. One is a 2D nationwide composite of Germany including C-Band Radar (2D) and Satellite information, the other a 3D local composite of the Bonn/Jülich area containing a high-resolution 3D X-Band Radar composite.

  14. Using Hierarchical Time Series Clustering Algorithm and Wavelet Classifier for Biometric Voice Classification

    PubMed Central

    Fong, Simon

    2012-01-01

    Voice biometrics has a long history in biosecurity applications such as verification and identification based on characteristics of the human voice. The other application called voice classification which has its important role in grouping unlabelled voice samples, however, has not been widely studied in research. Lately voice classification is found useful in phone monitoring, classifying speakers' gender, ethnicity and emotion states, and so forth. In this paper, a collection of computational algorithms are proposed to support voice classification; the algorithms are a combination of hierarchical clustering, dynamic time wrap transform, discrete wavelet transform, and decision tree. The proposed algorithms are relatively more transparent and interpretable than the existing ones, though many techniques such as Artificial Neural Networks, Support Vector Machine, and Hidden Markov Model (which inherently function like a black box) have been applied for voice verification and voice identification. Two datasets, one that is generated synthetically and the other one empirically collected from past voice recognition experiment, are used to verify and demonstrate the effectiveness of our proposed voice classification algorithm. PMID:22619492

  15. Automated spike sorting algorithm based on Laplacian eigenmaps and k-means clustering.

    PubMed

    Chah, E; Hok, V; Della-Chiesa, A; Miller, J J H; O'Mara, S M; Reilly, R B

    2011-02-01

    This study presents a new automatic spike sorting method based on feature extraction by Laplacian eigenmaps combined with k-means clustering. The performance of the proposed method was compared against previously reported algorithms such as principal component analysis (PCA) and amplitude-based feature extraction. Two types of classifier (namely k-means and classification expectation-maximization) were incorporated within the spike sorting algorithms, in order to find a suitable classifier for the feature sets. Simulated data sets and in-vivo tetrode multichannel recordings were employed to assess the performance of the spike sorting algorithms. The results show that the proposed algorithm yields significantly improved performance with mean sorting accuracy of 73% and sorting error of 10% compared to PCA which combined with k-means had a sorting accuracy of 58% and sorting error of 10%.A correction was made to this article on 22 February 2011. The spacing of the title was amended on the abstract page. No changes were made to the article PDF and the print version was unaffected.

  16. An Energy-Efficient Spectrum-Aware Reinforcement Learning-Based Clustering Algorithm for Cognitive Radio Sensor Networks.

    PubMed

    Mustapha, Ibrahim; Mohd Ali, Borhanuddin; Rasid, Mohd Fadlee A; Sali, Aduwati; Mohamad, Hafizal

    2015-08-13

    It is well-known that clustering partitions network into logical groups of nodes in order to achieve energy efficiency and to enhance dynamic channel access in cognitive radio through cooperative sensing. While the topic of energy efficiency has been well investigated in conventional wireless sensor networks, the latter has not been extensively explored. In this paper, we propose a reinforcement learning-based spectrum-aware clustering algorithm that allows a member node to learn the energy and cooperative sensing costs for neighboring clusters to achieve an optimal solution. Each member node selects an optimal cluster that satisfies pairwise constraints, minimizes network energy consumption and enhances channel sensing performance through an exploration technique. We first model the network energy consumption and then determine the optimal number of clusters for the network. The problem of selecting an optimal cluster is formulated as a Markov Decision Process (MDP) in the algorithm and the obtained simulation results show convergence, learning and adaptability of the algorithm to dynamic environment towards achieving an optimal solution. Performance comparisons of our algorithm with the Groupwise Spectrum Aware (GWSA)-based algorithm in terms of Sum of Square Error (SSE), complexity, network energy consumption and probability of detection indicate improved performance from the proposed approach. The results further reveal that an energy savings of 9% and a significant Primary User (PU) detection improvement can be achieved with the proposed approach.

  17. An Energy-Efficient Spectrum-Aware Reinforcement Learning-Based Clustering Algorithm for Cognitive Radio Sensor Networks

    PubMed Central

    Mustapha, Ibrahim; Ali, Borhanuddin Mohd; Rasid, Mohd Fadlee A.; Sali, Aduwati; Mohamad, Hafizal

    2015-01-01

    It is well-known that clustering partitions network into logical groups of nodes in order to achieve energy efficiency and to enhance dynamic channel access in cognitive radio through cooperative sensing. While the topic of energy efficiency has been well investigated in conventional wireless sensor networks, the latter has not been extensively explored. In this paper, we propose a reinforcement learning-based spectrum-aware clustering algorithm that allows a member node to learn the energy and cooperative sensing costs for neighboring clusters to achieve an optimal solution. Each member node selects an optimal cluster that satisfies pairwise constraints, minimizes network energy consumption and enhances channel sensing performance through an exploration technique. We first model the network energy consumption and then determine the optimal number of clusters for the network. The problem of selecting an optimal cluster is formulated as a Markov Decision Process (MDP) in the algorithm and the obtained simulation results show convergence, learning and adaptability of the algorithm to dynamic environment towards achieving an optimal solution. Performance comparisons of our algorithm with the Groupwise Spectrum Aware (GWSA)-based algorithm in terms of Sum of Square Error (SSE), complexity, network energy consumption and probability of detection indicate improved performance from the proposed approach. The results further reveal that an energy savings of 9% and a significant Primary User (PU) detection improvement can be achieved with the proposed approach. PMID:26287191

  18. The Hierarchical Distribution of the Young Stellar Clusters in Six Local Star-forming Galaxies

    NASA Astrophysics Data System (ADS)

    Grasha, K.; Calzetti, D.; Adamo, A.; Kim, H.; Elmegreen, B. G.; Gouliermis, D. A.; Dale, D. A.; Fumagalli, M.; Grebel, E. K.; Johnson, K. E.; Kahre, L.; Kennicutt, R. C.; Messa, M.; Pellerin, A.; Ryon, J. E.; Smith, L. J.; Shabani, F.; Thilker, D.; Ubeda, L.

    2017-05-01

    We present a study of the hierarchical clustering of the young stellar clusters in six local (3-15 Mpc) star-forming galaxies using Hubble Space Telescope broadband WFC3/UVIS UV and optical images from the Treasury Program LEGUS (Legacy ExtraGalactic UV Survey). We identified 3685 likely clusters and associations, each visually classified by their morphology, and we use the angular two-point correlation function to study the clustering of these stellar systems. We find that the spatial distribution of the young clusters and associations are clustered with respect to each other, forming large, unbound hierarchical star-forming complexes that are in general very young. The strength of the clustering decreases with increasing age of the star clusters and stellar associations, becoming more homogeneously distributed after ˜40-60 Myr and on scales larger than a few hundred parsecs. In all galaxies, the associations exhibit a global behavior that is distinct and more strongly correlated from compact clusters. Thus, populations of clusters are more evolved than associations in terms of their spatial distribution, traveling significantly from their birth site within a few tens of Myr, whereas associations show evidence of disruption occurring very quickly after their formation. The clustering of the stellar systems resembles that of a turbulent interstellar medium that drives the star formation process, correlating the components in unbound star-forming complexes in a hierarchical manner, dispersing shortly after formation, suggestive of a single, continuous mode of star form