Science.gov

Sample records for agglomerative clustering algorithm

  1. 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)

  2. Agglomerative clustering-based approach for two-dimensional phase unwrapping.

    PubMed

    Herráez, Miguel Arevalillo; Boticario, Jesús G; Lalor, Michael J; Burton, David R

    2005-03-01

    We describe a novel algorithm for two-dimensional phase unwrapping. The technique combines the principles of agglomerative clustering and use of heuristics to construct a discontinuous quality-guided path. Unlike other quality-guided algorithms, which establish the path at the start of the unwrapping process, our technique constructs the path as the unwrapping process evolves. This makes the technique less prone to error propagation, although it presents higher execution times than other existing algorithms. The algorithm reacts satisfactorily to random noise and breaks in the phase distribution. A variation of the algorithm is also presented that considerably reduces the execution time without affecting the results significantly.

  3. Deterministic algorithm with agglomerative heuristic for location problems

    NASA Astrophysics Data System (ADS)

    Kazakovtsev, L.; Stupina, A.

    2015-10-01

    Authors consider the clustering problem solved with the k-means method and p-median problem with various distance metrics. The p-median problem and the k-means problem as its special case are most popular models of the location theory. They are implemented for solving problems of clustering and many practically important logistic problems such as optimal factory or warehouse location, oil or gas wells, optimal drilling for oil offshore, steam generators in heavy oil fields. Authors propose new deterministic heuristic algorithm based on ideas of the Information Bottleneck Clustering and genetic algorithms with greedy heuristic. In this paper, results of running new algorithm on various data sets are given in comparison with known deterministic and stochastic methods. New algorithm is shown to be significantly faster than the Information Bottleneck Clustering method having analogous preciseness.

  4. Hierarchical Regional Disparities and Potential Sector Identification Using Modified Agglomerative Clustering

    NASA Astrophysics Data System (ADS)

    Munandar, T. A.; Azhari; Mushdholifah, A.; Arsyad, L.

    2017-03-01

    Disparities in regional development methods are commonly identified using the Klassen Typology and Location Quotient. Both methods typically use the data on the gross regional domestic product (GRDP) sectors of a particular region. The Klassen approach can identify regional disparities by classifying the GRDP sector data into four classes, namely Quadrants I, II, III, and IV. Each quadrant indicates a certain level of regional disparities based on the GRDP sector value of the said region. Meanwhile, the Location Quotient (LQ) is usually used to identify potential sectors in a particular region so as to determine which sectors are potential and which ones are not potential. LQ classifies each sector into three classes namely, the basic sector, the non-basic sector with a competitive advantage, and the non-basic sector which can only meet its own necessities. Both Klassen Typology and LQ are unable to visualize the relationship of achievements in the development clearly of each region and sector. This research aimed to develop a new approach to the identification of disparities in regional development in the form of hierarchical clustering. The method of Hierarchical Agglomerative Clustering (HAC) was employed as the basis of the hierarchical clustering model for identifying disparities in regional development. Modifications were made to HAC using the Klassen Typology and LQ. Then, HAC which had been modified using the Klassen Typology was called MHACK while HAC which had been modified using LQ was called MACLoQ. Both algorithms can be used to identify regional disparities (MHACK) and potential sectors (MACLoQ), respectively, in the form of hierarchical clusters. Based on the MHACK in 31 regencies in Central Java Province, it is identified that 3 regencies (Demak, Jepara, and Magelang City) fall into the category of developed and rapidly-growing regions, while the other 28 regencies fall into the category of developed but depressed regions. Results of the MACLo

  5. 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

  6. Combining analytical hierarchy process and agglomerative hierarchical clustering in search of expert consensus in green corridors development management.

    PubMed

    Shapira, Aviad; Shoshany, Maxim; Nir-Goldenberg, Sigal

    2013-07-01

    Environmental management and planning are instrumental in resolving conflicts arising between societal needs for economic development on the one hand and for open green landscapes on the other hand. Allocating green corridors between fragmented core green areas may provide a partial solution to these conflicts. Decisions regarding green corridor development require the assessment of alternative allocations based on multiple criteria evaluations. Analytical Hierarchy Process provides a methodology for both a structured and consistent extraction of such evaluations and for the search for consensus among experts regarding weights assigned to the different criteria. Implementing this methodology using 15 Israeli experts-landscape architects, regional planners, and geographers-revealed inherent differences in expert opinions in this field beyond professional divisions. The use of Agglomerative Hierarchical Clustering allowed to identify clusters representing common decisions regarding criterion weights. Aggregating the evaluations of these clusters revealed an important dichotomy between a pragmatist approach that emphasizes the weight of statutory criteria and an ecological approach that emphasizes the role of the natural conditions in allocating green landscape corridors.

  7. Classifying airborne radiometry data with Agglomerative Hierarchical Clustering: A tool for geological mapping in context of rainforest (French Guiana)

    NASA Astrophysics Data System (ADS)

    Martelet, G.; Truffert, C.; Tourlière, B.; Ledru, P.; Perrin, J.

    2006-09-01

    In highly weathered environments, it is crucial that geological maps provide information concerning both the regolith and the bedrock, for societal needs, such as land-use, mineral or water resources management. Often, geologists are facing the challenge of upgrading existing maps, as relevant information concerning weathering processes and pedogenesis is currently missing. In rugged areas in particular, where access to the field is difficult, ground observations are sparsely available, and need therefore to be complemented using methods based on remotely sensed data. For this purpose, we discuss the use of Agglomerative Hierarchical Clustering (AHC) on eU, K and eTh airborne gamma-ray spectrometry grids. The AHC process allows primarily to segment the geophysical maps into zones having coherent U, K and Th contents. The analysis of these contents are discussed in terms of geochemical signature for lithological attribution of classes, as well as the use of a dendrogram, which gives indications on the hierarchical relations between classes. Unsupervised classification maps resulting from AHC can be considered as spatial models of the distribution of the radioelement content in surface and sub-surface formations. The source of gamma rays emanating from the ground is primarily related to the geochemistry of the bedrock and secondarily to modifications of the radioelement distribution by weathering and other secondary mechanisms, such as mobilisation by wind or water. The interpretation of the obtained predictive classified maps, their U, K, Th contents, and the dendrogram, in light of available geological knowledge, allows to separate signatures related to regolith and solid geology. Consequently, classification maps can be integrated within a GIS environment and used by the geologist as a support for mapping bedrock lithologies and their alteration. We illustrate the AHC classification method in the region of Cayenne using high-resolution airborne radiometric data

  8. 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

  9. 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.

  10. 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)

  11. 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.

  12. 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.

  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. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. Agglomerative percolation on the Bethe lattice and the triangular cactus

    NASA Astrophysics Data System (ADS)

    Chae, Huiseung; Yook, Soon-Hyung; Kim, Yup

    2013-08-01

    Agglomerative percolation (AP) on the Bethe lattice and the triangular cactus is studied to establish the exact mean-field theory for AP. Using the self-consistent simulation method based on the exact self-consistent equations, the order parameter P∞ and the average cluster size S are measured. From the measured P∞ and S, the critical exponents βk and γk for k = 2 and 3 are evaluated. Here, βk and γk are the critical exponents for P∞ and S when the growth of clusters spontaneously breaks the Zk symmetry of the k-partite graph. The obtained values are β2 = 1.79(3), γ2 = 0.88(1), β3 = 1.35(5) and γ3 = 0.94(2). By comparing these exponents with those for ordinary percolation (β∞ = 1 and γ∞ = 1), we also find β∞ < β3 < β2 and γ∞ > γ3 > γ2. These results quantitatively verify the conjecture that the AP model belongs to a new universality class if the Zk symmetry is broken spontaneously, and the new universality class depends on k.

  12. 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

  13. 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

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. Greedy heuristic algorithm for solving series of eee components classification problems*

    NASA Astrophysics Data System (ADS)

    Kazakovtsev, A. L.; Antamoshkin, A. N.; Fedosov, V. V.

    2016-04-01

    Algorithms based on using the agglomerative greedy heuristics demonstrate precise and stable results for clustering problems based on k- means and p-median models. Such algorithms are successfully implemented in the processes of production of specialized EEE components for using in space systems which include testing each EEE device and detection of homogeneous production batches of the EEE components based on results of the tests using p-median models. In this paper, authors propose a new version of the genetic algorithm with the greedy agglomerative heuristic which allows solving series of problems. Such algorithm is useful for solving the k-means and p-median clustering problems when the number of clusters is unknown. Computational experiments on real data show that the preciseness of the result decreases insignificantly in comparison with the initial genetic algorithm for solving a single problem.

  2. 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.

  3. 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.

  4. 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.

  5. 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).

  6. 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.

  7. 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.

  8. Hierarchical clustering in minimum spanning trees.

    PubMed

    Yu, Meichen; Hillebrand, Arjan; Tewarie, Prejaas; Meier, Jil; van Dijk, Bob; Van Mieghem, Piet; Stam, Cornelis Jan

    2015-02-01

    The identification of clusters or communities in complex networks is a reappearing problem. The minimum spanning tree (MST), the tree connecting all nodes with minimum total weight, is regarded as an important transport backbone of the original weighted graph. We hypothesize that the clustering of the MST reveals insight in the hierarchical structure of weighted graphs. However, existing theories and algorithms have difficulties to define and identify clusters in trees. Here, we first define clustering in trees and then propose a tree agglomerative hierarchical clustering (TAHC) method for the detection of clusters in MSTs. We then demonstrate that the TAHC method can detect clusters in artificial trees, and also in MSTs of weighted social networks, for which the clusters are in agreement with the previously reported clusters of the original weighted networks. Our results therefore not only indicate that clusters can be found in MSTs, but also that the MSTs contain information about the underlying clusters of the original weighted network.

  9. Hierarchical clustering in minimum spanning trees

    NASA Astrophysics Data System (ADS)

    Yu, Meichen; Hillebrand, Arjan; Tewarie, Prejaas; Meier, Jil; van Dijk, Bob; Van Mieghem, Piet; Stam, Cornelis Jan

    2015-02-01

    The identification of clusters or communities in complex networks is a reappearing problem. The minimum spanning tree (MST), the tree connecting all nodes with minimum total weight, is regarded as an important transport backbone of the original weighted graph. We hypothesize that the clustering of the MST reveals insight in the hierarchical structure of weighted graphs. However, existing theories and algorithms have difficulties to define and identify clusters in trees. Here, we first define clustering in trees and then propose a tree agglomerative hierarchical clustering (TAHC) method for the detection of clusters in MSTs. We then demonstrate that the TAHC method can detect clusters in artificial trees, and also in MSTs of weighted social networks, for which the clusters are in agreement with the previously reported clusters of the original weighted networks. Our results therefore not only indicate that clusters can be found in MSTs, but also that the MSTs contain information about the underlying clusters of the original weighted network.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. The relative vertex clustering value - a new criterion for the fast discovery of functional modules in protein interaction networks

    PubMed Central

    2015-01-01

    Background Cellular processes are known to be modular and are realized by groups of proteins implicated in common biological functions. Such groups of proteins are called functional modules, and many community detection methods have been devised for their discovery from protein interaction networks (PINs) data. In current agglomerative clustering approaches, vertices with just a very few neighbors are often classified as separate clusters, which does not make sense biologically. Also, a major limitation of agglomerative techniques is that their computational efficiency do not scale well to large PINs. Finally, PIN data obtained from large scale experiments generally contain many false positives, and this makes it hard for agglomerative clustering methods to find the correct clusters, since they are known to be sensitive to noisy data. Results We propose a local similarity premetric, the relative vertex clustering value, as a new criterion allowing to decide when a node can be added to a given node's cluster and which addresses the above three issues. Based on this criterion, we introduce a novel and very fast agglomerative clustering technique, FAC-PIN, for discovering functional modules and protein complexes from a PIN data. Conclusions Our proposed FAC-PIN algorithm is applied to nine PIN data from eight different species including the yeast PIN, and the identified functional modules are validated using Gene Ontology (GO) annotations from DAVID Bioinformatics Resources. Identified protein complexes are also validated using experimentally verified complexes. Computational results show that FAC-PIN can discover functional modules or protein complexes from PINs more accurately and more efficiently than HC-PIN and CNM, the current state-of-the-art approaches for clustering PINs in an agglomerative manner. PMID:25734691

  16. 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

  17. 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.

  18. 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.

  19. 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.

  20. 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

  1. 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.

  2. 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.

  3. 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.

  4. 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%.

  5. 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.

  6. 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.

  7. 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…

  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. 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

  10. 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.

  11. 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.

  12. 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

  13. 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.

  14. 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

  15. 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.

  16. 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.

  17. 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.

  18. 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

  19. Towards an Evaluation of Air Surveillance Track Clustering Algorithms via External Cluster Quality Measures

    DTIC Science & Technology

    2013-01-01

    Index (Hubert & Arabie 1985) Range: [-1, 1] Similarity 2 FMI Fowlkes-Mallows Index (Fowlkes & Mallows 1983) Range: [0, 1] Similarity 3...distance between hand-crafted and algorithmic clusterings Clustering ARI FMI JC JMS MM NMI. RI VDM VI Mean-30k 0.6170 0.6628 0.4466 0.7208 29614 0.9579...0.7472 36312 0.9574 0.9985 1200 0.8556 Table 5: Similarity or distance between hand-crafted and random clusterings Clustering ARI FMI JC JMS MM NMI RI

  20. Hierarchical clustering techniques for image database organization and summarization

    NASA Astrophysics Data System (ADS)

    Vellaikal, Asha; Kuo, C.-C. Jay

    1998-10-01

    This paper investigates clustering techniques as a method of organizing image databases to support popular visual management functions such as searching, browsing and navigation. Different types of hierarchical agglomerative clustering techniques are studied as a method of organizing features space as well as summarizing image groups by the selection of a few appropriate representatives. Retrieval performance using both single and multiple level hierarchies are experimented with and the algorithms show an interesting relationship between the top k correct retrievals and the number of comparisons required. Some arguments are given to support the use of such cluster-based techniques for managing distributed image databases.

  1. 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.

  2. 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.

  3. 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%.

  4. Method for preventing plugging in the pyrolysis of agglomerative coals

    DOEpatents

    Green, Norman W.

    1979-01-23

    To prevent plugging in a pyrolysis operation where an agglomerative coal in a nondeleteriously reactive carrier gas is injected as a turbulent jet from an opening into an elongate pyrolysis reactor, the coal is comminuted to a size where the particles under operating conditions will detackify prior to contact with internal reactor surfaces while a secondary flow of fluid is introduced along the peripheral inner surface of the reactor to prevent backflow of the coal particles. The pyrolysis operation is depicted by two equations which enable preselection of conditions which insure prevention of reactor plugging.

  5. 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.

  6. 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.

  7. 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

  8. 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.

  9. 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.

  10. 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.

  11. 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

  12. 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.

  13. Data Clustering

    NASA Astrophysics Data System (ADS)

    Wagstaff, Kiri L.

    2012-03-01

    particular application involves considerations of the kind of data being analyzed, algorithm runtime efficiency, and how much prior knowledge is available about the problem domain, which can dictate the nature of clusters sought. Fundamentally, the clustering method and its representations of clusters carries with it a definition of what a cluster is, and it is important that this be aligned with the analysis goals for the problem at hand. In this chapter, I emphasize this point by identifying for each algorithm the cluster representation as a model, m_j , even for algorithms that are not typically thought of as creating a “model.” This chapter surveys a basic collection of clustering methods useful to any practitioner who is interested in applying clustering to a new data set. The algorithms include k-means (Section 25.2), EM (Section 25.3), agglomerative (Section 25.4), and spectral (Section 25.5) clustering, with side mentions of variants such as kernel k-means and divisive clustering. The chapter also discusses each algorithm’s strengths and limitations and provides pointers to additional in-depth reading for each subject. Section 25.6 discusses methods for incorporating domain knowledge into the clustering process. This chapter concludes with a brief survey of interesting applications of clustering methods to astronomy data (Section 25.7). The chapter begins with k-means because it is both generally accessible and so widely used that understanding it can be considered a necessary prerequisite for further work in the field. EM can be viewed as a more sophisticated version of k-means that uses a generative model for each cluster and probabilistic item assignments. Agglomerative clustering is the most basic form of hierarchical clustering and provides a basis for further exploration of algorithms in that vein. Spectral clustering permits a departure from feature-vector-based clustering and can operate on data sets instead represented as affinity, or similarity

  14. 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.

  15. 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

  16. 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.

  17. 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.

  18. Dynamically Incremental K-means++ Clustering Algorithm Based on Fuzzy Rough Set Theory

    NASA Astrophysics Data System (ADS)

    Li, Wei; Wang, Rujing; Jia, Xiufang; Jiang, Qing

    Being classic K-means++ clustering algorithm only for static data, dynamically incremental K-means++ clustering algorithm (DK-Means++) is presented based on fuzzy rough set theory in this paper. Firstly, in DK-Means++ clustering algorithm, the formula of similar degree is improved by weights computed by using of the important degree of attributes which are reduced on the basis of rough fuzzy set theory. Secondly, new data only need match granular which was clustered by K-means++ algorithm or seldom new data is clustered by classic K-means++ algorithm in global data. In this way, that all data is re-clustered each time in dynamic data set is avoided, so the efficiency of clustering is improved. Throughout our experiments showing, DK-Means++ algorithm can objectively and efficiently deal with clustering problem of dynamically incremental data.

  19. 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

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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

  13. 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.

  14. 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.

  15. 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.

  16. ARC: automated resource classifier for agglomerative functional classification of prokaryotic proteins using annotation texts.

    PubMed

    Gnanamani, Muthiah; Kumar, Naveen; Ramachandran, Srinivasan

    2007-08-01

    Functional classification of proteins is central to comparative genomics. The need for algorithms tuned to enable integrative interpretation of analytical data is felt globally. The availability of a general,automated software with built-in flexibility will significantly aid this activity. We have prepared ARC (Automated Resource Classifier), which is an open source software meeting the user requirements of flexibility. The default classification scheme based on keyword match is agglomerative and directs entries into any of the 7 basic non-overlapping functional classes: Cell wall, Cell membrane and Transporters (C), Cell division (D), Information (I), Translocation (L), Metabolism (M), Stress(R), Signal and communication (S) and 2 ancillary classes: Others (O) and Hypothetical (H). The keyword library of ARC was built serially by first drawing keywords from Bacillus subtilis and Escherichia coli K12. In subsequent steps,this library was further enriched by collecting terms from archaeal representative Archaeoglobus fulgidus, Gene Ontology, and Gene Symbols. ARC is 94.04% successful on 6,75,663 annotated proteins from 348 prokaryotes. Three examples are provided to illuminate the current perspectives on mycobacterial physiology and costs of proteins in 333 prokaryotes. ARC is available at http://arc.igib.res.in.

  17. Agglomerative Epigenetic Aberrations are a Common Event in Human Breast Cancer

    PubMed Central

    Petr, Novak; Taylor, Jensen; Oshiro Marc, M; Watts George, S; Kim Christina, J; Futscher Bernard, W

    2009-01-01

    Changes in DNA methylation patterns are a common characteristic of cancer cells. Recent studies suggest that DNA methylation affects not only discrete genes, but it can also affect large chromosomal regions, potentially leading to long range epigenetic silencing. It is unclear whether such long-range epigenetic events are relatively rare or frequent occurrences in cancer. Here we use a high-resolution promoter tiling array approach to analyze DNA methylation in breast cancer specimens and normal breast tissue to address this question. We identified 3506 cancer specific differentially methylated regions (DMR) in human breast cancer with 2033 being hypermethylation events and 1473 hypomethylation events. Most of these DMRs are recurrent in breast cancer; 90% of the identified DMRs occurred in at least 33% of the samples. Interestingly, we found a non-random spatial distribution of aberrantly methylated regions across the genome that showed a tendency to concentrate in relatively small genomic regions. Such agglomerates of hyper- and hypomethylated DMRs spanned up to several hundred kilobases and were frequently found at gene family clusters. The hypermethylation events usually occurred in the proximity of the transcription start site in CpG island promoters while hypomethylation events were frequently found in regions of segmental duplication. One example of a newly discovered agglomerate of hypermethylated DMRs associated with gene silencing in breast cancer that we examined in greater detail involved the protocadherin gene family clusters on chromosome 5 (PCDHA, PCDHB, and PCDHG). Taken together, our results suggest that agglomerative epigenetic aberrations are frequent events in human breast cancer. PMID:18922938

  18. 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…

  19. 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…

  20. 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.

  1. 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.

  2. 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.

  3. 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

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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

  11. 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.

  12. 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

  13. 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.

  14. 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

  15. 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.

  16. 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

  17. 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.

  18. 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.

  19. 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.

  20. 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

  1. 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.

  2. Improved initialisation of model-based clustering using Gaussian hierarchical partitions

    PubMed Central

    Scrucca, Luca; Raftery, Adrian E.

    2015-01-01

    Initialisation of the EM algorithm in model-based clustering is often crucial. Various starting points in the parameter space often lead to different local maxima of the likelihood function and, so to different clustering partitions. Among the several approaches available in the literature, model-based agglomerative hierarchical clustering is used to provide initial partitions in the popular mclust R package. This choice is computationally convenient and often yields good clustering partitions. However, in certain circumstances, poor initial partitions may cause the EM algorithm to converge to a local maximum of the likelihood function. We propose several simple and fast refinements based on data transformations and illustrate them through data examples. PMID:26949421

  3. A new clustering algorithm for scanning electron microscope images

    NASA Astrophysics Data System (ADS)

    Yousef, Amr; Duraisamy, Prakash; Karim, Mohammad

    2016-04-01

    A scanning electron microscope (SEM) is a type of electron microscope that produces images of a sample by scanning it with a focused beam of electrons. The electrons interact with the sample atoms, producing various signals that are collected by detectors. The gathered signals contain information about the sample's surface topography and composition. The electron beam is generally scanned in a raster scan pattern, and the beam's position is combined with the detected signal to produce an image. The most common configuration for an SEM produces a single value per pixel, with the results usually rendered as grayscale images. The captured images may be produced with insufficient brightness, anomalous contrast, jagged edges, and poor quality due to low signal-to-noise ratio, grained topography and poor surface details. The segmentation of the SEM images is a tackling problems in the presence of the previously mentioned distortions. In this paper, we are stressing on the clustering of these type of images. In that sense, we evaluate the performance of the well-known unsupervised clustering and classification techniques such as connectivity based clustering (hierarchical clustering), centroid-based clustering, distribution-based clustering and density-based clustering. Furthermore, we propose a new spatial fuzzy clustering technique that works efficiently on this type of images and compare its results against these regular techniques in terms of clustering validation metrics.

  4. 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.

  5. 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

  6. 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

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. High- and low-level hierarchical classification algorithm based on source separation process

    NASA Astrophysics Data System (ADS)

    Loghmari, Mohamed Anis; Karray, Emna; Naceur, Mohamed Saber

    2016-10-01

    High-dimensional data applications have earned great attention in recent years. We focus on remote sensing data analysis on high-dimensional space like hyperspectral data. From a methodological viewpoint, remote sensing data analysis is not a trivial task. Its complexity is caused by many factors, such as large spectral or spatial variability as well as the curse of dimensionality. The latter describes the problem of data sparseness. In this particular ill-posed problem, a reliable classification approach requires appropriate modeling of the classification process. The proposed approach is based on a hierarchical clustering algorithm in order to deal with remote sensing data in high-dimensional space. Indeed, one obvious method to perform dimensionality reduction is to use the independent component analysis process as a preprocessing step. The first particularity of our method is the special structure of its cluster tree. Most of the hierarchical algorithms associate leaves to individual clusters, and start from a large number of individual classes equal to the number of pixels; however, in our approach, leaves are associated with the most relevant sources which are represented according to mutually independent axes to specifically represent some land covers associated with a limited number of clusters. These sources contribute to the refinement of the clustering by providing complementary rather than redundant information. The second particularity of our approach is that at each level of the cluster tree, we combine both a high-level divisive clustering and a low-level agglomerative clustering. This approach reduces the computational cost since the high-level divisive clustering is controlled by a simple Boolean operator, and optimizes the clustering results since the low-level agglomerative clustering is guided by the most relevant independent sources. Then at each new step we obtain a new finer partition that will participate in the clustering process to enhance

  12. 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

  13. 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.

  14. 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)

  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. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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

  10. 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.

  11. 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

  12. 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.

  13. 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.

  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. 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.

  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. 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.

  18. 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

  19. 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

  20. 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.

  1. 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

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. Interactive Maximum Reliability Cluster Analysis.

    ERIC Educational Resources Information Center

    Mays, Robert

    1978-01-01

    A FORTRAN program for clustering variables using the alpha coefficient of reliability is described. For batch operation, a rule for stopping the agglomerative precedure is available. The conversational version of the program allows the user to intervene in the process in order to test the final solution for sensitivity to changes. (Author/JKS)

  15. 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.

  16. 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.

  17. 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.

  18. 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

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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

  6. 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.

  7. 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.

  8. 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

  9. [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.

  10. 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.

  11. 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

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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

  20. 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.

  1. 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.

  2. 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.

  3. 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

  4. Unsupervised classification of multivariate geostatistical data: Two algorithms

    NASA Astrophysics Data System (ADS)

    Romary, Thomas; Ors, Fabien; Rivoirard, Jacques; Deraisme, Jacques

    2015-12-01

    With the increasing development of remote sensing platforms and the evolution of sampling facilities in mining and oil industry, spatial datasets are becoming increasingly large, inform a growing number of variables and cover wider and wider areas. Therefore, it is often necessary to split the domain of study to account for radically different behaviors of the natural phenomenon over the domain and to simplify the subsequent modeling step. The definition of these areas can be seen as a problem of unsupervised classification, or clustering, where we try to divide the domain into homogeneous domains with respect to the values taken by the variables in hand. The application of classical clustering methods, designed for independent observations, does not ensure the spatial coherence of the resulting classes. Image segmentation methods, based on e.g. Markov random fields, are not adapted to irregularly sampled data. Other existing approaches, based on mixtures of Gaussian random functions estimated via the expectation-maximization algorithm, are limited to reasonable sample sizes and a small number of variables. In this work, we propose two algorithms based on adaptations of classical algorithms to multivariate geostatistical data. Both algorithms are model free and can handle large volumes of multivariate, irregularly spaced data. The first one proceeds by agglomerative hierarchical clustering. The spatial coherence is ensured by a proximity condition imposed for two clusters to merge. This proximity condition relies on a graph organizing the data in the coordinates space. The hierarchical algorithm can then be seen as a graph-partitioning algorithm. Following this interpretation, a spatial version of the spectral clustering algorithm is also proposed. The performances of both algorithms are assessed on toy examples and a mining dataset.

  5. 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).

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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

  12. 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…

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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

  19. 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.

  20. 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

  1. 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.

  2. 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

  3. MSClust: A Multi-Seeds Based Clustering Algorithm for microbiome profiling using 16S rRNA Sequence

    PubMed Central

    Chen, Wei; Cheng, Yongmei; Zhang, Clarence; Zhang, Shaowu; Zhao, Hongyu

    2013-01-01

    Recent developments of next generation sequencing technologies have led to rapid accumulation of 16s rRNA sequences for microbiome profiling. One key step in data processing is to cluster short sequences into operational taxonomic units (OTUs). Although many methods have been proposed for OTU inferences, a major challenge is the balance between inference accuracy and computational efficiency, where inference accuracy is often sacrificed to accommodate the need to analyze large numbers of sequences. Inspired by the hierarchical clustering method and a modified greedy network clustering algorithm, we propose a novel multi-seeds based heuristic clustering method, named MSClust, for OTU inference. MSClust first adaptively selects multi-seeds instead of one seed for each candidate cluster, and the reads are then processed using a greedy clustering strategy. Through many numerical examples, we demonstrate that MSClust enjoys less memory usage, and better biological accuracy compared to existing heuristic clustering methods while preserving efficiency and scalability. PMID:23899776

  4. Consumers' Kansei Needs Clustering Method for Product Emotional Design Based on Numerical Design Structure Matrix and Genetic Algorithms

    PubMed Central

    Chen, Deng-kai; Gu, Rong; Gu, Yu-feng; Yu, Sui-huai

    2016-01-01

    Consumers' Kansei needs reflect their perception about a product and always consist of a large number of adjectives. Reducing the dimension complexity of these needs to extract primary words not only enables the target product to be explicitly positioned, but also provides a convenient design basis for designers engaging in design work. Accordingly, this study employs a numerical design structure matrix (NDSM) by parameterizing a conventional DSM and integrating genetic algorithms to find optimum Kansei clusters. A four-point scale method is applied to assign link weights of every two Kansei adjectives as values of cells when constructing an NDSM. Genetic algorithms are used to cluster the Kansei NDSM and find optimum clusters. Furthermore, the process of the proposed method is presented. The details of the proposed approach are illustrated using an example of electronic scooter for Kansei needs clustering. The case study reveals that the proposed method is promising for clustering Kansei needs adjectives in product emotional design. PMID:27630709

  5. Consumers' Kansei Needs Clustering Method for Product Emotional Design Based on Numerical Design Structure Matrix and Genetic Algorithms.

    PubMed

    Yang, Yan-Pu; Chen, Deng-Kai; Gu, Rong; Gu, Yu-Feng; Yu, Sui-Huai

    2016-01-01

    Consumers' Kansei needs reflect their perception about a product and always consist of a large number of adjectives. Reducing the dimension complexity of these needs to extract primary words not only enables the target product to be explicitly positioned, but also provides a convenient design basis for designers engaging in design work. Accordingly, this study employs a numerical design structure matrix (NDSM) by parameterizing a conventional DSM and integrating genetic algorithms to find optimum Kansei clusters. A four-point scale method is applied to assign link weights of every two Kansei adjectives as values of cells when constructing an NDSM. Genetic algorithms are used to cluster the Kansei NDSM and find optimum clusters. Furthermore, the process of the proposed method is presented. The details of the proposed approach are illustrated using an example of electronic scooter for Kansei needs clustering. The case study reveals that the proposed method is promising for clustering Kansei needs adjectives in product emotional design.

  6. The effect of close relatives on unsupervised Bayesian clustering algorithms in population genetic structure analysis.

    PubMed

    Rodríguez-Ramilo, Silvia T; Wang, Jinliang

    2012-09-01

    The inference of population genetic structures is essential in many research areas in population genetics, conservation biology and evolutionary biology. Recently, unsupervised Bayesian clustering algorithms have been developed to detect a hidden population structure from genotypic data, assuming among others that individuals taken from the population are unrelated. Under this assumption, markers in a sample taken from a subpopulation can be considered to be in Hardy-Weinberg and linkage equilibrium. However, close relatives might be sampled from the same subpopulation, and consequently, might cause Hardy-Weinberg and linkage disequilibrium and thus bias a population genetic structure analysis. In this study, we used simulated and real data to investigate the impact of close relatives in a sample on Bayesian population structure analysis. We also showed that, when close relatives were identified by a pedigree reconstruction approach and removed, the accuracy of a population genetic structure analysis can be greatly improved. The results indicate that unsupervised Bayesian clustering algorithms cannot be used blindly to detect genetic structure in a sample with closely related individuals. Rather, when closely related individuals are suspected to be frequent in a sample, these individuals should be first identified and removed before conducting a population structure analysis.

  7. A Hybrid Spectral Clustering and Deep Neural Network Ensemble Algorithm for Intrusion Detection in Sensor Networks

    PubMed Central

    Ma, Tao; Wang, Fen; Cheng, Jianjun; Yu, Yang; Chen, Xiaoyun

    2016-01-01

    The development of intrusion detection systems (IDS) that are adapted to allow routers and network defence systems to detect malicious network traffic disguised as network protocols or normal access is a critical challenge. This paper proposes a novel approach called SCDNN, which combines spectral clustering (SC) and deep neural network (DNN) algorithms. First, the dataset is divided into k subsets based on sample similarity using cluster centres, as in SC. Next, the distance between data points in a testing set and the training set is measured based on similarity features and is fed into the deep neural network algorithm for intrusion detection. Six KDD-Cup99 and NSL-KDD datasets and a sensor network dataset were employed to test the performance of the model. These experimental results indicate that the SCDNN classifier not only performs better than backpropagation neural network (BPNN), support vector machine (SVM), random forest (RF) and Bayes tree models in detection accuracy and the types of abnormal attacks found. It also provides an effective tool of study and analysis of intrusion detection in large networks. PMID:27754380

  8. A Hybrid Spectral Clustering and Deep Neural Network Ensemble Algorithm for Intrusion Detection in Sensor Networks.

    PubMed

    Ma, Tao; Wang, Fen; Cheng, Jianjun; Yu, Yang; Chen, Xiaoyun

    2016-10-13

    The development of intrusion detection systems (IDS) that are adapted to allow routers and network defence systems to detect malicious network traffic disguised as network protocols or normal access is a critical challenge. This paper proposes a novel approach called SCDNN, which combines spectral clustering (SC) and deep neural network (DNN) algorithms. First, the dataset is divided into k subsets based on sample similarity using cluster centres, as in SC. Next, the distance between data points in a testing set and the training set is measured based on similarity features and is fed into the deep neural network algorithm for intrusion detection. Six KDD-Cup99 and NSL-KDD datasets and a sensor network dataset were employed to test the performance of the model. These experimental results indicate that the SCDNN classifier not only performs better than backpropagation neural network (BPNN), support vector machine (SVM), random forest (RF) and Bayes tree models in detection accuracy and the types of abnormal attacks found. It also provides an effective tool of study and analysis of intrusion detection in large networks.

  9. 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

  10. KANTS: a stigmergic ant algorithm for cluster analysis and swarm art.

    PubMed

    Fernandes, Carlos M; Mora, Antonio M; Merelo, Juan J; Rosa, Agostinho C

    2014-06-01

    KANTS is a swarm intelligence clustering algorithm inspired by the behavior of social insects. It uses stigmergy as a strategy for clustering large datasets and, as a result, displays a typical behavior of complex systems: self-organization and global patterns emerging from the local interaction of simple units. This paper introduces a simplified version of KANTS and describes recent experiments with the algorithm in the context of a contemporary artistic and scientific trend called swarm art, a type of generative art in which swarm intelligence systems are used to create artwork or ornamental objects. KANTS is used here for generating color drawings from the input data that represent real-world phenomena, such as electroencephalogram sleep data. However, the main proposal of this paper is an art project based on well-known abstract paintings, from which the chromatic values are extracted and used as input. Colors and shapes are therefore reorganized by KANTS, which generates its own interpretation of the original artworks. The project won the 2012 Evolutionary Art, Design, and Creativity Competition.

  11. A contiguity-enhanced k-means clustering algorithm for unsupervised multispectral image segmentation

    SciTech Connect

    Theiler, J.; Gisler, G.

    1997-07-01

    The recent and continuing construction of multi and hyper spectral imagers will provide detailed data cubes with information in both the spatial and spectral domain. This data shows great promise for remote sensing applications ranging from environmental and agricultural to national security interests. The reduction of this voluminous data to useful intermediate forms is necessary both for downlinking all those bits and for interpreting them. Smart onboard hardware is required, as well as sophisticated earth bound processing. A segmented image (in which the multispectral data in each pixel is classified into one of a small number of categories) is one kind of intermediate form which provides some measure of data compression. Traditional image segmentation algorithms treat pixels independently and cluster the pixels according only to their spectral information. This neglects the implicit spatial information that is available in the image. We will suggest a simple approach; a variant of the standard k-means algorithm which uses both spatial and spectral properties of the image. The segmented image has the property that pixels which are spatially contiguous are more likely to be in the same class than are random pairs of pixels. This property naturally comes at some cost in terms of the compactness of the clusters in the spectral domain, but we have found that the spatial contiguity and spectral compactness properties are nearly orthogonal, which means that we can make considerable improvements in the one with minimal loss in the other.

  12. Automated SNP genotype clustering algorithm to improve data completeness in high-throughput SNP genotyping datasets from custom arrays.

    PubMed

    Smith, Edward M; Littrell, Jack; Olivier, Michael

    2007-12-01

    High-throughput SNP genotyping platforms use automated genotype calling algorithms to assign genotypes. While these algorithms work efficiently for individual platforms, they are not compatible with other platforms, and have individual biases that result in missed genotype calls. Here we present data on the use of a second complementary SNP genotype clustering algorithm. The algorithm was originally designed for individual fluorescent SNP genotyping assays, and has been optimized to permit the clustering of large datasets generated from custom-designed Affymetrix SNP panels. In an analysis of data from a 3K array genotyped on 1,560 samples, the additional analysis increased the overall number of genotypes by over 45,000, significantly improving the completeness of the experimental data. This analysis suggests that the use of multiple genotype calling algorithms may be advisable in high-throughput SNP genotyping experiments. The software is written in Perl and is available from the corresponding author.

  13. 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

  14. Transition from exo- to endo- Cu absorption in CuSin clusters: A Genetic Algorithms Density Functional Theory (DFT) Study

    PubMed Central

    Oña, Ofelia B.; Ferraro, Marta B.; Facelli, Julio C.

    2010-01-01

    The characterization and prediction of the structures of metal silicon clusters is important for nanotechnology research because these clusters can be used as building blocks for nano devices, integrated circuits and solar cells. Several authors have postulated that there is a transition between exo to endo absorption of Cu in Sin clusters and showed that for n larger than 9 it is possible to find endohedral clusters. Unfortunately, no global searchers have confirmed this observation, which is based on local optimizations of plausible structures. Here we use parallel Genetic Algorithms (GA), as implemented in our MGAC software, directly coupled with DFT energy calculations to show that the global search of CuSin cluster structures does not find endohedral clusters for n < 8 but finds them for n ≥ 10. PMID:21785526

  15. `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.

  16. Molecular conformation of clusters by genetic algorithm using spatial operators and unlabeled distance data

    NASA Astrophysics Data System (ADS)

    Cherba, David M.

    A set of Genetic Algorithm (GA) operators based on spatial location concepts will provide improved performance for a class of NP hard search problems in N dimensional spaces. A set of spatial operators for use with genetic algorithms is proposed for a class of problems with real-valued genes that consist of N-dimensional homogeneous vectors. Evolutionary computation is capable of providing solutions to problems that would be intractable using more conventional methods. A subset of these problems is represented in real-valued three dimensional spaces or other more complex vector spaces. This thesis addresses a number of issues related to the natural influences that adjacent locations in these spaces have on the fitness functions used in genetic algorithms. A subset of building blocks (schema) will be utilized based on these natural influences. It will be shown that these operators can be described by a building block style of theory that supports the experiment results. Further, the spatial base operators naturally preserve the interactions between genes for this class of problems. Genes have a natural influence on each other based on proximity. To be an effective genetic algorithm, operators need to take these proximity effects into consideration in order to preserve good contributions to fitness. Failure to utilize these spatial relationships will lead to very poor performance of the genetic algorithm or require statistical methods to try to capture the relationships. As a demonstration of these spatial operators, this dissertation will focus on the conformation of molecular clusters, where each atom's location represents a gene with real-valued coordinates. Further, the algorithm presented will work from unlabeled distance information available from experiments with limited preparation. A set of theories will be presented that form the basis for prediction of operator effectiveness, population size and convergence for this class of problems. The theory will be

  17. Large-scale validation of a computer-aided polyp detection algorithm for CT colonography using cluster computing

    NASA Astrophysics Data System (ADS)

    Bitter, Ingmar; Brown, John E.; Brickman, Daniel; Summers, Ronald M.

    2004-04-01

    The presented method significantly reduces the time necessary to validate a computed tomographic colonography (CTC) computer aided detection (CAD) algorithm of colonic polyps applied to a large patient database. As the algorithm is being developed on Windows PCs and our target, a Beowulf cluster, is running on Linux PCs, we made the application dual platform compatible using a single source code tree. To maintain, share, and deploy source code, we used CVS (concurrent versions system) software. We built the libraries from their sources for each operating system. Next, we made the CTC CAD algorithm dual-platform compatible and validate that both Windows and Linux produced the same results. Eliminating system dependencies was mostly achieved using the Qt programming library, which encapsulates most of the system dependent functionality in order to present the same interface on either platform. Finally, we wrote scripts to execute the CTC CAD algorithm in parallel. Running hundreds of simultaneous copies of the CTC CAD algorithm on a Beowulf cluster computing network enables execution in less than four hours on our entire collection of over 2400 CT scans, as compared to a month a single PC. As a consequence, our complete patient database can be processed daily, boosting research productivity. Large scale validation of a computer aided polyp detection algorithm for CT colonography using cluster computing significantly improves the round trip time of algorithm improvement and revalidation.

  18. Relationship between clustering and algorithmic phase transitions in the random k-XORSAT model and its NP-complete extensions

    NASA Astrophysics Data System (ADS)

    Altarelli, F.; Monasson, R.; Zamponi, F.

    2008-01-01

    We study the performances of stochastic heuristic search algorithms on Uniquely Extendible Constraint Satisfaction Problems with random inputs. We show that, for any heuristic preserving the Poissonian nature of the underlying instance, the (heuristic-dependent) largest ratio αa of constraints per variables for which a search algorithm is likely to find solutions is smaller than the critical ratio αd above which solutions are clustered and highly correlated. In addition we show that the clustering ratio can be reached when the number k of variables per constraints goes to infinity by the so-called Generalized Unit Clause heuristic.

  19. [Analysis on principle of treatment of cough of yan zhenghua based on apriori and clustering algorithm].

    PubMed

    Wu, Jia-Rui; Guo, Wei-Xian; Zhang, Xiao-Meng; Yang, Bing; Zhang, Bing

    2014-02-01

    Based on the data mining methods of association rules and clustering algorithm, the 188 prescriptions for cough that built by Yan Zhenghua were collected and analyzed to get the frequency of drug usage and the relationship between drugs. From which we could conclude the experiences of Yan Zhenghua for the treatment of cough. The results of the analysis were that 20 core combinations were dig out, such as Bambusae Caulis in Taenias-Almond-Sactmarsh Aster. And there were 10 new prescriptions were found out, such as Sactmarsh Aster-Scutellariae Radix-Album Viscum-Bambusae Caulis in Taenian-Eriobotryae Folium. The results of the analysis were proved that Yan Zhenghua was good at curing cough by using the traditional Chinese medicine that can dispel wind and heat from the body, and remove heat from the lung to relieve cough.

  20. Evaluation of Modified Categorical Data Fuzzy Clustering Algorithm on the Wisconsin Breast Cancer Dataset

    PubMed Central

    2016-01-01

    The early diagnosis of breast cancer is an important step in a fight against the disease. Machine learning techniques have shown promise in improving our understanding of the disease. As medical datasets consist of data points which cannot be precisely assigned to a class, fuzzy methods have been useful for studying of these datasets. Sometimes breast cancer datasets are described by categorical features. Many fuzzy clustering algorithms have been developed for categorical datasets. However, in most of these methods Hamming distance is used to define the distance between the two categorical feature values. In this paper, we use a probabilistic distance measure for the distance computation among a pair of categorical feature values. Experiments demonstrate that the distance measure performs better than Hamming distance for Wisconsin breast cancer data. PMID:27022504

  1. OpenACC programs of the Swendsen-Wang multi-cluster spin flip algorithm

    NASA Astrophysics Data System (ADS)

    Komura, Yukihiro

    2015-12-01

    We present sample OpenACC programs of the Swendsen-Wang multi-cluster spin flip algorithm. OpenACC is a directive-based programming model for accelerators without requiring modification to the underlying CPU code itself. In this paper, we deal with the classical spin models as with the sample CUDA programs (Komura and Okabe, 2014), that is, two-dimensional (2D) Ising model, three-dimensional (3D) Ising model, 2D Potts model, 3D Potts model, 2D XY model and 3D XY model. We explain the details of sample OpenACC programs and compare the performance of the present OpenACC implementations with that of the CUDA implementations for the 2D and 3D Ising models and the 2D and 3D XY models.

  2. Hybrid clustering based fuzzy structure for vibration control - Part 1: A novel algorithm for building neuro-fuzzy system

    NASA Astrophysics Data System (ADS)

    Nguyen, Sy Dzung; Nguyen, Quoc Hung; Choi, Seung-Bok

    2015-01-01

    This paper presents a new algorithm for building an adaptive neuro-fuzzy inference system (ANFIS) from a training data set called B-ANFIS. In order to increase accuracy of the model, the following issues are executed. Firstly, a data merging rule is proposed to build and perform a data-clustering strategy. Subsequently, a combination of clustering processes in the input data space and in the joint input-output data space is presented. Crucial reason of this task is to overcome problems related to initialization and contradictory fuzzy rules, which usually happen when building ANFIS. The clustering process in the input data space is accomplished based on a proposed merging-possibilistic clustering (MPC) algorithm. The effectiveness of this process is evaluated to resume a clustering process in the joint input-output data space. The optimal parameters obtained after completion of the clustering process are used to build ANFIS. Simulations based on a numerical data, 'Daily Data of Stock A', and measured data sets of a smart damper are performed to analyze and estimate accuracy. In addition, convergence and robustness of the proposed algorithm are investigated based on both theoretical and testing approaches.

  3. 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.

  4. Study of cluster reconstruction and track fitting algorithms for CGEM-IT at BESIII

    NASA Astrophysics Data System (ADS)

    Guo, Yue; Wang, Liang-Liang; Ju, Xu-Dong; Wu, Ling-Hui; Xiu, Qing-Lei; Wang, Hai-Xia; Dong, Ming-Yi; Hu, Jing-Ran; Li, Wei-Dong; Li, Wei-Guo; Liu, Huai-Min; Qun, Ou-Yang; Shen, Xiao-Yan; Yuan, Ye; Zhang, Yao

    2016-01-01

    Considering the effects of aging on the existing Inner Drift Chamber (IDC) of BESIII, a GEM-based inner tracker, the Cylindrical-GEM Inner Tracker (CGEM-IT), is proposed to be designed and constructed as an upgrade candidate for the IDC. This paper introduces a full simulation package for the CGEM-IT with a simplified digitization model, and describes the development of software for cluster reconstruction and track fitting, using a track fitting algorithm based on the Kalman filter method. Preliminary results for the reconstruction algorithms which are obtained using a Monte Carlo sample of single muon events in the CGEM-IT, show that the CGEM-IT has comparable momentum resolution and transverse vertex resolution to the IDC, and a better z-direction resolution than the IDC. Supported by National Key Basic Research Program of China (2015CB856700), National Natural Science Foundation of China (11205184, 11205182) and Joint Funds of National Natural Science Foundation of China (U1232201)

  5. Cluster Analysis and Web-Based 3-D Visualization of Large-scale Geophysical Data

    NASA Astrophysics Data System (ADS)

    Kadlec, B. J.; Yuen, D. A.; Bollig, E. F.; Dzwinel, W.; da Silva, C. R.

    2004-05-01

    We present a problem-solving environment WEB-IS (Web-based Data Interrogative System), which we have developed for remote analysis and visualization of geophysical data [Garbow et. al., 2003]. WEB-IS employs agglomerative clustering methods intended for feature extraction and studying the predictions of large magnitude earthquake events. Data-mining is accomplished using a mutual nearest meighbor (MNN) algorithm for extracting event clusters of different density and shapes based on a hierarchical proximity measure. Clustering schemes used in molecular dynamics [Da Silva et. al., 2002] are also considered for increasing computational efficiency using a linked cell algorithm for creating a Verlet neighbor list (VNL) and extracting different cluster structures by applying a canonical backtracking search on the VNL. Space and time correlations between the events are visualized dynamically in 3-D through a filter by showing clusters at different timescales according to defined units of time ranging from days to years. This WEB-IS functionality was tested both on synthetic [Eneva and Ben-Zion, 1997] and actual earthquake catalogs of Japanese earthquakes and can be applied to the soft-computing data mining methods used in hydrology and geoinformatics. Da Silva, C.R.S., Justo, J.F., Fazzio, A., Phys Rev B, vol., 65, 2002. Eneva, M., Ben-Zion, Y.,J. Geophys. Res., 102, 17785-17795, 1997. Garbow, Z.A., Yuen, D.A., Erlebacher, G., Bollig, E.F., Kadlec, B.J., Vis. Geosci., 2003.

  6. Using the erroneous data clustering to improve the feature extraction weights of original image algorithms

    NASA Astrophysics Data System (ADS)

    Wu, Tin-Yu; Chang, Tse; Chu, Teng-Hao

    2017-02-01

    Many data mining adopts the form of Artificial Neural Network (ANN) to solve many problems, many problems will be involved in the process of training Artificial Neural Network, such as the number of samples with volume label, the time and performance of training, the number of hidden layers and Transfer function, if the compared data results are not expected, it cannot be known clearly that which dimension causes the deviation, the main reason is that Artificial Neural Network trains compared results through the form of modifying weight, and it is not a kind of training to improve the original algorithm for the extraction algorithm of image, but tend to obtain correct value aimed at the result plus the weigh; in terms of these problems, this paper will mainly put forward a method to assist in the image data analysis of Artificial Neural Network; normally, a parameter will be set as the value to extract feature vector during processing the image, which will be considered by us as weight, the experiment will use the value extracted from feature point of Speeded Up Robust Features (SURF) Image as the basis for training, SURF itself can extract different feature points according to extracted values, we will make initial semi-supervised clustering according to these values, and use Modified K - on his Neighbors (MFKNN) as training and classification, the matching mode of unknown images is not one-to-one complete comparison, but only compare group Centroid, its main purpose is to save its efficiency and speed up, and its retrieved data results will be observed and analyzed eventually; the method is mainly to make clustering and classification with the use of the nature of image feature point to give values to groups with high error rate to produce new feature points and put them into Input Layer of Artificial Neural Network for training, and finally comparative analysis is made with Back-Propagation Neural Network (BPN) of Genetic Algorithm-Artificial Neural Network

  7. AHIMSA - Ad hoc histogram information measure sensing algorithm for feature selection in the context of histogram inspired clustering techniques

    NASA Technical Reports Server (NTRS)

    Dasarathy, B. V.

    1976-01-01

    An algorithm is proposed for dimensionality reduction in the context of clustering techniques based on histogram analysis. The approach is based on an evaluation of the hills and valleys in the unidimensional histograms along the different features and provides an economical means of assessing the significance of the features in a nonparametric unsupervised data environment. The method has relevance to remote sensing applications.

  8. A modified possibilistic fuzzy c-means clustering algorithm for bias field estimation and segmentation of brain MR image.

    PubMed

    Ji, Ze-Xuan; Sun, Quan-Sen; Xia, De-Shen

    2011-07-01

    A modified possibilistic fuzzy c-means clustering algorithm is presented for fuzzy segmentation of magnetic resonance (MR) images that have been corrupted by intensity inhomogeneities and noise. By introducing a novel adaptive method to compute the weights of local spatial in the objective function, the new adaptive fuzzy clustering algorithm is capable of utilizing local contextual information to impose local spatial continuity, thus allowing the suppression of noise and helping to resolve classification ambiguity. To estimate the intensity inhomogeneity, the global intensity is introduced into the coherent local intensity clustering algorithm and takes the local and global intensity information into account. The segmentation target therefore is driven by two forces to smooth the derived optimal bias field and improve the accuracy of the segmentation task. The proposed method has been successfully applied to 3 T, 7 T, synthetic and real MR images with desirable results. Comparisons with other approaches demonstrate the superior performance of the proposed algorithm. Moreover, the proposed algorithm is robust to initialization, thereby allowing fully automatic applications.

  9. A Fast Exact k-Nearest Neighbors Algorithm for High Dimensional Search Using k-Means Clustering and Triangle Inequality

    PubMed Central

    Wang, Xueyi

    2011-01-01

    The k-nearest neighbors (k-NN) algorithm is a widely used machine learning method that finds nearest neighbors of a test object in a feature space. We present a new exact k-NN algorithm called kMkNN (k-Means for k-Nearest Neighbors) that uses the k-means clustering and the triangle inequality to accelerate the searching for nearest neighbors in a high dimensional space. The kMkNN algorithm has two stages. In the buildup stage, instead of using complex tree structures such as metric trees, kd-trees, or ball-tree, kMkNN uses a simple k-means clustering method to preprocess the training dataset. In the searching stage, given a query object, kMkNN finds nearest training objects starting from the nearest cluster to the query object and uses the triangle inequality to reduce the distance calculations. Experiments show that the performance of kMkNN is surprisingly good compared to the traditional k-NN algorithm and tree-based k-NN algorithms such as kd-trees and ball-trees. On a collection of 20 datasets with up to 106 records and 104 dimensions, kMkNN shows a 2-to 80-fold reduction of distance calculations and a 2- to 60-fold speedup over the traditional k-NN algorithm for 16 datasets. Furthermore, kMkNN performs significant better than a kd-tree based k-NN algorithm for all datasets and performs better than a ball-tree based k-NN algorithm for most datasets. The results show that kMkNN is effective for searching nearest neighbors in high dimensional spaces. PMID:22247818

  10. Adaptive partitioning by local density-peaks: An efficient density-based clustering algorithm for analyzing molecular dynamics trajectories.

    PubMed

    Liu, Song; Zhu, Lizhe; Sheong, Fu Kit; Wang, Wei; Huang, Xuhui

    2017-01-30

    We present an efficient density-based adaptive-resolution clustering method APLoD for analyzing large-scale molecular dynamics (MD) trajectories. APLoD performs the k-nearest-neighbors search to estimate the density of MD conformations in a local fashion, which can group MD conformations in the same high-density region into a cluster. APLoD greatly improves the popular density peaks algorithm by reducing the running time and the memory usage by 2-3 orders of magnitude for systems ranging from alanine dipeptide to a 370-residue Maltose-binding protein. In addition, we demonstrate that APLoD can produce clusters with various sizes that are adaptive to the underlying density (i.e., larger clusters at low-density regions, while smaller clusters at high-density regions), which is a clear advantage over other popular clustering algorithms including k-centers and k-medoids. We anticipate that APLoD can be widely applied to split ultra-large MD datasets containing millions of conformations for subsequent construction of Markov State Models. © 2016 Wiley Periodicals, Inc.

  11. The GSAM software: A global search algorithm of minima exploration for the investigation of low lying isomers of clusters

    SciTech Connect

    Marchal, Rémi; Carbonnière, Philippe; Pouchan, Claude

    2015-01-22

    The study of atomic clusters has become an increasingly active area of research in the recent years because of the fundamental interest in studying a completely new area that can bridge the gap between atomic and solid state physics. Due to their specific properties, such compounds are of great interest in the field of nanotechnology [1,2]. Here, we would present our GSAM algorithm based on a DFT exploration of the PES to find the low lying isomers of such compounds. This algorithm includes the generation of an intial set of structure from which the most relevant are selected. Moreover, an optimization process, called raking optimization, able to discard step by step all the non physically reasonnable configurations have been implemented to reduce the computational cost of this algorithm. Structural properties of Ga{sub n}Asm clusters will be presented as an illustration of the method.

  12. DHARMA - Discriminant hyperplane abstracting residuals minimization algorithm for separating clusters with fuzzy boundaries. [data points pattern recognition technique

    NASA Technical Reports Server (NTRS)

    Dasarathy, B. V.

    1976-01-01

    Learning of discriminant hyperplanes in imperfectly supervised or unsupervised training sample sets with unreliably labeled samples along the fuzzy joint boundaries between sample clusters is discussed, with the discriminant hyperplane designed to be a least-squares fit to the unreliably labeled data points. (Samples along the fuzzy boundary jump back and forth from one cluster to the other in recursive cluster stabilization and are considered unreliably labeled.) Minimization of the distances of these unreliably labeled samples from the hyperplanes does not sacrifice the ability to discriminate between classes represented by reliably labeled subsets of samples. An equivalent unconstrained linear inequality problem is formulated and algorithms for its solution are indicated. Landsat earth sensing data were used in confirming the validity and computational feasibility of the approach, which should be useful in deriving discriminant hyperplanes separating clusters with fuzzy boundaries, given supervised training sample sets with unreliably labeled boundary samples.

  13. An Improved Source-Scanning Algorithm for Locating Earthquake Clusters or Aftershock Sequences

    NASA Astrophysics Data System (ADS)

    Liao, Y.; Kao, H.; Hsu, S.

    2010-12-01

    The Source-scanning Algorithm (SSA) was originally introduced in 2004 to locate non-volcanic tremors. Its application was later expanded to the identification of earthquake rupture planes and the near-real-time detection and monitoring of landslides and mud/debris flows. In this study, we further improve SSA for the purpose of locating earthquake clusters or aftershock sequences when only a limited number of waveform observations are available. The main improvements include the application of a ground motion analyzer to separate P and S waves, the automatic determination of resolution based on the grid size and time step of the scanning process, and a modified brightness function to utilize constraints from multiple phases. Specifically, the improved SSA (named as ISSA) addresses two major issues related to locating earthquake clusters/aftershocks. The first one is the massive amount of both time and labour to locate a large number of seismic events manually. And the second one is to efficiently and correctly identify the same phase across the entire recording array when multiple events occur closely in time and space. To test the robustness of ISSA, we generate synthetic waveforms consisting of 3 separated events such that individual P and S phases arrive at different stations in different order, thus making correct phase picking nearly impossible. Using these very complicated waveforms as the input, the ISSA scans all model space for possible combination of time and location for the existence of seismic sources. The scanning results successfully associate various phases from each event at all stations, and correctly recover the input. To further demonstrate the advantage of ISSA, we apply it to the waveform data collected by a temporary OBS array for the aftershock sequence of an offshore earthquake southwest of Taiwan. The overall signal-to-noise ratio is inadequate for locating small events; and the precise arrival times of P and S phases are difficult to

  14. Determination of the Johnson-Cook Constitutive Model Parameters of Materials by Cluster Global Optimization Algorithm

    NASA Astrophysics Data System (ADS)

    Huang, Zhipeng; Gao, Lihong; Wang, Yangwei; Wang, Fuchi

    2016-09-01

    The Johnson-Cook (J-C) constitutive model is widely used in the finite element simulation, as this model shows the relationship between stress and strain in a simple way. In this paper, a cluster global optimization algorithm is proposed to determine the J-C constitutive model parameters of materials. A set of assumed parameters is used for the accuracy verification of the procedure. The parameters of two materials (401 steel and 823 steel) are determined. Results show that the procedure is reliable and effective. The relative error between the optimized and assumed parameters is no more than 4.02%, and the relative error between the optimized and assumed stress is 0.2% × 10-5. The J-C constitutive parameters can be determined more precisely and quickly than the traditional manual procedure. Furthermore, all the parameters can be simultaneously determined using several curves under different experimental conditions. A strategy is also proposed to accurately determine the constitutive parameters.

  15. Intensity-based signal separation algorithm for accuratequantification of clustered centrosomes in tissue sections

    SciTech Connect

    Fleisch, Markus C.; Maxell, Christopher A.; Kuper, Claudia K.; Brown, Erika T.; Parvin, Bahram; Barcellos-Hoff, Mary-Helen; Costes,Sylvain V.

    2006-03-08

    Centrosomes are small organelles that organize the mitoticspindle during cell division and are also involved in cell shape andpolarity. Within epithelial tumors, such as breast cancer, and somehematological tumors, centrosome abnormalities (CA) are common, occurearly in disease etiology, and correlate with chromosomal instability anddisease stage. In situ quantification of CA by optical microscopy ishampered by overlap and clustering of these organelles, which appear asfocal structures. CA has been frequently associated with Tp53 status inpremalignant lesions and tumors. Here we describe an approach toaccurately quantify centrosomes in tissue sections and tumors.Considering proliferation and baseline amplification rate the resultingpopulation based ratio of centrosomes per nucleus allow the approximationof the proportion of cells with CA. Using this technique we show that20-30 percent of cells have amplified centrosomes in Tp53 null mammarytumors. Combining fluorescence detection, deconvolution microscopy and amathematical algorithm applied to a maximum intensity projection we showthat this approach is superior to traditional investigator based visualanalysis or threshold-based techniques.

  16. 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.

  17. 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

  18. 3D Kirchhoff depth migration algorithm: A new scalable approach for parallelization on multicore CPU based cluster

    NASA Astrophysics Data System (ADS)

    Rastogi, Richa; Londhe, Ashutosh; Srivastava, Abhishek; Sirasala, Kirannmayi M.; Khonde, Kiran

    2017-03-01

    In this article, a new scalable 3D Kirchhoff depth migration algorithm is presented on state of the art multicore CPU based cluster. Parallelization of 3D Kirchhoff depth migration is challenging due to its high demand of compute time, memory, storage and I/O along with the need of their effective management. The most resource intensive modules of the algorithm are traveltime calculations and migration summation which exhibit an inherent trade off between compute time and other resources. The parallelization strategy of the algorithm largely depends on the storage of calculated traveltimes and its feeding mechanism to the migration process. The presented work is an extension of our previous work, wherein a 3D Kirchhoff depth migration application for multicore CPU based parallel system had been developed. Recently, we have worked on improving parallel performance of this application by re-designing the parallelization approach. The new algorithm is capable to efficiently migrate both prestack and poststack 3D data. It exhibits flexibility for migrating large number of traces within the available node memory and with minimal requirement of storage, I/O and inter-node communication. The resultant application is tested using 3D Overthrust data on PARAM Yuva II, which is a Xeon E5-2670 based multicore CPU cluster with 16 cores/node and 64 GB shared memory. Parallel performance of the algorithm is studied using different numerical experiments and the scalability results show striking improvement over its previous version. An impressive 49.05X speedup with 76.64% efficiency is achieved for 3D prestack data and 32.00X speedup with 50.00% efficiency for 3D poststack data, using 64 nodes. The results also demonstrate the effectiveness and robustness of the improved algorithm with high scalability and efficiency on a multicore CPU cluster.

  19. A Multi-Hop Energy Neutral Clustering Algorithm for Maximizing Network Information Gathering in Energy Harvesting Wireless Sensor Networks

    PubMed Central

    Yang, Liu; Lu, Yinzhi; Zhong, Yuanchang; Wu, Xuegang; Yang, Simon X.

    2015-01-01

    Energy resource limitation is a severe problem in traditional wireless sensor networks (WSNs) because it restricts the lifetime of network. Recently, the emergence of energy harvesting techniques has brought with them the expectation to overcome this problem. In particular, it is possible for a sensor node with energy harvesting abilities to work perpetually in an Energy Neutral state. In this paper, a Multi-hop Energy Neutral Clustering (MENC) algorithm is proposed to construct the optimal multi-hop clustering architecture in energy harvesting WSNs, with the goal of achieving perpetual network operation. All cluster heads (CHs) in the network act as routers to transmit data to base station (BS) cooperatively by a multi-hop communication method. In addition, by analyzing the energy consumption of intra- and inter-cluster data transmission, we give the energy neutrality constraints. Under these constraints, every sensor node can work in an energy neutral state, which in turn provides perpetual network operation. Furthermore, the minimum network data transmission cycle is mathematically derived using convex optimization techniques while the network information gathering is maximal. Simulation results show that our protocol can achieve perpetual network operation, so that the consistent data delivery is guaranteed. In addition, substantial improvements on the performance of network throughput are also achieved as compared to the famous traditional clustering protocol LEACH and recent energy harvesting aware clustering protocols. PMID:26712764

  20. A Multi-Hop Energy Neutral Clustering Algorithm for Maximizing Network Information Gathering in Energy Harvesting Wireless Sensor Networks.

    PubMed

    Yang, Liu; Lu, Yinzhi; Zhong, Yuanchang; Wu, Xuegang; Yang, Simon X

    2015-12-26

    Energy resource limitation is a severe problem in traditional wireless sensor networks (WSNs) because it restricts the lifetime of network. Recently, the emergence of energy harvesting techniques has brought with them the expectation to overcome this problem. In particular, it is possible for a sensor node with energy harvesting abilities to work perpetually in an Energy Neutral state. In this paper, a Multi-hop Energy Neutral Clustering (MENC) algorithm is proposed to construct the optimal multi-hop clustering architecture in energy harvesting WSNs, with the goal of achieving perpetual network operation. All cluster heads (CHs) in the network act as routers to transmit data to base station (BS) cooperatively by a multi-hop communication method. In addition, by analyzing the energy consumption of intra- and inter-cluster data transmission, we give the energy neutrality constraints. Under these constraints, every sensor node can work in an energy neutral state, which in turn provides perpetual network operation. Furthermore, the minimum network data transmission cycle is mathematically derived using convex optimization techniques while the network information gathering is maximal. Simulation results show that our protocol can achieve perpetual network operation, so that the consistent data delivery is guaranteed. In addition, substantial improvements on the performance of network throughput are also achieved as compared to the famous traditional clustering protocol LEACH and recent energy harvesting aware clustering protocols.

  1. Deconvoluting simulated metagenomes: the performance of hard- and soft- clustering algorithms applied to metagenomic chromosome conformation capture (3C)

    PubMed Central

    DeMaere, Matthew Z.

    2016-01-01

    Background Chromosome conformation capture, coupled with high throughput DNA sequencing in protocols like Hi-C and 3C-seq, has been proposed as a viable means of generating data to resolve the genomes of microorganisms living in naturally occuring environments. Metagenomic Hi-C and 3C-seq datasets have begun to emerge, but the feasibility of resolving genomes when closely related organisms (strain-level diversity) are present in the sample has not yet been systematically characterised. Methods We developed a computational simulation pipeline for metagenomic 3C and Hi-C sequencing to evaluate the accuracy of genomic reconstructions at, above, and below an operationally defined species boundary. We simulated datasets and measured accuracy over a wide range of parameters. Five clustering algorithms were evaluated (2 hard, 3 soft) using an adaptation of the extended B-cubed validation measure. Results When all genomes in a sample are below 95% sequence identity, all of the tested clustering algorithms performed well. When sequence data contains genomes above 95% identity (our operational definition of strain-level diversity), a naive soft-clustering extension of the Louvain method achieves the highest performance. Discussion Previously, only hard-clustering algorithms have been applied to metagenomic 3C and Hi-C data, yet none of these perform well when strain-level diversity exists in a metagenomic sample. Our simple extension of the Louvain method performed the best in these scenarios, however, accuracy remained well below the levels observed for samples without strain-level diversity. Strain resolution is also highly dependent on the amount of available 3C sequence data, suggesting that depth of sequencing must be carefully considered during experimental design. Finally, there appears to be great scope to improve the accuracy of strain resolution through further algorithm development. PMID:27843713

  2. New Nonequilibrium-to-Equilibrium Dynamical Scaling and Stretched-Exponential Critical Relaxation in Cluster Algorithms

    NASA Astrophysics Data System (ADS)

    Nonomura, Yoshihiko

    2014-11-01

    Nonequilibrium relaxation behaviors in the Ising model on a square lattice based on the Wolff algorithm are totally different from those based on local-update algorithms. In particular, the critical relaxation is described by the stretched-exponential decay. We propose a novel scaling procedure to connect nonequilibrium and equilibrium behaviors continuously, and find that the stretched-exponential scaling region in the Wolff algorithm is as wide as the power-law scaling region in local-update algorithms. We also find that relaxation to the spontaneous magnetization in the ordered phase is characterized by the exponential decay, not the stretched-exponential decay based on local-update algorithms.

  3. Effective Analysis of NGS Metagenomic Data with Ultra-Fast Clustering Algorithms (MICW - Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

    ScienceCinema

    Li, Weizhong [San Diego Supercomputer Center

    2016-07-12

    San Diego Supercomputer Center's Weizhong Li on "Effective Analysis of NGS Metagenomic Data with Ultra-fast Clustering Algorithms" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

  4. Delineation of river bed-surface patches by clustering high-resolution spatial grain size data

    NASA Astrophysics Data System (ADS)

    Nelson, Peter A.; Bellugi, Dino; Dietrich, William E.

    2014-01-01

    The beds of gravel-bed rivers commonly display distinct sorting patterns, which at length scales of ~ 0.1 - 1 channel widths appear to form an organization of patches or facies. This paper explores alternatives to traditional visual facies mapping by investigating methods of patch delineation in which clustering analysis is applied to a high-resolution grid of spatial grain-size distributions (GSDs) collected during a flume experiment. Specifically, we examine four clustering techniques: 1) partitional clustering of grain-size distributions with the k-means algorithm (assigning each GSD to a type of patch based solely on its distribution characteristics), 2) spatially-constrained agglomerative clustering ("growing" patches by merging adjacent GSDs, thus generating a hierarchical structure of patchiness), 3) spectral clustering using Normalized Cuts (using the spatial distance between GSDs and the distribution characteristics to generate a matrix describing the similarity between all GSDs, and using the eigenvalues of this matrix to divide the bed into patches), and 4) fuzzy clustering with the fuzzy c-means algorithm (assigning each GSD a membership probability to every patch type). For each clustering method, we calculate metrics describing how well-separated cluster-average GSDs are and how patches are arranged in space. We use these metrics to compute optimal clustering parameters, to compare the clustering methods against each other, and to compare clustering results with patches mapped visually during the flume experiment.All clustering methods produced better-separated patch GSDs than the visually-delineated patches. Although they do not produce crisp cluster assignment, fuzzy algorithms provide useful information that can characterize the uncertainty of a location on the bed belonging to any particular type of patch, and they can be used to characterize zones of transition from one patch to another. The extent to which spatial information influences

  5. Single-cluster algorithm for the site-bond-correlated Ising model

    NASA Astrophysics Data System (ADS)

    Campos, P. R. A.; Onody, R. N.

    1997-12-01

    We extend the Wolff algorithm to include correlated spin interactions in diluted magnetic systems. This algorithm is applied to study the site-bond-correlated Ising model on a two-dimensional square lattice. We use a finite-size scaling procedure to obtain the phase diagram in the temperature-concentration space. We also have verified that the autocorrelation time diminishes in the presence of dilution and correlation, showing that the Wolff algorithm performs even better in such situations.

  6. A sub-clustering algorithm based on spatial data correlation for energy conservation in wireless sensor networks.

    PubMed

    Tsai, Ming-Hui; Huang, Yueh-Min

    2014-11-18

    Wireless sensor networks (WSNs) have emerged as a promising solution for various applications due to their low cost and easy deployment. Typically, their limited power capability, i.e., battery powered, make WSNs encounter the challenge of extension of network lifetime. Many hierarchical protocols show better ability of energy efficiency in the literature. Besides, data reduction based on the correlation of sensed readings can efficiently reduce the amount of required transmissions. Therefore, we use a sub-clustering procedure based on spatial data correlation to further separate the hierarchical (clustered) architecture of a WSN. The proposed algorithm (2TC-cor) is composed of two procedures: the prediction model construction procedure and the sub-clustering procedure. The energy conservation benefits by the reduced transmissions, which are dependent on the prediction model. Also, the energy can be further conserved because of the representative mechanism of sub-clustering. As presented by simulation results, it shows that 2TC-cor can effectively conserve energy and monitor accurately the environment within an acceptable level.

  7. Fast clustering algorithm for large ECG data sets based on CS theory in combination with PCA and K-NN methods.

    PubMed

    Balouchestani, Mohammadreza; Krishnan, Sridhar

    2014-01-01

    Long-term recording of Electrocardiogram (ECG) signals plays an important role in health care systems for diagnostic and treatment purposes of heart diseases. Clustering and classification of collecting data are essential parts for detecting concealed information of P-QRS-T waves in the long-term ECG recording. Currently used algorithms do have their share of drawbacks: 1) clustering and classification cannot be done in real time; 2) they suffer from huge energy consumption and load of sampling. These drawbacks motivated us in developing novel optimized clustering algorithm which could easily scan large ECG datasets for establishing low power long-term ECG recording. In this paper, we present an advanced K-means clustering algorithm based on Compressed Sensing (CS) theory as a random sampling procedure. Then, two dimensionality reduction methods: Principal Component Analysis (PCA) and Linear Correlation Coefficient (LCC) followed by sorting the data using the K-Nearest Neighbours (K-NN) and Probabilistic Neural Network (PNN) classifiers are applied to the proposed algorithm. We show our algorithm based on PCA features in combination with K-NN classifier shows better performance than other methods. The proposed algorithm outperforms existing algorithms by increasing 11% classification accuracy. In addition, the proposed algorithm illustrates classification accuracy for K-NN and PNN classifiers, and a Receiver Operating Characteristics (ROC) area of 99.98%, 99.83%, and 99.75% respectively.

  8. A comparative study of DIGNET, average, complete, single hierarchical and k-means clustering algorithms in 2D face image recognition

    NASA Astrophysics Data System (ADS)

    Thanos, Konstantinos-Georgios; Thomopoulos, Stelios C. A.

    2014-06-01

    The study in this paper belongs to a more general research of discovering facial sub-clusters in different ethnicity face databases. These new sub-clusters along with other metadata (such as race, sex, etc.) lead to a vector for each face in the database where each vector component represents the likelihood of participation of a given face to each cluster. This vector is then used as a feature vector in a human identification and tracking system based on face and other biometrics. The first stage in this system involves a clustering method which evaluates and compares the clustering results of five different clustering algorithms (average, complete, single hierarchical algorithm, k-means and DIGNET), and selects the best strategy for each data collection. In this paper we present the comparative performance of clustering results of DIGNET and four clustering algorithms (average, complete, single hierarchical and k-means) on fabricated 2D and 3D samples, and on actual face images from various databases, using four different standard metrics. These metrics are the silhouette figure, the mean silhouette coefficient, the Hubert test Γ coefficient, and the classification accuracy for each clustering result. The results showed that, in general, DIGNET gives more trustworthy results than the other algorithms when the metrics values are above a specific acceptance threshold. However when the evaluation results metrics have values lower than the acceptance threshold but not too low (too low corresponds to ambiguous results or false results), then it is necessary for the clustering results to be verified by the other algorithms.

  9. 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.

  10. Optimal clustering of MGs based on droop controller for improving reliability using a hybrid of harmony search and genetic algorithms.

    PubMed

    Abedini, Mohammad; Moradi, Mohammad H; Hosseinian, S M

    2016-03-01

    This paper proposes a novel method to address reliability and technical problems of microgrids (MGs) based on designing a number of self-adequate autonomous sub-MGs via adopting MGs clustering thinking. In doing so, a multi-objective optimization problem is developed where power losses reduction, voltage profile improvement and reliability enhancement are considered as the objective functions. To solve the optimization problem a hybrid algorithm, named HS-GA, is provided, based on genetic and harmony search algorithms, and a load flow method is given to model different types of DGs as droop controller. The performance of the proposed method is evaluated in two case studies. The results provide support for the performance of the proposed method.

  11. Efficient Sparse Matrix Algorithm to Speed Up the Calculation of the Ladder Term in Coupled Cluster Programs.

    PubMed

    Pillió, Zoltán; Tajti, Attila; Szalay, Péter G

    2012-09-11

    A new algorithm is presented for the calculation of the ladder-type term of the coupled cluster singles and doubles (CCSD) equations using two-electron integrals in atomic orbital (AO) basis. The method is based on an orbital grouping scheme, which results in an optimal partitioning of the AO integral matrix into sparse and dense blocks allowing efficient matrix multiplication. Carefully chosen numerical tests have been performed to analyze the performance of all aspects of the new algorithm. It is shown that the suggested scheme allows an efficient utilization of modern highly parallel architectures and devices in CCSD calculations. Details of the implementation in the development version of CFOUR quantum chemical program package are also presented.

  12. A new algorithm to find earthquake clusters using neighboring cell connection and rate analysis.

    NASA Astrophysics Data System (ADS)

    Peng, W.; Toda, S.

    2015-12-01

    To study earthquake interaction, it is important to objectively find a group of earthquakes occurred closely in space and time. Earthquake clusters are chosen with previous techniques that characterize them as mainshock-aftershock sequences or swarm sequences by empirical laws (e.g., Omori-Utsu; ETAS) or direct assumptions about physical processes such as stress transfer, transient stress loading, and fluid migration. Recent papers instead proposed non-parameterized techniques such as a kernel-based smoothing method. The cumulative rate clustering method (CURATE, Jacobs et al., 2013) is one of the approaches without any direct assumptions. The CURATE method was applied in New Zealand and provided a good result for selecting the swarm sequences comparing with the ETAS model. However, it is still difficult to choose a proper confined area and a time interval for extracting sequences from the catalog. To avoid arbitrariness in space and time parameters, here we propose a new method modifying the CURATE approach. We first identify the spatial clusters by looking into the spatial distribution in a 2-D cell-gridded map. The spatial clusters defined as multiple neighboring cells, each of which contains at least one earthquake in a time period T. From the selected spatial clusters, we then evaluate temporal clustering which is defined as a transient increase of seismicity rate comparing to the rate before the target event. We tested this method focusing on shallow crustal seismicity, northern Honshu, Japan. We chose the parameter range from T = 1 to 100 days and cell size = 0.01°to 0.1°. As a result, the number of the clusters increase with longer T and larger cell size. By choosing the T = 30 days and cell size = 0.05°, we successfully selected the long-lasting aftershock sequences associated with the 2004 M6.8 Chuetsu and 2007 M6.8 Chuetsu-oki earthquakes, while other empirical models and CURATE method failed to decluster.

  13. Multi-GPU-based Swendsen-Wang multi-cluster algorithm for the simulation of two-dimensional q-state Potts model

    NASA Astrophysics Data System (ADS)

    Komura, Yukihiro; Okabe, Yutaka

    2013-01-01

    We present multiple GPU computing with the common unified device architecture (CUDA) for the Swendsen-Wang multi-cluster algorithm of two-dimensional (2D) q-state Potts model. Extending our algorithm for single GPU computing [Y. Komura, Y. Okabe, GPU-based Swendsen-Wang multi-cluster algorithm for the simulation of two-dimensional classical spin systems, Comput. Phys. Comm. 183 (2012) 1155-1161], we realize the GPU computation of the Swendsen-Wang multi-cluster algorithm for multiple GPUs. We implement our code on the large-scale open science supercomputer TSUBAME 2.0, and test the performance and the scalability of the simulation of the 2D Potts model. The performance on Tesla M2050 using 256 GPUs is obtained as 37.3 spin flips per a nano second for the q=2 Potts model (Ising model) at the critical temperature with the linear system size L=65536.

  14. A comparative analysis of clustering algorithms: O2 migration in truncated hemoglobin I from transition networks

    NASA Astrophysics Data System (ADS)

    Cazade, Pierre-André; Zheng, Wenwei; Prada-Gracia, Diego; Berezovska, Ganna; Rao, Francesco; Clementi, Cecilia; Meuwly, Markus

    2015-01-01

    The ligand migration network for O2-diffusion in truncated Hemoglobin N is analyzed based on three different clustering schemes. For coordinate-based clustering, the conventional k-means and the kinetics-based Markov Clustering (MCL) methods are employed, whereas the locally scaled diffusion map (LSDMap) method is a collective-variable-based approach. It is found that all three methods agree well in their geometrical definition of the most important docking site, and all experimentally known docking sites are recovered by all three methods. Also, for most of the states, their population coincides quite favourably, whereas the kinetics of and between the states differs. One of the major differences between k-means and MCL clustering on the one hand and LSDMap on the other is that the latter finds one large primary cluster containing the Xe1a, IS1, and ENT states. This is related to the fact that the motion within the state occurs on similar time scales, whereas structurally the state is found to be quite diverse. In agreement with previous explicit atomistic simulations, the Xe3 pocket is found to be a highly dynamical site which points to its potential role as a hub in the network. This is also highlighted in the fact that LSDMap cannot identify this state. First passage time distributions from MCL clusterings using a one- (ligand-position) and two-dimensional (ligand-position and protein-structure) descriptor suggest that ligand- and protein-motions are coupled. The benefits and drawbacks of the three methods are discussed in a comparative fashion and highlight that depending on the questions at hand the best-performing method for a particular data set may differ.

  15. A comparative analysis of clustering algorithms: O2 migration in truncated hemoglobin I from transition networks.

    PubMed

    Cazade, Pierre-André; Zheng, Wenwei; Prada-Gracia, Diego; Berezovska, Ganna; Rao, Francesco; Clementi, Cecilia; Meuwly, Markus

    2015-01-14

    The ligand migration network for O2-diffusion in truncated Hemoglobin N is analyzed based on three different clustering schemes. For coordinate-based clustering, the conventional k-means and the kinetics-based Markov Clustering (MCL) methods are employed, whereas the locally scaled diffusion map (LSDMap) method is a collective-variable-based approach. It is found that all three methods agree well in their geometrical definition of the most important docking site, and all experimentally known docking sites are recovered by all three methods. Also, for most of the states, their population coincides quite favourably, whereas the kinetics of and between the states differs. One of the major differences between k-means and MCL clustering on the one hand and LSDMap on the other is that the latter finds one large primary cluster containing the Xe1a, IS1, and ENT states. This is related to the fact that the motion within the state occurs on similar time scales, whereas structurally the state is found to be quite diverse. In agreement with previous explicit atomistic simulations, the Xe3 pocket is found to be a highly dynamical site which points to its potential role as a hub in the network. This is also highlighted in the fact that LSDMap cannot identify this state. First passage time distributions from MCL clusterings using a one- (ligand-position) and two-dimensional (ligand-position and protein-structure) descriptor suggest that ligand- and protein-motions are coupled. The benefits and drawbacks of the three methods are discussed in a comparative fashion and highlight that depending on the questions at hand the best-performing method for a particular data set may differ.

  16. Clustering social cues to determine social signals: developing learning algorithms using the "n-most likely states" approach

    NASA Astrophysics Data System (ADS)

    Best, Andrew; Kapalo, Katelynn A.; Warta, Samantha F.; Fiore, Stephen M.

    2016-05-01

    Human-robot teaming largely relies on the ability of machines to respond and relate to human social signals. Prior work in Social Signal Processing has drawn a distinction between social cues (discrete, observable features) and social signals (underlying meaning). For machines to attribute meaning to behavior, they must first understand some probabilistic relationship between the cues presented and the signal conveyed. Using data derived from a study in which participants identified a set of salient social signals in a simulated scenario and indicated the cues related to the perceived signals, we detail a learning algorithm, which clusters social cue observations and defines an "N-Most Likely States" set for each cluster. Since multiple signals may be co-present in a given simulation and a set of social cues often maps to multiple social signals, the "N-Most Likely States" approach provides a dramatic improvement over typical linear classifiers. We find that the target social signal appears in a "3 most-likely signals" set with up to 85% probability. This results in increased speed and accuracy on large amounts of data, which is critical for modeling social cognition mechanisms in robots to facilitate more natural human-robot interaction. These results also demonstrate the utility of such an approach in deployed scenarios where robots need to communicate with human teammates quickly and efficiently. In this paper, we detail our algorithm, comparative results, and offer potential applications for robot social signal detection and machine-aided human social signal detection.

  17. piClust: a density based piRNA clustering algorithm.

    PubMed

    Jung, Inuk; Park, Jong Chan; Kim, Sun

    2014-06-01

    Piwi-interacting RNAs (piRNAs) are recently discovered, endogenous small non-coding RNAs. piRNAs protect the genome from invasive transposable elements (TE) and sustain integrity of the genome in germ cell lineages. Small RNA-sequencing data can be used to detect piRNA activations in a cell under a specific condition. However, identification of cell specific piRNA activations requires sophisticated computational methods. As of now, there is only one computational method, proTRAC, to locate activated piRNAs from the sequencing data. proTRAC detects piRNA clusters based on a probabilistic analysis with assumption of a uniform distribution. Unfortunately, we were not able to locate activated piRNAs from our proprietary sequencing data in chicken germ cells using proTRAC. With a careful investigation on data sets, we found that a uniform or any statistical distribution for detecting piRNA clusters may not be assumed. Furthermore, small RNA-seq data contains many different types of RNAs which was not carefully taken into account in previous studies. To improve piRNA cluster identification, we developed piClust that uses a density based clustering approach without assumption of any parametric distribution. In previous studies, it is known that piRNAs exhibit a strong tendency of forming piRNA clusters in syntenic regions of the genome. Thus, the density based clustering approach is effective and robust to the existence of non-piRNAs or noise in the data. In experiments with piRNA data from human, mouse, rat and chicken, piClust was able to detect piRNA clusters from total small RNA-seq data from germ cell lines, while proTRAC was not successful. piClust outperformed proTRAC in terms of sensitivity and running time (up to 200 folds). piClust is currently available as a web service at http://epigenomics.snu.ac.kr/piclustweb.

  18. Efficient algorithms for solving the non-linear vibrational coupled-cluster equations using full and decomposed tensors.

    PubMed

    Madsen, Niels K; Godtliebsen, Ian H; Christiansen, Ove

    2017-04-07

    Vibrational coupled-cluster (VCC) theory provides an accurate method for calculating vibrational spectra and properties of small to medium-sized molecules. Obtaining these properties requires the solution of the non-linear VCC equations which can in some cases be hard to converge depending on the molecule, the basis set, and the vibrational state in question. We present and compare a range of different algorithms for solving the VCC equations ranging from a full Newton-Raphson method to approximate quasi-Newton models using an array of different convergence-acceleration schemes. The convergence properties and computational cost of the algorithms are compared for the optimization of VCC states. This includes both simple ground-state problems and difficult excited states with strong non-linearities. Furthermore, the effects of using tensor-decomposed solution vectors and residuals are investigated and discussed. The results show that for standard ground-state calculations, the conjugate residual with optimal trial vectors algorithm has the shortest time-to-solution although the full Newton-Raphson method converges in fewer macro-iterations. Using decomposed tensors does not affect the observed convergence rates in our test calculations as long as the tensors are decomposed to sufficient accuracy.

  19. Designing Topology-Aware Collective Communication Algorithms for Large Scale InfiniBand Clusters: Case Studies with Scatter and Gather

    SciTech Connect

    Kandalla, Krishna; Subramoni, Hari; Vishnu, Abhinav; Panda, Dhabaleswar K.

    2010-04-01

    Modern high performance computing systems are being increasingly deployed in a hierarchical fashion with multi-core computing platforms forming the base of the hierarchy. These systems are usually comprised of multiple racks, with each rack consisting of a finite number of chassis, with each chassis having multiple compute nodes or blades, based on multi-core architectures. The networks are also hierarchical with multiple levels of switches. Message exchange operations between processes that belong to different racks involve multiple hops across different switches and this directly affects the performance of collective operations. In this paper, we take on the challenges involved in detecting the topology of large scale InfiniBand clusters and leveraging this knowledge to design efficient topology-aware algorithms for collective operations. We also propose a communication model to analyze the communication costs involved in collective operations on large scale supercomputing systems. We have analyzed the performance characteristics of two collectives, MPI_Gather and MPI_Scatter on such systems and we have proposed topology-aware algorithms for these operations. Our experimental results have shown that the proposed algorithms can improve the performance of these collective operations by almost 54% at the micro-benchmark level.

  20. Comparison of Genetic Algorithm, Particle Swarm Optimization and Biogeography-based Optimization for Feature Selection to Classify Clusters of Microcalcifications

    NASA Astrophysics Data System (ADS)

    Khehra, Baljit Singh; Pharwaha, Amar Partap Singh

    2016-06-01

    Ductal carcinoma in situ (DCIS) is one type of breast cancer. Clusters of microcalcifications (MCCs) are symptoms of DCIS that are recognized by mammography. Selection of robust features vector is the process of selecting an optimal subset of features from a large number of available features in a given problem domain after the feature extraction and before any classification scheme. Feature selection reduces the feature space that improves the performance of classifier and decreases the computational burden imposed by using many features on classifier. Selection of an optimal subset of features from a large number of available features in a given problem domain is a difficult search problem. For n features, the total numbers of possible subsets of features are 2n. Thus, selection of an optimal subset of features problem belongs to the category of NP-hard problems. In this paper, an attempt is made to find the optimal subset of MCCs features from all possible subsets of features using genetic algorithm (GA), particle swarm optimization (PSO) and biogeography-based optimization (BBO). For simulation, a total of 380 benign and malignant MCCs samples have been selected from mammogram images of DDSM database. A total of 50 features extracted from benign and malignant MCCs samples are used in this study. In these algorithms, fitness function is correct classification rate of classifier. Support vector machine is used as a classifier. From experimental results, it is also observed that the performance of PSO-based and BBO-based algorithms to select an optimal subset of features for classifying MCCs as benign or malignant is better as compared to GA-based algorithm.

  1. Community Detection Algorithm Combining Stochastic Block Model and Attribute Data Clustering

    NASA Astrophysics Data System (ADS)

    Kataoka, Shun; Kobayashi, Takuto; Yasuda, Muneki; Tanaka, Kazuyuki

    2016-11-01

    We propose a new algorithm to detect the community structure in a network that utilizes both the network structure and vertex attribute data. Suppose we have the network structure together with the vertex attribute data, that is, the information assigned to each vertex associated with the community to which it belongs. The problem addressed this paper is the detection of the community structure from the information of both the network structure and the vertex attribute data. Our approach is based on the Bayesian approach that models the posterior probability distribution of the community labels. The detection of the community structure in our method is achieved by using belief propagation and an EM algorithm. We numerically verified the performance of our method using computer-generated networks and real-world networks.

  2. RoCaSCA: A contour tracing grid-based algorithm to identify similarity regions and clusters in spatial geographical data

    NASA Astrophysics Data System (ADS)

    Hazenberg, P.; Torfs, P. J. J. F.; Leijnse, H.; Uijlenhoet, R.

    2012-04-01

    Over the last decades the amount of spatial geographic data obtained from satellite and radar remote sensing, geographical and other types of spatial information has increased tremendously, making it impossible for a user to examine all in detail. Therefore, a considerable amount of research has focused on smart and efficient solutions to segment a spatial image into its dominant regions, extracting most essential information. The current research presents a new spatial image cluster identification method. The delineation of clusters is performed in two separate steps. First, we identify a regions outer contour using the properties of a rotating carpenter square. Secondly, we define all inner pixels belonging to a cluster based on the same principle, excluding inner contour regions if necessary. As such, a cluster identification method will be presented which has considerable similarity to some of the tracing type and connected component image segmentation algorithms developed in the literature during the last decade. However, since the characteristic shape of a carpenter square can easily be extended, the algorithm presented here does not strictly label neighboring pixels to the same component only. On the contrary, our algorithm is able to connect non-neighboring pixels for varying pixel distances as well. In addition, since our algorithm takes a continuous grid as input, it is possible to define transition pixels, that connect pixels that belong to a given cluster. Therefore, this newly developed algorithm presents a link between the traditional image segmentation methods implemented on binary grids and the partitional density and grid-based cluster identification methods that use continuous datasets. We will demonstrate the impact of this new cluster identification method for a number of typical geophysical cases ranging from global drought identification to weather radar based precipitation cell delineation.

  3. Improved CUDA programs for GPU computing of Swendsen-Wang multi-cluster spin flip algorithm: 2D and 3D Ising, Potts, and XY models

    NASA Astrophysics Data System (ADS)

    Komura, Yukihiro; Okabe, Yutaka

    2016-03-01

    We present new versions of sample CUDA programs for the GPU computing of the Swendsen-Wang multi-cluster spin flip algorithm. In this update, we add the method of GPU-based cluster-labeling algorithm without the use of conventional iteration (Komura, 2015) to those programs. For high-precision calculations, we also add a random-number generator in the cuRAND library. Moreover, we fix several bugs and remove the extra usage of shared memory in the kernel functions.

  4. [Analysis on principle of treatment of phlegm retention syndrome of Ma Peizhi based on apriori and clustering algorithm].

    PubMed

    Wu, Jia-Rui; Guo, Wei-Xian; Zhang, Xiao-Meng; Huang, Xiu-Qin; Yang, Bing

    2014-02-01

    Analyzed the prescriptions for phlegm retention syndrome that built by Ma Peizhi by the association rules and clustering algorithm, the frequency of drug usage and the relationship between drugs could be get. And from that we could conclude the experiences for phlegm retention syndrome of Ma Peizhi of menghe medical genre. The results of the analysis were that 18 core combinations were dig out, such as Citri Exocarpium Rubrum-Eriobotryae Folium-Citri Reticulatae Pericarpium. And there were 9 new prescriptions were found out such as Aurantii Fructus-Citri Exocarpium Rubium-Eriobotryae Folium-Citri Reticulatae Pericarpium. The results of the analysis were proved that Ma Peizhi of Menghe Medical Genre was good at curing phlegm retention syndrome by using the traditional Chinese medicine of mild and light, such as the medicines of mild tonification, and clearing damp and promoting diuresis.

  5. Parallel SOR Iterative Algorithms and Performance Evaluation on a Linux Cluster

    DTIC Science & Technology

    2005-06-01

    Red - Black two-color SOR implementation. Two other iterative methods , Jacobi method is preferred. Yanheh [4] showed that the and Gauss - Seidel (G-S...The optimal value of co lies in (0, 2). The choice 40 J +" of co = 1 corresponds to the Gauss - Seidel - j.1)( - 11 iteration. 2.2 Red - Black SOR...paper, a parallel algorithm for the structure of a matrix or a grid. However, the red - black SOR method with domain decomposition is multi-color

  6. GPUDePiCt: A Parallel Implementation of a Clustering Algorithm for Computing Degenerate Primers on Graphics Processing Units.

    PubMed

    Cickovski, Trevor; Flor, Tiffany; Irving-Sachs, Galen; Novikov, Philip; Parda, James; Narasimhan, Giri

    2015-01-01

    In order to make multiple copies of a target sequence in the laboratory, the technique of Polymerase Chain Reaction (PCR) requires the design of "primers", which are short fragments of nucleotides complementary to the flanking regions of the target sequence. If the same primer is to amplify multiple closely related target sequences, then it is necessary to make the primers "degenerate", which would allow it to hybridize to target sequences with a limited amount of variability that may have been caused by mutations. However, the PCR technique can only allow a limited amount of degeneracy, and therefore the design of degenerate primers requires the identification of reasonably well-conserved regions in the input sequences. We take an existing algorithm for designing degenerate primers that is based on clustering and parallelize it in a web-accessible software package GPUDePiCt, using a shared memory model and the computing power of Graphics Processing Units (GPUs). We test our implementation on large sets of aligned sequences from the human genome and show a multi-fold speedup for clustering using our hybrid GPU/CPU implementation over a pure CPU approach for these sequences, which consist of more than 7,500 nucleotides. We also demonstrate that this speedup is consistent over larger numbers and longer lengths of aligned sequences.

  7. A new time dependent density functional algorithm for large systems and plasmons in metal clusters

    SciTech Connect

    Baseggio, Oscar; Fronzoni, Giovanna; Stener, Mauro

    2015-07-14

    A new algorithm to solve the Time Dependent Density Functional Theory (TDDFT) equations in the space of the density fitting auxiliary basis set has been developed and implemented. The method extracts the spectrum from the imaginary part of the polarizability at any given photon energy, avoiding the bottleneck of Davidson diagonalization. The original idea which made the present scheme very efficient consists in the simplification of the double sum over occupied-virtual pairs in the definition of the dielectric susceptibility, allowing an easy calculation of such matrix as a linear combination of constant matrices with photon energy dependent coefficients. The method has been applied to very different systems in nature and size (from H{sub 2} to [Au{sub 147}]{sup −}). In all cases, the maximum deviations found for the excitation energies with respect to the Amsterdam density functional code are below 0.2 eV. The new algorithm has the merit not only to calculate the spectrum at whichever photon energy but also to allow a deep analysis of the results, in terms of transition contribution maps, Jacob plasmon scaling factor, and induced density analysis, which have been all implemented.

  8. A new time dependent density functional algorithm for large systems and plasmons in metal clusters

    NASA Astrophysics Data System (ADS)

    Baseggio, Oscar; Fronzoni, Giovanna; Stener, Mauro

    2015-07-01

    A new algorithm to solve the Time Dependent Density Functional Theory (TDDFT) equations in the space of the density fitting auxiliary basis set has been developed and implemented. The method extracts the spectrum from the imaginary part of the polarizability at any given photon energy, avoiding the bottleneck of Davidson diagonalization. The original idea which made the present scheme very efficient consists in the simplification of the double sum over occupied-virtual pairs in the definition of the dielectric susceptibility, allowing an easy calculation of such matrix as a linear combination of constant matrices with photon energy dependent coefficients. The method has been applied to very different systems in nature and size (from H2 to [Au147]-). In all cases, the maximum deviations found for the excitation energies with respect to the Amsterdam density functional code are below 0.2 eV. The new algorithm has the merit not only to calculate the spectrum at whichever photon energy but also to allow a deep analysis of the results, in terms of transition contribution maps, Jacob plasmon scaling factor, and induced density analysis, which have been all implemented.

  9. Clustering of CO and CO2 concentration from Sumatra peat fire haze using HYSPLIT and K-means algorithm

    NASA Astrophysics Data System (ADS)

    Ni’am, M.; Sitanggang, I. S.; Nuryanto, D. E.

    2017-01-01

    Peat fires in Indonesia could have a negative impact for human life such as the emergence of haze. Therefore, this research aims to analyze concentration of CO and CO2 due to peat fires in Sumatra in 2015 using the Hybrid Single-Particle Lagrangian Integrated Trajectory (HYSPLIT) and K-Means algorithm. The results of this study indicate that HYSPLIT can be used to obtain the concentration of CO and CO2 from the haze. Clustering using K-Means algorithm produces an average of the highest concentration of CO is 11.1471 μg/m3 and CO2 is 88.5882 μg/m3. Generally, pollutants have an average concentration of 0.0487 μg/m3 for CO and 0.3687 μg/m3 for CO2. The pollutant concentration is contained in 45 525 (95%) positions in haze trajectory and the haze spread starting from Riau to Nanggroe Aceh Darussalam.

  10. Vibrational absorption spectra from vibrational coupled cluster damped linear response functions calculated using an asymmetric Lanczos algorithm

    NASA Astrophysics Data System (ADS)

    Thomsen, Bo; Hansen, Mikkel Bo; Seidler, Peter; Christiansen, Ove

    2012-03-01

    We report the theory and implementation of vibrational coupled cluster (VCC) damped response functions. From the imaginary part of the damped VCC response function the absorption as function of frequency can be obtained, requiring formally the solution of the now complex VCC response equations. The absorption spectrum can in this formulation be seen as a matrix function of the characteristic VCC Jacobian response matrix. The asymmetric matrix version of the Lanczos method is used to generate a tridiagonal representation of the VCC response Jacobian. Solving the complex response equations in the relevant Lanczos space provides a method for calculating the VCC damped response functions and thereby subsequently the absorption spectra. The convergence behaviour of the algorithm is discussed theoretically and tested for different levels of completeness of the VCC expansion. Comparison is made with results from the recently reported [P. Seidler, M. B. Hansen, W. Györffy, D. Toffoli, and O. Christiansen, J. Chem. Phys. 132, 164105 (2010)] vibrational configuration interaction damped response function calculated using a symmetric Lanczos algorithm. Calculations of IR spectra of oxazole, cyclopropene, and uracil illustrate the usefulness of the new VCC based method.

  11. Cluster-algorithm renormalization-group study of universal fluctuations in the two-dimensional Ising model.

    PubMed

    Palma, G; Zambrano, D

    2008-12-01

    In this paper we propose a method to study critical systems numerically, which combines collective-mode algorithms and renormalization group on the lattice. This method is an improved version of the Monte Carlo renormalization group in the sense that it has all the advantages of cluster algorithms. As an application we considered the 2D Ising model and studied whether scale invariance or universality are possible underlying mechanisms responsible for the approximate "universal fluctuations" close to a so-called bulk temperature T(L) . "Universal fluctuations" were first proposed in the work of Bramwell, Holdsworth, and Pinton [Nature (London) 396, 552 (1998)] and stated that the probability density function of a global quantity for very dissimilar systems, such as a confined turbulent flow and a two-dimensional (2D) magnetic system, properly normalized to the first two moments, becomes similar to the "universal distribution," originally obtained for magnetization in the 2D XY model in the low-temperature region. The results for the critical exponents and the renormalization-group flow of the probability density function are very accurate and show no evidence to support that the approximate common shape of the PDF should be related to both scale invariance or universal behavior.

  12. Vibrational absorption spectra from vibrational coupled cluster damped linear response functions calculated using an asymmetric Lanczos algorithm.

    PubMed

    Thomsen, Bo; Hansen, Mikkel Bo; Seidler, Peter; Christiansen, Ove

    2012-03-28

    We report the theory and implementation of vibrational coupled cluster (VCC) damped response functions. From the imaginary part of the damped VCC response function the absorption as function of frequency can be obtained, requiring formally the solution of the now complex VCC response equations. The absorption spectrum can in this formulation be seen as a matrix function of the characteristic VCC Jacobian response matrix. The asymmetric matrix version of the Lanczos method is used to generate a tridiagonal representation of the VCC response Jacobian. Solving the complex response equations in the relevant Lanczos space provides a method for calculating the VCC damped response functions and thereby subsequently the absorption spectra. The convergence behaviour of the algorithm is discussed theoretically and tested for different levels of completeness of the VCC expansion. Comparison is made with results from the recently reported [P. Seidler, M. B. Hansen, W. Györffy, D. Toffoli, and O. Christiansen, J. Chem. Phys. 132, 164105 (2010)] vibrational configuration interaction damped response function calculated using a symmetric Lanczos algorithm. Calculations of IR spectra of oxazole, cyclopropene, and uracil illustrate the usefulness of the new VCC based method.

  13. Clustering and Differential Alignment Algorithm: Identification of Early Stage Regulators in the Arabidopsis thaliana Iron Deficiency Response

    PubMed Central

    Muhammad, Durreshahwar; Foret, Jessica; Brady, Siobhan M.; Ducoste, Joel J.; Tuck, James; Long, Terri A.; Williams, Cranos

    2015-01-01

    Time course transcriptome datasets are commonly used to predict key gene regulators associated with stress responses and to explore gene functionality. Techniques developed to extract causal relationships between genes from high throughput time course expression data are limited by low signal levels coupled with noise and sparseness in time points. We deal with these limitations by proposing the Cluster and Differential Alignment Algorithm (CDAA). This algorithm was designed to process transcriptome data by first grouping genes based on stages of activity and then using similarities in gene expression to predict influential connections between individual genes. Regulatory relationships are assigned based on pairwise alignment scores generated using the expression patterns of two genes and some inferred delay between the regulator and the observed activity of the target. We applied the CDAA to an iron deficiency time course microarray dataset to identify regulators that influence 7 target transcription factors known to participate in the Arabidopsis thaliana iron deficiency response. The algorithm predicted that 7 regulators previously unlinked to iron homeostasis influence the expression of these known transcription factors. We validated over half of predicted influential relationships using qRT-PCR expression analysis in mutant backgrounds. One predicted regulator-target relationship was shown to be a direct binding interaction according to yeast one-hybrid (Y1H) analysis. These results serve as a proof of concept emphasizing the utility of the CDAA for identifying unknown or missing nodes in regulatory cascades, providing the fundamental knowledge needed for constructing predictive gene regulatory networks. We propose that this tool can be used successfully for similar time course datasets to extract additional information and infer reliable regulatory connections for individual genes. PMID:26317202

  14. Larger water clusters with edges and corners on their way to ice: structural trends elucidated with an improved parallel evolutionary algorithm.

    PubMed

    Bandow, Bernhard; Hartke, Bernd

    2006-05-04

    For the difficult task of finding global minimum energy structures for molecular clusters of nontrivial size, we present a highly efficient parallel implementation of an evolutionary algorithm. By completely abandoning the traditional concept of generations and by replacing it with a less rigid pool concept, we have managed to eliminate serial bottlenecks completely and can operate the algorithm efficiently on an arbitrary number of parallel processes. Nevertheless, our new algorithm still realizes all of the main features of our old, successful implementation. First tests of the new algorithm are shown for the highly demanding problem of water clusters modeled by a potential with flexible, polarizable monomers (TTM2-F). For this problem, our new algorithm not only reproduces all of the global minima proposed previously in considerably less CPU time but also leads to improved proposals in several cases. These, in turn, qualitatively change our earlier predictions concerning the transitions from all-surface structures to cages with a single interior molecule, and from one to two interior molecules. Furthermore, we compare preliminary results up to n = 105 with locally optimized cuts from several ice modifications. This comparison indicates that relaxed ice structures may start to be competitive already at cluster sizes above n = 90.

  15. A Neural-Network Clustering-Based Algorithm for Privacy Preserving Data Mining

    NASA Astrophysics Data System (ADS)

    Tsiafoulis, S.; Zorkadis, V. C.; Karras, D. A.

    The increasing use of fast and efficient data mining algorithms in huge collections of personal data, facilitated through the exponential growth of technology, in particular in the field of electronic data storage media and processing power, has raised serious ethical, philosophical and legal issues related to privacy protection. To cope with these concerns, several privacy preserving methodologies have been proposed, classified in two categories, methodologies that aim at protecting the sensitive data and those that aim at protecting the mining results. In our work, we focus on sensitive data protection and compare existing techniques according to their anonymity degree achieved, the information loss suffered and their performance characteristics. The ℓ-diversity principle is combined with k-anonymity concepts, so that background information can not be exploited to successfully attack the privacy of data subjects data refer to. Based on Kohonen Self Organizing Feature Maps (SOMs), we firstly organize data sets in subspaces according to their information theoretical distance to each other, then create the most relevant classes paying special attention to rare sensitive attribute values, and finally generalize attribute values to the minimum extend required so that both the data disclosure probability and the information loss are possibly kept negligible. Furthermore, we propose information theoretical measures for assessing the anonymity degree achieved and empirical tests to demonstrate it.

  16. A binned clustering algorithm to detect high-Z material using cosmic muons

    NASA Astrophysics Data System (ADS)

    Thomay, C.; Velthuis, J. J.; Baesso, P.; Cussans, D.; Morris, P. A. W.; Steer, C.; Burns, J.; Quillin, S.; Stapleton, M.

    2013-10-01

    We present a novel approach to the detection of special nuclear material using cosmic rays. Muon Scattering Tomography (MST) is a method for using cosmic muons to scan cargo containers and vehicles for special nuclear material. Cosmic muons are abundant, highly penetrating, not harmful for organic tissue, cannot be screened against, and can easily be detected, which makes them highly suited to the use of cargo scanning. Muons undergo multiple Coulomb scattering when passing through material, and the amount of scattering is roughly proportional to the square of the atomic number Z of the material. By reconstructing incoming and outgoing tracks, we can obtain variables to identify high-Z material. In a real life application, this has to happen on a timescale of 1 min and thus with small numbers of muons. We have built a detector system using resistive plate chambers (RPCs): 12 layers of RPCs allow for the readout of 6 x and 6 y positions, by which we can reconstruct incoming and outgoing tracks. In this work we detail the performance of an algorithm by which we separate high-Z targets from low-Z background, both for real data from our prototype setup and for MC simulation of a cargo container-sized setup. (c) British Crown Owned Copyright 2013/AWE

  17. CoCMA: Energy-Efficient Coverage Control in Cluster-Based Wireless Sensor Networks Using a Memetic Algorithm

    PubMed Central

    Jiang, Joe-Air; Chen, Chia-Pang; Chuang, Cheng-Long; Lin, Tzu-Shiang; Tseng, Chwan-Lu; Yang, En-Cheng; Wang, Yung-Chung

    2009-01-01

    Deployment of wireless sensor networks (WSNs) has drawn much attention in recent years. Given the limited energy for sensor nodes, it is critical to implement WSNs with energy efficiency designs. Sensing coverage in networks, on the other hand, may degrade gradually over time after WSNs are activated. For mission-critical applications, therefore, energy-efficient coverage control should be taken into consideration to support the quality of service (QoS) of WSNs. Usually, coverage-controlling strategies present some challenging problems: (1) resolving the conflicts while determining which nodes should be turned off to conserve energy; (2) designing an optimal wake-up scheme that avoids awakening more nodes than necessary. In this paper, we implement an energy-efficient coverage control in cluster-based WSNs using a Memetic Algorithm (MA)-based approach, entitled CoCMA, to resolve the challenging problems. The CoCMA contains two optimization strategies: a MA-based schedule for sensor nodes and a wake-up scheme, which are responsible to prolong the network lifetime while maintaining coverage preservation. The MA-based schedule is applied to a given WSN to avoid unnecessary energy consumption caused by the redundant nodes. During the network operation, the wake-up scheme awakens sleeping sensor nodes to recover coverage hole caused by dead nodes. The performance evaluation of the proposed CoCMA was conducted on a cluster-based WSN (CWSN) under either a random or a uniform deployment of sensor nodes. Simulation results show that the performance yielded by the combination of MA and wake-up scheme is better than that in some existing approaches. Furthermore, CoCMA is able to activate fewer sensor nodes to monitor the required sensing area. PMID:22408561

  18. On the local optimal solutions of metabolic regulatory networks using information guided genetic algorithm approach and clustering analysis.

    PubMed

    Zheng, Ying; Yeh, Chen-Wei; Yang, Chi-Da; Jang, Shi-Shang; Chu, I-Ming

    2007-08-31

    Biological information generated by high-throughput technology has made systems approach feasible for many biological problems. By this approach, optimization of metabolic pathway has been successfully applied in the amino acid production. However, in this technique, gene modifications of metabolic control architecture as well as enzyme expression levels are coupled and result in a mixed integer nonlinear programming problem. Furthermore, the stoichiometric complexity of metabolic pathway, along with strong nonlinear behaviour of the regulatory kinetic models, directs a highly rugged contour in the whole optimization problem. There may exist local optimal solutions wherein the same level of production through different flux distributions compared with global optimum. The purpose of this work is to develop a novel stochastic optimization approach-information guided genetic algorithm (IGA) to discover the local optima with different levels of modification of the regulatory loop and production rates. The novelties of this work include the information theory, local search, and clustering analysis to discover the local optima which have physical meaning among the qualified solutions.

  19. SHARAKU: an algorithm for aligning and clustering read mapping profiles of deep sequencing in non-coding RNA processing

    PubMed Central

    Tsuchiya, Mariko; Amano, Kojiro; Abe, Masaya; Seki, Misato; Hase, Sumitaka; Sato, Kengo; Sakakibara, Yasubumi

    2016-01-01

    Motivation: Deep sequencing of the transcripts of regulatory non-coding RNA generates footprints of post-transcriptional processes. After obtaining sequence reads, the short reads are mapped to a reference genome, and specific mapping patterns can be detected called read mapping profiles, which are distinct from random non-functional degradation patterns. These patterns reflect the maturation processes that lead to the production of shorter RNA sequences. Recent next-generation sequencing studies have revealed not only the typical maturation process of miRNAs but also the various processing mechanisms of small RNAs derived from tRNAs and snoRNAs. Results: We developed an algorithm termed SHARAKU to align two read mapping profiles of next-generation sequencing outputs for non-coding RNAs. In contrast with previous work, SHARAKU incorporates the primary and secondary sequence structures into an alignment of read mapping profiles to allow for the detection of common processing patterns. Using a benchmark simulated dataset, SHARAKU exhibited superior performance to previous methods for correctly clustering the read mapping profiles with respect to 5′-end processing and 3′-end processing from degradation patterns and in detecting similar processing patterns in deriving the shorter RNAs. Further, using experimental data of small RNA sequencing for the common marmoset brain, SHARAKU succeeded in identifying the significant clusters of read mapping profiles for similar processing patterns of small derived RNA families expressed in the brain. Availability and Implementation: The source code of our program SHARAKU is available at http://www.dna.bio.keio.ac.jp/sharaku/, and the simulated dataset used in this work is available at the same link. Accession code: The sequence data from the whole RNA transcripts in the hippocampus of the left brain used in this work is available from the DNA DataBank of Japan (DDBJ) Sequence Read Archive (DRA) under the accession number DRA

  20. An evaluation of ISOCLS and CLASSY clustering algorithms for forest classification in northern Idaho. [Elk River quadrange of the Clearwater National Forest

    NASA Technical Reports Server (NTRS)

    Werth, L. F. (Principal Investigator)

    1981-01-01

    Both the iterative self-organizing clustering system (ISOCLS) and the CLASSY algorithms were applied to forest and nonforest classes for one 1:24,000 quadrangle map of northern Idaho and the classification and mapping accuracies were evaluated with 1:30,000 color infrared aerial photography. Confusion matrices for the two clustering algorithms were generated and studied to determine which is most applicable to forest and rangeland inventories in future projects. In an unsupervised mode, ISOCLS requires many trial-and-error runs to find the proper parameters to separate desired information classes. CLASSY tells more in a single run concerning the classes that can be separated, shows more promise for forest stratification than ISOCLS, and shows more promise for consistency. One major drawback to CLASSY is that important forest and range classes that are smaller than a minimum cluster size will be combined with other classes. The algorithm requires so much computer storage that only data sets as small as a quadrangle can be used at one time.

  1. Automated clustering of probe molecules from solvent mapping of protein surfaces: new algorithms applied to hot-spot mapping and structure-based drug design

    NASA Astrophysics Data System (ADS)

    Lerner, Michael G.; Meagher, Kristin L.; Carlson, Heather A.

    2008-10-01

    Use of solvent mapping, based on multiple-copy minimization (MCM) techniques, is common in structure-based drug discovery. The minima of small-molecule probes define locations for complementary interactions within a binding pocket. Here, we present improved methods for MCM. In particular, a Jarvis-Patrick (JP) method is outlined for grouping the final locations of minimized probes into physical clusters. This algorithm has been tested through a study of protein-protein interfaces, showing the process to be robust, deterministic, and fast in the mapping of protein "hot spots." Improvements in the initial placement of probe molecules are also described. A final application to HIV-1 protease shows how our automated technique can be used to partition data too complicated to analyze by hand. These new automated methods may be easily and quickly extended to other protein systems, and our clustering methodology may be readily incorporated into other clustering packages.

  2. The polarimetric entropy classification of SAR based on the clustering and signal noise ration

    NASA Astrophysics Data System (ADS)

    Shi, Lei; Yang, Jie; Lang, Fengkai

    2009-10-01

    Usually, Wishart H/α/A classification is an effective unsupervised classification method. However, the anisotropy parameter (A) is an unstable factor in the low signal noise ration (SNR) areas; at the same time, many clusters are useless to manually recognize. In order to avoid too many clusters to affect the manual recognition and the convergence of iteration and aiming at the drawback of the Wishart classification, in this paper, an enhancive unsupervised Wishart classification scheme for POLSAR data sets is introduced. The anisotropy parameter A is used to subdivide the target after H/α classification, this parameter has the ability to subdivide the homogeneity area in high SNR condition which can not be classified by using H/α. It is very useful to enhance the adaptability in difficult areas. Yet, the target polarimetric decomposition is affected by SNR before the classification; thus, the local homogeneity area's SNR evaluation is necessary. After using the direction of the edge detection template to examine the direction of POL-SAR images, the results can be processed to estimate SNR. The SNR could turn to a powerful tool to guide H/α/A classification. This scheme is able to correct the mistake judging of using A parameter such as eliminating much insignificant spot on the road and urban aggregation, even having a good performance in the complex forest. To convenience the manual recognition, an agglomerative clustering algorithm basing on the method of deviation-class is used to consolidate some clusters which are similar in 3by3 polarimetric coherency matrix. This classification scheme is applied to full polarimetric L band SAR image of Foulum area, Denmark.

  3. Coulomb explosion in dicationic noble gas clusters: A genetic algorithm-based approach to critical size estimation for the suppression of Coulomb explosion and prediction of dissociation channels

    NASA Astrophysics Data System (ADS)

    Nandy, Subhajit; Chaudhury, Pinaki; Bhattacharyya, S. P.

    2010-06-01

    We present a genetic algorithm based investigation of structural fragmentation in dicationic noble gas clusters, Arn+2, Krn+2, and Xen+2, where n denotes the size of the cluster. Dications are predicted to be stable above a threshold size of the cluster when positive charges are assumed to remain localized on two noble gas atoms and the Lennard-Jones potential along with bare Coulomb and ion-induced dipole interactions are taken into account for describing the potential energy surface. Our cutoff values are close to those obtained experimentally [P. Scheier and T. D. Mark, J. Chem. Phys. 11, 3056 (1987)] and theoretically [J. G. Gay and B. J. Berne, Phys. Rev. Lett. 49, 194 (1982)]. When the charges are allowed to be equally distributed over four noble gas atoms in the cluster and the nonpolarization interaction terms are allowed to remain unchanged, our method successfully identifies the size threshold for stability as well as the nature of the channels of dissociation as function of cluster size. In Arn2+, for example, fissionlike fragmentation is predicted for n =55 while for n =43, the predicted outcome is nonfission fragmentation in complete agreement with earlier work [Golberg et al., J. Chem. Phys. 100, 8277 (1994)].

  4. Cluster analysis of long time-series medical datasets

    NASA Astrophysics Data System (ADS)

    Hirano, Shoji; Tsumoto, Shusaku

    2004-04-01

    This paper presents a comparative study about the characteristics of clustering methods for inhomogeneous time-series medical datasets. Using various combinations of comparison methods and grouping methods, we performed clustering experiments of the hepatitis data set and evaluated validity of the results. The results suggested that (1) complete-linkage (CL) criterion in agglomerative hierarchical clustering (AHC) outperformed average-linkage (AL) criterion in terms of the interpretability of a dendrogram and clustering results, (2) combination of dynamic time warping (DTW) and CL-AHC constantly produced interpretable results, (3) combination of DTW and rough clustering (RC) would be used to find the core sequences of the clusters, (4) multiscale matching may suffer from the treatment of 'no-match' pairs, however, the problem may be eluded by using RC as a subsequent grouping method.

  5. Structural, spectroscopic aspects, and electronic properties of (TiO2)n clusters: a study based on the use of natural algorithms in association with quantum chemical methods.

    PubMed

    Ganguly Neogi, Soumya; Chaudhury, Pinaki

    2014-01-05

    In this article, we propose a stochastic search-based method, namely genetic algorithm (GA) and simulated annealing (SA) in conjunction with density functional theory (DFT) to evaluate global and local minimum structures of (TiO2)n clusters with n = 1-12. Once the structures are established, we evaluate the infrared spectroscopic modes, cluster formation energy, vertical excitation energy, vertical ionization potential, vertical electron affinity, highest occupied molecular orbital (HOMO)-lowest unoccupied molecular orbital (LUMO) gaps, and so forth. We show that an initial determination of structure using stochastic techniques (GA/SA), also popularly known as natural algorithms as their working principle mimics certain natural processes, and following it up with density functional calculations lead to high-quality structures for these systems. We have shown that the clusters tend to form three-dimensional networks. We compare our results with the available experimental and theoretical results. The results obtained from SA/GA-DFT technique agree well with available theoretical and experimental data of literature.

  6. An Effective Approach for Clustering InhA Molecular Dynamics Trajectory Using Substrate-Binding Cavity Features.

    PubMed

    De Paris, Renata; Quevedo, Christian V; Ruiz, Duncan D A; Norberto de Souza, Osmar

    2015-01-01

    Protein receptor conformations, obtained from molecular dynamics (MD) simulations, have become a promising treatment of its explicit flexibility in molecular docking experiments applied to drug discovery and development. However, incorporating the entire ensemble of MD conformations in docking experiments to screen large candidate compound libraries is currently an unfeasible task. Clustering algorithms have been widely used as a means to reduce such ensembles to a manageable size. Most studies investigate different algorithms using pairwise Root-Mean Square Deviation (RMSD) values for all, or part of the MD conformations. Nevertheless, the RMSD only may not be the most appropriate gauge to cluster conformations when the target receptor has a plastic active site, since they are influenced by changes that occur on other parts of the structure. Hence, we have applied two partitioning methods (k-means and k-medoids) and four agglomerative hierarchical methods (Complete linkage, Ward's, Unweighted Pair Group Method and Weighted Pair Group Method) to analyze and compare the quality of partitions between a data set composed of properties from an enzyme receptor substrate-binding cavity and two data sets created using different RMSD approaches. Ensembles of representative MD conformations were generated by selecting a medoid of each group from all partitions analyzed. We investigated the performance of our new method for evaluating binding conformation of drug candidates to the InhA enzyme, which were performed by cross-docking experiments between a 20 ns MD trajectory and 20 different ligands. Statistical analyses showed that the novel ensemble, which is represented by only 0.48% of the MD conformations, was able to reproduce 75% of all dynamic behaviors within the binding cavity for the docking experiments performed. Moreover, this new approach not only outperforms the other two RMSD-clustering solutions, but it also shows to be a promising strategy to distill

  7. An Effective Approach for Clustering InhA Molecular Dynamics Trajectory Using Substrate-Binding Cavity Features

    PubMed Central

    Ruiz, Duncan D. A.; Norberto de Souza, Osmar

    2015-01-01

    Protein receptor conformations, obtained from molecular dynamics (MD) simulations, have become a promising treatment of its explicit flexibility in molecular docking experiments applied to drug discovery and development. However, incorporating the entire ensemble of MD conformations in docking experiments to screen large candidate compound libraries is currently an unfeasible task. Clustering algorithms have been widely used as a means to reduce such ensembles to a manageable size. Most studies investigate different algorithms using pairwise Root-Mean Square Deviation (RMSD) values for all, or part of the MD conformations. Nevertheless, the RMSD only may not be the most appropriate gauge to cluster conformations when the target receptor has a plastic active site, since they are influenced by changes that occur on other parts of the structure. Hence, we have applied two partitioning methods (k-means and k-medoids) and four agglomerative hierarchical methods (Complete linkage, Ward’s, Unweighted Pair Group Method and Weighted Pair Group Method) to analyze and compare the quality of partitions between a data set composed of properties from an enzyme receptor substrate-binding cavity and two data sets created using different RMSD approaches. Ensembles of representative MD conformations were generated by selecting a medoid of each group from all partitions analyzed. We investigated the performance of our new method for evaluating binding conformation of drug candidates to the InhA enzyme, which were performed by cross-docking experiments between a 20 ns MD trajectory and 20 different ligands. Statistical analyses showed that the novel ensemble, which is represented by only 0.48% of the MD conformations, was able to reproduce 75% of all dynamic behaviors within the binding cavity for the docking experiments performed. Moreover, this new approach not only outperforms the other two RMSD-clustering solutions, but it also shows to be a promising strategy to distill

  8. Information Clustering Based on Fuzzy Multisets.

    ERIC Educational Resources Information Center

    Miyamoto, Sadaaki

    2003-01-01

    Proposes a fuzzy multiset model for information clustering with application to information retrieval on the World Wide Web. Highlights include search engines; term clustering; document clustering; algorithms for calculating cluster centers; theoretical properties concerning clustering algorithms; and examples to show how the algorithms work.…

  9. The tensor hypercontracted parametric reduced density matrix algorithm: coupled-cluster accuracy with O(r(4)) scaling.

    PubMed

    Shenvi, Neil; van Aggelen, Helen; Yang, Yang; Yang, Weitao; Schwerdtfeger, Christine; Mazziotti, David

    2013-08-07

    Tensor hypercontraction is a method that allows the representation of a high-rank tensor as a product of lower-rank tensors. In this paper, we show how tensor hypercontraction can be applied to both the electron repulsion integral tensor and the two-particle excitation amplitudes used in the parametric 2-electron reduced density matrix (p2RDM) algorithm. Because only O(r) auxiliary functions are needed in both of these approximations, our overall algorithm can be shown to scale as O(r(4)), where r is the number of single-particle basis functions. We apply our algorithm to several small molecules, hydrogen chains, and alkanes to demonstrate its low formal scaling and practical utility. Provided we use enough auxiliary functions, we obtain accuracy similar to that of the standard p2RDM algorithm, somewhere between that of CCSD and CCSD(T).

  10. A comparative analysis of clustering algorithms: O{sub 2} migration in truncated hemoglobin I from transition networks

    SciTech Connect

    Cazade, Pierre-André; Berezovska, Ganna; Meuwly, Markus; Zheng, Wenwei; Clementi, Cecilia; Prada-Gracia, Diego; Rao, Francesco

    2015-01-14

    The ligand migration network for O{sub 2}–diffusion in truncated Hemoglobin N is analyzed based on three different clustering schemes. For coordinate-based clustering, the conventional k–means and the kinetics-based Markov Clustering (MCL) methods are employed, whereas the locally scaled diffusion map (LSDMap) method is a collective-variable-based approach. It is found that all three methods agree well in their geometrical definition of the most important docking site, and all experimentally known docking sites are recovered by all three methods. Also, for most of the states, their population coincides quite favourably, whereas the kinetics of and between the states differs. One of the major differences between k–means and MCL clustering on the one hand and LSDMap on the other is that the latter finds one large primary cluster containing the Xe1a, IS1, and ENT states. This is related to the fact that the motion within the state occurs on similar time scales, whereas structurally the state is found to be quite diverse. In agreement with previous explicit atomistic simulations, the Xe3 pocket is found to be a highly dynamical site which points to its potential role as a hub in the network. This is also highlighted in the fact that LSDMap cannot identify this state. First passage time distributions from MCL clusterings using a one- (ligand-position) and two-dimensional (ligand-position and protein-structure) descriptor suggest that ligand- and protein-motions are coupled. The benefits and drawbacks of the three methods are discussed in a comparative fashion and highlight that depending on the questions at hand the best-performing method for a particular data set may differ.

  11. Knowledge discovery from patients’ behavior via clustering-classification algorithms based on weighted eRFM and CLV model: An empirical study in public health care services

    PubMed Central

    Zare Hosseini, Zeinab; Mohammadzadeh, Mahdi

    2016-01-01

    The rapid growing of information technology (IT) motivates and makes competitive advantages in health care industry. Nowadays, many hospitals try to build a successful customer relationship management (CRM) to recognize target and potential patients, increase patient loyalty and satisfaction and finally maximize their profitability. Many hospitals have large data warehouses containing customer demographic and transactions information. Data mining techniques can be used to analyze this data and discover hidden knowledge of customers. This research develops an extended RFM model, namely RFML (added parameter: Length) based on health care services for a public sector hospital in Iran with the idea that there is contrast between patient and customer loyalty, to estimate customer life time value (CLV) for each patient. We used Two-step and K-means algorithms as clustering methods and Decision tree (CHAID) as classification technique to segment the patients to find out target, potential and loyal customers in order to implement strengthen CRM. Two approaches are used for classification: first, the result of clustering is considered as Decision attribute in classification process and second, the result of segmentation based on CLV value of patients (estimated by RFML) is considered as Decision attribute. Finally the results of CHAID algorithm show the significant hidden rules and identify existing patterns of hospital consumers. PMID:27610177

  12. Computerized Segmentation and Characterization of Breast Lesions in Dynamic Contrast-Enhanced MR Images Using Fuzzy c-Means Clustering and Snake Algorithm

    PubMed Central

    Pang, Yachun; Li, Li; Hu, Wenyong; Peng, Yanxia; Liu, Lizhi; Shao, Yuanzhi

    2012-01-01

    This paper presents a novel two-step approach that incorporates fuzzy c-means (FCMs) clustering and gradient vector flow (GVF) snake algorithm for lesions contour segmentation on breast magnetic resonance imaging (BMRI). Manual delineation of the lesions by expert MR radiologists was taken as a reference standard in evaluating the computerized segmentation approach. The proposed algorithm was also compared with the FCMs clustering based method. With a database of 60 mass-like lesions (22 benign and 38 malignant cases), the proposed method demonstrated sufficiently good segmentation performance. The morphological and texture features were extracted and used to classify the benign and malignant lesions based on the proposed computerized segmentation contour and radiologists' delineation, respectively. Features extracted by the computerized characterization method were employed to differentiate the lesions with an area under the receiver-operating characteristic curve (AUC) of 0.968, in comparison with an AUC of 0.914 based on the features extracted from radiologists' delineation. The proposed method in current study can assist radiologists to delineate and characterize BMRI lesion, such as quantifying morphological and texture features and improving the objectivity and efficiency of BMRI interpretation with a certain clinical value. PMID:22952558

  13. SWIFT-scalable clustering for automated identification of rare cell populations in large, high-dimensional flow cytometry datasets, part 1: algorithm design.

    PubMed

    Naim, Iftekhar; Datta, Suprakash; Rebhahn, Jonathan; Cavenaugh, James S; Mosmann, Tim R; Sharma, Gaurav

    2014-05-01

    We present a model-based clustering method, SWIFT (Scalable Weighted Iterative Flow-clustering Technique), for digesting high-dimensional large-sized datasets obtained via modern flow cytometry into more compact representations that are well-suited for further automated or manual analysis. Key attributes of the method include the following: (a) the analysis is conducted in the multidimensional space retaining the semantics of the data, (b) an iterative weighted sampling procedure is utilized to maintain modest computational complexity and to retain discrimination of extremely small subpopulations (hundreds of cells from datasets containing tens of millions), and (c) a splitting and merging procedure is incorporated in the algorithm to preserve distinguishability between biologically distinct populations, while still providing a significant compaction relative to the original data. This article presents a detailed algorithmic description of SWIFT, outlining the application-driven motivations for the different design choices, a discussion of computational complexity of the different steps, and results obtained with SWIFT for synthetic data and relatively simple experimental data that allow validation of the desirable attributes. A companion paper (Part 2) highlights the use of SWIFT, in combination with additional computational tools, for more challenging biological problems.

  14. SWIFT—Scalable Clustering for Automated Identification of Rare Cell Populations in Large, High-Dimensional Flow Cytometry Datasets, Part 1: Algorithm Design

    PubMed Central

    Naim, Iftekhar; Datta, Suprakash; Rebhahn, Jonathan; Cavenaugh, James S; Mosmann, Tim R; Sharma, Gaurav

    2014-01-01

    We present a model-based clustering method, SWIFT (Scalable Weighted Iterative Flow-clustering Technique), for digesting high-dimensional large-sized datasets obtained via modern flow cytometry into more compact representations that are well-suited for further automated or manual analysis. Key attributes of the method include the following: (a) the analysis is conducted in the multidimensional space retaining the semantics of the data, (b) an iterative weighted sampling procedure is utilized to maintain modest computational complexity and to retain discrimination of extremely small subpopulations (hundreds of cells from datasets containing tens of millions), and (c) a splitting and merging procedure is incorporated in the algorithm to preserve distinguishability between biologically distinct populations, while still providing a significant compaction relative to the original data. This article presents a detailed algorithmic description of SWIFT, outlining the application-driven motivations for the different design choices, a discussion of computational complexity of the different steps, and results obtained with SWIFT for synthetic data and relatively simple experimental data that allow validation of the desirable attributes. A companion paper (Part 2) highlights the use of SWIFT, in combination with additional computational tools, for more challenging biological problems. © 2014 The Authors. Published by Wiley Periodicals Inc. PMID:24677621

  15. Knowledge discovery from patients' behavior via clustering-classification algorithms based on weighted eRFM and CLV model: An empirical study in public health care services.

    PubMed

    Zare Hosseini, Zeinab; Mohammadzadeh, Mahdi

    2016-01-01

    The rapid growing of information technology (IT) motivates and makes competitive advantages in health care industry. Nowadays, many hospitals try to build a successful customer relationship management (CRM) to recognize target and potential patients, increase patient loyalty and satisfaction and finally maximize their profitability. Many hospitals have large data warehouses containing customer demographic and transactions information. Data mining techniques can be used to analyze this data and discover hidden knowledge of customers. This research develops an extended RFM model, namely RFML (added parameter: Length) based on health care services for a public sector hospital in Iran with the idea that there is contrast between patient and customer loyalty, to estimate customer life time value (CLV) for each patient. We used Two-step and K-means algorithms as clustering methods and Decision tree (CHAID) as classification technique to segment the patients to find out target, potential and loyal customers in order to implement strengthen CRM. Two approaches are used for classification: first, the result of clustering is considered as Decision attribute in classification process and second, the result of segmentation based on CLV value of patients (estimated by RFML) is considered as Decision attribute. Finally the results of CHAID algorithm show the significant hidden rules and identify existing patterns of hospital consumers.

  16. Algorithm for the direct reconstruction of the dark matter correlation function from weak lensing and galaxy clustering

    SciTech Connect

    Baldauf, Tobias; Smith, Robert E.; Seljak, Uros; Mandelbaum, Rachel

    2010-03-15

    The clustering of matter on cosmological scales is an essential probe for studying the physical origin and composition of our Universe. To date, most of the direct studies have focused on shear-shear weak lensing correlations, but it is also possible to extract the dark matter clustering by combining galaxy-clustering and galaxy-galaxy-lensing measurements. In order to extract the required information, one must relate the observable galaxy distribution to the underlying dark matter distribution. In this study we develop in detail a method that can constrain the dark matter correlation function from galaxy clustering and galaxy-galaxy-lensing measurements, by focusing on the correlation coefficient between the galaxy and matter overdensity fields. Our goal is to develop an estimator that maximally correlates the two. To generate a mock galaxy catalogue for testing purposes, we use the halo occupation distribution approach applied to a large ensemble of N-body simulations to model preexisting SDSS luminous red galaxy sample observations. Using this mock catalogue, we show that a direct comparison between the excess surface mass density measured by lensing and its corresponding galaxy clustering quantity is not optimal. We develop a new statistic that suppresses the small-scale contributions to these observations and show that this new statistic leads to a cross-correlation coefficient that is within a few percent of unity down to 5h{sup -1} Mpc. Furthermore, the residual incoherence between the galaxy and matter fields can be explained using a theoretical model for scale-dependent galaxy bias, giving us a final estimator that is unbiased to within 1%, so that we can reconstruct the dark matter clustering power spectrum at this accuracy up to k{approx}1h Mpc{sup -1}. We also perform a comprehensive study of other physical effects that can affect the analysis, such as redshift space distortions and differences in radial windows between galaxy clustering and weak

  17. A new clustering strategy

    NASA Astrophysics Data System (ADS)

    Feng, Jian-xin; Tang, Jia-fu; Wang, Guang-xing

    2007-04-01

    On the basis of the analysis of clustering algorithm that had been proposed for MANET, a novel clustering strategy was proposed in this paper. With the trust defined by statistical hypothesis in probability theory and the cluster head selected by node trust and node mobility, this strategy can realize the function of the malicious nodes detection which was neglected by other clustering algorithms and overcome the deficiency of being incapable of implementing the relative mobility metric of corresponding nodes in the MOBIC algorithm caused by the fact that the receiving power of two consecutive HELLO packet cannot be measured. It's an effective solution to cluster MANET securely.

  18. Image-derived input function derived from a supervised clustering algorithm: methodology and validation in a clinical protocol using [11C](R)-rolipram.

    PubMed

    Lyoo, Chul Hyoung; Zanotti-Fregonara, Paolo; Zoghbi, Sami S; Liow, Jeih-San; Xu, Rong; Pike, Victor W; Zarate, Carlos A; Fujita, Masahiro; Innis, Robert B

    2014-01-01

    Image-derived input function (IDIF) obtained by manually drawing carotid arteries (manual-IDIF) can be reliably used in [(11)C](R)-rolipram positron emission tomography (PET) scans. However, manual-IDIF is time consuming and subject to inter- and intra-operator variability. To overcome this limitation, we developed a fully automated technique for deriving IDIF with a supervised clustering algorithm (SVCA). To validate this technique, 25 healthy controls and 26 patients with moderate to severe major depressive disorder (MDD) underwent T1-weighted brain magnetic resonance imaging (MRI) and a 90-minute [(11)C](R)-rolipram PET scan. For each subject, metabolite-corrected input function was measured from the radial artery. SVCA templates were obtained from 10 additional healthy subjects who underwent the same MRI and PET procedures. Cluster-IDIF was obtained as follows: 1) template mask images were created for carotid and surrounding tissue; 2) parametric image of weights for blood were created using SVCA; 3) mask images to the individual PET image were inversely normalized; 4) carotid and surrounding tissue time activity curves (TACs) were obtained from weighted and unweighted averages of each voxel activity in each mask, respectively; 5) partial volume effects and radiometabolites were corrected using individual arterial data at four points. Logan-distribution volume (V T/f P) values obtained by cluster-IDIF were similar to reference results obtained using arterial data, as well as those obtained using manual-IDIF; 39 of 51 subjects had a V T/f P error of <5%, and only one had error >10%. With automatic voxel selection, cluster-IDIF curves were less noisy than manual-IDIF and free of operator-related variability. Cluster-IDIF showed widespread decrease of about 20% [(11)C](R)-rolipram binding in the MDD group. Taken together, the results suggest that cluster-IDIF is a good alternative to full arterial input function for estimating Logan-V T/f P in [(11)C

  19. Image-Derived Input Function Derived from a Supervised Clustering Algorithm: Methodology and Validation in a Clinical Protocol Using [11C](R)-Rolipram

    PubMed Central

    Zoghbi, Sami S.; Liow, Jeih-San; Xu, Rong; Pike, Victor W.; Zarate, Carlos A.; Fujita, Masahiro; Innis, Robert B.

    2014-01-01

    Image-derived input function (IDIF) obtained by manually drawing carotid arteries (manual-IDIF) can be reliably used in [11C](R)-rolipram positron emission tomography (PET) scans. However, manual-IDIF is time consuming and subject to inter- and intra-operator variability. To overcome this limitation, we developed a fully automated technique for deriving IDIF with a supervised clustering algorithm (SVCA). To validate this technique, 25 healthy controls and 26 patients with moderate to severe major depressive disorder (MDD) underwent T1-weighted brain magnetic resonance imaging (MRI) and a 90-minute [11C](R)-rolipram PET scan. For each subject, metabolite-corrected input function was measured from the radial artery. SVCA templates were obtained from 10 additional healthy subjects who underwent the same MRI and PET procedures. Cluster-IDIF was obtained as follows: 1) template mask images were created for carotid and surrounding tissue; 2) parametric image of weights for blood were created using SVCA; 3) mask images to the individual PET image were inversely normalized; 4) carotid and surrounding tissue time activity curves (TACs) were obtained from weighted and unweighted averages of each voxel activity in each mask, respectively; 5) partial volume effects and radiometabolites were corrected using individual arterial data at four points. Logan-distribution volume (VT/fP) values obtained by cluster-IDIF were similar to reference results obtained using arterial data, as well as those obtained using manual-IDIF; 39 of 51 subjects had a VT/fP error of <5%, and only one had error >10%. With automatic voxel selection, cluster-IDIF curves were less noisy than manual-IDIF and free of operator-related variability. Cluster-IDIF showed widespread decrease of about 20% [11C](R)-rolipram binding in the MDD group. Taken together, the results suggest that cluster-IDIF is a good alternative to full arterial input function for estimating Logan-VT/fP in [11C](R)-rolipram PET clinical

  20. Optimal wavelength band clustering for multispectral iris recognition.

    PubMed

    Gong, Yazhuo; Zhang, David; Shi, Pengfei; Yan, Jingqi

    2012-07-01

    This work explores the possibility of clustering spectral wavelengths based on the maximum dissimilarity of iris textures. The eventual goal is to determine how many bands of spectral wavelengths will be enough for iris multispectral fusion and to find these bands that will provide higher performance of iris multispectral recognition. A multispectral acquisition system was first designed for imaging the iris at narrow spectral bands in the range of 420 to 940 nm. Next, a set of 60 human iris images that correspond to the right and left eyes of 30 different subjects were acquired for an analysis. Finally, we determined that 3 clusters were enough to represent the 10 feature bands of spectral wavelengths using the agglomerative clustering based on two-dimensional principal component analysis. The experimental results suggest (1) the number, center, and composition of clusters of spectral wavelengths and (2) the higher performance of iris multispectral recognition based on a three wavelengths-bands fusion.

  1. Using cluster analysis of cytokines to identify patterns of inflammation in hospitalized patients with community-acquired pneumonia: a pilot study

    PubMed Central

    Wiemken, Timothy L; Kelley, Robert R; Fernandez-Botran, Rafael; Mattingly, William A.; Arnold, Forest W.; Furmanek, Stephen P; Restrepo, Marcos I; Chalmers, James D; Peyrani, Paula; Cavallazzi, Rodrigo; Bordon, Jose; Aliberti, Stefano; Ramirez, Julio A.

    2017-01-01

    Introduction Patients with severe community-acquired pneumonia (CAP) are believed to have an exaggerated inflammatory response to bacterial infection. Therapies aiming to modulate the inflammatory response have been largely unsuccessful, perhaps reflecting that CAP is a heterogeneous disorder that cannot be modulated by a single anti-inflammatory approach. We hypothesize that the host inflammatory response to pneumonia may be characterized by distinct cytokine patterns, which can be harnessed for personalized therapies. Methods Here, we use hierarchical cluster analysis of cytokines to examine if patterns of inflammatory response in 13 hospitalized patients with CAP can be defined. This was a secondary data analysis of the Community-Acquired Pneumonia Inflammatory Study Group (CAPISG) database. The following cytokines were measured in plasma and sputum on the day of admission: interleukin (IL)-1β, IL-1 receptor antagonist (IL-1ra), IL-6, CXCL8 (IL-8), IL-10, IL-12p40, IL-17, interferon (IFN)γ, tumor necrosis factor (TNF)α, and CXCL10 (IP-10). Hierarchical agglomerative clustering algorithms were used to evaluate clusters of patients within plasma and sputum cytokine determinations. Results A total of thirteen patients were included in this pilot study. Cluster analysis identified distinct inflammatory response patterns of cytokines in the plasma, sputum, and the ratio of plasma to sputum. Conclusions Inflammatory response patterns in plasma and sputum can be identified in hospitalized patients with CAP. Characterization of the local and systemic inflammatory response may help to better discriminate patients for enrollment into clinical trials of immunomodulatory therapies. PMID:28393141

  2. Identification of column edges of DNA fragments by using K-means clustering and mean algorithm on lane histograms of DNA agarose gel electrophoresis images

    NASA Astrophysics Data System (ADS)

    Turan, Muhammed K.; Sehirli, Eftal; Elen, Abdullah; Karas, Ismail R.

    2015-07-01

    Gel electrophoresis (GE) is one of the most used method to separate DNA, RNA, protein molecules according to size, weight and quantity parameters in many areas such as genetics, molecular biology, biochemistry, microbiology. The main way to separate each molecule is to find borders of each molecule fragment. This paper presents a software application that show columns edges of DNA fragments in 3 steps. In the first step the application obtains lane histograms of agarose gel electrophoresis images by doing projection based on x-axis. In the second step, it utilizes k-means clustering algorithm to classify point values of lane histogram such as left side values, right side values and undesired values. In the third step, column edges of DNA fragments is shown by using mean algorithm and mathematical processes to separate DNA fragments from the background in a fully automated way. In addition to this, the application presents locations of DNA fragments and how many DNA fragments exist on images captured by a scientific camera.

  3. Analysis of Parallel Algorithms on SMP Node and Cluster of Workstations Using Parallel Programming Models with New Tile-based Method for Large Biological Datasets

    PubMed Central

    Shrimankar, D. D.; Sathe, S. R.

    2016-01-01

    Sequence alignment is an important tool for describing the relationships between DNA sequences. Many sequence alignment algorithms exist, differing in efficiency, in their models of the sequences, and in the relationship between sequences. The focus of this study is to obtain an optimal alignment between two sequences of biological data, particularly DNA sequences. The algorithm is discussed with particular emphasis on time, speedup, and efficiency optimizations. Parallel programming presents a number of critical challenges to application developers. Today’s supercomputer often consists of clusters of SMP nodes. Programming paradigms such as OpenMP and MPI are used to write parallel codes for such architectures. However, the OpenMP programs cannot be scaled for more than a single SMP node. However, programs written in MPI can have more than single SMP nodes. But such a programming paradigm has an overhead of internode communication. In this work, we explore the tradeoffs between using OpenMP and MPI. We demonstrate that the communication overhead incurs significantly even in OpenMP loop execution and increases with the number of cores participating. We also demonstrate a communication model to approximate the overhead from communication in OpenMP loops. Our results are astonishing and interesting to a large variety of input data files. We have developed our own load balancing and cache optimization technique for message passing model. Our experimental results show that our own developed techniques give optimum performance of our parallel algorithm for various sizes of input parameter, such as sequence size and tile size, on a wide variety of multicore architectures. PMID:27932868

  4. Analysis of Parallel Algorithms on SMP Node and Cluster of Workstations Using Parallel Programming Models with New Tile-based Method for Large Biological Datasets.

    PubMed

    Shrimankar, D D; Sathe, S R

    2016-01-01

    Sequence alignment is an important tool for describing the relationships between DNA sequences. Many sequence alignment algorithms exist, differing in efficiency, in their models of the sequences, and in the relationship between sequences. The focus of this study is to obtain an optimal alignment between two sequences of biological data, particularly DNA sequences. The algorithm is discussed with particular emphasis on time, speedup, and efficiency optimizations. Parallel programming presents a number of critical challenges to application developers. Today's supercomputer often consists of clusters of SMP nodes. Programming paradigms such as OpenMP and MPI are used to write parallel codes for such architectures. However, the OpenMP programs cannot be scaled for more than a single SMP node. However, programs written in MPI can have more than single SMP nodes. But such a programming paradigm has an overhead of internode communication. In this work, we explore the tradeoffs between using OpenMP and MPI. We demonstrate that the communication overhead incurs significantly even in OpenMP loop execution and increases with the number of cores participating. We also demonstrate a communication model to approximate the overhead from communication in OpenMP loops. Our results are astonishing and interesting to a large variety of input data files. We have developed our own load balancing and cache optimization technique for message passing model. Our experimental results show that our own developed techniques give optimum performance of our parallel algorithm for various sizes of input parameter, such as sequence size and tile size, on a wide variety of multicore architectures.

  5. An infared polarization image fusion method based on NSCT and fuzzy C-means clustering segmentation algorithms

    NASA Astrophysics Data System (ADS)

    Yu, Xuelian; Chen, Qian; Gu, Guohua; Qian, Weixian; Xu, Mengxi

    2014-11-01

    The integration between polarization and intensity images possessing complementary and discriminative information has emerged as a new and important research area. On the basis of the consideration that the resulting image has different clarity and layering requirement for the target and background, we propose a novel fusion method based on non-subsampled Contourlet transform (NSCT) and fuzzy C-means (FCM) segmentation for IR polarization and light intensity images. First, the polarization characteristic image is derived from fusion of the degree of polarization (DOP) and the angle of polarization (AOP) images using local standard variation and abrupt change degree (ACD) combined criteria. Then, the polarization characteristic image is segmented with FCM algorithm. Meanwhile, the two source images are respectively decomposed by NSCT. The regional energy-weighted and similarity measure are adopted to combine the low-frequency sub-band coefficients of the object. The high-frequency sub-band coefficients of the object boundaries are integrated through the maximum selection rule. In addition, the high-frequency sub-band coefficients of internal objects are integrated by utilizing local variation, matching measure and region feature weighting. The weighted average and maximum rules are employed independently in fusing the low-frequency and high-frequency components of the background. Finally, an inverse NSCT operation is accomplished and the final fused image is obtained. The experimental results illustrate that the proposed IR polarization image fusion algorithm can yield an improved performance in terms of the contrast between artificial target and cluttered background and a more detailed representation of the depicted scene.

  6. Geomorphological activity at a rock glacier front detected with a 3D density-based clustering algorithm

    NASA Astrophysics Data System (ADS)

    Micheletti, Natan; Tonini, Marj; Lane, Stuart N.

    2017-02-01

    Acquisition of high density point clouds using terrestrial laser scanners (TLSs) has become commonplace in geomorphic science. The derived point clouds are often interpolated onto regular grids and the grids compared to detect change (i.e. erosion and deposition/advancement movements). This procedure is necessary for some applications (e.g. digital terrain analysis), but it inevitably leads to a certain loss of potentially valuable information contained within the point clouds. In the present study, an alternative methodology for geomorphological analysis and feature detection from point clouds is proposed. It rests on the use of the Density-Based Spatial Clustering of Applications with Noise (DBSCAN), applied to TLS data for a rock glacier front slope in the Swiss Alps. The proposed methods allowed the detection and isolation of movements directly from point clouds which yield to accuracies in the following computation of volumes that depend only on the actual registered distance between points. We demonstrated that these values are more conservative than volumes computed with the traditional DEM comparison. The results are illustrated for the summer of 2015, a season of enhanced geomorphic activity associated with exceptionally high temperatures.

  7. Adaptive Clustering of Hypermedia Documents.

    ERIC Educational Resources Information Center

    Johnson, Andrew; Fotouhi, Farshad

    1996-01-01

    Discussion of hypermedia systems focuses on a comparison of two types of adaptive algorithm (genetic algorithm and neural network) in clustering hypermedia documents. These clusters allow the user to index into the nodes to find needed information more quickly, since clustering is "personalized" based on the user's paths rather than…

  8. Matlab Cluster Ensemble Toolbox

    SciTech Connect

    Sapio, Vincent De; Kegelmeyer, Philip

    2009-04-27

    This is a Matlab toolbox for investigating the application of cluster ensembles to data classification, with the objective of improving the accuracy and/or speed of clustering. The toolbox divides the cluster ensemble problem into four areas, providing functionality for each. These include, (1) synthetic data generation, (2) clustering to generate individual data partitions and similarity matrices, (3) consensus function generation and final clustering to generate ensemble data partitioning, and (4) implementation of accuracy metrics. With regard to data generation, Gaussian data of arbitrary dimension can be generated. The kcenters algorithm can then be used to generate individual data partitions by either, (a) subsampling the data and clustering each subsample, or by (b) randomly initializing the algorithm and generating a clustering for each initialization. In either case an overall similarity matrix can be computed using a consensus function operating on the individual similarity matrices. A final clustering can be performed and performance metrics are provided for evaluation purposes.

  9. Development of a radiation track structure clustering algorithm for the prediction of DNA DSB yields and radiation induced cell death in Eukaryotic cells.

    PubMed

    Douglass, Michael; Bezak, Eva; Penfold, Scott

    2015-04-21

    The preliminary framework of a combined radiobiological model is developed and calibrated in the current work. The model simulates the production of individual cells forming a tumour, the spatial distribution of individual ionization events (using Geant4-DNA) and the stochastic biochemical repair of DNA double strand breaks (DSBs) leading to the prediction of survival or death of individual cells. In the current work, we expand upon a previously developed tumour generation and irradiation model to include a stochastic ionization damage clustering and DNA lesion repair model. The Geant4 code enabled the positions of each ionization event in the cells to be simulated and recorded for analysis. An algorithm was developed to cluster the ionization events in each cell into simple and complex double strand breaks. The two lesion kinetic (TLK) model was then adapted to predict DSB repair kinetics and the resultant cell survival curve. The parameters in the cell survival model were then calibrated using experimental cell survival data of V79 cells after low energy proton irradiation. A monolayer of V79 cells was simulated using the tumour generation code developed previously. The cells were then irradiated by protons with mean energies of 0.76 MeV and 1.9 MeV using a customized version of Geant4. By replicating the experimental parameters of a low energy proton irradiation experiment and calibrating the model with two sets of data, the model is now capable of predicting V79 cell survival after low energy (<2 MeV) proton irradiation for a custom set of input parameters. The novelty of this model is the realistic cellular geometry which can be irradiated using Geant4-DNA and the method in which the double strand breaks are predicted from clustering the spatial distribution of ionisation events. Unlike the original TLK model which calculates a tumour average cell survival probability, the cell survival probability is calculated for each cell in the geometric tumour model

  10. CUDA programs for the GPU computing of the Swendsen-Wang multi-cluster spin flip algorithm: 2D and 3D Ising, Potts, and XY models

    NASA Astrophysics Data System (ADS)

    Komura, Yukihiro; Okabe, Yutaka

    2014-03-01

    We present sample CUDA programs for the GPU computing of the Swendsen-Wang multi-cluster spin flip algorithm. We deal with the classical spin models; the Ising model, the q-state Potts model, and the classical XY model. As for the lattice, both the 2D (square) lattice and the 3D (simple cubic) lattice are treated. We already reported the idea of the GPU implementation for 2D models (Komura and Okabe, 2012). We here explain the details of sample programs, and discuss the performance of the present GPU implementation for the 3D Ising and XY models. We also show the calculated results of the moment ratio for these models, and discuss phase transitions. Catalogue identifier: AERM_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AERM_v1_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 5632 No. of bytes in distributed program, including test data, etc.: 14688 Distribution format: tar.gz Programming language: C, CUDA. Computer: System with an NVIDIA CUDA enabled GPU. Operating system: System with an NVIDIA CUDA enabled GPU. Classification: 23. External routines: NVIDIA CUDA Toolkit 3.0 or newer Nature of problem: Monte Carlo simulation of classical spin systems. Ising, q-state Potts model, and the classical XY model are treated for both two-dimensional and three-dimensional lattices. Solution method: GPU-based Swendsen-Wang multi-cluster spin flip Monte Carlo method. The CUDA implementation for the cluster-labeling is based on the work by Hawick et al. [1] and that by Kalentev et al. [2]. Restrictions: The system size is limited depending on the memory of a GPU. Running time: For the parameters used in the sample programs, it takes about a minute for each program. Of course, it depends on the system size, the number of Monte Carlo steps, etc. References: [1] K

  11. Development of a radiation track structure clustering algorithm for the prediction of DNA DSB yields and radiation induced cell death in Eukaryotic cells

    NASA Astrophysics Data System (ADS)

    Douglass, Michael; Bezak, Eva; Penfold, Scott

    2015-04-01

    The preliminary framework of a combined radiobiological model is developed and calibrated in the current work. The model simulates the production of individual cells forming a tumour, the spatial distribution of individual ionization events (using Geant4-DNA) and the stochastic biochemical repair of DNA double strand breaks (DSBs) leading to the prediction of survival or death of individual cells. In the current work, we expand upon a previously developed tumour generation and irradiation model to include a stochastic ionization damage clustering and DNA lesion repair model. The Geant4 code enabled the positions of each ionization event in the cells to be simulated and recorded for analysis. An algorithm was developed to cluster the ionization events in each cell into simple and complex double strand breaks. The two lesion kinetic (TLK) model was then adapted to predict DSB repair kinetics and the resultant cell survival curve. The parameters in the cell survival model were then calibrated using experimental cell survival data of V79 cells after low energy proton irradiation. A monolayer of V79 cells was simulated using the tumour generation code developed previously. The cells were then irradiated by protons with mean energies of 0.76 MeV and 1.9 MeV using a customized version of Geant4. By replicating the experimental parameters of a low energy proton irradiation experiment and calibrating the model with two sets of data, the model is now capable of predicting V79 cell survival after low energy (<2 MeV) proton irradiation for a custom set of input parameters. The novelty of this model is the realistic cellular geometry which can be irradiated using Geant4-DNA and the method in which the double strand breaks are predicted from clustering the spatial distribution of ionisation events. Unlike the original TLK model which calculates a tumour average cell survival probability, the cell survival probability is calculated for each cell in the geometric tumour model

  12. Waveforms clustering and single-station location of microearthquake multiplets recorded in the northern Sicilian offshore region

    NASA Astrophysics Data System (ADS)

    D'Alessandro, Antonino; Mangano, Giorgio; D'Anna, Giuseppe; Luzio, Dario

    2013-09-01

    In 2009 December, the OBSLab-INGV (Istituto Nazionale di Geofisica e Vulcanologia) deployed an Ocean Bottom Seismometer with Hydrophone (OBS/H) near the epicentral area of the main shock of the Palermo seismic sequence of 2002. The monitoring activity had a total duration of about 8 months. During this experiment, the OBS/H recorded 247 very local microearthquakes, whose local magnitude is between -0.5 and 2.5 and TS - TP delay time between 0.2 and 5 s, almost all of which were undetected by the Italian National Seismic Network. This local microseismicity has been analysed using an innovative clustering technique that exploits the similarity between the waveforms generated by different events. The clustering technique implemented, based on hierarchical agglomerative algorithms, nearest neighbour technique and dendrogram representation, allowed us to identify nine distinct multiplets characterized by a high degree of similarity between the waveforms. The microevents were located through an improved single-station location (SSL) technique based on the polarization analysis of the 3C signals and on the estimation of the TS - TP time. In the new SSL technique, an unbiased covariance matrix was defined and a ray tracer-based determination of the epicentral distance and hypocentral depth was proposed. All the multiplets were generated by events with hypocentres that were very close to each other. However, not all the identified clusters are also clustered in the time-magnitude domain. It was also observed that some multiplets have clouds of hypocentres overlapping each other. These clusters, indistinguishable without the application of a waveforms clustering technique, show differences in the waveforms that must be attributed to differences in the focal mechanisms which generated the waveforms. The local seismic events recorded are typical of a seismicity generated by a volume characterized by a highly complex fracturing pattern and by an important role in the dynamics

  13. Identification of new candidate drugs for lung cancer using chemical-chemical interactions, chemical-protein interactions and a K-means clustering algorithm.

    PubMed

    Lu, Jing; Chen, Lei; Yin, Jun; Huang, Tao; Bi, Yi; Kong, Xiangyin; Zheng, Mingyue; Cai, Yu-Dong

    2016-01-01

    Lung cancer, characterized by uncontrolled cell growth in the lung tissue, is the leading cause of global cancer deaths. Until now, effective treatment of this disease is limited. Many synthetic compounds have emerged with the advancement of combinatorial chemistry. Identification of effective lung cancer candidate drug compounds among them is a great challenge. Thus, it is necessary to build effective computational methods that can assist us in selecting for potential lung cancer drug compounds. In this study, a computational method was proposed to tackle this problem. The chemical-chemical interactions and chemical-protein interactions were utilized to select candidate drug compounds that have close associations with approved lung cancer drugs and lung cancer-related genes. A permutation test and K-means clustering algorithm were employed to exclude candidate drugs with low possibilities to treat lung cancer. The final analysis suggests that the remaining drug compounds have potential anti-lung cancer activities and most of them have structural dissimilarity with approved drugs for lung cancer.

  14. Evaluation of machine learning algorithms for classification of primary biological aerosol using a new UV-LIF spectrometer

    NASA Astrophysics Data System (ADS)

    Ruske, Simon; Topping, David O.; Foot, Virginia E.; Kaye, Paul H.; Stanley, Warren R.; Crawford, Ian; Morse, Andrew P.; Gallagher, Martin W.

    2017-03-01

    Characterisation of bioaerosols has important implications within environment and public health sectors. Recent developments in ultraviolet light-induced fluorescence (UV-LIF) detectors such as the Wideband Integrated Bioaerosol Spectrometer (WIBS) and the newly introduced Multiparameter Bioaerosol Spectrometer (MBS) have allowed for the real-time collection of fluorescence, size and morphology measurements for the purpose of discriminating between bacteria, fungal spores and pollen.This new generation of instruments has enabled ever larger data sets to be compiled with the aim of studying more complex environments. In real world data sets, particularly those from an urban environment, the population may be dominated by non-biological fluorescent interferents, bringing into question the accuracy of measurements of quantities such as concentrations. It is therefore imperative that we validate the performance of different algorithms which can be used for the task of classification.For unsupervised learning we tested hierarchical agglomerative clustering with various different linkages. For supervised learning, 11 methods were tested, including decision trees, ensemble methods (random forests, gradient boosting and AdaBoost), two implementations for support vector machines (libsvm and liblinear) and Gaussian methods (Gaussian naïve Bayesian, quadratic and linear discriminant analysis, the k-nearest neighbours algorithm and artificial neural networks).The methods were applied to two different data sets produced using the new MBS, which provides multichannel UV-LIF fluorescence signatures for single airborne biological particles. The first data set contained mixed PSLs and the second contained a variety of laboratory-generated aerosol.Clustering in general performs slightly worse than the supervised learning methods, correctly classifying, at best, only 67. 6 and 91. 1 % for the two data sets respectively. For supervised learning the gradient boosting algorithm was

  15. Abdominal adipose tissue quantification on water-suppressed and non-water-suppressed MRI at 3T using semi-automated FCM clustering algorithm

    NASA Astrophysics Data System (ADS)

    Valaparla, Sunil K.; Peng, Qi; Gao, Feng; Clarke, Geoffrey D.

    2014-03-01

    Accurate measurements of human body fat distribution are desirable because excessive body fat is associated with impaired insulin sensitivity, type 2 diabetes mellitus (T2DM) and cardiovascular disease. In this study, we hypothesized that the performance of water suppressed (WS) MRI is superior to non-water suppressed (NWS) MRI for volumetric assessment of abdominal subcutaneous (SAT), intramuscular (IMAT), visceral (VAT), and total (TAT) adipose tissues. We acquired T1-weighted images on a 3T MRI system (TIM Trio, Siemens), which was analyzed using semi-automated segmentation software that employs a fuzzy c-means (FCM) clustering algorithm. Sixteen contiguous axial slices, centered at the L4-L5 level of the abdomen, were acquired in eight T2DM subjects with water suppression (WS) and without (NWS). Histograms from WS images show improved separation of non-fatty tissue pixels from fatty tissue pixels, compared to NWS images. Paired t-tests of WS versus NWS showed a statistically significant lower volume of lipid in the WS images for VAT (145.3 cc less, p=0.006) and IMAT (305 cc less, p<0.001), but not SAT (14.1 cc more, NS). WS measurements of TAT also resulted in lower fat volumes (436.1 cc less, p=0.002). There is strong correlation between WS and NWS quantification methods for SAT measurements (r=0.999), but poorer correlation for VAT studies (r=0.845). These results suggest that NWS pulse sequences may overestimate adipose tissue volumes and that WS pulse sequences are more desirable due to the higher contrast generated between fatty and non-fatty tissues.

  16. A comparison of performance of automatic cloud coverage assessment algorithm for Formosat-2 image using clustering-based and spatial thresholding methods

    NASA Astrophysics Data System (ADS)

    Hsu, Kuo-Hsien

    2012-11-01

    Formosat-2 image is a kind of high-spatial-resolution (2 meters GSD) remote sensing satellite data, which includes one panchromatic band and four multispectral bands (Blue, Green, Red, near-infrared). An essential sector in the daily processing of received Formosat-2 image is to estimate the cloud statistic of image using Automatic Cloud Coverage Assessment (ACCA) algorithm. The information of cloud statistic of image is subsequently recorded as an important metadata for image product catalog. In this paper, we propose an ACCA method with two consecutive stages: preprocessing and post-processing analysis. For pre-processing analysis, the un-supervised K-means classification, Sobel's method, thresholding method, non-cloudy pixels reexamination, and cross-band filter method are implemented in sequence for cloud statistic determination. For post-processing analysis, Box-Counting fractal method is implemented. In other words, the cloud statistic is firstly determined via pre-processing analysis, the correctness of cloud statistic of image of different spectral band is eventually cross-examined qualitatively and quantitatively via post-processing analysis. The selection of an appropriate thresholding method is very critical to the result of ACCA method. Therefore, in this work, We firstly conduct a series of experiments of the clustering-based and spatial thresholding methods that include Otsu's, Local Entropy(LE), Joint Entropy(JE), Global Entropy(GE), and Global Relative Entropy(GRE) method, for performance comparison. The result shows that Otsu's and GE methods both perform better than others for Formosat-2 image. Additionally, our proposed ACCA method by selecting Otsu's method as the threshoding method has successfully extracted the cloudy pixels of Formosat-2 image for accurate cloud statistic estimation.

  17. Haplotyping Problem, A Clustering Approach

    SciTech Connect

    Eslahchi, Changiz; Sadeghi, Mehdi; Pezeshk, Hamid; Kargar, Mehdi; Poormohammadi, Hadi

    2007-09-06

    Construction of two haplotypes from a set of Single Nucleotide Polymorphism (SNP) fragments is called haplotype reconstruction problem. One of the most popular computational model for this problem is Minimum Error Correction (MEC). Since MEC is an NP-hard problem, here we propose a novel heuristic algorithm based on clustering analysis in data mining for haplotype reconstruction problem. Based on hamming distance and similarity between two fragments, our iterative algorithm produces two clusters of fragments; then, in each iteration, the algorithm assigns a fragment to one of the clusters. Our results suggest that the algorithm has less reconstruction error rate in comparison with other algorithms.

  18. Haplotyping Problem, A Clustering Approach

    NASA Astrophysics Data System (ADS)

    Eslahchi, Changiz; Sadeghi, Mehdi; Pezeshk, Hamid; Kargar, Mehdi; Poormohammadi, Hadi

    2007-09-01

    Construction of two haplotypes from a set of Single Nucleotide Polymorphism (SNP) fragments is called haplotype reconstruction problem. One of the most popular computational model for this problem is Minimum Error Correction (MEC). Since MEC is an NP-hard problem, here we propose a novel heuristic algorithm based on clustering analysis in data mining for haplotype reconstruction problem. Based on hamming distance and similarity between two fragments, our iterative algorithm produces two clusters of fragments; then, in each iteration, the algorithm assigns a fragment to one of the clusters. Our results suggest that the algorithm has less reconstruction error rate in comparison with other algorithms.

  19. Overview on techniques in cluster analysis.

    PubMed

    Frades, Itziar; Matthiesen, Rune

    2010-01-01

    Clustering is the unsupervised, semisupervised, and supervised classification of patterns into groups. The clustering problem has been addressed in many contexts and disciplines. Cluster analysis encompasses different methods and algorithms for grouping objects of similar kinds into respective categories. In this chapter, we describe a number of methods and algorithms for cluster analysis in a stepwise framework. The steps of a typical clustering analysis process include sequentially pattern representation, the choice of the similarity measure, the choice of the clustering algorithm, the assessment of the output, and the representation of the clusters.

  20. Single-cluster dynamics for the random-cluster model

    NASA Astrophysics Data System (ADS)

    Deng, Youjin; Qian, Xiaofeng; Blöte, Henk W. J.

    2009-09-01

    We formulate a single-cluster Monte Carlo algorithm for the simulation of the random-cluster model. This algorithm is a generalization of the Wolff single-cluster method for the q -state Potts model to noninteger values q>1 . Its results for static quantities are in a satisfactory agreement with those of the existing Swendsen-Wang-Chayes-Machta (SWCM) algorithm, which involves a full-cluster decomposition of random-cluster configurations. We explore the critical dynamics of this algorithm for several two-dimensional Potts and random-cluster models. For integer q , the single-cluster algorithm can be reduced to the Wolff algorithm, for which case we find that the autocorrelation functions decay almost purely exponentially, with dynamic exponents zexp=0.07 (1), 0.521 (7), and 1.007 (9) for q=2 , 3, and 4, respectively. For noninteger q , the dynamical behavior of the single-cluster algorithm appears to be very dissimilar to that of the SWCM algorithm. For large critical systems, the autocorrelation function displays a range of power-law behavior as a function of time. The dynamic exponents are relatively large. We provide an explanation for this peculiar dynamic behavior.

  1. Single-cluster dynamics for the random-cluster model.

    PubMed

    Deng, Youjin; Qian, Xiaofeng; Blöte, Henk W J

    2009-09-01

    We formulate a single-cluster Monte Carlo algorithm for the simulation of the random-cluster model. This algorithm is a generalization of the Wolff single-cluster method for the q-state Potts model to noninteger values q>1. Its results for static quantities are in a satisfactory agreement with those of the existing Swendsen-Wang-Chayes-Machta (SWCM) algorithm, which involves a full-cluster decomposition of random-cluster configurations. We explore the critical dynamics of this algorithm for several two-dimensional Potts and random-cluster models. For integer q, the single-cluster algorithm can be reduced to the Wolff algorithm, for which case we find that the autocorrelation functions decay almost purely exponentially, with dynamic exponents z(exp)=0.07 (1), 0.521 (7), and 1.007 (9) for q=2, 3, and 4, respectively. For noninteger q, the dynamical behavior of the single-cluster algorithm appears to be very dissimilar to that of the SWCM algorithm. For large critical systems, the autocorrelation function displays a range of power-law behavior as a function of time. The dynamic exponents are relatively large. We provide an explanation for this peculiar dynamic behavior.

  2. A Linear Algebra Measure of Cluster Quality.

    ERIC Educational Resources Information Center

    Mather, Laura A.

    2000-01-01

    Discussion of models for information retrieval focuses on an application of linear algebra to text clustering, namely, a metric for measuring cluster quality based on the theory that cluster quality is proportional to the number of terms that are disjoint across the clusters. Explains term-document matrices and clustering algorithms. (Author/LRW)

  3. Extending DFT-based genetic algorithms by atom-to-place re-assignment via perturbation theory: A systematic and unbiased approach to structures of mixed-metallic clusters

    SciTech Connect

    Weigend, Florian

    2014-10-07

    Energy surfaces of metal clusters usually show a large variety of local minima. For homo-metallic species the energetically lowest can be found reliably with genetic algorithms, in combination with density functional theory without system-specific parameters. For mixed-metallic clusters this is much more difficult, as for a given arrangement of nuclei one has to find additionally the best of many possibilities of assigning different metal types to the individual positions. In the framework of electronic structure methods this second issue is treatable at comparably low cost at least for elements with similar atomic number by means of first-order perturbation theory, as shown previously [F. Weigend, C. Schrodt, and R. Ahlrichs, J. Chem. Phys. 121, 10380 (2004)]. In the present contribution the extension of a genetic algorithm with the re-assignment of atom types to atom sites is proposed and tested for the search of the global minima of PtHf{sub 12} and [LaPb{sub 7}Bi{sub 7}]{sup 4−}. For both cases the (putative) global minimum is reliably found with the extended technique, which is not the case for the “pure” genetic algorithm.

  4. Extending DFT-based genetic algorithms by atom-to-place re-assignment via perturbation theory: a systematic and unbiased approach to structures of mixed-metallic clusters.

    PubMed

    Weigend, Florian

    2014-10-07

    Energy surfaces of metal clusters usually show a large variety of local minima. For homo-metallic species the energetically lowest can be found reliably with genetic algorithms, in combination with density functional theory without system-specific parameters. For mixed-metallic clusters this is much more difficult, as for a given arrangement of nuclei one has to find additionally the best of many possibilities of assigning different metal types to the individual positions. In the framework of electronic structure methods this second issue is treatable at comparably low cost at least for elements with similar atomic number by means of first-order perturbation theory, as shown previously [F. Weigend, C. Schrodt, and R. Ahlrichs, J. Chem. Phys. 121, 10380 (2004)]. In the present contribution the extension of a genetic algorithm with the re-assignment of atom types to atom sites is proposed and tested for the search of the global minima of PtHf12 and [LaPb7Bi7](4-). For both cases the (putative) global minimum is reliably found with the extended technique, which is not the case for the "pure" genetic algorithm.

  5. Fuzzy Subspace Clustering

    NASA Astrophysics Data System (ADS)

    Borgelt, Christian

    In clustering we often face the situation that only a subset of the available attributes is relevant for forming clusters, even though this may not be known beforehand. In such cases it is desirable to have a clustering algorithm that automatically weights attributes or even selects a proper subset. In this paper I study such an approach for fuzzy clustering, which is based on the idea to transfer an alternative to the fuzzifier (Klawonn and Höppner, What is fuzzy about fuzzy clustering? Understanding and improving the concept of the fuzzifier, In: Proc. 5th Int. Symp. on Intelligent Data Analysis, 254-264, Springer, Berlin, 2003) to attribute weighting fuzzy clustering (Keller and Klawonn, Int J Uncertain Fuzziness Knowl Based Syst 8:735-746, 2000). In addition, by reformulating Gustafson-Kessel fuzzy clustering, a scheme for weighting and selecting principal axes can be obtained. While in Borgelt (Feature weighting and feature selection in fuzzy clustering, In: Proc. 17th IEEE Int. Conf. on Fuzzy Systems, IEEE Press, Piscataway, NJ, 2008) I already presented such an approach for a global selection of attributes and principal axes, this paper extends it to a cluster-specific selection, thus arriving at a fuzzy subspace clustering algorithm (Parsons, Haque, and Liu, 2004).

  6. Unconventional methods for clustering

    NASA Astrophysics Data System (ADS)

    Kotyrba, Martin

    2016-06-01

    Cluster analysis or clustering is a task of grouping a set of objects in such a way that objects in the same group (called a cluster) are more similar (in some sense or another) to each other than to those in other groups (clusters). It is the main task of exploratory data mining and a common technique for statistical data analysis used in many fields, including machine learning, pattern recognition, image analysis, information retrieval, and bioinformatics. The topic of this paper is one of the modern methods of clustering namely SOM (Self Organising Map). The paper describes the theory needed to understand the principle of clustering and descriptions of algorithm used with clustering in our experiments.

  7. Use of multiple cluster analysis methods to explore the validity of a community outcomes concept map.

    PubMed

    Orsi, Rebecca

    2017-02-01

    Concept mapping is now a commonly-used technique for articulating and evaluating programmatic outcomes. However, research regarding validity of knowledge and outcomes produced with concept mapping is sparse. The current study describes quantitative validity analyses using a concept mapping dataset. We sought to increase the validity of concept mapping evaluation results by running multiple cluster analysis methods and then using several metrics to choose from among solutions. We present four different clustering methods based on analyses using the R statistical software package: partitioning around medoids (PAM), fuzzy analysis (FANNY), agglomerative nesting (AGNES) and divisive analysis (DIANA). We then used the Dunn and Davies-Bouldin indices to assist in choosing a valid cluster solution for a concept mapping outcomes evaluation. We conclude that the validity of the outcomes map is high, based on the analyses described. Finally, we discuss areas for further concept mapping methods research.

  8. Brightest Cluster Galaxy Identification

    NASA Astrophysics Data System (ADS)

    Leisman, Luke; Haarsma, D. B.; Sebald, D. A.; ACCEPT Team

    2011-01-01

    Brightest cluster galaxies (BCGs) play an important role in several fields of astronomical research. The literature includes many different methods and criteria for identifying the BCG in the cluster, such as choosing the brightest galaxy, the galaxy nearest the X-ray peak, or the galaxy with the most extended profile. Here we examine a sample of 75 clusters from the Archive of Chandra Cluster Entropy Profile Tables (ACCEPT) and the Sloan Digital Sky Survey (SDSS), measuring masked magnitudes and profiles for BCG candidates in each cluster. We first identified galaxies by hand; in 15% of clusters at least one team member selected a different galaxy than the others.We also applied 6 other identification methods to the ACCEPT sample; in 30% of clusters at least one of these methods selected a different galaxy than the other methods. We then developed an algorithm that weighs brightness, profile, and proximity to the X-ray peak and centroid. This algorithm incorporates the advantages of by-hand identification (weighing multiple properties) and automated selection (repeatable and consistent). The BCG population chosen by the algorithm is more uniform in its properties than populations selected by other methods, particularly in the relation between absolute magnitude (a proxy for galaxy mass) and average gas temperature (a proxy for cluster mass). This work supported by a Barry M. Goldwater Scholarship and a Sid Jansma Summer Research Fellowship.

  9. A 3D Voronoi+Gapper Galaxy Cluster Finder in Redshift Space to z≈ 0.2 I: An Algorithm Optimized for the 2dFGRS

    NASA Astrophysics Data System (ADS)

    Pereira, Sebastián; Campusano, Luis E.; Hitschfeld-Kahler, Nancy; Pizarro, Daniel; Haines, Christopher P.; Clowes, Roger G.; Marinello, Gabriel; Söchting, Ilona K.

    2017-04-01

    This paper is the first in a series, presenting a new galaxy cluster finder based on a three-dimensional Voronoi Tesselation plus a maximum likelihood estimator, followed by gapping-filtering in radial velocity(VoML+G). The scientific aim of the series is a reassessment of the diversity of optical clusters in the local universe. A mock galaxy database mimicking the southern strip of the magnitude(blue)-limited 2dF Galaxy Redshift Survey (2dFGRS), for the redshift range 0.009 < z < 0.22, is built on the basis of the Millennium Simulation of the LCDM cosmology and a reference catalog of “Millennium clusters,” spannning across the 1.0 × 1012–1.0 × 1015 M ⊙ h ‑1 dark matter (DM) halo mass range, is recorded. The validation of VoML+G is performed through its application to the mock data and the ensuing determination of the completeness and purity of the cluster detections by comparison with the reference catalog. The execution of VoML+G over the 2dFGRS mock data identified 1614 clusters, 22% with N g ≥ 10, 64 percent with 10 > N g ≥ 5, and 14% with N g < 5. The ensemble of VoML+G clusters has a ∼59% completeness and a ∼66% purity, whereas the subsample with N g ≥ 10, to z ∼ 0.14, has greatly improved mean rates of ∼75% and ∼90%, respectively. The VoML+G cluster velocity dispersions are found to be compatible with those corresponding to “Millennium clusters” over the 300–1000 km s‑1 interval, i.e., for cluster halo masses in excess of ∼3.0 × 1013 M ⊙ h ‑1.

  10. Advanced modularity-specialized label propagation algorithm for detecting communities in networks

    NASA Astrophysics Data System (ADS)

    Liu, X.; Murata, T.

    2010-04-01

    A modularity-specialized label propagation algorithm (LPAm) for detecting network communities was recently proposed. This promising algorithm offers some desirable qualities. However, LPAm favors community divisions where all communities are similar in total degree and thus it is prone to get stuck in poor local maxima in the modularity space. To escape local maxima, we employ a multistep greedy agglomerative algorithm (MSG) that can merge multiple pairs of communities at a time. Combining LPAm and MSG, we propose an advanced modularity-specialized label propagation algorithm (LPAm+). Experiments show that LPAm+ successfully detects communities with higher modularity values than ever reported in two commonly used real-world networks. Moreover, LPAm+ offers a fair compromise between accuracy and speed.

  11. Algorithms and Algorithmic Languages.

    ERIC Educational Resources Information Center

    Veselov, V. M.; Koprov, V. M.

    This paper is intended as an introduction to a number of problems connected with the description of algorithms and algorithmic languages, particularly the syntaxes and semantics of algorithmic languages. The terms "letter, word, alphabet" are defined and described. The concept of the algorithm is defined and the relation between the algorithm and…

  12. Using Self-Organizing Neural Network Map Combined with Ward's Clustering Algorithm for Visualization of Students' Cognitive Structural Models about Aliveness Concept

    PubMed Central

    Ugulu, Ilker; Aydin, Halil

    2016-01-01

    We propose an approach to clustering and visualization of students' cognitive structural models. We use the self-organizing map (SOM) combined with Ward's clustering to conduct cluster analysis. In the study carried out on 100 subjects, a conceptual understanding test consisting of open-ended questions was used as a data collection tool. The results of analyses indicated that students constructed the aliveness concept by associating it predominantly with human. Motion appeared as the most frequently associated term with the aliveness concept. The results suggest that the aliveness concept has been constructed using anthropocentric and animistic cognitive structures. In the next step, we used the data obtained from the conceptual understanding test for training the SOM. Consequently, we propose a visualization method about cognitive structure of the aliveness concept. PMID:26819579

  13. Two generalizations of Kohonen clustering

    NASA Technical Reports Server (NTRS)

    Bezdek, James C.; Pal, Nikhil R.; Tsao, Eric C. K.

    1993-01-01

    The relationship between the sequential hard c-means (SHCM), learning vector quantization (LVQ), and fuzzy c-means (FCM) clustering algorithms is discussed. LVQ and SHCM suffer from several major problems. For example, they depend heavily on initialization. If the initial values of the cluster centers are outside the convex hull of the input data, such algorithms, even if they terminate, may not produce meaningful results in terms of prototypes for cluster representation. This is due in part to the fact that they update only the winning prototype for every input vector. The impact and interaction of these two families with Kohonen's self-organizing feature mapping (SOFM), which is not a clustering method, but which often leads ideas to clustering algorithms is discussed. Then two generalizations of LVQ that are explicitly designed as clustering algorithms are presented; these algorithms are referred to as generalized LVQ = GLVQ; and fuzzy LVQ = FLVQ. Learning rules are derived to optimize an objective function whose goal is to produce 'good clusters'. GLVQ/FLVQ (may) update every node in the clustering net for each input vector. Neither GLVQ nor FLVQ depends upon a choice for the update neighborhood or learning rate distribution - these are taken care of automatically. Segmentation of a gray tone image is used as a typical application of these algorithms to illustrate the performance of GLVQ/FLVQ.

  14. Cluster Headache

    MedlinePlus

    Cluster headache Overview By Mayo Clinic Staff Cluster headaches, which occur in cyclical patterns or clusters, are one of the most painful types of headache. A cluster headache commonly awakens you ...

  15. Information-based clustering

    PubMed Central

    Slonim, Noam; Atwal, Gurinder Singh; Tkačik, Gašper; Bialek, William

    2005-01-01

    In an age of increasingly large data sets, investigators in many different disciplines have turned to clustering as a tool for data analysis and exploration. Existing clustering methods, however, typically depend on several nontrivial assumptions about the structure of data. Here, we reformulate the clustering problem from an information theoretic perspective that avoids many of these assumptions. In particular, our formulation obviates the need for defining a cluster “prototype,” does not require an a priori similarity metric, is invariant to changes in the representation of the data, and naturally captures nonlinear relations. We apply this approach to different domains and find that it consistently produces clusters that are more coherent than those extracted by existing algorithms. Finally, our approach provides a way of clustering based on collective notions of similarity rather than the traditional pairwise measures. PMID:16352721

  16. Brain Tissue Classification Based on Diffusion Tensor Imaging: A Comparative Study Between Some Clustering Algorithms and Their Effect on Different Diffusion Tensor Imaging Scalar Indices

    PubMed Central

    Elaff, Ihab

    2016-01-01

    Background Brain segmentation from diffusion tensor imaging (DTI) into white matter (WM), gray matter (GM), and cerebrospinal fluid (CSF) with acceptable results is subjected to many factors. Objectives The most important issue in brain segmentation from DTI images is the selection of suitable scalar indices that best describe the required tissue in the images. Specifying suitable clustering method and suitable number of clusters of the selected method are other factors which affects the segmentation process significantly. Materials and Methods The segmentation process is evaluated using four different clustering methods with different number of clusters where some DTI scalar indices for 10 human brains are processed. Results The aim was to produce results with less segmentation error and a lower computational cost while attempting to minimizing boundary overlapping and minimizing the effect of artifacts due to macroscale scanning. Conclusion The volume ratios of the best produced outputs with respect to the total brain size are 16.7% ± 3.53% for CSF, 35.05% ± 1.13% for WM, and 48.2% ± 2.88% for GM. PMID:27703655

  17. Bayesian Decision Theoretical Framework for Clustering

    ERIC Educational Resources Information Center

    Chen, Mo

    2011-01-01

    In this thesis, we establish a novel probabilistic framework for the data clustering problem from the perspective of Bayesian decision theory. The Bayesian decision theory view justifies the important questions: what is a cluster and what a clustering algorithm should optimize. We prove that the spectral clustering (to be specific, the…

  18. Quasi-Likelihood Techniques in a Logistic Regression Equation for Identifying Simulium damnosum s.l. Larval Habitats Intra-cluster Covariates in Togo

    PubMed Central

    JACOB, BENJAMIN G.; NOVAK, ROBERT J.; TOE, LAURENT; SANFO, MOUSSA S.; AFRIYIE, ABENA N.; IBRAHIM, MOHAMMED A.; GRIFFITH, DANIEL A.; UNNASCH, THOMAS R.

    2013-01-01

    The standard methods for regression analyses of clustered riverine larval habitat data of Simulium damnosum s.l. a major black-fly vector of Onchoceriasis, postulate models relating observational ecological-sampled parameter estimators to prolific habitats without accounting for residual intra-cluster error correlation effects. Generally, this correlation comes from two sources: (1) the design of the random effects and their assumed covariance from the multiple levels within the regression model; and, (2) the correlation structure of the residuals. Unfortunately, inconspicuous errors in residual intra-cluster correlation estimates can overstate precision in forecasted S.damnosum s.l. riverine larval habitat explanatory attributes regardless how they are treated (e.g., independent, autoregressive, Toeplitz, etc). In this research, the geographical locations for multiple riverine-based S. damnosum s.l. larval ecosystem habitats sampled from 2 pre-established epidemiological sites in Togo were identified and recorded from July 2009 to June 2010. Initially the data was aggregated into proc genmod. An agglomerative hierarchical residual cluster-based analysis was then performed. The sampled clustered study site data was then analyzed for statistical correlations using Monthly Biting Rates (MBR). Euclidean distance measurements and terrain-related geomorphological statistics were then generated in ArcGIS. A digital overlay was then performed also in ArcGIS using the georeferenced ground coordinates of high and low density clusters stratified by Annual Biting Rates (ABR). This data was overlain onto multitemporal sub-meter pixel resolution satellite data (i.e., QuickBird 0.61m wavbands ). Orthogonal spatial filter eigenvectors were then generated in SAS/GIS. Univariate and non-linear regression-based models (i.e., Logistic, Poisson and Negative Binomial) were also employed to determine probability distributions and to identify statistically significant parameter

  19. Quasi-Likelihood Techniques in a Logistic Regression Equation for Identifying Simulium damnosum s.l. Larval Habitats Intra-cluster Covariates in Togo.

    PubMed

    Jacob, Benjamin G; Novak, Robert J; Toe, Laurent; Sanfo, Moussa S; Afriyie, Abena N; Ibrahim, Mohammed A; Griffith, Daniel A; Unnasch, Thomas R

    2012-01-01

    The standard methods for regression analyses of clustered riverine larval habitat data of Simulium damnosum s.l. a major black-fly vector of Onchoceriasis, postulate models relating observational ecological-sampled parameter estimators to prolific habitats without accounting for residual intra-cluster error correlation effects. Generally, this correlation comes from two sources: (1) the design of the random effects and their assumed covariance from the multiple levels within the regression model; and, (2) the correlation structure of the residuals. Unfortunately, inconspicuous errors in residual intra-cluster correlation estimates can overstate precision in forecasted S.damnosum s.l. riverine larval habitat explanatory attributes regardless how they are treated (e.g., independent, autoregressive, Toeplitz, etc). In this research, the geographical locations for multiple riverine-based S. damnosum s.l. larval ecosystem habitats sampled from 2 pre-established epidemiological sites in Togo were identified and recorded from July 2009 to June 2010. Initially the data was aggregated into proc genmod. An agglomerative hierarchical residual cluster-based analysis was then performed. The sampled clustered study site data was then analyzed for statistical correlations using Monthly Biting Rates (MBR). Euclidean distance measurements and terrain-related geomorphological statistics were then generated in ArcGIS. A digital overlay was then performed also in ArcGIS using the georeferenced ground coordinates of high and low density clusters stratified by Annual Biting Rates (ABR). This data was overlain onto multitemporal sub-meter pixel resolution satellite data (i.e., QuickBird 0.61m wavbands ). Orthogonal spatial filter eigenvectors were then generated in SAS/GIS. Univariate and non-linear regression-based models (i.e., Logistic, Poisson and Negative Binomial) were also employed to determine probability distributions and to identify statistically significant parameter

  20. Convex Clustering: An Attractive Alternative to Hierarchical Clustering

    PubMed Central

    Chen, Gary K.; Chi, Eric C.; Ranola, John Michael O.; Lange, Kenneth

    2015-01-01

    The primary goal in cluster analysis is to discover natural groupings of objects. The field of cluster analysis is crowded with diverse methods that make special assumptions about data and address different scientific aims. Despite its shortcomings in accuracy, hierarchical clustering is the dominant clustering method in bioinformatics. Biologists find the trees constructed by hierarchical clustering visually appealing and in tune with their evolutionary perspective. Hierarchical clustering operates on multiple scales simultaneously. This is essential, for instance, in transcriptome data, where one may be interested in making qualitative inferences about how lower-order relationships like gene modules lead to higher-order relationships like pathways or biological processes. The recently developed method of convex clustering preserves the visual appeal of hierarchical clustering while ameliorating its propensity to make false inferences in the presence of outliers and noise. The solution paths generated by convex clustering reveal relationships between clusters that are hidden by static methods such as k-means clustering. The current paper derives and tests a novel proximal distance algorithm for minimizing the objective function of convex clustering. The algorithm separates parameters, accommodates missing data, and supports prior information on relationships. Our program CONVEXCLUSTER incorporating the algorithm is implemented on ATI and nVidia graphics processing units (GPUs) for maximal speed. Several biological examples illustrate the strengths of convex clustering and the ability of the proximal distance algorithm to handle high-dimensional problems. CONVEXCLUSTER can be freely downloaded from the UCLA Human Genetics web site at http://www.genetics.ucla.edu/software/ PMID:25965340

  1. Star Clusters within FIRE

    NASA Astrophysics Data System (ADS)

    Perez, Adrianna; Moreno, Jorge; Naiman, Jill; Ramirez-Ruiz, Enrico; Hopkins, Philip F.

    2017-01-01

    In this work, we analyze the environments surrounding star clusters of simulated merging galaxies. Our framework employs Feedback In Realistic Environments (FIRE) model (Hopkins et al., 2014). The FIRE project is a high resolution cosmological simulation that resolves star forming regions and incorporates stellar feedback in a physically realistic way. The project focuses on analyzing the properties of the star clusters formed in merging galaxies. The locations of these star clusters are identified with astrodendro.py, a publicly available dendrogram algorithm. Once star cluster properties are extracted, they will be used to create a sub-grid (smaller than the resolution scale of FIRE) of gas confinement in these clusters. Then, we can examine how the star clusters interact with these available gas reservoirs (either by accreting this mass or blowing it out via feedback), which will determine many properties of the cluster (star formation history, compact object accretion, etc). These simulations will further our understanding of star formation within stellar clusters during galaxy evolution. In the future, we aim to enhance sub-grid prescriptions for feedback specific to processes within star clusters; such as, interaction with stellar winds and gas accretion onto black holes and neutron stars.

  2. Subspace K-means clustering.

    PubMed

    Timmerman, Marieke E; Ceulemans, Eva; De Roover, Kim; Van Leeuwen, Karla

    2013-12-01

    To achieve an insightful clustering of multivariate data, we propose subspace K-means. Its central idea is to model the centroids and cluster residuals in reduced spaces, which allows for dealing with a wide range of cluster types and yields rich interpretations of the clusters. We review the existing related clustering methods, including deterministic, stochastic, and unsupervised learning approaches. To evaluate subspace K-means, we performed a comparative simulation study, in which we manipulated the overlap of subspaces, the between-cluster variance, and the error variance. The study shows that the subspace K-means algorithm is sensitive to local minima but that the problem can be reasonably dealt with by using partitions of various cluster procedures as a starting point for the algorithm. Subspace K-means performs very well in recovering the true clustering across all conditions considered and appears to be superior to its competitor methods: K-means, reduced K-means, factorial K-means, mixtures of factor analyzers (MFA), and MCLUST. The best competitor method, MFA, showed a performance similar to that of subspace K-means in easy conditions but deteriorated in more difficult ones. Using data from a study on parental behavior, we show that subspace K-means analysis provides a rich insight into the cluster characteristics, in terms of both the relative positions of the clusters (via the centroids) and the shape of the clusters (via the within-cluster residuals).

  3. Galaxy cluster's rotation

    NASA Astrophysics Data System (ADS)

    Manolopoulou, M.; Plionis, M.

    2017-03-01

    We study the possible rotation of cluster galaxies, developing, testing, and applying a novel algorithm which identifies rotation, if such does exist, as well as its rotational centre, its axis orientation, rotational velocity amplitude, and, finally, the clockwise or counterclockwise direction of rotation on the plane of the sky. To validate our algorithms we construct realistic Monte Carlo mock rotating clusters and confirm that our method provides robust indications of rotation. We then apply our methodology on a sample of Abell clusters with z ≲ 0.1 with member galaxies selected from the Sloan Digital Sky Survey DR10 spectroscopic data base. After excluding a number of substructured clusters, which could provide erroneous indications of rotation, and taking into account the expected fraction of misidentified coherent substructure velocities for rotation, provided by our Monte Carlo simulation analysis, we find that ∼23 per cent of our clusters are rotating under a set of strict criteria. Loosening the strictness of the criteria, on the expense of introducing spurious rotation indications, we find this fraction increasing to ∼28 per cent. We correlate our rotation indicators with the cluster dynamical state, provided either by their Bautz-Morgan type or by their X-ray isophotal shape and find for those clusters showing rotation within 1.5 h^{-1}_{70} Mpc that the significance of their rotation is related to the dynamically younger phases of cluster formation but after the initial anisotropic accretion and merging has been completed. Finally, finding rotational modes in galaxy clusters could lead to the necessity of correcting the dynamical cluster mass calculations.

  4. Swarm Intelligence in Text Document Clustering

    SciTech Connect

    Cui, Xiaohui; Potok, Thomas E

    2008-01-01

    Social animals or insects in nature often exhibit a form of emergent collective behavior. The research field that attempts to design algorithms or distributed problem-solving devices inspired by the collective behavior of social insect colonies is called Swarm Intelligence. Compared to the traditional algorithms, the swarm algorithms are usually flexible, robust, decentralized and self-organized. These characters make the swarm algorithms suitable for solving complex problems, such as document collection clustering. The major challenge of today's information society is being overwhelmed with information on any topic they are searching for. Fast and high-quality document clustering algorithms play an important role in helping users to effectively navigate, summarize, and organize the overwhelmed information. In this chapter, we introduce three nature inspired swarm intelligence clustering approaches for document clustering analysis. These clustering algorithms use stochastic and heuristic principles discovered from observing bird flocks, fish schools and ant food forage.

  5. CLUSTER CHEMISTRY

    SciTech Connect

    Muetterties, Earl L.

    1980-05-01

    Metal cluster chemistry is one of the most rapidly developing areas of inorganic and organometallic chemistry. Prior to 1960 only a few metal clusters were well characterized. However, shortly after the early development of boron cluster chemistry, the field of metal cluster chemistry began to grow at a very rapid rate and a structural and a qualitative theoretical understanding of clusters came quickly. Analyzed here is the chemistry and the general significance of clusters with particular emphasis on the cluster research within my group. The importance of coordinately unsaturated, very reactive metal clusters is the major subject of discussion.

  6. Precipitation, pH and metal load in AMD river basins: an application of fuzzy clustering algorithms to the process characterization.

    PubMed

    Grande, J A; Andújar, J M; Aroba, J; de la Torre, M L; Beltrán, R

    2005-04-01

    In the present work, Acid Mine Drainage (AMD) processes in the Chorrito Stream, which flows into the Cobica River (Iberian Pyrite Belt, Southwest Spain) are characterized by means of clustering techniques based on fuzzy logic. Also, pH behavior in contrast to precipitation is clearly explained, proving that the influence of rainfall inputs on the acidity and, as a result, on the metal load of a riverbed undergoing AMD processes highly depends on the moment when it occurs. In general, the riverbed dynamic behavior is the response to the sum of instant stimuli produced by isolated rainfall, the seasonal memory depending on the moment of the target hydrological year and, finally, the own inertia of the river basin, as a result of an accumulation process caused by age-long mining activity.

  7. Toward Parallel Document Clustering

    SciTech Connect

    Mogill, Jace A.; Haglin, David J.

    2011-09-01

    A key challenge to automated clustering of documents in large text corpora is the high cost of comparing documents in a multimillion dimensional document space. The Anchors Hierarchy is a fast data structure and algorithm for localizing data based on a triangle inequality obeying distance metric, the algorithm strives to minimize the number of distance calculations needed to cluster the documents into “anchors” around reference documents called “pivots”. We extend the original algorithm to increase the amount of available parallelism and consider two implementations: a complex data structure which affords efficient searching, and a simple data structure which requires repeated sorting. The sorting implementation is integrated with a text corpora “Bag of Words” program and initial performance results of end-to-end a document processing workflow are reported.

  8. The global Minmax k-means algorithm.

    PubMed

    Wang, Xiaoyan; Bai, Yanping

    2016-01-01

    The global k-means algorithm is an incremental approach to clustering that dynamically adds one cluster center at a time through a deterministic global search procedure from suitable initial positions, and employs k-means to minimize the sum of the intra-cluster variances. However the global k-means algorithm sometimes results singleton clusters and the initial positions sometimes are bad, after a bad initialization, poor local optimal can be easily obtained by k-means algorithm. In this paper, we modified the global k-means algorithm to eliminate the singleton clusters at first, and then we apply MinMax k-means clustering error method to global k-means algorithm to overcome the effect of bad initialization, proposed the global Minmax k-means algorithm. The proposed clustering method is tested on some popular data sets and compared to the k-means algorithm, the global k-means algorithm and the MinMax k-means algorithm. The experiment results show our proposed algorithm outperforms other algorithms mentioned in the paper.

  9. An Efficient, FPGA-Based, Cluster Detection Algorithm Implementation for a Strip Detector Readout System in a Time Projection Chamber Polarimeter

    NASA Technical Reports Server (NTRS)

    Gregory, Kyle J.; Hill, Joanne E. (Editor); Black, J. Kevin; Baumgartner, Wayne H.; Jahoda, Keith

    2016-01-01

    A fundamental challenge in a spaceborne application of a gas-based Time Projection Chamber (TPC) for observation of X-ray polarization is handling the large amount of data collected. The TPC polarimeter described uses the APV-25 Application Specific Integrated Circuit (ASIC) to readout a strip detector. Two dimensional photoelectron track images are created with a time projection technique and used to determine the polarization of the incident X-rays. The detector produces a 128x30 pixel image per photon interaction with each pixel registering 12 bits of collected charge. This creates challenging requirements for data storage and downlink bandwidth with only a modest incidence of photons and can have a significant impact on the overall mission cost. An approach is described for locating and isolating the photoelectron track within the detector image, yielding a much smaller data product, typically between 8x8 pixels and 20x20 pixels. This approach is implemented using a Microsemi RT-ProASIC3-3000 Field-Programmable Gate Array (FPGA), clocked at 20 MHz and utilizing 10.7k logic gates (14% of FPGA), 20 Block RAMs (17% of FPGA), and no external RAM. Results will be presented, demonstrating successful photoelectron track cluster detection with minimal impact to detector dead-time.

  10. Join-Graph Propagation Algorithms

    PubMed Central

    Mateescu, Robert; Kask, Kalev; Gogate, Vibhav; Dechter, Rina

    2010-01-01

    The paper investigates parameterized approximate message-passing schemes that are based on bounded inference and are inspired by Pearl's belief propagation algorithm (BP). We start with the bounded inference mini-clustering algorithm and then move to the iterative scheme called Iterative Join-Graph Propagation (IJGP), that combines both iteration and bounded inference. Algorithm IJGP belongs to the class of Generalized Belief Propagation algorithms, a framework that allowed connections with approximate algorithms from statistical physics and is shown empirically to surpass the performance of mini-clustering and belief propagation, as well as a number of other state-of-the-art algorithms on several classes of networks. We also provide insight into the accuracy of iterative BP and IJGP by relating these algorithms to well known classes of constraint propagation schemes. PMID:20740057

  11. A GMBCG galaxy cluster catalog of 55,880 rich clusters from SDSS DR7

    SciTech Connect

    Hao, Jiangang; McKay, Timothy A.; Koester, Benjamin P.; Rykoff, Eli S.; Rozo, Eduardo; Annis, James; Wechsler, Risa H.; Evrard, August; Siegel, Seth R.; Becker, Matthew; Busha, Michael; /Fermilab /Michigan U. /Chicago U., Astron. Astrophys. Ctr. /UC, Santa Barbara /KICP, Chicago /KIPAC, Menlo Park /SLAC /Caltech /Brookhaven

    2010-08-01

    We present a large catalog of optically selected galaxy clusters from the application of a new Gaussian Mixture Brightest Cluster Galaxy (GMBCG) algorithm to SDSS Data Release 7 data. The algorithm detects clusters by identifying the red sequence plus Brightest Cluster Galaxy (BCG) feature, which is unique for galaxy clusters and does not exist among field galaxies. Red sequence clustering in color space is detected using an Error Corrected Gaussian Mixture Model. We run GMBCG on 8240 square degrees of photometric data from SDSS DR7 to assemble the largest ever optical galaxy cluster catalog, consisting of over 55,000 rich clusters across the redshift range from 0.1 < z < 0.55. We present Monte Carlo tests of completeness and purity and perform cross-matching with X-ray clusters and with the maxBCG sample at low redshift. These tests indicate high completeness and purity across the full redshift range for clusters with 15 or more members.

  12. A GMBCG Galaxy Cluster Catalog of 55,424 Rich Clusters from SDSS DR7

    SciTech Connect

    Hao, Jiangang; McKay, Timothy A.; Koester, Benjamin P.; Rykoff, Eli S.; Rozo, Eduardo; Annis, James; Wechsler, Risa H.; Evrard, August; Siegel, Seth R.; Becker, Matthew; Busha, Michael; Gerdes, David; Johnston, David E.; Sheldon, Erin; /Brookhaven

    2011-08-22

    We present a large catalog of optically selected galaxy clusters from the application of a new Gaussian Mixture Brightest Cluster Galaxy (GMBCG) algorithm to SDSS Data Release 7 data. The algorithm detects clusters by identifying the red sequence plus Brightest Cluster Galaxy (BCG) feature, which is unique for galaxy clusters and does not exist among field galaxies. Red sequence clustering in color space is detected using an Error Corrected Gaussian Mixture Model. We run GMBCG on 8240 square degrees of photometric data from SDSS DR7 to assemble the largest ever optical galaxy cluster catalog, consisting of over 55,000 rich clusters across the redshift range from 0.1 < z < 0.55. We present Monte Carlo tests of completeness and purity and perform cross-matching with X-ray clusters and with the maxBCG sample at low redshift. These tests indicate high completeness and purity across the full redshift range for clusters with 15 or more members.

  13. Hybrid cluster identification

    NASA Astrophysics Data System (ADS)

    Martín-Herrero, J.

    2004-10-01

    I present a hybrid method for the labelling of clusters in two-dimensional lattices, which combines the recursive approach with iterative scanning to reduce the stack size required by the pure recursive technique, while keeping its benefits: single pass and straightforward cluster characterization and percolation detection parallel to the labelling. While the capacity to hold the entire lattice in memory is usually regarded as the major constraint for the applicability of the recursive technique, the required stack size is the real limiting factor. Resorting to recursion only for the transverse direction greatly reduces the recursion depth and therefore the required stack. It also enhances the overall performance of the recursive technique, as is shown by results on a set of uniform random binary lattices and on a set of samples of the Ising model. I also show how this technique may replace the recursive technique in Wolff's cluster algorithm, decreasing the risk of stack overflow and increasing its speed, and the Hoshen-Kopelman algorithm in the Swendsen-Wang cluster algorithm, allowing effortless characterization during generation of the samples and increasing its speed.

  14. Absolute classification with unsupervised clustering

    NASA Technical Reports Server (NTRS)

    Jeon, Byeungwoo; Landgrebe, D. A.

    1992-01-01

    An absolute classification algorithm is proposed in which the class definition through training samples or otherwise is required only for a particular class of interest. The absolute classification is considered as a problem of unsupervised clustering when one cluster is known initially. The definitions and statistics of the other classes are automatically developed through the weighted unsupervised clustering procedure, which is developed to keep the cluster corresponding to the class of interest from losing its identity as the class of interest. Once all the classes are developed, a conventional relative classifier such as the maximum-likelihood classifier is used in the classification.

  15. Segmenting Student Markets with a Student Satisfaction and Priorities Survey.

    ERIC Educational Resources Information Center

    Borden, Victor M. H.

    1995-01-01

    A market segmentation analysis of 872 university students compared 2 hierarchical clustering procedures for deriving market segments: 1 using matching-type measures and an agglomerative clustering algorithm, and 1 using the chi-square based automatic interaction detection. Results and implications for planning, evaluating, and improving academic…

  16. Cluster headache

    MedlinePlus

    Histamine headache; Headache - histamine; Migrainous neuralgia; Headache - cluster; Horton's headache; Vascular headache - cluster ... be related to the body's sudden release of histamine (chemical in the body released during an allergic ...

  17. Ranking inter-relationships between clusters

    NASA Astrophysics Data System (ADS)

    Wang, Tingting; Chen, Feng; Phoebe Chen, Yi-Ping

    2011-12-01

    The evaluation of the relationships between clusters is important to identify vital unknown information in many real-life applications, such as in the fields of crime detection, evolution trees, metallurgical industry and biology engraftment. This article proposes a method called 'mode pattern + mutual information' to rank the inter-relationship between clusters. The idea of the mode pattern is used to find outstanding objects from each cluster, and the mutual information criterion measures the close proximity of a pair of clusters. Our approach is different from the conventional algorithms of classifying and clustering, because our focus is not to classify objects into different clusters, but instead, we aim to rank the inter-relationship between clusters when the clusters are given. We conducted experiments on a wide range of real-life datasets, including image data and cancer diagnosis data. The experimental results show that our algorithm is effective and promising.

  18. Meaningful Clusters

    SciTech Connect

    Sanfilippo, Antonio P.; Calapristi, Augustin J.; Crow, Vernon L.; Hetzler, Elizabeth G.; Turner, Alan E.

    2004-05-26

    We present an approach to the disambiguation of cluster labels that capitalizes on the notion of semantic similarity to assign WordNet senses to cluster labels. The approach provides interesting insights on how document clustering can provide the basis for developing a novel approach to word sense disambiguation.

  19. Splitting Methods for Convex Clustering

    PubMed Central

    Chi, Eric C.; Lange, Kenneth

    2016-01-01

    Clustering is a fundamental problem in many scientific applications. Standard methods such as k-means, Gaussian mixture models, and hierarchical clustering, however, are beset by local minima, which are sometimes drastically suboptimal. Recently introduced convex relaxations of k-means and hierarchical clustering shrink cluster centroids toward one another and ensure a unique global minimizer. In this work we present two splitting methods for solving the convex clustering problem. The first is an instance of the alternating direction method of multipliers (ADMM); the second is an instance of the alternating minimization algorithm (AMA). In contrast to previously considered algorithms, our ADMM and AMA formulations provide simple and unified frameworks for solving the convex clustering problem under the previously studied norms and open the door to potentially novel norms. We demonstrate the performance of our algorithm on both simulated and real data examples. While the differences between the two algorithms appear to be minor on the surface, complexity analysis and numerical experiments show AMA to be significantly more efficient. This article has supplemental materials available online. PMID:27087770

  20. About the Clusters Program

    EPA Pesticide Factsheets

    The Environmental Technology Innovation Clusters Program advises cluster organizations, encourages collaboration between clusters, tracks U.S. environmental technology clusters, and connects EPA programs to cluster needs.

  1. Structural transitions in clusters.

    PubMed

    Hartke, Bernd

    2002-05-03

    If one adds more particles to a cluster, the energetically optimal structure is neither preserved nor does it change in a continuous fashion. Instead, one finds several cluster size regions where one structural principle dominates almost without exception, and rather narrow boundary regions in-between. The structure of the solid is usually reached only at relatively large sizes, after more than one structural transition. The occurrence of this general phenomenon of size-dependent structural transitions does not seem to depend on the nature of the particles, it is found for atomic, molecular, homogeneous, and heterogeneous clusters alike. Clearly, it is a collective many-body phenomenon which can in principle be calculated but not understood in a fully reductionistic manner. Actual calculations with sufficient accuracy are not feasible today, because of the enormous computational expense, even when unconventional evolutionary algorithms are employed for global geometry optimization. Therefore, simple rules for cluster structures are highly desirable. In fact, we are dealing here not just with the academic quest for linkages between cluster structure and features of the potential energy surface, but structural transitions in clusters are also of immediate relevance for many natural and industrial processes, ranging from crystal growth all the way to nanotechnology. This article provides an exemplary overview of research on this topic, from simple model systems where first qualitative explanations start to be successful, up to more realistic complex systems which are still beyond our understanding.

  2. Clustering Millions of Faces by Identity.

    PubMed

    Otto, Charles; Wang, Dayong; Jain, Anil

    2017-03-07

    Given a large collection of unlabeled face images, we address the problem of clustering faces into an unknown number of identities. This problem is of interest in social media, law enforcement, and other applications, where the number of faces can be of the order of hundreds of million, while the number of identities (clusters) can range from a few thousand to millions. To address the challenges of run-time complexity and cluster quality, we present an approximate Rank-Order clustering algorithm that performs better than popular clustering algorithms (k-Means and Spectral). Our experiments include clustering up to 123 million face images into over 10 million clusters. Clustering results are analyzed in terms of external (known face labels) and internal (unknown face labels) quality measures, and run-time. Our algorithm achieves an F-measure of 0:87 on the LFW benchmark (13K faces of 5; 749 individuals), which drops to 0:27 on the largest dataset considered (13K faces in LFW + 123M distractor images). Additionally, we show that frames in the YouTube benchmark can be clustered with an F-measure of 0:71. An internal per-cluster quality measure is developed to rank individual clusters for manual exploration of high quality clusters that are compact and isolated.

  3. ConsensusCluster: a software tool for unsupervised cluster discovery in numerical data.

    PubMed

    Seiler, Michael; Huang, C Chris; Szalma, Sandor; Bhanot, Gyan

    2010-02-01

    We have created a stand-alone software tool, ConsensusCluster, for the analysis of high-dimensional single nucleotide polymorphism (SNP) and gene expression microarray data. Our software implements the consensus clustering algorithm and principal component analysis to stratify the data into a given number of robust clusters. The robustness is achieved by combining clustering results from data and sample resampling as well as by averaging over various algorithms and parameter settings to achieve accurate, stable clustering results. We have implemented several different clustering algorithms in the software, including K-Means, Partition Around Medoids, Self-Organizing Map, and Hierarchical clustering methods. After clustering the data, ConsensusCluster generates a consensus matrix heatmap to give a useful visual representation of cluster membership, and automatically generates a log of selected features that distinguish each pair of clusters. ConsensusCluster gives more robust and more reliable clusters than common software packages and, therefore, is a powerful unsupervised learning tool that finds hidden patterns in data that might shed light on its biological interpretation. This software is free and available from http://code.google.com/p/consensus-cluster .

  4. Discriminative clustering via extreme learning machine.

    PubMed

    Huang, Gao; Liu, Tianchi; Yang, Yan; Lin, Zhiping; Song, Shiji; Wu, Cheng

    2015-10-01

    Discriminative clustering is an unsupervised learning framework which introduces the discriminative learning rule of supervised classification into clustering. The underlying assumption is that a good partition (clustering) of the data should yield high discrimination, namely, the partitioned data can be easily classified by some classification algorithms. In this paper, we propose three discriminative clustering approaches based on Extreme Learning Machine (ELM). The first algorithm iteratively trains weighted ELM (W-ELM) classifier to gradually maximize the data discrimination. The second and third methods are both built on Fisher's Linear Discriminant Analysis (LDA); but one approach adopts alternative optimization, while the other leverages kernel k-means. We show that the proposed algorithms can be easily implemented, and yield competitive clustering accuracy on real world data sets compared to state-of-the-art clustering methods.

  5. Clustering granulometric features

    NASA Astrophysics Data System (ADS)

    Brun, Marcel; Balagurunathan, Yoganand; Barrera, Junior; Dougherty, Edward R.

    2002-05-01

    Granulometric features have been widely used for classification, segmentation and recently in estimation of parameters in shape models. In this paper we study the inference of clustering based on granulometric features for a collection of structuring probes in the context of random models. We use random Boolean models to represent grains of different shapes and structure. It is known that granulometric features are excellent descriptors of shape and structure of grains. Inference based on clustering these features helps to analyze the consistency of these features and clustering algorithms. This greatly aids in classifier design and feature selection. Features and the order of their addition play a role in reducing the inference errors. We study four different types of feature addition methods and the effect of replication in reducing the inference errors.

  6. A statistical algorithm showing coenzyme Q10 and citrate synthase as biomarkers for mitochondrial respiratory chain enzyme activities.

    PubMed

    Yubero, D; Adin, A; Montero, R; Jou, C; Jiménez-Mallebrera, C; García-Cazorla, A; Nascimento, A; O'Callaghan, M M; Montoya, J; Gort, L; Navas, P; Ribes, A; Ugarte, M D; Artuch, R

    2016-12-01

    Laboratory data interpretation for the assessment of complex biological systems remains a great challenge, as occurs in mitochondrial function research studies. The classical biochemical data interpretation of patients versus reference values may be insufficient, and in fact the current classifications of mitochondrial patients are still done on basis of probability criteria. We have developed and applied a mathematic agglomerative algorithm to search for correlations among the different biochemical variables of the mitochondrial respiratory chain in order to identify populations displaying correlation coefficients >0.95. We demonstrated that coenzyme Q10 may be a better biomarker of mitochondrial respiratory chain enzyme activities than the citrate synthase activity. Furthermore, the application of this algorithm may be useful to re-classify mitochondrial patients or to explore associations among other biochemical variables from different biological systems.

  7. Partially supervised speaker clustering.

    PubMed

    Tang, Hao; Chu, Stephen Mingyu; Hasegawa-Johnson, Mark; Huang, Thomas S

    2012-05-01

    model-based distance metrics, 2) our advocated use of the cosine distance metric yields consistent increases in the speaker clustering performance as compared to the commonly used euclidean distance metric, 3) our partially supervised speaker clustering concept and strategies significantly improve the speaker clustering performance over the baselines, and 4) our proposed LSDA algorithm further leads to state-of-the-art speaker clustering performance.

  8. Clustering gene expression data using a diffraction‐inspired framework

    PubMed Central

    2012-01-01

    Background The recent developments in microarray technology has allowed for the simultaneous measurement of gene expression levels. The large amount of captured data challenges conventional statistical tools for analysing and finding inherent correlations between genes and samples. The unsupervised clustering approach is often used, resulting in the development of a wide variety of algorithms. Typical clustering algorithms require selecting certain parameters to operate, for instance the number of expected clusters, as well as defining a similarity measure to quantify the distance between data points. The diffraction‐based clustering algorithm however is designed to overcome this necessity for user‐defined parameters, as it is able to automatically search the data for any underlying structure. Methods The diffraction‐based clustering algorithm presented in this paper is tested using five well‐known expression datasets pertaining to cancerous tissue samples. The clustering results are then compared to those results obtained from conventional algorithms such as the k‐means, fuzzy c‐means, self‐organising map, hierarchical clustering algorithm, Gaussian mixture model and density‐based spatial clustering of applications with noise (DBSCAN). The performance of each algorithm is measured using an average external criterion and an average validity index. Results The diffraction‐based clustering algorithm is shown to be independent of the number of clusters as the algorithm searches the feature space and requires no form of parameter selection. The results show that the diffraction‐based clustering algorithm performs significantly better on the real biological datasets compared to the other existing algorithms. Conclusion The results of the diffraction‐based clustering algorithm presented in this paper suggest that the method can provide researchers with a new tool for successfully analysing microarray data. PMID:23164195

  9. A compilation of jet finding algorithms

    SciTech Connect

    Flaugher, B.; Meier, K.

    1992-12-31

    Technical descriptions of jet finding algorithms currently in use in p{anti p} collider experiments (CDF, UA1, UA2), e{sup +}e{sup {minus}} experiments and Monte-Carlo event generators (LUND programs, ISAJET) have been collected. For the hadron collider experiments, the clustering methods fall into two categories: cone algorithms and nearest-neighbor algorithms. In addition, UA2 has employed a combination of both methods for some analysis. While there are clearly differences between the cone and nearest-neighbor algorithms, the authors have found that there are also differences among the cone algorithms in the details of how the centroid of a cone cluster is located and how the E{sub T} and P{sub T} of the jet are defined. The most commonly used jet algorithm in electron-positron experiments is the JADE-type cluster algorithm. Five various incarnations of this approach have been described.

  10. Analyzing geographic clustered response

    SciTech Connect

    Merrill, D.W.; Selvin, S.; Mohr, M.S.

    1991-08-01

    In the study of geographic disease clusters, an alternative to traditional methods based on rates is to analyze case locations on a transformed map in which population density is everywhere equal. Although the analyst's task is thereby simplified, the specification of the density equalizing map projection (DEMP) itself is not simple and continues to be the subject of considerable research. Here a new DEMP algorithm is described, which avoids some of the difficulties of earlier approaches. The new algorithm (a) avoids illegal overlapping of transformed polygons; (b) finds the unique solution that minimizes map distortion; (c) provides constant magnification over each map polygon; (d) defines a continuous transformation over the entire map domain; (e) defines an inverse transformation; (f) can accept optional constraints such as fixed boundaries; and (g) can use commercially supported minimization software. Work is continuing to improve computing efficiency and improve the algorithm. 21 refs., 15 figs., 2 tabs.

  11. Segmentation of color images based on the gravitational clustering concept

    NASA Astrophysics Data System (ADS)

    Lai, Andrew H.; Yung, H. C.

    1998-03-01

    A new clustering algorithm derived from the Markovian model of the gravitational clustering concept is proposed that works in the RGB measurement space for color image. To enable the model to be applicable in image segmentation, the new algorithm imposes a clustering constraint at each clustering iteration to control and determine the formation of multiple clusters. Using such constraint to limit the attraction between clusters, a termination condition can be easily defined. The new clustering algorithm is evaluated objectively and subjectively on three different images against the K-means clustering algorithm, the recursive histogram clustering algorithm for color, the Hedley-Yan algorithm, and the widely used seed-based region growing algorithm. From the evaluation, it is observed that the new algorithm exhibits the following characteristics: (1) its objective measurement figures are comparable with the best in this group of segmentation algorithms; (2) it generates smoother region boundaries; (3) the segmented boundaries align closely with the original boundaries; and (4) it forms a meaningful number of segmented regions.

  12. Iterative Discovery of Multiple AlternativeClustering Views.

    PubMed

    Donglin Niu; Dy, Jennifer G; Jordan, Michael I

    2014-07-01

    Complex data can be grouped and interpreted in many different ways. Most existing clustering algorithms, however, only find one clustering solution, and provide little guidance to data analysts who may not be satisfied with that single clustering and may wish to explore alternatives. We introduce a novel approach that provides several clustering solutions to the user for the purposes of exploratory data analysis. Our approach additionally captures the notion that alternative clusterings may reside in different subspaces (or views). We present an algorithm that simultaneously finds these subspaces and the corresponding clusterings. The algorithm is based on an optimization procedure that incorporates terms for cluster quality and novelty relative to previously discovered clustering solutions. We present a range of experiments that compare our approach to alternatives and explore the connections between simultaneous and iterative modes of discovery of multiple clusterings.

  13. Geometric Clustering and its Applications

    DTIC Science & Technology

    2013-10-31

    limited theoretical treatment exists. As a by- product , we present the first R-tree based algorithm for Rfn. Our algorithms do not assume that either P...student, James McClain. On a related subject, we made progress on accurate localization of RFID tags in three dimensions [7]. 4 Clustering on Road...Hekimian-Williams, B. Grant, Xiuwen Liu, Zhenghao Zhang, and P. Kumar. Accurate localization of rfid tags using phase difference. In RFID , 2010 IEEE

  14. The SMART CLUSTER METHOD - adaptive earthquake cluster analysis and declustering

    NASA Astrophysics Data System (ADS)

    Schaefer, Andreas; Daniell, James; Wenzel, Friedemann

    2016-04-01

    Earthquake declustering is an essential part of almost any statistical analysis of spatial and temporal properties of seismic activity with usual applications comprising of probabilistic seismic hazard assessments (PSHAs) and earthquake prediction methods. The nature of earthquake clusters and subsequent declustering of earthquake catalogues plays a crucial role in determining the magnitude-dependent earthquake return period and its respective spatial variation. Various methods have been developed to address this issue from other researchers. These have differing ranges of complexity ranging from rather simple statistical window methods to complex epidemic models. This study introduces the smart cluster method (SCM), a new methodology to identify earthquake clusters, which uses an adaptive point process for spatio-temporal identification. Hereby, an adaptive search algorithm for data point clusters is adopted. It uses the earthquake density in the spatio-temporal neighbourhood of each event to adjust the search properties. The identified clusters are subsequently analysed to determine directional anisotropy, focussing on a strong correlation along the rupture plane and adjusts its search space with respect to directional properties. In the case of rapid subsequent ruptures like the 1992 Landers sequence or the 2010/2011 Darfield-Christchurch events, an adaptive classification procedure is applied to disassemble subsequent ruptures which may have been grouped into an individual cluster using near-field searches, support vector machines and temporal splitting. The steering parameters of the search behaviour are linked to local earthquake properties like magnitude of completeness, earthquake density and Gutenberg-Richter parameters. The method is capable of identifying and classifying earthquake clusters in space and time. It is tested and validated using earthquake data from California and New Zealand. As a result of the cluster identification process, each event in

  15. Genetic algorithms

    NASA Technical Reports Server (NTRS)

    Wang, Lui; Bayer, Steven E.

    1991-01-01

    Genetic algorithms are mathematical, highly parallel, adaptive search procedures (i.e., problem solving methods) based loosely on the processes of natural genetics and Darwinian survival of the fittest. Basic genetic algorithms concepts are introduced, genetic algorithm applications are introduced, and results are presented from a project to develop a software tool that will enable the widespread use of genetic algorithm technology.

  16. 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.

  17. Feature Clustering for Accelerating Parallel Coordinate Descent

    SciTech Connect

    Scherrer, Chad; Tewari, Ambuj; Halappanavar, Mahantesh; Haglin, David J.

    2012-12-06

    We demonstrate an approach for accelerating calculation of the regularization path for L1 sparse logistic regression problems. We show the benefit of feature clustering as a preconditioning step for parallel block-greedy coordinate descent algorithms.

  18. Ckmeans.1d.dp: Optimal k-means Clustering in One Dimension by Dynamic Programming.

    PubMed

    Wang, Haizhou; Song, Mingzhou

    2011-12-01

    The heuristic k-means algorithm, widely used for cluster analysis, does not guarantee optimality. We developed a dynamic programming algorithm for optimal one-dimensional clustering. The algorithm is implemented as an R package called Ckmeans.1d.dp. We demonstrate its advantage in optimality and runtime over the standard iterative k-means algorithm.

  19. A local search for a graph clustering problem

    NASA Astrophysics Data System (ADS)

    Navrotskaya, Anna; Il'ev, Victor

    2016-10-01

    In the clustering problems one has to partition a given set of objects (a data set) into some subsets (called clusters) taking into consideration only similarity of the objects. One of most visual formalizations of clustering is graph clustering, that is grouping the vertices of a graph into clusters taking into consideration the edge structure of the graph whose vertices are objects and edges represent similarities between the objects. In the graph k-clustering problem the number of clusters does not exceed k and the goal is to minimize the number of edges between clusters and the number of missing edges within clusters. This problem is NP-hard for any k ≥ 2. We propose a polynomial time (2k-1)-approximation algorithm for graph k-clustering. Then we apply a local search procedure to the feasible solution found by this algorithm and hold experimental research of obtained heuristics.

  20. Quintuplet Cluster

    NASA Technical Reports Server (NTRS)

    1999-01-01

    Penetrating 25,000 light-years of obscuring dust and myriad stars, NASA's Hubble Space Telescope has provided the clearest view yet of one of the largest young clusters of stars inside our Milky Way galaxy, located less than 100 light-years from the very center of the Galaxy. Having the equivalent mass greater than 10,000 stars like our sun, the monster cluster is ten times larger than typical young star clusters scattered throughout our Milky Way. It is destined to be ripped apart in just a few million years by gravitational tidal forces in the galaxy's core. But in its brief lifetime it shines more brightly than any other star cluster in the Galaxy. Quintuplet Cluster is 4 million years old. It has stars on the verge of blowing up as supernovae. It is the home of the brightest star seen in the galaxy, called the Pistol star. This image was taken in infrared light by Hubble's NICMOS camera in September 1997. The false colors correspond to infrared wavelengths. The galactic center stars are white, the red stars are enshrouded in dust or behind dust, and the blue stars are foreground stars between us and the Milky Way's center. The cluster is hidden from direct view behind black dust clouds in the constellation Sagittarius. If the cluster could be seen from earth it would appear to the naked eye as a 3rd magnitude star, 1/6th of a full moon's diameter apart.

  1. Voting-based consensus clustering for combining multiple clusterings of chemical structures

    PubMed Central

    2012-01-01

    Background Although many consensus clustering methods have been successfully used for combining multiple classifiers in many areas such as machine learning, applied statistics, pattern recognition and bioinformatics, few consensus clustering methods have been applied for combining multiple clusterings of chemical structures. It is known that any individual clustering method will not always give the best results for all types of applications. So, in this paper, three voting and graph-based consensus clusterings were used for combining multiple clusterings of chemical structures to enhance the ability of separating biologically active molecules from inactive ones in each cluster. Results The cumulative voting-based aggregation algorithm (CVAA), cluster-based similarity partitioning algorithm (CSPA) and hyper-graph partitioning algorithm (HGPA) were examined. The F-measure and Quality Partition Index method (QPI) were used to evaluate the clusterings and the results were compared to the Ward’s clustering method. The MDL Drug Data Report (MDDR) dataset was used for experiments and was represented by two 2D fingerprints, ALOGP and ECFP_4. The performance of voting-based consensus clustering method outperformed the Ward’s method using F-measure and QPI method for both ALOGP and ECFP_4 fingerprints, while the graph-based consensus clustering methods outperformed the Ward’s method only for ALOGP using QPI. The Jaccard and Euclidean distance measures were the methods of choice to generate the ensembles, which give the highest values for both criteria. Conclusions The results of the experiments show that consensus clustering methods can improve the effectiveness of chemical structures clusterings. The cumulative voting-based aggregation algorithm (CVAA) was the method of choice among consensus clustering methods. PMID:23244782

  2. SMART: Unique Splitting-While-Merging Framework for Gene Clustering

    PubMed Central

    Fa, Rui; Roberts, David J.; Nandi, Asoke K.

    2014-01-01

    Successful clustering algorithms are highly dependent on parameter settings. The clustering performance degrades significantly unless parameters are properly set, and yet, it is difficult to set these parameters a priori. To address this issue, in this paper, we propose a unique splitting-while-merging clustering framework, named “splitting merging awareness tactics” (SMART), which does not require any a priori knowledge of either the number of clusters or even the possible range of this number. Unlike existing self-splitting algorithms, which over-cluster the dataset to a large number of clusters and then merge some similar clusters, our framework has the ability to split and merge clusters automatically during the process and produces the the most reliable clustering results, by intrinsically integrating many clustering techniques and tasks. The SMART framework is implemented with two distinct clustering paradigms in two algorithms: competitive learning and finite mixture model. Nevertheless, within the proposed SMART framework, many other algorithms can be derived for different clustering paradigms. The minimum message length algorithm is integrated into the framework as the clustering selection criterion. The usefulness of the SMART framework and its algorithms is tested in demonstration datasets and simulated gene expression datasets. Moreover, two real microarray gene expression datasets are studied using this approach. Based on the performance of many metrics, all numerical results show that SMART is superior to compared existing self-splitting algorithms and traditional algorithms. Three main properties of the proposed SMART framework are summarized as: (1) needing no parameters dependent on the respective dataset or a priori knowledge about the datasets, (2) extendible to many different applications, (3) offering superior performance compared with counterpart algorithms. PMID:24714159

  3. Spitzer Clusters

    NASA Astrophysics Data System (ADS)

    Krick, Kessica

    This proposal is a specific response to the strategic goal of NASA's research program to "discover how the universe works and explore how the universe evolved into its present form." Towards this goal, we propose to mine the Spitzer archive for all observations of galaxy groups and clusters for the purpose of studying galaxy evolution in clusters, contamination rates for Sunyaev Zeldovich cluster surveys, and to provide a database of Spitzer observed clusters to the broader community. Funding from this proposal will go towards two years of support for a Postdoc to do this work. After searching the Spitzer Heritage Archive, we have found 194 unique galaxy groups and clusters that have data from both the Infrared array camera (IRAC; Fazio et al. 2004) at 3.6 - 8 microns and the multiband imaging photometer for Spitzer (MIPS; Rieke et al. 2004) at 24microns. This large sample will add value beyond the individual datasets because it will be a larger sample of IR clusters than ever before and will have sufficient diversity in mass, redshift, and dynamical state to allow us to differentiate amongst the effects of these cluster properties. An infrared sample is important because it is unaffected by dust extinction while at the same time is an excellent measure of both stellar mass (IRAC wavelengths) and star formation rate (MIPS wavelengths). Additionally, IRAC can be used to differentiate star forming galaxies (SFG) from active galactic nuclei (AGN), due to their different spectral shapes in this wavelength regime. Specifically, we intend to identify SFG and AGN in galaxy groups and clusters. Groups and clusters differ from the field because the galaxy densities are higher, there is a large potential well due mainly to the mass of the dark matter, and there is hot X-ray gas (the intracluster medium; ICM). We will examine the impact of these differences in environment on galaxy formation by comparing cluster properties of AGN and SFG to those in the field. Also, we will

  4. Convalescing Cluster Configuration Using a Superlative Framework

    PubMed Central

    Sabitha, R.; Karthik, S.

    2015-01-01

    Competent data mining methods are vital to discover knowledge from databases which are built as a result of enormous growth of data. Various techniques of data mining are applied to obtain knowledge from these databases. Data clustering is one such descriptive data mining technique which guides in partitioning data objects into disjoint segments. K-means algorithm is a versatile algorithm among the various approaches used in data clustering. The algorithm and its diverse adaptation methods suffer certain problems in their performance. To overcome these issues a superlative algorithm has been proposed in this paper to perform data clustering. The specific feature of the proposed algorithm is discretizing the dataset, thereby improving the accuracy of clustering, and also adopting the binary search initialization method to generate cluster centroids. The generated centroids are fed as input to K-means approach which iteratively segments the data objects into respective clusters. The clustered results are measured for accuracy and validity. Experiments conducted by testing the approach on datasets from the UC Irvine Machine Learning Repository evidently show that the accuracy and validity measure is higher than the other two approaches, namely, simple K-means and Binary Search method. Thus, the proposed approach proves that discretization process will improve the efficacy of descriptive data mining tasks. PMID:26543895

  5. Pattern Clustering Using a Swarm Intelligence Approach

    NASA Astrophysics Data System (ADS)

    Das, Swagatam; Abraham, Ajith

    Clustering aims at representing large datasets by a fewer number of prototypes or clusters. It brings simplicity in modeling data and thus plays a central role in the process of knowledge discovery and data mining. Data mining tasks, in these days, require fast and accurate partitioning of huge datasets, which may come with a variety of attributes or features. This, in turn, imposes severe computational requirements on the relevant clustering techniques. A family of bio-inspired algorithms, well-known as Swarm Intelligence (SI) has recently emerged that meets these requirements and has successfully been applied to a number of real world clustering problems. This chapter explores the role of SI in clustering different kinds of datasets. It finally describes a new SI technique for partitioning a linearly non-separable dataset into an optimal number of clusters in the kernel- induced feature space. Computer simulations undertaken in this research have also been provided to demonstrate the effectiveness of the proposed algorithm.

  6. Galaxy Clusters

    NASA Astrophysics Data System (ADS)

    Miller, Christopher J. Miller

    2012-03-01

    There are many examples of clustering in astronomy. Stars in our own galaxy are often seen as being gravitationally bound into tight globular or open clusters. The Solar System's Trojan asteroids cluster at the gravitational Langrangian in front of Jupiter’s orbit. On the largest of scales, we find gravitationally bound clusters of galaxies, the Virgo cluster (in the constellation of Virgo at a distance of ˜50 million light years) being a prime nearby example. The Virgo cluster subtends an angle of nearly 8◦ on the sky and is known to contain over a thousand member galaxies. Galaxy clusters play an important role in our understanding of theUniverse. Clusters exist at peaks in the three-dimensional large-scale matter density field. Their sky (2D) locations are easy to detect in astronomical imaging data and their mean galaxy redshifts (redshift is related to the third spatial dimension: distance) are often better (spectroscopically) and cheaper (photometrically) when compared with the entire galaxy population in large sky surveys. Photometric redshift (z) [Photometric techniques use the broad band filter magnitudes of a galaxy to estimate the redshift. Spectroscopic techniques use the galaxy spectra and emission/absorption line features to measure the redshift] determinations of galaxies within clusters are accurate to better than delta_z = 0.05 [7] and when studied as a cluster population, the central galaxies form a line in color-magnitude space (called the the E/S0 ridgeline and visible in Figure 16.3) that contains galaxies with similar stellar populations [15]. The shape of this E/S0 ridgeline enables astronomers to measure the cluster redshift to within delta_z = 0.01 [23]. The most accurate cluster redshift determinations come from spectroscopy of the member galaxies, where only a fraction of the members need to be spectroscopically observed [25,42] to get an accurate redshift to the whole system. If light traces mass in the Universe, then the locations

  7. On evaluating clustering procedures for use in classification

    NASA Technical Reports Server (NTRS)

    Pore, M. D.; Moritz, T. E.; Register, D. T.; Yao, S. S.; Eppler, W. G. (Principal Investigator)

    1979-01-01

    The problem of evaluating clustering algorithms and their respective computer programs for use in a preprocessing step for classification is addressed. In clustering for classification the probability of correct classification is suggested as the ultimate measure of accuracy on training data. A means of implementing this criterion and a measure of cluster purity are discussed. Examples are given. A procedure for cluster labeling that is based on cluster purity and sample size is presented.

  8. [Cluster analysis and its application].

    PubMed

    Půlpán, Zdenĕk

    2002-01-01

    The study exploits knowledge-oriented and context-based modification of well-known algorithms of (fuzzy) clustering. The role of fuzzy sets is inherently inclined towards coping with linguistic domain knowledge also. We try hard to obtain from rich diverse data and knowledge new information about enviroment that is being explored.

  9. DICON: interactive visual analysis of multidimensional clusters.

    PubMed

    Cao, Nan; Gotz, David; Sun, Jimeng; Qu, Huamin

    2011-12-01

    Clustering as a fundamental data analysis technique has been widely used in many analytic applications. However, it is often difficult for users to understand and evaluate multidimensional clustering results, especially the quality of clusters and their semantics. For large and complex data, high-level statistical information about the clusters is often needed for users to evaluate cluster quality while a detailed display of multidimensional attributes of the data is necessary to understand the meaning of clusters. In this paper, we introduce DICON, an icon-based cluster visualization that embeds statistical information into a multi-attribute display to facilitate cluster interpretation, evaluation, and comparison. We design a treemap-like icon to represent a multidimensional cluster, and the quality of the cluster can be conveniently evaluated with the embedded statistical information. We further develop a novel layout algorithm which can generate similar icons for similar clusters, making comparisons of clusters easier. User interaction and clutter reduction are integrated into the system to help users more effectively analyze and refine clustering results for large datasets. We demonstrate the power of DICON through a user study and a case study in the healthcare domain. Our evaluation shows the benefits of the technique, especially in support of complex multidimensional cluster analysis.

  10. Unbridled growth of spin-glass clusters

    NASA Astrophysics Data System (ADS)

    Kessler, David A.; Bretz, Michael

    1990-03-01

    We investigate the application of the recent cluster-based acceleration methods of Wolff and of Kandel et al. to the problem of simulating spin glasses. We find the techniques offer no improvement as the clusters generated by these algorithms are infinitely large or interact infinitely strongly, respectively. We comment on the reasons for this failure.

  11. Star clusters

    NASA Astrophysics Data System (ADS)

    Labhardt, Lukas; Binggeli, Bruno

    Star clusters are at the heart of astronomy, being key objects for our understanding of stellar evolution and galactic structure. Observations with the Hubble Space Telescope and other modern equipment have revealed fascinating new facts about these galactic building blocks. This book provides two comprehensive and up-to-date, pedagogically designed reviews on star clusters by two well-known experts in the field. Bruce Carney presents our current knowledge of the relative and absolute ages of globular clusters and the chemical history of our Galaxy. Bill Harris addresses globular clusters in external galaxies and their use as tracers of galaxy formation and cosmic distance indicators. The book is written for graduate students as well as professionals in astronomy and astrophysics.

  12. Occupational Clusters.

    ERIC Educational Resources Information Center

    Pottawattamie County School System, Council Bluffs, IA.

    The 15 occupational clusters (transportation, fine arts and humanities, communications and media, personal service occupations, construction, hospitality and recreation, health occupations, marine science occupations, consumer and homemaking-related occupations, agribusiness and natural resources, environment, public service, business and office…

  13. Cluster generator

    DOEpatents

    Donchev, Todor I.; Petrov, Ivan G.

    2011-05-31

    Described herein is an apparatus and a method for producing atom clusters based on a gas discharge within a hollow cathode. The hollow cathode includes one or more walls. The one or more walls define a sputtering chamber within the hollow cathode and include a material to be sputtered. A hollow anode is positioned at an end of the sputtering chamber, and atom clusters are formed when a gas discharge is generated between the hollow anode and the hollow cathode.

  14. Stream Clustering of Growing Objects

    NASA Astrophysics Data System (ADS)

    Siddiqui, Zaigham Faraz; Spiliopoulou, Myra

    We study incremental clustering of objects that grow and accumulate over time. The objects come from a multi-table stream e.g. streams of Customer and Transaction. As the Transactions stream accumulates, the Customers’ profiles grow. First, we use an incremental propositionalisation to convert the multi-table stream into a single-table stream upon which we apply clustering. For this purpose, we develop an online version of K-Means algorithm that can handle these swelling objects and any new objects that arrive. The algorithm also monitors the quality of the model and performs re-clustering when it deteriorates. We evaluate our method on the PKDD Challenge 1999 dataset.

  15. A Bayesian Alternative to Mutual Information for the Hierarchical Clustering of Dependent Random Variables

    PubMed Central

    Marrelec, Guillaume; Messé, Arnaud; Bellec, Pierre

    2015-01-01

    The use of mutual information as a similarity measure in agglomerative hierarchical clustering (AHC) raises an important issue: some correction needs to be applied for the dimensionality of variables. In this work, we formulate the decision of merging dependent multivariate normal variables in an AHC procedure as a Bayesian model comparison. We found that the Bayesian formulation naturally shrinks the empirical covariance matrix towards a matrix set a priori (e.g., the identity), provides an automated stopping rule, and corrects for dimensionality using a term that scales up the measure as a function of the dimensionality of the variables. Also, the resulting log Bayes factor is asymptotically proportional to the plug-in estimate of mutual information, with an additive correction for dimensionality in agreement with the Bayesian information criterion. We investigated the behavior of these Bayesian alternatives (in exact and asymptotic forms) to mutual information on simulated and real data. An encouraging result was first derived on simulations: the hierarchical clustering based on the log Bayes factor outperformed off-the-shelf clustering techniques as well as raw and normalized mutual information in terms of classification accuracy. On a toy example, we found that the Bayesian approaches led to results that were similar to those of mutual information clustering techniques, with the advantage of an automated thresholding. On real functional magnetic resonance imaging (fMRI) datasets measuring brain activity, it identified clusters consistent with the established outcome of standard procedures. On this application, normalized mutual information had a highly atypical behavior, in the sense that it systematically favored very large clusters. These initial experiments suggest that the proposed Bayesian alternatives to mutual information are a useful new tool for hierarchical clustering. PMID:26406245

  16. Clustering with shallow trees

    NASA Astrophysics Data System (ADS)

    Bailly-Bechet, M.; Bradde, S.; Braunstein, A.; Flaxman, A.; Foini, L.; Zecchina, R.

    2009-12-01

    We propose a new method for obtaining hierarchical clustering based on the optimization of a cost function over trees of limited depth, and we derive a message-passing method that allows one to use it efficiently. The method and the associated algorithm can be interpreted as a natural interpolation between two well-known approaches, namely that of single linkage and the recently presented affinity propagation. We analyse using this general scheme three biological/medical structured data sets (human population based on genetic information, proteins based on sequences and verbal autopsies) and show that the interpolation technique provides new insight.

  17. Clustering PPI data by combining FA and SHC method

    PubMed Central

    2015-01-01

    Clustering is one of main methods to identify functional modules from protein-protein interaction (PPI) data. Nevertheless traditional clustering methods may not be effective for clustering PPI data. In this paper, we proposed a novel method for clustering PPI data by combining firefly algorithm (FA) and synchronization-based hierarchical clustering (SHC) algorithm. Firstly, the PPI data are preprocessed via spectral clustering (SC) which transforms the high-dimensional similarity matrix into a low dimension matrix. Then the SHC algorithm is used to perform clustering. In SHC algorithm, hierarchical clustering is achieved by enlarging the neighborhood radius of synchronized objects continuously, while the hierarchical search is very difficult to find the optimal neighborhood radius of synchronization and the efficiency is not high. So we adopt the firefly algorithm to determine the optimal threshold of the neighborhood radius of synchronization automatically. The proposed algorithm is tested on the MIPS PPI dataset. The results show that our proposed algorithm is better than the traditional algorithms in precision, recall and f-measure value. PMID:25707632

  18. Clustering PPI data by combining FA and SHC method.

    PubMed

    Lei, Xiujuan; Ying, Chao; Wu, Fang-Xiang; Xu, Jin

    2015-01-01

    Clustering is one of main methods to identify functional modules from protein-protein interaction (PPI) data. Nevertheless traditional clustering methods may not be effective for clustering PPI data. In this paper, we proposed a novel method for clustering PPI data by combining firefly algorithm (FA) and synchronization-based hierarchical clustering (SHC) algorithm. Firstly, the PPI data are preprocessed via spectral clustering (SC) which transforms the high-dimensional similarity matrix into a low dimension matrix. Then the SHC algorithm is used to perform clustering. In SHC algorithm, hierarchical clustering is achieved by enlarging the neighborhood radius of synchronized objects continuously, while the hierarchical search is very difficult to find the optimal neighborhood radius of synchronization and the efficiency is not high. So we adopt the firefly algorithm to determine the optimal threshold of the neighborhood radius of synchronization automatically. The proposed algorithm is tested on the MIPS PPI dataset. The results show that our proposed algorithm is better than the traditional algorithms in precision, recall and f-measure value.

  19. Quantum Algorithms

    NASA Technical Reports Server (NTRS)

    Abrams, D.; Williams, C.

    1999-01-01

    This thesis describes several new quantum algorithms. These include a polynomial time algorithm that uses a quantum fast Fourier transform to find eigenvalues and eigenvectors of a Hamiltonian operator, and that can be applied in cases for which all know classical algorithms require exponential time.

  20. Detecting galaxy clusters in the DLS and CARS: a Bayesian cluster finder

    NASA Astrophysics Data System (ADS)

    Ascaso, B.; Wittman, D.; Benítez, N.

    2011-11-01

    The detection of galaxy clusters in present and future surveys enables measuring mass-to-light ratios, clustering properties or galaxy cluster abundances and therefore, constraining cosmological parameters. We present a new technique for detecting galaxy clusters, which is based on the Matched Filter Algorithm from a Bayesian point of view. The method is able to determine the position, redshift and richness of the cluster through the maximization of a filter depending on galaxy luminosity, density and photometric redshift combined with a galaxy cluster prior. We tested the algorithm through realistic mock galaxy catalogs, revealing that the detections are 100% complete and 80% pure for clusters up to z < 1.2 and richer than λ ≥ 25 (Abell richness ≥ 0). We applied the algorithm to the CFHTLS Archive Research Survey (CARS) data, recovering similar detections as previously published using the same data plus additional clusters that are very probably real. We also applied this algorithm to the Deep Lens Survey (DLS), obtaining the first sample of optical-selected galaxy in this survey. The sample is complete up to redshift 0.7 and we detect more than 780 cluster candidates up to redshift 1.2. We conclude by discussing the differences between previous weak lensing detections in this survey and optical detections in both samples.

  1. Handwritten text line segmentation by spectral clustering

    NASA Astrophysics Data System (ADS)

    Han, Xuecheng; Yao, Hui; Zhong, Guoqiang

    2017-02-01

    Since handwritten text lines are generally skewed and not obviously separated, text line segmentation of handwritten document images is still a challenging problem. In this paper, we propose a novel text line segmentation algorithm based on the spectral clustering. Given a handwritten document image, we convert it to a binary image first, and then compute the adjacent matrix of the pixel points. We apply spectral clustering on this similarity metric and use the orthogonal kmeans clustering algorithm to group the text lines. Experiments on Chinese handwritten documents database (HIT-MW) demonstrate the effectiveness of the proposed method.

  2. When is Constrained Clustering Beneficial, and Why?

    NASA Technical Reports Server (NTRS)

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

    2006-01-01

    Several researchers have shown that constraints can improve the results of a variety of clustering algorithms. However, there can be a large variation in this improvement, even for a fixed number of constraints for a given data set. We present the first attempt to provide insight into this phenomenon by characterizing two constraint set properties: informativeness and coherence. We show that these measures can help explain why some constraint sets are more beneficial to clustering algorithms than others. Since they can be computed prior to clustering, these measures can aid in deciding which constraints to use in practice.

  3. Breaking the hierarchy - a new cluster selection mechanism for hierarchical clustering methods

    PubMed Central

    Zahoránszky, László A; Katona, Gyula Y; Hári, Péter; Málnási-Csizmadia, András; Zweig, Katharina A; Zahoránszky-Köhalmi, Gergely

    2009-01-01

    Background Hierarchical clustering methods like Ward's method have been used since decades to understand biological and chemical data sets. In order to get a partition of the data set, it is necessary to choose an optimal level of the hierarchy by a so-called level selection algorithm. In 2005, a new kind of hierarchical clustering method was introduced by Palla et al. that differs in two ways from Ward's method: it can be used on data on which no full similarity matrix is defined and it can produce overlapping clusters, i.e., allow for multiple membership of items in clusters. These features are optimal for biological and chemical data sets but until now no level selection algorithm has been published for this method. Results In this article we provide a general selection scheme, the level independent clustering selection method, called LInCS. With it, clusters can be selected from any level in quadratic time with respect to the number of clusters. Since hierarchically clustered data is not necessarily associated with a similarity measure, the selection is based on a graph theoretic notion of cohesive clusters. We present results of our method on two data sets, a set of drug like molecules and set of protein-protein interaction (PPI) data. In both cases the method provides a clustering with very good sensitivity and specificity values according to a given reference clustering. Moreover, we can show for the PPI data set that our graph theoretic cohesiveness measure indeed chooses biologically homogeneous clusters and disregards inhomogeneous ones in most cases. We finally discuss how the method can be generalized to other hierarchical clustering methods to allow for a level independent cluster selection. Conclusion Using our new cluster selection method together with the method by Palla et al. provides a new interesting clustering mechanism that allows to compute overlapping clusters, which is especially valuable for biological and chemical data sets. PMID:19840391

  4. An Evaluation of Cluster Analytic Approaches to Initial Model Specification.

    ERIC Educational Resources Information Center

    Bacon, Donald R.

    2001-01-01

    Evaluated the performance of several alternative cluster analytic approaches to initial model specification using population parameter analyses and a Monte Carlo simulation. Of the six cluster approaches evaluated, the one using the correlations of item correlations as a proximity metric and average linking as a clustering algorithm performed the…

  5. The APM Galaxy Survey - V. Catalogues of galaxy clusters

    NASA Astrophysics Data System (ADS)

    Dalton, G. B.; Maddox, S. J.; Sutherland, W. J.; Efstathiou, G.

    1997-08-01

    We describe the construction of catalogues of galaxy clusters from the APM Galaxy survey using an automated algorithm based on Abell-like selection criteria. We investigate the effects of varying several parameters in our selection algorithm, including the magnitude range and radius from the cluster centre used to estimate the cluster richnesses. We quantify the accuracy of the photometric distance estimates by comparing them with measured redshifts, and we investigate the stability and completeness of the resulting catalogues. We find that the angular correlation functions for different cluster catalogues are in good agreement with one another, and are also consistent with the observed amplitude of the spatial correlation function of rich clusters.

  6. Considerations on the thermal performances of ribbed channels by means of a novel dynamic method for hierarchical clustering

    NASA Astrophysics Data System (ADS)

    Niro, A.; Fustinoni, D.; Vignati, F.; Gramazio, P.; Ciminà, S.

    2016-09-01

    The investigation of ribbed surfaces for the enhancement of heat transfer in forced convection allowed to observe that different geometries may lead to comparable performances. Due to the lack of an underlying structure of the data, a novel method for data clustering is introduced here, to assess to what extent comparable performances can be achieved using different rib geometries. The clustering method is an agglomerative technique, based on the inclusion of each configuration in another ones bounding box, whose size depends dynamically on the Nusselt number and the pumping power. The method is applied to a large database experimentally obtained at ThermALab of Politecnico di Milano, in order to identify the Nusselt number and the friction factor for diverse-rib configurations in a large-aspect ratio channel with low-Reynolds flows. The clusters are determined, and the resulting families of configurations are used to assess the possible effects of the rib geometry on the thermal and fluid-dynamic performances. The clustering analysis results suggest interesting considerations.

  7. Bipartite graph partitioning and data clustering

    SciTech Connect

    Zha, Hongyuan; He, Xiaofeng; Ding, Chris; Gu, Ming; Simon, Horst D.

    2001-05-07

    Many data types arising from data mining applications can be modeled as bipartite graphs, examples include terms and documents in a text corpus, customers and purchasing items in market basket analysis and reviewers and movies in a movie recommender system. In this paper, the authors propose a new data clustering method based on partitioning the underlying biopartite graph. The partition is constructed by minimizing a normalized sum of edge weights between unmatched pairs of vertices of the bipartite graph. They show that an approximate solution to the minimization problem can be obtained by computing a partial singular value decomposition (SVD) of the associated edge weight matrix of the bipartite graph. They point out the connection of their clustering algorithm to correspondence analysis used in multivariate analysis. They also briefly discuss the issue of assigning data objects to multiple clusters. In the experimental results, they apply their clustering algorithm to the problem of document clustering to illustrate its effectiveness and efficiency.

  8. Clustering of High Throughput Gene Expression Data

    PubMed Central

    Pirim, Harun; Ekşioğlu, Burak; Perkins, Andy; Yüceer, Çetin

    2012-01-01

    High throughput biological data need to be processed, analyzed, and interpreted to address problems in life sciences. Bioinformatics, computational biology, and systems biology deal with biological problems using computational methods. Clustering is one of the methods used to gain insight into biological processes, particularly at the genomics level. Clearly, clustering can be used in many areas of biological data analysis. However, this paper presents a review of the current clustering algorithms designed especially for analyzing gene expression data. It is also intended to introduce one of the main problems in bioinformatics - clustering gene expression data - to the operations research community. PMID:23144527

  9. Scaling law of Wolff cluster surface energy

    NASA Astrophysics Data System (ADS)

    Hsiao, Pai-Yi; Monceau, Pascal

    2003-05-01

    We study the scaling properties of the clusters grown by the Wolff algorithm on seven different Sierpinski-type fractals of Hausdorff dimension 1cluster follows a power law with respect to the lattice size. Moreover, we investigate the probability density distribution of the surface energy of the Wolff cluster and are able to establish a different scaling relation. It enables us to introduce an exponent that is associated to the surface energy of the Wolff cluster. Finally, this exponent is linked to a dynamical exponent via an inequality.

  10. SAR image segmentation with entropy ranking based adaptive semi-supervised spectral clustering

    NASA Astrophysics Data System (ADS)

    Zhang, Xiangrong; Yang, Jie; Hou, Biao; Jiao, Licheng

    2010-10-01

    Spectral clustering has become one of the most popular modern clustering algorithms in recent years. In this paper, a new algorithm named entropy ranking based adaptive semi-supervised spectral clustering for SAR image segmentation is proposed. We focus not only on finding a suitable scaling parameter but also determining automatically the cluster number with the entropy ranking theory. Also, two kinds of constrains must-link and cannot-link based semi-supervised spectral clustering is applied to gain better segmentation results. Experimental results on SAR images show that the proposed method outperforms other spectral clustering algorithms.

  11. Learner Typologies Development Using OIndex and Data Mining Based Clustering Techniques

    ERIC Educational Resources Information Center

    Luan, Jing

    2004-01-01

    This explorative data mining project used distance based clustering algorithm to study 3 indicators, called OIndex, of student behavioral data and stabilized at a 6-cluster scenario following an exhaustive explorative study of 4, 5, and 6 cluster scenarios produced by K-Means and TwoStep algorithms. Using principles in data mining, the study…

  12. New Star Clusters Discovered in the GLIMPSE Survey

    NASA Astrophysics Data System (ADS)

    Mercer, E. P.; Clemens, D. P.; Meade, M. R.; Babler, B. L.; Indebetouw, R.; Whitney, B. A.; Watson, C.; Wolfire, M. G.; Wolff, M. J.; Bania, T. M.; Benjamin, R. A.; Cohen, M.; Dickey, J. M.; Jackson, J. M.; Kobulnicky, H. A.; Mathis, J. S.; Stauffer, J. R.; Stolovy, S. R.; Uzpen, B.; Churchwell, E. B.

    2005-12-01

    A systematic and automated search of the extensive GLIMPSE mid-infrared survey data of the inner Galaxy was carried out to uncover new star clusters. This search has yielded 59 new clusters. Using our automated search algorithm, these clusters were identified as significant localized overdensities in the GLIMPSE point-source catalog (GLMC) and archive (GLMA). Subsequent visual inspection of the GLIMPSE image mosaics confirmed the existence of these clusters plus an additional 33 heavily embedded clusters missed by our detection algorithm, for a total of 92 newly discovered clusters. These previously uncataloged clusters range in type from heavily embedded to fully exposed clusters. More than half of the clusters have memberships exceeding 35 stars, and nearly all the clusters have diameters of 3' or less. The Galactic latitude distribution of the clusters reveals that the majority are concentrated toward the Galactic midplane. There is an asymmetry in the number of clusters located above and below the midplane, with more clusters detected below the midplane. We also observe an asymmetry in the number of clusters detected in the northern and southern halves of the Galaxy, with more than twice as many clusters detected in the south.

  13. Matlab Cluster Ensemble Toolbox v. 1.0

    SciTech Connect

    2009-04-27

    This is a Matlab toolbox for investigating the application of cluster ensembles to data classification, with the objective of improving the accuracy and/or speed of clustering. The toolbox divides the cluster ensemble problem into four areas, providing functionality for each. These include, (1) synthetic data generation, (2) clustering to generate individual data partitions and similarity matrices, (3) consensus function generation and final clustering to generate ensemble data partitioning, and (4) implementation of accuracy metrics. With regard to data generation, Gaussian data of arbitrary dimension can be generated. The kcenters algorithm can then be used to generate individual data partitions by either, (a) subsampling the data and clustering each subsample, or by (b) randomly initializing the algorithm and generating a clustering for each initialization. In either case an overall similarity matrix can be computed using a consensus function operating on the individual similarity matrices. A final clustering can be performed and performance metrics are provided for evaluation purposes.

  14. Complementary ensemble clustering of biomedical data.

    PubMed

    Fodeh, Samah Jamal; Brandt, Cynthia; Luong, Thai Binh; Haddad, Ali; Schultz, Martin; Murphy, Terrence; Krauthammer, Michael

    2013-06-01

    The rapidly growing availability of electronic biomedical data has increased the need for innovative data mining methods. Clustering in particular has been an active area of research in many different application areas, with existing clustering algorithms mostly focusing on one modality or representation of the data. Complementary ensemble clustering (CEC) is a recently introduced framework in which Kmeans is applied to a weighted, linear combination of the coassociation matrices obtained from separate ensemble clustering of different data modalities. The strength of CEC is its extraction of information from multiple aspects of the data when forming the final clusters. This study assesses the utility of CEC in biomedical data, which often have multiple data modalities, e.g., text and images, by applying CEC to two distinct biomedical datasets (PubMed images and radiology reports) that each have two modalities. Referent to five different clustering approaches based on the Kmeans algorithm, CEC exhibited equal or better performance in the metrics of micro-averaged precision and Normalized Mutual Information across both datasets. The reference methods included clustering of single modalities as well as ensemble clustering of separate and merged data modalities. Our experimental results suggest that CEC is equivalent or more efficient than comparable Kmeans based clustering methods using either single or merged data modalities.

  15. Maximum Margin Clustering of Hyperspectral Data

    NASA Astrophysics Data System (ADS)

    Niazmardi, S.; Safari, A.; Homayouni, S.

    2013-09-01

    In recent decades, large margin methods such as Support Vector Machines (SVMs) are supposed to be the state-of-the-art of supervised learning methods for classification of hyperspectral data. However, the results of these algorithms mainly depend on the quality and quantity of available training data. To tackle down the problems associated with the training data, the researcher put effort into extending the capability of large margin algorithms for unsupervised learning. One of the recent proposed algorithms is Maximum Margin Clustering (MMC). The MMC is an unsupervised SVMs algorithm that simultaneously estimates both the labels and the hyperplane parameters. Nevertheless, the optimization of the MMC algorithm is a non-convex problem. Most of the existing MMC methods rely on the reformulating and the relaxing of the non-convex optimization problem as semi-definite programs (SDP), which are computationally very expensive and only can handle small data sets. Moreover, most of these algorithms are two-class classification, which cannot be used for classification of remotely sensed data. In this paper, a new MMC algorithm is used that solve the original non-convex problem using Alternative Optimization method. This algorithm is also extended for multi-class classification and its performance is evaluated. The results of the proposed algorithm show that the algorithm has acceptable results for hyperspectral data clustering.

  16. Cluster bulleticity

    NASA Astrophysics Data System (ADS)

    Massey, Richard; Kitching, Thomas; Nagai, Daisuke

    2011-05-01

    The unique properties of dark matter are revealed during collisions between clusters of galaxies, such as the bullet cluster (1E 0657-56) and baby bullet (MACS J0025-12). These systems provide evidence for an additional, invisible mass in the separation between the distributions of their total mass, measured via gravitational lensing, and their ordinary 'baryonic' matter, measured via its X-ray emission. Unfortunately, the information available from these systems is limited by their rarity. Constraints on the properties of dark matter, such as its interaction cross-section, are therefore restricted by uncertainties in the individual systems' impact velocity, impact parameter and orientation with respect to the line of sight. Here we develop a complementary, statistical measurement in which every piece of substructure falling into every massive cluster is treated as a bullet. We define 'bulleticity' as the mean separation between dark matter and ordinary matter, and we measure the signal in hydrodynamical simulations. The phase space of substructure orbits also exhibits symmetries that provide an equivalent control test. Any detection of bulleticity in real data would indicate a difference in the interaction cross-sections of baryonic and dark matter that may rule out hypotheses of non-particulate dark matter that are otherwise able to model individual systems. A subsequent measurement of bulleticity could constrain the dark matter cross-section. Even with conservative estimates, the existing Hubble Space Telescope archive should yield an independent constraint tighter than that from the bullet cluster. This technique is then trivially extendable to and benefits enormously from larger, future surveys.

  17. Multiple Manifold Clustering Using Curvature Constrained Path

    PubMed Central

    Babaeian, Amir; Bayestehtashk, Alireza; Bandarabadi, Mojtaba

    2015-01-01

    The problem of multiple surface clustering is a challenging task, particularly when the surfaces intersect. Available methods such as Isomap fail to capture the true shape of the surface near by the intersection and result in incorrect clustering. The Isomap algorithm uses shortest path between points. The main draw back of the shortest path algorithm is due to the lack of curvature constrained where causes to have a path between points on different surfaces. In this paper we tackle this problem by imposing a curvature constraint to the shortest path algorithm used in Isomap. The algorithm chooses several landmark nodes at random and then checks whether there is a curvature constrained path between each landmark node and every other node in the neighborhood graph. We build a binary feature vector for each point where each entry represents the connectivity of that point to a particular landmark. Then the binary feature vectors could be used as a input of conventional clustering algorithm such as hierarchical clustering. We apply our method to simulated and some real datasets and show, it performs comparably to the best methods such as K-manifold and spectral multi-manifold clustering. PMID:26375819

  18. Using clustering for document reconstruction

    NASA Astrophysics Data System (ADS)

    Ukovich, Anna; Zacchigna, Alessandra; Ramponi, Giovanni; Schoier, Gabriella

    2006-02-01

    In the forensics and investigative science fields there may arise the need of reconstructing documents which have been destroyed by means of a shredder. In a computer-based reconstruction, the pieces are described by numerical features, which represent the visual content of the strips. Usually, the pieces of different pages have been mixed. We propose an approach for the reconstruction which performs a first clustering on the strips to ease the successive matching, be it manual (with the help of a computer) or automatic. A number of features, extracted by means of image processing algorithms, have been selected for this aim. The results show the effectiveness of the features and of the proposed clustering algorithm.

  19. Mean-field behavior of cluster dynamics

    NASA Astrophysics Data System (ADS)

    Persky, N.; Ben-Av, R.; Kanter, I.; Domany, E.

    1996-09-01

    The dynamic behavior of cluster algorithms is analyzed in the classical mean-field limit. Rigorous analytical results below Tc establish that the dynamic exponent has the value zSW=1 for the Swendsen-Wang algorithm and zW=0 for the Wolff algorithm. An efficient Monte Carlo implementation is introduced, adapted for using these algorithms for fully connected graphs. Extensive simulations both above and below Tc demonstrate scaling and evaluate the finite-size scaling function by means of a rather impressive collapse of the data.

  20. Canonical PSO Based K-Means Clustering Approach for Real Datasets.

    PubMed

    Dey, Lopamudra; Chakraborty, Sanjay

    2014-01-01

    "Clustering" the significance and application of this technique is spread over various fields. Clustering is an unsupervised process in data mining, that is why the proper evaluation of the results and measuring the compactness and separability of the clusters are important issues. The procedure of evaluating the results of a clustering algorithm is known as cluster validity measure. Different types of indexes are used to solve different types of problems and indices selection depends on the kind of available data. This paper first proposes Canonical PSO based K-means clustering algorithm and also analyses some important clustering indices (intercluster, intracluster) and then evaluates the effects of those indices on real-time air pollution database, wholesale customer, wine, and vehicle datasets using typical K-means, Canonical PSO based K-means, simple PSO based K-means, DBSCAN, and Hierarchical clustering algorithms. This paper also describes the nature of the clusters and finally compares the performances of these clustering algorithms according to the validity assessment. It also defines which algorithm will be more desirable among all these algorithms to make proper compact clusters on this particular real life datasets. It actually deals with the behaviour of these clustering algorithms with respect to validation indexes and represents their results of evaluation in terms of mathematical and graphical forms.

  1. Adaptive cluster detection

    NASA Astrophysics Data System (ADS)

    Friedenberg, David

    2010-10-01

    the rate of falsely detected active regions. Additionally we examine the more general field of clustering and develop a framework for clustering algorithms based around diffusion maps. Diffusion maps can be used to project high-dimensional data into a lower dimensional space while preserving much of the structure in the data. We demonstrate how diffusion maps can be used to solve clustering problems and examine the influence of tuning parameters on the results. We introduce two novel methods, the self-tuning diffusion map which replaces the global scaling parameter in the typical diffusion map framework with a local scaling parameter and an algorithm for automatically selecting tuning parameters based on a cross-validation style score called prediction strength. The methods are tested on several example datasets.

  2. CiSE: a circular spring embedder layout algorithm.

    PubMed

    Dogrusoz, Ugur; Belviranli, Mehmet E; Dilek, Alptug

    2013-06-01

    We present a new algorithm for automatic layout of clustered graphs using a circular style. The algorithm tries to determine optimal location and orientation of individual clusters intrinsically within a modified spring embedder. Heuristics such as reversal of the order of nodes in a cluster and swap of neighboring node pairs in the same cluster are employed intermittently to further relax the spring embedder system, resulting in reduced inter-cluster edge crossings. Unlike other algorithms generating circular drawings, our algorithm does not require the quotient graph to be acyclic, nor does it sacrifice the edge crossing number of individual clusters to improve respective positioning of the clusters. Moreover, it reduces the total area required by a cluster by using the space inside the associated circle. Experimental results show that the execution time and quality of the produced drawings with respect to commonly accepted layout criteria are quite satisfactory, surpassing previous algorithms. The algorithm has also been successfully implemented and made publicly available as part of a compound and clustered graph editing and layout tool named CHISIO.

  3. A GMBCG GALAXY CLUSTER CATALOG OF 55,424 RICH CLUSTERS FROM SDSS DR7

    SciTech Connect

    Hao Jiangang; Annis, James; Johnston, David E.; McKay, Timothy A.; Evrard, August; Siegel, Seth R.; Gerdes, David; Koester, Benjamin P.; Rykoff, Eli S.; Rozo, Eduardo; Wechsler, Risa H.; Busha, Michael; Becker, Matthew; Sheldon, Erin

    2010-12-15

    We present a large catalog of optically selected galaxy clusters from the application of a new Gaussian Mixture Brightest Cluster Galaxy (GMBCG) algorithm to SDSS Data Release 7 data. The algorithm detects clusters by identifying the red-sequence plus brightest cluster galaxy (BCG) feature, which is unique for galaxy clusters and does not exist among field galaxies. Red-sequence clustering in color space is detected using an Error Corrected Gaussian Mixture Model. We run GMBCG on 8240 deg{sup 2} of photometric data from SDSS DR7 to assemble the largest ever optical galaxy cluster catalog, consisting of over 55,000 rich clusters across the redshift range from 0.1 < z < 0.55. We present Monte Carlo tests of completeness and purity and perform cross-matching with X-ray clusters and with the maxBCG sample at low redshift. These tests indicate high completeness and purity across the full redshift range for clusters with 15 or more members.

  4. Collaborative Clustering for Sensor Networks

    NASA Technical Reports Server (NTRS)

    Wagstaff. Loro :/; Green Jillian; Lane, Terran

    2011-01-01

    Traditionally, nodes in a sensor network simply collect data and then pass it on to a centralized node that archives, distributes, and possibly analyzes the data. However, analysis at the individual nodes could enable faster detection of anomalies or other interesting events, as well as faster responses such as sending out alerts or increasing the data collection rate. There is an additional opportunity for increased performance if individual nodes can communicate directly with their neighbors. Previously, a method was developed by which machine learning classification algorithms could collaborate to achieve high performance autonomously (without requiring human intervention). This method worked for supervised learning algorithms, in which labeled data is used to train models. The learners collaborated by exchanging labels describing the data. The new advance enables clustering algorithms, which do not use labeled data, to also collaborate. This is achieved by defining a new language for collaboration that uses pair-wise constraints to encode useful information for other learners. These constraints specify that two items must, or cannot, be placed into the same cluster. Previous work has shown that clustering with these constraints (in isolation) already improves performance. In the problem formulation, each learner resides at a different node in the sensor network and makes observations (collects data) independently of the other learners. Each learner clusters its data and then selects a pair of items about which it is uncertain and uses them to query its neighbors. The resulting feedback (a must and cannot constraint from each neighbor) is combined by the learner into a consensus constraint, and it then reclusters its data while incorporating the new constraint. A strategy was also proposed for cleaning the resulting constraint sets, which may contain conflicting constraints; this improves performance significantly. This approach has been applied to collaborative

  5. Scheduling algorithms

    NASA Astrophysics Data System (ADS)

    Wolfe, William J.; Wood, David; Sorensen, Stephen E.

    1996-12-01

    This paper discusses automated scheduling as it applies to complex domains such as factories, transportation, and communications systems. The window-constrained-packing problem is introduced as an ideal model of the scheduling trade offs. Specific algorithms are compared in terms of simplicity, speed, and accuracy. In particular, dispatch, look-ahead, and genetic algorithms are statistically compared on randomly generated job sets. The conclusion is that dispatch methods are fast and fairly accurate; while modern algorithms, such as genetic and simulate annealing, have excessive run times, and are too complex to be practical.

  6. Haplotyping algorithms

    SciTech Connect

    Sobel, E.; Lange, K.; O`Connell, J.R.

    1996-12-31

    Haplotyping is the logical process of inferring gene flow in a pedigree based on phenotyping results at a small number of genetic loci. This paper formalizes the haplotyping problem and suggests four algorithms for haplotype reconstruction. These algorithms range from exhaustive enumeration of all haplotype vectors to combinatorial optimization by simulated annealing. Application of the algorithms to published genetic analyses shows that manual haplotyping is often erroneous. Haplotyping is employed in screening pedigrees for phenotyping errors and in positional cloning of disease genes from conserved haplotypes in population isolates. 26 refs., 6 figs., 3 tabs.

  7. A data-driven approach to estimating the number of clusters in hierarchical clustering

    PubMed Central

    Zambelli, Antoine E.

    2016-01-01

    DNA microarray and gene expression problems often require a researcher to perform clustering on their data in a bid to better understand its structure. In cases where the number of clusters is not known, one can resort to hierarchical clustering methods. However, there currently exist very few automated algorithms for determining the true number of clusters in the data. We propose two new methods (mode and maximum difference) for estimating the number of clusters in a hierarchical clustering framework to create a fully automated process with no human intervention. These methods are compared to the established elbow and gap statistic algorithms using simulated datasets and the Biobase Gene ExpressionSet. We also explore a data mixing procedure inspired by cross validation techniques. We find that the overall performance of the maximum difference method is comparable or greater to that of the gap statistic in multi-cluster scenarios, and achieves that performance at a fraction of the computational cost. This method also responds well to our mixing procedure, which opens the door to future research. We conclude that both the mode and maximum difference methods warrant further study related to their mixing and cross-validation potential. We particularly recommend the use of the maximum difference method in multi-cluster scenarios given its accuracy and execution times, and present it as an alternative to existing algorithms.

  8. Clustering with Missing Values: No Imputation Required

    NASA Technical Reports Server (NTRS)

    Wagstaff, Kiri

    2004-01-01

    Clustering algorithms can identify groups in large data sets, such as star catalogs and hyperspectral images. In general, clustering methods cannot analyze items that have missing data values. Common solutions either fill in the missing values (imputation) or ignore the missing data (marginalization). Imputed values are treated as just as reliable as the truly observed data, but they are only as good as the assumptions used to create them. In contrast, we present a method for encoding partially observed features as a set of supplemental soft constraints and introduce the KSC algorithm, which incorporates constraints into the clustering process. In experiments on artificial data and data from the Sloan Digital Sky Survey, we show that soft constraints are an effective way to enable clustering with missing values.

  9. Entropy-based cluster validation and estimation of the number of clusters in gene expression data.

    PubMed

    Novoselova, Natalia; Tom, Igor

    2012-10-01

    Many external and internal validity measures have been proposed in order to estimate the number of clusters in gene expression data but as a rule they do not consider the analysis of the stability of the groupings produced by a clustering algorithm. Based on the approach assessing the predictive power or stability of a partitioning, we propose the new measure of cluster validation and the selection procedure to determine the suitable number of clusters. The validity measure is based on the estimation of the "clearness" of the consensus matrix, which is the result of a resampling clustering scheme or consensus clustering. According to the proposed selection procedure the stable clustering result is determined with the reference to the validity measure for the null hypothesis encoding for the absence of clusters. The final number of clusters is selected by analyzing the distance between the validity plots for initial and permutated data sets. We applied the selection procedure to estimate the clustering results on several datasets. As a result the proposed procedure produced an accurate and robust estimate of the number of clusters, which are in agreement with the biological knowledge and gold standards of cluster quality.

  10. Reactive Collision Avoidance Algorithm

    NASA Technical Reports Server (NTRS)

    Scharf, Daniel; Acikmese, Behcet; Ploen, Scott; Hadaegh, Fred

    2010-01-01

    The reactive collision avoidance (RCA) algorithm allows a spacecraft to find a fuel-optimal trajectory for avoiding an arbitrary number of colliding spacecraft in real time while accounting for acceleration limits. In addition to spacecraft, the technology can be used for vehicles that can accelerate in any direction, such as helicopters and submersibles. In contrast to existing, passive algorithms that simultaneously design trajectories for a cluster of vehicles working to achieve a common goal, RCA is implemented onboard spacecraft only when an imminent collision is detected, and then plans a collision avoidance maneuver for only that host vehicle, thus preventing a collision in an off-nominal situation for which passive algorithms cannot. An example scenario for such a situation might be when a spacecraft in the cluster is approaching another one, but enters safe mode and begins to drift. Functionally, the RCA detects colliding spacecraft, plans an evasion trajectory by solving the Evasion Trajectory Problem (ETP), and then recovers after the collision is avoided. A direct optimization approach was used to develop the algorithm so it can run in real time. In this innovation, a parameterized class of avoidance trajectories is specified, and then the optimal trajectory is found by searching over the parameters. The class of trajectories is selected as bang-off-bang as motivated by optimal control theory. That is, an avoiding spacecraft first applies full acceleration in a constant direction, then coasts, and finally applies full acceleration to stop. The parameter optimization problem can be solved offline and stored as a look-up table of values. Using a look-up table allows the algorithm to run in real time. Given a colliding spacecraft, the properties of the collision geometry serve as indices of the look-up table that gives the optimal trajectory. For multiple colliding spacecraft, the set of trajectories that avoid all spacecraft is rapidly searched on

  11. A spatial dirichlet process mixture model for clustering population genetics data.

    PubMed

    Reich, Brian J; Bondell, Howard D

    2011-06-01

    Identifying homogeneous groups of individuals is an important problem in population genetics. Recently, several methods have been proposed that exploit spatial information to improve clustering algorithms. In this article, we develop a Bayesian clustering algorithm based on the Dirichlet process prior that uses both genetic and spatial information to classify individuals into homogeneous clusters for further study. We study the performance of our method using a simulation study and use our model to cluster wolverines in Western Montana using microsatellite data.

  12. Q+: characterizing the structure of young star clusters

    NASA Astrophysics Data System (ADS)

    Jaffa, S. E.; Whitworth, A. P.; Lomax, O.

    2017-04-01

    Many young star clusters appear to be fractal, i.e. they appear to be concentrated in a nested hierarchy of clusters within clusters. We present a new algorithm for statistically analysing the distribution of stars to quantify the level of substructure. We suggest that, even at the simplest level, the internal structure of a fractal cluster requires the specification of three parameters. (i) The 3D fractal dimension, D, measures the extent to which the clusters on one level of the nested hierarchy fill the volume of their parent cluster. (ii) The number of levels, L, reflects the finite ratio between the linear size of the large root-cluster at the top of the hierarchy, and the smallest leaf-clusters at the bottom of the hierarchy. (iii) The volume-density scaling exponent, C = -d ln [δ n]/d ln [L] measures the factor by which the excess density, δn, in a structure of scale L, exceeds that of the background formed by larger structures; it is similar, but not exactly equivalent, to the exponent in Larson's scaling relation between density and size for molecular clouds. We describe an algorithm that can be used to constrain the values of (D,L,C) and apply this method to artificial and observed clusters. We show that this algorithm is able to reliably describe the three-dimensional structure of an artificial star cluster from the two-dimensional projection, and quantify the varied structures observed in real and simulated clusters.

  13. A Short Survey of Document Structure Similarity Algorithms

    SciTech Connect

    Buttler, D

    2004-02-27

    This paper provides a brief survey of document structural similarity algorithms, including the optimal Tree Edit Distance algorithm and various approximation algorithms. The approximation algorithms include the simple weighted tag similarity algorithm, Fourier transforms of the structure, and a new application of the shingle technique to structural similarity. We show three surprising results. First, the Fourier transform technique proves to be the least accurate of any of approximation algorithms, while also being slowest. Second, optimal Tree Edit Distance algorithms may not be the best technique for clustering pages from different sites. Third, the simplest approximation to structure may be the most effective and efficient mechanism for many applications.

  14. Canonical PSO Based K-Means Clustering Approach for Real Datasets

    PubMed Central

    Dey, Lopamudra; Chakraborty, Sanjay

    2014-01-01

    “Clustering” the significance and application of this technique is spread over various fields. Clustering is an unsupervised process in data mining, that is why the proper evaluation of the results and measuring the compactness and separability of the clusters are important issues. The procedure of evaluating the results of a clustering algorithm is known as cluster validity measure. Different types of indexes are used to solve different types of problems and indices selection depends on the kind of available data. This paper first proposes Canonical PSO based K-means clustering algorithm and also analyses some important clustering indices (intercluster, intracluster) and then evaluates the effects of those indices on real-time air pollution database, wholesale customer, wine, and vehicle datasets using typical K-means, Canonical PSO based K-means, simple PSO based K-means, DBSCAN, and Hierarchical clustering algorithms. This paper also describes the nature of the clusters and finally compares the performances of these clustering algorithms according to the validity assessment. It also defines which algorithm will be more desirable among all these algorithms to make proper compact clusters on this particular real life datasets. It actually deals with the behaviour of these clustering algorithms with respect to validation indexes and represents their results of evaluation in terms of mathematical and graphical forms. PMID:27355083

  15. Estimating the Concrete Compressive Strength Using Hard Clustering and Fuzzy Clustering Based Regression Techniques

    PubMed Central

    Nagwani, Naresh Kumar; Deo, Shirish V.

    2014-01-01

    Understanding of the compressive strength of concrete is important for activities like construction arrangement, prestressing operations, and proportioning new mixtures and for the quality assurance. Regression techniques are most widely used for prediction tasks where relationship between the independent variables and dependent (prediction) variable is identified. The accuracy of the regression techniques for prediction can be improved if clustering can be used along with regression. Clustering along with regression will ensure the more accurate curve fitting between the dependent and independent variables. In this work cluster regression technique is applied for estimating the compressive strength of the concrete and a novel state of the art is proposed for predicting the concrete compressive strength. The objective of this work is to demonstrate that clustering along with regression ensures less prediction errors for estimating the concrete compressive strength. The proposed technique consists of two major stages: in the first stage, clustering is used to group the similar characteristics concrete data and then in the second stage regression techniques are applied over these clusters (groups) to predict the compressive strength from individual clusters. It is found from experiments that clustering along with regression techniques gives minimum errors for predicting compressive strength of concrete; also fuzzy clustering algorithm C-means performs better than K-means algorithm. PMID:25374939

  16. Estimating the concrete compressive strength using hard clustering and fuzzy clustering based regression techniques.

    PubMed

    Nagwani, Naresh Kumar; Deo, Shirish V

    2014-01-01

    Understanding of the compressive strength of concrete is important for activities like construction arrangement, prestressing operations, and proportioning new mixtures and for the quality assurance. Regression techniques are most widely used for prediction tasks where relationship between the independent variables and dependent (prediction) variable is identified. The accuracy of the regression techniques for prediction can be improved if clustering can be used along with regression. Clustering along with regression will ensure the more accurate curve fitting between the dependent and independent variables. In this work cluster regression technique is applied for estimating the compressive strength of the concrete and a novel state of the art is proposed for predicting the concrete compressive strength. The objective of this work is to demonstrate that clustering along with regression ensures less prediction errors for estimating the concrete compressive strength. The proposed technique consists of two major stages: in the first stage, clustering is used to group the similar characteristics concrete data and then in the second stage regression techniques are applied over these clusters (groups) to predict the compressive strength from individual clusters. It is found from experiments that clustering along with regression techniques gives minimum errors for predicting compressive strength of concrete; also fuzzy clustering algorithm C-means performs better than K-means algorithm.

  17. Modified distance in average linkage based on M-estimator and MADn criteria in hierarchical cluster analysis

    NASA Astrophysics Data System (ADS)

    Muda, Nora; Othman, Abdul Rahman

    2015-10-01

    The process of grouping a set of objects into classes of similar objects is called clustering. It divides a large group of observations into smaller groups so that the observations within each group are relatively similar and the observations in different groups are relatively dissimilar. In this study, an agglomerative method in hierarchical cluster analysis is chosen and clusters were constructed by using an average linkage technique. An average linkage technique requires distance between clusters, which is calculated based on the average distance between all pairs of points, one group with another group. In calculating the average distance, the distance will not be robust when there is an outlier. Therefore, the average distance in average linkage needs to be modified in order to overcome the problem of outlier. Therefore, the criteria of outlier detection based on MADn criteria is used and the average distance is recalculated without the outlier. Next, the distance in average linkage is calculated based on a modified one step M-estimator (MOM). The groups of cluster are presented in dendrogram graph. To evaluate the goodness of a modified distance in the average linkage clustering, the bootstrap analysis is conducted on the dendrogram graph and the bootstrap value (BP) are assessed for each branch in dendrogram that formed the group, to ensure the reliability of the branches constructed. This study found that the average linkage technique with modified distance is significantly superior than the usual average linkage technique, if there is an outlier. Both of these techniques are said to be similar if there is no outlier.

  18. Clustering of polarization-encoded images.

    PubMed

    Zallat, Jihad; Collet, Christophe; Takakura, Yoshitate

    2004-01-10

    Polarization-encoded imaging consists of the distributed measurements of polarization parameters for each pixel of an image. We address clustering of multidimensional polarization-encoded images. The spatial coherence of polarization information is considered. Two methods of analysis are proposed: polarization contrast enhancement and a more-sophisticated image-processing algorithm based on a Markovian model. The proposed algorithms are applied and validated with two different Mueller images acquired by a fully polarimetric imaging system.

  19. Minimum spanning trees for gene expression data clustering.

    PubMed

    Xu, Y; Olman, V; Xu, D

    2001-01-01

    This paper describes a new framework for microarray gene-expression data clustering. The foundation of this framework is a minimum spanning tree (MST) representation of a set of multi-dimensional gene expression data. A key property of this representation is that each cluster of the expression data corresponds to one subtree of the MST, which rigorously converts a multi-dimensional clustering problem to a tree partitioning problem. We have demonstrated that though the inter-data relationship is greatly simplified in the MST representation, no essential information is lost for the purpose of clustering. Two key advantages in representing a set of multi-dimensional data as an MST are: (1) the simple structure of a tree facilitates efficient implementations of rigorous clustering algorithms, which otherwise are highly computationally challenging; and (2) as an MST-based clustering does not depend on detailed geometric shape of a cluster, it can overcome many of the problems faced by classical clustering algorithms. Based on the MST representation, we have developed a number of rigorous and efficient clustering algorithms, including two with guaranteed global optimality. We have implemented these algorithms as a computer software EXCAVATOR. To demonstrate its effectiveness, we have tested it on two data sets, i.e., expression data from yeast Saccharomyces cerevisiae, and Arabidopsis expression data in response to chitin elicitation.

  20. Clustering Short Time-Series Microarray

    NASA Astrophysics Data System (ADS)

    Ping, Loh Wei; Hasan, Yahya Abu

    2008-01-01

    Most microarray analyses are carried out on static gene expressions. However, the dynamical study of microarrays has lately gained more attention. Most researches on time-series microarray emphasize on the bioscience and medical aspects but few from the numerical aspect. This study attempts to analyze short time-series microarray mathematically using STEM clustering tool which formally preprocess data followed by clustering. We next introduce the Circular Mould Distance (CMD) algorithm with combinations of both preprocessing and clustering analysis. Both methods are subsequently compared in terms of efficiencies.

  1. A Clustering Graph Generator

    SciTech Connect

    Winlaw, Manda; De Sterck, Hans; Sanders, Geoffrey

    2015-10-26

    In very simple terms a network can be de ned as a collection of points joined together by lines. Thus, networks can be used to represent connections between entities in a wide variety of elds including engi- neering, science, medicine, and sociology. Many large real-world networks share a surprising number of properties, leading to a strong interest in model development research and techniques for building synthetic networks have been developed, that capture these similarities and replicate real-world graphs. Modeling these real-world networks serves two purposes. First, building models that mimic the patterns and prop- erties of real networks helps to understand the implications of these patterns and helps determine which patterns are important. If we develop a generative process to synthesize real networks we can also examine which growth processes are plausible and which are not. Secondly, high-quality, large-scale network data is often not available, because of economic, legal, technological, or other obstacles [7]. Thus, there are many instances where the systems of interest cannot be represented by a single exemplar network. As one example, consider the eld of cybersecurity, where systems require testing across diverse threat scenarios and validation across diverse network structures. In these cases, where there is no single exemplar network, the systems must instead be modeled as a collection of networks in which the variation among them may be just as important as their common features. By developing processes to build synthetic models, so-called graph generators, we can build synthetic networks that capture both the essential features of a system and realistic variability. Then we can use such synthetic graphs to perform tasks such as simulations, analysis, and decision making. We can also use synthetic graphs to performance test graph analysis algorithms, including clustering algorithms and anomaly detection algorithms.

  2. Fuzzy C-Means Clustering and Energy Efficient Cluster Head Selection for Cooperative Sensor Network.

    PubMed

    Bhatti, Dost Muhammad Saqib; Saeed, Nasir; Nam, Haewoon

    2016-09-09

    We propose a novel cluster based cooperative spectrum sensing algorithm to save the wastage of energy, in which clusters are formed using fuzzy c-means (FCM) clustering and a cluster head (CH) is selected based on a sensor's location within each cluster, its location with respect to fusion center (FC), its signal-to-noise ratio (SNR) and its residual energy. The sensing information of a single sensor is not reliable enough due to shadowing and fading. To overcome these issues, cooperative spectrum sensing schemes were proposed to take advantage of spatial diversity. For cooperative spectrum sensing, all sensors sense the spectrum and report the sensed energy to FC for the final decision. However, it increases the energy consumption of the network when a large number of sensors need to cooperate; in addition to that, the efficiency of the network is also reduced. The proposed algorithm makes the cluster and selects the CHs such that very little amount of network energy is consumed and the highest efficiency of the network is achieved. Using the proposed algorithm maximum probability of detection under an imperfect channel is accomplished with minimum energy consumption as compared to conventional clustering schemes.

  3. Fuzzy C-Means Clustering and Energy Efficient Cluster Head Selection for Cooperative Sensor Network

    PubMed Central

    Bhatti, Dost Muhammad Saqib; Saeed, Nasir; Nam, Haewoon

    2016-01-01

    We propose a novel cluster based cooperative spectrum sensing algorithm to save the wastage of energy, in which clusters are formed using fuzzy c-means (FCM) clustering and a cluster head (CH) is selected based on a sensor’s location within each cluster, its location with respect to fusion center (FC), its signal-to-noise ratio (SNR) and its residual energy. The sensing information of a single sensor is not reliable enough due to shadowing and fading. To overcome these issues, cooperative spectrum sensing schemes were proposed to take advantage of spatial diversity. For cooperative spectrum sensing, all sensors sense the spectrum and report the sensed energy to FC for the final decision. However, it increases the energy consumption of the network when a large number of sensors need to cooperate; in addition to that, the efficiency of the network is also reduced. The proposed algorithm makes the cluster and selects the CHs such that very little amount of network energy is consumed and the highest efficiency of the network is achieved. Using the proposed algorithm maximum probability of detection under an imperfect channel is accomplished with minimum energy consumption as compared to conventional clustering schemes. PMID:27618061

  4. A fast meteor detection algorithm

    NASA Astrophysics Data System (ADS)

    Gural, P.

    2016-01-01

    A low latency meteor detection algorithm for use with fast steering mirrors had been previously developed to track and telescopically follow meteors in real-time (Gural, 2007). It has been rewritten as a generic clustering and tracking software module for meteor detection that meets both the demanding throughput requirements of a Raspberry Pi while also maintaining a high probability of detection. The software interface is generalized to work with various forms of front-end video pre-processing approaches and provides a rich product set of parameterized line detection metrics. Discussion will include the Maximum Temporal Pixel (MTP) compression technique as a fast thresholding option for feeding the detection module, the detection algorithm trade for maximum processing throughput, details on the clustering and tracking methodology, processing products, performance metrics, and a general interface description.

  5. Cluster headache

    PubMed Central

    Leroux, Elizabeth; Ducros, Anne

    2008-01-01

    Cluster headache (CH) is a primary headache disease characterized by recurrent short-lasting attacks (15 to 180 minutes) of excruciating unilateral periorbital pain accompanied by ipsilateral autonomic signs (lacrimation, nasal congestion, ptosis, miosis, lid edema, redness of the eye). It affects young adults, predominantly males. Prevalence is estimated at 0.5–1.0/1,000. CH has a circannual and circadian periodicity, attacks being clustered (hence the name) in bouts that can occur during specific months of the year. Alcohol is the only dietary trigger of CH, strong odors (mainly solvents and cigarette smoke) and napping may also trigger CH attacks. During bouts, attacks may happen at precise hours, especially during the night. During the attacks, patients tend to be restless. CH may be episodic or chronic, depending on the presence of remission periods. CH is associated with trigeminovascular activation and neuroendocrine and vegetative disturbances, however, the precise cautive mechanisms remain unknown. Involvement of the hypothalamus (a structure regulating endocrine function and sleep-wake rhythms) has been confirmed, explaining, at least in part, the cyclic aspects of CH. The disease is familial in about 10% of cases. Genetic factors play a role in CH susceptibility, and a causative role has been suggested for the hypocretin receptor gene. Diagnosis is clinical. Differential diagnoses include other primary headache diseases such as migraine, paroxysmal hemicrania and SUNCT syndrome. At present, there is no curative treatment. There are efficient treatments to shorten the painful attacks (acute treatments) and to reduce the number of daily attacks (prophylactic treatments). Acute treatment is based on subcutaneous administration of sumatriptan and high-flow oxygen. Verapamil, lithium, methysergide, prednisone, greater occipital nerve blocks and topiramate may be used for prophylaxis. In refractory cases, deep-brain stimulation of the hypothalamus and

  6. Formation of Cluster Complexes by Cluster-Cluster-Collisions

    NASA Astrophysics Data System (ADS)

    Ichihashi, Masahiko; Odaka, Hideho

    2015-03-01

    Multi-element clusters are interested in their chemical and physical properties, and it is expected that they are utilized as catalysts, for example. Their properties critically depend on the size, composition and atomic ordering, and it should be important to adjust the above parameters for their functionality. One of the ways to form a multi-element cluster is to employ a low-energy collision between clusters. Here, we show characteristic results obtained in the collision between a neutral Ar cluster and a size-selected Co cluster ion. Low-energy collision experiment was accomplished by using a newly developed merging-beam apparatus. Cobalt cluster ions were produced by laser ablation, and mass-selected. On the other hand, argon clusters were prepared by the supersonic expansion of Ar gas. Both cluster beams were merged together in an ion guide, and ionic cluster complexes were mass-analyzed. In the collision of Co2+ and ArN, Co2Arn+ (n = 1 - 30) were observed, and the total intensity of Co2Arn+ (n >= 1) is inversely proportional to the relative velocity between Co2+ and ArN. This suggests that the charge-induced dipole interaction between Co2+ and a neutral Ar cluster is dominant in the formation of the cluster complex, Co2+Arn.

  7. Impact of heuristics in clustering large biological networks.

    PubMed

    Shafin, Md Kishwar; Kabir, Kazi Lutful; Ridwan, Iffatur; Anannya, Tasmiah Tamzid; Karim, Rashid Saadman; Hoque, Mohammad Mozammel; Rahman, M Sohel

    2015-12-01

    Traditional clustering algorithms often exhibit poor performance for large networks. On the contrary, greedy algorithms are found to be relatively efficient while uncovering functional modules from large biological networks. The quality of the clusters produced by these greedy techniques largely depends on the underlying heuristics employed. Different heuristics based on different attributes and properties perform differently in terms of the quality of the clusters produced. This motivates us to design new heuristics for clustering large networks. In this paper, we have proposed two new heuristics and analyzed the performance thereof after incorporating those with three different combinations in a recently celebrated greedy clustering algorithm named SPICi. We have extensively analyzed the effectiveness of these new variants. The results are found to be promising.

  8. Dynamical Mass Measurements of Contaminated Galaxy Clusters Using Machine Learning

    NASA Astrophysics Data System (ADS)

    Ntampaka, Michelle; Trac, Hy; Sutherland, Dougal; Fromenteau, Sebastien; Poczos, Barnabas; Schneider, Jeff

    2016-01-01

    Galaxy clusters are a rich source of information for examining fundamental astrophysical processes and cosmological parameters, however, employing clusters as cosmological probes requires accurate mass measurements derived from cluster observables. We study dynamical mass measurements of galaxy clusters contaminated by interlopers, and show that a modern machine learning (ML) algorithm can predict masses by better than a factor of two compared to a standard scaling relation approach. We create a mock catalog from Multidark's publicly-available N-body MDPL1 simulation where a simple cylindrical cut around the cluster center allows interlopers to contaminate the clusters. In the standard approach, we use a power law scaling relation to infer cluster mass from galaxy line of sight (LOS) velocity dispersion. The presence of interlopers in the catalog produces a wide, flat fractional mass error distribution, with width = 2.13. We employ the Support Distribution Machine (SDM) class of algorithms to learn from distributions of data to predict single values. Applied to distributions of galaxy observables such as LOS velocity and projected distance from the cluster center, SDM yields better than a factor-of-two improvement (width = 0.67). Remarkably, SDM applied to contaminated clusters is better able to recover masses than even a scaling relation approach applied to uncontaminated clusters. We show that the SDM method more accurately reproduces the cluster mass function, making it a valuable tool for employing cluster observations to evaluate cosmological models.

  9. ASteCA: Automated Stellar Cluster Analysis

    NASA Astrophysics Data System (ADS)

    Perren, G. I.; Vázquez, R. A.; Piatti, A. E.

    2015-04-01

    We present the Automated Stellar Cluster Analysis package (ASteCA), a suit of tools designed to fully automate the standard tests applied on stellar clusters to determine their basic parameters. The set of functions included in the code make use of positional and photometric data to obtain precise and objective values for a given cluster's center coordinates, radius, luminosity function and integrated color magnitude, as well as characterizing through a statistical estimator its probability of being a true physical cluster rather than a random overdensity of field stars. ASteCA incorporates a Bayesian field star decontamination algorithm capable of assigning membership probabilities using photometric data alone. An isochrone fitting process based on the generation of synthetic clusters from theoretical isochrones and selection of the best fit through a genetic algorithm is also present, which allows ASteCA to provide accurate estimates for a cluster's metallicity, age, extinction and distance values along with its uncertainties. To validate the code we applied it on a large set of over 400 synthetic MASSCLEAN clusters with varying degrees of field star contamination as well as a smaller set of 20 observed Milky Way open clusters (Berkeley 7, Bochum 11, Czernik 26, Czernik 30, Haffner 11, Haffner 19, NGC 133, NGC 2236, NGC 2264, NGC 2324, NGC 2421, NGC 2627, NGC 6231, NGC 6383, NGC 6705, Ruprecht 1, Tombaugh 1, Trumpler 1, Trumpler 5 and Trumpler 14) studied in the literature. The results show that ASteCA is able to recover cluster parameters with an acceptable precision even for those clusters affected by substantial field star contamination. ASteCA is written in Python and is made available as an open source code which can be downloaded ready to be used from its official site.

  10. Scattering properties of dense clusters of colloidal nanoparticles.

    PubMed

    Lattuada, Marco; Ehrl, Lyonel

    2009-04-30

    In this work, we present a new methodology to accurately calculate scattering properties of fractal clusters with arbitrary large fractal dimension, d(f) (up to 3), and arbitrary primary particle size and material optical properties. Our approach is based on a combination of Monte Carlo simulations to generate cluster structures and mean-field T-matrix theory for the calculation of scattering properties. We have used a conventional cluster-cluster aggregation algorithm to generate clusters with d(f) up to 2.1, a tunable cluster-cluster aggregation algorithm for clusters with d(f) up to 2.5 and a newly developed Voronoi tessellation-based densification algorithm for clusters with d(f) up to 3. The scattering properties of clusters have been computed by means of mean-field T-matrix code (proposed by Botet; et al. Appl. Opt. 1997, 36 , 8791 - 8797 ), which can account for intracluster multiple scattering at a very low computational cost, thus overcoming the major limitations of commonly used Rayleigh-Debye-Gans (RDG) theory. The results of the calculations show significant deviations of the scattering cross sections and zero-angle intensities as compared to RDG theory for large primary particle sizes and high d(f). Good accuracies of the method have been confirmed by comparisons with full T-matrix calculations. The proposed approach is an ideal compromise between accuracy and high computational efficiency, and is suitable for inversion of experimental scattering data.

  11. Algorithms for Automated DNA Assembly

    DTIC Science & Technology

    2010-01-01

    polyketide synthase gene cluster. Proc. Natl Acad. Sci. USA, 101, 15573–15578. 16. Shetty,R.P., Endy,D. and Knight,T.F. Jr (2008) Engineering BioBrick vectors...correct theoretical construction scheme is de- veloped manually, it is likely to be suboptimal by any number of cost metrics. Modular, robust and...to an exhaustive search on a small synthetic dataset and our results show that our algorithms can quickly find an optimal solution. Comparison with

  12. Algorithm development

    NASA Technical Reports Server (NTRS)

    Barth, Timothy J.; Lomax, Harvard

    1987-01-01

    The past decade has seen considerable activity in algorithm development for the Navier-Stokes equations. This has resulted in a wide variety of useful new techniques. Some examples for the numerical solution of the Navier-Stokes equations are presented, divided into two parts. One is devoted to the incompressible Navier-Stokes equations, and the other to the compressible form.

  13. Approximation algorithms

    PubMed Central

    Schulz, Andreas S.; Shmoys, David B.; Williamson, David P.

    1997-01-01

    Increasing global competition, rapidly changing markets, and greater consumer awareness have altered the way in which corporations do business. To become more efficient, many industries have sought to model some operational aspects by gigantic optimization problems. It is not atypical to encounter models that capture 106 separate “yes” or “no” decisions to be made. Although one could, in principle, try all 2106 possible solutions to find the optimal one, such a method would be impractically slow. Unfortunately, for most of these models, no algorithms are known that find optimal solutions with reasonable computation times. Typically, industry must rely on solutions of unguaranteed quality that are constructed in an ad hoc manner. Fortunately, for some of these models there are good approximation algorithms: algorithms that produce solutions quickly that are provably close to optimal. Over the past 6 years, there has been a sequence of major breakthroughs in our understanding of the design of approximation algorithms and of limits to obtaining such performance guarantees; this area has been one of the most flourishing areas of discrete mathematics and theoretical computer science. PMID:9370525

  14. Research on recommendation system based on interest clustering

    NASA Astrophysics Data System (ADS)

    Yu, Yunfei; Zhou, Yinghua

    2017-03-01

    Traditional collaborative filtering algorithm does not take into account the user's interest factors, at the same time, it has the problem of sparse data, poor scalability and so on, which directly affects the quality of the recommendation. This paper proposes a collaborative filtering recommendation algorithm based on user interest clustering. Firstly, according to the user's existing score, a method is used to compute the interest degree of the user. Secondly, a clustering algorithm is used to divide the users into clusters. Finally, a collaborative filtering algorithm is used to recommend movie, it effectively improves data sparsity and real-time of problem. The experimental results exhibit that the proposed algorithm shows a great improvement in the recommendation accuracy.

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

    PubMed

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

    2013-01-01

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

  16. 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.

  17. BioCluster: tool for identification and clustering of Enterobacteriaceae based on biochemical data.

    PubMed

    Abdullah, Ahmed; Sabbir Alam, S M; Sultana, Munawar; Hossain, M Anwar

    2015-06-01

    Presumptive identification of different Enterobacteriaceae species is routinely achieved based on biochemical properties. Traditional practice includes manual comparison of each biochemical property of the unknown sample with known reference samples and inference of its identity based on the maximum similarity pattern with the known samples. This process is labor-intensive, time-consuming, error-prone, and subjective. Therefore, automation of sorting and similarity in calculation would be advantageous. Here we present a MATLAB-based graphical user interface (GUI) tool named BioCluster. This tool was designed for automated clustering and identification of Enterobacteriaceae based on biochemical test results. In this tool, we used two types of algorithms, i.e., traditional hierarchical clustering (HC) and the Improved Hierarchical Clustering (IHC), a modified algorithm that was developed specifically for the clustering and identification of Enterobacteriaceae species. IHC takes into account the variability in result of 1-47 biochemical tests within this Enterobacteriaceae family. This tool also provides different options to optimize the clustering in a user-friendly way. Using computer-generated synthetic data and some real data, we have demonstrated that BioCluster has high accuracy in clustering and identifying enterobacterial species based on biochemical test data. This tool can be freely downloaded at http://microbialgen.du.ac.bd/biocluster/.

  18. Segmentation of MRI Brain Images with an Improved Harmony Searching Algorithm

    PubMed Central

    Yang, Zhang; Li, Guo; Weifeng, Ding

    2016-01-01

    The harmony searching (HS) algorithm is a kind of optimization search algorithm currently applied in many practical problems. The HS algorithm constantly revises variables in the harmony database and the probability of different values that can be used to complete iteration convergence to achieve the optimal effect. Accordingly, this study proposed a modified algorithm to improve the efficiency of the algorithm. First, a rough set algorithm was employed to improve the convergence and accuracy of the HS algorithm. Then, the optimal value was obtained using the improved HS algorithm. The optimal value of convergence was employed as the initial value of the fuzzy clustering algorithm for segmenting magnetic resonance imaging (MRI) brain images. Experimental results showed that the improved HS algorithm attained better convergence and more accurate results than those of the original HS algorithm. In our study, the MRI image segmentation effect of the improved algorithm was superior to that of the original fuzzy clustering method. PMID:27403428

  19. Segmentation of MRI Brain Images with an Improved Harmony Searching Algorithm.

    PubMed

    Yang, Zhang; Shufan, Ye; Li, Guo; Weifeng, Ding

    2016-01-01

    The harmony searching (HS) algorithm is a kind of optimization search algorithm currently applied in many practical problems. The HS algorithm constantly revises variables in the harmony database and the probability of different values that can be used to complete iteration convergence to achieve the optimal effect. Accordingly, this study proposed a modified algorithm to improve the efficiency of the algorithm. First, a rough set algorithm was employed to improve the convergence and accuracy of the HS algorithm. Then, the optimal value was obtained using the improved HS algorithm. The optimal value of convergence was employed as the initial value of the fuzzy clustering algorithm for segmenting magnetic resonance imaging (MRI) brain images. Experimental results showed that the improved HS algorithm attained better convergence and more accurate results than those of the original HS algorithm. In our study, the MRI image segmentation effect of the improved algorithm was superior to that of the original fuzzy clustering method.

  20. Applications of Clustering to Information System Design.

    ERIC Educational Resources Information Center

    Stanfel, Larry E.

    1983-01-01

    Describes methods for effecting the partition of information systems consisting of many components and interconnections into subsystems which are later made to interface with one another achieving an overall system. Clustering algorithms for the specific case of information systems are obtained and exemplified. Twenty-seven references are…