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Exploiting homogeneity in protein sequence clusters for construction of protein family hierarchies

PATTERN RECOGNITION 2006年第12期39卷 2356-2369页

作者： Chen, Chien-Yu Chung, Wen-Chin Su, Chung-Tsai Natl Taiwan Univ Dept Bioind Mechatron Engn Taipei 106 Taiwan Natl Taiwan Univ Dept Comp Sci & Informat Engn Taipei 106 Taiwan

In the field of proteomics, protein hierarchies based on sequence analysis have been extensively applied to automate the annotations of new proteins and facilitate the discovery and analysis of protein families. However, the presence of ambiguous similarities in large databases increases the difficulty of delivering protein family hierarchies with favorable sensitivity and specificity. This work develops the HomoClust algorithm that exploits the homogeneity of protein sequences in generating protein family hierarchies. HomoClust improves the clustering quality of traditional hierarchical clustering algorithms by adopting different clustering mechanisms for different levels of sequence similarity. With considering homogeneity detection during clustering process, HomoClust increases the sensitivity of protein clusters without a drop in high specificity. (c) 2006 Pattern Recognition Society. Published by Elsevier Ltd. All rights reserved.

关键词： protein sequence clustering family analysis twilight zone hierarchical algorithm

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ICCAP - A linear time sparsification and reordering algorithm for 3-D BEM capacitance extraction

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IEEE TRANSACTIONS ON MICROWAVE THEORY AND TECHNIQUES 2006年第7期54卷 3060-3068页

作者： Jiang, Rong Chang, Yi-Hao Chen, Charlie Chung-Ping Cadence Design Syst Inc San Jose CA 95131 USA Etron Technol Corp Memory Design Dev Hsinchu Taiwan Natl Taiwan Univ Dept Elect Engn Taipei 106 Taiwan Natl Taiwan Univ Grad Inst Elect Engn Taipei 106 Taiwan

This paper presents an efficient, simple, hierarchical, and sparse three-dimensional capacitance extraction algorithm, i.e., ICCAP. Most previous capacitance extraction algorithms, such as FastCap and HiCap, introduce intermediate variables to facilitate the hierarchical potential calculation, but still preserve the basic panels as basis. In this paper, we. discover that those intermediate variables are a fundamentally much better basis than leaf panels. As a result, we are able to explicitly construct the sparse potential coefficient matrix and solve it with linear memory and linear run time in comparison with the most recent hierarchical O(nlogn) approach in PHiCap. Furthermore, the explicit sparse formulation of a potential matrix not only enables the usage of preconditioned Krylov subspace iterative methods, but also the reordering technique. A new reordering technique, i.e., level-oriented reordering (LOR), is proposed to further reduce over 20% of memory consumption and run time compared with no reordering techniques applied. In fact, LOR is even better than the state-of-the-art minimum degree reordering and more efficient. Without complicated orthonormalization matrix computation, ICCAP is very simple, efficient, and accurate. Experimental results demonstrate the superior run time and memory consumption over previous approaches while achieving similar accuracy.

关键词： basis boundary-element method (BEM) capacitance extraction hierarchical algorithm interconnect interconnect modeling parasitic extraction reordering

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Parameters extraction for MIS structure with protective layer by double-image Green's function method

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INTERNATIONAL JOURNAL OF ELECTRONICS 2005年第9期92卷 553-559页

作者： Dai, WL Li, ZF Fan, Y Shanghai Jiao Tong Univ Dept Elect Engn Shanghai 200030 Peoples R China Univ Elect Sci & Technol China Sch Elect Engn Chengdu 610054 Peoples R China

In this paper, a new double- image Green's function approach is proposed to compute the frequency- dependent capacitance and conductance for the interconnects based on metal- insulator- semiconductor ( MIS) structure with a protective layer. The hierarchical algorithm is also adopted to speed the calculation of the infinite series resulted from the double- image Green's function. The parameters gained from this new approach are shown to be in good agreement with the data obtained by full- wave method and total charge Green's function method.

关键词： protective MIS double-image Green's function hierarchical algorithm

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A k-populations algorithm for clustering categorical data

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PATTERN RECOGNITION 2005年第7期38卷 1131-1134页

作者： Kim, DW Lee, K Lee, D Lee, KH Korea Adv Inst Sci & Technol Dept BioSyst Taejon 305701 South Korea Korea Adv Inst Sci & Technol Adv Informat Technol Res Ctr Taejon 305701 South Korea Korea Adv Inst Sci & Technol Dept Elect Engn & Comp Sci Taejon 305701 South Korea

In this paper, the conventional k-modes-type algorithms for clustering categorical data are extended by representing the clusters of categorical data with k-populations instead of the hard-type centroids used in the conventional algorithms. Use of a population-based centroid representation makes it possible to preserve the uncertainty inherent in data sets as long as possible before actual decisions are made. The k-populations algorithm was found to give markedly better clustering results through various experiments. (c) 2005 Pattern Recognition Society. Published by Elsevier Ltd. All rights reserved.

关键词： clustering categorical data hierarchical algorithm k-modes algorithm fuzzy k-modes algorithm

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Study and improvement on hierarchical algorithm of association rule

Study and improvement on hierarchical algorithm of associati...

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Conference on Data Mining and Knowledge Discovery - Theory, Tools, and Technology IV

作者： Zhong, L Xia, HX Yuan, JL Wuhan Univ Technol Dept Comp Wuhan 430070 Peoples R China

ISBN: (纸本)0819444804

This paper introduces the problem of data mining association rules. We adopt the iterative method to enlarge the size of the item set gradually and describe the hierarchical algorithm in detail. The hierarchical algorithm produces a larger provisional sets based on the obtained frequent item sets and make sure that those provisional sets which will never be frequent item set are ignored under the premise of the known information. Finally, an improving algorithm by decreasing the times of scanning databases is proposed. It's an improving algorithm which is to combine the last several procedures of iteration into a single scan of the database D. Mainly because that the more backwards the iterative processes approach the end, the less the provisional sets are there.

关键词： data mining association rule hierarchical algorithm frequency degree confidence degree

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Fast Two-Dimensional Parameters Extraction for Interconnects in Arbitrary Dielectric Layers by hierarchical algorithm

Fast Two-Dimensional Parameters Extraction for Interconnects...

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2002海峡两岸三地无线科技研讨会

作者： DAI Wen-liang, LI Zheng-fan, LI Fu-hua Department of Electronic Engineering, Shanghai Jiaotong University, Shanghai, 200030, China

Instead of using the total charge Green抯 function method directly to compute the two-dimensional parameters of interconnects in multi-dielectric media, the Appel抯 hierarchical algorithm is adopted to

关键词： boundary element method hierarchical algorithm total charge Green抯 function method

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Parameter convergence in nonlinearly parameterized systems

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IEEE TRANSACTIONS ON AUTOMATIC CONTROL 2003年第3期48卷 397-412页

作者： Cao, CY Annaswamy, AM Kojic, A MIT Dept Mech Engn Act Adapt Control Lab Cambridge MA 02139 USA Robert Bosch Corp Palo Alto CA 94130 USA

A large class of problems in parameter estimation concerns nonlinearly parametrized systems. Over the past few years, a stability framework for estimation and control of such systems has been established. We address the issue of parameter convergence in such systems in this paper. Systems with both convex/concave and general parameterizations are considered. In the former case, sufficient conditions are derived under which parameter estimates converge to their true values using a min-max algorithm as in a previous. work by Armaswamy et al. In the latter case, to achieve parameter convergence a hierarchical min-max algorithm is proposed where the lower level consists of a min-max algorithm and the higher level component updates the bounds on the parameter region within which the unknown parameter is known to lie. Using this hierarchical algorithm, a necessary and sufficient condition is established for global parameter convergence in systems with a general nonlinear parameterization. In both cases, the conditions needed are shown to be stronger than linear persistent excitation conditions that guarantee parameter convergence in linearly parametrized systems. Explanations and examples of these conditions and simulation results are included to illustrate the nature of these conditions. A general definition of nonlinear persistent excitation that leads. to parameter convergence is proposed at the end of this paper.

关键词： convex persistent excitation convex/concave parameterization hierarchical algorithm nonlinear parameterization nonlinear persistent excitation parameter convergence parameter estimation

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Topology preserving top-down compression of 2D vector fields using bintree and triangular quadtrees

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IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS 2003年第4期9卷 433-442页

作者： Lodha, SK Faaland, NM Renteria, JC Univ Calif Santa Cruz Dept Comp Sci Santa Cruz CA 95064 USA Army Res Lab Aberdeen MD USA

We present a hierarchical top-down refinement algorithm for compressing 2D vector fields that preserves topology. Our approach is to reconstruct the data set using adaptive refinement that considers topology. The algorithms start with little data and subdivide regions that are most likely to reconstruct the original topology of the given data set. We use two different refinement techniques. The first technique uses bintree subdivision and linear interpolation. The second algorithm is driven by triangular quadtree subdivision with Coons patch quadratic interpolation. We employ local error metrics to measure the quality of compression and as a global metric we compute Earth Mover's Distance (EMD) to measure the deviation from the original topology. Experiments with both analytic and simulated data sets are presented. Results indicate that one can obtain significant compression with low errors without losing topological information. Advantages and disadvantages of different topology preserving compression algorithms are also discussed in the paper.

关键词： vector fields compression topology top-down bintree quadtree hierarchical algorithm

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Modelling a distributed fusion system for intelligent alarm analysis

Journal of the Institution of Engineers (India), Part CP: Co...

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Journal of the Institution of Engineers (India), Part CP: Computer Engineering Division 2002年第NOV.期82卷 46-49页

作者： Shalinie, S.M. Dept. of Computer Science and Eng. Thiagarajar College of Engineering Madurai 625 015 Tamil Nadu India

Multisensor data fusion is necessary to integrate data from different sensors and extract the relevant information on the targets. While a centralized processing approach is theoretically optimal, there are significant advantages in distributing the fusion operations over multiple processing nodes. This paper discusses architectures for distributed fusion, whereby each node processes the data from its own set of sensors and communicates with other nodes to improve on the estimates. Information flow in distributed fusion systems is modelled using information graph. The approach is verified for intelligent alarm analysis process.

关键词： Alarm analysis Distributed approach Fuzzy logic hierarchical algorithm Multisensor

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A hierarchical computation model for distributed shared-memory machines 9

A hierarchical computation model for distributed shared-memo...

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9th Euromicro Workshop on Parallel and Distributed Processing

作者： Rauber, T Rünger, G Univ Halle Wittenberg Inst Informat D-06099 Halle Germany

ISBN: (纸本)0769509886

We present a computation model to describe a clustered memory hierarchy of distributed shared memory machines. The computation model includes the access to shared data stored in different levels of the hierarchy as well as the transfer of entire blocks of data between different levels of the memory. Pure shared memory machines and pure message passing machines can be expressed within the model. As example we use the model to analyze a hierarchical matrix multiplication algorithm.

关键词： shared-memory model distributed shared memory memory hierarchy hierarchical algorithm

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