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  • 1
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    Forests, Vol. 5, Pages 3087-3106: Dendrochronological Potential in a Semi-Deciduous Rainforest: The Case of Pericopsis elata in Central Africa (2014)
    MDPI Publishing
    In: Forests
    Details
    Publication Date: 2014-12-13
    Description: The long-lived pioneer species Pericopsis elata is one of the rare tropical timbers on the list of the Convention on International Trade of Endangered Species, supporting the need for accurate and reliable growth data. In one planted and one natural forest in the Democratic Republic of Congo, respectively four and 37 Pericopsis stem disks were collected. The tree-ring series of planted trees were used to confirm annual tree-ring formation. For the natural forest, a tree-ring chronology with 24 stem disks ranged from 1852 up to 2008. This chronology was compared with time-series of local precipitation, resulting in a significant correlation with the second half of the rainy season (September–November). This seasonal precipitation was related with sea surface temperatures of the West Indian Ocean. Higher precipitation during El Niño years corresponded with higher tree-ring indices but differences were not significant. In addition, pointer years were rare and did not have a consistent link with extreme climatic conditions. The existence of annual tree rings encourages further tree-ring analyses of P. elata and other flagship timber species in order to further document climate-growth responses and to provide the long-term framework that is needed for sustainable management planning.
    Electronic ISSN: 1999-4907
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Published by MDPI Publishing
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  • 2
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    Detection of Replication Origin Sites in Herpesvirus Genomes by Clustering and Scoring of Palindromes with Quadratic Entropy Measures (2014)
    Institute of Electrical and Electronics Engineers (IEEE)
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    Publication Date: 2014-12-13
    Description: Replication in herpesvirus genomes is a major concern of public health as they multiply rapidly during the lytic phase of infection that cause maximum damage to the host cells. Earlier research has established that sites of replication origin are dominated by high concentration of rare palindrome sequences of DNA. Computational methods are devised based on scoring to determine the concentration of palindromes. In this paper, we propose both extraction and localization of rare palindromes in an automated manner. Discrete Cosine Transform (DCT-II), a widely recognized image compression algorithm is utilized here to extract palindromic sequences based on their reverse complimentary symmetry property of existence. We formulate a novel approach to localize the rare palindrome clusters by devising a Minimum Quadratic Entropy (MQE) measure based on the Renyi’s Quadratic Entropy (RQE) function. Experimental results over a large number of herpesvirus genomes show that the RQE based scoring of rare palindromes have higher order of sensitivity, and lesser false alarm in detecting concentration of rare palindromes and thereby sites of replication origin.
    Print ISSN: 1545-5963
    Electronic ISSN: 1557-9964
    Topics: Biology , Computer Science
    Published by Institute of Electrical and Electronics Engineers (IEEE) on behalf of The IEEE Computational Intelligence Society ; The IEEE Computer Society ; The IEEE Control Systems Society ; The IEEE Engineering in Medicine and Biology Society ; The Association for Computing Machinery.
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  • 3
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    Determining Semantically Related Significant Genes (2014)
    Institute of Electrical and Electronics Engineers (IEEE)
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    Publication Date: 2014-12-13
    Description: GO relation embodies some aspects of existence dependency. If GO term x is existence-dependent on GO term y , the presence of y implies the presence of x . Therefore, the genes annotated with the function of the GO term y are usually functionally and semantically related to the genes annotated with the function of the GO term x . A large number of gene set enrichment analysis methods have been developed in recent years for analyzing gene sets enrichment. However, most of these methods overlook the structural dependencies between GO terms in GO graph by not considering the concept of existence dependency. We propose in this paper a biological search engine called RSGSearch that identifies enriched sets of genes annotated with different functions using the concept of existence dependency. We observe that GO term x cannot be existence-dependent on GO term y , if x and y have the same specificity (biological characteristics). After encoding into a numeric format the contributions of GO terms annotating target genes to the semantics of their lowest common ancestors (LCAs), RSGSearch uses microarray experiment to identify the most significant LCA that annotates the result genes. We evaluated RSGSearch experimentally and compared it with five gene set enrichment systems. Results showed marked improvement.
    Print ISSN: 1545-5963
    Electronic ISSN: 1557-9964
    Topics: Biology , Computer Science
    Published by Institute of Electrical and Electronics Engineers (IEEE) on behalf of The IEEE Computational Intelligence Society ; The IEEE Computer Society ; The IEEE Control Systems Society ; The IEEE Engineering in Medicine and Biology Society ; The Association for Computing Machinery.
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  • 4
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    Nonparametric Tikhonov Regularized NMF and Its Application in Cancer Clustering (2014)
    Institute of Electrical and Electronics Engineers (IEEE)
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    Publication Date: 2014-12-13
    Description: The Tikhonov regularized nonnegative matrix factorization (TNMF) is an NMF objective function that enforces smoothness on the computed solutions, and has been successfully applied to many problem domains including text mining, spectral data analysis, and cancer clustering. There is, however, an issue that is still insufficiently addressed in the development of TNMF algorithms, i.e., how to develop mechanisms that can learn the regularization parameters directly from the data sets. The common approach is to use fixed values based on a priori knowledge about the problem domains. However, from the linear inverse problems study it is known that the quality of the solutions of the Tikhonov regularized least square problems depends heavily on the choosing of appropriate regularization parameters. Since least squares are the building blocks of the NMF, it can be expected that similar situation also applies to the NMF. In this paper, we propose two formulas to automatically learn the regularization parameters from the data set based on the L-curve approach. We also develop a convergent algorithm for the TNMF based on the additive update rules. Finally, we demonstrate the use of the proposed algorithm in cancer clustering tasks.
    Print ISSN: 1545-5963
    Electronic ISSN: 1557-9964
    Topics: Biology , Computer Science
    Published by Institute of Electrical and Electronics Engineers (IEEE) on behalf of The IEEE Computational Intelligence Society ; The IEEE Computer Society ; The IEEE Control Systems Society ; The IEEE Engineering in Medicine and Biology Society ; The Association for Computing Machinery.
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  • 5
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    On the Number of Ranked Species Trees Producing Anomalous Ranked Gene Trees (2014)
    Institute of Electrical and Electronics Engineers (IEEE)
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    Publication Date: 2014-12-13
    Description: Analysis of probability distributions conditional on species trees has demonstrated the existence of anomalous ranked gene trees (ARGTs), ranked gene trees that are more probable than the ranked gene tree that accords with the ranked species tree. Here, to improve the characterization of ARGTs, we study enumerative and probabilistic properties of two classes of ranked labeled species trees, focusing on the presence or avoidance of certain subtree patterns associated with the production of ARGTs. We provide exact enumerations and asymptotic estimates for cardinalities of these sets of trees, showing that as the number of species increases without bound, the fraction of all ranked labeled species trees that are ARGT-producing approaches $1$ . This result extends beyond earlier existence results to provide a probabilistic claim about the frequency of ARGTs.
    Print ISSN: 1545-5963
    Electronic ISSN: 1557-9964
    Topics: Biology , Computer Science
    Published by Institute of Electrical and Electronics Engineers (IEEE) on behalf of The IEEE Computational Intelligence Society ; The IEEE Computer Society ; The IEEE Control Systems Society ; The IEEE Engineering in Medicine and Biology Society ; The Association for Computing Machinery.
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  • 6
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    Shifting-and-Scaling Correlation Based Biclustering Algorithm (2014)
    Institute of Electrical and Electronics Engineers (IEEE)
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    Publication Date: 2014-12-13
    Description: The existence of various types of correlations among the expressions of a group of biologically significant genes poses challenges in developing effective methods of gene expression data analysis. The initial focus of computational biologists was to work with only absolute and shifting correlations. However, researchers have found that the ability to handle shifting-and-scaling correlation enables them to extract more biologically relevant and interesting patterns from gene microarray data. In this paper, we introduce an effective shifting-and-scaling correlation measure named Shifting and Scaling Similarity (SSSim), which can detect highly correlated gene pairs in any gene expression data. We also introduce a technique named Intensive Correlation Search (ICS) biclustering algorithm, which uses SSSim to extract biologically significant biclusters from a gene expression data set. The technique performs satisfactorily with a number of benchmarked gene expression data sets when evaluated in terms of functional categories in Gene Ontology database.
    Print ISSN: 1545-5963
    Electronic ISSN: 1557-9964
    Topics: Biology , Computer Science
    Published by Institute of Electrical and Electronics Engineers (IEEE) on behalf of The IEEE Computational Intelligence Society ; The IEEE Computer Society ; The IEEE Control Systems Society ; The IEEE Engineering in Medicine and Biology Society ; The Association for Computing Machinery.
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  • 7
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    ILP/SMT-Based Method for Design of Boolean Networks Based on Singleton Attractors (2014)
    Institute of Electrical and Electronics Engineers (IEEE)
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    Publication Date: 2014-12-13
    Description: Attractors in gene regulatory networks represent cell types or states of cells. In system biology and synthetic biology, it is important to generate gene regulatory networks with desired attractors. In this paper, we focus on a singleton attractor, which is also called a fixed point. Using a Boolean network (BN) model, we consider the problem of finding Boolean functions such that the system has desired singleton attractors and has no undesired singleton attractors. To solve this problem, we propose a matrix-based representation of BNs. Using this representation, the problem of finding Boolean functions can be rewritten as an Integer Linear Programming (ILP) problem and a Satisfiability Modulo Theories (SMT) problem. Furthermore, the effectiveness of the proposed method is shown by a numerical example on a WNT5A network, which is related to melanoma. The proposed method provides us a basic method for design of gene regulatory networks.
    Print ISSN: 1545-5963
    Electronic ISSN: 1557-9964
    Topics: Biology , Computer Science
    Published by Institute of Electrical and Electronics Engineers (IEEE) on behalf of The IEEE Computational Intelligence Society ; The IEEE Computer Society ; The IEEE Control Systems Society ; The IEEE Engineering in Medicine and Biology Society ; The Association for Computing Machinery.
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  • 8
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    Improving Detection of Driver Genes: Power-Law Null Model of Copy Number Variation in Cancer (2014)
    Institute of Electrical and Electronics Engineers (IEEE)
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    Publication Date: 2014-12-13
    Description: In this paper, we study Copy Number Variation (CNV) data.The underlying process generating CNV segments is generally assumed to be memory-less, giving rise to an exponential distribution of segment lengths. In this paper, we provide evidence from cancer patient data, which suggests that this generative model is too simplistic , and that segment lengths follow a power-law distribution instead . We conjecture a simple preferential attachment generative model that provides the basis for the observed power-law distribution. We then show how an existing statistical method for detecting cancer driver genes can be improved by incorporating the power-law distribution in the null model.
    Print ISSN: 1545-5963
    Electronic ISSN: 1557-9964
    Topics: Biology , Computer Science
    Published by Institute of Electrical and Electronics Engineers (IEEE) on behalf of The IEEE Computational Intelligence Society ; The IEEE Computer Society ; The IEEE Control Systems Society ; The IEEE Engineering in Medicine and Biology Society ; The Association for Computing Machinery.
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  • 9
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    On Representing Protein Folding Patterns Using Non-Linear Parametric Curves (2014)
    Institute of Electrical and Electronics Engineers (IEEE)
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    Publication Date: 2014-12-13
    Description: Proteins fold into complex three-dimensional shapes. Simplified representations of their shapes are central to rationalise, compare, classify, and interpret protein structures. Traditional methods to abstract protein folding patterns rely on representing their standard secondary structural elements (helices and strands of sheet) using line segments. This results in ignoring a significant proportion of structural information. The motivation of this research is to derive mathematically rigorous and biologically meaningful abstractions of protein folding patterns that maximize the economy of structural description and minimize the loss of structural information. We report on a novel method to describe a protein as a non-overlapping set of parametric three dimensional curves of varying length and complexity. Our approach to this problem is supported by information theory and uses the statistical framework of minimum message length (MML) inference. We demonstrate the effectiveness of our non-linear abstraction to support efficient and effective comparison of protein folding patterns on a large scale.
    Print ISSN: 1545-5963
    Electronic ISSN: 1557-9964
    Topics: Biology , Computer Science
    Published by Institute of Electrical and Electronics Engineers (IEEE) on behalf of The IEEE Computational Intelligence Society ; The IEEE Computer Society ; The IEEE Control Systems Society ; The IEEE Engineering in Medicine and Biology Society ; The Association for Computing Machinery.
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  • 10
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    Organized Modularity in the Interactome: Evidence from the Analysis of Dynamic Organization in the Cell Cycle (2014)
    Institute of Electrical and Electronics Engineers (IEEE)
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    Publication Date: 2014-12-13
    Description: The organization of global protein interaction networks (PINs) has been extensively studied and heatedly debated. We revisited this issue in the context of the analysis of dynamic organization of a PIN in the yeast cell cycle. Statistically significant bimodality was observed when analyzing the distribution of the differences in expression peak between periodically expressed partners. A close look at their behavior revealed that date and party hubs derived from this analysis have some distinct features. There are no significant differences between them in terms of protein essentiality, expression correlation and semantic similarity derived from gene ontology (GO) biological process hierarchy. However, date hubs exhibit significantly greater values than party hubs in terms of semantic similarity derived from both GO molecular function and cellular component hierarchies. Relating to three-dimensional structures, we found that both single- and multi-interface proteins could become date hubs coordinating multiple functions performed at different times while party hubs are mainly multi-interface proteins. Furthermore, we constructed and analyzed a PPI network specific to the human cell cycle and highlighted that the dynamic organization in human interactome is far more complex than the dichotomy of hubs observed in the yeast cell cycle.
    Print ISSN: 1545-5963
    Electronic ISSN: 1557-9964
    Topics: Biology , Computer Science
    Published by Institute of Electrical and Electronics Engineers (IEEE) on behalf of The IEEE Computational Intelligence Society ; The IEEE Computer Society ; The IEEE Control Systems Society ; The IEEE Engineering in Medicine and Biology Society ; The Association for Computing Machinery.
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  • 11
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    Big data processing in computational biology and bioinformatics (2014)
    Institute of Electrical and Electronics Engineers (IEEE)
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    Publication Date: 2014-12-13
    Print ISSN: 1545-5963
    Electronic ISSN: 1557-9964
    Topics: Biology , Computer Science
    Published by Institute of Electrical and Electronics Engineers (IEEE) on behalf of The IEEE Computational Intelligence Society ; The IEEE Computer Society ; The IEEE Control Systems Society ; The IEEE Engineering in Medicine and Biology Society ; The Association for Computing Machinery.
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  • 12
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    Analysis of Biological data (2014)
    Institute of Electrical and Electronics Engineers (IEEE)
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    Publication Date: 2014-12-13
    Print ISSN: 1545-5963
    Electronic ISSN: 1557-9964
    Topics: Biology , Computer Science
    Published by Institute of Electrical and Electronics Engineers (IEEE) on behalf of The IEEE Computational Intelligence Society ; The IEEE Computer Society ; The IEEE Control Systems Society ; The IEEE Engineering in Medicine and Biology Society ; The Association for Computing Machinery.
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  • 13
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    IEEE Transactions on Pattern Analysis and Machine Intelligence Information for Authors (2014)
    Institute of Electrical and Electronics Engineers (IEEE)
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    Publication Date: 2014-12-13
    Print ISSN: 1545-5963
    Electronic ISSN: 1557-9964
    Topics: Biology , Computer Science
    Published by Institute of Electrical and Electronics Engineers (IEEE) on behalf of The IEEE Computational Intelligence Society ; The IEEE Computer Society ; The IEEE Control Systems Society ; The IEEE Engineering in Medicine and Biology Society ; The Association for Computing Machinery.
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  • 14
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    Selected Articles from the 2012 IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS 2012) (2014)
    Institute of Electrical and Electronics Engineers (IEEE)
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    Publication Date: 2014-12-13
    Description: The articles in this special section were presented at the 2012 IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS 2012) that was held in Washington DC from December 2nd to 4th.
    Print ISSN: 1545-5963
    Electronic ISSN: 1557-9964
    Topics: Biology , Computer Science
    Published by Institute of Electrical and Electronics Engineers (IEEE) on behalf of The IEEE Computational Intelligence Society ; The IEEE Computer Society ; The IEEE Control Systems Society ; The IEEE Engineering in Medicine and Biology Society ; The Association for Computing Machinery.
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  • 15
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    Accelerate RDP RAID-6 Scaling by Reducing Disk I/Os and XOR Operations (2014)
    Institute of Electrical and Electronics Engineers (IEEE)
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    Publication Date: 2014-12-13
    Description: Disk additions to an RAID-6 storage system can increase the I/O parallelism and expand the storage capacity simultaneously. To regain load balance among all disks including old and new, RAID-6 scaling requires moving certain data blocks onto newly added disks. Existing approaches to RAID-6 scaling, restricted by preserving a round-robin data distribution, require migrating all the data, which results in an expensive cost for RAID-6 scaling. In this paper, we propose RS6—a new approach to accelerating RDP RAID-6 scaling by reducing disk I/Os and XOR operations. First, RS6 minimizes the number of data blocks to be moved while maintaining a uniform data distribution across all data disks. Second, RS6 piggybacks parity updates during data migration to reduce the cost of maintaining consistent parities. Third, RS6 selects parameters of data migration so as to reduce disk I/Os for parity updates. Our mathematical analysis indicates that RS6 provides uniform data distribution, minimal data migration, and fast data addressing. We also conducted extensive simulation experiments to quantitatively characterize the properties of RS6. The results show that, compared with existing “moving-everything” Round-Robin approaches, RS6 reduces the number of blocks to be moved by 60.0%–88.9%, and saves the migration time by 40.27%–69.88%.
    Print ISSN: 0018-9340
    Electronic ISSN: 1557-9956
    Topics: Computer Science
    Published by Institute of Electrical and Electronics Engineers (IEEE) on behalf of The IEEE Computer Society.
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  • 16
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    A Time Fairness-Based MAC Algorithm for Throughput Maximization in 802.11 Networks (2014)
    Institute of Electrical and Electronics Engineers (IEEE)
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    Publication Date: 2014-12-13
    Description: This paper focuses on designing a distributed medium access control algorithm for fairly sharing network resources among contending stations in an 802.11 wireless network. Because the notion of fairness is not universal and there lacks a rigorous analysis on the relationships among the four types of most popular fairness criteria, we first mathematically prove that there exist certain connections between these types of fairness criteria. We then propose an efficient medium access algorithm that aims at achieving time fairness and throughput enhancement in a fully distributed manner. The core idea of our proposed algorithm lies in that each station needs to select an appropriate contention window size so as to fairly share the channel occupancy time and maximize the throughput under the time fairness constraint. The derivation of the proper contention window size is addressed rigorously. We evaluate the performance of our proposed algorithm through an extensive simulation study, and the evaluation results demonstrate that our proposed algorithm leads to nearly perfect time fairness, high throughput, and low collision overhead.
    Print ISSN: 0018-9340
    Electronic ISSN: 1557-9956
    Topics: Computer Science
    Published by Institute of Electrical and Electronics Engineers (IEEE) on behalf of The IEEE Computer Society.
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  • 17
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    Adaptive Voltage Scaling with In-Situ Detectors in Commercial FPGAs (2014)
    Institute of Electrical and Electronics Engineers (IEEE)
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    Publication Date: 2014-12-13
    Description: This paper investigates the limits of adaptive voltage scaling (AVS) applied to commercial FPGAs which do not specifically support voltage adaptation. An adaptive power architecture based on a modified design flow is created with in-situ detectors and dynamic reconfiguration of clock management resources. AVS is a power-saving technique that enables a device to regulate its own voltage and frequency based on workload, process and operating conditions in a closed-loop configuration. It results in significant improved energy profiles compared with dynamic voltage frequency scaling (DVFS) in which the device uses a number of pre-calculated valid working points. The results of deploying AVS in FPGAs with in-situ detectors shows power and energy savings exceeding 85 percent compared with nominal voltage operation at the same frequency. The in-situ detector approach compares favorably with critical path replication based on delay lines since it avoids the need of cumbersome and error-prone delay line calibration.
    Print ISSN: 0018-9340
    Electronic ISSN: 1557-9956
    Topics: Computer Science
    Published by Institute of Electrical and Electronics Engineers (IEEE) on behalf of The IEEE Computer Society.
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  • 18
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    Forests, Vol. 5, Pages 3222-3240: Comparison of Three Ideal Point-Based Multi-Criteria Decision Methods for Afforestation Planning (2014)
    MDPI Publishing
    In: Forests
    Details
    Publication Date: 2014-12-16
    Description: Three ideal point-based multi-criteria decision methods (MCDM), i.e., iterative ideal point thresholding (IIPT), compromise programming (CP) and a newly-proposed CP variant, called balanced compromise programming (BCP), were applied to the Tabacay catchment in Ecuador with the aim of finding a distribution of land use types (LUT) that optimizes regional land performance. This performance was expressed in terms of several conflicting on-site ecosystem services (ESS), namely water conservation, soil protection, carbon storage and monetary income. IIPT selects the best performing LUT on a per-land unit basis, that is the assignment of a LUT to a land unit is completely independent with respect to other land units. CP and BCP, on the other hand, aim at optimizing the integrated regional performance. These methods produce a LUT distribution that is as close as possible to the absolute optimal performance that would be achieved when conflict among ESS is not considered. In general, similar results were obtained with CP and BCP. This was not the case when the results produced by these two methods were contrasted with IIPT. For most ESS under consideration, CP and BCP produced balanced results that were closer to the absolute optimal values when compared to IIPT. We conclude from our results that, when optimization of land performance at a regional scale is at stake, CP-derived models emerge as the preferable option over IIPT, especially when balanced solutions are a requirement.
    Electronic ISSN: 1999-4907
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
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  • 19
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    Forests, Vol. 5, Pages 3241-3256: Simulation of Quaking Aspen Potential Fire Behavior in Northern Utah, USA (2014)
    MDPI Publishing
    In: Forests
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    Publication Date: 2014-12-16
    Description: Current understanding of aspen fire ecology in western North America includes the paradoxical characterization that aspen-dominated stands, although often regenerated following fire, are “fire-proof”. We tested this idea by predicting potential fire behavior across a gradient of aspen dominance in northern Utah using the Forest Vegetation Simulator and the Fire and Fuels Extension. The wind speeds necessary for crowning (crown-to-crown fire spread) and torching (surface to crown fire spread) were evaluated to test the hypothesis that predicted fire behavior is influenced by the proportion of aspen in the stand. Results showed a strong effect of species composition on crowning, but only under moderate fire weather, where aspen-dominated stands were unlikely to crown or torch. Although rarely observed in actual fires, conifer-dominated stands were likely to crown but not to torch, an example of “hysteresis” in crown fire behavior. Results support the hypothesis that potential crown fire behavior varies across a gradient of aspen dominance and fire weather, where it was likely under extreme and severe fire weather, and unlikely under moderate and high fire weather. Furthermore, the “fire-proof” nature of aspen stands broke down across the gradient of aspen dominance and fire weather.
    Electronic ISSN: 1999-4907
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
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  • 20
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    BitPAl: a bit-parallel, general integer-scoring sequence alignment algorithm (2014)
    Oxford University Press
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    Publication Date: 2014-11-07
    Description: Motivation: Mapping of high-throughput sequencing data and other bulk sequence comparison applications have motivated a search for high-efficiency sequence alignment algorithms. The bit-parallel approach represents individual cells in an alignment scoring matrix as bits in computer words and emulates the calculation of scores by a series of logic operations composed of AND, OR, XOR, complement, shift and addition. Bit-parallelism has been successfully applied to the longest common subsequence (LCS) and edit-distance problems, producing fast algorithms in practice. Results: We have developed BitPAl, a bit-parallel algorithm for general, integer-scoring global alignment. Integer-scoring schemes assign integer weights for match, mismatch and insertion/deletion. The BitPAl method uses structural properties in the relationship between adjacent scores in the scoring matrix to construct classes of efficient algorithms, each designed for a particular set of weights. In timed tests, we show that BitPAl runs 7–25 times faster than a standard iterative algorithm. Availability and implementation: Source code is freely available for download at http://lobstah.bu.edu/BitPAl/BitPAl.html . BitPAl is implemented in C and runs on all major operating systems. Contact : jloving@bu.edu or yhernand@bu.edu or gbenson@bu.edu Supplementary information : Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 21
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    gCUP: rapid GPU-based HIV-1 co-receptor usage prediction for next-generation sequencing (2014)
    Oxford University Press
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    Publication Date: 2014-11-07
    Description: : Next-generation sequencing (NGS) has a large potential in HIV diagnostics, and genotypic prediction models have been developed and successfully tested in the recent years. However, albeit being highly accurate, these computational models lack computational efficiency to reach their full potential. In this study, we demonstrate the use of graphics processing units (GPUs) in combination with a computational prediction model for HIV tropism. Our new model named gCUP, parallelized and optimized for GPU, is highly accurate and can classify 〉175 000 sequences per second on an NVIDIA GeForce GTX 460. The computational efficiency of our new model is the next step to enable NGS technologies to reach clinical significance in HIV diagnostics. Moreover, our approach is not limited to HIV tropism prediction, but can also be easily adapted to other settings, e.g. drug resistance prediction. Availability and implementation: The source code can be downloaded at http://www.heiderlab.de Contact: d.heider@wz-straubing.de
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 22
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    Fast construction of FM-index for long sequence reads (2014)
    Oxford University Press
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    Publication Date: 2014-11-07
    Description: : We present a new method to incrementally construct the FM-index for both short and long sequence reads, up to the size of a genome. It is the first algorithm that can build the index while implicitly sorting the sequences in the reverse (complement) lexicographical order without a separate sorting step. The implementation is among the fastest for indexing short reads and the only one that practically works for reads of averaged kilobases in length. Availability and implementation: https://github.com/lh3/ropebwt2 Contact: hengli@broadinstitute.org
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
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  • 23
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    AliView: a fast and lightweight alignment viewer and editor for large datasets (2014)
    Oxford University Press
    Details
    Publication Date: 2014-11-07
    Description: : AliView is an alignment viewer and editor designed to meet the requirements of next-generation sequencing era phylogenetic datasets. AliView handles alignments of unlimited size in the formats most commonly used, i.e. FASTA, Phylip, Nexus, Clustal and MSF. The intuitive graphical interface makes it easy to inspect, sort, delete, merge and realign sequences as part of the manual filtering process of large datasets. AliView also works as an easy-to-use alignment editor for small as well as large datasets. Availability and implementation: AliView is released as open-source software under the GNU General Public License, version 3.0 (GPLv3), and is available at GitHub ( www.github.com/AliView ). The program is cross-platform and extensively tested on Linux, Mac OS X and Windows systems. Downloads and help are available at http://ormbunkar.se/aliview Contact: anders.larsson@ebc.uu.se Supplementary information: Supplementary data are available at Bioinformatics online.
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    Trowel: a fast and accurate error correction module for Illumina sequencing reads (2014)
    Oxford University Press
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    Publication Date: 2014-11-07
    Description: Motivation: The ability to accurately read the order of nucleotides in DNA and RNA is fundamental for modern biology. Errors in next-generation sequencing can lead to many artifacts, from erroneous genome assemblies to mistaken inferences about RNA editing. Uneven coverage in datasets also contributes to false corrections. Result: We introduce Trowel, a massively parallelized and highly efficient error correction module for Illumina read data. Trowel both corrects erroneous base calls and boosts base qualities based on the k -mer spectrum. With high-quality k -mers and relevant base information, Trowel achieves high accuracy for different short read sequencing applications.The latency in the data path has been significantly reduced because of efficient data access and data structures. In performance evaluations, Trowel was highly competitive with other tools regardless of coverage, genome size read length and fragment size. Availability and implementation: Trowel is written in C++ and is provided under the General Public License v3.0 (GPLv3). It is available at http://trowel-ec.sourceforge.net . Contact: euncheon.lim@tue.mpg.de or weigel@tue.mpg.de Supplementary information: Supplementary data are available at Bioinformatics online.
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    MEGADOCK 4.0: an ultra-high-performance protein-protein docking software for heterogeneous supercomputers (2014)
    Oxford University Press
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    Publication Date: 2014-11-07
    Description: : The application of protein–protein docking in large-scale interactome analysis is a major challenge in structural bioinformatics and requires huge computing resources. In this work, we present MEGADOCK 4.0, an FFT-based docking software that makes extensive use of recent heterogeneous supercomputers and shows powerful, scalable performance of 〉97% strong scaling. Availability and Implementation: MEGADOCK 4.0 is written in C++ with OpenMPI and NVIDIA CUDA 5.0 (or later) and is freely available to all academic and non-profit users at: http://www.bi.cs.titech.ac.jp/megadock . Contact: akiyama@cs.titech.ac.jp Supplementary information: Supplementary data are available at Bioinformatics online
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    Detection of active transcription factor binding sites with the combination of DNase hypersensitivity and histone modifications (2014)
    Oxford University Press
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    Publication Date: 2014-11-07
    Description: Motivation: The identification of active transcriptional regulatory elements is crucial to understand regulatory networks driving cellular processes such as cell development and the onset of diseases. It has recently been shown that chromatin structure information, such as DNase I hypersensitivity (DHS) or histone modifications, significantly improves cell-specific predictions of transcription factor binding sites. However, no method has so far successfully combined both DHS and histone modification data to perform active binding site prediction. Results: We propose here a method based on hidden Markov models to integrate DHS and histone modifications occupancy for the detection of open chromatin regions and active binding sites. We have created a framework that includes treatment of genomic signals, model training and genome-wide application. In a comparative analysis, our method obtained a good trade-off between sensitivity versus specificity and superior area under the curve statistics than competing methods. Moreover, our technique does not require further training or sequence information to generate binding location predictions. Therefore, the method can be easily applied on new cell types and allow flexible downstream analysis such as de novo motif finding. Availability and implementation: Our framework is available as part of the Regulatory Genomics Toolbox. The software information and all benchmarking data are available at http://costalab.org/wp/dh-hmm . Contact: ivan.costa@rwth-aachen.de or eduardo.gusmao@rwth-aachen.de Supplementary information: Supplementary data are available at Bioinformatics online.
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    A method for de novo nucleic acid diagnostic target discovery (2014)
    Oxford University Press
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    Publication Date: 2014-11-07
    Description: Motivation: A proper target or marker is essential in any diagnosis (e.g. an infection or cancer). An ideal diagnostic target should be both conserved in and unique to the pathogen. Currently, these targets can only be identified manually, which is time-consuming and usually error-prone. Because of the increasingly frequent occurrences of emerging epidemics and multidrug-resistant ‘superbugs’, a rapid diagnostic target identification process is needed. Results: A new method that can identify uniquely conserved regions (UCRs) as candidate diagnostic targets for a selected group of organisms solely from their genomic sequences has been developed and successfully tested. Using a sequence-indexing algorithm to identify UCRs and a k -mer integer-mapping model for computational efficiency, this method has successfully identified UCRs within the bacteria domain for 15 test groups, including pathogenic, probiotic, commensal and extremophilic bacterial species or strains. Based on the identified UCRs, new diagnostic primer sets were designed, and their specificity and efficiency were tested by polymerase chain reaction amplifications from both pure isolates and samples containing mixed cultures. Availability and implementation: The UCRs identified for the 15 bacterial species are now freely available at http://ucr.synblex.com . The source code of the programs used in this study is accessible at http://ucr.synblex.com/bacterialIdSourceCode.d.zip Contact: yazhousun@synblex.com Supplementary Information: Supplementary data are available at Bioinformatics online.
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    Quantitative method for the assignment of hinge and shear mechanism in protein domain movements (2014)
    Oxford University Press
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    Publication Date: 2014-11-07
    Description: Motivation: A popular method for classification of protein domain movements apportions them into two main types: those with a ‘hinge’ mechanism and those with a ‘shear’ mechanism. The intuitive assignment of domain movements to these classes has limited the number of domain movements that can be classified in this way. Furthermore, whether intended or not, the term ‘shear’ is often interpreted to mean a relative translation of the domains. Results: Numbers of occurrences of four different types of residue contact changes between domains were optimally combined by logistic regression using the training set of domain movements intuitively classified as hinge and shear to produce a predictor for hinge and shear. This predictor was applied to give a 10-fold increase in the number of examples over the number previously available with a high degree of precision. It is shown that overall a relative translation of domains is rare, and that there is no difference between hinge and shear mechanisms in this respect. However, the shear set contains significantly more examples of domains having a relative twisting movement than the hinge set. The angle of rotation is also shown to be a good discriminator between the two mechanisms. Availability and implementation: Results are free to browse at http://www.cmp.uea.ac.uk/dyndom/interface/ . Contact: sjh@cmp.uea.ac.uk . Supplementary information: Supplementary data are available at Bioinformatics online.
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    Network-based analysis of genotype-phenotype correlations between different inheritance modes (2014)
    Oxford University Press
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    Publication Date: 2014-11-07
    Description: Motivation: Recent studies on human disease have revealed that aberrant interaction between proteins probably underlies a substantial number of human genetic diseases. This suggests a need to investigate disease inheritance mode using interaction, and based on which to refresh our conceptual understanding of a series of properties regarding inheritance mode of human disease. Results: We observed a strong correlation between the number of protein interactions and the likelihood of a gene causing any dominant diseases or multiple dominant diseases, whereas no correlation was observed between protein interaction and the likelihood of a gene causing recessive diseases. We found that dominant diseases are more likely to be associated with disruption of important interactions. These suggest inheritance mode should be understood using protein interaction. We therefore reviewed the previous studies and refined an interaction model of inheritance mode, and then confirmed that this model is largely reasonable using new evidences. With these findings, we found that the inheritance mode of human genetic diseases can be predicted using protein interaction. By integrating the systems biology perspectives with the classical disease genetics paradigm, our study provides some new insights into genotype–phenotype correlations. Contact: haodapeng@ems.hrbmu.edu.cn or biofomeng@hotmail.com Supplementary information: Supplementary data are available at Bioinformatics online.
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    Drug/Cell-line Browser: interactive canvas visualization of cancer drug/cell-line viability assay datasets (2014)
    Oxford University Press
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    Publication Date: 2014-11-07
    Description: : Recently, several high profile studies collected cell viability data from panels of cancer cell lines treated with many drugs applied at different concentrations. Such drug sensitivity data for cancer cell lines provide suggestive treatments for different types and subtypes of cancer. Visualization of these datasets can reveal patterns that may not be obvious by examining the data without such efforts. Here we introduce Drug/Cell-line Browser (DCB), an online interactive HTML5 data visualization tool for interacting with three of the recently published datasets of cancer cell lines/drug-viability studies. DCB uses clustering and canvas visualization of the drugs and the cell lines, as well as a bar graph that summarizes drug effectiveness for the tissue of origin or the cancer subtypes for single or multiple drugs. DCB can help in understanding drug response patterns and prioritizing drug/cancer cell line interactions by tissue of origin or cancer subtype. Availability and implementation: DCB is an open source Web-based tool that is freely available at: http://www.maayanlab.net/LINCS/DCB Contact: avi.maayan@mssm.edu Supplementary information: Supplementary data are available at Bioinformatics online.
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    A Linear Time Pessimistic Diagnosis Algorithm for Hypermesh Multiprocessor Systems under the PMC Model (2014)
    Institute of Electrical and Electronics Engineers (IEEE)
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    Publication Date: 2014-11-08
    Description: In microprocessor-based systems, such as the cloud computing infrastructure, high reliability is essential. As multiprocessor systems become more widespread and increasingly complex, system-level diagnosis will increasingly be adopted to determine their robustness. In this paper, we consider a pessimistic diagnostic strategy for hypermesh multiprocessor systems under the PMC model. The pessimistic strategy is a diagnostic process whereby all faulty processors are correctly identified and at most one fault-free processor may be misjudged to be a faulty processor. We first determine the pessimistic diagnosability of a hypermesh to be ${2}{{n}}({{k}} - {1}) - {{k}}$ . We then propose an efficient pessimistic diagnostic algorithm to identify at most ${ 2}{{n}}({{k}} - { 1}) - {{k}}$ faults in ${{O}}({{N}})$ time, where ${mbi{k}}$ is the radix, ${mbi{n}}$ is the number of dimensions, and ${{N}} = {{k^n}}$ is the total number of processors. This result is superior to the best precise diagnostic algorithm, which runs in ${{O}}({{N}}{log _{{k}}}{{N}})$ time. Furthermore, the Cartesian product network, a subgraph of the hypermesh and the proposed algorithm can be employed to determine faults in the product network.
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    A General Technique for Top- $k$ Geometric Intersection Query Problems (2014)
    Institute of Electrical and Electronics Engineers (IEEE)
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    Publication Date: 2014-11-08
    Description: In a top- $k$ Geometric Intersection Query (top- $k$ GIQ) problem, a set of $n$ weighted, geometric objects in ${bb R}^d$ is to be pre-processed into a compact data structure so that for any query geometric object, $q$ , and integer $k>0$ , the $k$ largest-weight objects intersected by $q$ can be reported efficiently. While the top- $k$ problem has been studied extensively for non-geometric problems (e.g., recommender systems), the geometric version has received little attention. This paper gives a general technique to solve any top-
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    A Rough Set-Based Method for Updating Decision Rules on Attribute Values’ Coarsening and Refining (2014)
    Institute of Electrical and Electronics Engineers (IEEE)
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    Publication Date: 2014-11-08
    Description: Rule induction method based on rough set theory (RST) has received much attention recently since it may generate a minimal set of rules from the decision system for real-life applications by using of attribute reduction and approximations. The decision system may vary with time, e.g., the variation of objects, attributes and attribute values. The reduction and approximations of the decision system may alter on Attribute Values’ Coarsening and Refining (AVCR), a kind of variation of attribute values, which results in the alteration of decision rules simultaneously. This paper aims for dynamic maintenance of decision rules $w.r.t.$ AVCR. The definition of minimal discernibility attribute set is proposed firstly, which aims to improve the efficiency of attribute reduction in RST. Then, principles of updating decision rules in case of AVCR are discussed. Furthermore, the rough set-based methods for updating decision rules in the inconsistent decision system are proposed. The complexity analysis and extensive experiments on UCI data sets have verified the effectiveness and efficiency of the proposed methods.
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    A Unifying Framework for Mining Approximate Top- (k) Binary Patterns (2014)
    Institute of Electrical and Electronics Engineers (IEEE)
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    Publication Date: 2014-11-08
    Description: A major mining task for binary matrixes is the extraction of approximate top- (k) patterns that are able to concisely describe the input data. The top- (k) pattern discovery problem is commonly stated as an optimization one, where the goal is to minimize a given cost function, see the accuracy of the data description. In this work, we review several greedy algorithms, and discuss PaNDa + , an algorithmic framework able to optimize different cost functions generalized into a unifying formulation. We evaluated the goodness of the algorithm by measuring the quality of the extracted patterns. We adapted standard quality measures to assess the capability of the algorithm to discover both the items and transactions of the patterns embedded in the data. The evaluation was conducted on synthetic data, where patterns were artificially embedded, and on real-world text collection, where each document is labeled with a topic. Finally, in order to qualitatively evaluate the usefulness of the discovered patterns, we exploited PaNDa + to detect overlapping communities in a bipartite network. The results show that PaNDa + is able to discover high-quality patterns in both synthetic and real-world datasets.
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    Co-Evolution of Multi-Typed Objects in Dynamic Star Networks (2014)
    Institute of Electrical and Electronics Engineers (IEEE)
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    Publication Date: 2014-11-08
    Description: Mining network evolution has emerged as an intriguing research topic in many domains such as data mining, social networks, and machine learning. While a bulk of research has focused on mining evolutionary patterns of homogeneous networks (e.g., networks of friends), however, most real-world networks are heterogeneous, containing objects of different types, such as authors, papers, venues, and terms in a bibliographic network. Modeling co-evolution of multityped objects can capture richer information than that on single-typed objects alone. For example, studying co-evolution of authors, venues, and terms in a bibliographic network can tell better the evolution of research areas than just examining co-author network or term network alone. In this paper, we study mining co-evolution of multityped objects in a special type of heterogeneous networks, called star networks, and examine how the multityped objects influence each other in the network evolution. A hierarchical Dirichlet process mixture model-based evolution model is proposed, which detects the co-evolution of multityped objects in the form of multityped cluster evolution in dynamic star networks. An efficient inference algorithm is provided to learn the proposed model. Experiments on several real networks (DBLP, Twitter, and Delicious) validate the effectiveness of the model and the scalability of the algorithm.
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    A New Strategy of Cost-Free Learning in the Class Imbalance Problem (2014)
    Institute of Electrical and Electronics Engineers (IEEE)
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    Publication Date: 2014-11-08
    Description: In this work, we define cost-free learning (CFL) formally in comparison with cost-sensitive learning (CSL). The main difference between them is that a CFL approach seeks optimal classification results without requiring any cost information, even in the class imbalance problem. In fact, several CFL approaches exist in the related studies, such as sampling and some criteria-based approaches. However, to our best knowledge, none of the existing CFL and CSL approaches are able to process the abstaining classifications properly when no information is given about errors and rejects. Based on information theory, we propose a novel CFL which seeks to maximize normalized mutual information of the targets and the decision outputs of classifiers. Using the strategy, we can handle binary/multi-class classifications with/without abstaining. Significant features are observed from the new strategy. While the degree of class imbalance is changing, the proposed strategy is able to balance the errors and rejects accordingly and automatically. Another advantage of the strategy is its ability of deriving optimal rejection thresholds for abstaining classifications and the “equivalent” costs in binary classifications. The connection between rejection thresholds and ROC curve is explored. Empirical investigation is made on several benchmark data sets in comparison with other existing approaches. The classification results demonstrate a promising perspective of the strategy in machine learning.
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    Discovery of Temporal Associations in Multivariate Time Series (2014)
    Institute of Electrical and Electronics Engineers (IEEE)
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    Publication Date: 2014-11-08
    Description: Multivariate time series are common in many application domains, particularly in industrial processes with a large number of sensors installed for process monitoring and control. Often, such data encapsulate complex relations among individual series. This paper presents a new type of patterns in multivariate time series, referred to as temporal associations, to capture a wide range of local relations along and across individual series. A scalable algorithm is developed to discover frequent associations by incorporating (1) redundancy pruning of patterns in single time series and (2) two conditions to avoid over-counting the occurrences of associations, thus greatly reducing the space and runtime complexity of the discovery process. A statistical significance measure is also introduced for ranking and post-pruning discovered associations. To evaluate the proposed method, synthetic data sets and a real world data set taken from the time series mining repository as well as a large data set obtained from a delayed coking plant are used. The experiments demonstrated that the discovered associations capture the local relations in multiple time series and that the proposed method is scalable to large data sets.
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    BTM: Topic Modeling over Short Texts (2014)
    Institute of Electrical and Electronics Engineers (IEEE)
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    Publication Date: 2014-11-08
    Description: Short texts are popular on today’s web, especially with the emergence of social media. Inferring topics from large scale short texts becomes a critical but challenging task for many content analysis tasks. Conventional topic models such as latent Dirichlet allocation (LDA) and probabilistic latent semantic analysis (PLSA) learn topics from document-level word co-occurrences by modeling each document as a mixture of topics, whose inference suffers from the sparsity of word co-occurrence patterns in short texts. In this paper, we propose a novel way for short text topic modeling, referred as biterm topic model (BTM) . BTM learns topics by directly modeling the generation of word co-occurrence patterns (i.e., biterms) in the corpus, making the inference effective with the rich corpus-level information. To cope with large scale short text data, we further introduce two online algorithms for BTM for efficient topic learning. Experiments on real-word short text collections show that BTM can discover more prominent and coherent topics, and significantly outperform the state-of-the-art baselines. We also demonstrate the appealing performance of the two online BTM algorithms on both time efficiency and topic learning.
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    Evaluation of Hierarchical Interestingness Measures for Mining Pairwise Generalized Association Rules (2014)
    Institute of Electrical and Electronics Engineers (IEEE)
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    Publication Date: 2014-11-08
    Description: In the literature about association analysis, many interestingness measures have been proposed to assess the quality of obtained association rules in order to select a small set of the most interesting among them. In the particular case of hierarchically organized items and generalized association rules connecting them, a measure that dealt appropriately with the hierarchy would be advantageous. Here we present the further developments of a new class of such hierarchical interestingness measures and compare them with a large set of conventional measures and with three hierarchical pruning methods from the literature. The aim is to find interesting pairwise generalized association rules connecting the concepts of multiple ontologies. Interested in the broad empirical evaluation of interestingness measures, we compared the rules obtained by 37 methods on four real world data sets against predefined ground truth sets of associations. To this end, we adopted a framework of instance-based ontology matching and extended the set of performance measures by two novel measures: relation learning recall and precision which take into account hierarchical relationships.
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    Highly Comparative Feature-Based Time-Series Classification (2014)
    Institute of Electrical and Electronics Engineers (IEEE)
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    Publication Date: 2014-11-08
    Description: A highly comparative, feature-based approach to time series classification is introduced that uses an extensive database of algorithms to extract thousands of interpretable features from time series. These features are derived from across the scientific time-series analysis literature, and include summaries of time series in terms of their correlation structure, distribution, entropy, stationarity, scaling properties, and fits to a range of time-series models. After computing thousands of features for each time series in a training set, those that are most informative of the class structure are selected using greedy forward feature selection with a linear classifier. The resulting feature-based classifiers automatically learn the differences between classes using a reduced number of time-series properties, and circumvent the need to calculate distances between time series. Representing time series in this way results in orders of magnitude of dimensionality reduction, allowing the method to perform well on very large data sets containing long time series or time series of different lengths. For many of the data sets studied, classification performance exceeded that of conventional instance-based classifiers, including one nearest neighbor classifiers using euclidean distances and dynamic time warping and, most importantly, the features selected provide an understanding of the properties of the data set, insight that can guide further scientific investigation.
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    An Unsupervised Feature Selection Framework for Social Media Data (2014)
    Institute of Electrical and Electronics Engineers (IEEE)
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    Publication Date: 2014-11-08
    Description: The explosive usage of social media produces massive amount of unlabeled and high-dimensional data. Feature selection has been proven to be effective in dealing with high-dimensional data for efficient learning and data mining. Unsupervised feature selection remains a challenging task due to the absence of label information based on which feature relevance is often assessed. The unique characteristics of social media data further complicate the already challenging problem of unsupervised feature selection, e.g., social media data is inherently linked, which makes invalid the independent and identically distributed assumption, bringing about new challenges to unsupervised feature selection algorithms. In this paper, we investigate a novel problem of feature selection for social media data in an unsupervised scenario. In particular, we analyze the differences between social media data and traditional attribute-value data, investigate how the relations extracted from linked data can be exploited to help select relevant features, and propose a novel unsupervised feature selection framework, LUFS, for linked social media data. We systematically design and conduct systemic experiments to evaluate the proposed framework on data sets from real-world social media websites. The empirical study demonstrates the effectiveness and potential of our proposed framework.
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    Process Discovery Algorithms Using Numerical Abstract Domains (2014)
    Institute of Electrical and Electronics Engineers (IEEE)
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    Publication Date: 2014-11-08
    Description: The discovery of process models from event logs has emerged as one of the crucial problems for enabling the continuous support in the life-cycle of an information system. However, in a decade of process discovery research, the algorithms and tools that have appeared are known to have strong limitations in several dimensions. The size of the logs and the formal properties of the model discovered are the two main challenges nowadays. In this paper we propose the use of numerical abstract domains for tackling these two problems, for the particular case of the discovery of Petri nets. First, numerical abstract domains enable the discovery of general process models, requiring no knowledge (e.g., the bound of the Petri net to derive) for the discovery algorithm. Second, by using divide and conquer techniques we are able to control the size of the process discovery problems. The methods proposed in this paper have been implemented in a prototype tool and experiments are reported illustrating the significance of this fresh view of the process discovery problem.
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    SlashBurn: Graph Compression and Mining beyond Caveman Communities (2014)
    Institute of Electrical and Electronics Engineers (IEEE)
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    Publication Date: 2014-11-08
    Description: Given a real world graph, how should we lay-out its edges? How can we compress it? These questions are closely related, and the typical approach so far is to find clique-like communities, like the ‘cavemen graph’, and compress them. We show that the block-diagonal mental image of the ‘cavemen graph’ is the wrong paradigm, in full agreement with earlier results that real world graphs have no good cuts. Instead, we propose to envision graphs as a collection of hubs connecting spokes, with super-hubs connecting the hubs, and so on, recursively. Based on the idea, we propose the SlashBurn method to recursively split a graph into hubs and spokes connected only by the hubs. We also propose techniques to select the hubs and give an ordering to the spokes, in addition to the basic SlashBurn. We give theoretical analysis of the proposed hub selection methods. Our view point has several advantages: (a) it avoids the ‘no good cuts’ problem, (b) it gives better compression, and (c) it leads to faster execution times for matrix-vector operations, which are the back-bone of most graph processing tools. Through experiments, we show that SlashBurn consistently outperforms other methods for all data sets, resulting in better compression and faster running time. Moreover, we show that SlashBurn with the appropriate spokes ordering can further improve compression while hardly sacrificing the running time.
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    Task Trail: An Effective Segmentation of User Search Behavior (2014)
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    Publication Date: 2014-11-08
    Description: In this paper, we introduce “task trail” to understand user search behaviors. We define a task to be an atomic user information need, whereas a task trail represents all user activities within that particular task, such as query reformulations, URL clicks. Previously, web search logs have been studied mainly at session or query level where users may submit several queries within one task and handle several tasks within one session. Although previous studies have addressed the problem of task identification, little is known about the advantage of using task over session or query for search applications. In this paper, we conduct extensive analyses and comparisons to evaluate the effectiveness of task trails in several search applications: determining user satisfaction, predicting user search interests, and suggesting related queries. Experiments on large scale data sets of a commercial search engine show that: (1) Task trail performs better than session and query trails in determining user satisfaction; (2) Task trail increases webpage utilities of end users comparing to session and query trails; (3) Task trails are comparable to query trails but more sensitive than session trails in measuring different ranking functions; (4) Query terms from the same task are more topically consistent to each other than query terms from different tasks; (5) Query suggestion based on task trail is a good complement of query suggestions based on session trail and click-through bipartite. The findings in this paper verify the need of extracting task trails from web search logs and enhance applications in search and recommendation systems.
    Print ISSN: 1041-4347
    Electronic ISSN: 1558-2191
    Topics: Computer Science
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    Overcoming Asymmetry in Entity Graphs (2014)
    Institute of Electrical and Electronics Engineers (IEEE)
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    Publication Date: 2014-11-08
    Description: This paper studies the problem of mining named entity translations by aligning comparable corpora. Current state-of-the-art approaches mine a translation pair by aligning an entity graph in one language to another based on node similarity or propagated similarity of related entities. However, they, building on the assumption of “symmetry”, quickly deteriorate on “weakly” comparable corpora with some asymmetry. In this paper, we pursue two directions for overcoming relation and entity asymmetry respectively. The first approach starts from weakly comparable corpora (for high recall) then ensures precision by selective propagation only to entities of symmetric relations. The second approach starts from parallel corpora (for high precision) then enhances recall by extending the translation matrix based on node similarity and contextual similarity. Our experimental results on English-Chinese corpora show that both approaches are effective and complementary. Our combined approach outperforms the best-performing baseline in terms of F1-score by up to 0.28.
    Print ISSN: 1041-4347
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    Topics: Computer Science
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    Knowledge Acquisition Method Based on Singular Value Decomposition for Human Motion Analysis (2014)
    Institute of Electrical and Electronics Engineers (IEEE)
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    Publication Date: 2014-11-08
    Description: The knowledge remembered by the human body and reflected by the dexterity of body motion is called embodied knowledge. In this paper, we propose a new method using singular value decomposition for extracting embodied knowledge from the time-series data of the motion. We compose a matrix from the time-series data and use the left singular vectors of the matrix as the patterns of the motion and the singular values as a scalar, by which each corresponding left singular vector affects the matrix. Two experiments were conducted to validate the method. One is a gesture recognition experiment in which we categorize gesture motions by two kinds of models with indexes of similarity and estimation that use left singular vectors. The proposed method obtained a higher correct categorization ratio than principal component analysis (PCA) and correlation efficiency (CE). The other is an ambulation evaluation experiment in which we distinguished the levels of walking disability. The first singular values derived from the walking acceleration were suggested to be a reliable criterion to evaluate walking disability. Finally we discuss the characteristic and significance of the embodied knowledge extraction using the singular value decomposition proposed in this paper.
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    Efficiently Supporting Edit Distance Based String Similarity Search Using B $^+$ -Trees (2014)
    Institute of Electrical and Electronics Engineers (IEEE)
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    Publication Date: 2014-11-08
    Description: Edit distance is widely used for measuring the similarity between two strings. As a primitive operation, edit distance based string similarity search is to find strings in a collection that are similar to a given query string using edit distance. Existing approaches for answering such string similarity queries follow the filter-and-verify framework by using various indexes. Typically, most approaches assume that indexes and data sets are maintained in main memory. To overcome this limitation, in this paper, we propose B $^+$ -tree based approaches to answer edit distance based string similarity queries, and hence, our approaches can be easily integrated into existing RDBMSs. In general, we answer string similarity search using pruning techniques employed in the metric space in that edit distance is a metric. First, we split the string collection into partitions according to a set of reference strings. Then, we index strings in all partitions using a single B $^+$ -tree based on the distances of these strings to their corresponding reference strings. Finally, we propose two approaches to efficiently answer range and KNN queries, respectively, based on the B $^+$ -tree. We prove that the optimal partitioning of the data set is an NP-hard problem, and therefore propose a heuristic approach for selecting the reference strings greedily and present an optimal partition assignment strategy to minimize the expected number of strings that need to be verified during the query evaluation. Through extensive experiments over a variety of real data sets, we demonstrate that our B $^+$ -tree based approaches provide superior performance over state-of-the-art techniques on both range and KNN queries in most cases.
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    Toward Scalable Indexing for Top- (k) Queries (2014)
    Institute of Electrical and Electronics Engineers (IEEE)
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    Publication Date: 2014-11-08
    Description: A top- k query retrieves the best (k) tuples by assigning scores for each tuple in a target relation with respect to a user-specific scoring function. This paper studies the problem of constructing an indexing structure for supporting top- k queries over varying scoring functions and retrieval sizes. The existing research efforts can be categorized into three approaches: list- , layer- , and view-based approaches. In this paper, we mainly focus on the layer-based approach that pre-materializes tuples into consecutive multiple layers. We first propose a dual-resolution layer that consists of coarse-level and fine-level layers. Specifically, we build coarse-level layers using skylines , and divide each coarse-level layer into fine-level sublayers using convex skylines . To make our proposed dual-resolution layer scalable , we then address the following optimization directions: 1) index construction; 2) disk-based storage scheme; 3) the design of the virtual layer; and 4) index maintenance for tuple updates. Our evaluation results show that our proposed method is more scalable than the state-of-the-art methods.
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    The Need for Indigenous Voices in Discourse about Introduced Species: Insights from a Controversy over Wild Horses (2014)
    White Horse Press
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    Publication Date: 2014-11-05
    Print ISSN: 0963-2719
    Electronic ISSN: 1752-7015
    Topics: Energy, Environment Protection, Nuclear Power Engineering , Philosophy
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    Ethical Intuitions, Welfare, and Permaculture (2014)
    White Horse Press
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    Publication Date: 2014-11-05
    Description: This article is currently available as a free download on ingentaconnect
    Print ISSN: 0963-2719
    Electronic ISSN: 1752-7015
    Topics: Energy, Environment Protection, Nuclear Power Engineering , Philosophy
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    Alien Invasive Species Management: Stakeholder Perceptions of the Barents Sea King Crab (2014)
    White Horse Press
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    Publication Date: 2014-11-05
    Print ISSN: 0963-2719
    Electronic ISSN: 1752-7015
    Topics: Energy, Environment Protection, Nuclear Power Engineering , Philosophy
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    Plants in Ethics: Why Flourishing Deserves Moral Respect (2014)
    White Horse Press
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    Publication Date: 2014-11-05
    Print ISSN: 0963-2719
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    Topics: Energy, Environment Protection, Nuclear Power Engineering , Philosophy
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    Should We Move the Whitebark Pine? Assisted Migration, Ethics and Global Environmental Change (2014)
    White Horse Press
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    Publication Date: 2014-11-05
    Print ISSN: 0963-2719
    Electronic ISSN: 1752-7015
    Topics: Energy, Environment Protection, Nuclear Power Engineering , Philosophy
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    Reviews (2014)
    White Horse Press
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    Publication Date: 2014-11-05
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    Topics: Energy, Environment Protection, Nuclear Power Engineering , Philosophy
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    The Blind Hens' Challenge: Does It Undermine the View That Only Welfare Matters in Our Dealings with Animals? (2014)
    White Horse Press
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    Publication Date: 2014-11-05
    Print ISSN: 0963-2719
    Electronic ISSN: 1752-7015
    Topics: Energy, Environment Protection, Nuclear Power Engineering , Philosophy
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    Future Internet, Vol. 6, Pages 688-716: The ARCOMEM Architecture for Social- and Semantic-Driven Web Archiving (2014)
    MDPI Publishing
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    Publication Date: 2014-11-05
    Description: The constantly growing amount ofWeb content and the success of the SocialWeb lead to increasing needs for Web archiving. These needs go beyond the pure preservationo of Web pages. Web archives are turning into “community memories” that aim at building a better understanding of the public view on, e.g., celebrities, court decisions and other events. Due to the size of the Web, the traditional “collect-all” strategy is in many cases not the best method to build Web archives. In this paper, we present the ARCOMEM (From Future Internet 2014, 6 689 Collect-All Archives to Community Memories) architecture and implementation that uses semantic information, such as entities, topics and events, complemented with information from the Social Web to guide a novel Web crawler. The resulting archives are automatically enriched with semantic meta-information to ease the access and allow retrieval based on conditions that involve high-level concepts..
    Electronic ISSN: 1999-5903
    Topics: Computer Science
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    Latent Feature Decompositions for Integrative Analysis of Multi-Platform Genomic Data (2014)
    Institute of Electrical and Electronics Engineers (IEEE)
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    Publication Date: 2014-12-13
    Description: Increased availability of multi-platform genomics data on matched samples has sparked research efforts to discover how diverse molecular features interact both within and between platforms. In addition, simultaneous measurements of genetic and epigenetic characteristics illuminate the roles their complex relationships play in disease progression and outcomes. However, integrative methods for diverse genomics data are faced with the challenges of ultra-high dimensionality and the existence of complex interactions both within and between platforms. We propose a novel modeling framework for integrative analysis based on decompositions of the large number of platform-specific features into a smaller number of latent features. Subsequently we build a predictive model for clinical outcomes accounting for both within- and between-platform interactions based on Bayesian model averaging procedures. Principal components, partial least squares and non-negative matrix factorization as well as sparse counterparts of each are used to define the latent features, and the performance of these decompositions is compared both on real and simulated data. The latent feature interactions are shown to preserve interactions between the original features and not only aid prediction but also allow explicit selection of outcome-related features. The methods are motivated by and applied to a glioblastoma multiforme data set from The Cancer Genome Atlas to predict patient survival times integrating gene expression, microRNA, copy number and methylation data. For the glioblastoma data, we find a high concordance between our selected prognostic genes and genes with known associations with glioblastoma. In addition, our model discovers several relevant cross-platform interactions such as copy number variation associated gene dosing and epigenetic regulation through promoter methylation. On simulated data, we show that our proposed method successfully incorporates interactions within and between g- nomic platforms to aid accurate prediction and variable selection. Our methods perform best when principal components are used to define the latent features.
    Print ISSN: 1545-5963
    Electronic ISSN: 1557-9964
    Topics: Biology , Computer Science
    Published by Institute of Electrical and Electronics Engineers (IEEE) on behalf of The IEEE Computational Intelligence Society ; The IEEE Computer Society ; The IEEE Control Systems Society ; The IEEE Engineering in Medicine and Biology Society ; The Association for Computing Machinery.
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    A Novel En-Route Filtering Scheme Against False Data Injection Attacks in Cyber-Physical Networked Systems (2014)
    Institute of Electrical and Electronics Engineers (IEEE)
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    Publication Date: 2014-12-13
    Description: In Cyber-Physical Networked Systems (CPNS), the adversary can inject false measurements into the controller through compromised sensor nodes, which not only threaten the security of the system, but also consume network resources. To deal with this issue, a number of en-route filtering schemes have been designed for wireless sensor networks. However, these schemes either lack resilience to the number of compromised nodes or depend on the statically configured routes and node localization, which are not suitable for CPNS. In this paper, we propose a Polynomial-based Compromise-Resilient En-route Filtering scheme (PCREF), which can filter false injected data effectively and achieve a high resilience to the number of compromised nodes without relying on static routes and node localization. PCREF adopts polynomials instead of Message Authentication Codes (MACs) for endorsing measurement reports to achieve resilience to attacks. Each node stores two types of polynomials: authentication polynomial and check polynomial, derived from the primitive polynomial, and used for endorsing and verifying the measurement reports. Through extensive theoretical analysis and experiments, our data shows that PCREF achieves better filtering capacity and resilience to the large number of compromised nodes in comparison to the existing schemes.
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    RRAM Defect Modeling and Failure Analysis Based on March Test and a Novel Squeeze-Search Scheme (2014)
    Institute of Electrical and Electronics Engineers (IEEE)
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    Publication Date: 2014-12-13
    Description: The Resistive Random Access Memory (RRAM) is a new type of non-volatile memory based on the resistive memory device. Researchers are currently moving from resistive device development to memory circuit design and implementation, hoping to fabricate memory chips that can be deployed in the market in the near future. However, so far the low manufacturing yield is still a major issue. In this paper, we propose defect and fault models specific to RRAM, i.e., the Over-Forming (OF) defect and the Read-One-Disturb (R1D) fault. We then propose a March algorithm to cover these defects and faults in addition to the conventional RAM faults, which is called March C*. We also develop a novel squeeze-search scheme to identify the OF defect, which leads to the Stuck-At Fault (SAF). The proposed test algorithm is applied to a first-cut 4-Mb HfO 2 -based RRAM test chip. Results show that OF defects and R1D faults do exist in the RRAM chip. We also identify specific failure patterns from the test results, which are shown to be induced by multiple short defects between bit-lines. By identifying the defects and faults, designers and process engineers can improve the RRAM yield in a more cost-effective way.
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    Requester-Based Spin Lock: A Scalable and Energy Efficient Locking Scheme on Multicore Systems (2014)
    Institute of Electrical and Electronics Engineers (IEEE)
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    Publication Date: 2014-12-13
    Description: In response to the increasing ubiquity of multicore processors, applications are usually designed or deployed to make each core busy. Unfortunately, lock contention within operating systems can limit the scalability of multicore systems so severely that an increase in the number of cores can actually lead to reduced performance (i.e., scalability collapse). Existing lock implementations have disadvantages in scalability, power consumption, and energy efficiency. In this paper, we observe that the number of tasks requesting a lock has a significant correlation with the occurrence of scalability collapse. Based on this observation, a lock implementation that allows tasks waiting for a lock to either spin or enter a power-saving state based on the number of requesters is proposed. Our lock protocol is called requester-based lock and is implemented in the Linux kernel to replace its default spin lock. Based on the results of a sensitivity analysis, we find that the best policy, in practice, for a task waiting for a lock to be granted is to enter the power-saving state immediately after noticing the lock cannot be acquired. Our requester-based lock scheme is evaluated using intensive benchmarking on AMD 32-core and Intel 40-core systems. Experimental results suggest that our lock avoids scalability collapse completely for most applications and shows better scalability, power consumption, and energy efficiency than previous work. Besides, the requester-based lock is extensible, which means using together with other kinds of spin locks can provide better scalability and energy efficiency.
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    Selecting an Optimal Fault Tolerance Strategy for Reliable Service-Oriented Systems with Local and Global Constraints (2014)
    Institute of Electrical and Electronics Engineers (IEEE)
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    Publication Date: 2014-12-13
    Description: Functionally equivalent web services can be composed to form more reliable service-oriented systems. However, the choice of fault tolerance strategy can have a significant effect on the quality-of-service (QoS) of the resulting service-oriented systems. In this paper, we investigate the problem of selecting an optimal fault tolerance strategy for building reliable service-oriented systems. We formulate the user requirements as local and global constraints and model the selection of fault tolerance strategy as an optimization problem. A heuristic algorithm is proposed to efficiently solve the optimization problem. Fault tolerance strategy selection for semantically related tasks is also investigated in this paper. Large-scale real-world experiments are conducted to illustrate the benefits of the proposed approach. The experimental results show that our problem modeling approach and the proposed selection algorithm make it feasible to manage the fault tolerance of complex service-oriented systems both efficiently and effectively.
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    Software Support and Evaluation of Hardware Transactional Memory on Blue Gene/Q (2014)
    Institute of Electrical and Electronics Engineers (IEEE)
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    Publication Date: 2014-12-13
    Description: This paper describes an end-to-end system implementation of a transactional memory (TM) programming model on top of the hardware transactional memory (HTM) of the Blue Gene/Q machine. The TM programming model supports most C/C++ programming constructs using a best-effort HTM and the help of a complete software stack including the compiler, the kernel, and the TM runtime. An extensive evaluation of the STAMP and the RMS-TM benchmark suites on BG/Q is the first of its kind in understanding characteristics of running TM workloads on real hardware TM. The study reveals several interesting insights on the overhead and the scalability of BG/Q HTM with respect to sequential execution, coarse-grain locking, and software TM.
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    Completely Pinpointing the Missing RFID Tags in a Time-Efficient Way (2014)
    Institute of Electrical and Electronics Engineers (IEEE)
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    Publication Date: 2014-12-13
    Description: Radio Frequency Identification (RFID) technology has been widely used in inventory management in many scenarios, e.g., warehouses, retail stores, hospitals, etc. This paper investigates a challenging problem of complete identification of missing tags in large-scale RFID systems. Although this problem has attracted extensive attention from academy and industry, the existing work can hardly satisfy the stringent real-time requirements. In this paper, a Slot Filter-based Missing Tag Identification (SFMTI) protocol is proposed to reconcile some expected collision slots into singleton slots and filter out the expected empty slots as well as the unreconcilable collision slots, thereby achieving the improved time-efficiency. The theoretical analysis is conducted to minimize the execution time of the proposed SFMTI. We then propose a cost-effective method to extend SFMTI to the multi-reader scenarios. The extensive simulation experiments and performance results demonstrate that the proposed SFMTI protocol outperforms the most promising Iterative ID-free Protocol (IIP) by reducing nearly 45% of the required execution time, and is just within a factor of 1.18 from the lower bound of the minimum execution time.
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    Testing Open Defects in Memristor-Based Memories (2014)
    Institute of Electrical and Electronics Engineers (IEEE)
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    Publication Date: 2014-12-13
    Description: Memristor-based memory technology, also referred to as resistive RAM (RRAM), is one of the emerging memory technologies potentially to replace conventional semiconductor memories such as SRAM, DRAM, and flash. Existing research on such novel circuits focuses mainly on the integration between CMOS and non-CMOS, fabrication techniques, and reliability improvement. However, research on (manufacturing) test for yield and quality improvement is still in its infancy stage. This paper presents fault analysis and modeling for open defects based on electrical simulation, introduces fault models, and proposes test approaches for RRAMs. The fault analysis reveals that unique faults occur in addition to some conventional memory faults, and the detection of such unique faults cannot be guaranteed with just the application of traditional march tests. The paper also presents a new Design-for-Testability (DfT) concept to facilitate the detection of the unique faults. Two DfT schemes are developed by exploiting the access time duration and supply voltage level of the RRAM cells, and their simulation results show that the fault coverage can be increased with minor circuit modification. As the fault behavior may vary due to process variations, the DfT schemes are extended to be programmable to track the changes and further improve the fault/defect coverage.
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    Time Series Characterization of Gaming Workload for Runtime Power Management (2014)
    Institute of Electrical and Electronics Engineers (IEEE)
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    Publication Date: 2014-12-13
    Description: Runtime power management using dynamic voltage and frequency scaling (DVFS) has been extensively studied for video processing applications. But there is only a little work on game power management although gaming applications are now widely run on battery-operated portable devices like mobile phones. Taking a cue from video power management, where PID controllers have been successfully used, they were recently applied to game workload prediction and DVFS. However, the use of hand-tuned PID controller gains on relatively short game plays left open questions on the robustness of the controller and the sensitivity of prediction quality on the choice of the gain values. In this paper, we try to systematically answer these questions. We first show that from the space of PID controller gain values, only a small subset leads to good game quality and power savings. Further, the choice of this set highly depends on the scene and the game application. For most gain values the controller becomes unstable, which can lead to large oscillations in the processor’s frequency setting and thereby poor results. We then study a number of time series models, such as a Least Mean Squares (LMS) Linear Predictor and its generalizations in the form of Autoregressive Moving Average (ARMA) models. These models learn most of the relevant model parameters iteratively as the game progresses, thereby dramatically reducing the complexity of manual parameter estimation. This makes them deployable in real setups, where all game plays and even game applications are not a priori known. We have evaluated each of these models (PID, LMS, and ARMA) for a variety of games—ranging from Quake II to more recent closed-source games such as Crysis, Need for Speed—Shift and World in Conflict—with very encouraging results. To the best of our knowledge, this is the first work that systematically explores (a) the feasibility of manually tuning PID controller parameters for p- wer management, (b) time series models for workload prediction for gaming applications, and (c) power management for closed-source games.
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    Efficient Privacy-Preserving Ciphertext-Policy Attribute Based-Encryption and Broadcast Encryption (2014)
    Institute of Electrical and Electronics Engineers (IEEE)
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    Publication Date: 2014-12-13
    Description: Ciphertext Policy Attribute-Based Encryption (CP-ABE) enforces expressive data access policies and each policy consists of a number of attributes. Most existing CP-ABE schemes incur a very large ciphertext size, which increases linearly with respect to the number of attributes in the access policy. Recently, Herranz proposed a construction of CP-ABE with constant ciphertext. However, Herranz do not consider the recipients’ anonymity and the access policies are exposed to potential malicious attackers. On the other hand, existing privacy preserving schemes protect the anonymity but require bulky, linearly increasing ciphertext size. In this paper, we proposed a new construction of CP-ABE, named Privacy Preserving Constant CP-ABE (denoted as PP-CP-ABE) that significantly reduces the ciphertext to a constant size with any given number of attributes. Furthermore, PP-CP-ABE leverages a hidden policy construction such that the recipients’ privacy is preserved efficiently. As far as we know, PP-CP-ABE is the first construction with such properties. Furthermore, we developed a Privacy Preserving Attribute-Based Broadcast Encryption (PP-AB-BE) scheme. Compared to existing Broadcast Encryption (BE) schemes, PP-AB-BE is more flexible because a broadcasted message can be encrypted by an expressive hidden access policy, either with or without explicit specifying the receivers. Moreover, PP-AB-BE significantly reduces the storage and communication overhead to the order of ${mbi {O}}(log {mbi {N}})$ , where ${mbi {N}}$ is the system size. Also, we proved, using information theoretical approaches, PP-AB-BE attains minimal bound on storage overhead for each user to cover all possible subgroups in the communication system.
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    Stabilizing CPU Frequency and Voltage for Temperature-Aware DVFS in Mobile Devices (2014)
    Institute of Electrical and Electronics Engineers (IEEE)
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    Publication Date: 2014-12-13
    Description: Recent mobile devices adopt high-performance processors to support various functions. As a side effect, higher performance inevitably leads to power density increase, eventually resulting in thermal problems. In order to alleviate the thermal problems, off-the-shelf mobile devices rely on dynamic voltage-frequency scaling (DVFS)-based dynamic thermal management (DTM) schemes. Unfortunately, in the DVFS-based DTM schemes, an excessive number of DTM operations worsen not only performance but also power efficiency. In this paper, we propose a temperature-aware DVFS scheme for Android-based mobile devices to optimize power or performance depending on the option. We evaluate our scheme in the off-the-shelf mobile device. Our evaluation results show that our scheme saves energy consumption by 12.7%, on average, when we use the power optimizing option. Our scheme also enhances the performance by 6.3%, on average, by using the performance optimizing scheme, still reducing the energy consumption by 6.7%.
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    2014 Index IEEE Transactions on Computers Vol. 63 (2014)
    Institute of Electrical and Electronics Engineers (IEEE)
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    Publication Date: 2014-12-13
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    Comment on “High Speed Parallel Decimal Multiplication With Redundant Internal Encodings” (2014)
    Institute of Electrical and Electronics Engineers (IEEE)
    Details
    Publication Date: 2014-12-13
    Description: Han propose a new method for parallel decimal multiplication with redundant partial products. They compare the performance of their multiplier with some previous relevant works, based on analytical and synthesis results. We have noted that the claimed critical delay path in (IEEE Trans. Computers, vol. 62, no. 5, pp. 956–968, May 2013) is faster than the actual critical delay path. Therefore, comparison results seem to be deceptive. For example, our accurate analytical evaluation devaluated the claimed speed advantage over the multiplier of (Microelectronics J., vol. 40, no. 10, pp. 1471–1481, Oct. 2009). Furthermore, we synthesized both multipliers, to show synthesis results confirm those of analytical evaluation.
    Print ISSN: 0018-9340
    Electronic ISSN: 1557-9956
    Topics: Computer Science
    Published by Institute of Electrical and Electronics Engineers (IEEE) on behalf of The IEEE Computer Society.
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    Exploring Metasystems (2014)
    Institute of Electrical and Electronics Engineers (IEEE)
    Details
    Publication Date: 2014-12-06
    Description: Learn about metasystems, their characteristics, and the challenges IT professionals and systems engineers face in designing and managing such systems.
    Print ISSN: 1520-9202
    Electronic ISSN: 1941-045X
    Topics: Computer Science
    Published by Institute of Electrical and Electronics Engineers (IEEE) on behalf of The IEEE Computer Society.
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    Employing Enterprise Architecture for Applications Assurance (2014)
    Institute of Electrical and Electronics Engineers (IEEE)
    Details
    Publication Date: 2014-12-06
    Description: Before writing a single line of code, software engineers can increase application assurance by instituting the practice recommendations articulated in their enterprise architecture. Many Common Weakness Enumerations (CWEs) can be addressed in the architecture and design phases of the development life cycle. Architectural and design flaws found late in the SDLC can be costly to repair; often, these flaws are so baked into the application that they're resistant to code patches. The only viable response might be to catalogue their existence for a later redesign of the application. Moreover, patches to flaws can inject additional defects as well as alert adversaries to the existence of these flaws.
    Print ISSN: 1520-9202
    Electronic ISSN: 1941-045X
    Topics: Computer Science
    Published by Institute of Electrical and Electronics Engineers (IEEE) on behalf of The IEEE Computer Society.
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    Algorithms, Vol. 7, Pages 685-702: Fusion of Multiple Pyroelectric Characteristics for Human Body Identification (2014)
    MDPI Publishing
    Details
    Publication Date: 2014-12-19
    Description: Due to instability and poor identification ability of single pyroelectric infrared (PIR) detector for human target identification, this paper proposes a new approach to fuse the information collected from multiple PIR sensors for human identification. Firstly, Fast Fourier Transform (FFT), Short Time Fourier Transform (STFT), Wavelet Transform (WT) and Wavelet Packet Transform (WPT) are adopted to extract features of the human body, which can be achieved by single PIR sensor. Then, we apply Principal Component Analysis (PCA) and Support Vector Machine (SVM) to reduce the characteristic dimensions and to classify the human targets, respectively. Finally, Fuzzy Comprehensive Evaluation (FCE) is utilized to fuse recognition results from multiple PIR sensors to finalize human identification. The pyroelectric characteristics under scenarios with different people and/or different paths are analyzed by various experiments, and the recognition results with/without fusion procedure are also shown and compared. The experimental results demonstrate our scheme has improved efficiency for human identification.
    Electronic ISSN: 1999-4893
    Topics: Computer Science
    Published by MDPI Publishing
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    The Indian Banking Community Cloud (2014)
    Institute of Electrical and Electronics Engineers (IEEE)
    Details
    Publication Date: 2014-12-06
    Description: Cloud computing provides flexibility and agility to meet growing business needs in a dynamic and competitive landscape. Banking, financial services, and insurance sector organizations are interested in exploring cloud services as a technology, provided that security and privacy are ensured. One solution is a community cloud, in which cloud services are targeted for organizations with common objectives and security controls. The Indian Banking Community Cloud (IBCC) initiative of the Institute for Development and Research in Banking Technology in Hyderabad, India, provides cloud-based services exclusively for Indian banks. In this article, the authors describe the IBCC architecture, along with its implementation details, cloud services offered, security and disaster-recovery aspects, deployment challenges, and future work. This article is part of a special issue on advancing cloud computing.
    Print ISSN: 1520-9202
    Electronic ISSN: 1941-045X
    Topics: Computer Science
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    Automated Semantic Tagging of Textual Content (2014)
    Institute of Electrical and Electronics Engineers (IEEE)
    Details
    Publication Date: 2014-12-06
    Description: Motivated by a continually increasing demand for applications that depend on machine comprehension of text-based content, researchers in both academia and industry have developed innovative solutions for automated information extraction from text. In this article, the authors focus on a subset of such tools--semantic taggers--that not only extract and disambiguate entities mentioned in the text but also identify topics that unambiguously describe the text's main themes. The authors offer insight into the process of semantic tagging, the capabilities and specificities of today's semantic taggers, and also indicate some of the criteria to be considered when choosing a tagger.
    Print ISSN: 1520-9202
    Electronic ISSN: 1941-045X
    Topics: Computer Science
    Published by Institute of Electrical and Electronics Engineers (IEEE) on behalf of The IEEE Computer Society.
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    Cost-Benefit Analysis of Datacenter Consolidation Using Virtualization (2014)
    Institute of Electrical and Electronics Engineers (IEEE)
    Details
    Publication Date: 2014-12-06
    Description: The objectives of datacenter consolidation are cost reduction and superior services. A datacenter consolidation plan includes minimizing investments in IT infrastructure and buildings and reducing power consumption related to cooling. Such a process requires scalable planning and implementation. Virtualization is the most popular and cost-effective technology for datacenter consolidation. In this article, the author runs a cost-benefit analysis of virtualization and datacenter consolidation using the Global Virtual datacenter online calculator and VMware's ROI CO ((for) return on investment/total cost of ownership) calculator version 3.0.
    Print ISSN: 1520-9202
    Electronic ISSN: 1941-045X
    Topics: Computer Science
    Published by Institute of Electrical and Electronics Engineers (IEEE) on behalf of The IEEE Computer Society.
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    Computational Networks: Challenging Traditional Program Management (2014)
    Institute of Electrical and Electronics Engineers (IEEE)
    Details
    Publication Date: 2014-12-06
    Description: The adoption of various converging trends in IT, such as cloud computing, the Internet of Things (IoT), crypto-currency, autonomous systems, and big data, challenge traditional notions of program management and highlight the importance of computational networks.
    Print ISSN: 1520-9202
    Electronic ISSN: 1941-045X
    Topics: Computer Science
    Published by Institute of Electrical and Electronics Engineers (IEEE) on behalf of The IEEE Computer Society.
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    [Masthead] (2014)
    Institute of Electrical and Electronics Engineers (IEEE)
    Details
    Publication Date: 2014-12-06
    Description: Provides a listing of current staff, committee members and society officers.
    Print ISSN: 1520-9202
    Electronic ISSN: 1941-045X
    Topics: Computer Science
    Published by Institute of Electrical and Electronics Engineers (IEEE) on behalf of The IEEE Computer Society.
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    Farmland Prices: Is This Time Different? (2014)
    Oxford University Press
    Details
    Publication Date: 2014-12-03
    Description: The historical behavior of farmland prices, rental rates, and rates of return are examined by treating farmland as an asset with an infinitely long life. It is found that high (low) farmland prices relative to rents have historically preceded extended periods of low (high) net rates of return, rather than greater (smaller) growth in rents. Our analysis shows that this attribute is shared with stocks and housing, and the financial literature provides ample evidence that other assets feature it as well. The long-run relationship linking farmland prices, rents, and rates of return is analyzed. Based on this relationship, we conclude that recent trends are unlikely to be sustainable. The study explores the expected paths that farmland prices and rates of return might follow if they were to eventually conform to the average values observed in the historical sample, and concludes with a discussion of the policy implications. Recommendations for policy makers include close monitoring of farmland lending practices and institutions to allow early identification of potential problems, and identifying in advance appropriate interventions in case recent farmland market trends were to suddenly change.
    Keywords: Q14 - Agricultural Finance
    Print ISSN: 2040-5790
    Electronic ISSN: 2040-5804
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
    Published by Oxford University Press
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    Subscription Page (2014)
    Oxford University Press
    Details
    Publication Date: 2014-12-03
    Print ISSN: 2040-5790
    Electronic ISSN: 2040-5804
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
    Published by Oxford University Press
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    Some Comments on "Taxes, Subsidies, and Advertising Efficacy in Changing Eating Behavior: An Experimental Study" (2014)
    Oxford University Press
    Details
    Publication Date: 2014-12-03
    Print ISSN: 2040-5790
    Electronic ISSN: 2040-5804
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
    Published by Oxford University Press
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    Hispanic American Opinions toward Immigration and Immigration Policy Reform Proposals (2014)
    Oxford University Press
    Details
    Publication Date: 2014-12-03
    Description: This study presents evidence from a survey and choice experiment on the preferences of Hispanic immigrants who entered the United States illegally for different immigration reform proposal attributes. Key components of the current competing US Senate and House immigration reform bills are considered including pathways to legal permanent residence, temporary work visas, family visitation rights, and access to medical care. The results quantify the value Hispanic immigrants place on different policy attributes and suggest that longer-term work visas are highly valued. Ability to legally work in the United States and a pathway to citizenship are substantially more valued than social services such as medical care and social security benefits.
    Keywords: J15 - Economics of Minorities and Races ; Non-labor Discrimination, K37 - Immigration Law, Q18 - Agricultural Policy ; Food Policy
    Print ISSN: 2040-5790
    Electronic ISSN: 2040-5804
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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    What to Do about the "Cult of Statistical Significance"? A Renewable Fuel Application using the Neyman-Pearson Protocol (2014)
    Oxford University Press
    Details
    Publication Date: 2014-12-03
    Description: This research adapts the Neyman-Pearson testing protocol commonly used in biomedical research for ex post evaluation of the employment impacts of new ethanol bio-refineries in the U.S. Great Plains and the Midwest. By calculating the power of the test, the suggested protocol may provide policy-relevant information, even in the event of nonsignificant findings. The main obstacle to applying this protocol has been the need to posit an explicit alternative distribution, which runs counter to the empiricist tradition of mainstream econometrics. We resolve this problem by applying a data generating process with known parameters anchored to sample data to compute power.
    Keywords: C12 - Hypothesis Testing, Q42 - Alternative Energy Sources, R11 - Regional Economic Activity: Growth, Development, and Changes
    Print ISSN: 2040-5790
    Electronic ISSN: 2040-5804
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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    Reply to Comment on Taxes, Subsidies, and Advertising Efficacy in Changing Eating Behavior: An Experimental Study (2014)
    Oxford University Press
    Details
    Publication Date: 2014-12-03
    Keywords: C91 - Laboratory, Individual Behavior, I18 - Government Policy ; Regulation ; Public Health
    Print ISSN: 2040-5790
    Electronic ISSN: 2040-5804
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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    Characterization of structural variants with single molecule and hybrid sequencing approaches (2014)
    Oxford University Press
    Details
    Publication Date: 2014-12-04
    Description: Motivation : Structural variation is common in human and cancer genomes. High-throughput DNA sequencing has enabled genome-scale surveys of structural variation. However, the short reads produced by these technologies limit the study of complex variants, particularly those involving repetitive regions. Recent ‘third-generation’ sequencing technologies provide single-molecule templates and longer sequencing reads, but at the cost of higher per-nucleotide error rates. Results : We present MultiBreak-SV, an algorithm to detect structural variants (SVs) from single molecule sequencing data, paired read sequencing data, or a combination of sequencing data from different platforms. We demonstrate that combining low-coverage third-generation data from Pacific Biosciences (PacBio) with high-coverage paired read data is advantageous on simulated chromosomes. We apply MultiBreak-SV to PacBio data from four human fosmids and show that it detects known SVs with high sensitivity and specificity. Finally, we perform a whole-genome analysis on PacBio data from a complete hydatidiform mole cell line and predict 1002 high-probability SVs, over half of which are confirmed by an Illumina-based assembly. Availability and implementation : MultiBreak-SV is available at http://compbio.cs.brown.edu/software/ . Contact : annaritz@vt.edu or braphael@cs.brown.edu Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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    MindTheGap: integrated detection and assembly of short and long insertions (2014)
    Oxford University Press
    Details
    Publication Date: 2014-12-04
    Description: Motivation: Insertions play an important role in genome evolution. However, such variants are difficult to detect from short-read sequencing data, especially when they exceed the paired-end insert size. Many approaches have been proposed to call short insertion variants based on paired-end mapping. However, there remains a lack of practical methods to detect and assemble long variants. Results: We propose here an original method, called M ind T he G ap , for the integrated detection and assembly of insertion variants from re-sequencing data. Importantly, it is designed to call insertions of any size, whether they are novel or duplicated, homozygous or heterozygous in the donor genome. M ind T he G ap uses an efficient k -mer-based method to detect insertion sites in a reference genome, and subsequently assemble them from the donor reads. M ind T he G ap showed high recall and precision on simulated datasets of various genome complexities. When applied to real Caenorhabditis elegans and human NA12878 datasets, M ind T he G ap detected and correctly assembled insertions 〉1 kb, using at most 14 GB of memory. Availability and implementation: http://mindthegap.genouest.org Contact: guillaume.rizk@inria.fr or claire.lemaitre@inria.fr
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
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    Quantifying tumor heterogeneity in whole-genome and whole-exome sequencing data (2014)
    Oxford University Press
    Details
    Publication Date: 2014-12-04
    Description: Motivation: Most tumor samples are a heterogeneous mixture of cells, including admixture by normal (non-cancerous) cells and subpopulations of cancerous cells with different complements of somatic aberrations. This intra-tumor heterogeneity complicates the analysis of somatic aberrations in DNA sequencing data from tumor samples. Results: We describe an algorithm called THetA2 that infers the composition of a tumor sample—including not only tumor purity but also the number and content of tumor subpopulations—directly from both whole-genome (WGS) and whole-exome (WXS) high-throughput DNA sequencing data. This algorithm builds on our earlier Tumor Heterogeneity Analysis (THetA) algorithm in several important directions. These include improved ability to analyze highly rearranged genomes using a variety of data types: both WGS sequencing (including low ~7 x coverage) and WXS sequencing. We apply our improved THetA2 algorithm to WGS (including low-pass) and WXS sequence data from 18 samples from The Cancer Genome Atlas (TCGA). We find that the improved algorithm is substantially faster and identifies numerous tumor samples containing subclonal populations in the TCGA data, including in one highly rearranged sample for which other tumor purity estimation algorithms were unable to estimate tumor purity. Availability and implementation: An implementation of THetA2 is available at http://compbio.cs.brown.edu/software Contact: layla@cs.brown.edu or braphael@brown.edu Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
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    Forests, Vol. 5, Pages 2996-3021: From Co-Management to Landscape Governance: Whither Ghana’s Modified Taungya System? (2014)
    MDPI Publishing
    In: Forests
    Details
    Publication Date: 2014-12-05
    Description: Natural resource management literature has documented three paradigm shifts over the past decade: from co-management to adaptive co-management and adaptive governance respectively and, more recently, towards landscape governance. The latter is conceived as a governance approach towards negotiated land use at the landscape level to deal with global challenges such as food insecurity, climate change and biodiversity loss. There is not a lot of clarity about how co-management systems could actually evolve into landscape governance. This paper aims to address the gap by exploring how a stalled co-management system for the reforestation of degraded forest areas—the modified taungya system (MTS) in Ghana—could be revitalised and redesigned as a landscape approach. Drawing on case studies and expert consultation, the performance of the national MTS and the MTS under the Community Forestry Management Project is reviewed with regard to five principles (integrated approach, multi-stakeholder negotiation, polycentric governance, continual learning and adaptive capacity) and three enabling conditions (social capital, bridging organisations and long-term funding) distilled from the literature. The authors conclude that some of these principles and conditions were met under the Community Forestry Management Project, but that continual learning, transcending jurisdictional boundaries, developing adaptive capacity, and long-term funding and benefits still pose challenges.
    Electronic ISSN: 1999-4907
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
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    Aligning Technology and Market Drivers in an Open Source Standards Testing Program (2014)
    Institute of Electrical and Electronics Engineers (IEEE)
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    Publication Date: 2014-12-06
    Description: In creating the Open Networking Foundation's conformance testing program for the OpenFlow networking specification, economic, technological, and market drivers must be harmonized, allowing for the simultaneous development of consumer confidence, industry competition, and trustworthy product validation.
    Print ISSN: 0018-9162
    Electronic ISSN: 1558-0814
    Topics: Computer Science
    Published by Institute of Electrical and Electronics Engineers (IEEE) on behalf of The IEEE Computer Society.
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    Why Clouds Give Me a Case of the Vapors (2014)
    Institute of Electrical and Electronics Engineers (IEEE)
    Details
    Publication Date: 2014-12-06
    Description: Recently, Apple admitted that revealing photos of celebrities had been released on the Internet due to security breaches associated with its iCloud and Find My iPhone systems.
    Print ISSN: 0018-9162
    Electronic ISSN: 1558-0814
    Topics: Computer Science
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    Understanding Integrity Level Concepts (2014)
    Institute of Electrical and Electronics Engineers (IEEE)
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    Publication Date: 2014-12-06
    Description: An integrity level defines a required level of confidence that a system satisfies critical properties related to relevant risk criteria. However, integrity level terms and definitions differ across industry sectors, and this hampers a common understanding and application of integrity levels.
    Print ISSN: 0018-9162
    Electronic ISSN: 1558-0814
    Topics: Computer Science
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    COOL Chips XVIII (2014)
    Institute of Electrical and Electronics Engineers (IEEE)
    Details
    Publication Date: 2014-12-06
    Description: Describes the above-named upcoming conference event. May include topics to be covered or calls for papers.
    Print ISSN: 0018-9162
    Electronic ISSN: 1558-0814
    Topics: Computer Science
    Published by Institute of Electrical and Electronics Engineers (IEEE) on behalf of The IEEE Computer Society.
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    When Open Source Meets Network Control Planes (2014)
    Institute of Electrical and Electronics Engineers (IEEE)
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    Publication Date: 2014-12-06
    Description: Software-defined networking opens up new possibilities for architectures based on open source components, promising improved orchestration and agility, lower operational costs, and--most important--a wave of innovation. The Web extra at http://youtu.be/pdG2btcyyK8 is a video in which authors Christian Esteve Rothenberg, Roy Chua, and Thomas Nadeau present a slideshow and discuss how software-defined networking opens up new possibilities for architectures based on open-source components, promising improved orchestration and agility, lower operational costs, and a new wave of innovation.
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    Topics: Computer Science
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    Energy Efficiency in the Wild: Why Datacenters Fear Power Management (2014)
    Institute of Electrical and Electronics Engineers (IEEE)
    Details
    Publication Date: 2014-12-06
    Description: Why do dynamic power-management technologies that dramatically improve datacenter server energy efficiency continue to go unleveraged?
    Print ISSN: 0018-9162
    Electronic ISSN: 1558-0814
    Topics: Computer Science
    Published by Institute of Electrical and Electronics Engineers (IEEE) on behalf of The IEEE Computer Society.
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    Theory-Guided Data Science for Climate Change (2014)
    Institute of Electrical and Electronics Engineers (IEEE)
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    Publication Date: 2014-12-06
    Description: To adequately address climate change, we need novel data-science methods that account for the spatiotemporal and physical nature of climate phenomena. Only then will we be able to move from statistical analysis to scientific insights.
    Print ISSN: 0018-9162
    Electronic ISSN: 1558-0814
    Topics: Computer Science
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    The External Environment (2014)
    Institute of Electrical and Electronics Engineers (IEEE)
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    Publication Date: 2014-12-06
    Description: Amateur software developers might lack precise technical skills, but they bring detailed knowledge of their environments to the table. The first Web extra at http://youtu.be/r-kIJQu4iDQ is an audio recording of author David Alan Grier reading his Errant Hashtag column in which he discusses how amateur software developers might lack precise technical skills but bring detailed knowledge of their environments to the table. The second Web extra at http://youtu.be/EDKeN9mVfwk is an audio recording of author David Alan Grier discussing a recent report on electronic voting by the Atlantic Council, a Washington DC think tank, that shows that e-voting is still a risk that citizens of democracies and engineers should take into account.
    Print ISSN: 0018-9162
    Electronic ISSN: 1558-0814
    Topics: Computer Science
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    Computer Highlights Society Magazines (2014)
    Institute of Electrical and Electronics Engineers (IEEE)
    Details
    Publication Date: 2014-12-06
    Description: A summary of articles recently published in IEEE Computer Society magazines.
    Print ISSN: 0018-9162
    Electronic ISSN: 1558-0814
    Topics: Computer Science
    Published by Institute of Electrical and Electronics Engineers (IEEE) on behalf of The IEEE Computer Society.
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    Forests, Vol. 5, Pages 3022-3030: Current Challenges and Perspectives for Governing Forest Restoration (2014)
    MDPI Publishing
    In: Forests
    Details
    Publication Date: 2014-12-06
    Description: Negotiation, reconciliation of multiple scales through both ecological and social dimensions and minimization of power imbalances are considered critical challenges to overcome for effective governance of forest restoration. Finding the right mix of “command and control” in forest restoration vs. “environmental governance”, which includes non-state actors, regulatory flexibility, and market based instruments is at the heart of these challenges. This Special Issue attempts at shedding light on these challenges with case studies from South and Central America, Africa, and Asia. Some provide within-country as well as cross-country comparisons. A few others present case studies at the household level. Both policy and legal constraints towards implementing forest restoration are also discussed as a function of top down vs. bottom up approaches. The effectiveness of payments for environmental services is examined as catalyzers of forest restoration initiatives. Finally, two papers deal with the legal and policy constraints in making restoration through natural regeneration a viable and cost-effective tool. In the face of renewed perspectives for expanding forest restoration programs globally, governance issues will likely play a key role in eventually determining success. As many of the papers in this Special Issue suggest, the fate of forest restoration outcomes is, more often than not, associated with overall governance challenges, some of which are often overlooked particularly across multiple scales.
    Electronic ISSN: 1999-4907
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Published by MDPI Publishing
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    State of the Journal Editorial (2014)
    Institute of Electrical and Electronics Engineers (IEEE)
    Details
    Publication Date: 2014-12-06
    Print ISSN: 1041-4347
    Electronic ISSN: 1558-2191
    Topics: Computer Science
    Published by Institute of Electrical and Electronics Engineers (IEEE) on behalf of The IEEE Computer Society.
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    Are Data Sets Like Documents?: Evaluating Similarity-Based Ranked Search over Scientific Data (2014)
    Institute of Electrical and Electronics Engineers (IEEE)
    Details
    Publication Date: 2014-12-06
    Description: The past decade has seen a dramatic increase in the amount of data captured and made available to scientists for research. This increase amplifies the difficulty scientists face in finding the data most relevant to their information needs. In prior work, we hypothesized that Information Retrieval-style ranked search can be applied to data sets to help a scientist discover the most relevant data amongst the thousands of data sets in many formats, much like text-based ranked search helps users make sense of the vast number of Internet documents. To test this hypothesis, we explored the use of ranked search for scientific data using an existing multi-terabyte observational archive as our test-bed. In this paper, we investigate whether the concept of varying relevance, and therefore ranked search, applies to numeric data—that is, are data sets are enough like documents for Information Retrieval techniques and evaluation measures to apply? We present a user study that demonstrates that data set similarity resonates with users as a basis for relevance and, therefore, for ranked search. We evaluate a prototype implementation of ranked search over data sets with a second user study and demonstrate that ranked search improves a scientist's ability to find needed data.
    Print ISSN: 1041-4347
    Electronic ISSN: 1558-2191
    Topics: Computer Science
    Published by Institute of Electrical and Electronics Engineers (IEEE) on behalf of The IEEE Computer Society.
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    An Effective GPU-Based Approach to Probabilistic Query Confidence Computation (2014)
    Institute of Electrical and Electronics Engineers (IEEE)
    Details
    Publication Date: 2014-12-06
    Description: In recent years, probabilistic data management has received a lot of attention due to several applications that deal with uncertain data: RFID systems, sensor networks, data cleaning, scientific and biomedical data management, and approximate schema mappings. Query evaluation is a challenging problem in probabilistic databases, proved to be #P-hard. A general method for query evaluation is based on the lineage of the query and reduces the query evaluation problem to computing the probability of a propositional formula. The main approaches proposed in the literature to approximate probabilistic queries confidence computation are based on Monte Carlo simulation, or formula compilation into decision diagrams (e.g., d-trees). The former executes a polynomial, but with too many, iterations, while the latter is polynomial for easy queries, but may be exponential in the worst case. We designed a new optimized Monte Carlo algorithm that drastically reduces the number of iterations and proposed an efficient parallel version that we implemented on GPU. Thanks to the elevated degree of parallelism provided by the GPU, combined with the linear speedup of our algorithm, we managed to reduce significantly the long running time required by a sequential Monte Carlo algorithm. Experimental results show that our algorithm is so efficient as to be comparable with the formula compilation approach, but with the significant advantage of avoiding exponential behavior.
    Print ISSN: 1041-4347
    Electronic ISSN: 1558-2191
    Topics: Computer Science
    Published by Institute of Electrical and Electronics Engineers (IEEE) on behalf of The IEEE Computer Society.
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