ppxscal/embedding_network huggingface dataset:
Variation in the correlation of G + C composition with synonymous codon usage bias among bacteria
Authors: Haruo Suzuki, Rintaro Saito, Masaru Tomita
Venue: EURASIP Journal on Bioinformatics and Systems Biology (2007)

G + C composition at the third codon position (GC3) is widely reported to be correlated with synonymous codon usage bias. However, no quantitative attempt has been made to compare the extent of this correlation among different genomes. Here, we applied Shannon entropy from information theory to measure the degree of GC3 bias and that of synonymous codon usage bias of each gene. The strength of the correlation of GC3 with synonymous codon usage bias, quantified by a correlation coefficient, varied widely among bacterial genomes, ranging from -0.07 to 0.95. Previous analyses suggesting that the relationship between GC3 and synonymous codon usage bias is independent of species are thus inconsistent with the more detailed analyses obtained here for individual species.
Business modeling using SQL spreadsheets
Authors: Andrew Witkowski, Srikanth Bellamkonda, Tolga Bozkaya, Nathan Folkert, Abhinav Gupta, Lei Sheng, Sankar Subramanian
Venue: Proceedings of the 29th international conference on Very large data bases - Volume 29 (2003)

One of the critical deficiencies of SQL is the lack of support for array and spreadsheet like calculations which are frequent in OLAP and Business Modeling applications. Applications relying on SQL have to emulate these calculations using joins, UNION operations, Window Functions and complex CASE expressions. The designated place in SQL for algebraic calculations is the SELECT clause, which is extremely limiting and forces applications to generate queries with nested views, subqueries and complex joins. This distributes Business Modeling computations across many query blocks, making applications coded in SQL hard to develop. The limitations of RDBMS have been filled by spreadsheets and specialized MOLAP engines which are good at formulas for mathematical modeling but lack the formalism of the relational model, are difficult to manage, and exhibit scalability problems. This demo presents a scalable, mathematically rigorous, and performant SQL extensions for Relational Business Modeling, called the SQL Spreadsheet. We present examples of typical Business Modeling computations with SQL spreadsheet and compare them with the ones using standard SQL showing performance advantages and ease of programming for the former. We will show a scalability example where data is processed in parallel and will present a new class of query optimizations applicable to SQL spreadsheet.
Synthesis: Dreams ? Programs
Authors: Z. Manna
Venue: IEEE Transactions on Software Engineering (1979)

Deductive techniques are presented for deriving programs systematically from given specifications. The specifications express the purpose of the desired program without giving any hint of the algorithm to be employed. The basic approach is to transform the specifications repeatedly according to certain rules, until a satisfactory program is produced. The rules are guided by a number of strategic controls. These techniques have been incorporated in a running program-synthesis system, called DEDALUS.
Hybrid Intelligent and Adaptive Sensor Systems with Improved Noise Invulnerability by Dynamically Reconfigurable Matched Sensor Electronics
Authors: Senthil Kumar Lakshmanan, Andreas Konig
Venue: Proceedings of the 7th International Conference on Hybrid Intelligent Systems (2007)

Hybrid intelligent sensor systems and networks are composed of modules of tightly co-operating software and hardware components. Bio-inspired information processing is embodied in algorithms as well as dedicated electronics for intelligent processing and system adaptation. This paper focuses on the challenges imposed on the small yet irreplaceable analog and mixed signal components in such a sensor system, which are prone to deviation and degradations. Novel architectures combine issues of rapid-prototyping, trimming, fault-tolerance, and self-repair. However, the common reconfiguration approaches cannot deal efficiently with real-world noise problems. This paper adapts effective solution strategies to advanced sensor electronics for hybrid intelligent and adaptive sensor systems in a 0.35ìm CMOS technology and reports on the design of a novel generic chip.
A High-Speed Threshold Gate Multiplier
Authors: S. A. Kent
Venue: IEEE Transactions on Computers (1977)

A design for a multiplier is proposed which utilizes the extended switching properties of threshold elements. High-speed adders capable of adding more than two summands are constructed using minimal numbers of threshold gates. These are used to sum the partial products generated in the multiplication of two numbers. Several levels of these adders may be combined to reduce the number of summands to two without incurring any carry propagation delay. When the final addition is then performed to yield the product, the carry ripple delay is a minimum. The entire network uses fewer logic elements than in the iterative array approach and gives a significantly faster processing time.
Optimal Cluster-Cluster Design for Sensor Network with Guaranteed Capacity and Fault Tolerance
Authors: Bin Zeng, Jun Wei, Tao Hu
Venue: Proceedings of the Eighth ACIS International Conference on Software Engineering, Artificial Intelligence, Networking, and Parallel/Distributed Computing - Volume 01 (2007)

Sensor networks have recently gained a lot of attention from the research community. To ensure scalability sensor networks are often partitioned into clusters, each managed by a cluster head. Since sensors self-organize in the form of clusters within a hierarchal wireless sensor network, it is necessary for a sensor node to perform target tracking cooperating with a set of sensors that belong to another cluster. The increased flexibility allows for efficient and optimized use of sensor nodes. While most of the previous research focused on the optimal communication of sensors in one cluster, very little attention has been paid to the efficiency of cooperation among the clusters. This paper proposes a heuristic algorithm of designing optimal structure across clusters to allow the inter-cluster flow of communication and resource sharing under reliability constraints. Such a guarantee simultaneously provides fault tolerance against node failures and high capacity through multi-path routing.
On the number of principal components: A test of dimensionality based on measurements of similarity between matrices
Authors: Stéphane Dray
Venue: Computational Statistics Data Analysis (2008)

An important problem in principal component analysis (PCA) is the estimation of the correct number of components to retain. PCA is most often used to reduce a set of observed variables to a new set of variables of lower dimensionality. The choice of this dimensionality is a crucial step for the interpretation of results or subsequent analyses, because it could lead to a loss of information (underestimation) or the introduction of random noise (overestimation). New techniques are proposed to evaluate the dimensionality in PCA. They are based on similarity measurements, singular value decomposition and permutation procedures. A simulation study is conducted to evaluate the relative merits of the proposed approaches. Results showed that one method based on the RV coefficient is very accurate and seems to be more efficient than other existing approaches.
Investigating learning styles in the online educational environment
Authors: Jack P. Krichen
Venue: Proceedings of the 8th ACM SIGITE conference on Information technology education (2007)

As the majority of traditional educational institutions move toward some version of online instruction and institutions devoted totally to online instruction emerge, it is imperative that the mechanisms of this instruction support the needs of current and future cadres of online learners. The rational for investigating learning styles in this context is presented focusing on the characteristics of the online learner population and the tendency of this population to be more "at risk" and less traditional then learners in a typical university setting. The theoretical foundations for anticipating benefits from utilizing learning styles in the online context are articulated. The potential for utilizing information technology to facilitate utilization of learning styles in this environment is explored. Finally, a research model for exploring the effectiveness and level of learner satisfaction with using learning styles in this context is presented.
Fast evaluation of time domain fields in sub-wavelength source/observer distributions using accelerated Cartesian expansions (ACE)
Authors: M. Vikram, B. Shanker
Venue: Journal of Computational Physics (2007)

Time domain integral equation solvers for transient scattering from electrically large objects have benefitted significantly from acceleration techniques like the plane wave time domain (PWTD) algorithm; these techniques reduce the asymptotic CPU and memory cost. However, PWTD breaks down when used in the analysis of structures that have subwavelength features or features whose length scales are orders of magnitude smaller than the smallest wavelength in the incident pulse. Instances of these occurring in electromagnetics range from antenna topologies, to feed structures, etc. In this regime, it is the geometric constraints that dictate the computational complexity, as opposed to the wavelength of interest. In this work, we present an approach for efficient analysis of such sub-wavelength source/observer distributions in time domain. The methodology that we seek to exploit is the recently developed algorithm based on Cartesian expansions for accelerating the computation of potentials of the form R^@n. In this paper, we present an efficient methodology for computing these polynomials for two different scenarios; where the size of the domain spans the distance travelled by light in (i) one time step and (ii) multiple time steps. These algorithms are cast within the framework of both uniform and non-uniform distributions. Results that demonstrate the efficiency and convergence of the proposed algorithm are presented.
A Sharp Upper Bound for the Number of Spanning Trees of a Graph
Authors: Kinkar Ch. Das
Venue: Graphs and Combinatorics (2007)

Let G = (V,E) be a simple graph with n vertices, e edges and d1 be the highest degree. Further let &lambda;i, i = 1,2,...,n be the non-increasing eigenvalues of the Laplacian matrix of the graph G. In this paper, we obtain the following result: For connected graph G, &lambda;2 = &lambda;3 = ... = &lambda;n-1 if and only if G is a complete graph or a star graph or a (d1,d1) complete bipartite graph. Also we establish the following upper bound for the number of spanning trees of G on n, e and d1 only: t(G) &le; (2e-d1-1 / n-2)n-2. The equality holds if and only if G is a star graph or a complete graph. Earlier bounds by Grimmett [5], Grone and Merris [6], Nosal [11], and Kelmans [2] were sharp for complete graphs only. Also our bound depends on n, e and d1 only.
Decomposition properties in fluid queues
Authors: Yujing Wu, Weibo Gong, Don Towsley
Venue: Performance Evaluation (2008)

We discover two decomposition properties in certain fluid queues. In a queue fed by burst flows, the impact of flow dynamics over shorter timescales on the mean buffer length can be separated from the impact of flow dynamics over larger timescales. A queue with multiple inputs can be decomposed into multiple simpler queues and the two systems have the same mean buffer length. This study may find applications in fast evaluation and resource management of computer networks.
Applying query expansion to a bilingual search engine
Authors: Ratchaneekorn Theva-aksorn, Nuttanart Facundes
Venue: Proceedings of the third conference on IASTED International Conference: Advances in Computer Science and Technology (2007)

Nowadays, distributed information in the form of linguistic resources is accessible throughout the internet. Search engines have become crucial for information retrieval since users need to find and retrieve relevant information in various languages and forms. The objective of this paper is to investigate the application of query expansion technique to improve cross-language information retrieval in English and Thai. As the method of evaluation of query expansion, we investigate whether the expanded terms are useful for the search.
On Temporal Path Conditions in Dependence Graphs
Authors: Andreas Lochbihler, Gregor Snelting
Venue: Proceedings of the Seventh IEEE International Working Conference on Source Code Analysis and Manipulation (2007)

Program dependence graphs are a well-established device to represent possible information flow in a program. Path conditions in dependence graphs have been proposed to express more detailed circumstances of a particular flow; they provide precise necessary conditions for information flow along a path or chop in a dependence graph. Ordinary boolean path conditions however cannot express temporal properties, e.g. that for a specific flow it is necessary that some condition holds, and later another specific condition holds. In this contribution, we introduce temporal path conditions, which extend ordinary path conditions by temporal operators in order to express temporal dependencies between conditions for a flow. We present motivating examples, generation and simplification rules, application of model checking to generate witnesses for a specific flow, and a case study. We prove the following soundness property: if a temporal path condition for a path is satisfiable, then the ordinary boolean path condition for the path is satis fiable. The converse does not hold, indicating that temporal path conditions are more precise.
Direct-Projected AR Based Interactive User Interface for Medical Surgery
Authors: Byung-Kuk Seo, Moon-Hyun Lee, Hanhoon Park, Jong-Il Park, Young Soo Kim
Venue: Proceedings of the 17th International Conference on Artificial Reality and Telexistence (2007)

In the field of computer aided surgery, augmented reality (AR) technology has been successfully used for enhancing accuracy of surgery and making surgeons convenient by visually assisting them in performing a number of complicated and time-consuming medical operations. However, there are still medical operations that do not receive the benefit of AR technology. As a representative one, surgeons still use an ink pen when they mark surgical targets for scheduling an operation. The ink pen is inconvenient because the mark drawn by the foreign matter is not easily modified or deleted. And the ink pen is also unlikely to be sanitary. In this paper, we propose an interactive user interface based on direct-projected augmented reality (DirectAR) technology for handling all these problems with the ink pen and its validity is shown in experimental results.
Can citation analysis of web publications better detect research fronts?
Authors: Dangzhi Zhao, Andreas Strotmann
Venue: Journal of the American Society for Information Science and Technology (2007)

We present evidence that in some research fields, research published in journals and reported on the Web may collectively represent different evolutionary stages of the field, with journals lagging a few years behind the Web on average, and that a "two-tier" scholarly communication system may therefore be evolving. We conclude that in such fields, (a) for detecting current research fronts, author co-citation analyses (ACA) using articles published on the Web as a data source can outperform traditional ACAs using articles published in journals as data, and that (b) as a result, it is important to use multiple data sources in citation analysis studies of scholarly communication for a complete picture of communication patterns. Our evidence stems from comparing the respective intellectual structures of the XML research field, a subfield of computer science, as revealed from three sets of ACA covering two time periods: (a) from the field's beginnings in 1996 to 2001, and (b) from 2001 to 2006. For the first time period, we analyze research articles both from journals as indexed by the Science Citation Index (SCI) and from the Web as indexed by CiteSeer. We follow up by an ACA of SCI data for the second time period. We find that most trends in the evolution of this field from the first to the second time period that we find when comparing ACA results from the SCI between the two time periods already were apparent in the ACA results from CiteSeer during the first time period.
Globase.KOM - A P2P Overlay for Fully Retrievable Location-based Search
Authors: Aleksandra Kova!cevi, Nicolas Liebau, Ralf Steinmetz
Venue: Proceedings of the Seventh IEEE International Conference on Peer-to-Peer Computing (2007)

Location based services are becoming increasingly pop- ular as devices that determine geographical position be- come more available to end users. The main problem of existing solutions to location-based search is keeping infor- mation updated requires centralized maintenance at spe- cific times. Therefore, retrieved results do not include all objects that exist in reality. A peer-to-peer (P2P) approach can easily overcome this issue as peers are responsible for the information users are searching for. Unfortunately, cur- rent state-of-the-art overlays cannot fulfill the requirements for efficient and fully retrievable location-based search. In this paper we present Globase.KOM, a hierarchical tree- based P2P overlay that enables fully retrievable location- based overlay operations which proved to be highly efficient and logarithmically scalable.
Sequential Program Prefetching in Memory Hierarchies
Authors: A. J. Smith
Venue: Computer (1978)

Memory transfers due to a cache miss are costly. Prefetching all memory references in very fast computers can increase the effective CPU speed by 10 to 25 percent.
A generic fuzzy aggregation operator: rules extraction from and insertion into artificial neural networks
Authors: C. J. Mantas
Venue: Soft Computing - A Fusion of Foundations, Methodologies and Applications (2007)

Multilayered feedforward artificial neural networks (ANNs) are black boxes. Several methods have been published to extract a fuzzy system from a network, where the input&#x2013;output mapping of the fuzzy system is equivalent to the mapping of the ANN. These methods are generalized by means of a new fuzzy aggregation operator. It is defined by using the activation function of a network. This fact lets to choose among several standard aggregation operators. A method to extract fuzzy rules from ANNs is presented by using this new operator. The insertion of fuzzy knowledge with linguistic hedges into an ANN is also defined thanks to this operator.
Interactive evolution for cochlear implants fitting
Authors: Pierrick Legrand, Claire Bourgeois-Republique, Vincent Péan, Esther Harboun-Cohen, Jacques Levy-Vehel, Bruno Frachet, Evelyne Lutton, Pierre Collet
Venue: Genetic Programming and Evolvable Machines (2007)

Cochlear implants (CI) are devices that become more and more sophisticated and adapted to the need of patients, but at the same time they become more and more difficult to parameterize. After a deaf patient has been surgically implanted, a specialised medical practitioner has to spend hours during months to precisely fit the implant to the patient. This process is a complex one implying two intertwined tasks: the practitioner has to tune the parameters of the device (optimisation) while the patient's brain needs to adapt to the new data he receives (learning). This paper presents a study that intends to make the implant more adaptable to environment (auditive ecology) and to simplify the process of fitting. Real experiments on volunteer implanted patients are presented, that show the efficiency of interactive evolution for this purpose.
A Method for Solving the Visibility Problem
Authors: Christoph Hornung
Venue: IEEE Computer Graphics and Applications (1984)

Faster solutions to 3-D visibility problems and better distribution of multiprocessor systems can be achieved when this new connectivity data algorithm is used.
Supply switching with ground collapse: simultaneous control of subthreshold and gate leakage current in nanometer-scale CMOS circuits
Authors: Youngsoo Shin, Sewan Heo, Hyung-Ock Kim, Jung Yun Choi
Venue: IEEE Transactions on Very Large Scale Integration (VLSI) Systems (2007)

Power gating has been widely used to reduce subthreshold leakage. However, the efficiency of power gating degrades very fast with technology scaling, which we demonstrate by experiment. This is due to the gate leakage of circuits specific to power gating, such as storage elements and output interface circuits with a data-retention capability. A new scheme called supply switching with ground collapse is proposed to control both gate and subthreshold leakage in nanometer-scale CMOS circuits. Compared to power gating, the leakage is cut by a factor of 6.3 with 65-nm and 8.6 with 45-nm technology. Various issues in implementing the proposed scheme using standard-cell elements are addressed, from register transfer level to layout. These include the choice of standby supply voltage with circuits that support it, a power network architecture for designs based on standard-cell elements, a current switch design methodology, several circuit elements specific to the proposed scheme, and the design flow that encompasses all the components. The proposed design flow is demonstrated on a commercial design with 90-nm technology, and the leakage saving by a factor of 32 is observed with 3% and 6% of increase in area and wirelength, respectively.
Noise Problems in Testing VLSI Hardware
Authors: Kofi Torku, Dave Kiesling
Venue: IEEE Design Test (1985)

Noise resulting from the switching of high-current, off-product drivers in VLSI circuits cause substantial problems duringmanufacturing test and may lead to zero yield. These problems, seldom addressed during product design, can be mitigated oreliminated either during the design phase or at mauufacturing test. In this article, we present some of our experiences withnoise during manufacturing test, and discuss several solutions to the problem. These remedies include such manufacturing testoptions as relaxing the test specification, or ?guardbanding? which requires both substantial study of the impact on qualityand continual tracking of the problem level; modifying the test program to eliminate the need for a guardband; or having thelogic designer create a new set of functional test patterns specifically designed to avoid simultaneously switching drivers.We also examine alternative design methods for use during both product and tester design.
Pulmonary Diffusion A Model Study
Authors: L. Braun
Venue: Computer (1977)

Compared to even the most complex engineering systems, physiological systems are enormously difficult ones in which to conduct direct parametric studies. In this paper, we look at the application of computer simulation techniques to the study of pulmonary diffusion a physiological process that is especially difficult to study in vivo ( i.e., experiments conducted on a living subject).