ppxscal/embedding_network huggingface dataset:
ELISA-BASE
Authors: Amanda M. White, James R. Collett, Shannon L. Seurynck-Servoss, Don S. Daly, Richard C. Zangar
Venue: Bioinformatics (2009)

Summary:ELISA-BASE is an open source database for capturing, organizing and analyzing enzyme-linked immunosorbent assay (ELISA) microarray data. ELISA-BASE is an extension of the BioArray Software Environment (BASE) database system. Availability: http://www.pnl.gov/statistics/ProMAT/ELISA-BASE.stm. Contact: amanda.white@pnl.gov
Optimal placement and routing strategies for resilient two-tiered sensor networks
Authors: Ataul Bari, Arunita Jaekel, Subir Bandyopadhyay
Venue: Wireless Communications Mobile Computing (2009)

In hierarchical sensor networks using relay nodes, sensor nodes are arranged in clusters and higher powered relay nodes can be used as cluster heads. The lifetime of such a network is determined primarily by the lifetime of the relay nodes. In this paper, we propose two new integer linear programs (ILPs) formulations for optimal data gathering, which maximize the lifetime of the upper tier relay node network. Unlike most previous approaches considered in the literature, our formulations can generate optimal solutions under the non-flow-splitting model. Experimental results demonstrate that our approach can significantly extend network lifetime, compared to traditional routing schemes, for the non-flow-splitting model. The lifetime can be further enhanced by periodic updates of the routing strategy based on the residual energy at each relay node. The proposed rescheduling scheme can be used to handle single or multiple relay node failures. We have also presented a very simple and straightforward algorithm for the placement of relay nodes. The placement algorithm guarantees that all the sensor nodes can communicate with at least one relay node and that the relay node network is at least 2-connected. This means that failure of a single relay node will not disconnect the network, and data may be routed around the failed node. The worst case performance of the placement algorithm is bounded by a constant with respect to any optimum placement algorithm. Copyright &copy; 2008 John Wiley & Sons, Ltd.
Solving partial differential equations using sinc methods
Authors: Thomas Shores, David Swanson
Venue:  (2008)

Sinc methods, since their introduction, have shown great theoretical promise as highly accurate methods for a wide range of numerical tasks. They have proven to have exponential convergence for ordinary differential equations and partial differential equations. However, there are few large-scale numerical implementations of sinc methods due to the density and size of the resulting matrix equations. We have developed a package, SincLib, which provides significant computational improvements for sinc-based PDE solutions in n-dimensions. We apply these speedups to several problems on different types of computational hardware. We additionally discuss domain decomposition as a method for attacking problems which are not differentiable at points. Throughout the dissertation, we apply our work to problems arising from the Schr&ouml;dinger equation and the Poisson equation.
Experimental Study of the Usefulness of External Face Features for Face Classification
Authors: Àgata Lapedriza, David Masip, Jordi Vitrià
Venue: Proceeding of the 2005 conference on Artificial Intelligence Research and Development (2005)

In general face classification problems, only the internal features of the face are commonly used, rejecting the information located at head, chin, and ears, since due to their variability is not easy to extract this information. In this paper, a complete scheme based on a Top-Down reconstruction algorithm to extract External Features of face images is proposed. We use the Non negative Matrix Factorization (NMF) algorithm to obtain the final coefficients that encode the external information and using this codification the faces are classified. Our experimental results in different face classification problems show that the information contributed by the external features is significant and useful for classification purposes.
Event-triggered strategies for industrial control over wireless networks
Authors: Maben Rabi, Karl H. Johansson
Venue: Proceedings of the 4th Annual International Conference on Wireless Internet (2008)

New event-based sampling strategies can support the efficient use of radio resources in wireless control systems. Motivated by the recent introduction of wireless network nodes in process control industry, we consider the particular demands these closed-loop systems set on the wireless communication and the influence the communication has on the control performance. In the paper, it is pointed out that by letting sensor nodes transmit only when needed, it is possible to minimize the communication bandwidth utilization in these systems. We show how classical control strategies commonly based on periodic sampling, such as proportional-integral-derivative control and minimum variance control, can be cast in an event-based setting in which decentralized communication decisions are taken suitable for commonly used contention-based medium access control protocols. Event-triggered sampling for estimation is also reviewed. Simulated examples illustrate the results.
How Many Bootstrap Replicates Are Necessary?
Authors: Nicholas D. Pattengale, Masoud Alipour, Olaf R. Bininda-Emonds, Bernard M. Moret, Alexandros Stamatakis
Venue: Proceedings of the 13th Annual International Conference on Research in Computational Molecular Biology (2009)

Phylogenetic Bootstrapping (BS) is a standard technique for inferring confidence values on phylogenetic trees that is based on reconstructing many trees from minor variations of the input data, trees called replicates. BS is used with all phylogenetic reconstruction approaches, but we focus here on the most popular, Maximum Likelihood (ML). Because ML inference is so computationally demanding, it has proved too expensive to date to assess the impact of the number of replicates used in BS on the quality of the support values. For the same reason, a rather small number (typically 100) of BS replicates are computed in real-world studies. Stamatakis et al. recently introduced a BS algorithm that is 1---2 orders of magnitude faster than previous techniques, while yielding qualitatively comparable support values, making an experimental study possible.In this paper, we propose stopping criteria, that is, thresholds computed at runtime to determine when enough replicates have been generated, and report on the first large-scale experimental study to assess the effect of the number of replicates on the quality of support values, including the performance of our proposed criteria. We run our tests on 17 diverse real-world DNA, single-gene as well as multi-gene, datasets, that include between 125 and 2,554 sequences. We find that our stopping criteria typically stop computations after 100---500 replicates (although the most conservative criterion may continue for several thousand replicates) while producing support values that correlate at better than 99.5% with the reference values on the best ML trees. Significantly, we also find that the stopping criteria can recommend very different numbers of replicates for different datasets of comparable sizes.Our results are thus two-fold: (i) they give the first experimental assessment of the effect of the number of BS replicates on the quality of support values returned through bootstrapping; and (ii) they validate our proposals for stopping criteria. Practitioners will no longer have to enter a guess nor worry about the quality of support values; moreover, with most counts of replicates in the 100---500 range, robust BS under ML inference becomes computationally practical for most datasets. The complete test suite is available at http://lcbb.epfl.ch/BS.tar.bz2 and BS with our stopping criteria is included in RAxML 7.1.0.
Simulation of Industrial Systems: Discrete Event Simulation Using Excel/VBA, 1st edition
Authors: David Elizandro, Hamdy Taha
Venue:  (2007)

In any production environment, discrete event simulation is a powerful tool for the analysis, planning, and operating of a manufacturing facility. Operations managers can use simulation to improve their production systems by eliminating bottlenecks, reducing cycle time and cost, and increasing capacity utilization. Offering a hands-on tutorial on how to model traditional applications to optimize production operations, Simulation of Industrial Systems: Discrete Event Simulation Using Excel/VBA Introduces the Design Environment for Event Driven Simulation (DEEDS), an original simulator, which facilitates the modeling of complex situations using four (self-contained) nodes: source, queue, facility, and delay. Demonstrates how to use discrete event simulation as a powerful tool for the analysis, planning, design, and operation of diverse production systems Shows how to model application areas such as facilities layout, material handling, inventory control, scheduling, maintenance, quality control, and supply chain logistics Integrates the design of experiments and optimization techniques for improving production systems With the comprehensive instruction provided within these pages, in combination with the flexibility of the DEEDS program environment, operations managers will be able to harness the power of discrete event simulation to streamline their production environments. The authors have created a website with a variety of teaching aids that professors will be able to access
Convergence estimates of a projection-difference method for an operator-differential equation
Authors: Polina Vinogradova
Venue: Journal of Computational and Applied Mathematics (2009)

This article investigates the projection-difference method for a Cauchy problem for a linear operator-differential equation with a leading self-adjoint operator A(t) and a subordinate linear operator K(t) in Hilbert space. This method leads to the solution of a system of linear algebraic equations on each time level; moreover, the projection subspaces are linear spans of eigenvectors of an operator similar to A(t). The convergence estimates are obtained. The application of the developed method for solving the initial boundary value problem is given.
UML-Based Model-Driven Development for HSDPA Design
Authors: Jesús Martínez, Pedro Merino, Alberto Salmerón, Francisco Malpartida
Venue: IEEE Software (2009)

This article examines using model-driven development (MDD) with UML for communication protocols. The authors believe this approach is essential for reducing the costs of developing, maintaining, and evolving complex software systems. However, is this statement valid for communication protocol software? Such software's stringent performance and robustness requirements are critical for embedded devices in modern mobile and cellular networks. To compare UML-based MDD with a code-centric approach, the authors developed two versions of a fully functional High-Speed Downlink Packet Access (HSDPA) prototype. Experiments show that the development process was easier with UML-based MDD than with the code-centric approach, without sacrificing performance.
SUSE Linux Enterprise Server Security
Authors: Jason Eckert, Novell
Venue:  (2007)

The release of Novell's SUSE Linux Enterprise Server version 10 (SLES 10) marked a new era for the Open Source server. SLES 10 was developed with interoperability in mind. It can be integrated seamlessly into existing network environments, both Open Source and proprietary. It provides a manageable, stable, secure, and affordable network environment. Novell has become an affordable and attractive alternative server operating system for corporate environments. Companies such as Marriott, CNN, Circuit City, HP, Dell, and Publix have adopted SLES 10, and now Industry certification bodies are recognizing the benefits of SLES 10 as well. Security Certified Program, an industry-recognized network security certification body that does training with the Department of Defense, will be adopting SLES 10 in January 2007. With the increased demand for SLES 10 and the absolute necessity of securing networks, there is an increased demand for trained SLES 10 network professionals. SUSE Linux Enterprise Server Security introduces network professionals to the many security features of the new server program, and it contains Course Technology's proven academic pedagogy, making this the ideal classroom solution for teaching Novell.
Requirements engineering for multi-channel services: the SEB method and its application to a multi-channel bank
Authors: Lia Patr&#x00ed;cio, Jo&#x00e3;o Falc&#x00e3;o e Cunha, Raymond P. Fisk
Venue: Requirements Engineering (2009)

The widespread usage of technology for service provision to customers has created a new and challenging environment for the design of interactive systems, with the emergence of technology enabled multi-channel services. Requirements engineers involved in the design of such service systems must actively work together with interaction designers and service managers to better integrate customer service experience and technology components, requiring unifying methods and tools within the emerging field of service science management and engineering. This paper proposes the service experience blueprint (SEB), a multidisciplinary method for the design of technology enabled multi-channel service systems and illustrates its application in two examples of redesign of banking services that involved an extensive study with more than 4,000 bank customers. The SEB method is based on concepts and tools from RE and interaction design, such as goal-oriented analysis and conceptual modeling, but also uses methods developed in the service and marketing fields, such as service blueprinting. SEB brings marketing research methods to the requirements process, as they can provide a useful contribution for the elicitation of customer experience requirements in service environments. By bringing together goal-oriented modeling and use case modeling from requirements engineering, with service blueprinting from service design, the SEB method contributes to creating a shared understanding and a unifying language to better support the design of new technology enabled multi-channel service systems, where technology and service issues are deeply intertwined.
Improvement of software reliability modeling predictions by the detection and removal of test outliers
Authors: Nasser H. Abosaq, Walter Bond
Venue: Proceedings of the 47th Annual Southeast Regional Conference (2009)

Modeling the times between failure of software under test is one method for predicting when the software will be ready for release. For various reasons such as poorly written test cases, a chosen software reliability model may over-estimate the mean time to the next failure (MTTF). When a test case shows a longer time to the next defect, it biases the estimation of MTTF and that failure time can be considered to be an outlier. In this paper, order statistics is used to construct a bound such that the probability that the kth largest values (relative to their positions in the ordered series) in the failure dataset will exceed that bound is fixed at a small level of significance. The simulation of contaminated datasets is used in the research to validate the proposed approach. Also, real failure datasets with actual Time To Failure (TTF) data are used to demonstrate the approach.
Understanding and capturing people's privacy policies in a mobile social networking application
Authors: Norman Sadeh, Jason Hong, Lorrie Cranor, Ian Fette, Patrick Kelley, Madhu Prabaker, Jinghai Rao
Venue: Personal and Ubiquitous Computing (2009)

A number of mobile applications have emerged that allow users to locate one another. However, people have expressed concerns about the privacy implications associated with this class of software, suggesting that broad adoption may only happen to the extent that these concerns are adequately addressed. In this article, we report on our work on PeopleFinder, an application that enables cell phone and laptop users to selectively share their locations with others (e.g. friends, family, and colleagues). The objective of our work has been to better understand people's attitudes and behaviors towards privacy as they interact with such an application, and to explore technologies that empower users to more effectively and efficiently specify their privacy preferences (or "policies"). These technologies include user interfaces for specifying rules and auditing disclosures, as well as machine learning techniques to refine user policies based on their feedback. We present evaluations of these technologies in the context of one laboratory study and three field studies.
Reducing outer joins
Authors: Gerhard Hill, Andrew Ross
Venue: The VLDB Journal &mdash; The International Journal on Very Large Data Bases (2009)

We present a method for transforming some outer joins to inner joins and describe a generalized semijoin reduction technique. The first part of the paper shows how to transform a given outer join query whose join graph is a tree to an equivalent inner join query. The method uses derived relations and join predicates. Derived relations contain columns corresponding to join conditions and may have virtual row identifiers, rows and attribute values. The constructed inner join query, after elimination of virtual row identifiers, has the same join tuples as the outer join query. Both the theoretical maximum number of virtual rows and the average number in practice are shown to be low. The method confines consideration of the non-associativity of outer joins to a single step. The second part of the paper generalizes to outer joins the well known technique of semijoin reduction of inner joins. It does so by defining the notions of influencing and needing, and using them to define full reduction and reduction plans. The technique is applied here to perform one step of the method presented in the first part. Semijoin reduction is useful in practice for executing join queries in distributed databases.
Division-based rainfall-runoff simulations with BP neural networks and Xinanjiang model
Authors: Qin Ju, Zhongbo Yu, Zhenchun Hao, Gengxin Ou, Jian Zhao, Dedong Liu
Venue: Neurocomputing (2009)

The application of artificial neural network (ANN) to rainfall-runoff simulations has provided promising results in recent years. However, it is difficult to obtain satisfying results by using raw data for the direct prediction of the time series of streamflows. To improve simulating daily streamflow with back-propagation (BP) neural networks, the whole data set in this study is divided into two independent groups, flood period and non-flood period. The approaches and techniques of applying the division-based BP (DBP) in runoff simulation are presented in this paper. A comparison of the DBP model to the primitive BP model and the Xinanjiang model was also conducted to evaluate the effectiveness of the improvement. The numerical experimental results indicate that DBP model still overestimated flow peak, but improved considerably the streamflow simulation in the non-flood period.
Qucs: A GPL software package for circuit simulation, compact device modelling and circuit macromodelling from DC to RF and beyond
Authors: M. E. Brinson, S. Jahn
Venue: International Journal of Numerical Modelling: Electronic Networks, Devices and Fields (2009)

The &lsquo;Quite universal circuit simulator&rsquo; (Qucs) is an open source circuit simulator supporting Verilog-A compact model standardization. This paper describes a number of compact semiconductor device and circuit macromodelling techniques that have been implemented in recent Qucs releases, stressing those techniques that are not found in SPICE 2g6 or 3f5. It also introduces a novel hierarchical approach to Verilog-A compact model and circuit macromodel construction based on non-linear equation-defined devices, linear-controlled sources and noise generators embedded in subcircuits. To illustrate the new approach, the properties and models of a number of components with electrical and non-electrical characteristics are described. These models demonstrate how recent trends in open source simulation technology use embedded equations as integral elements in component and physical process models. Copyright &copy; 2008 John Wiley & Sons, Ltd.
Empirical evaluation of software development productivity in high performance computing
Authors: John R. Gilbert
Venue:  (2008)

Although advances in parallel hardware continue to deliver a measurable increase in execution performance, corresponding improvements in the programmability and thereby productivity of HPC systems remain hard to quantify. Several factors such as the parallel programming language, the hardware architecture, and programmer aptitude influence the achieved performance and the required effort. While there exists a rich body of work to characterize system and application performance, the effect of factors such as programming languages and programmer workflows on performance and productivity is poorly understood. Traditional benchmarks narrowly focus on raw performance and fail to evaluate these factors.This dissertation presents an empirical approach to study the effect of these factors, especially programming languages, on productivity using experimental studies with human subjects. We leverage the development experience of students in HPC classroom studies to collect empirical data for our experimental analysis. Collecting high-quality data across multiple classroom studies is a challenging problem. We present a data collection methodology and an operational system that captures an accurate and concise view of the development workflow. Our system uses instrumented tools along with a high-level development framework to capture development activities of subjects with minimal intrusiveness. We address practical issues such as reproducibility, noise, and privacy that arise during data analysis. Using our system, we have consistently collected several high-quality datasets during a series of replicated studies.The dissertation presents a statistical approach for using this data to formally evaluate several hypotheses about the relative productivity of two parallel language extensions, MPI and UPC, that represent two mainstream parallel programming models. We formulate hypothesis tests for comparing the performance and productivity of these two models and present several statistically significant results. While the statistical method analyzes the data related to the developed software, a workflow model explains the development process and effort of the programmer. We propose a Hidden Markov Model to representatively model the workflow followed by subjects when using a given programming language. We present results from training and building these models on our datasets. We also describe GRID*p, a MATLAB-based programming environment that demonstrates the productivity and performance of high-level development tools for large-scale computations on the Grid. Results of developing two typical parallel applications show that GRID*p delivers promising performance for highly parallel applications with minimal development effort.
Beyond viewpoint: X3D camera nodes for digital cinematography
Authors: Jeffrey D. Weekley, Don Brutzman
Venue: Proceedings of the 14th International Conference on 3D Web Technology (2009)

This paper describes four candidate X3D extension nodes: Camera, Shot, Movement and OfflineRendering. An X3D lexicon for camera movements is defined so that individuals directing virtual cameras in X3D can directly apply terms that film directors and cinematographers understand. This approach greatly simplifies the technical tasks involved in creating precise camera animations and setting up still images for digital photography. Further, candidate methods are examined for implementing Depth of Field for focus control. Moving beyond the typical clumsiness of Viewpoint control can enable authors to create compelling still and moving images from X3D scenes.