ppxscal/embedding_network huggingface dataset:
A Lightweight Middleware Monitor for Distributed Scientific Workflows
Authors: Sergio Manuel Serra da Cruz, Fabricio Nogueira da Silva, Luiz M. R. Gadelha Jr., Maria Claudia Reis Cavalcanti, Maria Luiza M. Campos, Marta Mattoso
Venue: Proceedings of the 2008 Eighth IEEE International Symposium on Cluster Computing and the Grid (2008)

Monitoring the execution of distributed tasks within the workflow execution is not easy and is frequently controlled manually. This work presents a lightweight middleware monitor to design and control the parallel execution of tasks from a distributed scientific workflow. This middleware can be connected into a workflow management system. This middleware implementation is evaluated with the Kepler workflow management system, by including new modules to control and monitor the distributed execution of the tasks. These middleware modules were added to a bioinformatics workflow to monitor parallel BLAST executions. Results show potential to high performance process execution while preserving the original features of the workflow.
CFD-based application of the Nyquist criterion to thermo-acoustic instabilities
Authors: J. Kopitz, W. Polifke
Venue: Journal of Computational Physics (2008)

A novel approach for the analysis of self-excited instabilities in thermo-acoustic systems is proposed. Combining computational fluid dynamics with low-order acoustic modeling, the open-loop transfer function of the system under investigation is computed. The system eigenmodes and the linear stability characteristics are then deduced from a Nyquist plot. The method is suitable for systems where - due to geometrical complexities or non-compact regions of heat release - a low-order formulation is not appropriate or not available. Explicit knowledge of the frequency response or the transfer matrix of the heat source is not required. Further advantages of the new approach are discussed in the paper. To establish proof of concept, the method is validated against a simple model of a Rijke tube. Over the frequency range considered, frequencies and growth rates of stable as well as unstable eigenmodes are predicted accurately. The new method, combining flow simulation, low-order acoustic modeling and control theory, makes possible a comprehensive analysis of acoustic stability behavior of complex thermo-acoustic systems at comparatively modest computational cost.
From nsdl 1.0 to nsdl 2.0: towards a comprehensive cyberinfrastructure for teaching and learning
Authors: David J. McArthur, Lee L. Zia
Venue: Proceedings of the 8th ACM/IEEE-CS joint conference on Digital libraries (2008)

NSDL is a premier provider of digital educational collections and services, which has been supported by NSF for eight years. As a mature program, NSDL has reached a point where it could either change direction or wind down. In this paper we argue there are reasons to continue the program and we outline several possible new program directions. These build on NSDL's learning platform, and they also look towards NSF's emerging interest in supporting work at the intersection of cyberinfrastructure and education. We consider NSDL's potential roles in several grand challenges that confront education, including: tailoring educational resources to students' needs, providing educators with a cyber-teaching environment, developing a cyber-workbench for researchers, and integrating education research and practice.
Scheduling Dynamic Workflows onto Clusters of Clusters using Postponing
Authors: Sascha Hunold, Thomas Rauber, Frederic Suter
Venue: Proceedings of the 2008 Eighth IEEE International Symposium on Cluster Computing and the Grid (2008)

In this article, we revisit the problem of scheduling dynamically generated directed acyclic graphs (DAGs)of multi-processor tasks (M-tasks). A DAG is a basic model for expressing workflows applications where each node represents a task of the workflow. We present a novel algorithm (DMHEFT) for scheduling dynamically generated DAGs onto a heterogeneous collection of clusters. The scheduling decisions are based on the predicted runtime of an M-task as well as the estimationof the redistribution costs between data-dependent tasks. The algorithm also takes care of unfavorable placements of M-tasks by considering the postponing of ready tasks even if idle processors are available. We evaluate the scheduling algorithm by comparing the resulting makespans to the results obtained by using others cheduling algorithms, such as RePA and MHEFT.
Sample size and power calculations based on generalized linear mixed models with correlated binary outcomes
Authors: Qianyu Dang, Sati Mazumdar, Patricia R. Houck
Venue: Computer Methods and Programs in Biomedicine (2008)

The generalized linear mixed model (GLIMMIX) provides a powerful technique to model correlated outcomes with different types of distributions. The model can now be easily implemented with SAS PROC GLIMMIX in version 9.1. For binary outcomes, linearization methods of penalized quasi-likelihood (PQL) or marginal quasi-likelihood (MQL) provide relatively accurate variance estimates for fixed effects. Using GLIMMIX based on these linearization methods, we derived formulas for power and sample size calculations for longitudinal designs with attrition over time. We found that the power and sample size estimates depend on the within-subject correlation and the size of random effects. In this article, we present tables of minimum sample sizes commonly used to test hypotheses for longitudinal studies. A simulation study was used to compare the results. We also provide a Web link to the SAS macro that we developed to compute power and sample sizes for correlated binary outcomes.
On the network complexity of selection
Authors: C. G. Plaxton
Venue: Proceedings of the 30th Annual Symposium on Foundations of Computer Science (1989)

The sequential complexity of determining the kth largest out of a given set of n keys is known to be linear. Thus, given a p-processor parallel machine, it is asked whether or not an O(n/p) selection algorithm can be devised for that machine. An Omega ((n/p) log log p+log p) lower bound is obtained for selection on any network that satisfies a particular low expansion property. The class of networks satisfying this property includes all of the common network families, such as the tree, multidimensional mesh, hypercube, butterfly, and shuffle-exchange. When n/p is sufficiently large (e.g. greater than log/sup 2/p on the butterfly, hypercube, and shuffle-exchange), this result is matched by the upper bound given previously by the author (Proc. 1st Ann. ACM Symp. on Parallel Algorithms and Architecture p.64-73, 1989).
Efficient algorithms and methods to solve dynamic MINs stability problem using stable matching with complete ties
Authors: Nitin, Ashok Subramanian
Venue: Journal of Discrete Algorithms (2008)

We claimed that Stable Matching problems are the same as problems about stable configurations of Multi-stage Interconnection Networks (MINs). We solved the Regular and Irregular MINs Stability Problems using the approaches and solutions provided by the Stable Matching Problem. Specifically we have used Stable Marriage Problem as an example of Stable Matching. Two algorithms are proposed:-the first algorithm generates the MINs Preferences List in O(n^2) time and second algorithm produces a set of most Optimal Pairs of the Switching Elements (SEs), derived from the MINs Preferences List in O(n) time. Consequences include new algorithms for finding a Stable Matching between the SEs, an understanding of the difference between MINs Stability and Unstability problems, Algorithms used for generating the Preference Lists for the MINs, methods, and procedures used for deriving the Optimal Pairs from the MINs Preference Lists, and solving ties between them.
Mind your manners: socially appropriate wireless key establishment for groups
Authors: Cynthia Kuo, Ahren Studer, Adrian Perrig
Venue: Proceedings of the first ACM conference on Wireless network security (2008)

Group communication is inherently a social activity. However, existing protocols for group key establishment often fail to consider important social dynamics. This paper examines the human requirements for wireless group key establishment. We identify seven social and situational factors which impact group formation. Using these factors, we examine the requirements of four common classes of group communications. Each scenario imposes a unique set of requirements on wireless group key establishment.
A Fast Accuracy Crystal Identification Method Based on Fuzzy C-Means (FCM) Clustering Algorithm for MicroPET
Authors: Xiaowen Kang, Xishan Sun, Shi Wang, Yaqiang Liu, Yan Xia, Rong Zhou, Zhaoxia Wu, Yongjie Jin
Venue: Proceedings of the 2008 International Conference on BioMedical Engineering and Informatics - Volume 01 (2008)

A high resolution detector is being developed for our small animal position emission tomography (MicroPET). The detector unit consist of 8×8 crystal blocks, coupled to four photomultiplier tubes (PMTs).Each scintillation event is mapped in a two dimensional (2-D) position through the relative ratio of the output signals of the PMTs. Crystal Look-up table (CLT) used in ThuMicroPET scanner defines the matching relation between signal position of a detected event to a corresponding detector pixel location. It has a direct impact on imaging quality and brings significant influence to the gantry overall performance. However, the currently used method involves a lot of human interaction for CLT corrections, and cannot be implemented as a general process due to its complexity. This paper introduces a fast accuracy method based on Fuzzy C-Means (FCM) Clustering Algorithm for crystal identification. In the FCM, a cluster center and a fuzzy partition matrix of individual events in the 2-D position are defined. By iteratively updating the cluster centers and the membership grades for each event, we can move the cluster center to the right location in a short time, based on minimizing objective function that represents the distance from any given events to a cluster center weighted by its membership grade. The preliminary result shows that FCM can be used effectively in CLT construction, which significantly reduces the time, and brings excellent accuracy than we expected.
Persistent changes in NDVI between 1982 and 2003 over India using AVHRR GIMMS (Global Inventory Modeling and Mapping Studies) data
Authors: A. T. Jeyaseelan, P. S. Roy, S. S. Young
Venue: International Journal of Remote Sensing (2007)

The preliminary results of Normalized Difference Vegetation Index (NDVI) change studies over India using data from Advanced Very High Resolution Radiometer Global Inventory Modeling and Mapping Studies (AVHRR GIMMS) between 1982 and 2003 are presented. The three methodologies of univariate differencing, temporal profiling and anomaly analysis were undertaken. Univariate differencing was used to determine overall NDVI change between 1982 and 2003. A persistence filter was used to filter out ephemeral changes. The temporal profile analyses were carried out over different meteorological subdivisions to compare changes in NDVI with rainfall patterns. In the anomaly analysis, the areas of change were analysed over different land cover categories derived from IRS-WiFS data. The preliminary results indicate that positive trends in vegetation change occurred over most parts of the country and these changes appear not to be highly correlated with rainfall data, indicating that land cover transformations may be the major driving force behind the changes. The land cover classifications experiencing the greatest increasing NDVI were tropical thorn forests and intensive agriculture and the land cover experiencing very slow growth included current jhum, tropical moist deciduous and temperate evergreen forest. Five-year moving averages indicate a general increase in NDVI from 1986 to 1998 and then declining thereafter. This is a concern in most of the meteorological subdivisions.
Measurement repository for Scrum-based software development process
Authors: Viljan Mahnic, Natasa Zabkar
Venue: Proceedings of the 2nd WSEAS International Conference on Computer Engineering and Applications (2008)

A measurement repository design for Scrum-based software development process is presented. A meta-model of Scrum is shown first that serves as a basis for the development of the repository data model. Then the mapping between CMMI practices and Scrum is presented for the Measurement and Analysis (MA) Process Area, including the specification of base and derived measures. This is followed by the description of the repository design for collecting and storing project data and measurement results.
Facelets Essentials: Guide to JavaServer Faces View Definition Framework (Firstpress), 1 edition
Authors: Bruno Aranda, Zubin Wadia
Venue:  (2008)

Facelets is a templating language developed from the ground up with JavaServer Faces in mind. Created in response to the many concerns involving JSP when building JavaServer Faces views, Facelets steps outside of the JSP specification and provides a highly performant, JSFcentric view technology. Facelets top properties, templating, reuse, and ease of development, allows it to help making JSF a technology suitable for largescale projects. One of the first things a developer using Facelets finds is that it immediately leads to a reduction in UI code. Facelets Essentials, the first book on Facelets, introduces you to its importance, architecture, and relationship to JSF and the Apache MyFaces web framework. Learn to create your first application using the power and flexibility Facelets offers. Then, master and apply its basic and advanced features including Unified Expression Language, templating and reuse, custom tag development, and more. What youll learn See why you should use Facelets and the Facelets architecture. Ccreate your first application with Facelets. Use the Facelets Unified Expression Language. Explore Facelets templating and reuse, as well as the tag reference and custom tag development. Create composition components. Extend the ViewHandler. And more Who is this book for? This book is for Java web developers who are using or experienced with JSF and perhaps learning to use the MyFaces web framework.
Using Trustworthy and Referee Agents to Secure Multi-Agent Systems
Authors: Jamal Bentahar, Babak Khosravifar
Venue: Proceedings of the Fifth International Conference on Information Technology: New Generations (2008)

Security is a crucial factor in multi-agent systems where agents dynamically leave and enter the system. In this paper, we continue our work on security for agent-based systems by proposing a new trust model allowing agents to decide about a target agent. The model combines two techniques: using reports provided by the trustworthy agents regarding to direct and indirect interaction histories, and using reports provided by the referee agents in the form of recommendations. In addition, after a periodic time, the actual behavior of the target agent is checked against the provided information by others to adjust their credibility. The paper considers different parameters for computing trust, which is represented as a quantitative value.
A semi-random multiple decision-tree algorithm for mining data streams
Authors: Xue-Gang Hu, Pei-pei Li, Xin-Dong Wu, Gong-Qing Wu
Venue: Journal of Computer Science and Technology (2007)

Mining with streaming data is a hot topic in data mining. When performing classification on data streams, traditional classification algorithms based on decision trees, such as ID3 and C4.5, have a relatively poor efficiency in both time and space due to the characteristics of streaming data. There are some advantages in time and space when using random decision trees. An incremental algorithm for mining data streams, SRMTDS (Semi-Random Multiple decision Trees for Data Streams), based on random decision trees is proposed in this paper. SRMTDS uses the inequality of Hoeffding bounds to choose the minimum number of split-examples, a heuristic method to compute the information gain for obtaining the split thresholds of numerical attributes, and a Naïve Bayes classifier to estimate the class labels of tree leaves. Our extensive experimental study shows that SRMTDS has an improved performance in time, space, accuracy and the anti-noise capability in comparison with VFDTc, a state-of-the-art decision-tree algorithm for classifying data streams.
Hidden space-based nonlinear discriminant feature extraction method
Authors: Caikou Chen, Jingyu Yang
Venue: International Journal of Computer Mathematics (2007)

A novel nonlinear feature extraction method based on the scatter difference criterion in hidden space is developed. The main idea is that the original input space is first mapped into a hidden space through a hidden function, which is still referred to as the kernel function in the proposed method, and, in this space, feature extraction is conducted using the difference of between-class scatter and within-class scatter as the discriminant criterion. Different from the existing kernel-based feature extraction methods, the kernel functions used in the proposed method are not required to satisfy Mercer's theorem so that they can be chosen from a wide range. What is more important is that, due to the adoption of the scatter difference as the discriminant criterion for feature extraction, the proposed method essentially avoids the small sample size problem usually encountered in kernel Fisher discriminant analysis. Finally, extensive experiments have been performed on a subset of the FERET face database and the CENPARMI handwritten digital database. The experimental results indicate that the proposed method outperforms traditional scatter difference discriminant analysis in recognition performance.
Heat treatment for bearings: scheduling strategies and distributed decision support system
Authors: B. R. S. M. Jothi, Sachin B. Patkar
Venue: Proceedings of the 9th WSEAS International Conference on Systems (2005)

Scheduling and Production Planning problems are typically large in scale and fairly complex. A decision support system for such an operations research (OR) problem makes a good case study to be implemented using the web enabled, enterprise scale facilities of Java 2 Enterprise Edition (J2EE) and Simple Object Access Protocol (SOAP). We propose mathematical programming models as well as design and analyze certain specialized algorithms for special versions of these problems. In general, we use a powerful grade Mixed Integer Programming (MIP) solver, which we have web-enabled in our distributed decision support system, to solve the MIP models created by our system. Reusing web infrastructure can drastically lower the cost of setting up these application and allows us to reuse all kinds of tools originally built for the web.
The international workshop on software architectures and mobility (SAM 2008)
Authors: Licia Capra, Rami Bahsoon, Wolfgang Emmerich, Mohamed E. Fayad
Venue: Companion of the 30th international conference on Software engineering (2008)

E-businesses are increasingly facing the need of porting the provision of their e-services to mobile customers. Evolving requirements, such as reliability, security, scalability, performance and privacy, from fixed to mobile settings, has revealed new and important challenges. This is due to the behavioral constraints that mobility poses, and that were not faced in traditional distributed settings. Examples include: dynamic network topology, changes in location, constrained resource availability, communication protocols heterogeneity, unstable connectivity, and so forth. Industrial practice is demonstrating that such transition is not straightforward and tends to be costly. In particular, the evolution may "break" the software system architecture, thus calling for substantial and expensive changes. Even when the system is (re)built from scratch, it is unclear if and how the state-of-the-art in software architectures relate to the requirements and concerns brought forward by mobile software systems. Likewise, there is still a lack of systematic software engineering methods and techniques which can assist in developing and evolving mobile software systems. The goal of this workshop is to address these gaps by strengthening the cross fertilization of advances from requirements and domain engineering, software architectures, and middleware to systematically develop and evolve architectures supporting mobility.
Towards an Integration of Low-Level Timing Analysis and Model-Based Code Generation
Authors: Christian Ferdinand, Reinhold Heckmann, Hans-Jörg Wolff, Christian Renz, Manabendra Gupta, Oleg Parshin
Venue: Proceedings of the Second International Symposium on Leveraging Applications of Formal Methods, Verification and Validation (2006)

Software developers in the automotive sector must achieve high quality objectives. Many design and implementation errors are avoided by synthesizing code from model-based software specifications using automatic code generators such as ETAS' ASCET. To verify non-functional properties of the implementation, model-based design processes should be complemented with static program analysis tools like AbsInt's StackAnalyzer and timing analyzer aiT. ASCET, StackAnalyzer and aiT can be integrated in a way that the analysis results for code generated by ASCETare conveniently accessible from within the ASCET development environment. This gives ASCET users a direct feedback on the effects of their design decisions on resource usage, allowing to select more efficient designs and implementation methods. In the paper, we present the tools, the experimental integration, preliminary results and plans for further tool integration.
MULTISCALE AGENT-BASED SIMULATION FOR CHONDROGENIC PATTERN FORMATION IN VITRO
Authors: Scott Christley, Xuelian Zhu, Stuart A. Newman, Mark S. Alber
Venue: Cybernetics and Systems (2007)

Mathematical and computational multiscale models are becoming increasingly important investigative tools in developmental biological research. During certain developmental processes cells that start out as independent entities interact to form multicellular structures. Cells of the embryonic vertebrate limb in high-density culture undergo chondrogenic pattern formation, which results in the formation of regularly-spaced "islands" of cartilage analogous to the cartilage primordia of the developing limb skeleton. In this article we describe a discrete, agent-based stochastic model for studying the behavior of limb bud precartilage mesenchymal cells in vitro. This model, like an earlier one, employs a biologically motivated reaction-diffusion process and cell-matrix adhesion as the basis of self-organizing pattern formation, but constitutes an improvement in biological fidelity over previous descriptions in that it is multiscale (i.e., cell and molecular dynamics occur on distinct scales), and the cells are represented as spatially extended objects. The improved model reproduces a broader set of results of the micromass culture system than the previous one and discloses multiple dynamical regimes that suggest new biological experiments.