ppxscal/embedding_network huggingface dataset:
Model-based analysis of interferon-β induced signaling pathway
Authors: Jaroslaw Smieja, Mohammad Jamaluddin, Allan R. Brasier, Marek Kimmel
Venue: Bioinformatics (2008)

Motivation: Interferon-β induced JAK-STAT signaling pathways contribute to mucosal immune recognition and an anti-viral state. Though the main molecular mechanisms constituting these pathways are known, neither the detailed structure of the regulatory network, nor its dynamics has yet been investigated. The objective of this work is to build a mathematical model for the pathway that would serve two purposes: (1) to reproduce experimental results in simulation of both early and late response to Interferon-β stimulation and (2) to explain experimental phenomena generating new hypotheses about regulatory mechanisms that cannot yet be tested experimentally. Results: Experimentally determined time dependent changes in the major components of this pathway were used to build a mathematical model describing pathway dynamics in the form of ordinary differential equations. The experimental results suggested existence of unknown negative control mechanisms that were tested numerically using the model. Together, experimental and numerical data show that the epithelial JAK-STAT pathway might be subjected to previously unknown dynamic negative control mechanisms: (1) activation of dormant phosphatases and (2) inhibition of nuclear import of IRF1. Availability: The model, written in Matlab, is available online at www.stat.rice.edu/~jsmieja/IFN Contact: jaroslaw.smieja@polsl.pl Supplementary information:Supplementary data are available at Bioinformatics online.
Structure and development of plans in computer text editing
Authors: Scott P. Robertson, John B. Black
Venue: Human-computer interaction (1986)

When people learn such a complex skill as computer text editing, they are learning a set of goals and the plans for accomplishing those goals. In this experiment we examined the structure and development of simple text-editing goals and plans. Long interkeystroke times were found to be associated with plan boundaries. The longest times were found between keystrokes separating superordinate goals, whereas less significant time increases appeared between keystrokes at subgoal boundaries. Changes in the patterns of interkeystroke times showed plan restructuring with experience.
Robust stability analysis for 2-D continuous-time systems via parameter-dependent Lyapunov functions
Authors: M. Alfidi, A. Hmamed
Venue: WSEAS Transactions on Systems and Control (2007)

New sufficient conditions to test stability of 2-D linear continuos-time systems described by Roesser model with polytopic uncertainty are presented in this paper. Robust stability is guaranteed by the existence of a parameter-dependent Lyapunov function obtained from the feasibility of a set of Linear Matrix Inequalities(LMIs), formulated at the vertices of the uncertainty polytope. Two conditions are presented, and the results are compared with the analysis based on quadratic stability (same Lyapunov function for the entire set of uncertainties). Several examples are presented to illustrate the results.
A correlation factor based islanding detection method for distributed synchronous generators
Authors: Wen-Yeau Chang
Venue: WSEAS TRANSACTIONS on SYSTEMS (2008)

This paper proposes a new correlation factor based islanding detection method for use of grid-connected distributed synchronous generator. The proposed correlation factor method is based on voltage fluctuation injection, which can be obtained through regulating the field current of the distributed synchronous generator periodically. The correlation factor between the periodic regulating signal and the perturbed voltage is then used as an islanding detection index. When distributed synchronous generator is grid-interconnected, the correlation factor is lower than a threshold value. In contrast, as an islanding occurs, the correlation factor would become much higher than the threshold value. In this paper, experiments are conducted to illustrate the principles of the proposed technique. The test results show that the new proposed method is reliable, economical, and easy for implementation for islanding detection of distributed synchronous generator.
Go with Microsoft Office 2003: Brief
Authors: John Preston, Sally Preston, Robert L. Ferrett
Venue:  (2007)

For Introductory Computer courses in Microsoft Office 2003 or courses in Computer Concepts with a lab component for Microsoft Office 2003 applications. Teach the course YOU want in LESS TIME. The primary goal of the GO! Series is ease of implementation, with an approach that is based on clearly-defined projects for students and a one of a kind supplements package.
Reduction of the Rosenbrock matrix in analysis of invariant zeros of the linear MIMO-System
Authors: M. Sh. Misrikhanov, V. N. Ryabchenko
Venue: Automation and Remote Control (2008)

The problem is considered of reduction of the Rosenbrock matrix in analysis of invariant zeros of a linear multidimensional dynamical system with many inputs and many outputs. Approaches to the Rosenbrock matrix reduction are compared, which are carried out with the aid of the transformation of initial system equations to the Yokoyama canonical form and on the basis of zero divisors of numerical matrices. It is shown that the approach to the Rosenbrock matrix reduction on the basis of zero divisors is less arduous and offers the possibility of obtaining a well-posed problem in eigenvalues of the generalized linear bundle, while the reduction on the basis of subspaces of A.N. Krylov leads to the problem in eigenvalues of the nonlinear (polynomial) bundle of matrices, and its stipulation is generally rather poor. Various versions of the reduced matrices are presented, which are obtained in accordance with properties of the dynamical system. Properties of the Rosenbrock reduced matrices are analyzed.
Adapting information retrieval to query contexts
Authors: Jing Bai, Jian-Yun Nie
Venue: Information Processing and Management: an International Journal (2008)

In current IR approaches documents are retrieved only according to the terms specified in the query. The same answers are returned for the same query whatever the user and the search goal are. In reality, many other contextual factors strongly influence document's relevance and they should be taken into account in IR operations. This paper proposes a method, based on language modeling, to integrate several contextual factors so that document ranking will be adapted to the specific query contexts. We will consider three contextual factors in this paper: the topic domain of the query, the characteristics of the document collection, as well as context words within the query. Each contextual factor is used to generate a new query language model to specify some aspect of the information need. All these query models are then combined together to produce a more complete model for the underlying information need. Our experiments on TREC collections show that each contextual factor can positively influence the IR effectiveness and the combined model results in the highest effectiveness. This study shows that it is both beneficial and feasible to integrate more contextual factors in the current IR practice.
Projection theorem for Banach and locally convex spaces
Authors: V. V. Semenov
Venue: Cybernetics and Systems Analysis (2008)

The problem of representing linear functionals and linear operators using a given bilinear mapping is considered. For linear continuous functionals and linear compact operators that act in Banach and locally convex spaces, theorems on their representability using a given bilinear operator are formulated. Our results generalize the classical Lax-Milgram theorem.
An efficient A* algorithm for the directed linear arrangement problem
Authors: Derchian Tsaih, Guangming Wu, Chiehyao Chang, Shaoshin Hung, Chinshan Wu, Huiling Lin
Venue: WSEAS Transactions on Computers (2008)

In this paper we present an efficient A* algorithm to solve the Directed Linear Arrangement Problem. By using a branch and bound technique to embed a given directed acyclic graph into a layerwise partition search graph, the optimal directed ordering is then be identified through a A* shortest path search in the embedding graph. We developed a hybrid DC+BDS algorithm to approximate the optimal linear arrangement solution, which includes directed clustering and bidirectional sort technique. Along with a lower bound based on the maximum flow technique, this approximation solution is used as an upper bound to prune the state space during the A* search. In order to reduce the memory requirement of the A* search, we also discuss a implementation of the relay node technique from Zhou and Hansen [22].
Graceful database schema evolution: the PRISM workbench
Authors: Carlo A. Curino, Hyun J. Moon, Carlo Zaniolo
Venue: Proceedings of the VLDB Endowment (2008)

Supporting graceful schema evolution represents an unsolved problem for traditional information systems that is further exacerbated in web information systems, such as Wikipedia and public scientific databases: in these projects based on multiparty cooperation the frequency of database schema changes has increased while tolerance for downtimes has nearly disappeared. As of today, schema evolution remains an error-prone and time-consuming undertaking, because the DB Administrator (DBA) lacks the methods and tools needed to manage and automate this endeavor by (i) predicting and evaluating the effects of the proposed schema changes, (ii) rewriting queries and applications to operate on the new schema, and (iii) migrating the database. Our PRISM system takes a big first step toward addressing this pressing need by providing: (i) a language of Schema Modification Operators to express concisely complex schema changes, (ii) tools that allow the DBA to evaluate the effects of such changes, (iii) optimized translation of old queries to work on the new schema version, (iv) automatic data migration, and (v) full documentation of intervened changes as needed to support data provenance, database flash back, and historical queries. PRISM solves these problems by integrating recent theoretical advances on mapping composition and invertibility, into a design that also achieves usability and scalability. Wikipedia and its 170+ schema versions provided an invaluable testbed for validating PRISM tools and their ability to support legacy queries.
Automatic quality of experience measuring on video delivering networks
Authors: Daniel De Vera, Pablo Rodríguez-Bocca, Gerardo Rubino
Venue: ACM SIGMETRICS Performance Evaluation Review (2008)

This article describes a full video delivery network monitoring suite. Our monitoring tool offers a new view of a video delivery network, based on the quality as perceived by final users (what is nowadays called Quality of Experience, in short QoE). We measure the perceived quality at the client side by means of the recently proposed PSQA technology, by studying the video flows at the frame level. The developed monitoring suite is a completely free-software application, based on well-known technologies such as Simple Network Management Protocol or Round Robin Databases, which can be executed in various operating systems. In this short article we explain the tool implementation and we present some of the measurements performed with it.
Towards a High Performance Implementation of MPI-IO on the Lustre File System
Authors: Phillip Dickens, Jeremy Logan
Venue: Proceedings of the OTM 2008 Confederated International Conferences, CoopIS, DOA, GADA, IS, and ODBASE 2008. Part I on On the Move to Meaningful Internet Systems: (2008)

Lustre is becoming an increasingly important file system for large-scale computing clusters. The problem is that many data-intensive applications use MPI-IO for their I/O requirements, and it has been well documented that MPI-IO performs poorly in a Lustre file system environment. However, the reasons for such poor performance are not currently well understood. We believe that the primary reason for poor performance is that the assumptions underpinning most of the parallel I/O optimizations implemented in MPI-IO do not hold in a Lustre environment. Perhaps the most important assumption that appears to be incorrect is that optimal performance is obtained by performing large, contiguous I/O operations. Our research suggests that this is often the worst approach to take in a Lustre file system. In fact, we found that the best performance is sometimes achieved when each process performs a series of smaller, non-contiguous I/O requests. In this paper, we provide experimental results showing that such assumptions do not apply in Lustre, and explore new approaches that appear to provide significantly better performance.
Adaptive redundancy for data propagation exploiting dynamic sensory mobility
Authors: Athanasios Kinalis, Sotiris Nikoletseas
Venue: Proceedings of the 11th international symposium on Modeling, analysis and simulation of wireless and mobile systems (2008)

Motivated by emerging applications, we consider sensor networks where the sensors themselves (not just the sinks) are mobile. We focus on mobility scenarios characterized by heterogeneous, highly changing mobility roles in the network. To capture these high dynamics we propose a novel network parameter, the mobility level, which, although simple and local, quite accurately takes into account both the spatial and speed characteristics of motion. We then propose adaptive data dissemination protocols that use the mobility level estimation to improve performance. By basically exploiting high mobility (redundant message ferrying) as a cost-effective replacement of flooding, e.g., the sensors tend to dynamically propagate less data in the presence of high mobility, while nodes of high mobility are favored for moving data around. These dissemination schemes are enhanced by a distance-sensitive probabilistic message flooding inhibition mechanism that further reduces communication cost, especially for fast nodes of high mobility level, and as distance to data destination decreases. Our simulation findings demonstrate significant performance gains of our protocols compared to non-adaptive protocols, i.e., adaptation increases the success rate and reduces latency (even by 15%) while at the same time significantly reducing energy dissipation (in most cases by even 40%). Also, our adaptive schemes achieve significantly higher message delivery ratio and satisfactory energy-latency trade-offs when compared to flooding when sensor nodes have limited message queues.
Ensemble of support vector machines for land cover classification
Authors: M. Pal
Venue: International Journal of Remote Sensing (2008)

This letter presents the results of two different ensemble approaches to increase the accuracy of land cover classification using support vector machines. Finite ensemble approaches, based on boosting and bagging and infinite ensemble created by embedding the infinite hypothesis in the kernel of support vector machines, are discussed. Results suggest that the infinite ensemble approach provides a significant increase in the classification accuracy in comparison to the radial basis function kernel-based support vector machines. While using finite ensemble approaches, bagging works well and provides a comparable performance to the infinite ensemble approach, whereas boosting decreases the performance of support vector machines. Comparison in terms of computational cost suggests that finite ensemble approaches require a large processing time in comparison to the infinite ensemble approach.
Web Information Retrieval Support Systems: The Future of Web Search
Authors: Orland Hoeber
Venue: Proceedings of the 2008 IEEE/WIC/ACM International Conference on Web Intelligence and Intelligent Agent Technology - Volume 03 (2008)

The primary focus of Web Information Retrieval Support Systems (WIRSS) are to address the aspects of search that consider the specific needs and goals of the individuals conducting Web searches. WIRSS moves beyond the traditional focus of automated searching within digital collections, applying intelligent methods and Web-based technologies to assist users in specifying their information needs, evaluating and exploring search results, and managing the information they find. The goal of this paper is to provide an overview of some of the key issues, challenges, and opportunities in WIRSS research.
Solving modern mixed-size placement instances
Authors: Jarrod A. Roy, Aaron N. Ng, Rajat Aggarwal, Venky Ramachandran, Igor L. Markov
Venue: Integration, the VLSI Journal (2009)

Physical design of modern systems-on-chip is extremely challenging. Such digital integrated circuits often contain tens of millions of logic gates, intellectual property blocks, embedded memories and custom register-transfer level (RTL) blocks. At current and future technology nodes, their power and performance are impacted, more than ever, by the placement of their modules. However, our experiments show that traditional techniques for placement and floorplanning, and existing academic tools cannot reliably solve the placement task. To study this problem, we identify particularly difficult industrial instances and reproduce the failures of existing tools by modifying pre-existing benchmark instances. Furthermore, we propose algorithms that facilitate placement of these difficult instances. Empirically, our techniques consistently produce legal placements, and on instances where comparison is possible, reduce wirelength by 13% over Capo 9.4 and 31% over PATOMA 1.0-the pre-existing tools that most frequently produce legal placements in our experiments.
VistaClara
Authors: Robert Kincaid, Allan Kuchinsky, Michael Creech
Venue: Bioinformatics (2008)

Summary: VistaClara is a plug-in for Cytoscape which provides a more flexible means to visualize gene and protein expression within a network context. An extended attribute browser is provided in the form of a graphical and interactive permutation matrix that resembles the heat map displays popular in gene-expression analysis. This extended browser permits a variety of display options and interactions not currently available in Cytoscape. Availability: http://chianti.ucsd.edu/cyto_web/plugins/index.php Contact: robert_kincaid@agilent.com
XML Methods for Validation of Temporal Properties on Message Traces with Data
Authors: Sylvain Hallé, Roger Villemaire
Venue: Proceedings of the OTM 2008 Confederated International Conferences, CoopIS, DOA, GADA, IS, and ODBASE 2008. Part I on On the Move to Meaningful Internet Systems: (2008)

We perform trace validation of LTL formulæ by exclusively using readily-available XML technologies. We first provide a translation between LTL and a subset of the XML Query Language XQuery, and show that an efficient validation of LTL formulæ can be achieved through the evaluation of XQuery expressions. Moreover, since LTL maps to a small fragment of XQuery, we show that that extending it to LTL-FO + , which includes full first-order quantification over message contents, can be supported without additional cost. All these capabilities, which come "for free" in any web service environment providing a standard XQuery engine, are tested using a representative choreography scenario.
Dynamical modeling and multi-experiment fitting with PottersWheel
Authors: Thomas Maiwald, Jens Timmer
Venue: Bioinformatics (2008)

Motivation: Modelers in Systems Biology need a flexible framework that allows them to easily create new dynamic models, investigate their properties and fit several experimental datasets simultaneously. Multi-experiment-fitting is a powerful approach to estimate parameter values, to check the validity of a given model, and to discriminate competing model hypotheses. It requires high-performance integration of ordinary differential equations and robust optimization. Results: We here present the comprehensive modeling framework Potters-Wheel (PW) including novel functionalities to satisfy these requirements with strong emphasis on the inverse problem, i.e. data-based modeling of partially observed and noisy systems like signal transduction pathways and metabolic networks. PW is designed as a MATLAB toolbox and includes numerous user interfaces. Deterministic and stochastic optimization routines are combined by fitting in logarithmic parameter space allowing for robust parameter calibration. Model investigation includes statistical tests for model-data-compliance, model discrimination, identifiability analysis and calculation of Hessian-and Monte-Carlo-based parameter confidence limits. A rich application programming interface is available for customization within own MATLAB code. Within an extensive performance analysis, we identified and significantly improved an integrator–optimizer pair which decreases the fitting duration for a realistic benchmark model by a factor over 3000 compared to MATLAB with optimization toolbox. Availability: PottersWheel is freely available for academic usage at http://www.PottersWheel.de/. The website contains a detailed documentation and introductory videos. The program has been intensively used since 2005 on Windows, Linux and Macintosh computers and does not require special MATLAB toolboxes. Contact: maiwald@fdm.uni-freiburg.de Supplementary information:Supplementary data are available at Bioinformatics online.
Managing requirements inter-dependency for software product line derivation
Authors: David Sellier, Mike Mannion, Jason Xabier Mansell
Venue: Requirements Engineering (2008)

Software Product Line Engineering (SPLE) can reduce software development costs, reduce time to market and improve product quality. A software product line is a set of software products sharing a set of common features but containing variation points. Successful SPLE requires making selection decisions at variation points effectively and efficiently. A significant challenge is how to identify, represent and manage the inter-dependency of selection decisions for requirements. We developed the concept of a meta-model for requirement decision models to bring formalism and consistency to the structure and to model inter-dependencies between requirement selection decisions. Here we present a meta-model for requirement selection decisions that includes inter-dependencies and we use a mobile phone worked example to illustrate our approach. To support our method, we developed two separate tools, V-Define (for domain decision model construction) and V-Resolve (for new product derivation). Finally the results of a metal processing product line case study using the tools are described.
Hierarchical pathfinding and AI-based learning approach in strategy game design
Authors: LeMinh Duc, Amandeep Singh Sidhu, Narendra S. Chaudhari
Venue: International Journal of Computer Games Technology (2008)

Strategy game and simulation application are an exciting area with many opportunities for study and research. Currently most of the existing games and simulations apply hard coded rules so the intelligence of the computer generated forces is limited. After some time, player gets used to the simulation making it less attractive and challenging. It is also costly and tedious to incorporate new rules for an existing game. The main motivation behind this research project is to improve the quality of artificial intelligence- (AI-) based on various techniques such as qualitative spatial reasoning (Forbus et al., 2002), near-optimal hierarchical pathfinding (HPA*) (Botea et al., 2004), and reinforcement learning (RL) (Sutton and Barto, 1998).