ppxscal/embedding_network huggingface dataset:
A Proposal for Task Parallelism in OpenMP
Authors: Eduard Ayguadé, Nawal Copty, Alejandro Duran, Jay Hoeflinger, Yuan Lin, Federico Massaioli, Ernesto Su, Priya Unnikrishnan, Guansong Zhang
Venue: Proceedings of the 3rd international workshop on OpenMP: A Practical Programming Model for the Multi-Core Era (2007)

This paper presents a novel proposal to define task parallelism in OpenMP. Task parallelism has been lacking in the OpenMP language for a number of years already. As we show, this makes certain kinds of applications difficult to parallelize, inefficient or both. A subcommittee of the OpenMP language committee, with representatives from a number of organizations, prepared this proposal to give OpenMP a way to handle unstructured parallelism. While defining the proposal we had three design goals: simplicity of use, simplicity of specification and consistency with the rest of OpenMP. Unfortunately, these goals were in conflict many times during our discussions. The paper describes the proposal, some of the problems we faced, the different alternatives, and the rationale for our choices. We show how to use the proposal to parallelize some of the classical examples of task parallelism, like pointer chasing and recursive functions.
Development of routing protocols for the solar-powered autonomous underwater vehicle (SAUV) platform
Authors: Radim Bartoš, Steven G. Chappell, Rick J. Komerska, Matthew M. Haag, Sai S. Mupparapu, Emmanuel Agu, Ian Katz
Venue: Wireless Communications Mobile Computing (2008)

The solar-powered autonomous underwater vehicle (SAUV) platform has been developed over the past several years as a means to achieve long-endurance cooperative missions, and the design of mobile routing protocols has become one of the main areas of focus during this process. This paper reports on the lessons learned from the design, simulation-based evaluation, and field testing of two protocols. Two areas for possible improvements are proposed and evaluated using simulations. Finally, we present suggestions drawn from field experience for improving the design, simulation, and evaluation of protocols for use in a harsh underwater environment. Copyright &copy; 2008 John Wiley & Sons, Ltd.
On the Identification of Wiener Systems Having Saturation-like Functions with Positive Slopes
Authors: Rimantas Pupeikis
Venue: Informatica (2005)

The aim of the given paper is the development of an approach for parametric identification of Wiener systems with piecewise linear nonlinearities, i.e., when the linear part with unknown parameters is followed by a saturation-like function with unknown slopes. It is shown here that by a simple data reordering and by a following data partition the problem of identification of a nonlinear Wiener system could be reduced to a linear parametric estimation problem. Afterwards, estimates of the unknown parameters of linear regression models are calculated by processing respective particles of input-output data. A technique based on ordinary least squares (LS) is proposed here for the estimation of parameters of linear and nonlinear parts of the Wiener system, including the unknown threshold of piecewise nonlinearity, too. The results of numerical simulation and identification obtained by processing observations of input-output signals of a discrete-time Wiener system with a piecewise nonlinearity by computer are given.
0.374 Pflop/s trillion-particle kinetic modeling of laser plasma interaction on Roadrunner
Authors: K. J. Bowers, B. J. Albright, B. Bergen, L. Yin, K. J. Barker, D. J. Kerbyson
Venue: Proceedings of the 2008 ACM/IEEE conference on Supercomputing (2008)

We demonstrate the outstanding performance and scalability of the VPIC kinetic plasma modeling code on the heterogeneous IBM Roadrunner supercomputer at Los Alamos National Laboratory. VPIC is a three-dimensional, relativistic, electromagnetic, particle-in-cell (PIC) code that self-consistently evolves a kinetic plasma. VPIC simulations of laser plasma interaction were conducted at unprecedented fidelity and scale---up to 1.0 x 1012 particles on as many as 136 x 106 voxels---to model accurately the particle trapping physics occurring within a laser-driven hohlraum in an inertial confinement fusion experiment. During a parameter study of laser reflectivity as a function of laser intensity under experimentally realizable hohlraum conditions [1], we measured sustained performance exceeding 0.374 Pflop/s (s.p.) with the inner loop itself achieving 0.488 Pflop/s (s.p.). Given the increasing importance of data motion limitations, it is notable that this was measured in a PIC calculation---a technique that typically requires more data motion per computation than other techniques (such as dense matrix calculations, molecular dynamics N-body calculations and Monte-Carlo calculations) often used to demonstrate supercomputer performance. This capability opens up the exciting possibility of using VPIC to model, from first-principles, an issue critical to the success of the multi-billion dollar DOE/NNSA National Ignition Facility.
Children's Interactions with Animated Agents in an Intelligent Tutoring System
Authors: Judy Robertson, Beth Cross, Hamish Macleod, Peter Wiemer-Hastings
Venue: International Journal of Artificial Intelligence in Education (2004)

Although animated pedagogical agents are frequently found in intelligent tutoring systems and interactive learning environments, their effect on users?attitudes and learning requires further investigation. This paper reports findings of a field study designed to investigate the impact of animated pedagogical agents on primary school children's attitudes to and interactions with the StoryStation system. Sixty pupils used either a version of StoryStation with an animated agent interface or an equivalent one with a normal graphical user interface to write a story. Analysis of questionnaire data indicated that pupils who used the agent version rated StoryStation more highly than those who used the non-agent version. Analysis of program use revealed that girls tended to interact more with the agent version, while boys tended to interact more with the non-agent version.
A Coupled Chemo-Thermo-Hydro-Mechanical Constitutive Model for Porous Media
Authors: Zejia Liu, Xikui Li, Liqun Tang
Venue: Proceedings of the 7th international conference on Computational Science, Part III: ICCS 2007 (2007)

Basing on the existing thermo-hydro-mechanical constitutive model presented in reference[1], and the chemo-mechanical constitutive model presented in reference[2], a coupled chemo-thermo-hydro-mechanical(CTHM) constitutive model of porous media is developed in the present paper. The chemoplastic and thermoplastic coupling behavior is considered in the present constitutive model. The present coupled CTHM constitutive model has been integrated into the coupled thermo-hydro-mechanical mathematical model including contaminant translation in porous media. The numerical results are illustrated to particularly emphasize the effects of the contaminant concentration and temperature to the coupled CTHM system in porous media.
A privacy-aware trajectory tracking query engine
Authors: Aris Gkoulalas-Divanis, Vassilios S. Verykios
Venue: ACM SIGKDD Explorations Newsletter (2008)

Advances in telecommunications and GPS sensors technology have made possible the collection of data like time series of locations, related to the movement of individuals. The analysis of this, so-called trajectory data, is beneficial both for the individuals (e.g., through location-based services) and for the community as a whole (e.g., decision support for urban planning or traffic control). However, because of the very nature of this data, strict safeguards must be enforced to ensure the privacy of the individuals, whose movement is recorded. In this paper, we present a privacy-aware trajectory tracking query engine that offers strict guarantees about what can be observed by untrusted third parties. Through the query engine, subscribed users can gain restricted access to an in-house trajectory data warehouse, to perform certain analysis tasks. In addition to regular queries involving non-spatial non-temporal attributes, the engine supports a variety of spatiotemporal queries, including range queries, nearest neighbor queries and queries for aggregate statistics. The query results are augmented with fake trajectory data (dummies) to fulfil the requirements of K-anonymity. Through qualitative analysis, we prove the effectiveness of our approach towards blocking certain types of attacks, while minimally distorting the dataset.
Small amplitude limit cycles of symmetric cubic systems
Authors: Terence R. Blows
Venue: Computers Mathematics with Applications (2008)

Hilbert's Sixteenth Problem concerns the number and relative position of limit cycles in a planar polynomial system of differential equations. We show, using multiple Hopf bifurcation from multiple fine foci, that limit cycle configurations of types (3, 3, -2, -2) and (2, 2, 1, 1, -1) occur in symmetric cubic systems.
Risk assessment in practice: A real case study
Authors: Marco Benini, Sabrina Sicari
Venue: Computer Communications (2008)

The aim of this work is to evaluate the risk of an external attack to the network of our Department in the University. Thus, this work wants to complement the results in [M. Benini, S. Sicari, A mathematical framework for risk assessment, in: H. Labiod, M. Badra (Eds.), New Technologies, Mobility and Security, Signals and Communication, Springer-Verlag, May 2007, pp. 459-469] where a mathematical framework justifying our risk assessment method has been presented. Hence, this article describes a detailed account of our experience where the instruments, the techniques and the results are described and evaluated.
Significance-Driven Graph Clustering
Authors: Marco Gaertler, Robert Görke, Dorothea Wagner
Venue: Proceedings of the 3rd international conference on Algorithmic Aspects in Information and Management (2007)

Modularity, the recently defined quality measure for clusterings, has attained instant popularity in the fields of social and natural sciences. We revisit the rationale behind the definition of modularity and explore the founding paradigm. This paradigm is based on the trade-off between the achieved quality and the expected quality of a clustering with respect to networks with similar intrinsic structure. We experimentally evaluate realizations of this paradigm systematically, including modularity, and describe efficient algorithms for their optimization. We confirm the feasibility of the resulting generality by a first systematic analysis of the behavior of these realizations on both artificial and on real-world data, arriving at remarkably good results of community detection.
Ranking for Approximated XQuery Full-Text Queries
Authors: Giacomo Buratti, Danilo Montesi
Venue: Proceedings of the 25th British national conference on Databases: Sharing Data, Information and Knowledge (2008)

Treating structural conditions included in an XQuery Full-Text expression as desiderata rather than mandatory constraints could be beneficial for better answering user's informational needs. Using an approximated semantics requires however a mechanism for calculating a score for each resulting tree, and an algorithm for efficiently finding the best results. Both these issues are explored in this paper. We present algorithms for query evaluation that uses a threshold approach in order to improve performance; the algorithms rely on some properties of the functions used to calculate the score. Moreover, we propose a method, based on the new concepts of Path Edit Distance and Comparison Satisfaction Ratio, for calculating the structural score of a tree that partially satisfies conditions over tree structure and element values.
Agile Computer Control of a Complex Experiment
Authors: Gaël Varoquaux
Venue: Computing in Science and Engineering (2008)

This article introduces techniques and tools useful for writing an experiment's control framework. In particular, the author discusses how to use the Python language to control hardware.
An International Look at Virtual Citizenship
Authors: Drew Robb
Venue: IT Professional (2003)

Comprehensive strategies in India and Europe guide the movement of government services online.
Adaptive Planning for Supply Chain Networks
Authors: Michael Andreev, George Rzevski, Petr Skobelev, Peter Shveykin, Alexander Tsarev, Andrew Tugashev
Venue: Proceedings of the 3rd international conference on Industrial Applications of Holonic and Multi-Agent Systems: Holonic and Multi-Agent Systems for Manufacturing (2007)

This paper describes methodology, toolset and case studies of adaptive planning for supply chain networks based on the holistic approach, multi-agent technology and ontological modeling. The set of tools for the development of adaptive planners can be used for a wide range of applications. Case studies are included describing applications inr adaptive airport logistics, factory planning, laundry scheduling and pharmaceutical logistics.
Adapting wireless sensor networks to obstructed and concave environments
Authors: Li Xiao
Venue:  (2007)

The advances of electronic circuits make it possible to achieve intelligent computation in small devices at low cost, which enables the development of wireless sensor networks in recent years. Wireless sensor networks consist of large volume of sensors deployed in a field and have broad applications in collecting data from the physical world. In practice, wireless sensor networks are often deployed in complicated enviromnents including obstructed or concave areas, where radio signals are interfered or blocked by obstructions, which leads to irregular communication patterns or concave network topologies. In this dissertation, we systematically investigate how system performance are affected by complicated environmental factors, and develop a suite of solutions in sensor localization and data communications that can be applied to sensor networks deployed in obstructed and concave environments. Sensor Localization provides fundamental support for sensor network protocols and applications. However, localization results can be severely distorted by complicated environments, where distance measurements may have large errors because radio or ultrasound signals are blocked, reflected, or distracted by obstructions. To address these problems, we propose the virtual ruler approach to filter out the incorrect distances in the measurement step. We further propose the upper bound approach in localization algorithms to eliminate the impact of incorrect distance measurements. It is a challenging task to realize packet routing in a wireless sensor network, because only small routing states can be maintained in a sensor's limited memory space. Location aware routing has been proposed to realize scalable packet routing by greedy forwarding based on a small set of neighbors' positions. However, location aware routing has low routing success rate when sensors are deployed into obstructed and concave environments. To improve the routing success rate of the greedy forwarding, we propose the topology aware routing that uses the graph embedding to efficiently encode a network topology into small size routing states. We further improve the end to end routing performance by encoding the expected number of transmissions to small routing states. Radio packets may be lost in transmission because radio signals are susceptible to environmental interference. We propose the receiver-centric protocol to realize reliable data transmission for sensor networks with high throughput and low overhead. The receiver-centric protocol utilizes the broadcast nature of radio signals and multihop forwarding of sensor networks. Since the communication throughput can also be reduced by radio interference among neighboring sensors, we further enforce channel access scheduling to CSMA protocol to mitigate channel interference. The channel access scheduling proposed in this dissertation is specially designed based on the tree structure that is naturally formed in data collection of a sensor network, and therefore outperforms other MAC protocols designed for general purposes.
A New Hardware Friendly Vector Distance Evaluation Function for Vector Classifiers
Authors: Hiroomi Hikawa, Kaori Kugimiya
Venue: Neural Information Processing: 14th International Conference, ICONIP 2007, Kitakyushu, Japan, November 13-16, 2007, Revised Selected Papers, Part II (2008)

This paper proposes a new vector distance evaluation function for vector classifications. The proposed distance evaluation function is the weighted sum of the differences between vector elements. The weight values are determined according to whether the input vector element is in the neighborhood of the prototype vector element or not. If the element is not within the neighborhood, then the weight is selected so that the distance measure is less significant The proposed distance measure is applied to a hardware vector classifier system and its feasibility is verified by simulations and circuit size evaluation. These simulations and evaluations reveal that the performance of the classifier with the proposed method is better than that of the Manhattan distance classifier and slightly inferior to Gaussian classifier. While providing respectable performance on the classification, the evaluation function can be easily implemented in hardware.
Entity Ranking from Annotated Text Collections Using Multitype Topic Models
Authors: Hitohiro Shiozaki, Koji Eguchi
Venue: Focused Access to XML Documents: 6th International Workshop of the Initiative for the Evaluation of XML Retrieval, INEX 2007 Dagstuhl Castle, Germany, December 17-19, 2007. Selected Papers (2008)

Very recently, topic model-based retrieval methods have produced good results using Latent Dirichlet Allocation (LDA) model or its variants in language modeling framework. However, for the task of retrieving annotated documents when using the LDA-based methods, some post-processing is required outside the model in order to make use of multiple word types that are specified by the annotations. In this paper, we explore new retrieval methods using a `multitype topic model' that can directly handle multiple word types, such as annotated entities, category labels and other words that are typically used in Wikipedia. We investigate how to effectively apply the multitype topic model to retrieve documents from an annotated collection, and show the effectiveness of our methods through experiments on entity ranking using a Wikipedia collection.
A Multi-ojbective Evolutionary Algorithm with Extended MGG Model and Distance-Based Density Measure
Authors: Youyun Ao, Hongqin Chi
Venue: Proceedings of the 2008 Second International Conference on Genetic and Evolutionary Computing (2008)

A multi-objective evolutionary algorithm with extended minimal generation gap (MGG) model and distance-based density measure is given, which we call DMOEA. DMOEA employs a new technique to estimate the distance between two individuals in the objective space, further, finds the K nearest neighbors on either side of certain individual along one focused objective, calculates the sum of the distances to the K nearest neighbors for the crowding density of the individual, and prunes the set of non-dominated solutions one by one according to the crowding density with the purpose of maintaining the diversity of solutions when the number of non-dominated solutions in the set is more than its capacity. Furthermore, DMOEA extends MGG model with simplex crossover to generate the new population, which can improve the search efficiency. DMOEA has been compared with three other state-of-the-art algorithms, DEMO, NSGA-II, and SPEA2 on a set of representative test problems.
Re-assessing the Value of Adaptive Navigation Support in E-Learning Context
Authors: Sergey Sosnovsky, Peter Brusilovsky, Danielle H. Lee, Vladimir Zadorozhny, Xin Zhou
Venue: Proceedings of the 5th international conference on Adaptive Hypermedia and Adaptive Web-Based Systems (2008)

In a recent study, we discovered a new effect of adaptive navigation support in the context of E-learning: the ability to motivate students to work more with non-mandatory educational content. The results presented in this paper extend the limits of our earlier findings. We describe the implementation of adaptive navigation support for the SQL domain, and report the results of the classroom evaluation of our approach. Among other issues, we investigate whether the use in parallel of two different types of navigation support could change the nature or the magnitude of the previously observed effect. Our study confirms the motivational value of navigation support in the new domain. We observe the increase of this effect after adding the concept-based navigation layer to the existing topic-based adaptive navigation service. The results of the navigational pattern analysis allow us to determine the major source of this increase.
A Unified View of Matrix Factorization Models
Authors: Ajit P. Singh, Geoffrey J. Gordon
Venue: Proceedings of the European conference on Machine Learning and Knowledge Discovery in Databases - Part II (2008)

We present a unified view of matrix factorization that frames the differences among popular methods, such as NMF, Weighted SVD, E-PCA, MMMF, pLSI, pLSI-pHITS, Bregman co-clustering, and many others, in terms of a small number of modeling choices. Many of these approaches can be viewed as minimizing a generalized Bregman divergence, and we show that (i) a straightforward alternating projection algorithm can be applied to almost any model in our unified view; (ii) the Hessian for each projection has special structure that makes a Newton projection feasible, even when there are equality constraints on the factors, which allows for matrix co-clustering; and (iii) alternating projections can be generalized to simultaneously factor a set of matrices that share dimensions. These observations immediately yield new optimization algorithms for the above factorization methods, and suggest novel generalizations of these methods such as incorporating row and column biases, and adding or relaxing clustering constraints.
A Framework to Understand the Mechanism of Toxicity
Authors: Wenhui Huang, Liqing Zhang
Venue: Proceedings of the 4th international conference on Intelligent Computing: Advanced Intelligent Computing Theories and Applications - with Aspects of Artificial Intelligence (2008)

Computational identification of the mechanisms of drug toxicity is a very challenging problem. Little progress has been made thus far. In this work, we propose a novel framework to identify proteins involved in the chosen toxicities. Specifically, we used the proteins (bait proteins) that have been identified empirically to be involved in the toxicities to fish out additional proteins that might be strongly associated with the bait proteins in the protein-protein interaction network. We applied our method to 14 toxicities and manually validated two toxicities including bleeding disorders and urinary disorders. Literature research indicates that most of the newly identified proteins are involved in the toxicities in some degrees, and the networks identified are consistent with the known studies related to the toxicities.
Grammar Morphisms and Weakly Adhesive Categories
Authors: Tobias Heindel
Venue: Proceedings of the 4th international conference on Graph Transformations (2008)

In the area of specification and modelling of concurrent systems, Petri nets have become a standard tool, and they still work behind the scenes in tools for graph transformation systems (cf. [1]). Moreover there is still potential for crossfertilization between the graph transformation and Petri net community. Even a better understanding of adhesive categories [2] and the related concepts of [3] seems possible in light of the proposed notion of weakly adhesive categories [4], which has emerged during work on the generalization of the co-reflective semantics of Petri nets to the realm of graph transformation and adhesive rewriting systems.