ppxscal/embedding_network huggingface dataset:
The PlaNet consortium: a network of European plant databases connecting plant genome data in an integrated biological knowledge resource: Conference Reviews
Authors: H. Schoof, R. Ernst, K. F. X. Mayer
Venue: Comparative and Functional Genomics (2004)

The completion of the Arabidopsis genome and the large collections of other plant sequences generated in recent years have sparked extensive functional genomics efforts. However, the utilization of this data is inefficient, as data sources are distributed and heterogeneous and efforts at data integration are lagging behind. PlaNet aims to overcome the limitations of individual efforts as well as the limitations of heterogeneous, independent data collections. PlaNet is a distributed effort among European bioinformatics groups and plant molecular biologists to establish a comprehensive integrated database in a collaborative network. Objectives are the implementation of infrastructure and data sources to capture plant genomic information into a comprehensive, integrated platform. This will facilitate the systematic exploration of Arabidopsis and other plants. New methods for data exchange, database integration and access are being developed to create a highly integrated, federated data resource for research. The connection between the individual resources is realized with BioMOBY. BioMOBY provides an architecture for the discovery and distribution of biological data through web services. While knowledge is centralized, data is maintained at its primary source without a need for warehousing. To standardize nomenclature and data representation, ontologies and generic data models are defined in interaction with the relevant communities. Minimal data models should make it simple to allow broad integration, while inheritance allows detail and depth to be added to more complex data objects without losing integration. To allow expert annotation and keep databases curated, local and remote annotation interfaces are provided. Easy and direct access to all data is key to the project. Copyright &copy; 2004 John Wiley & Sons, Ltd.
Three Practical Ways to Improve Your Network
Authors: Kevin Miller
Venue: Proceedings of the 17th USENIX conference on System administration (2003)

This paper presents three simple techniques for improving network service using relatively unknown features of many existing networks. The resulting system provides greater reliability, enhanced security, and ease of management. First, it addresses the application of IP anycast to provide reliable recursive DNS service. Next, it explains the use of unicast reverse path forwarding and its usefulness in preventing local nodes from originating packets with spoofed source addresses. Finally, it explains how unicast reverse path forwarding can be used to quickly and easily apply source address filters on your network. As an added benefit, some of these features provide mechanisms to conform a network to Best Common Practices (BCP) of network operators.
Adaptive sampling for sensor networks
Authors: Ankur Jain, Edward Y. Chang
Venue: Proceeedings of the 1st international workshop on Data management for sensor networks: in conjunction with VLDB 2004 (2004)

A distributed data-stream architecture finds application in sensor networks for monitoring environment and activities. In such a network, large numbers of sensors deliver continuous data to a central server. The rate at which the data is sampled at each sensor affects the communication resource and the computational load at the central server. In this paper, we propose a novel adaptive sampling technique where the sampling rate at each sensor adapts to the streaming-data characteristics. Our approach employs a Kalman-Filter (KF)-based estimation technique wherein the sensor can use the KF estimation error to adaptively adjust its sampling rate within a given range, autonomously. When the desired sampling rate violates the range, a new sampling rate is requested from the server. The server allocates new sampling rates under the constraint of available resources such that KF estimation error over all the active streaming sensors is minimized. Through empirical studies, we demonstrate the flexibility and effectiveness of our model.
Grid-enabled data warehousing for molecular engineering
Authors: Werner Dubitzky, Damian McCourt, Mykola Galushka, Mathilde Romberg, Bernd Schuller
Venue: Parallel Computing (2004)

Molecular engineering is concerned with the design and manufacturing of novel chemical compounds and materials. Molecular engineering for drug development is complex, time-consuming, and expensive. To lower costs and improve the overall drug development process, information technology (IT) is increasingly employed in the molecular engineering phase. Key IT components for molecular engineering include public and proprietary databases containing information on molecular structures and properties and computational models capable of calculating global properties of molecular structures based on structural and other descriptors characterizing the compound. Recently data mining and data warehousing have become critical tools in the molecular engineering process. Increasingly, some of the computational resources--such as data and information bases, computational models, compute power to execute these models, specialized data mining algorithms--required to develop a new compound are not available locally, but accessible via the global computing network infrastructure. This paper describes a Grid-based approach to molecular engineering. Focus of this paper is placed on the data warehousing of the OpenMolGRID system.
Visualizing Demographic Trajectories with Self-Organizing Maps
Authors: André Skupin, Ron Hagelman
Venue: Geoinformatica (2005)

In recent years, the proliferation of multi-temporal census data products and the increased capabilities of geospatial analysis and visualization techniques have encouraged longitudinal analyses of socioeconomic census data. Traditional cartographic methods for illustrating socioeconomic change tend to rely either on comparison of multiple temporal snapshots or on explicit representation of the magnitude of change occurring between different time periods. This paper proposes to add another perspective to the visualization of temporal change, by linking multi-temporal observations to a geometric configuration that is not based on geographic space, but on a spatialized representation of n-dimensional attribute space. The presented methodology aims at providing a cognitively plausible representation of changes occurring inside census areas by representing their attribute space trajectories as line features traversing a two-dimensional display space. First, the self-organizing map (SOM) method is used to transform n-dimensional data such that the resulting two-dimensional configuration can be represented with standard GIS data structures. Then, individual census observations are mapped onto the neural network and linked as temporal vertices to represent attribute space trajectories as directed graphs. This method is demonstrated for a data set containing 254 counties and 32 demographic variables. Various transformations and visual results are presented and discussed in the paper, from the visualization of individual component planes and trajectory clusters to the mapping of different attributes onto temporal trajectories.
Species Over a Finite Field
Authors: Anthony Henderson
Venue: Journal of Algebraic Combinatorics: An International Journal (2005)

We generalize Joyal's theory of species to the case of functors from the groupoid of finite sets to the category of varieties over Fq. These have cycle index series defined by counting fixed points of twisted Frobenius maps. We give an application to configuration spaces.
A role-based infrastructure management system: design and implementation: Research Articles
Authors: Dongwan Shin, Gail-Joon Ahn, Sangrae Cho, Seunghun Jin
Venue: Concurrency and Computation: Practice Experience (2004)

Over the last decade there has been a tremendous advance in the theory and practice of role-based access control (RBAC). One of the most significant aspects of RBAC can be viewed from its management of permissions on the basis of roles rather than individual users. Consequently, it reduces administrative costs and potential errors. The management of roles in various RBAC implementations, however, tends to be conducted on an ad hoc basis, closely coupled with a certain context of system environments. This paper discusses the development of a system whose purpose is to help manage a valid set of roles with assigned users and permissions for role-based authorization infrastructures. We have designed and implemented the system, called RolePartner. This system enables role administrators to build and configure various components of a RBAC model so as to embody organizational access control policies which can be separated from different enforcement mechanisms. Hence the system helps make it possible to lay a foundation for role-based authorization infrastructures. Three methodological constituents are introduced for our purposes, together with the design and implementation issues. The system has a role-centric view for easily managing constrained and hierarchical roles as well as assigned users and permissions. An LDAP-accessible directory service was used for a role database. We show that the system can be seamlessly integrated with an existing privilege-based authorization infrastructure. Copyright &copy; 2004 John Wiley & Sons, Ltd.
Securing the PlanetLab Distributed Testbed: How to Manage Security in an Environment with No Firewalls, with All Users Having Root, and No Direct Physical Control of Any System
Authors: Paul Brett, Mic Bowman, Jeff Sedayao, Robert Adams, Rob Knauerhause, Aaron Klingaman
Venue: Proceedings of the 18th USENIX conference on System administration (2004)

PlanetLab is a globally distributed network of hosts designed to support the deployment and evaluation of planetary scale applications. Support for planetary applications development poses several security challenges to the team maintaining PlanetLab. The planetary nature of PlanetLab mandates nodes distributed across the globe, far from the physical control of the team. The application development requirements force every user to have access to the equivalent of root on each machine, and use of firewalls is discouraged. If an account is compromised, PlanetLab administrators needed a way to track the actions of users on the nodes. If an entire node is compromised, then the administrators need a way to regain control despite the lack of physical access. Encryption was built into PlanetLab to ensure confidentiality and integrity of system downloads. A special reset packet, combined with keeping a boot CD in the machine, enables PlanetLab system administrators to remotely regain control of machines if they are compromised and return to the nodes into a safe known state. The Linux VServer implementation is used to provide root access to PlanetLab users for development purposes while isolating users from each other. A network abstraction layer provides accounting of traffic and allows safe access to raw sockets. These mechanisms have proven very useful in managing PlanetLab. After a compromise of large numbers of PlanetLab hosts, control of the PlanetLab network was regained in 10 minutes. The compromise spawned a review of PlanetLab security, which pointed out a number of flaws. The need for a central site for maintaining PlanetLab was cited as a key weakness. Future work includes distributing the functions of PlanetLab's central administrative database and improving integrity checks.
Generating Driving Directions for Intelligent Vehicles Interfaces
Authors: Barbara Di Eugenio, Michael J. Trolio
Venue: Proceedings of the 12th IEEE International Conference and Workshops on Engineering of Computer-Based Systems (2005)

Much effort is taking place today to understand the best type of interface between a driver and his/her intelligent vehicle, e.g. the best combination of input / output modalities [1, 2, 3, 5, 6, 13]. In a scenario in which an in-vehicle system answers the driverýs queries perhaps with a mixture of speech and graphical displays such as maps, there is an orthogonal issue that needs to be addressed: of all the information collected to answer the query, how much should be communicated and at what level of detail. In this paper, we discuss a system that provides driving directions (in written form) to a user, and its evaluation. Traditional literature provides an abundance of optimal algorithms that can be applied to a representation of a territory to generate text output for navigating between two arbitrary termini within that territory. In addition to the termini, the output generally consists of the minimal chain of intermediate landmarks and interconnecting roadways. By using simple templates, the algorithm can then realize this "essential" information into text. A prime example is MapQuest, the well-known web-based application (www.mapquest.com) that uses the NavTech geographical database for generating route directions within the United States. The final output, however, lacks the type of cueing that occurs in discourse between two people exchanging route information [4, 16]. In this paper, we show that providing those additional cues improves wayfiding performance: simulated drivers had fewer incorrect turns when following enhanced directions than those following essential directions. We will describe the software system we developed, that can generate both essential and enhanced directios. It consists mainly of 1) a route generator that uses factual map data to generate routes, and 2) a natural language front-end. Using this software system and two sample groups, a single-factor experiment was conducted comparing the effectiveness of essential vs. enhanced form directions in wayfinding. Most notable in the experiment was the difference in incorrect turns, a measure of wayfinding; it approached significance in favor of the experimental group, namely, of the group that read enhanced directions. There were no other significant or marginally significant differences in the other measures we collected. More details on the software system and the experiment described in this paper can be found in [14].
Sensorimotor Control of Biped Locomotion
Authors: Chandana Paul
Venue: Adaptive Behavior - Animals, Animats, Software Agents, Robots, Adaptive Systems (2005)

Human locomotion is extremely adaptive and robust to changes in environment, body size, and morphology. The control of this highly adaptive system is thought to be performed by central pattern generators, supported by a system of sensorimotor connections called reflexes. Several studies on central pattern generators have been conducted, alone and in concert with reflexes. However, controllers based on direct sensorimotor reflexes have not been given much attention, as they have probably been considered too simple for the task of controlling a biped. In this paper, however, we present results to the contrary. It is shown that a purely sensorimotor neural network, that is one with direct connections between sensors and motors can produce gait in an eight degree-of-freedom simulated lower body biped. Further analysis indicates that proprioceptive information is useful but not essential for the control of walking, while cutaneous information is essential. The final experiments show that sensorimotor control of biped walking can be accomplished using a network with only two cutaneous inputs and four neurons. The results suggest that reflexes may play a large role in rhythm generation, in addition to central pattern generators. The results also demonstrate the importance of sensorimotor reflexes in adaptive behavior.
Impact Of External Security Measures On Data Access Implementation With Online Database Management System
Authors: Moses Garuba, Anteneh Girma
Venue: Proceedings of the International Conference on Information Technology: Coding and Computing (ITCC'05) - Volume I - Volume 01 (2005)

The creation and phenomenal growth of the Internet has spawned the emergence of a global information society. The scientific, engineering, and educational communities are all using the internet as an indispensable tool for collaboration and rapid dissemination of information on advances and practice at all levels of scientific and engineering endeavors. Critical national infrastructures supporting such vital areas like banking, communications, and defense are growing progressively more dependent upon internet-based application. All of these benefits that the Internet can provide are subject to disruption by Internet-based cyber attacks that use the speed and global connectivity of the global computer network to cross national boundaries with ease. The local and global implications of an increasingly critical societal dependence on the Internet makes necessary the ability to deter, or to minimize, the effect of cyber attacks, by enhancing the security. The implementation of additional layers to enhance security in either a client/server or online database management system environment does have an impact onthe response time for queries. The research presented in this paper was conducted at Howard University as part of a research project at the graduate school.
Scalable Hardware-Based Multicast Trees
Authors: Salvador Coll, Duato Duato, Fabrizio Petrini, Francisco J. Mora
Venue: Proceedings of the 2003 ACM/IEEE conference on Supercomputing (2003)

This paper presents an algorithm for implementing optimal hardware-based multicast trees, on networks that provide hardware support for collective communication. Although the proposed methodology can be generalized to a wide class of networks, we apply our methodology to the Quadrics network, a state-of-the-art network that provides hardware-based multicast communication. The proposed mechanism is intended to improve the performance of the collective communication patterns on the network, in those cases where the hardware support can not be directly used, for instance, due to some faulty nodes. This scheme provides significant reduction on multicast latencies compared to the original system primitives, which use multicast trees based on unicast communication. A backtracking algorithm to find the optimal solution to the problem is presented. In addition, a greedy algorithm is presented and shown to provide near optimal solutions. Finally, our experimental results show the good performance and scalability of the proposed multicast tree in comparison to the traditional unicast-based multicast trees. Our multicast mechanism doubles barrier synchronization and broadcasts performance when compared to the production-level MPI library.
Hyperbolic conservation laws with space-dependent fluxes: II. general study of numerical fluxes
Authors: Peng Zhang, Ru-Xun Liu
Venue: Journal of Computational and Applied Mathematics (2005)

Following the previous paper, this one continues to study numerical approximations to the space-dependent flux functions in hyperbolic conservation laws. The investigation is based on the wave propagation behavior, Riemann problem, steady flows, hyperbolic properties, cell entropy inequalities, along with such well known numerical fluxes as the Godunov, Local Lax-Friedrichs and Engquist-Osher. All these give rise to correct description for the consistency and monotonicity of numerical fluxes, which ensure properly confined numerical solutions. Numerical examples show that the accordingly designed fluxes resolve discontinuities and smooth solutions very precisely.
An exact algorithm for the elementary shortest path problem with resource constraints: Application to some vehicle routing problems
Venue: Networks (2004)

In this article, we propose a solution procedure for the Elementary Shortest Path Problem with Resource Constraints &lpar;ESPPRC&rpar;. A relaxed version of this problem in which the path does not have to be elementary has been the backbone of a number of solution procedures based on column generation for several important problems, such as vehicle routing and crew pairing. In many cases relaxing the restriction of an elementary path resulted in optimal solutions in a reasonable computation time. However, for a number of other problems, the elementary path restriction has too much impact on the solution to be relaxed or might even be necessary. We propose an exact solution procedure for the ESPPRC, which extends the classical label correcting algorithm originally developed for the relaxed &lpar;nonelementary&rpar; path version of this problem. We present computational experiments of this algorithm for our specific problem and embedded in a column generation scheme for the classical Vehicle Routing Problem with Time Windows. &copy; 2004 Wiley Periodicals, Inc. NETWORKS, Vol. 44&lpar;3&rpar;, 216&ndash;229 2004
An Algorithm of Dynamic Resource Reservation for Multimedia Wireless Communication
Authors: Ying-Hong Wang, Kuo-Jan Tseng, Yi Hsieh
Venue: Proceedings of the 19th International Conference on Advanced Information Networking and Applications - Volume 2 (2005)

Wireless communication that provides voice only is not sufficient to support the necessity of user. In the future, the major of advantage of third generation wireless communication (3G) are providing packet data communication, mobile internet, and mobile multimedia data communication. This kind of data type requires more bandwidth to transmit data. Sometimes, the communication would be encountered the transmitting block because the new cell has no enough resource allocating to Mobile Station (MS or MH) in handoff. How to reduce the losing probability of data packets in wireless communication networks is important things which can raise the Quality of Service (QoS) and degrade the time and resource consume. In this paper, a resource reservation method is proposed to improve QoS and resource switching management to reduce data packet loss for multimedia communication at handoff operation.
k-means projective clustering
Authors: Pankaj K. Agarwal, Nabil H. Mustafa
Venue: Proceedings of the twenty-third ACM SIGMOD-SIGACT-SIGART symposium on Principles of database systems (2004)

In many applications it is desirable to cluster high dimensional data along various subspaces, which we refer to as projective clustering. We propose a new objective function for projective clustering, taking into account the inherent trade-off between the dimension of a subspace and the induced clustering error. We then present an extension of the k-means clustering algorithm for projective clustering in arbitrary subspaces, and also propose techniques to avoid local minima. Unlike previous algorithms, ours can choose the dimension of each cluster independently and automatically. Furthermore, experimental results show that our algorithm is significantly more accurate than the previous approaches.
On the effect of a configuration choice on the performance of a mirrored storage system
Authors: Eitan Bachmat, Tao Kai Lam
Venue: Journal of Parallel and Distributed Computing (2005)

In this paper, we study the effect of various configuration choices on the performance of a mirrored disk array. We introduce a large class of semistructured configurations which provide good seek minimization and bandwidth. We study their properties with respect to both online and offline mirroring algorithms. We also prove a theorem concerning the load balancing capabilities of random or semistructured configurations with several data copies. We show that almost the entire bandwidth of the storage system can be exploited once we increase the number of copies. In an appendix we explain a common error which appears in much of the literature concerning this subject.