ppxscal/embedding_network huggingface dataset:
In Services: Data Management for In Silico Workflows
Authors: Fabricio Nogueira da Silva, Maria Claudia Cavalcanti, Alberto M. R. Davila
Venue: Proceedings of the 17th International Conference on Database and Expert Systems Applications (2006)

Scientific workflows are emerging as a suitable practice to support bioinformatics experiments. Specially, in distributed environments, where workflow steps are located at different sites, workflows can create an independent and interoperable environment between the scientific applications and databases, when combined with the Web Services technology. Web Services have been useful as legacy code wrappers, in order to facilitate distributed workflow definition and orchestration. However, there is an increasing need to address workflow intermediate data management. This work presents the In Services system that provides support for bioinformatics workflows redefinition. This redefinition enables the user to include specific data management services, according to his needs. These services are able to filter, store and retrieve data that are generated in each workflow execution step.
Proceedings of the second international workshop on Computing education research
Venue: International Computing Education Research Workshop (2006)

It is our great pleasure to welcome you to the 2nd International Computing Education Research Workshop, sponsored by the ACM Special Interest Group in Computer Science Education (SIGCSE)---ICER 2006. This second workshop highlights a growing community of computing education researchers and a developing corpus of high-quality research.The call for papers attracted 23 submissions from Australia, Canada, Europe, and the United States. The program committee accepted 13 papers that demonstrate a wide range of methods to ask a variety of different questions about how people come to understand computing. The program begins with a discussion with Thomas R. G. Green, one of the pioneer researchers in computing education research.
Extracting Topic Maps from Web Histories by Clustering with Web Structure and Contents
Authors: Motohiro Mase, Seiji Yamada
Venue: Proceedings of the 2006 IEEE/WIC/ACM international conference on Web Intelligence and Intelligent Agent Technology (2006)

In this paper, we propose a clustering method to extract Topic Maps from the Web browsing history. We improve the structure-based hierarchical clustering method using the contents similarity of the pages and the weight by the types of links and the hierarchical difference of the directories in which the pages are located. The topic maps show the topics that user has seen or not in Web browsing and the relationships between the topics. Using the Web browsing history, we experimentally extract the topic map and evaluate it.
Acquisition-based simulation
Authors: Grant Martin, Jeffrey Schamburg, Michael J. Kwinn,  Jr.
Venue: Proceedings of the 37th conference on Winter simulation (2005)

The Army acquisition community requires high-resolution simulations that represent the dismounted infantry soldier in enough detail to conduct an analysis of alternatives (AOA) for individual weapons and equipment. These models must also be capable of assessing future, proposed capabilities and technologies. Previous work established a detailed, representative set of soldier functions which should be modeled, as well as proposed coordination among three different models. This paper describes the technique used for implementing that coordination on behalf of the acquisition community. It does so in two parts. First, we discuss the methodology used to transforming the needs of the acquisition community into analysis needs. Second, we describe how we integrated the soldier functions into those analysis needs to derive simulation requirements. We will conclude with a discussion of how effective the technique has been in practice.
Decision Trees for Probability Estimation: An Empirical Study
Authors: Han Liang, Harry Zhang, Yuhong Yan
Venue: Proceedings of the 18th IEEE International Conference on Tools with Artificial Intelligence (2006)

Accurate probability estimation generated by learning models is desirable in some practical applications, such as medical diagnosis. In this paper, we empirically study traditional decision-tree learning models and their variants in terms of probability estimation, measured by Conditional Log Likelihood (CLL). Furthermore, we also compare decision tree learning with other kinds of representative learning: na¨ýve Bayes, Na¨ýve Bayes Tree, Bayesian Network, K-Nearest Neighbors and Support Vector Machine with respect to probability estimation. From our experiments, we have several interesting observations. First, among various decision-tree learning models, C4.4 is the best in yielding precise probability estimation measured by CLL, although its performance is not good in terms of other evaluation criteria, such as accuracy and ranking. We provide an explanation for this and reveal the nature of CLL. Second, compared with other popular models, C4.4 achieves the best CLL. Finally, CLL does not dominate another wellestablished relevant measurement AUC (the Area Under the Curve of Receiver Operating Characteristics), which suggests that different decision-tree learning models should be used for different objectives. Our experiments are conducted on the basis of 36 UCI sample sets that cover a wide range of domains and data characteristics. We run all the models within a machine learning platform - Weka.
Aeneid: agent emergent network intrusion detection
Authors: James Cannady
Venue:  (2006)

Computer networks continue to be the targets of numerous types of attacks, which can expose sensitive data or simply deny service to legitimate users. Current intrusion detection technologies utilize signature bases that allow them to rapidly and accurately identify known attacks. This, however, leaves them vulnerable to previously unknown attacks. An adaptive approach, capable of recognizing novel attacks, is warranted. The proposed research presents an adaptive agent-based intrusion detection system. The approach is innovative in several respects: the agents self-organize into a scale-free peer-to-peer network, emergent behavior is facilitated by allowing simple communication between the agents, and the system is adaptive both to recognize new attacks and to the loss of agents, and can withstand the loss of up to 25% of its agents without impairing its functionality. This combination of innovations represents a significant advance in the application of artificial intelligence techniques to intrusion detection.
Parson's programming puzzles: a fun and effective learning tool for first programming courses
Authors: Dale Parsons, Patricia Haden
Venue: Proceedings of the 8th Austalian conference on Computing education - Volume 52 (2006)

Mastery of basic syntactic and logical constructs is an essential part of learning to program. Unfortunately, practice exercises for programming basics can be very tedious, making it difficult to motivate students. In this paper we describe Parson's Programming Puzzles, an automated, interactive tool that provides practice with basic programming principles in an entertaining puzzle-like format. Careful design of the items in the puzzles allows the tutor to highlight particular topics and common programming errors. Since each puzzle solution is a complete sample of well-written code, use of the tool exposes students to good programming practice. This paper discusses the motivation of Parson's Programming Puzzles, and gives several examples. We describe the web-based authoring tool used to build the puzzles, and present our plans for future development.
K-MCore for Multicasting on Mobile Ad Hoc Networks
Authors: Yamin Li, Shietung Peng, Wanming Chu
Venue: Proceedings of the Seventh International Conference on Parallel and Distributed Computing, Applications and Technologies (2006)

A k-cluster of a tree includes a single path and k-1 subpaths growing from that path. A k-MCore is a k-cluster that minimizes the sum of the distances of all vertices to the cluster plus the size of the cluster. This structure is motivated by the applications on overlay multicasting. The overlay multicast protocol constructs a virtual mesh spanning all member nodes of a multicast group. It employs standard unicast routing and forwarding to fulfill multicast functionality. In this paper, we propose effective distributed algorithms for constructing k-MCore on a tree network. The k-MCore is more stable and easier to maintain than the spanning tree in virtual mesh. The simulation results show that our approach handles the flexibility and mobility issues in an overlay multicast protocol effectively, especially when the group size is large.
Validation of the re-design of a manufacturing work cell using simulation
Authors: Carrie Grimard, Jon H. Marvel, Charles R. Standridge
Venue: Proceedings of the 37th conference on Winter simulation (2005)

Simulation can be used to validate the design or redesign of any complex system before it is implemented. Validation evidence is obtained if the simulation demonstrates that the system operation corresponds to its design. This evidence includes comparing both detailed system behavior and performance measure values to those stated in the design. The application of simulation to validating the redesign of an injector assembly and calibration production area is discussed. Simulation is necessary to validate the initial estimate of cell throughput since a single worker must perform multiple operations at multiple workstations. The feasibility of the pattern of movement by this worker between stations must be demonstrated and alternative patterns assessed. Controls on the amount of work in process inventory in the cell must be validated. Modeling challenges unique to part movement using one-piece flow, work in process inventory control, and the movement of both workers and parts are discussed.
The cyclic multi-peg Tower of Hanoi
Authors: Daniel Berend, Amir Sapir
Venue: ACM Transactions on Algorithms (TALG) (2006)

Variants of the classical Tower of Hanoi problem evolved in various directions. Allowing more than 3 pegs, and imposing limitations on the possible moves among the pegs, are two of these. Here, we deal with the case of h&ge;3 pegs arranged on a circle, where moves are allowed only from a peg to the next peg (in the clockwise direction). Unlike the multi-peg problem without restrictions on moves between pegs, the complexity of this variant as a function of the number of disks is exponential. We find explicit lower and upper bounds for its complexity for any h, and show how this complexity can be estimated arbitrarily well for any specific h.
A Camera-Projector System for Robot Positioning by Visual Servoing
Authors: Jordi Pages, Christophe Collewet, Francois Chaumette, Joaquim Salvi
Venue: Proceedings of the 2006 Conference on Computer Vision and Pattern Recognition Workshop (2006)

Positioning a robot with respect to objects by using data provided by a camera is a well known technique called visual servoing. In order to perform a task, the object must exhibit visual features which can be extracted from different points of view. Then, visual servoing is object-dependent as it depends on the object appearance. Therefore, performing the positioning task is not possible in presence of nontextured objets or objets for which extracting visual features is too complex or too costly. This paper proposes a solution to tackle this limitation inherent to the current visual servoing techniques. Our proposal is based on the coded structured light approach as a reliable and fast way to solve the correspondence problem. In this case, a coded light pattern is projected providing robust visual features independently of the object appearance.
Chaotic maps generating white noise
Authors: A. F. Goloubentsev, V. M. Anikin, Y. A. Barulina
Venue: Proceedings of the 2003 International Conference on Physics and Control - Volume 2 (2003)

Some one-dimensional chaotic maps having delta-autocorrelation function are considered. New examples of exact endomophisms generating discrete white noise for a continuous range of a parameter are obtained. They may be treated as generalizations of the Chebyshev polynomial T/sub 2/(x), x /spl epsi/ (-1,1) of the first kind. The using such difference equations may be preferable to construct chaotic generators of pseudorandom sequences.
Computation in networks of passively mobile finite-state sensors
Authors: Dana Angluin, James Aspnes, Zoë Diamadi, Michael J. Fischer, René Peralta
Venue: Distributed Computing (2006)

The computational power of networks of small resource-limited mobile agents is explored. Two new models of computation based on pairwise interactions of finite-state agents in populations of finite but unbounded size are defined. With a fairness condition on interactions, the concept of stable computation of a function or predicate is defined. Protocols are given that stably compute any predicate in the class definable by formulas of Presburger arithmetic, which includes Boolean combinations of threshold-k, majority, and equivalence modulo m. All stably computable predicates are shown to be in NL. Assuming uniform random sampling of interacting pairs yields the model of conjugating automata. Any counter machine with O (1) counters of capacity O (n) can be simulated with high probability by a conjugating automaton in a population of size n. All predicates computable with high probability in this model are shown to be in P; they can also be computed by a randomized logspace machine in exponential time. Several open problems and promising future directions are discussed.
Disruption tolerant shell
Authors: Martin Lukac, Lewis Girod, Deborah Estrin
Venue: Proceedings of the 2006 SIGCOMM workshop on Challenged networks (2006)

Wireless network technology is being applied to a wide range of scientific and engineering problems and across a wide dynamic range of spatial scales. When node placement is constrained by the application (e.g, coupled to sensor placement needs), and can not rely on pre-existing infrastructure (e.g., cellular infrastructure or power-lines), such systems may experience erratic link qualities and intermittent node disconnection. These characteristics, combined with unpredictable environmental conditions, make it difficult to rely upon traditional end to end connections for regular high bandwidth data acquisition and for system management and configuration. We have implemented and deployed such a "challenged network" system of 50 nodes for use by seismologists along a part of the Mesoamerican Subduction Experiment (MASE) broadband seismic array, stretching 500 KM from Acapulco to Tampico through Mexico city. In addition to supporting Delay Tolerant data transfer of relatively high bandwidth seismic data, our system includes a reliable asynchronous remote shell interface (referred to as Disruption Tolerant Shell, DTS) to accomplish the management on these types of system. We present the implementation of this solution and its evaluation on a 13 node portion of the MASE network.
Enabling HPC E-Science via Integrated Grid Infrastructure
Authors: Phil Andrews, Martin Margo, Amit Chourasia, John Towns
Venue: Proceedings of the Second IEEE International Conference on e-Science and Grid Computing (2006)

High Performance Computing E-Science has numerous requirements well in excess of the normal environment sufficient for routine computations. The data requirements in particular may be in the multiterabyte regime, with transfer rates in the several Gb/s or more range. Such data capabilities may only be available at a single location. On the other hand, understanding the data, via data-mining and visualization may require completely different facilities, while the actual data production may be only possible at yet a third location. The use of Global File System with multi-Gb/s speeds and hundreds of TeraBytes capacity can help the scientific researchers, but the simultaneous utilization of several systems also requires a reasonably sophisticated co-scheduling capability. In this paper, we show how the TeraGrid is combining massive computational clusters, a Global File System, very powerful visualization systems, and a co-scheduler to enable massive E-Science in a very coordinated and usable manner.
Human Carrying Status in Visual Surveillance
Authors: Dacheng Tao, Xuelong Li, Stephen J. Maybank, Xindong Wu
Venue: Proceedings of the 2006 IEEE Computer Society Conference on Computer Vision and Pattern Recognition - Volume 2 (2006)

A person's gait changes when he or she is carrying an object such as a bag, suitcase or rucksack. As a result, human identification and tracking are made more difficult because the averaged gait image is too simple to represent the carrying status. Therefore, in this paper we first introduce a set of Gabor based human gait appearance models, because Gabor functions are similar to the receptive field profiles in the mammalian cortical simple cells. The very high dimensionality of the feature space makes training difficult. In order to solve this problem we propose a general tensor discriminant analysis (GTDA), which seamlessly incorporates the object (Gabor based human gait appearance model) structure information as a natural constraint. GTDA differs from the previous tensor based discriminant analysis methods in that the training converges. Existing methods fail to converge in the training stage. This makes them unsuitable for practical tasks. Experiments are carried out on the USF baseline data set to recognize a human's ID from the gait silhouette. The proposed Gabor gait incorporated with GTDA is demonstrated to significantly outperform the existing appearance-based methods.
With J: the Hodge Podge machine
Authors: Cliff Reiter
Venue: ACM SIGAPL APL Quote Quad (2004)

Cellular automata are collections of cells arranged in some manner such that each cell contains a value that is updated from generation to generation according to a local rule. The Game of Life [1-5,7,15] is perhaps the best known cellular automaton. It is based upon a rectangular arrangement of cells that are either 0 or 1, along with simple rules of evolution: if a cell is 0 and has exactly 3 immediate neighbors then it becomes a 1; if a cell is 0 and has exactly 2 or 3 immediate neighbors that are 1, then the cell remains 1; otherwise, the cell becomes or remains 0. The Game of Life is incredibly intriguing, giving rise to complex behavior that is visually stimulating, mathematically interesting and, moreover, it is known to be capable of universal computation. Despite the fact that at a basic level it was designed to model alive and dead cells, it is primarily a toy model in the sense that it does not model any physical behavior well.
Covert Reorienting and Inhibition of Return: An Event-Related fMRI Study
Authors: Jöran Lepsien, Stefan Pollmann
Venue: Journal of Cognitive Neuroscience (2002)

Using event-related fMRI, we analyzed the functional neuroanatomy of covert reorienting and inhibition of return (IOR). Covert reorienting to a target appearing within 250 msec after an invalid contralateral location cue elicited increased activation in the left fronto-polar cortex (LFPC), right anterior and left posterior middle frontal gyrus, and right cerebellum, areas that have previously been associated with attentional processes, specifically attentional change. In contrast, IOR, which leads to prolonged response times to targets that appear at the cued location at a stimulus-onset-asynchrony (SOA)>250 msec, was accompanied by increased activation in brain areas involved in oculomotor programming, such as the right medial frontal gyrus (supplementary eye field; SEF) and the right inferior precentral sulcus (frontal eye field; FEF), supporting the oculomotor bias theory of IOR. Pre-SEF and pre-FEF areas were involved both in covert reorienting and IOR. The supramarginal gyri were bilaterally involved in IOR, with the right supramarginal gyrus additionally involved in covert reorienting.
Towards user-friendly mobile browsing
Authors: Timo Lehtonen, Said Benamar, Vesa Laamanen, Ilkka Luoma, Olli Ruotsalainen, Jaakko Salonen, Tommi MikkonenP
Venue: Proceedings of the 2nd international workshop on Advanced architectures and algorithms for internet delivery and applications (2006)

User experience of Web browsing on a mobile device is affected by low bandwidth, low CPU performance and small screen. This is not an essential technical restriction, as some help can be provided by running the browser engine on the server side instead of the mobile client. The approach of Tut-Mobi system introduced in this paper is such that the server side component residing in the fixed network processes the page to a format that consists of page miniature and page element data. Using this method, it is possible to save up to 90 percent of bandwidth, which makes navigating the web pages a considerably faster. This allows practical browsing of complex web pages even with a mobile device. Moreover, user experience is better, because the original layout of the page is saved which makes it easy to browse familiar sites.
Etudes in non-interactive zero-knowledge
Authors: Abhi Shelat
Venue:  (2005)

IN A ZERO-KNOWLEDGE PROOF [GMR85], Prover interactively convinces Verifier that theorem &pi; is true in such a way that (a) a corrupt Prover cannot convince Verifier of a false theorem and (b) a corrupt Verifier cannot "learn" anything other than the fact that &pi; is true. In a NON-INTERACTIVE ZERO-KNOWLEDGE PROOF [BFM 88], the Prover must do the above by sending only a single message to Verifier! To make this possible, Prover and Verifier are not tabula rasa, but rather born with some setup information. Much in the fashion of a musical &Eacute;TUDE, in this thesis, we explore several variations on the setup assumptions for non-interactive zero-knowledge in order to enjoy a richer understanding. Our labor brings forth: (1) various unconditional characterizations of computational and statistical NIZK proofs, (2) new constructions that have practical applications to non-malleable encryption and CCA2 encryption, (3) new constructions which form the building blocks of "fair" versions of interactive zero-knowledge and collusion-free multi-party computation protocols, (4) and conceptual contributions which underlie the recent works on how cryptography can be used to achieve equilibrium in game theory. (Copies available exclusively from MIT Libraries, Rm. 14-0551, Cambridge, MA 02139-4307. Ph. 617-253-5668; Fax 617-253-1690.)
Virtual disk based centralized management for enterprise networks
Authors: Yuezhi Zhou, Yaoxue Zhang, Yinglian Xie
Venue: Proceedings of the 2006 SIGCOMM workshop on Internet network management (2006)

The rapid advances in hardware, software, and networks have made the management of enterprise network systems an increasingly challenging task. Due to the tight coupling between hardware, software, and data, every one of the hundreds or thousands of PCs that are connected in an enterprise environment has to be administered individually, leading to high Total Cost of Ownership (TCO). We argue that centralized management with distributed, diskless clients, yet centralized repositories of all software and data can reduce the management complexity with reduced software maintenance time, improved system availability, and enhanced security. We instantiate such paradigm with a diskless, thick client based system that supports heterogeneous OSes including Windows---the dominant commodity OS in the current market. The prototype requires no or minimum OS modification, nor application modification. Our initial deployment and experiment results demonstrate that our approach is a feasible and efficient solution for managing enterprise network systems.
A random construction for permutation codes and the covering radius
Authors: Peter Keevash, Cheng Yeaw Ku
Venue: Designs, Codes and Cryptography (2006)

We analyse a probabilistic argument that gives a semi-random construction for a permutation code on n symbols with distance n ¿ s and size ¿(s!(log n)1/2), and a bound on the covering radius for sets of permutations in terms of a certain frequency parameter.