ppxscal/embedding_network huggingface dataset:
Visualization of Lattice-Based Protein Folding Simulations
Authors: Sebastian Potzsch, Gerik Scheuermann, Peter F. Stadler, Michael T. Wolfinger, Christoph Flamm
Venue: Proceedings of the conference on Information Visualization (2006)

Analysis of the spatial structure of proteins including folding processes is a challenge for modern bioinformatics. Due to limited experimental access to folding processes, computer simulations are a standard approach. Since realistic continuous (all-atom) simulations are far too expensive, lattice based protein folding simulations are a common coarse-graining. In this paper, we present a visualization tool for lattice based protein folding simulations. The system is based on Shneiderman's mantra "Overview first, zoom and filter, details on demand" and uses a collection of information visualization techniques including multiple views, focus+context and table lenses which have been tailored towards our data. We demonstrate the potential of information visualization techniques for providing insight into such simulations.
Measurement of a Translation and a Rotation of a Tooth after an Orthodontic Treatment Using GA
Authors: S. Nakajima, H. Arimoto H. Rensha, T. Toriu
Venue: Proceedings of the First International Conference on Innovative Computing, Information and Control - Volume 1 (2006)

The purpose of our study is measurement of the value of the translation and the rotation between the corresponding teeth of digital dental models before and after an orthodontic treatment. We used digital models from plaster models digitized by 3D scanner, and divide the polygons into several teeth using our original GUI. We measured the distance from a polygon in the jaw before the treatment to the nearest polygon in the after jaw and consider the distance as a fitness value. We got the best motion (translation and rotation) parameters using GA and reported them as the measurement of the tooth motion after the treatment. And we checked the accuracy of the result.
SemCrypt - Ensuring Privacy of Electronic Documents Through Semantic-Based Encrypted Query Processing
Authors: Michael Schrefl, Katharina Grun, Jurgen Dorn
Venue: Proceedings of the 21st International Conference on Data Engineering Workshops (2005)

The trend towards outsourcing increases the number of documents stored at external service providers. This storage model, however, raises privacy and security concerns because the service providers cannot be trusted with respect to maintaining the privacy of the documents. The research project SemCrypt^1 explores techniques for processing queries and updates over encrypted XML documents stored at untrusted servers. By performing encryption and decryption only on the client and not on the server, SemCrypt guarantees that neither the document structure nor the document content are disclosed on the server. Filtering query results and processing as much as possible of the query/update statement on the server does not depend on special encryption techniques. Instead, the chosen approach exploits the structural semantics of XML documents and uses standard, well-proven encryption techniques. SemCrypt thus enables to query and update encrypted XML documents on untrusted servers while ensuring data privacy.
TouchSync: Lightweight Synchronization for Ad-Hoc Mobile Collaboration
Authors: Vassil Roussev, Gabriel Perez Priego, Golden G. III Richard
Venue: Proceedings of the International Symposium on Collaborative Technologies and Systems (2006)

For current generation of PDA and smart phone devices, wireless capabilities are practically a standard feature. Consequently, they should be able to support users in their spontaneous daily interactions. Yet, the original host-centric model of data synchronization is still entrenched, thereby depriving users of adequate support for ad-hoc collaboration. In our view, what is needed is a more relaxed and intuitive sharing model that reflects the semistructured nature of informal user interactions. We present TouchSynca lightweight framework that allows users to easily form an ad-hoc group and automatically share data on their devices. The framework provides a flexible sharing mechanism that allows various single-user applications to be easily adapted for collaboration. Adapted applications completely retain their original user interaction functions, while the infrastructure provides generic collaboration tools for session management and privacy control. We discuss both the overall design of the framework and an implementation for PalmOS and Bluetooth. We also present implementation results from the adaptation of three common applications to support meetings.
Concepts for Cooperative Knowledge Spaces in Mathematics and Natural Sciences
Authors: Sabine Cikic, Uwe Sinha, Sabina Jeschke
Venue: Proceedings of the 2006 International Conference on Cyberworlds (2006)

Cooperative knowledge spaces have a high potential to improve eLTR (eLearning, eTeaching and eResearch) at universities. Since there are few implementations deployed, notably in the fields of mathematics, natural sciences, and engineering, we propose a concept for field-specific knowledge spaces for those disciplines - "ViCToR"-Spaces (Virtual Cooperation in Teaching and Research for Mathematics, Natural Sciences and Engineering). ViCToR-Spaces present novel collaborative working environments for knowledge gain and research, supporting well-established forms of scientific and technological cooperation without geographical or technological boundaries. In this article, we will describe the requirements for ViCToR-Spaces, the components that are already available, and further developments.
Route planning and threat avoidance through cognitive robotics
Authors: Brad Best
Venue: Proceedings of the 36th conference on Winter simulation (2004)

This simulation case study demonstrates the use of the ACT-R cognitive modeling framework for robotic control in a real environment and virtual avatar control in a virtual environment. The model performs spatial tasks ranging from simple mobility and obstacle avoidance to more complex behaviors such as route planning while avoiding threats.
MUSHI: a multi-device framework for collaborative inquiry learning
Authors: Leilah Lyons, Joseph Lee, Christopher Quintana, Elliot Soloway
Venue: Proceedings of the 7th international conference on Learning sciences (2006)

We present the MUSHI (Multi-User Simulation with Handheld Integration) framework, which was designed to support middle and high school students in the acquisition of scientific concepts rooted in complex, multi-scalar phenomena. In designing a learning environment that is conducive to collaborative inquiry learning, we have combined a dynamic simulation with wirelessly-connected handheld devices. This is a novel use of technology, so we first had to ensure that this new multi-device paradigm would not, via extraneous cognitive load, interfere with inquiry learning tasks. In this pilot study, we confirmed that the multi-device interface can be used by the lower age range of our target demographic, and that its use does not impair the execution of inquiry learning tasks of the sort we have designed for the learning environment. We also observed the collaborative behaviors that naturally emerged from the use of MUSHI, to develop recommendations for scaffolding collaborative inquiry tasks.
An Event-related Neuroimaging Study Distinguishing Form and Content in Sentence Processing
Authors: W. Ni, R. T. Constable, W. E. Mencl, K. R. Pugh, R. K. Fulbright, S. E. Shaywitz, B. A. Shaywitz, J. C. Gore, D. Shankweiler
Venue: Journal of Cognitive Neuroscience (2000)

Two coordinated experiments using functional Magnetic Resonance Imaging (fMRI) investigated whether the brain represents language form (grammatical structure) separately from its meaning content (semantics). While in the scanner, 14 young, unimpaired adults listened to simple sentences that were either nonanomalous or contained a grammatical error (for example, *Trees can grew.), or a semantic anomaly (for example, *Trees can eat.). A same/different tone pitch judgment task provided a baseline that isolated brain activity associated with linguistic processing from background activity generated by attention to the task and analysis of the auditory input. Sites selectively activated by sentence processing were found in both hemispheres in inferior frontal, middle, and superior frontal, superior temporal, and temporo-parietal regions. Effects of syntactic and semantic anomalies were differentiated by some nonoverlapping areas of activation: Syntactic anomaly triggered significantly increased activity in and around Broca&rsquo;s area, whereas semantic anomaly activated several other sites anteriorly and posteriorly, among them Wernicke&rsquo;s area. These dissociations occurred when listeners were not required to attend to the anomaly. The results confirm that linguistic operations in sentence processing can be isolated from nonlinguistic operations and support the hypothesis of a specialization for syntactic processing.
A Novel Stochastic Algorithm for Scheduling QoS-Constrained Workflows in a Web Service-Oriented Grid
Authors: Yash Patel, John Darlington
Venue: Proceedings of the 2006 IEEE/WIC/ACM international conference on Web Intelligence and Intelligent Agent Technology (2006)

The success of web services has influenced the way in which Grid applications are being written. Grid users often submit their applications in the form of workflows with certain Quality of Service (QoS) requirements imposed on the workflows. These workflows detail the composition of web services and the level of service required from the Grid. This paper addresses scheduling technique, which aims to satisfy QoS requirements of Grid workflows with a sufficient guarantee. We model a web service as a G/G/k queue and obtain scheduling solutions for workflow tasks by solving an ILP (Integer Linear Program), which is the traditional method. We further develop a novel 2-stage stochastic program, which is capable of dealing with the volatile nature of the Grid and adapting the selection of the services during the lifetime of the workflows. We also present a stochastic algorithm which obtains scheduling solutions for workflow tasks. We present experimental results comparing our approaches, showing that the 2-stage stochastic programming approach performs consistently better than other traditional approaches.
Dependable Multithreaded Processing Using Runtime Validation
Authors: Kaiyu Chen, Sharad Malik
Venue: Proceedings of the 12th Pacific Rim International Symposium on Dependable Computing (2006)

Modern processors face growing verification and reliability challenges posed by increasing microarchitecture complexity and aggressive technology scaling. While viable approaches have been proposed to address these challenges in the context of uniprocessors, little work has been done for emerging multithreaded processors. Multithreading raises new issues for validation due to inter-thread interactions and inherent complexity of the underlying hardware. We propose an extension of the DIVA approach [1], which employs a simple checker processor to effectively validate the complex superscalar processor, to perform instructionlevel runtime validation for both intra-thread and interthread correctness properties for multithreaded execution. We present the validation methodology using a representative simultaneous-multithreaded (SMT) architecture, and briefly discuss its general applicability to other forms of multithreading. Detailed timing simulation shows this solution has low performance penalty, while providing general robustness against both operational and functional errors with relatively small hardware overhead.
Brain Activity during Episodic Retrieval of Autobiographical and Laboratory Events: An fMRI Study using a Novel Photo Paradigm
Authors: Roberto Cabeza, Steve E. Prince, Sander M. Daselaar, Daniel L. Greenberg, Matthew Budde, Florin Dolcos, Kevin S. Labar, David C. Rubin
Venue: Journal of Cognitive Neuroscience (2004)

Functional neuroimaging studies of episodic memory retrieval generally measure brain activity while participants remember items encountered in the laboratory (''controlled laboratory condition'') or events from their own life (''open autobiographical condition''). Differences in activation between these conditions may reflect differences in retrieval processes, memory remoteness, emotional content, retrieval success, self-referential processing, visual/spatial memory, and recollection. To clarify the nature of these differences, a functional MRI study was conducted using a novel ''photo paradigm,'' which allows greater control over the autobiographical condition, including a measure of retrieval accuracy. Undergraduate students took photos in specified campus locations (''controlled autobiographical condition''), viewed in the laboratory similar photos taken by other participants (controlled laboratory condition), and were then scanned while recognizing the two kinds of photos. Both conditions activated a common episodic memory network that included medial temporal and prefrontal regions. Compared with the controlled laboratory condition, the controlled autobiographical condition elicited greater activity in regions associated with self-referential processing (medial prefrontal cortex), visual/spatial memory (visual and parahippocampal regions), and recollection (hippocampus). The photo paradigm provides a way of investigating the functional neuroanatomy of real-life episodic memory under rigorous experimental control.
A Protocol for Secure Content Distribution in Pure P2P Networks
Authors: Esther Palomar, Juan M. Estevez-Tapiador, Julio C. Hernandez-Castro, Arturo Ribagorda
Venue: Proceedings of the 17th International Conference on Database and Expert Systems Applications (2006)

A significant challenge for Peer-to-Peer (P2P) systems is maintaining the correctness and consistency of their global data structures and shared contents as peers independently and unpredictably join and leave the system. In such networks, it is necessary that some security mechanisms will be applied with the aim of avoiding attacks based on nonauthorized content modifications. In this paper, we propose a content authentication protocol for pure P2P networks. The scheme also incorporates a rational content access procedure based on proofs of computational effort. Our proposal relies on a set of peers playing the role of a certification authority, since it is unrealistic to assume that appropriate trusted third parties can be deployed in such environments.
Status and Perspective of Intelligent System Design Automation
Authors: Andreas Konig
Venue: Proceedings of the Sixth International Conference on Hybrid Intelligent Systems (2006)

Intelligent systems have become both ubiquitous and more and more powerful and complex in the last decade. They base on an increasing variety of sensorial input, hybrid algorithms, and integrated, electronic embodiment. In particular, with the rapid advance of wireless and low-power implementation, new application fields, such as sensor networks or ambient intelligence gain momentum. While efficient design techniques are well established for microtechnique and -electronic system realization, the heart of an intelligent system, i.e., the structure from sensorial input to decision making, is still predominantly assembled in an expert driven, manual way. This represents a tedious, labor-intensive approach, which tends to end in locally optimal solutions due to the restricted covering of the potential search space implied by the problem and available sensors and algorithms. Consequently, the challenge of automated intelligent system design has been picked up exploiting obvious techniques from machine learning, i.e., neural networks, and more general optimization techniques based on appropriate assessment and optimization. The latter approach in particular is applied together with classical and advanced multi-dimensional signal processing. The talk will summarize important work contributed to that emerging field. The importance of hybrid approaches, including evolutionary optimization techniques, for effective and efficient, feasible system designs under embedding/integration constraints, e.g., power dissipation, will be pointed out. Then a proprietary approach and design methodology developed in the last nine years will be presented and demonstrated by examples from vision and other sensorial application systems. In addition to the obvious rapid-prototyping benefit, this approach and the underlying learning architecture together with appropriate hardware platforms offers improved robustness and fault-tolerance.
Coverage and connectivity in three-dimensional networks
Authors: S. M. Nazrul Alam, Zygmunt J. Haas
Venue: Proceedings of the 12th annual international conference on Mobile computing and networking (2006)

Although most wireless terrestrial networks are based on two-dimensional (2D) design, in reality, such networks operate in three-dimensions (3D). Since most often the size (i.e., the length and the width) of such terrestrial networks is significantly larger than the differences in the third dimension (i.e., the height) of the nodes, the 2D assumption is somewhat justified and usually it does not lead to major inaccuracies. However, in some environments, this is not the case; the underwater, atmospheric, or space communications being such apparent examples. In fact, recent interest in underwater acoustic ad hoc and sensor networks hints at the need to understand how to design networks in 3D. Unfortunately, the design of 3D networks is surprisingly more difficult than the design of 2D networks. For example, proofs of Kelvin's conjecture and Kepler's conjecture required centuries of research to achieve breakthroughs, whereas their 2D counterparts are trivial to solve. In this paper, we consider the coverage and connectivity issues of 3D networks, where the goal is to find a node placement strategy with 100% sensing coverage of a 3D space, while minimizing the number of nodes required for surveillance. Our results indicate that the use of the Voronoi tessellation of 3D space to create truncated octahedral cells results in the best strategy. In this truncated octahedron placement strategy, the transmission range must be at least 1.7889 times the sensing range in order to maintain connectivity among nodes. If the transmission range is between 1.4142 and 1.7889 times the sensing range, then a hexagonal prism placement strategy or a rhombic dodecahedron placement strategy should be used. Although the required number of nodes in the hexagonal prism and the rhombic dodecahedron placement strategies is the same, this number is 43.25% higher than the number of nodes required by the truncated octahedron placement strategy. We verify by simulation that our placement strategies indeed guarantee ubiquitous coverage. We believe that our approach and our results presented in this paper could be used for extending the processes of 2D network design to 3D networks.
Adding Semantics to Email Clustering
Authors: Hua Li, Dou Shen, Benyu Zhang, Zheng Chen, Qiang Yang
Venue: Proceedings of the Sixth International Conference on Data Mining (2006)

This paper presents a novel algorithm to cluster emails according to their contents and the sentence styles of their subject lines. In our algorithm, natural language processing techniques and frequent itemset mining techniques are utilized to automatically generate meaningful generalized sentence patterns (GSPs) from subjects of emails. Then we put forward a novel unsupervised approach which treats GSPs as pseudo class labels and conduct email clustering in a supervised manner, although no human labeling is involved. Our proposed algorithm is not only expected to improve the clustering performance, it can also provide meaningful descriptions of the resulted clusters by the GSPs. Experimental results on open dataset (Enron email dataset) and a personal email dataset collected by ourselves demonstrate that the proposed algorithm outperforms the K-means algorithm in terms of the popular measurement F1. Furthermore, the cluster naming readability is improved by 68.5% on the personal email dataset.
Temporal Data Mining in Dynamic Feature Spaces
Authors: Brent Wenerstrom, Christophe Giraud-Carrier
Venue: Proceedings of the Sixth International Conference on Data Mining (2006)

Many interesting real-world applications for temporal data mining are hindered by concept drift. One particular form of concept drift is characterized by changes to the underlying feature space. Seemingly little has been done in this area. This paper presents FAE, an incremental ensemble approach to mining data subject to such concept drift. Empirical results on large data streams demonstrate promise.
Numerical Computations in US Undergraduate Physics Courses
Authors: Robert G. Fuller
Venue: Computing in Science and Engineering (2006)

A recent study using email and Web surveys gathered responses from physics faculty members across the US about their use of numerical computations in the classroom. Responses showed a strong commitment to computational activities from some physics faculty, and a frustration over the lack of such activities from others.
A role-based analysis model for the evaluation of novices' programming knowledge development
Authors: Pauli Byckling, Jorma Sajaniemi
Venue: Proceedings of the second international workshop on Computing education research (2006)

The development of high level programming knowledge is not well known and there are no direct techniques to evaluate and measure it. Measurement of programming skills is mostly based on the evaluation of programs written by students but the final programs do not reveal the correctness of students' mental models of programming concepts. This paper presents a new analysis model that can be used to evaluate students' mental models based on their program writing protocols with three different measures. The analysis model is based on the concept of roles of variables and extends the methodology of Rist's theory of schema expansion in programming but has a better coverage and is more finely grained than Rist's model. This paper also reports a study in which the applicability and the general validity of the model was studied by following the emergence of novice students' programming knowledge during their first programming course. The results suggest that the model is generally applicable for analyzing programming knowledge in novice level and that the three measures can be applied when focusing on different aspects of this knowledge.
Here Be Dragons
Authors: Fred B. Schneider
Venue: IEEE Security and Privacy (2006)

This isn't the first time we've been told that the world is flat. In ancient times, ships that set sail for new worlds either returned or didn't: those that returned hadn't sailed far enough, and those that didn't must have sailed over the edge and fallen off, where, as popular belief held, dragons awaited them.
Time-Free and Timer-Based Assumptions Can Be Combined to Obtain Eventual Leadership
Authors: Achour Mostefaoui, Michel Raynal, Corentin Travers
Venue: IEEE Transactions on Parallel and Distributed Systems (2006)

Leader-based protocols rest on a primitive able to provide the processes with the same unique leader. Such protocols are very common in distributed computing to solve synchronization or coordination problems. Unfortunately, providing such a primitive is far from being trivial in asynchronous distributed systems prone to process crashes. (It is even impossible in fault-prone purely asynchronous systems.) To circumvent this difficulty, several protocols have been proposed that build a leader facility on top of an asynchronous distributed system enriched with additional assumptions. The protocols proposed so far consider either additional assumptions based on synchrony or additional assumptions on the pattern of the messages that are exchanged. Considering systems with n processes and up to f process crashes, 1\leq f