ppxscal/embedding_network huggingface dataset:
Fast, small and reliable self-assembly
Authors: Ashish Goel
Venue:  (2005)

Self-assembly is an emerging computing paradigm potentially useful in fields that range from electronics and nanorobotics to biology. A promising approach for designing and building practical Self-assembly systems in the lab is to combine carefully designed DNA molecules [21, 22, 18]. In addition to all the practical problems to be solved in the lab, the design of Self-assembly systems seems to require to consider higher level issues. These considerations are analogous to designing and analyzing algorithms. Self-assembly can be thought of as a program running on a digital computer [12, 14, 20, 15, 16, 3, 4]. We can try to optimize Self-assembly systems, as we can try to optimize conventional programs. Another aspect to be considered is robustness. Lab experiments suggest that error detection and/or correction mechanisms are needed. We show that the problem of optimizing for space is NP-complete in the Tile Assembly model. We describe how to analyze the running time for some families of Self-assembly systems, such as partial-order systems. We conjecture that optimizing for time by selecting concentrations functions is #P-hard and we show approximation techniques that allow efficient optimizations. We define invadable systems in the Tile assembly model, that allow error correction based on strand invasion. We show an efficient counter construction that solves an open problem formulated in [3]. We describe progress towards finding an optimal size counter. We describe the mixers systems model of Self-assembly, which is based on differential equations. The mixer systems is a generalization of Reaction-networks, introduced by Martin Feinberg [9]. We prove basic properties of this new model related to the range of their solutions and about the existence of nontrivial polynomial conservation laws.
Augmenting Existing Virtual Environments with Plausible Naturalistic Clutter
Authors: R. A. Broughton, T. L. J. Howard
Venue: Proceedings of the 2005 International Conference on Cyberworlds (2005)

We present an approach for enriching a Virtual Environment by augmenting it with the kind of naturalistic clutter often found in real-world scenes. Rather than manually specifying clutter distribution, our semi-automatic procedural approach seeks to add plausible clutter with minimal user-interaction, and few constraints on the format in which the Virtual Environment is specified. We suggest that the integration of suitable and plausible clutter to a Virtual Environment increases realism at low cost.
Protecting TFRC from a Selfish Receiver
Authors: Manfred Georg, Sergey Gorinsky
Venue: Proceedings of the Joint International Conference on Autonomic and Autonomous Systems and International Conference on Networking and Services (2005)

This paper examines operation of TFRC (TCP-Friendly Rate Control) in scenarios where the receiver is untrustworthy and can misbehave to receive data at an unfairly high rate at the expense of competing traffic. Several attacks are considered for a selfish receiver to take advantage of TFRC. After confirming experimentally that the identified receiver attacks are effective, we design Robust TCP-Friendly Rate Control (RTFRC), a TFRC variant resilient to the attacks. We also show that additional attacks targeted directly at RTFRC are unable to compromise the protocol.
Iterative Image Restoration Combining Total Variation Minimization and a Second-Order Functional
Authors: Marius Lysaker, Xue-Cheng Tai
Venue: International Journal of Computer Vision (2006)

A noise removal technique using partial differential equations (PDEs) is proposed here. It combines the Total Variational (TV) filter with a fourth-order PDE filter. The combined technique is able to preserve edges and at the same time avoid the staircase effect in smooth regions. A weighting function is used in an iterative way to combine the solutions of the TV-filter and the fourth-order filter. Numerical experiments confirm that the new method is able to use less restrictive time step than the fourth-order filter. Numerical examples using images with objects consisting of edge, flat and intermediate regions illustrate advantages of the proposed model.
Visualization of Graphs with Associated Timeseries Data
Authors: Purvi Saraiya, Peter Lee, Chris North
Venue: Proceedings of the Proceedings of the 2005 IEEE Symposium on Information Visualization (2005)

The most common approach to support analysis of graphs with associated time series data include: overlay of data on graph vertices for one timepoint at a time by manipulating a visual property (e.g. color) of the vertex, along with sliders or some such mechanism to animate the graph for other timepoints. Alternatively, data from all the timepoints can be overlaid simultaneously by embedding small charts into graph vertices. These graph visualizations may also be linked to other visualizations (e.g., parallel co-ordinates) using brushing and linking. This paper describes a study performed to evaluate and rank graph+timeseries visualization options based on users' performance time and accuracy of responses on predefined tasks. The results suggest that overlaying data on graph vertices one timepoint at a time may lead to more accurate performance for tasks involving analysis of a graph at a single timepoint, and comparisons between graph vertices for two distinct timepoints. Overlaying data simultaneously for all the timepoints on graph vertices may lead to more accurate and faster performance for tasks involving searching for outlier vertices displaying different behavior than the rest of the graph vertices for all timepoints. Single views have advantage over multiple views on tasks that require topological information. Also, the number of attributes displayed on nodes has a non trivial influence on accuracy of responses, whereas the number of visualizations affect the performance time.
ViCAT: Visualisation and Interaction on a Collaborative Access Table
Authors: Fang Chen, Peter Eades, Julien Epps, Serge Lichman, Benjamin Close, Peter Hutterer, Masa Takatsuka, Bruce Thomas, Mike Wu
Venue: Proceedings of the First IEEE International Workshop on Horizontal Interactive Human-Computer Systems (2006)

Despite many years of research in the area of human-computer interaction, there are still remarkably few computing platforms in existence that permit remote collaboration over various software applications in an intense manner. Visualisation and Interaction on a Collaborative Access Table (ViCAT) is a new project whose aim is to allow intense collaboration between multiple users at multiple remotely located sites, as if the users were gathered around a physical table. This paper introduces the ViCAT design philosophy and how it addresses the mixed presence groupware concept, and then describes the relationship between the ViCAT project and current horizontal interactive human-computer systems research.
Evolving agents for network centric warfare
Authors: Ang Yang, Hussein A. Abbass, Ruhul Sarker
Venue: Proceedings of the 2005 workshops on Genetic and evolutionary computation (2005)

The advances in information technology largely influence our life style in various aspects. The changes in the underlying economics, information technology, business processes and organizations are affecting the very character of war and are leading to the fundamental shift from platform-centric warfare to network centric warfare (NCW), also known as network centric operation (NCO) [1]. Since its emergence in 1983 [10], the debate between proponents and opponents is hotly continuous. The proponents suggest that networked entities may produce information superiority, which in turn dramatically increases combat power. The theory that power is increasingly derived from information sharing, knowledge sharing and command speeding up has been supported by results of recent military operational experience [4]. The advantages of NCW have been recognized as:Small-size networked forces can perform missions effectively at a lower cost;
Q-learning of sequential attention for visual object recognition from informative local descriptors
Authors: Lucas Paletta, Gerald Fritz, Christin Seifert
Venue: Proceedings of the 22nd international conference on Machine learning (2005)

This work provides a framework for learning sequential attention in real-world visual object recognition, using an architecture of three processing stages. The first stage rejects irrelevant local descriptors based on an information theoretic saliency measure, providing candidates for foci of interest (FOI). The second stage investigates the information in the FOI using a codebook matcher and providing weak object hypotheses. The third stage integrates local information via shifts of attention, resulting in chains of descriptor-action pairs that characterize object discrimination. A Q-learner adapts then from explorative search and evaluative feedback from entropy decreases on the attention sequences, eventually prioritizing shifts that lead to a geometry of descriptor-action scanpaths that is highly discriminative with respect to object recognition. The methodology is successfully evaluated on indoors (COIL-20 database) and outdoors (TSG-20 database) imagery, demonstrating significant impact by learning, outperforming standard local descriptor based methods both in recognition accuracy and processing time.
The Social Side of Services
Authors: Steve Vinoski
Venue: IEEE Internet Computing (2006)

In addition to the technical issues you'll face with SOA, nontechnical factors have a far greater influence on project success than technologists care to admit.
Design and evaluation of activity model-based groupware: methodological issues
Authors: Nadia Gauducheau, Eddie Soulier, Myriam Lewkowicz
Venue: Proceedings of the 14th IEEE International Workshops on Enabling Technologies: Infrastructure for Collaborative Enterprise (2005)

This article presents methodological issues on evaluation related to the design process of the tool being evaluated. We emphasize the different variables which are important to take into account, and the links between them. We illustrate our approach with the presentation of a groupware for collective sensemaking (Sum'it Up) based on a theoretical activity model coming from social sciences, and a first evaluation of this groupware.
Segmentation of Connected Handwritten Numerals by Graph Representation
Authors: Misako Suwa
Venue: Proceedings of the Eighth International Conference on Document Analysis and Recognition (2005)

This paper proposes a new algorithm for separating a touching pair of digits by using the graphrepresentation of the pattern. The segmentation can be regarded as grouping these edges and vertices into two disconnected sub-graphs. This process is executed by applying graph theory methods and certain heuristic rules. Since the boundaries of patterns are determined along the edges, the shapes of the segmented digits can be restored with high quality. The algorithm can segment not only simply connected cases but also multiply connected ones. The results of the performance evaluation using the NIST database are also presented.
Model Checking An Entire Linux Distribution for Security Violations
Authors: Benjamin Schwarz, Hao Chen, David Wagner, Jeremy Lin, Wei Tu, Geoff Morrison, Jacob West
Venue: Proceedings of the 21st Annual Computer Security Applications Conference (2005)

Software model checking has become a popular tool for verifying programs' behavior. Recent results suggest that it is viable for finding and eradicating security bugs quickly. However, even state-of-the-art model checkers are limited in use when they report an overwhelming number of false positives, or when their lengthy running time dwarfs other software development processes. In this paper we report our experiences with software model checking for security properties on an extremely large scale-an entire Linux distribution consisting of 839 packages and 60 million lines of code. To date, we have discovered 108 exploitable bugs. Our results indicate that model checking can be both a feasible and integral part of the software development process.
Tracking Single Quantum Dots in Live Cells with Minimal Paths
Authors: Stephane Bonneau, Maxime Dahan, Laurent D. Cohen
Venue: Proceedings of the 2005 IEEE Computer Society Conference on Computer Vision and Pattern Recognition (CVPR'05) - Workshops - Volume 03 (2005)

We present here a novel method for automatically detecting and tracking semi-conductor quantum dots (QDs) in sequences of fluorescence images. QDs are new nanometersized fluorescent probes with great prospects for ultrasensitive biological imaging. When specifically attached to a biomolecule, they can be observed and tracked in live cells at the single molecule level over unprecedented durations. Due to QD complex optical properties, such as fluorescence intermittency, the quantitative analysis of image stacks is however challenging and requires advanced algorithms. Our tracking approach, instead of a frame by frame analysis, is based on perceptual grouping in a spatio-temporal volume. By applying a detection process based on an image fluorescence model, we first obtain a set of unstructured points. Individual molecular trajectories are then considered as minimal paths in a Riemannian metric derived from the fluorescence image stack. These paths are computed with the Fast Marching method, and few parameters are required. We illustrate our approach by showing experimental results issued from the tracking of individual glycine receptors in the membrane of live neurons.
FAR: Face-aware routing for mobicast in large-scale sensor networks
Authors: Qingfeng Huang, Sangeeta Bhattacharya, Chenyang Lu, Gruia-Catalin Roman
Venue: ACM Transactions on Sensor Networks (TOSN) (2005)

This article presents FAR, a Face-Aware Routing protocol for mobicast---a spatiotemporal variant of multicast tailored for sensor networks with environmental mobility. FAR features face-routing and timed-forwarding for delivering a message to a mobile delivery zone. Both analytical and statistical results show that FAR achieves reliable spatial and just-in-time message delivery with only moderate communication and memory overhead. This article also presents a novel distributed algorithm for spatial neighborhood discovery for FAR bootstrapping. The spatiotemporal performance and reliability of FAR are demonstrated via network simulations.
RelaXML: Bidirectional Transfer Between Relational and XML Data
Authors: Steffen Ulso Knudsen, Torben Bach Pedersen, Christian Thomsen, Kristian Torp
Venue: Proceedings of the 9th International Database Engineering & Application Symposium (2005)

In modern enterprises, almost all data is stored in relational databases. Additionally, most enterprises increasingly collaborate with other enterprises in long-running read-write workflows, primarily through XML-based data exchange technologies such as web services. However, bidirectional XML data exchange is cumbersome and must often be hand-coded, at considerable expense. This paper remedies the situation by proposing RELAXML, an automatic and effective approach to bidirectional XML-based exchange of relational data. RELAXML supports re-use through multiple inheritance, and handles both export of relational data to XML documents and (re-)import of XML documents with a large degree of flexibility in terms of the SQL statements and XML document structures supported. Import and export are formally defined so as to avoid semantic problems, and algorithms to implement both are given. A performance study shows that the approach has a reasonable overhead compared to hand-coded programs.
Hand Gesture Extraction by Active Shape Models
Authors: Nianjun Liu, Brian C. Lovell
Venue: Proceedings of the Digital Image Computing on Techniques and Applications (2005)

The paper applied active statistical model for hand gesture extraction and recognition. After the hand contours are found out by a real-time segmenting and tracking system, a set of feature points (Landmarks) are marked out automatically and manually along the contour. A set of feature vectors will be normalized and aligned and then trained by Principle Component Analysis (PCA). Mean shape, eigen-values and eigenvectors are computed out and composed of active shape model. When the model parameter is adjusted continually, various shape contours are generated to match the hand edges extracted from the original images. The gesture is finally recognized after well matching.
Bit-level partial evaluation of synchronous circuits
Authors: Sarah Thompson, Alan Mycroft
Venue: Proceedings of the 2006 ACM SIGPLAN symposium on Partial evaluation and semantics-based program manipulation (2006)

Partial evaluation has been known for some time to be very effective when applied to software; in this paper we demonstrate that it can also be usefully applied to hardware. We present a bit-level algorithm that supports the offline partial evaluation of synchronous digital circuits. Full PE of combinational logic is noted to be equivalent to Boolean minimisation. A loop unrolling technique, supporting both partial and full unrolling, is described. Experimental results are given, showing that partial evaluation of a simple micro-processor against a ROM image is equivalent to compiling the ROM program directly into low level hardware.
NHPP models for categorized software defects: Research Articles
Authors: Zhaohui Liu, Nalini Ravishanker, Bonnie K. Ray
Venue: Applied Stochastic Models in Business and Industry (2005)

We develop NHPP models to characterize categorized event data, with application to modelling the discovery process for categorized software defects. Conditioning on the total number of defects, multivariate models are proposed for modelling the defects by type. A latent vector autoregressive structure is used to characterize dependencies among the different types. We show how Bayesian inference can be achieved via MCMC procedures, with a posterior prediction-based L-measure used for model selection. The results are illustrated for defects of different types found during the System Test phase of a large operating system software development project. Copyright &copy; 2005 John Wiley & Sons, Ltd.
Testing Web Services by XML Perturbation
Authors: Wuzhi Xu, Jeff Offutt, Juan Luo
Venue: Proceedings of the 16th IEEE International Symposium on Software Reliability Engineering (2005)

The eXtensible Markup Language (XML) is widely used to transmit data across the Internet. XML schemas are used to define the syntax of XML messages. XML-based applications can receive messages from arbitrary applications, as long as they follow the protocol defined by the schema. A receiving application must either validate XML messages, process the data in the XML message without validation, or modify the XML message to ensure that it conforms to the XML schema. A problem for developers is how well the application performs the validation, data processing, and, when necessary, transformation. This paper describes and gives examples of a method to generate tests for XML-based communication by modifying and then instantiating XML schemas. The modified schemas are based on precisely definedschema primitive perturbation operators.
Efficient Query Evaluation on Large Textual Collections in a Peer-to-Peer Environment
Authors: Jiangong Zhang, Torsten Suel
Venue: Proceedings of the Fifth IEEE International Conference on Peer-to-Peer Computing (2005)

We study the problem of evaluating ranked (top-k) queries on textual collections ranging from multiple giga-bytes to terabytes in size. We focus on the case of a global index organization in a highly distributed environment, and consider a class of ranking functions that includes common variants of the Cosine and Okapi measures. The main bottleneck in such a scenario is the amount of communication required during query evaluation. We propose several efficient query evaluation schemes and evaluate their performance. Our results on real search engine query traces and over 120 million web pages show that after careful optimization such queries can be evaluated at a reasonable cost, while challenges remain for even larger collections and more general classes of ranking functions.
Documents and Services: From the Historical Points of Document Media as Extension of Human Body
Authors: Jun Miyazaki
Venue: Proceedings of the Eighth International Conference on Document Analysis and Recognition (2005)

Starting from the history of document media, especially from the point of the relationship between document media and human bodies. Document media can be seen as extension of body. We see how document media have been evolved with human interaction. And how human bodies have been extended by document media. But recently we have lost those historical obtained senses in electronic documents. Some thoughts for recovering those senses will be presented. Next, an example of document media in workplace is described. We will see how workplace affect the interaction between document media and human being as services. Finally, the future of document media and its services are briefly forecasted.
A New Network Availability Algorithm for WDM Optical Networks
Authors: Rongping Lin, Sheng Wang, Lemin Li, Lei Guo
Venue: Proceedings of the The Fifth International Conference on Computer and Information Technology (2005)

As the need of network users for high-availability increase, how to evaluate the network availability justly becomes an on edge problem. Under the dynamic connections, a new Network Availability Algorithm (NAA), which considers the high network performance, for WDM optical networks is proposed. It is practically to the users and operators of the network. Simulation results show that NAA not only is correct but also is efficient.
A tutorial view of simulation model development
Authors: Richard E. Nance
Venue: ACM SIGSIM Simulation Digest (1984)

Working from the background of simulation language developments, we develop an understanding of the current status of simulation model development. Factors characterizing the current status include a shift in emphasis from program to model, more commitment to modeling tools, and the lingering impedance of simulation language isolation. Current and future needs are identified. Specific approaches to meeting these needs are cited in an extensive description of current research, and in summary we conclude that the technology of simulation model development is in a transitional period that portends more rapid changes for the future.
Arithmetic Meyer sets and finite automata
Authors: Shigeki Akiyama, Frédérique Bassino, Christiane Frougny
Venue: Information and Computation (2005)

Non-standard number representation has proved to be useful in the speed-up of some algorithms, and in the modelization of solids called quasicrystals. Using tools from automata theory, we study the set Zβ of β-integers, that is, the set of real numbers which have a zero fractional part when expanded in a real base β, for a given β > 1. In particular, when β is a Pisot number--like the golden mean--, the set Zβ is a Meyer set, which implies that there exists a finite set F (which depends only on β) such that Zβ - Zβ ⊂ Zβ + F. Such a finite set F, even of minimal size, is not uniquely determined. In this paper, we give a method to construct the sets F and an algorithm, whose complexity is exponential in time and space, to minimize their size. We also give a finite transducer that performs the decomposition of the elements of Zβ - Zβ as a sum belonging to Zβ + F.