ppxscal/embedding_network huggingface dataset:
ClawHMMER: A Streaming HMMer-Search Implementatio
Authors: Daniel Reiter Horn, Mike Houston, Pat Hanrahan
Venue: Proceedings of the 2005 ACM/IEEE conference on Supercomputing (2005)

The proliferation of biological sequence data has motivated the need for an extremely fast probabilistic sequence search. One method for performing this search involves evaluating the Viterbi probability of a hidden Markov model (HMM) of a desired sequence family for each sequence in a protein database. However, one of the difficulties with current implementations is the time required to search large databases. Many current and upcoming architectures offering large amounts of compute power are designed with data-parallel execution and streaming in mind. We present a streaming algorithm for evaluating an HMM's Viterbi probability and refine it for the specific HMM used in biological sequence search. We implement our streaming algorithm in the Brook language, allowing us to execute the algorithm on graphics processors. We demonstrate that this streaming algorithm on graphics processors can outperform available CPU implementations. We also demonstrate this implementation running on a 16 node graphics cluster.
Enhancing efficiency in the health care industry
Authors: Stephan Kudyba, G. Brent Hamar, William M. Gandy
Venue: Communications of the ACM (2005)

Using critical data and predictive modeling can help identify high-risk candidates in a total health plan population.
Shading and Shadowing of Architecture in Mixed Reality
Authors: Tetsuya Kakuta, Takeshi Oishi, Katsushi Ikeuchi
Venue: Proceedings of the 4th IEEE/ACM International Symposium on Mixed and Augmented Reality (2005)

We propose a simple method to express shading and shadowing of virtual objects in Mixed Reality especially appropriate for static architecture models in outdoor scenes. We create the shadows of the virtual objects in a fast and efficient way using a set of pre-rendered basis images and shadowing planes. The proposed method is limited in interactivity but can operate in near real-time.
Layout based document image retrieval by means of XY tree reduction
Authors: Simone Marinai, Emanuele Marino, Giovanni Soda
Venue: Proceedings of the Eighth International Conference on Document Analysis and Recognition (2005)

We analyze a system for the retrieval of document images on the basis of layout similarity. Layout objects are extracted and represented with the XY tree. Page similarity is computed with a tree-edit distance algorithm. The peculiarity of the approach is the use of tree grammars to model the variations in the tree which are due to segmentation algorithms or to structural differences between documents with similar layout. A few class-independent grammatical rules are used to modify each tree and obtain a reduced tree that is supposed to preserve the most relevant features of the page.
A Robust Approach to Sequence Classification
Authors: Ming Li, Ronan Sleep
Venue: Proceedings of the 17th IEEE International Conference on Tools with Artificial Intelligence (2005)

We report results for classification of representations of music, spoken words, and text documents. Experimental comparisons with other state-of-the-art algorithms yield improved results for all three examples. We use a Support Vector Machine (SVM) as our classifier in all experiments. This is driven by a kernel matrix of similarity measures between the sequences. Our similarity measure is based on n-grams of varying length (multi-grams), weighted to reflect discrimination ability. To alleviate the problem of the exponential growth of feature size with n, we use a modified LZ78 algorithm [1] to guide feature selection. Our method exhibits good performance over the three widely distinct tasks reported here, and is very computationally efficient and may therefore be useful in real time applications.
On-Demand Broadcast Algorithms with Caching on Improving Response Time for Real-Time Information Dispatch Systems
Authors: Chui Ying Hui, Joseph Kee-Yin Ng, Victor Chung-Sing Lee
Venue: Proceedings of the 11th IEEE International Conference on Embedded and Real-Time Computing Systems and Applications (2005)

This paper presents a performance study on various broadcast algorithms and caching strategies for on-time delivery of data in a Real-Time Information Dispatch System. The objective of the study is not just aiming at on-time delivery, but to improve the response time on the data requests. We propose and perform a series of simulation experiments, using real traffic data from the access log of the official web site for FIFA 2002 World Cup. Simulation results show that our proposed broadcast algorithm not only succeeds in providing good on-time delivery of data but at the same time provides 2 to 3 times of improvement in response time over traditional scheduling algorithms like First-In-First-Out (FIFO) and Earliest-Deadline-First (EDF).The simulation results also show that our proposed caching strategy provides further improvement in percentage of requests finished in time over traditional caching strategy like Least Recently Used (LRU).
SOI planar photonic crystal fabrication: Etching through SiO2/Si/SiO2 layer systems using fluorocarbon plasmas
Authors: A. P. Milenin, C. Jamois, T. Geppert, U. Gösele, R. B. Wehrspohn
Venue: Microelectronic Engineering (2005)

Dry plasma etching of sub-micron structures in a SiO"2/Si/SiO"2 layer system using Cr as a mask was performed in a fluorocarbon plasma. It was determined that the best anisotropy could be achieved in the most electropositive plasma. A gas composition yielding the desired SOI planar photonic crystal structures was optimized from the available process gases, Ar, He, O"2, SF"6, CF"4, c-C"4F"8, CHF"3, using DC bias data sets. Application of the c-C"4F"8/(noble gas) chemistry allowed fabrication of the desired SOI planar photonic crystal. The average etching rates for the pores and ridge waveguide regions were about 71 and 97nm/min, respectively, while the average SiO"2/Si/SiO"2 to Cr etching selectivity for the ridge waveguide region was about 33:1 in case of the c-C"4F"8/90%Ar plasma with optimized parameters.
"Some criteria for classification and evaluation of discrete event simulation languages"
Authors: Wolfgang Kreutzer
Venue: ACM SIGSIM Simulation Digest (1977)

In order to describe (model) a given system in a more or less disciplined way, some kind of formal or informal "system description language", providing a "world view" for concept articulation and communication will be explicitely or implicitely used. To appreciate the importance of an "appropriate" frame of reference, it should be considered, that a system description methodology will necessarily be used as a device for structuring the thinking of its users. The severe problems encountered by large-scale software development projects have recently led to widespread recognition of the importance of structuring and levels of abstraction as a method supporting reliable engineering of systems; /DENNING74/.
Data Masking: A New Approach for Steganography?
Authors: Regunathan Radhakrishnan, Mehdi Kharrazi, Nasir Memon
Venue: Journal of VLSI Signal Processing Systems (2005)

It is well known that encryption provides secure channels for communicating entities. However, due to lack of covertness on these channels, an eavesdropper can identify encrypted streams through statistical tests and capture them for further cryptanalysis. Hence, the communicating entities can use steganography to achieve covertness. In this paper we propose a new form of multimedia steganography called data masking. Instead of embedding a secret message into a multimedia object, as in traditional multimedia steganography, we process the entire secret message to make it appear statistically similar to a multimedia object itself. Thereby we foil an eavesdropper who is primarily applying statistical tests to detect encrypted communication channels. We show that our approach can potentially give a covert channel capacity which is an order of magnitude higher than traditional steganography. Our experiments also show that steganalyzers trained with stego objects of known steganographic have a low detection accuracy for datamasked multimedia objects.
Making Practical Use of IPv6 Anycasting: Mobile IPv6 Based approach
Authors: Masakazu Hashimoto, Shingo Ata, Hiroshi Kitamura, Masayuki Murata
Venue: Proceedings of the International Symposium on Applications on Internet (2006)

Anycast is a new IPv6 function in which an anycast address can be assigned to multiple nodes that provide the same service. The Anycast packet is transmitted to one appropriate node selected out of all the nodes assigned to the same anycast address. Although it is expected that anycast will be used in various ways, the use of anycast is quite limited today. This is because anycast functionalities are still unclear, and it is difficult to realize a global anycast that requires existing routing protocols to be radically changed. In this paper, we clarify and classify some essential anycast issues and propose a new and practical communication architecture, based on Mobile IPv6 architecture, that overcomes the anycast difficulties.
On location independent representations and self-organization
Authors: Ivan Garibay, Annie S. Wu, Ozlem Garibay
Venue: Proceedings of the 2005 workshops on Genetic and evolutionary computation (2005)

We study the self-organization of genomic symbols on a genetic algorithm with a location independent representation&mdash;the Proportional Genetic Algorithm (PGA) [2]. Self-organization of genomic symbols is possible because location independent representations ensure the absence of selective pressure for a particular order. We hypothesize that self-similarity emerges because self-similar genomes are more robust with respect to crossover and mutation and because it favors positive correlations between the form and quality of candidate solutions.
Pruning Social Networks Using Structural Properties and Descriptive Attributes
Authors: Lisa Singh, Lise Getoor, Louis Licamele
Venue: Proceedings of the Fifth IEEE International Conference on Data Mining (2005)

Scale is often an issue with understanding and making sense of large social networks. Here we investigate methods for pruning social networks by determining the most relevant relationships. We measure importance in terms of predictive accuracy on a set of target attributes of the social network. Our goal is to create a pruned network that models only the most informative affiliations and relationships. We present methods for pruning networks based on both structural properties and descriptive attributes demonstrate it on a network of NASDAQ and NYSE businesses and on a bibliographic network.
Axioms for bigraphical structure
Authors: Robin Milner
Venue: Mathematical Structures in Computer Science (2005)

This paper axiomatises the structure of bigraphs, and proves that the resulting theory is complete. Bigraphs are graphs with double structure, representing locality and connectivity. They have been shown to represent dynamic theories for the $\pi$-calculus, mobile ambients and Petri nets in a way that is faithful to each of those models of discrete behaviour. While the main purpose of bigraphs is to understand mobile systems, a prerequisite for this understanding is a well-behaved theory of the structure of states in such systems. The algebra of bigraph structure is surprisingly simple, as this paper demonstrates; this is because bigraphs treat locality and connectivity orthogonally.
Resource allocation schemes and performance evaluation models for wavelength division multiplexed optical networks
Authors: Mostafa Bassiouni
Venue:  (2005)

Wavelength division multiplexed (WDM) optical networks are rapidly becoming the technology of choice in network infrastructure and next-generation Internet architectures. WDM networks have the potential to provide unprecedented bandwidth, reduce processing cost, achieve protocol transparency, and enable efficient failure handling. This dissertation addresses the important issues of improving the performance and enhancing the reliability of WDM networks as well as modeling and evaluating the performance of these networks. Optical wavelength conversion is one of the emerging WDM enabling technologies that can significantly improve bandwidth utilization in optical networks. A new approach for the sparse placement of full wavelength converters based on the concept of k-Dominating Set (k-DS) of graphs is presented. The k-DS approach is also extended to the case of limited conversion capability using three scalable and cost-effective switch designs: flexible node-sharing, strict node-sharing and static mapping. Compared to full search algorithms previously proposed in the literature, the K-DS approach has better blocking performance, has better time complexity and avoids the local minimum problem. The performance benefit of the K-DS approach is demonstrated by extensive simulation. Fiber delay line (FDL) is another emerging WDM technology that can be used to obtain limited optical buffering capability. A placement algorithm, k-WDS, for the sparse placement of FDLs at a set of selected nodes in Optical Burst Switching (OBS) networks is proposed. The algorithm can handle both uniform and non-uniform traffic patterns. Extensive performance tests have shown that k-WDS provides more efficient placement of optical fiber delay lines than the well-known approach of placing the resources at nodes with the highest experienced burst loss. Performance results that compare the benefit of using FDLs versus using optical wavelength converters (OWCs) are presented. A new algorithm, A-WDS, for the placement of an arbitrary numbers of FDLs and OWCs is introduced and is evaluated under different non-uniform traffic loads. This dissertation also introduces a new cost-effective optical switch design using FDL and a QoS-enhanced JET (just enough time) protocol suitable for optical burst switched WDM networks. The enhanced JET protocol allows classes of traffic to benefit from FDLs and OWCs while minimizing the end-to-end delay for high priority bursts. (Abstract shortened by UMI.)
CRAWDAD: A Community Resource for Archiving Wireless Data at Dartmouth
Authors: David Kotz, Tristan Henderson
Venue: IEEE Pervasive Computing (2005)

Wireless network researchers are seriously starved for data about how real users, applications, and devices use real networks under real network conditions. CRAWDAD (Community Resource for Archiving Wireless Data at Dartmouth) is a new National Science Foundation-funded project to build a wireless-network data archive for the research community. It will host wireless data and provide tools and documents to make collecting and using the data easy. This resource should help researchers identify and evaluate real and interesting problems in mobile and pervasive computing. To learn more about CRAWDAD and discuss its direction, about 30 interested people gathered at a workshop held in conjunction with MobiCom 2005.
Balanced Multicasting: High-throughput Communication for Grid Applications
Authors: Mathijs den Burger, Thilo Kielmann, Henri E. Bal
Venue: Proceedings of the 2005 ACM/IEEE conference on Supercomputing (2005)

Many grid applications need to transfer large amounts of data between the geographically distributed sites of a grid environment. Network heterogeneity between these sites makes throughput optimization of data transfers to multiple sites (multicast) hard or even impossible. We present a technique called balanced multicasting that uses monitoring information for both bandwidth capacity and achievable bandwidth to compute balanced multicast trees at runtime that use application-level traffic shaping at the sender side to avoid self-induced congestion. Our experimental evaluation shows that our approach outperforms existing multicast strategies by large margins.
High reynolds number simulation and drag reduction techniques
Authors: George Em Karniadakis
Venue:  (2005)

The first part of this thesis is an attempt to perform high Reynolds number DNS and large Eddy Simulation (LES). In order to conduct DNS at high Reynolds number, we have implemented and benchmarked several different parallel models. Domain decomposition has been done in either stream-wise only or in both stream-wise and span-wise directions, based on MPI or OpenMP to parallelize the code. In order to overcome in part the limitations of Reynolds number on DNS, LES has been implemented whereby the large scale dynamics of flow are accurately simulated, but the small scale features are parameterized by an approximate model. LES requires fewer grid points and less computer time for a simulation. We have conducted relatively high Reynolds number DNS, and LES at Re* = 600,1000 using the Spectral Vanishing Viscosity (SVV) method. SVV has been combined with standard and dynamic Smagorinsky models. In order to improve the numerical stability, SVV has been implemented implicitly. The LES results have been compared with DNS, and show that SVV has potential to be a good approach for LES. In the second half of thesis, we have investigated several turbulent drag reduction techniques using DNS. Turbulence drag reduction by adding micro-bubbles into a turbulent boundary layer has been well established in experiments. However, it has been difficult until now to capture such effects in numerical simulations due to a lack of an accurate interaction model between turbulence and micro-bubbles. In this thesis, a series of DNS of small bubbles seeded in turbulent channel flow at average volume fractions of up to 13% have been carried out. The results show that about 10% drag reduction is reached. This is consistent with low speed and low void fraction experiments, but significantly less than 70% to 80% reductions in skin friction reported in some experiments. A nondeformable, spherical bubble shape has been assumed, and the Force Coupling Method (FCM) has been used to simulate bubbles in turbulent flow. It is found that the bubble size should be small enough to produce a sustained level of drag reduction over time. Drag reduction effects have been investigated in detail at different Reynolds numbers. Finally, motivated by the apparently lower levels of drag reduction found in the numerical simulation as compared to many experiments, we consider the possibility of other physical process not captured so far. One such process is a partial slip flow condition at the wall. A slip boundary condition can arise from effects of hydrophobic surfaces or the formation of a thin gas film on the wall. The simulation results show that a large level of drag reduction can be achieved by applying slip boundary condition. The effect of combining slip boundary conditions with micro-bubbles has also been investigated, and a detailed analysis has been carried out. (Abstract shortened by UMI.)
From Searching to Browsing through Multimodal Documents Linking
Authors: Delila Mekhaldi, Denis Lalanne, Rolf Ingold
Venue: Proceedings of the Eighth International Conference on Document Analysis and Recognition (2005)

Relationships that link static documents discussed during meetings to the corresponding speech transcripts can be of various kinds. The most important one, thematic links, quotations and references are presented in this paper. Thematic links are detected via extraction is based on the detection of segments of documents that are quoted in the speech transcript. References, made by speakers to documents, are performed via a matching process between referring expressions detected in the speech transcript, and corresponding documents logical blocks. Finally, a framework that combines these links and an evaluation of the links complementarity are presented.
MIT Simpl
Authors: Malcolm M. Jones
Venue: ACM SIGSIM Simulation Digest (1973)

Simpl is a simulation system (i.e., a specialized programming language and an associated run-time support system) specifically designed to provide a high degree of interaction between an individual researcher and a complex simulation model, in all the stages of the simulation process, by taking advantage of the sophisticated interaction possible in a modern, on-line, man-computer environment.
Building Evidence Graphs for Network Forensics Analysis
Authors: Wei Wang, Thomas E. Daniels
Venue: Proceedings of the 21st Annual Computer Security Applications Conference (2005)

In this paper, we present techniques for a network forensics analysis mechanism that includes effective evidence presentation, manipulation and automated reasoning. We propose the evidence graph as a novel graph model to facilitate the presentation and manipulation of intrusion evidence. For automated evidence analysis, we develop a hierarchical reasoning framework that includes local reasoning and global reasoning. Local reasoning aims to infer the roles of suspicious hosts from local observations. Global reasoning aims to identify group of strongly correlated hosts in the attack and derive their relationships. By using the evidence graph model, we effectively integrate analyst feedback into the automated reasoning process. Experimental results demonstrate the potential and effectiveness of our proposed approaches.
Wikis: a rapidly growing phenomenon in the German-speaking school community
Authors: Beat Doebeli Honegger
Venue: Proceedings of the 2005 international symposium on Wikis (2005)

In the first part we describe the dissemination of wikis in the German-speaking school community with a special focus on Switzerland, the most active German-speaking country using wikis in schools. In the second part we examine what foundations have to be laid for a further propagation of wikis in the German-speaking school community as an example of a non English-speaking community.
Sharp interface Cartesian grid method II: A technique for simulating droplet interactions with surfaces of arbitrary shape
Authors: H. Liu, S. Krishnan, S. Marella, H. S. Udaykumar
Venue: Journal of Computational Physics (2005)

A fixed-grid, sharp interface method is developed to simulate droplet impact and spreading on surfaces of arbitrary shape. A finite-difference technique is used to discretize the incompressible Navier-Stokes equations on a Cartesian grid. To compute flow around embedded solid boundaries, a previously developed sharp interface method for solid immersed boundaries is used. The ghost fluid method (GFM) is used for fluid-fluid interfaces. The model accounts for the effects of discontinuities such as density and viscosity jumps and singular sources such as surface tension in both bubble and droplet simulations. With a level-set representation of the propagating interface, large deformations of the boundary can be handled easily. The model successfully captures the essential features of interactions between fluid-fluid and solid-fluid phases during impact and spreading. Moving contact lines are modeled with contact angle hysteresis and contact line motion on non-planar surfaces is computed. Experimental observations and other simulation results are used to validate the calculations.
Static Analysis for Computing Escapability and Mutability for Java Components
Authors: Aiwu Shi, Gleb Naumovich
Venue: Proceedings of the Fifth IEEE International Workshop on Source Code Analysis and Manipulation (2005)

A common theme in information security is protection of trusted software components against unauthorized access by untrusted users. In the context of distributed object technologies, such as Enterprise Java Beans, this means preventing leaks of sensitive information to untrusted users, as well as preventing untrusted users from modifying sensitive information. In this paper, we propose an approach for identification and classification of potentially sensitive information that can leak out of trusted software components to untrusted parties. Unlike the current approaches to securing information flow by extending the type system, our technique is based on static points-to, data and control-dependence, and object mutability analyses.