ppxscal/embedding_network huggingface dataset:
MUSCLE: Multiple Sequence Alignment with Improved Accuracy and Speed
Authors: Robert C. Edgar
Venue: Proceedings of the 2004 IEEE Computational Systems Bioinformatics Conference (2004)

We present MUSCLE, a new program for creating multiple alignments of protein sequences. MUSCLE achieves the highest scores so far reported on four alignment benchmarks: Balibase, PREFAB, SABmark and SMART, achieving accuracy from 1% to 2.5% higher than T-Coffee and execution times that are generally lower than CLUSTALW for typical input data. With options designed for high-throughput applications, MUSCLE gives average accuracy statistically indistinguishable from T-Coffee and is the fastest published method for large numbers of sequences, able to align 5,000 sequences of length 300 in 7 minutes on a desktop computer. MUSCLE is freely available at http://www.drive5.com /muscle.
Formally Designing Web Services for Mobile Team Collaboration
Authors: Schahram Dustdar, Pascal Fenkam
Venue: Proceedings of the 30th EUROMICRO Conference (2004)

We illustrate a symbiotic relationship between existing model oriented specificationtechniques and web services. Through the formal re-design of a platform for mobile team collaboration, we investigate the suitability of existing formal specification and verification techniques to web services. In general, this preliminary work suggests that a lot is still to be done on understanding the computationalbehavior of web services, hence on specifying and verifying them.
2002 Academy Award winner for best animated short "The ChubbChubbs!"
Venue: ACM SIGGRAPH 2003 video review on Electronic theater program on Electronic theater program - Volume 144 (2003)

When Sony Pictures Imageworks president Tim Sarnoff encouraged company artists and animators to create an original story, "The ChubbChubbs!" was conceived. Imageworks' first all-CG short introduces the alien inhabitants of the Planet Glorf: Meeper, the earnest but oh so awkward hero, the singing Diva, the Zyzaks and the ChubbChubbs. In this debut short, Meeper valiantly tries to warn the patrons of the Ale-E-Inn, an intergalatic watering hole with its own constellation of stars, of impending danger only to find himself face to face with the toughest creatures in the universe. "The ChubbChubbs!" began as a test of Imageworks' production pipeline and went on to win an Academy Award&reg; for Best Animated Short Film. Copyright held by creator.
An Architectural Framework for Providing Reliability and Security Support
Authors: N. Nakka, Z. Kalbarczyk, R. K. Iyer, J. Xu
Venue: Proceedings of the 2004 International Conference on Dependable Systems and Networks (2004)

This paper explores hardware-implemented error-detection and security mechanisms embedded as modules in a hardware-level framework called the Reliability andSecurity Engine (RSE), which is implemented as an integralpart of a modern microprocessor. The RSE interacts with theprocessor through an input/output interface. The CHECKinstruction, a special extension of the instruction set architectureof the processor, is the interface of the application withthe RSE. The detection mechanisms described here in detailare: (1) the Memory Layout Randomization (MLR) module,which randomizes the memory layout of a process in order tofoil attackers who assume a fixed system layout, (2) the DataDependency Tracking (DDT) module, which tracks the dependenciesamong threads of a process and maintains checkpointsof shared memory pages in order to rollback thethreads when an offending (potentially malicious) thread isterminated, and (3) the Instruction Checker module (ICM),which checks an instruction for its validity or the control-flowof the program just as the instruction enters the pipeline forexecution. Performance simulations for the studied modulesindicate low overhead of the proposed solutions.
EXPERT: expedited simulation exploiting program behavior repetition
Authors: Wei Liu, Michael C. Huang
Venue: Proceedings of the 18th annual international conference on Supercomputing (2004)

Studying program behavior is a central component in architectural designs. In this paper, we study and exploit one aspect of program behavior, the behavior repetition, to expedite simulation. Detailed architectural simulation can be long and computationally expensive. Various alternatives are commonly used to simulate a much smaller instruction stream to evaluate design choices: using a reduced input set or simulating only a small window of the instruction stream. In this paper, we propose to reduce the amount of detailed simulation by avoiding simulating repeated code sections that demonstrate stable behavior. By characterizing program behavior repetition and use the information to select a subset of instructions for detailed simulation, we can significantly speed up the process without affecting the accuracy. In most cases, simulation time of full-length SPEC CPU2000 benchmarks is reduced from hundreds of hours to a few hours. The average error incurred is only about 1% or less for a range of metrics.
Motivation-Based Selection of Negotiation Partners
Authors: Steve Munroe, Michael Luck, Mark d'Inverno
Venue: Proceedings of the Third International Joint Conference on Autonomous Agents and Multiagent Systems - Volume 3 (2004)

Negotiation is key to resolving conflicts, allocating resources and establishing cooperation in systems of self-interested agents. Often, an agent may have to select between different potential negotiation partners, and identifying which offers the best chance of a successful negotiation is a challenging task. However, poor selection of partners can result in failure or in inefficient outcomes. To that end, this paper describes a motivation-based mechanism to evaluate and select between negotiation candidates. This is achieved by a twofold process: first, acceptable candidates are identified using motivation-based thresholds on objective scoring measures; second, the importance of issues is considered, and expected performance measures are evaluated accordingly. The mechanism is described and empirically evaluated.
Stimulation Signal Processing for Intraocular Vision Implants
Authors: Andreas Schmid
Venue: Proceedings of the 17th IEEE Symposium on Computer-Based Medical Systems (2004)

Intraocular vision implants offer potential cure for several 100,000 blind people, including blind patients suffering from corneal opacity, accidents, fire, explosion, and alkali burn.Wireless, fully implantable, intraocular vision implant systems are capable of applying optical stimulation patterns to the photoreceptor layer of blind patients' retinas. The opticalstimulation patterns are derived in real-time from a live video feed. This paper presents theessential component of these intraocular stimulation systems - the digital signal processingthat emulates the healthy eye and replaces the defective parts of the blind patients' eyes. Theimplementation is based on the comprehensive mathematical description of the photoreceptor encoding process. During this process, the live video feed is transformed in real-time bythe photoreceptor encoding function to implement the temporal and spatial properties of pigment bleaching, horizontal cell feedback, Michaelson-Menton transduction, cone response, and inhibitory horizontal cell feedback. To customize the stimulation data for transmission to the micro-display, the source coding process also performs spatial downsampling and luminance dynamics reduction.
Age of computers: game-based teaching of computer fundamentals
Authors: Lasse Natvig, Steinar Line
Venue: Proceedings of the 9th annual SIGCSE conference on Innovation and technology in computer science education (2004)

Age of Computers (AoC) is a new approach to the learning activities that supplements the auditorium lectures in a computer fundamentals course with 250 students. It is a computer game that presents the students a diverse set of problems from the course topics linked to computer history. It is implemented as set of dynamic web pages retrieved from a database. A prototype was used in 2003, and the feedback is positive and a strong motivation for continuing the project. The paper describes AoC, its use and implementation.
Pathway Mapping with Operon Information: An Integer-Programming Method
Authors: Fenglou Mao, Zhengchang Su, Victor Olman, David Chuang, Ying Xu
Venue: Proceedings of the 2004 IEEE Computational Systems Bioinformatics Conference (2004)

Biological pathway mapping is an important problem in the post-genomic era. We now present a new algorithm for pathway mapping in microbes. The algorithm considers not only sequence similarity among the template and target genes, but also the operon structures in the target genome. We formulated the mapping problem as a graph finding problem, and solved it by an Integer-Programming (IP) method. The goal is to minimize a linear object function subject to six constraints, such that maximal sequence similarity among the template and target genes are achieved, and at the same time, a minimal number of operons are covered in the target genome. Compared to our previous Minimal Spanning Tree (MST) algorithm, the IP method has the following advantages: i) It is much faster and thus can map larger pathway involving a much large set of genes. ii) The IP method looks into the details of genes in the operons, and consequently avoids the many-to-one mapping mistakes that sometimes occur in the MST algorithm. We have compiled a large pathway training set to optimize the parameters of the program, and tested it by mapping 16 complex pathways from BioCyc onto E.coli K12 genome and the results are very promising.
Discovery of Web Services in a Federated Registry Environment
Authors: Kaarthik Sivashanmugam, Kunal Verma, Amit Sheth
Venue: Proceedings of the IEEE International Conference on Web Services (2004)

The potential of a large scale growth of private andsemi-private registries is creating the need for aninfrastructure which can support discovery andpublication over a group of autonomous registries.Recent versions of UDDI have made changes toaccommodate interactions between distributedregistries. In this paper, we discuss METEOR-S Webservice Discovery Infrastructure, which provides anontology-based infrastructure to access a group ofregistries that are divided based on business domainsand grouped into federations. We also discuss how Webservice discovery is carried out within a federation.
Improving Cache Performance in Mobile Computing Networks through Dynamic Object Relocation
Authors: Kwong Yuen Lai, Zahir Tari, Peter Bertok
Venue: Proceedings of the Parallel and Distributed Systems, Tenth International Conference (2004)

Caching improves the performance of web servers byplacing frequently accessed data at intermediate nodesclose to web clients. Similarly, in a mobile network, accessdelay can be reduced by caching data objects near themobile clients. Existing caching techniques used for webservers are unsuitable for mobile networks because they donot deal with the issue of client mobility. To ensure cacheperformance is not affected by client movement, object relocationtechniques can be used to dynamically relocate dataobjects so they remain close to the moving client. Existingrelocation techniques rely on path predictions to help makerelocation decisions. However, the inaccuracy of path predictiontechniques result in high relocation overhead andincreased access delay after each handover.In this paper, we propose two new object relocation techniquesto deal with the problem of poor path predictions andhigh object relocation overhead. The first technique called2PR (Two-Phase Relocation) compensates for the inaccuracyof existing path prediction algorithms by temporarilyrelocating data objects to a common parent node until theclient's location is confirmed. The second technique, calledROLP (Return-path Object-List Passing), reduces the trafficoverhead associated with object relocation by using coordinationmessages between nodes. Test results show that2PR and ROLP reduce the penalty of poor path predictionsand significantly reduces the overhead associated withcache relocation compared to existing schemes.
Equal processing and equal setup time cases of scheduling parallel machines with a single server
Authors: Amir H. Abdekhodaee, Andrew Wirth, Heng Soon Gan
Venue: Computers and Operations Research (2004)

This paper considers the deterministic problem of scheduling two-operation non-preemptable jobs on two identical semi-automatic machines. A single server is available to carry out the first (or setup) operation. The second operation is executed automatically, without the server. The general problem of makespan minimization is NP-hard in the strong sense. Two special cases which arise in practice, the equal processing times and regular equal setup times problems turn out to be closely linked to the restricted set partitioning problem. This link is used to show that they are NP-hard in the ordinary sense, and to construct a tight lower bound and two highly effective O(n log n) heuristics.
Differential rational normal forms and a reduction algorithm for hyperexponential func
Authors: Keith Geddes, Ha Le, Ziming Li
Venue: Proceedings of the 2004 international symposium on Symbolic and algebraic computation (2004)

We describe differential rational normal forms of a rational function and their properties. Based on these normal forms, we present an algorithm which, given a hyperexponential function T(x), constructs two hyperexponential functions T;1;(x) and T;2;(x) such that T(x) = T;1;'(x) + T;2;(x) and T;2;(x) is minimal in some sense. The algorithm can be used to accelerate the differential Gosper's algorithm and to compute right factors of the telescopers.
Non-Photorealistic Outdoor Scene Rendering: Techniques and Application
Authors: Irene Liew Suet Fun, Mohd Shahrizal Sunar, Abdullah Bade
Venue: Proceedings of the International Conference on Computer Graphics, Imaging and Visualization (2004)

Many researches in Non-Photorealistic Rendering (NPR) have been done to investigate a variety of techniques to simulate the styles of hand-drawn artists. Many applications in industrial, architectural, animated film production, technical design, and computer graphics designs have focused on rendering 3D models to depict non-photorealism. Most of them are based on rendering characters and object-based. This paper investigates on non-photorealistic rendering techniques for 3D outdoor scenes. Outdoor scene composed of a large extent of natural phenomena of landscapes, plants, trees, mountains, buildings, and many more. Techniques discussed in this paper include silhouette and cartoon-shaded renderings. Silhouette rendering implements Brute Force approach to determine the silhouette edges. Cel-shading algorithm in cartoon rendering renders the objects in the scene by manipulating directional or positional lightings with texture-shaded to give the scene cartoon look.
A hybrid-based texture synthesis approach
Authors: Chang-Hsing Wu, Yueh-Yi Lai, Wen-Kai Tai
Venue: The Visual Computer: International Journal of Computer Graphics (2004)

Texture synthesis has been an active research area in computer graphics, vision, and image processing. A hybrid texture synthesis approach that combines the strength of Ashikhmin&#x2019;s [1] and Liang&#x2019;s [11] algorithms is presented in this paper. Using patches from the input sample texture to extend the input itself, more suitable valid candidate pixels in the input sample can be more precisely determined. An extra original position array is used to record the valid pixel position in the extended region of input sample texture such that the candidate pixel can be retrieved efficiently. Pasting patches with more global information of texture features to initialize the output texture, the texture synthesis process tends to grow larger pieces in the output texture so that the perceptual similarity is reserved as much as possible. Many classes of textures have been used to test our approach. As the experimental results showed, the proposed hybrid approach effectively and efficiently synthesizes high-quality textures from a wide variety of textures.
Scaling IR-system evaluation using term relevance sets
Authors: Einat Amitay, David Carmel, Ronny Lempel, Aya Soffer
Venue: Proceedings of the 27th annual international ACM SIGIR conference on Research and development in information retrieval (2004)

This paper describes an evaluation method based on Term Relevance Sets Trels that measures an IR system's quality by examining the content of the retrieved results rather than by looking for pre-specified relevant pages. Trels consist of a list of terms believed to be relevant for a particular query as well as a list of irrelevant terms. The proposed method does not involve any document relevance judgments, and as such is not adversely affected by changes to the underlying collection. Therefore, it can better scale to very large, dynamic collections such as the Web. Moreover, this method can evaluate a system's effectiveness on an updatable "live" collection, or on collections derived from different data sources. Our experiments show that the proposed method is very highly correlated with official TREC measures.
Adaptive Routing of QoS-Constrained Media Streams over Scalable Overlay Topologies
Venue: Proceedings of the 10th IEEE Real-Time and Embedded Technology and Applications Symposium (2004)

Current research on Internet-based distributed systemsemphasizes the scalability of overlay topologies for efficientsearch and retrieval of data items, as well as routingamongst peers. However, most existing approaches fail toaddress the transport of data across these logical networksin accordance with quality of service (QoS) constraints.Consequently, this paper investigates the use of scalableoverlay topologies for routing real-time media streams betweenpublishers and potentially many thousands of subscribers.Specifically, we analyze the costs of using k-aryn-cubes for QoS-constrained routing. Given a numberof nodes in a distributed system, we calculate the optimalk-ary n-cube structure for minimizing the averagedistance between any pair of nodes. Using this structure,we describe a greedy algorithm that selects paths betweennodes in accordance with the real-time delays along physicallinks. We show this method improves the routing latenciesby as much as 40%, compared to approaches that donot consider physical link costs. Additionally, we discussan approach that dynamically repositions nodes in logicalspace, to improve the likelihood of meeting service requirementson data routed between publishers and subscribers.
TCP Offload to the Rescue
Authors: Andy Currid
Venue: Queue (2004)

In recent years, TCP/IP offload engines, known as TOEs, have attracted a good deal of industry attention and a sizable share of venture capital dollars. A TOE is a specialized network device that implements a significant portion of the TCP/IP protocol in hardware, thereby offloading TCP/IP processing from software running on a general-purpose CPU. This article examines the reasons behind the interest in TOEs and looks at challenges involved in their implementation and deployment.
Continuous K-Nearest Neighbor Search for Moving Objects
Authors: Yifan Li, Jiong Yang, Jiawei Han
Venue: Proceedings of the 16th International Conference on Scientific and Statistical Database Management (2004)

The paper describes a new method of continuously monitoringthe k nearest neighbors of a given object in the mobileenvironment.Instead of monitoring all k nearest neighbors,we choose to monitor the k-th (nearest) neighbor sincethe necessary condition of changes in the KNN is the changeof the k-th neighbor.In addition, rather than in the originalspace, we consider the moving objects in a transformedtime-distance (TD) space, where each object is representedby a curve.A beach-line algorithm is developed to monitorthe change of the k-th neighbor, which enables us to maintainthe KNN incrementally.An extensive empirical studyshows that the beach-line algorithm outperforms the mostefficient existing algorithm by a wide margin, especiallywhen k or n (the total number of objects) is large.
Adaptive passivity of nonlinear systems using time-varying gains
Authors: M. A. Duarte-Mermoud, R. Castro-Linares, A. Castillo-Facuse
Venue: Dynamics and Control (2001)

In this paper, an adaptive controller with time-varying gains is proposed to solve the problem of making a single-input single-output (SISO) nonlinear system, with explicit linear parametric uncertainty, equivalent to a passive system. Some stability issues associated to the resultant closed-loop passive system are also discussed. The results obtained are applied to two examples, a third order nonlinear system and a model of a magnetic levitation system, to show the controller methodology design.
Optimal Randomizer Efficiency in the Bounded-Storage Model
Authors: Stefan Dziembowski, Ueli Maurer
Venue: Journal of Cryptology (2004)

In the bounded-storage model for information-theoretically secure encryption and key-agreement one can prove the security of a cipher based on the sole assumption that the adversary&#x2019;s storage capacity is bounded, say by $s$ bits, even if her computational power is unlimited. Assume that a random $t$-bit string $R$ is either publicly available (e.g., the signal of a deep-space radio source) or broadcast by one of the legitimate parties. If $s < t$, the adversary can store only partial information about $R$. The legitimate sender Alice and receiver Bob, sharing a short secret key $K$ initially, can therefore potentially generate a very long $n$-bit one-time pad $X$ with $n\gg|K|$ about which the adversary has essentially no information.All \looseness = &#x2013;1 previous results in the bounded-storage model were partial or far from optimal, for one of the following reasons: either the secret key $K$ had to be longer than the derived one-time pad ($n < |K|$), or $t$ had to be extremely large ($t > ns$), or the adversary was assumed to be able to store only $s$ actual bits of $R$ rather than arbitrary $s$ bits of information about $R$, or the adversary received a non-negligible amount of information about $X$. In this paper we prove the first non-restricted security result in the bounded-storage model: $K$ is short, $X$ is very long, and $t$ needs to be only moderately larger than $s + n$. In fact, $s/t$ can be arbitrarily close to $1$ and hence the storage bound is essentially optimal. The security can be proved also if $R$ is not uniformly random, provided that the min-entropy of $R$ is sufficiently greater than $s$.
Implicit queries (IQ) for contextualized search
Authors: Susan Dumais, Edward Cutrell, Raman Sarin, Eric Horvitz
Venue: Proceedings of the 27th annual international ACM SIGIR conference on Research and development in information retrieval (2004)

The Implicit Query (IQ) prototype is a system which automatically generates context-sensitive searches based on a user's current computing activities. In the demo, we show IQ running when users are reading or composing email. Queries are automatically generated by analyzing the email message, and results are presented in a small pane adjacent to the current window to provide peripheral awareness of related information.
All-Nearest-Neighbors Queries in Spatial Databases
Authors: Jun Zhang, Nikos Mamoulis, Dimitris Papadias, Yufei Tao
Venue: Proceedings of the 16th International Conference on Scientific and Statistical Database Management (2004)

Given two sets A and B of multidimensional objects, theall-nearest-neighbors (ANN) query retrieves for eachobject in A its nearest neighbor in B. Although thisoperation is common in several applications, it has notreceived much attention in the database literature. Inthis paper we study alternative methods for processingANN queries depending on whether A and B areindexed. Our algorithms are evaluated throughextensive experimentation using synthetic and realdatasets. The performance studies show that they arean order of magnitude faster than a previous approachbased on closest-pairs query processing.