ppxscal/embedding_network huggingface dataset:
Comparison of Current BLAST Software on Nucleotide Sequences
Authors: I. Elizabeth Cha, Eric C. Rouchka
Venue: Proceedings of the 19th IEEE International Parallel and Distributed Processing Symposium (IPDPS'05) - Workshop 7 - Volume 08 (2005)

The computational power needed for searching exponentially growing databases, such as GenBank, has increased dramatically. Three different implementations of the most widely used sequence alignment tool, known as BLAST (Basic Local Alignment Search Tool), are studied for their efficiency on nucleotide-nucleotide comparisons. The performance of these implementations are evaluated using target databases and query sequences of varying lengths and number of entries constructed from human genomic and EST sequences. In general, WU BLAST was found to be most efficient when the database and query composition are unknown. NCBI BLAST appears to work best when the database contains a small number of sequences, while mpiBLAST shows the power of database distribution when the number of bases per target database is large. The optimal number of compute nodes in mpiBLAST varies depending upon the database, yet in the cases studied, remains surprisingly low.
Virtual laboratories for collaborative working in environment water
Authors: K.-Peter Holz, Gerald Hildebrandt, Tzveta Neltchinova
Venue: Proceedings of the 5th international conference on Computer systems and technologies (2004)

Modern information and communication technology (ICT) enables new technical solutions to support collaboration in environmental engineering over distance. The establishment of 'virtual laboratories' including application of Internet based project platforms, distributed team work and collaboration methods require new kinds of soft skills, knowledge and experience and a new 'technological culture' to be generated just by doing - a task for education, training and profession in Hydro-Informatics. This is a challenge for the European dimension, where in future experts and engineers from different countries with different languages, different mentalities as well as different specialization and professional experience have to collaborate in research teaching and practice. Training of collaborating in such new environment is the challenge of the courses HydroWeb and HydroEurope which by collaboration of 23 universities world-wide will help to establish common high quality university teaching courses and establish links between students from the involved countries.The students are solving a given environmental engineering task in distributed teams in the Internet. The students acquired in this course experience in interdisciplinary team work, net based project co-ordination and Web based reporting. They strengthened their social competence to collaborate in heterogeneous teams with members of different habits, nationalities, ages, educational backgrounds. The described experiment might be the basis to introduce Web based collaborative engineering in the regular course programme of water-environment related curricula at universities.
A Distributed Ontology Framework in the Semantic Grid Environment
Authors: Andrew Flahive, Wenny Rahayu, David Taniar, Bernady Apduhan
Venue: Proceedings of the 19th International Conference on Advanced Information Networking and Applications - Volume 2 (2005)

This paper explores a distributed ontology framework for tailoring ontologies in the Semantic Grid environment. The framework is divided into five main categories; Ontology Processing, Ontology Location, Ontology Connection, Usersý Connection and Algorithm Location. A number of possible scenarios are discussed following two Case Studies that indicate how the framework can be manipulated and used in various situations. This framework will help developers design tools for tailoring ontologies in the Semantic Grid Environment.
A Continuous Model for Multistore Competitive Location
Authors: Abdullah Dasci, Gilbert Laporte
Venue: Operations Research (2005)

This paper presents a simple model to determine the location strategies of two retail firms planning to open a number of stores in a geographical market. Firms try to maximize their profit under a leader-follower type competition in which the number of stores is made endogenous by the introduction of fixed costs. A novel methodology is developed in which firms' strategies are defined in terms of their location densities. This methodology leads to a model that is solvable analytically, and to several results on competitive location strategies. First, it is shown that if the follower decides to enter a market, he enters at least as strongly as the leader. Second, the leader can effectively deter entry even if she is severely cost-disadvantaged. However, in some cases the leader is better off by allowing the follower to enter the market. Third, the leader may also let the follower enter the market in some situations where she has a cost advantage. It is also shown that in situations where both firms enter the market, their location strategies are quite insensitive to model parameters.
Adaptive Reservoir Evolutionary Algorithm: An Evolutionary On-Line Adaptation Scheme for Global Function Optimization
Authors: C. Munteanu, A. C. Rosa
Venue: Journal of Heuristics (2004)

This paper introduces a novel global optimization heuristic algorithm based on the basic paradigms of Evolutionary Algorithms (EA). The algorithm greatly extends a previous strategy proposed by the authors in Munteanu and Lazarescu (1998). In the newly designed algorithm the exploration/exploitation of the search space is adapted on-line based on the current features of the landscape that is being searched. The on-line adaptation mechanism involves a decision process as to whether more exploitation or exploration is needed depending on the current progress of the algorithm and on the current estimated potential of discovering better solutions. The convergence with probability 1 in finite time and discrete space is analyzed, as well as an extensive comparison with other evolutionary optimization heuristics is performed on a set of test functions.
Time-Accurate Aerodynamic Modeling of Synthetic Jets for Projectile Control
Authors: Jubaraj Sahu
Venue: Proceedings of the 2004 Users Group Conference (2004)

This paper describes a computational study undertaken to determine the aerodynamic effectof tiny unsteady synthetic jets as a means to provide the control authority needed to maneuver a spinning projectile at low subsonic speeds. Advanced Navier-Stokes computational techniques have been developed and used to obtain numerical solutions for the unsteady jet-interaction flow field at subsonic speeds and small angles of attack. Unsteady numerical results show the effect of the jet on the flow field and on the aerodynamic coefficients. The unsteady jet is shown to substantially alter the flow field both near the jet and the base region of the projectile that in turn affects the forces and moments even at zero degree angle of attack. The results have shown the potential of computational fluid dynamics to provide insight into the jet interaction flow fields and provided guidance as to the locations and sizes of the jets to generate the maximum control authority to maneuver a projectile to hit its target with precision.
Using an interaction model as a resource for communication in design
Authors: Maíra Greco de Paula, Bruno Santana da Silva, Simone Diniz Junqueira Barbosa
Venue: CHI '05 extended abstracts on Human factors in computing systems (2005)

Many design models and representations have been proposed to support user-centered system design, such as scenarios, use cases, and prototypes. With these artifacts, designers typically deal with representations of fragments of the application, and sometimes have difficulties communicating with one another about design decisions. To face some of the communication challenges during design, we believe that we could use a global view of the system's apparent behavior, from the users' point of view. Such a representation would serve as a common reference for HCI designers from different disciplinary backgrounds, helping to foster communication among them. In our goal to promote a shared understanding of the application, we have investigated different professionals' usage of MoLIC, an interaction modeling language that follows an interaction-as-conversation metaphor. MoLIC allows designers to build a blueprint of all the interactions that may take place when the application is used.
An Efficient Selected Feature Set for the Middle Age Persian Character Recognition
Authors: S. Alirezaee, H. Aghaeinia, M. Ahmadi, K. Faez
Venue: Proceedings of the 33rd Applied Imagery Pattern Recognition Workshop (2004)

In this paper, a morphological based method for recognition of handwritten middle Persian characters is presented. After pre-processing and noise cancellation, Morphological erosion operator with many structure elements is applied. The structure elements are with variable length lines at directions 0, 45, 90, 135 degrees. A five element feature set has been defined so: (1) relative energy of eroded version with respect to the original image energy (REL_ENG), (2) displacement of the center of mass (CM_DIS), (3) minimum eigenvalue (EIG_MIN), (4) maximum eigenvalue (EIG_MAX) and (5) its direction (EIG-DIR). These features are used to design a feedforward neural network with one hidden layer. The best classification error is about 2.39% (97.61% recognition rate), and is achieved with 150 neurons for the hidden layer.
A Portable Fingertip Tactile Feedback Array " Transmission System Reliability and Modelling
Authors: I. Sarakoglou, N. Tsagarakis, D. G. Caldwell
Venue: Proceedings of the First Joint Eurohaptics Conference and Symposium on Haptic Interfaces for Virtual Environment and Teleoperator Systems (2005)

In this paper we present our work towards the realization of a portable- wearable tactile display in the form of a 4 x 4 pin array actuated by miniature remotely (forearm) located motors. The display introduced has a capacity for force generation at up to 3N per tactor and pin displacements of 2.5mm. The bandwidth at this 2.5mm displacement is greater than 15Hz with significantly higher frequency with lower displacements needed in texture simulation. The total weight of the device is approximately 275g of which less than 10g are loading the finger.
Text Data Mining: A Case Study
Authors: Charles Wesley Ford, Chia-Chu Chiang, Hao Wu, Radhika R. Chilka, John R. Talburt
Venue: Proceedings of the International Conference on Information Technology: Coding and Computing (ITCC'05) - Volume I - Volume 01 (2005)

A vast amount of data is available on the web. Many companies have started to mine this data to augment datasets used in production. This paper presents an industry study for one such text data mining. The study and analysis of the extracted data from the web could be used to help improve products and services. A prototype has been completed and benched marked in the laboratory.
Cartesian closed stable categories
Authors: Ni Liu, Sheng-Gang Li
Venue: Information Sciences&mdash;Informatics and Computer Science: An International Journal (2005)

The aim of this paper is to establish some Cartesian closed categories which are between the two Cartesian closed categories: SLP (the category of L-domains and stable functions) and DI (the full subcategory of SLP whose objects are all dI-domains). First we show that the exponentials of every full subcategory of SLP are exactly the spaces of stable functions. Then we prove that the full subcategories SDMBC, SDCBC and SDABC of SLP which contain DI are all Cartesian closed, where the objects of SDMBC (resp., SDCBC, SDABC) are all distributive bc-domains which are meet-continuous (resp., continuous, algebraic). We also obtain many non-Cartesian closed full subcategories of SLP and present some reflective relations between those categories concerned.
A practical pattern recovery approach based on both structural and behavioral analysis
Authors: Heyuan Huang, Shensheng Zhang, Jian Cao, Yonghong Duan
Venue: Journal of Systems and Software (2005)

While the merit of using design patterns is clear for forward engineering, we could also benefit from design pattern recovery in program understanding and reverse engineering. In this paper, we present a practical approach to enlarge the recoverable scope and improve precision ratio of pattern recovery. To specify both structural aspect and behavioral aspect of design patterns, we introduce traditional predicate logic combined with Allen's interval-based temporal logic as our theory foundation. The formal specifications could be conveniently converted into Prolog representations to support pattern recovery. To illustrate how to specify and recover design patterns in our approach, we take one example for each category of design patterns. Moreover, we give a taxonomy of design patterns based on the analysis in our approach to show its applicable scope. To validate our approach, we have developed a tool named PRAssistor and analyzed two well-known open source frameworks. The experiment results show that most of the patterns addressed in our taxonomy have been recovered. Besides larger recoverable scope, the recovery precision of our approach is much higher than others. Furthermore, we consider that our approach and tool could be promisingly extended to support "Debug at Design Level" and "Pattern-Driven Refactoring".
Clustering methods as partial solutions to the space allocation problem
Authors: Robert Simpson Frew
Venue: ACM SIGDA Newsletter (1976)

The paper presents a three phase approach to the space allocation problem. The first phase is to identify the activities that can be considered as members of component groups by classification methods. Secondly to find organizational form for each of the groups and to locate the members into the layout. Thirdly to find organizational form for the whole system and to locate the groups in the system.
Detection and Reaction to Unplanned Operational Events in Large Scale Distributed Real-Time Embedded Systems
Authors: Jianming Ye, Joe Loyall, Rick Schantz, Gary Duzan
Venue: Proceedings of the 19th IEEE International Parallel and Distributed Processing Symposium (IPDPS'05) - Workshop 2 - Volume 03 (2005)

In recent years, we have seen an increase in the use of embedded systems in large distributed systems, often designed and optimized for critical real-time controls. These systems of systems often include multiple end-to-end application streams and share heterogeneous, constrained resources. Unlike most non-distributed, static, closed embedded systems, these systems operate in highly dynamic environments and need to be able to react in real-time to changes in missions, conditions and operating environments. Today more and more of these mission-critical distributed real-time embedded (DRE) systems are becoming Quality of Service (QoS) enabled, thus providing predictable, adaptable, and managed behaviors. Due to the dynamic and distributed nature of DRE systems, unplanned events can occur that could significantly impact the behavior and performance of these systems. Examples of unplanned events are significantly less than expected available resources, system failures, unexpected service demands, and events completely outside the system scope which have unanticipated side effects on its operation.
Communicating Quality of Service Requirements to an Object-Based Storage Device
Authors: Kevin KleinOsowski, Tom Ruwart, David J. Lilja
Venue: Proceedings of the 22nd IEEE / 13th NASA Goddard Conference on Mass Storage Systems and Technologies (2005)

Obtaining consistent bandwidth with predictable latency from disk-based storage systems has proven difficult due to the storage system's inability to understand Quality of Service (QoS) requirements. In this paper, we present a feasibility study of QoS with the Object-based Storage Device (OSD) specification. We look at OSD's ability to provide QoS guarantees for consistent bandwidth with predictable latency. Included in this paper is a description of QoS requirements of a sample application and how these requirements are translated into parameters that are then communicated to, and interpreted by, the OSD. Implementation problems lead to the failure of a hard real-time QoS model, but this failure is not due to the OSD protocol. The paper concludes with a description of how well the Revision 9 OSD standard (OSDR9) is able to accommodate QoS. We provide suggestions for improving the OSD specification and its ability to communicate QoS requirements.
epsilon-SSVR: A Smooth Support Vector Machine for epsilon-Insensitive Regression
Authors: Yuh-Jye Lee, Wen-Feng Hsieh, Chien-Ming Huang
Venue: IEEE Transactions on Knowledge and Data Engineering (2005)

A new smoothing strategy for solving \epsilon{\hbox{-}}{\rm{support}} vector regression (\epsilon{\hbox{-}}{\rm{SVR}}), tolerating a small error in fitting a given data set linearly or nonlinearly, is proposed in this paper. Conventionally, \epsilon{\hbox{-}}{\rm{SVR}} is formulated as a constrained minimization problem, namely, a convex quadratic programming problem. We apply the smoothing techniques that have been used for solving the support vector machine for classification, to replace the \epsilon{\hbox{-}}{\rm{insensitive}} loss function by an accurate smooth approximation. This will allow us to solve \epsilon{\hbox{-}}{\rm{SVR}} as an unconstrained minimization problem directly. We term this reformulated problem as \epsilon{\hbox{-}}{\rm{smooth}} support vector regression (\epsilon{\hbox{-}}{\rm{SSVR}}). We also prescribe a Newton-Armijo algorithm that has been shown to be convergent globally and quadratically to solve our \epsilon{\hbox{-}}{\rm{SSVR}}. In order to handle the case of nonlinear regression with a massive data set, we also introduce the reduced kernel technique in this paper to avoid the computational difficulties in dealing with a huge and fully dense kernel matrix. Numerical results and comparisons are given to demonstrate the effectiveness and speed of the algorithm.
Modeling and Simulation of a LFVC Scheduler
Authors: Antonio Marcos Alberti
Venue: Proceedings of the 38th annual Symposium on Simulation (2005)

Service disciplines that approximate GPS have had a lot of success satisfying QoS isolation among connections in integrated services networks. In the past years, several of such disciplines were developed. However, to maintain a delay little bigger than GPS, with a fair throughput and a good worst-case fairness while reducing computational overhead is a big challenge. LFVC appears to be the first service discipline that optimizes these factors. This motivated us to implement an original LFVC model in the context of an ATM network model, originally developed to trustworthily evaluate QoS in ATM networks. LFVC expands this model and improves its quality, since LFVC is capable to isolate traffic and capture service differences among connections. In addition, LFVC interacts with other models of this model set, producing better simulation results. The paper also presents a model validation and a performance evaluation of the LFVC scheduler.
A Technical Comparison of IPSec and SSL
Authors: AbdelNasir Alshamsi, Takamichi Saito
Venue: Proceedings of the 19th International Conference on Advanced Information Networking and Applications - Volume 2 (2005)

IPSec (IP Security) and SSL (Secure Socket layer) have been the most robust and most potential tools available for securing communications over theInternet. Both IPSec and SSL have advantages andshortcomings. Yet no paper has been found comparing the two protocols in terms of characteristic andfunctionality. Our objective is to present an analysis of security and performance properties for IPSec and SSL.
Name creation implements restriction in the &pi;-calculus
Authors: Yoshinobu Kawabe, Ken Mano, Eiichi Horita, Kiyoshi Kogure
Venue: Systems and Computers in Japan (2005)

The &pi;-calculus is a process algebra that is capable of expressing the dynamic connection of communication links between processes. In this paper, we describe a methodology for implementing the communication links necessary for implementing the &pi;-calculus. In the &pi;-calculus, the communication links are formalized using the notion of name restriction, while in the implementation communication links are easily handled by name creation. No formal proof is given for their equivalence. Moreover, for the &pi;-calculus augmented with data types, there is a counterexample of the equivalence. In this paper, we argue the restriction under which the equivalence holds for the &pi;-calculus augmented with data types. &copy; 2005 Wiley Periodicals, Inc. Syst Comp Jpn, 36(2): 78&ndash;91, 2005; Published online in Wiley InterScience (). DOI 10.1002&sol;scj.10302
Improvement of Power-Performance Efficiency for High-End Computing
Authors: Rong Ge, Xizhou Feng, Kirk W. Cameron
Venue: Proceedings of the 19th IEEE International Parallel and Distributed Processing Symposium (IPDPS'05) - Workshop 11 - Volume 12 (2005)

Left unchecked, the fundamental drive to increase peak performance using tens of thousands of power hungry components will lead to intolerable operating costs and failure rates. Recent work has shown application characteristics of single-processor, memorybound non-interactive codes and distributed, interactive web services can be exploited to conserve power and energy with minimal performance impact. Our novel approach is to exploit parallel performance inefficiencies characteristic of non-interactive, distributed scientific applications, conserving energy using DVS (dynamic voltage scaling) without impacting time-to-solution (TTS) significantly, reducing cost and improving reliability. We present a software framework to analyze and optimize distributed power-performance using DVS implemented on a 16-node Centrino-based cluster. Using various DVS strategies we achieve application-dependent overall system energy savings as large as 25% with as little as 2% performance impact.
Shape segmentation using local slippage analysis
Authors: Natasha Gelfand, Leonidas J. Guibas
Venue: Proceedings of the 2004 Eurographics/ACM SIGGRAPH symposium on Geometry processing (2004)

We propose a method for segmentation of 3D scanned shapes into simple geometric parts. Given an input point cloud, our method computes a set of components which possess one or more slippable motions: rigid motions which, when applied to a shape, slide the transformed version against the stationary version without forming any gaps. Slippable shapes include rotationally and translationally symmetrical shapes such as planes, spheres, and cylinders, which are often found as components of scanned mechanical parts. We show how to determine the slippable motions of a given shape by computing eigenvalues of a certain symmetric matrix derived from the points and normals of the shape. Our algorithm then discovers slippable components in the input data by computing local slippage signatures at a set of points of the input and iteratively aggregating regions with matching slippable motions. We demonstrate the performance of our algorithm for reverse engineering surfaces of mechanical parts.