ppxscal/embedding_network huggingface dataset:
Statistical Methods for the Discovery of Co-Operative Transcription Factors: The Co-bind Code Revised
Authors: Giovanni Lavorgna, Paolo Palazzari, Alessandro Marongiu, Vittorio Rosato, Simone Melchionna, Paolo Verrecchia
Venue: Proceedings of the 19th IEEE International Parallel and Distributed Processing Symposium (IPDPS'05) - Workshop 7 - Volume 08 (2005)

Discovering co-operative Transcription Factors (TF's) within the genome is a computationally challenging problem, tackled through Monte Carlo-like analysis by the Co-Bind code, developed at the Department of Genetics of the St. Louis Washington University. Due to its statistical nature, Co-Bind is characterized by very long execution times, order of days on current high-end workstations, and could benefit from parallelization and a wise optimization, performed at both the algorithmic and coding levels. This work presents the results achieved by parallelizing Co-Bind and optimising the parallel code and shows that, on a 16-processor architecture, a speedup greater than two orders of magnitude is achieved with respect to the serial version released by the code's authors.
Interleaved semantic interpretation in environment-based parsing
Authors: William Schuler
Venue: Proceedings of the 19th international conference on Computational linguistics - Volume 1 (2002)

This paper extends a polynomial-time parsing algorithm that resolves structural ambiguity in input sentences by calculating and comparing the denotations of rival constituents, given some model of the application environment (Schuler, 2001). The algorithm is extended to incorporate a full set of logical operators, including quantifiers and conjunctions, into this calculation without increasing the complexity of the overall algorithm beyond polynomial time, both in terms of the length of the input and the number of entities in the environment model.
Qwerty-like 3x4 keypad layouts for mobile phone
Authors: Sunyu Hwang, Geehyuk Lee
Venue: CHI '05 extended abstracts on Human factors in computing systems (2005)

Most computer users are accustomed to the QWERTY keyboard layout. This study was started from the hypothesis that a user's skill in a QWERTY keyboard may be transferred to a 3x4 keypad environment. In order to test the hypothesis, we designed an experiment where users are instructed to type a series of sentences on a "blank" keypad after they were informed that the underlying layout is either QWERTY-like or ABC-type (alphabetical). We observed a more localized layout of typed characters over keys in the QWERTY-like case than in the ABC case. Encouraged by the results, we carried out a series of experiments in order to compare a QWERTY-like layout and an ABC-type layout, and obtained consistently better learning curves and better final typing speeds with a QWERTY-like keypad. As an effort to explain the results, we carried out an eye-gaze analysis for the two cases, and the results are presented.
Non-speech sound and paralinguistic parameters in mobile speech applications
Authors: Peter Fröhlich
Venue: CHI '05 extended abstracts on Human factors in computing systems (2005)

This paper describes the background, research questions and methodology of user studies on the integration of non-speech sound and paralinguistic parameters in speech-enabled applications. Preliminary results are summarized and future directions are discussed.
Minimizing development and maintenance costs in supporting persistently optimized BLAS
Authors: R. Clint Whaley, Antoine Petitet
Venue: Software&mdash;Practice Experience (2005)

The Basic Linear Algebra Subprograms &lpar;BLAS&rpar; define one of the most heavily used performance-critical APIs in scientific computing today. It has long been understood that the most important of these routines, the dense Level 3 BLAS, may be written efficiently given a highly optimized general matrix multiply routine. In this paper, however, we show that an even larger set of operations can be efficiently maintained using a much simpler matrix multiply kernel. Indeed, this is how our own project, ATLAS &lpar;which provides one of the most widely used BLAS implementations in use today&rpar;, supports a large variety of performance-critical routines. Copyright &copy; 2004 John Wiley & Sons, Ltd.
Bow Spring/Tendon Actuation for Low Cost Haptic Interfaces
Authors: Dale A. Lawrence, Lucy Y. Pao, Sutha Aphanuphong
Venue: Proceedings of the First Joint Eurohaptics Conference and Symposium on Haptic Interfaces for Virtual Environment and Teleoperator Systems (2005)

This paper describes a novel bow spring and tendon actuator design for a haptic interface that provides high-bandwidth force transmission to the fingers, with a large range of motion. This is combined with a low-cost stepper motor and a low-cost optical encoder, along with self-calibration and control compensation to produce a smooth force source with excellent hard virtual wall rendering capabilities. Four techniques are discussed to compensate for bow spring, friction, and ripple torques in the actuator. Experimental results quantify the achieved force rendering quality of each technique, and provide a measure of hard virtual surface rendering quality in one degree of freedom.
Architecture Reviews: Practice and Experience
Authors: Joseph F. Maranzano, Sandra A. Rozsypal, Gus H. Zimmerman, Guy W. Warnken, Patricia E. Wirth, David M. Weiss
Venue: IEEE Software (2005)

Architecture reviews have evolved over the past decade to become a critical part of continuing efforts to improve the software development process and the systems it produces. The reviews identify project problems before they become costly to fix and provide timely information to upper management so that they can make better-informed decisions. Development managers who want to establish architecture reviews as part of their development methodology will find that the process isn't difficult to implement, especially with experienced domain experts and a willing management team.
Plagiarism or Ignorance? You Decide
Authors: Sorel Reisman
Venue: IT Professional (2005)

Many undergraduates might be committing plagiarism in ignorance. New policies at CSUFunderscore instruction, rather than crime detection.
Lightweight Morphing Support for Evolving Middleware Data Exchanges in Distributed Applications
Authors: Sandip Agarwala, Greg Eisenhauer, Karsten Schwan
Venue: Proceedings of the 25th IEEE International Conference on Distributed Computing Systems (2005)

Most systems must evolve as their missions or roles change and/or as they adapt to new execution environments. When evolving large distributed applications, it is particularly difficult to make changes to the data formats that underlie their componentsý communications, because such ýformat evolutioný can affect all or many application components. Prior approaches to the problem of implementing changes in the communications of a deployed system have relied upon ad-hoc solutions or on protocol negotiation to avoid message format mismatches. Unfortunately, such solutions tend to increase the complexity of application code. This paper presents a novel approach to the problem of data format evolution that combines meta-data about the data being exchanged with dynamic binary code generation to create a robust data exchange system that naturally supports application evolution. The idea is to specialize the communications of application components by dynamically generating the code that can automatically transform incoming data into forms that receiving components can understand. A realistic example in the context of publish/subscribe middleware is used to illustrate how this technique can be applied to enhance interoperability between different version of distributed applications.
Support Vector Machine and Generalized Regression Neural Network Based Classification Fusion Models for Cancer Diagnosis
Authors: Muhammad Shoaib B. Sehgal, Iqbal Gondal, Laurence Dooley
Venue: Proceedings of the Fourth International Conference on Hybrid Intelligent Systems (2004)

This paper presents decision-based fusion models to classify BRCA1, BRCA2 and Sporadic genetic mutations for breast and ovarian cancer. Different ensembles of base classifiers using the stacked generalization technique have been proposed including Support Vector Machines (SVM) with linear, polynomial and radial base function kernels. A Generalized Regression Neural Networks (GRNN) is then applied to predict the mutation type based on the outputs of base classifiers, and experimental results will show that the new proposed fusion methodology for selecting the best and removing weak classifiers outperforms single classification models.
A Software Development Support Portal (SDSP) Based on a Peer-to-Peer Platform - A Case Study
Authors: W. C. Wong, Eric Moy, Mohammad Eyadat
Venue: Proceedings of the International Conference on Information Technology: Coding and Computing (ITCC'05) - Volume II - Volume 02 (2005)

As more and more organizations and companies increasingly outsource system development projects offshore the complexity of management and support increases proportionally. Traditional software development support tools are no longer sufficient to support a geographically and culturally diversified development team. Furthermore, to increase the chance of success, clients and stakeholders should be invited to participate in every step of the development. There is a need of a software development support portal (SDSP) to tie all the pieces together. In this paper, we propose a software development support portal that is designed and implemented based on a commercially available Peer-to-Peer (P2P) platform.
Visualization of mobile object environments
Authors: Yaniv Frishman, Ayellet Tal
Venue: Proceedings of the 2005 ACM symposium on Software visualization (2005)

This paper presents a system for visualizing mobile object frameworks. In such frameworks, the objects can migrate to remote hosts, along with their state and behavior, while the application is running. An innovative graph-based visualization is used to depict the physical and the logical connections in the distributed object network. Scalability is achieved by using a focus+context technique jointly with a user-steered clustering algorithm. In addition, an event synchronization model for mobile objects is presented. The system has been applied to visualizing several mobile object applications.
Priority inversion in multi processor systems due to protected actions
Authors: Gustaf Naeser
Venue: ACM SIGAda Ada Letters (2005)

The use of multiple processors give rise to new issues regarding old problems of the Ada95 design.In this paper we discuss how serviceing of protected actions, due to unspecified dispatching, can lead to unbounded priority inversion in systems with multiple processors. We also discuss different ways to resolve the problem.
An efficient quality of service routing algorithm for delay-sensitive applications
Authors: Wei Liu, Wenjing Lou, Yuguang Fang
Venue: Computer Networks: The International Journal of Computer and Telecommunications Networking (2005)

It is well known that the Delay-Constrained Least-Cost (DCLC) unicast routing problem is NP-complete, hence various heuristic algorithms have been developed for this problem. In this paper, we propose a more efficient distributed algorithm, namely, Selection-Function-based DCLC (SF-DCLC), based on a novel selection function for the DCLC problem. The proposed SF-DCLC algorithm requires limited network state information at each node and is always able to find a loop-free path satisfying the delay bound if such paths exist. Simulation study shows that SF-DCLC is not as sensitive to the delay bound and the size of networks as some other DCLC routing algorithms, and has very low cost-inefficiency compared to the optimal one in various network scenarios we have studied. A noteworthy feature of SFDCLC is that SF-DCLC has very high probability of finding the optimal solution in polynomial time with low computational complexity and message complexity.
A Formal Method for Program Slicing
Authors: Yingzhou Zhang, Baowen Xu, Jose Emilio Labra Gayo
Venue: Proceedings of the 2005 Australian conference on Software Engineering (2005)

Program slicing is a well-known program analysis technique that extracts the elements of a program related to a particular computation. Based on modular monadic semantics of a programming language, this paper presents a new formal method for slicing, called modular monadic slicing, by abstracting the computation of slicing as a slice monad transformer. With the use of slice transformer, the feature of program slicing can be combined in a modular way into semantic descriptions of the program analyzed. According to these, this paper gives both monadic dynamic and static slicing algorithms. They compute program slices directly on abstract syntax, without the needs to explicitly construct intermediate structures such as dependence graphs, or to record an execution history in dynamic slicing algorithm.
Spread spectrum watermarking technique for information system securing
Authors: Todor Todorov
Venue: Proceedings of the 5th international conference on Computer systems and technologies (2004)

In this paper we consider a computer information system and a way to realize the security of the data in it with digital watermarking. A technique for spread spectrum watermarking is presented and its realization with MathLAB 6.5 is shown.
A Novel Fingerprint Matching Method Based on the Hough Transform without Quantization of the Hough Space
Authors: Jin Qi, Zhongchao Shi, Xuying Zhao, Yangsheng Wang
Venue: Proceedings of the Third International Conference on Image and Graphics (2004)

In contrast to the conventional usage of the Hough transform for fingerprint alignment, our novel Hough transform-based fingerprint registration algorithm proposed in this paper doesnýt need to discretize the Hough space when estimating the parameters of the rigid transformation between two fingerprint impressions. In our algorithm the parameters (rotation, .. translation and .. translation) of the transform (rigid transform considered) can be estimated separately. In addition, the orientation fields from the fingerprints, instead of the minutiae, are used to estimate the most optimal rotation parameter. The experimental results obtained on the public domain collections of fingerprint images, FVC2002 db2 set A (800 fingerprints) and db3 set A (800 fingerprints) , show that the new fingerprint registration algorithm presented by us in this paper is faster and more effective compared to the conventional generalized Hough transform-based fingerprint alignment method.
Dynamics of Team Member Replacements from Complex Systems Theory
Authors: Daniel J. Lacks
Venue: Computational Mathematical Organization Theory (2005)

Simulations based on the NK model are carried out to address team member replacements that follow tweaking (i.e., gradual changes) of the strategy of the team leader. For simple teams in which the team members do not interact, team member replacements occur independently. However, for teams in which team members interact with other team members, team member replacements occur as cascades. In these cascades, the replacement of one team member triggers the replacement of another, which triggers the replacement of yet another, and so on. These cascades of team member replacements are largest for teams with intermediate complexity, in which each member interacts with between $${\frac{1}{4}}$$ and $${\frac{1}{2}}$$ of the other team members. The cascades are roughly independent of team size, and so smaller teams are more volatile in that the cascades affect a larger fraction of the team.
Introduction
Authors: Anand Desai
Venue: Communications of the ACM (2005)

It is common knowledge that individuals, the communities in which we live, and the organizations we create adapt over time and changing conditions. It is also generally understood that organizations, communities, and individuals are all complex entities. To state that organizations are adaptive complex enterprises (ACE) is neither novel nor new: What is new, however, is that we now have a language and a set of constructs that allow us to formally conceptualize and discuss these concepts. (See the sidebar for a brief discussion of the terms adaptive complex enterprises and complex adaptive systems.)
Power-Aware Communication Optimization for Networks-on-Chips with Voltage Scalable Links
Authors: Dongkun Shin, Jihong Kim
Venue: Proceedings of the international conference on Hardware/Software Codesign and System Synthesis: 2004 (2004)

Networks-on-Chip (NOC) is emerging as a practical development platform for future systems-on-chip products. We propose an energy-efficient static algorithm which optimizes the energy consumption of task communications in NoCs with voltage scalable links. In order to find optimal link speeds, the proposed algorithm (based on a genetic formulation) globally explores the design space of NOC-based systems, including task assignment, tile mapping, routing path allocation, task scheduling and link speed assignment. Experimental results show that the proposed design technique can reduce energy consumption by 28% on average compared with existing techniques.
Cooperative approach for mobile application adaptability based on MobileJMS
Authors: Mejdi Kaddour, Laurent Pautet
Venue: Proceedings of the 1st French-speaking conference on Mobility and ubiquity computing (2004)

Application adaptability to context changes has emerged as an absolute necessary criteria in the design of successful mobile systems. In this context, we investigate in this paper various factors to be taken into account to reach this goal. We propose an approach based on the cooperation between applications and the MobileJMS middleware which we developed previously. First, applications specify their requirements and constraints in terms of quality of service. Second, middleware provides primitives which fulfill these requirements and constraints. This equation is completed by the correlation between the quality of the service and the execution context of the applications.
ABSTRACTS OF INTEREST
Authors: Susanne M. Humphrey, Ben Shneiderman
Venue: ACM SIGCHI Bulletin (1993)

The following abstracts were selected from a computer search using the BRS Information Technologies retrieval services of the Dissertation Abstracts International (DAI) database produced by University Microfilms International.Unless otherwise specified, paper or microform copies of dissertations may be ordered, using the UMI order number, from University Microfilms International, Dissertation Copies, Post Office Box 1764, Ann Arbor, MI 488106; telephone for U.S. (except Michigan, Hawaii, or Alaska): 800/521-3042, for Canada: 800/268-6090. Price lists, ordering, and shipping information are in the introduction to the published DAI. An alternative source for copies is sometimes provided at the end of the abstract.The dissertation titles and abstracts contained here are published with permission of University Microfilms International, publishers of Dissertation Abstracts International (copyright 1985 by University Microfilms International), and may not be reproduced without their prior permission.
A Fracture Mechanics Approach to Haptic Synthesis of Tissue Cutting with Scissors
Authors: Mohsen Mahvash, Allison M. Okamura
Venue: Proceedings of the First Joint Eurohaptics Conference and Symposium on Haptic Interfaces for Virtual Environment and Teleoperator Systems (2005)

An analytical model for cutting of a plate of material with a pair of scissors is presented in terms of concepts of contact and fracture mechanics. The forces of contact between the blade of the scissors and the plate are expressed by a nonlinear function of deflection at the crack front multiplied by the length of the contact region between the blade and the plate. The cutting model captures the combined effect of multiple fracture modes. The level of deflection that causes fracture is obtained using an energy approach. The cutting model predicts that, during fracture, force and torque responses of the scissors depend on the toughness and geometry of the plate, but do not depend on the stiffness of the plate. The model is used for haptic synthesis of interaction between a pair of scissors and a virtual plate. An implementation of the model is presented for the case of surgical scissors in contact with skin. The simulation results are compared to previous experimental data, demonstrating the realism of the cutting model behavior. This haptic rendering technique is computationally efficient and can be applied to real-time simulation.
Solutions for increasing the number of PC parallel port control and selecting lines
Authors: Mircea Popa
Venue: Proceedings of the 5th international conference on Computer systems and technologies (2004)

The paper approaches the problem of control and selecting possibilities offered by the PC parallel port. Although it is the most frequently used PC port for controlling external applications, the parallel port has severe limitations in generating chip select and control signals. Their number can be increased by using the parallel port data lines, extra hardware and specific routines. Higher speed can be obtained if the EPP and ECP modes are used. Techniques for increasing the number of chip select and control signals generated by the PC parallel port are presented and analyzed.
MieLog: A Highly Interactive Visual Log Browser Using Information Visualization and Statistical Analysis
Venue: Proceedings of the 16th USENIX conference on System administration (2002)

System administration has become an increasingly important function, with the fundamental task being the inspection of computer log-files. It is not, however, easy to perform such tasks for two reasons. One is the high recognition load of log contents due to the massive amount of textual data. It is a tedious, time-consuming and often error-prone task to read through them. The other problem is the difficulty in extracting unusual messages from the log. If an administrator does not have the knowledge or experience, he or she cannot readily recognize unusual log messages. To help address these issues, we have developed a highly interactive visual log browser called "MieLog." MieLog uses two techniques for manual log inspection tasks: information visualization and statistical analysis. Information visualization is helpful in reducing the recognition load because it provides an alternative method of interpreting textual information without reading. Statistical analysis enables the extraction of unusual log messages without domain specific knowledge. We will give three examples that illustrate the ability of the MieLog system to isolate unusual messages more easily than before.