ppxscal/embedding_network huggingface dataset:
Guaranteed inconsistency avoidance during software evolution
Authors: Keith Gallagher, Mark Harman, Sebastin Danicic
Venue: Journal of Software Maintenance: Research and Practice (2003)

The attempt to design and integrate consistent changes to an existing system is the essence of software maintenance. Software developers also confront similar problems: there are changes during testing and the release of new system builds. Whether in development or maintenance, changes to evolving systems must be made consistently; that is, without damaging correct computations. It is difficult for the programmer to ascertain the complete effect of a code change; the programmer may make a change to a program that is syntactically and semantically legal, but which has ripples into the parts of the program that were intended to remain unchanged.Using the standard denotational semantics for procedural programming languages, this paper formalizes decomposition slicing, which identifies interferences between software components and isolates the components to be changed. We enumerate the conditions for changing one component in ways that will guarantee that changes to it will not interact inconsistently and prove that changes made under these conditions are sound. Thus, the programmer can then execute changes secure in the knowledge that the semantics of the new system are guaranteed to be consistent with the projection of the semantics of the original for which it behaved correctly. Validating that the changes do not interfere not only guarantees consistency with respect to previous unchanging behaviors, but can also be achieved with a complexity proportional to the size of the change to be made.
Frequent-subsequence-based prediction of outer membrane proteins
Authors: Rong She, Fei Chen, Ke Wang, Martin Ester, Jennifer L. Gardy, Fiona S. L. Brinkman
Venue: Proceedings of the ninth ACM SIGKDD international conference on Knowledge discovery and data mining (2003)

A number of medically important disease-causing bacteria (collectively called Gram-negative bacteria) are noted for the extra "outer" membrane that surrounds their cell. Proteins resident in this membrane (outer membrane proteins, or OMPs) are of primary research interest for antibiotic and vaccine drug design as they are on the surface of the bacteria and so are the most accessible targets to develop new drugs against. With the development of genome sequencing technology and bioinformatics, biologists can now deduce all the proteins that are likely produced in a given bacteria and have attempted to classify where proteins are located in a bacterial cell. However such protein localization programs are currently least accurate when predicting OMPs, and so there is a current need for the development of a better OMP classifier. Data mining research suggests that the use of frequent patterns has good performance in aiding the development of accurate and efficient classification algorithms. In this paper, we present two methods to identify OMPs based on frequent subsequences and test them on all Gram-negative bacterial proteins whose localizations have been determined by biological experiments. One classifier follows an association rule approach, while the other is based on support vector machines (SVMs). We compare the proposed methods with the state-of-the-art methods in the biological domain. The results demonstrate that our methods are better both in terms of accurately identifying OMPs and providing biological insights that increase our understanding of the structures and functions of these important proteins.
Bi-CMOS Opto-Electronic Reception System for Application in High-Frequencies
Authors: J. Martínez-Castillo, A. Díaz-Sánchez, A. Torres-Jácome, R. S. Murphy-Arteaga, J. L. Finol
Venue: Proceedings of the 14th International Conference on Electronics, Communications and Computers (2004)

Two opto-electronics integrated circuits (OEIC) arepresented. CMOS transimpedance amplifier (TIA)structures based on the common-gate topology, usingnegative feedback with the integration of a siliconphotodiode, are discussed. Simulations were performedusing BSIM3V3, modified BSIM3v3, and EKV modelsfor high-frequency applications. Experimental andsimulation results were performed for a 0.8 µm SiBiCMOS AMS process, using HSPICE and CADENCEsimulators. Experimental results, obtained from S-parameters,show a transimpedance gain of 40 dB and abandwidth of 1.9 GHz.
Making the case for case-based learning in computer information systems
Authors: Morgan M. Jennings, Charles H. Mawhinney, Janos Fustos
Venue: Current issues in IT education (2003)

In this chapter, we report the results of a study comparing current student's perceptions of computer information systems with student's perceptions of 12 years past. We found that students continue to prefer more interaction than they perceive an IS career to provide. Given this we (1) report on some programs available in high schools to interest students in a CIS career and (2) discuss case or problem-based learning as a means to provide students with the interaction they desire and show them that it is an integral part of a CIS career.
Fundamental Limits of Reconstruction-Based Superresolution Algorithms under Local Translation
Authors: Zhouchen Lin, Heung-Yeung Shum
Venue: IEEE Transactions on Pattern Analysis and Machine Intelligence (2004)

Abstract--Superresolution is a technique that can produce images of a higher resolution than that of the originally captured ones. Nevertheless, improvement in resolution using such a technique is very limited in practice. This makes it significant to study the problem: ¿Do fundamental limits exist for superresolution?¿ In this paper, we focus on a major class of superresolution algorithms, called the reconstruction-based algorithms, which compute high-resolution images by simulating the image formation process. Assuming local translation among low-resolution images, this paper is the first attempt to determine the explicit limits of reconstruction-based algorithms, under both real and synthetic conditions. Based on the perturbation theory of linear systems, we obtain the superresolution limits from the conditioning analysis of the coefficient matrix. Moreover, we determine the number of low-resolution images that are sufficient to achieve the limit. Both real and synthetic experiments are carried out to verify our analysis.
Cluster rendering of skewed datasets via visualization
Authors: Keke Chen, Ling Liu
Venue: Proceedings of the 2003 ACM symposium on Applied computing (2003)

Information Visualization is commonly recognized as a useful method for understanding sophistication in large datasets. In this paper, we introduce a flexible clustering approach with visualization techniques, aiming at the datasets that have skewed cluster distribution. This paper has three contributions. First, we propose a framework Vista that incorporates information visualization methods into the clustering process in order to enhance the understanding of the intermediate clustering results and allow user to revise the clustering results easily. Second, we develop a visualization model that maps multidimensional dataset to 2D visualizations while preserving or partially preserving clusters. Third, based on the visualization model, a set of operating rules are proposed to guide the user rendering clusters efficiently. Experiments show that the Vista system can yield lower error rates for real datasets than typical automated algorithms.
Speeding-up Hirschberg and Hunt-Szymanski LCS algorithms
Authors: Maxime Crochemore, Costas S. Ilipoulos, Yoan J. Pinzon
Venue: Fundamenta Informaticae (2002)

Two algorithms are presented that solve the problem of recovering the longest common subsequence of two strings. The first algorithm is an improvement of Hirschberg's divide-and-conquer algorithm. The second algorithm is an improvement of Hunt-Szymanski algorithm based on an efficient computation of all dominant match points. These two algorithms use bit-vector operations and are shown to work very efficiently in practice.
Function and behavior representation in conceptual mechanical design
Authors: Y.-M. Deng
Venue: Artificial Intelligence for Engineering Design, Analysis and Manufacturing (2002)

Conceptual design seeks to deliver design concepts that implement desired functions. Function and behavior are two dominant terms used in the research of this design phase. However, there are still some fundamental ambiguities and confusions over their representation, which have greatly hindered the interchange of research ideas and the development of design synthesis strategies. For conceptual design of mechanical products specifically, this paper attempts to clarify these ambiguities. It classifies function as purpose function and action function and relates them to the different levels of design hierarchy and abstraction. It distinguishes between semantic and syntactic representations of function and behavior and summarizes basic representation schemes. It also proposes an input&ndash;output action transformation scheme for semantic function representation and an input&ndash;output flow of action scheme for semantic behavior representation. Based on these discoveries, a refined framework is proposed for conceptual mechanical product design, where a function&ndash;decomposition&ndash;mapping process is elaborated to demonstrate the necessities and usefulness of the presented work.
Methods for the semantic analysis of document markup
Authors: Petra Saskia Bayerl, Harald Lüngen, Daniela Goecke, Andreas Witt, Daniel Naber
Venue: Proceedings of the 2003 ACM symposium on Document engineering (2003)

We present an approach on how to investigate what kind of semantic information is regularly associated with the structural markup of scientific articles. This approach addresses the need for an explicit formal description of the semantics of text-oriented XML-documents. The domain of our investigation is a corpus of scientific articles from psychology and linguistics from both English and German online available journals.For our analyses, we provide XML-markup representing two kinds of semantic levels: the thematic level (i.e.\ topics in the text world that the article is about) and the functional or rhetorical level. Our hypothesis is that these semantic levels correlate with the articles' document structure also represented in XML. Articles have been annotated with the appropriate information. Each of the three informational levels is modelled in a separate XML document, since in our domain, the different description levels might conflict so that it is impossible to model them within a single XML document.For comparing and mining the resulting multi-layered\linebreak XML annotations of one article, a Prolog-based approach is used. It focusses on the comparison of XML markup that is distributed among different documents. Prolog predicates have been defined for inferring relations between levels of information that are modelled in separate XML documents. We demonstrate how the Prolog tool is applied in our corpus analyses.
Nurturing Next-Generation Computer Scientists
Authors: Paul Fishwick
Venue: Computer (2003)

Can merging fine arts and computer science create modern-day successors to Leonardo da Vinci?
Parlay X Web Services
Authors: H. Lofthouse, M. J. Yates, R. Stretch
Venue: BT Technology Journal (2004)

The Parlay X specification describes a number of Web Services that will provide a simple interface to telephony and other systems. Other telephony interface initiatives have addressed the needs of complex and niche applications. The Parlay X initiative has set out to address the needs of the wider population of application developers. These application developers should be able to create telephony applications with little or no knowledge of the underlying network. Version 1 of the specification is complete and should be released to the public in the near future. This version covers third-party call control, SMS, multimedia messaging, payment, account management, user status and user location. This paper discusses the motivation for these new initiatives and presents an overview of the specifications and also gives an insight into the implementations available.
A prototype debugger for Hermes
Authors: David Taylor
Venue: Proceedings of the 1992 conference of the Centre for Advanced Studies on Collaborative research - Volume 2 (1992)

Hemes programs consist of many processes interacting with each other through primitive operations defined as part of the language. Understanding the behaviour of a Hermes program, in order to debug it, requires understanding the interactions between processes. Other aspects of debugging are little different from debugging in a conventional, sequential-programming environment. A debugger prototype has been constructed that provides a display of interprocess interactions in Hermes. This paper describes the facilities of the debugger prototype and its interaction with a running Hermes program. The internal structure of the debugger and the additional facilities that would be required to extend it to a complete debugger are also briefly described.
Matching data dissemination algorithms to application requirements
Authors: John Heidemann, Fabio Silva, Deborah Estrin
Venue: Proceedings of the 1st international conference on Embedded networked sensor systems (2003)

A distinguishing characteristic of wireless sensor networks is the opportunity to exploit characteristics of the application at lower layers. This approach is encouraged by device resource constraints, and acceptable because devices are inexpensive and numerous enough that they can be dedicated to specific applications. Many data dissemination protocols have been proposed for multi-hop communication in sensor networks, each evaluated in some scenario. The premise of this paper is that, if protocols are designed to exploit application requirements, then no one protocol can be optimized for all applications.Instead, a family of protocols are needed, with guidance to match protocol to application. We show through field experiments with two tracking applications that choice of diffusion algorithm can affect application performance by 40--60%. These applications motivate the design of two new diffusion algorithms: push and one-phase pull diffusion. We describe these algorithms in comparison to previous algorithms, then systematically explore their performance as the number of sinks and sources, the traffic rate and node placement varies, and with and without geographic proximity in node placement and with and without geographically scoped communication. We characterize algorithm performance and highlight the effect of the choice of algorithm parameters. The end result of this work are guidelines to help application developers to match dissemination algorithms to application performance requirements.
Local supercomputing training in the computational sciences using remote national centers
Authors: Floyd B. Hanson
Venue: Future Generation Computer Systems (2003)

Local training for high performance computing using remote national supercomputing centers is quite different from training at the centers themselves or using local machines. The local site computing and communication resources are a fraction of those available at the national centers. However, training at the local site has the potential of training more computational science and engineering students in high performance computing by including those who are unable to travel to the national center for training. The experience gained from supercomputing courses and workshops in the last 17 years at the University of Illinois at Chicago is described. These courses serve as the kernel in the program for training computational science and engineering students. Many training techniques are illustrated, such as key local user's guides and starter problems that would be portable to other local sites. Training techniques are continually evolving to keep up with rapid changes in supercomputing. An essential feature of this program is the use of real supercomputer time on several supercomputer platforms at national centers with emphasis in solving large scale problems.
Improve Multi-Instance Neural Networks through Feature Selection
Authors: Min-Ling Zhang, Zhi-Hua Zhou
Venue: Neural Processing Letters (2004)

Multi-instance learning is regarded as a new learning framework where the training examples are bags composed of instances without labels, and the task is to predict the labels of unseen bags through analyzing the training bags with known labels. Recently, a multi-instance neural network BP-MIP was proposed. In this paper, BP-MIP is improved through adopting two different feature selection techniques, i.e. feature scaling with Diverse Density and feature reduction with principal component analysis. In detail, before feature vectors are fed to a BP-MIP neural network, they are scaled by the feature weights found by running Diverse Density on the training data, or projected by a linear transformation matrix formed by principal component analysis. Experiments show that these feature selection mechanisms can significantly improve the performance of BP-MIP.
Learning, Innovation and IT-Usage -- A Research Approach to Regional Development
Authors: Anders Edström, Mikael Lind, Jan Ljungberg
Venue: Proceedings of the Proceedings of the 37th Annual Hawaii International Conference on System Sciences (HICSS'04) - Track 8 - Volume 8 (2004)

Regional clusters of companies are becoming an increasingly important focus of government industrial policy makers and researchers. A cluster is a network of companies in an industrial sector where suppliers, customers, consultants, etc. interact together with regional policymakers and universities. Sometimes the individual firms compete, and sometimes theycollaborate. The delimited characteristics of a cluster to a regional area and an industrial sector, makes it possible to view the cluster as an arena or laboratory. The concept of regions as laboratories, which is the base for the present paper, does not have a policy orientation. Instead, it stresses the interactive and cooperative aspects, which emerge organically in a regional cluster. The paper presents the formation of a research arena in cooperation between the University College of Borås and the industry organization of Swedish mail order companies for studies of learning and innovations in IT usage within the cluster. The strategy to establish the arena, formulation of research questions and initial experiences are presented.
Finite element analysis for weakly coupled magneto-thermo-mechanical phenomena in shell structures
Authors: J. K. Sakellaris
Venue: Proceedings of the international conference on Computational methods in sciences and engineering (2003)

In a previous paper it was shown that, the use of the surface impedances concept, widely used already, can contribute to the construction of a universal model for eddy currents modeling in thin layers. This is the most fundamental part for a systematic approach on constructing an appropriate type of finite element analysis for weakly coupled magneto - thermo - mechanical phenomena in shell structures. At this point it would be very interesting, to remind, that this technique has been initially used for thin layers modeling. Such a structure can be represented by two surfaces with self - impedances Zaa and Zbb respectively, accompanied by a transfer impedance Ztr taking into account the interdependence of the phenomena on the two surfaces. Hence, the previous paper was devoted to the presentation of this universal model, which is accompanied by a new type of elements for its implementation. A second and a third part followed. The second part dealt with one directional coupling of magnetic and thermal phenomena, whilst the third one with one directional coupling of magnetic and mechanical phenomena very briefly and this the point from which, this paper starts.
Deductive Schedulability Verification Methodology of Real-Time Software using both Refinement Verification and Hybrid Automata
Authors: Satoshi Yamane
Venue: Proceedings of the 27th Annual International Conference on Computer Software and Applications (2003)

Real-time software runs over real-time operating systems,and guaranteeing qualities is difficult. As timing constraintsand resource allocations are strict, it is necessary to verifyschedulability, safety and liveness properties. In this paper,we formally specify real-time software using hybrid automataand verify its schedulability using both deductive refinementtheory and scheduling theory. In this case, the above real-timesoftware consists of periodic processes and a fixed-prioritypreemptive scheduling policy on one CPU. Using our proposedmethods, we can uniformally and easily specify real-timesoftware and verify its schedulability based on hybridautomata. Moreover, we can verify its schedulability at designstage.
&#x0022;Type/Token-taken&#x0022; informetrics: some comments and further examples
Authors: Quentin L. Burrell
Venue: Journal of the American Society for Information Science and Technology (2003)

Egghe has propounded the notion of Type/Token-Taken (T/TT) informetrics. In this note we show how his ideas relate to ones that are already well known in informetrics and resolve some of the specific problems posed.
An Adaptive Middleware for Context-Sensitive Communications for Real-Time Applications in Ubiquitous Computing Environments
Authors: Stephen S. Yau, Fariaz Karim
Venue: Real-Time Systems (2004)

Context-sensitivity is an important expected capability in applications in ubiquitous computing (ubicomp) environments. These applications need to use different contextual information from the user, host device, on board sensors, network, and the ambient environments to systematically adapt their actions. In addition, some context-sensitive applications may use specific contextual conditions to trigger impromptu and possibly short-lived interactions with applications in other devices. This property, referred to as context-sensitive or context-aware communications, allows applications to form short-range mobile ad hoc networks consisting of mobile and stationary devices, sensors, and other computing resources. Real-time applications, especially those having reactive behavior, running on embedded devices and requiring context-sensitive communications support, pose new challenges related to systematic representation of specific contexts, associations of contexts with real-time actions, timely context data collection and propagation, and transparent context-sensitive connection establishment. An object-based middleware can be effective to meet these challenges if such a middleware can provide a well-defined development framework as well as lightweight runtime services. In this paper, an adaptive and object-based middleware, called reconfigurable context-sensitive middleware (RCSM) is presented to facilitate context-sensitive communications in ubicomp environments. To facilitates context-sensitive communications, RCSM provides a context-aware interface definition language for specifying context-sensitive interfaces of real-time objects, an object container framework for generating interfaces-specific context-analyzers, and a context-sensitive object request broker for context-sensitive object discovery and impromptu connection management. RCSM is adaptive in the sense that depending on the context-sensitive behavior of the applications, it adapts its object discovery and connection management mechanisms.