ppxscal/embedding_network huggingface dataset:
Similar_Join: extending DBMS with a bio-specific operator
Authors: Jake Yue Chen, John V. Carlis
Venue: Proceedings of the 2003 ACM symposium on Applied computing (2003)

Existing sequence comparison software applications lack adequate automation, abstraction, performance, and flexibility. Users need a new way of studying and applying sequence comparisons in the post-genomics era. We invented and developed a new bio-specific Database Management System (DBMS) operator, Similar_Join, to abstract the labor-intensive batch sequence similarity search task into a syntactically concise database operation. We implemented the Similar_Join operator as part of a relational operator package. This implementation enabled us to write simple PL/SQL scripts within the DBMS to accomplish routine sequence similarity searches conveniently, for example, a "batch BLAST" that compares 7,000 human genes against 500,000 human Expressed Sequence Tags (EST) in a few hours. We also implemented a simple version of Similar_Join as a database operator in the extended data cartridge of Oracle 8i object-relational DBMS. When fully integrated into SQL language extensions, we demonstrated this operator could enable biology users to achieve interesting complex biological queries previously impossible inside the DBMS.
P2P with JXTA-Java pipes
Authors: Jean-Marc Seigneur, Gregory Biegel, Christian Damsgaard Jensen
Venue: Proceedings of the 2nd international conference on Principles and practice of programming in Java (2003)

The peer-to-peer (p2p) paradigm is attracting increasing attention from both the research community and software engineers, due to potential performance, reliability and scalability improvements. This paper emphasizes that JXTA can help teachers to teach p2p with Java. This paper also presents an approach for performance analysis of JXTA pipes - one of the key abstractions in JXTA, which has not yet been fully evaluated. It explains how to assess a pipe and demonstrates performance results of the JXTA-Java implementation. In doing so, this paper assists software developers in estimating the overall performance and scalability of JXTA, and the suitability of choosing JXTA for their specific application.
Semantic Conflict Resolution Ontology (SCROL): An Ontology for Detecting and Resolving Data and Schema-Level Semantic Conflicts
Authors: Sudha Ram, Jinsoo Park
Venue: IEEE Transactions on Knowledge and Data Engineering (2004)

Abstract--Establishing semantic interoperability among heterogeneous information sources has been a critical issue in the database community for the past two decades. Despite the critical importance, current approaches to semantic interoperability of heterogeneous databases have not been sufficiently effective. We propose a common ontology called Semantic Conflict Resolution Ontology (SCROL) that addresses the inherent difficulties in the conventional approaches, i.e., federated schema and domain ontology approaches. SCROL provides a systematic method for automatically detecting and resolving various semantic conflicts in heterogeneous databases. SCROL provides a dynamic mechanism of comparing and manipulating contextual knowledge of each information source, which is useful in achieving semantic interoperability among heterogeneous databases. We show how SCROL is used for detecting and resolving semantic conflicts between semantically equivalent schema and data elements. In addition, we present evaluation results to show that SCROL can be successfully used to automate the process of identifying and resolving semantic conflicts.
Information Retrieval with Distributed Databases: Analytic Models of Performance
Authors: Robert M. Losee, Lewis Church Jr.
Venue: IEEE Transactions on Parallel and Distributed Systems (2004)

Abstract--The major emphasis of this paper is on analytical techniques for predicting the performance of various collection fusion scenarios. Knowledge of analytical models of information retrieval system performance, both with single processors and with multiple processors, increases our understanding of the parameters (e.g., number of documents, ranking algorithms, stemming algorithms, stop word lists, etc.) affecting system behavior. While there is a growing literature on the implementation of distributed information retrieval systems and digital libraries, little research has focused on analytic models of performance. We analytically describe the performance for single and multiple processors, both when different processors have the same parameter values and when they have different values. The use of different ranking algorithms and parameter values at different sites is examined.
Advanced LCD Timing Controller IC with Memory-Assisted Response Time Compensation
Authors: Richard McCartney, Nikhil Balram
Venue: Proceedings of the 17th International Conference on VLSI Design (2004)

The electro-optic response times of the principal LCDmodes are not fast enough for video applications. Applyinga one-frame acceleration voltage, in lieu of the correctvideo command, can compensate the slow response time.This paper discusses the operation and design choices of atiming controller with an embedded LCD response timecompensator (RTC).
Finding an optimal path without growing the tree
Authors: Danny Z. Chen, Ovidiu Daescu, Xiaobo Hu, Jinhui Xu
Venue: Journal of Algorithms (2003)

For problems on computing an optimal path as well as its length in a certain setting, the "standard" approach for finding an actual optimal path is by building (or "growing") a single-source optimal path tree. In this paper, we study a class of optimal path problems with the following phenomenon: The space complexity of the algorithms for reporting the lengths of single-source optimal paths for these problems is asymptotically smaller than the space complexity of the "standard" tree-growing algorithms for finding actual optimal paths. We present a general and efficient algorithmic paradigm for finding an actual optimal path for such problems without having to grow a single-source optimal path tree. Our paradigm is based on the "marriage-before-conquer" strategy, the prune-and-search technique, and a new data structure called clipped trees. The paradigm enables us to compute an actual path for a number of optimal path problems and dynamic programming problems in computational geometry, graph theory, and combinatorial optimization. Our algorithmic solutions improve the space bounds (in certain cases, the time bounds as well) of the previously best known algorithms, and settle some open problems. Our techniques are likely to be applicable to other problems.
A RUP-based software process supporting progressive implementation
Authors: Tiago Lima Massoni, Augusto Cesar Alves Sampaio, Paulo Henrique Monteiro Borba
Venue: UML and the unified process (2003)

This chapter introduces an extension of the Rational Unified Process (RUP) with a method that supports the progressive, and separate, implementation of three different aspects: persistence, distribution, and concurrence control. This complements RUP with a specific implementation method, called Progressive Implementation Method (Pim), and helps to tame the complexity of applications that are persistent, distributed, and concurrent. By gradually and separately implementing, testing, and validating such applications, we obtain two major benefits: the impact caused by the requirements changes during development is reduced and testing and debugging are simplified. In addition, the authors hope to contribute to solving the lack of a specific implementation method in RUP.
Mining multiple phenotype structures underlying gene expression profiles
Authors: Chun Tang, Aidong Zhang
Venue: Proceedings of the twelfth international conference on Information and knowledge management (2003)

DNA microarray technology is now widely used in basic biomedical research for mRNA expression profiling and are increasingly being used to explore patterns of gene expression in clinical research. Automatically detecting phenotype structures from gene expression profiles can provide deep insight into the nature of many diseases as well as lead in the development of new drugs. While most of the previous studies focus on only mining empirical phenotype structure which the experiment controls, it is also interesting to detect possible hidden phenotype structures underlying gene expression profiles.Since the number of samples is usually limited, such data sets are very sparse in high-dimensional gene space. Furthermore, most of the genes of interest are buried in large amount of noise. Unsupervised phenotype structure discovery of such sparse high-dimensional data sets present interesting but challenging problems. In this paper, we propose the model of simultaneously mining both empirical and hidden phenotype structures from gene expression data. We demonstrate the effectiveness and efficiency of the proposed method on various real-world data sets.
High Performance Compression of Hyperspectral Imagery with Reduced Search Complexity in the Compressed Domain
Authors: Francesco Rizzo, Bruno Carpentieri, Giovanni Motta, James A. Storer
Venue: Proceedings of the Conference on Data Compression (2004)

In previous work we considered LPVQ, a compression algorithm based on LocallyOptimal Partitioned Vector Quantization that can be used to compress hyperspectral images byapplying partitioned VQ to the spectral signatures (e.g., to the 224 16-bit values of a NASAAVIRIS pixel) and then encoding error information with a threshold that can be varied from highquality lossy to near lossless to lossless (e.g., 50-to-1 lossy, 10-to-1 near lossless, or 3-to-1lossless). An advantage of LPVQ is extremely fast decoding (table lookup followed by entropydecoding), but it is at the cost of more complex encoding. Here we present a new low complexityalgorithm for hyperspectral image compression, called SLSQ, that employs linear predictiontargeted at spectral correlation followed by entropy coding of the prediction error. We thenconsider how SLSQ can be combined with LPVQ in a scenario commonly arising in practice. Inthis scenario, a low-complexity lossless encoder on the remote acquisition platform compressesthe data for transmission to a central computing facility, where it is processed and recoded usingLPVQ, so that the compressed data can be distributed to the final users at various quality levels.The VQ indices of the LPVQ form a lossy compressed image of only about 2% of the originalsize; this small image can be employed to greatly reduce the time for browsing and classification.
Introducing reliability in content-based publish-subscribe through epidemic algorithms
Authors: Paolo Costa, Matteo Migliavacca, Gian Pietro Picco, Gianpaolo Cugola
Venue: Proceedings of the 2nd international workshop on Distributed event-based systems (2003)

Distributed content-based publish-subscribe middleware provides the necessary decoupling, flexibility, expressiveness, and scalability required by modern distributed applications. Unfortunately, this middleware usually does not provide reliability, especially in the presence of highly reconfigurable scenarios. Indeed, this problem has been thus far largely disregarded by the research community and solutions developed in other contexts are not immediately applicable.In this paper, we tackle the problem of introducing reliability in content-based publish-subscribe in dynamic environments by exploiting epidemic algorithms, whose characteristics in terms of decentralization, scalability, and resilience to topological changes resonate with our problem.
Experiences with a tablet PC based lecture presentation system in computer science courses
Authors: Richard Anderson, Ruth Anderson, Beth Simon, Steven A. Wolfman, Tammy VanDeGrift, Ken Yasuhara
Venue: Proceedings of the 35th SIGCSE technical symposium on Computer science education (2004)

Computer science instructors frequently teach using slides displayed with a computer and a data projector. This has many advantages, e.g., ability to present prepared materials and ease of switching the display to a development environment during mid-presentation. However, existing computer-based presentation systems severely limit flexibility in delivery, hindering instructors' extemporaneous adaptation of their presentations to match their audiences. One major limitation of computer-based systems is lack of support for high-quality handwriting over slides, as with overhead projectors and other manual presentation systems. We developed and deployed Classroom Presenter, a Tablet PC-based presentation system that (1) combines the advantages of existing computer-based and manual presentation systems and (2) builds on these systems, introducing novel affordances. Classroom Presenter has been used in 25 Computer Science courses at three universities. In this paper we describe the system, summarize results from its deployment, and detail several novel uses of the system by instructors in computer science courses.
Some attacks upon authenticated group key agreement protocols
Authors: Olivier Pereira, Jean-Jacques Quisquater
Venue: Journal of Computer Security (2003)

During the last few years, a number of authenticated group key agreement protocols have been proposed in the literature. We observed that the efforts in this domain were mostly dedicated to the improvement of their performance in term of bandwidth or computational requirements, but that there were very few systematic studies on their security properties. In this paper, we tried to develop a systematic way to analyse protocol suites extending the Diffie-Hellman key-exchange scheme to a group setting and presented in the context of the Cliques project. This led us to propose a very simple machinery that allowed us to manually pinpoint several unpublished attacks against the main security properties claimed in the definition of these protocols (implicit key agreement, perfect forward secrecy, resistance to known-key attacks).
Distance-regular circulants
Authors: Štefko Miklavič, Primož Potočnik
Venue: European Journal of Combinatorics (2003)

A classification of strongly regular Cayley graphs of cyclic group was independently achieved by Bridges and Mena (Ars Combin. 8 (1979) 143), Hughes, van Lint and Wilson (Announcement at the Seventh British Combinatorial Conference (1979)), and Ma (Discrete Math. 52 (1984) 75). Here we discuss their results in a more general setting of distance-regular Cayley graphs, and give the complete classification of distance-regular Cayley graphs of cyclic groups. In particular, we prove that a Cayley graph of a cyclic group is distance-regular if and only if it is isomorphic to a cycle, or a complete graph, or a complete multipartite graph, or a complete bipartite graph on a twice an odd number of vertices with a matching removed, or the Paley graph with a prime number of vertices.
Response-Time Analysis of Composite Web Services
Authors: Daniel A. Menascé
Venue: IEEE Internet Computing (2004)

A single Internet application can invoke many different Web services for example, the metasearch engine WebSifter uses several online ontologies to refine a user's request into a more meaningful query and then submits that query to various search engines in parallel. We call such applications composite Web services. As I discussed in a previous column, many important challenges stem from the quality-of-service issues in composite Web services. In this column, I address the impact of slow services on the overall response time of a transaction that uses several Web services in parallel.
Controllability Mechanism for Object-Oriented Software Testing
Authors: Anita Goel, S. C. Gupta, S. K. Wasan
Venue: Proceedings of the Tenth Asia-Pacific Software Engineering Conference Software Engineering Conference (2003)

This paper presents a controllability mechanism thatfacilitates creation of difficult-to-achieve states, forexecution of state specific tests, during object-orientedsoftware testing. Provisions are made in the softwareduring the design phase and coded during the codingphase of software development. The mechanism requirescreating the control environment and incorporatingcontrol commands in the software during softwaredevelopment. The paper illustrates the control mechanismusing three examples, each requiring a unique controlenvironment to attain the difficult-to-create states.
A categorical framework for finite state machines
Authors: Peter Hines
Venue: Mathematical Structures in Computer Science (2003)

We provide a consistent way of looking at a range of finite state machines and their algebraic models. Our claim is that the natural representation of transitions of finite state machines is in terms of monoid homomorphisms, and distinct generalisation processes that can be applied to finite state machines correspond to distinct categorical generalisation processes at the level of the algebraic models.The generalisations we consider are those from deterministic to non-deterministic machines, from one-way to two-way machines, and from read-only machines to read&sol;write machines. Hence the finite state machines we consider, and provide algebraic models for, are (deterministic and non-deterministic) finite state automata, two-way automata, Mealy machines, and bounded Turing machines.The categorical constructions corresponding to these generalisation processes are, respectively: altering the base category from functions to relations, applying the Geometry of Interaction, or Int construction, and a categorical process, which we refer to as the Comp construction, that uses the tensor on monoidal categories to construct graded categories.
Synthesis of Partitioned Shared Memory Architectures for Energy-Efficient Multi-Processor SoC
Authors: Kimish Patel, Enrico Macii, Massimo Poncino
Venue: Proceedings of the conference on Design, automation and test in Europe - Volume 1 (2004)

Accesses to the shared memory in multi-processor systems-on-chip represent a significant performance bottleneck. Multi-port memories are a common solution to this problem, because they allow to parallelize accesses. However, they are not an energy-efficient solution.We propose an energy-efficient shared-memory architecture that can be used as a substitute for multi-port memories, which is based on an application-driven partitioning of the shared address space into a multi-bank architecture.Experiments on a set of parallel benchmarks show energy savings of about 56% with respect to a dual-port memory artchitecture, at a very limited performance penalty.
Detecting pattern-based outliers
Authors: Tianming Hu, Sam Y. Sung
Venue: Pattern Recognition Letters (2003)

Outlier detection targets those exceptional data that deviate from the general pattern. Besides high density clustering, there is another pattern called low density regularity. Thus, there are two types of outliers w.r.t. them. We propose two techniques: one to identify the two patterns and the other to detect the corresponding outliers.
Using SMIL to encode interactive, peer-level multimedia annotations
Authors: Dick C. A. Bulterman
Venue: Proceedings of the 2003 ACM symposium on Document engineering (2003)

This paper discusses applying facilities in SMIL 2.0 to the problem of annotating multimedia presentations. Rather than viewing annotations as collections of (abstract) meta-informa-tion for use in indexing, retrieval or semantic processing, we view annotations as a set of peer-level content with temporal and spatial relationships that are important in presenting a coherent story to a user. The composite nature of the collection of media is essential to the nature of peer-level annotations: you would typically annotate a single media item much differently than that same media item in the context of a total presentation.This paper focuses on the document engineering aspects of the annotation system. We do not consider any particular user interface for creating the annotations or any back-end storage architecture to save/search the annotations. Instead, we focus on how annotations can be represented within a common document architecture and we consider means of providing docu-ment facilities that meet the requirements of our user model. We present our work in the context of a medical patient dossier example.
Satellite system simulation
Authors: Franco Davoli, Mario Marchese
Venue: Applied system simulation: methodologies and applications (2003)

The chapter highlights techniques to simulate the behavior of real-time and non real-time satellite systems and clarifies possible application fields and motivations. Communication systems and, in particular, satellite components have increased their complexity. Simulation is a reality to explore new solutions without increasing hazards and costs: long phases of space missions are completely dedicated to forecast the behavior of the systems to be implemented and simulations are widely used. The chapter focuses on methods to evaluate the efficiency of a simulator, underlines some traffic models suited to simulate communication systems and explains particular topics where the authors have direct experience. A couple of tools are presented applied to the satellite environment: a C-language based non-real-time software simulator and a real-time simulator (emulator), where real machines can be attached to the tool, so as to avoid traffic modeling. Performance results are reported to better explain the concepts of the chapter.
Study on strand space model theory
Authors: Qing Guang Ji, Si Han Qing, Yong Bin Zhou, Deng Guo Feng
Venue: Journal of Computer Science and Technology (2003)

The growing interest in the application of formal methods of cryptographic protocol analysis has led to the development of a number of different ways for analyzing protocol. In this paper, it is strictly proved that if for any strand, there exists at least one bundle containing it, then an entity authentication protocol is secure in strand space model (SSM) with some small extensions. Unfortunately, the results of attack scenario demonstrate that this protocol and the Yahalom protocol and its modification are de facto insecure. By analyzing the reasons of failure of formal inference in strand space model, some deficiencies in original SSM are pointed out. In order to break through these limitations of analytic capability of SSM, the generalized strand space model (GSSM) induced by some protocol is proposed. In this model, some new classes of strands, oracle strands, high order oracle strands etc., are developed, and some notions are formalized strictly in GSSM, such as protocol attacks, valid protocol run and successful protocol run. GSSM can then be used to further analyze the entity authentication protocol. This analysis sheds light on why this protocol would be vulnerable while it illustrates that GSSM not only can prove security protocol correct, but also can be efficiently used to construct protocol attacks. It is also pointed out that using other protocol to attack some given protocol is essentially the same as the case of using the most of protocol itself.
Hardware support for user-access control on an object-oriented processor
Authors: K. M. Lo, P. L. Mok, W. S. Yu, Anthony S. Fong
Venue: Proceedings of the 1st international symposium on Information and communication technologies (2003)

JAVA is relatively a new Object-Oriented Programming (OOP) language. It has most of the advantages of Object-Oriented languages such as encapsulation, polymorphism, dynamic binding and inheritance. Consequently programs developed by JAVA are more reliable and secure. However, as traditional computer architectures RISC and CISC do not provide much hardware support for OOP, their performance for OOP is notoriously poor.jHISC is developed to target for JAVA and bases on High Level Instruction Set Computer (HISC) which supports Object-Oriented Programming (OOP) in hardware level. With jHISC architecture, software developer can take the advantages of OOP without the performance penalty.In this paper, a new algorithm of security management is introduced for jHISC. The algorithm can maximize the hardware supports to OOP of jHISC, to further improve the security and performance of JAVA program.