ppxscal/embedding_network huggingface dataset:
Enhancing the visualization process with principal component analysis to support the exploration of trends
Authors: Wolfgang Müller, Thomas Nocke, Heidrun Schumann
Venue: Proceedings of the 2006 Asia-Pacific Symposium on Information Visualisation - Volume 60 (2006)

This paper describes the integration of the Principal Component Analysis into the Visualization Process. Although, the combination of Principal Component Analysis (PCA) and visual methods is a common approach to the analysis of high-dimensional datasets, it is mostly limited to a pure preprocessing step for dimension reduction. In this paper we will discuss, how PCA results can be used to control all steps of the visualization pipeline to generate more effective visual representations, and thus, a higher degree of understanding of the PCA values as well as of original data.
Keynote II
Authors: C. Anderson
Venue: Proceedings of the 2004 IEEE International Symposium on Performance Analysis of Systems and Software (2004)

Memory hierarchy performance, specifically cache memory capacity, is a constraining factor in the performance of modern computers. This paper presents the results of two-level cache memory simulations and examines the impact of exclusive caching on system performance. Exclusive caching enables higher capacity with the same cache area by eliminating redundant copies. The experiments presented compare an exclusive cache hierarchy with an inclusive cache hierarchy utilizing similar L1 and L2 parameters. Experiments indicate that significant performance advantages can be gained for some benchmark through the use of an exclusive organization. The performance differences are illustrated using the L2 cache misses and execution time metrics. The most significant improvement shown is a 16% reduction in execution time, with an average reduction of 8% for the smallest cache configuration tested. With equal size victim buffer and victim cache for exclusive and inclusive cache hierarchies respectively, some benchmarks show increased execution time for exclusive caches because a victim cache can reduce conflict misses significantly while a victim buffer can introduce worst-case penalties. Considering the inconsistent performance improvement, the increased complexity of an exclusive cache hierarchy needs to be justified based upon the specifics of the application and system.
A Grid of Language Resource Repositories
Authors: Daan Broeder, Remco van Veenendaal, David Nathan, Sven Stromqvist
Venue: Proceedings of the Second IEEE International Conference on e-Science and Grid Computing (2006)

The DAM-LR (Distributed Access Management for Language Resources) project aims at virtually integrating various European language resource archives that allow users to navigate and operate in a single unified domain of language resources. This type of integration introduces Grid technology to the humanities disciplines and forms a federation of archives. It is the basis for establishing a research infrastructure for language resources which will finally enable eHumanities. Currently, the complete architecture is designed based on a few well-known components and some components have already been tested. Based on the technological insights gathered and due to discussions within the international DELAMAN (Digital Endangered Languages and Music Archives Network) network the ethical and organizational basis for such a federation is defined.
Dual security-based image steganography
Authors: Chun-Shien Lu
Venue: Proceedings of the 2003 International Conference on Multimedia and Expo - Volume 1 (2003)

In this paper, an image steganographic method with security level confined to a dual security criterion is addressed. Dual security is designed to be measured by kurtosis in the spatial domain and by relative entropy in the frequency domain, simultaneously. Messages are encoded into the wavelet domain by adjusting the magnitude (least few significant bits) relationship between four neighboring child nodes (called permutations of order representations) to satisfy the dual security criterion. Relationship between security, perceptual fidelity, and capacity are investigated on various images.
Co-evolution of Agent-Oriented Conceptual Models and CASO Agent Programs
Authors: Aniruddha Dasgupta, Aneesh Krishna, Aditya K. Ghose
Venue: Proceedings of the IEEE/WIC/ACM international conference on Intelligent Agent Technology (2006)

Agent-Oriented conceptual modelling notations are highly effective in representing requirements from an intentional stance and answering questions such as what goals exist, how key actors depend on each other and what alternatives must be considered. In this paper, we suggest an approach to executing i* models by translating these into set of interacting agents implemented in the CASO language. In addition, we suggest a hybrid modelling, or co-evolution, approach in which i* models and CASO agent programs are concurrently maintained and updated, while retaining some modicum of loose consistency between the two. This allows us to benefit from the complementary representational capabilities of the two frameworks.
MetaOn - Ontology Driven Metadata Construction and Management for Intelligent Search in Text and Image Collections
Authors: Haralampos Karanikas, Nikos Pelekis, Dimitris K. Iakovidis, Ioannis Kopanakis, Thomas Mavroudakis, Yannis Theodoridis
Venue: Proceedings of the 17th International Conference on Database and Expert Systems Applications (2006)

State of the art in multimedia technology focuses in managing data collected from various sources, including documents, images, video, and speech. Therefore the effective management, analysis and mining of such heterogeneous data requires the combination of various techniques. In this paper we present an overview of the recently funded MetaOn project. The core objective of MetaOn is to construct and integrate semantically rich metadata collections extracted from documents images and linguistic resources, to facilitate intelligent search and analysis. The proposed MetaOn framework involves, ontology-based information extraction and data mining, semi-automatic construction of domain specific ontologies, content-based image indexing and retrieval, and metadata management. The Hellenic history has been chosen as a challenging application case study.
Motion Segmentation by Spatiotemporal Smoothness Using 5D Tensor Voting
Authors: Changki Min, Gerard Medioni
Venue: Proceedings of the 2006 Conference on Computer Vision and Pattern Recognition Workshop (2006)

Our goal is to recover temporal trajectories of all pixels in a reference image for the given image sequence, and segment the image based on motion similarities. These trajectories can be visualized by observing the 3D (x, y, t) spatiotemporal volume. The mathematical formalism describing the evolution of pixels in time is that of fiber bundles, but it is difficult to implement directly. Instead, we express the problem in a higher dimensional 5D space, in which pixels with coherent apparent motion produce smooth 3D layers. The coordinates in this 5D space are (x, y, t, vx, vy). It is initially populated by peaks of correlation. We then enforce smoothness both in the spatial and temporal domains simultaneously, using the tensor voting framework. Unlike the previous 4D approach which uses only two frames, we fully take advantage of the temporal information through multiple images, and it significantly improves the motion analysis results. The approach is generic, in the sense that it does not make restrictive assumptions on the observed scene or on the camera motion. We present some results on real data sets, and they are very good on even challenging image sequences such as serious occlusion.
A Joinless Approach for Mining Spatial Colocation Patterns
Authors: Jin Soung Yoo, Shashi Shekhar
Venue: IEEE Transactions on Knowledge and Data Engineering (2006)

Spatial colocations represent the subsets of features which are frequently located together in geographic space. Colocation pattern discovery presents challenges since spatial objects are embedded in a continuous space, whereas classical data is often discrete. A large fraction of the computation time is devoted to identifying the instances of colocation patterns. We propose a novel joinless approach for efficient colocation pattern mining. The joinless colocation mining algorithm uses an instance-lookup scheme instead of an expensive spatial or an instance join operation for identifying colocation instances. We prove the joinless algorithm is correct and complete in finding colocation rules. We also describe a partial join approach for a spatial data set often clustered in neighborhood areas. We provide the algebraic cost models to characterize the performance dominance zones of the joinless method and the partial join method with a current join-based colocation mining method, and compare their computational complexities. In the experimental evaluation, using synthetic and real-world data sets, our methods performed more efficiently than the join-based method and show more scalability in dense data.
Investigating Organisational Structures with Networks of Planning Agents
Authors: Anthony Dekker, Lavindra de Silva
Venue: Proceedings of the International Conference on Computational Inteligence for Modelling Control and Automation and International Conference on Intelligent Agents Web Technologies and International Commerce (2006)

In this paper, we present a simulation model specifically for investigating formal and informal organisational structures. CAVALIER-NPA (Networks of Planning Agents) is an agent-based simulation written in Java, where agents can communicate and do BDI-based planning. We describe a simple experiment which explores the impact of planning time, communications delays, and workload sharing on a simple mission. Analysis of the experimental results underlines the importance of efficient communication, the balance between planning and reactive behaviour, and the benefits of workload sharing within informal organisational networks.
The Generation of E-Learning Exercise Problems from Subject Ontologies
Authors: Edmond Holohan, Mark Melia, Declan McMullen, Claus Pahl
Venue: Proceedings of the Sixth IEEE International Conference on Advanced Learning Technologies (2006)

The teaching/ learning of cognitive skills, such as problem-solving, is an important goal in most forms of education. In well-structured subject areas certain exercise problem types may be precisely described by means of machine-processable knowledge structures or ontologies. These ontologies can readily be used to generate individual problem examples for the student, where each problem consists of a question and its solution. An example is given from the subject domain of computer databases.
Analysis of Clustering and Routing Overhead for Clustered Mobile Ad Hoc Networks
Authors: Mingqiang Xue, Inn-Inn Er, Winston K. G. Seah
Venue: Proceedings of the 26th IEEE International Conference on Distributed Computing Systems (2006)

This paper presents an analysis of the control overhead involved in clustering and routing for one-hop clustered mobile ad hoc networks. Previous work on the analysis of control overhead incurred by clustering algorithms focused mainly on the derivation of control overhead in the Knuth big-O notation with respect to network size. However, we observe that the control overhead in a clustered network is closely related to different network parameters, e.g. node mobility, node transmission range, network size, and network density. We present an analysis that captures the effects of different network parameters on the control overhead. The results of our work can provide valuable insights into the amount of overhead that clustering algorithms may incur in different network environments. This facilitates the design of efficient clustering algorithms in order to minimize the control overhead.
The Optimisation of Thresholding Techniques for the Identification of Choroidal Neovascular Membranes in Exudative Age-Related Macular Degeneration
Authors: E Brankin, P McCuIlagh, N Black, W Patton, A Muldrew
Venue: Proceedings of the 19th IEEE Symposium on Computer-Based Medical Systems (2006)

The application of image processing to the investigation of Age-related Macular Degeneration (AMD) has focused on detecting focal drusen deposits in retinal images. This research investigates algorithmic approaches in order to detect choroidal neovascularisation (CNV) from retinal fluorescein angiograms in exudative AMD, the most severe form of the disease. A combination of the 'Sobel' edge detection algorithm combined with thresholding produced the best qualitative segmentation, as verified by a trained ophthalmic grader. This study confirms that image processing can be used to identzfi certain types of CNV in retinal images particularly those that are hyperfluorescent. Further work is necessary to quantify the total lesion and characterise the clinically significant sub-components: classic or occult leakage, blood or exudate.
Low-Overhead Run-Time Memory Leak Detection and Recovery
Authors: Timothy Tsai, Kalyan Vaidyanathan, Kenny Gross
Venue: Proceedings of the 12th Pacific Rim International Symposium on Dependable Computing (2006)

Memory leaks are known to be a major cause of reliability and performance issues in software. This paper describes a run-time scheme that detects and removes memory leaks with minimal performance overhead and with no modifications to application source code. The scheme consists of a first stage where a pattern recognition technique proactively detects subtle memory leaks, followed by a more resourceintensive second stage that scans the memory space of an application and removes detected memory leaks. The pattern recognition technique in the first stage is based on the multivariate state estimation technique (MSET) which provides accurate detection of subtle memory leaks with very little overhead. The second stage is only activated when problems are identified by the first stage. For our prototype, this second stage is based on debugging and analysis tools provided by Solaris 10. Due to the low-overhead impact of the first stage, the system can be monitored for memory leaks without incurring noticeable performance degradation. We present and discuss some results from our unique proactive detection and debugging methodology.
Between Art and Architecture: The Interactive Skin
Authors: Jules Moloney
Venue: Proceedings of the conference on Information Visualization (2006)

There are two current approaches to the realisation of interactive building 'skins': in architecture so called intelligent facades are being designed with an environmental science agenda; while in a parallel line of inquiry, artists are experimenting with media facades. It is proposed here that there is common ground between reactive environmental facades and data driven screens, in that both involve the design of kinetic process. Selected examples from kinetic and generative art provide useful precursors for such an approach and these provide the background to a framework for the design of interactive building skins. The aim is to locate the design parameters for practice where the art / architectural skin is a process based system, rather than a static object.
Mainstream Games in the Multi-agent Classroom
Authors: Celso de Melo, Rui Prada, Guilherme Raimundo, Joana Paulo Pardal, Helena Sofia Pinto, Ana Paiva
Venue: Proceedings of the IEEE/WIC/ACM international conference on Intelligent Agent Technology (2006)

Computer games make learning fun and support learning through doing. Edutainment software tries to capitalize on this however, it has failed in reaching the levels of motivation and engagement seen in mainstream games. In this context, we have integrated a mainstream first-person shooter game, Counter-Strike, into the curriculum of our Autonomous Agents and Multi-agent Systems course. In this paper we describe this integration and a platform to support the creation of Counter-Strike agents. In addition, a questionnaire was posed to our students to assess the success of our approach. Results show that students found the idea of applying a first-person- shooter game motivating and the integration with the curriculum useful for their education.
A conceptual solution for representing time in data warehouse dimensions
Authors: Elzbieta Malinowski, Esteban Zimányi
Venue: Proceedings of the 3rd Asia-Pacific conference on Conceptual modelling - Volume 53 (2006)

Data Warehouses (DWs) use an omnipresent time dimension for keeping track of changes in measure values. However, this dimension cannot be used to model changes in other dimensions. On the other hand, Temporal Databases (TDBs) have been successfully used for modelling time-varying information. Bringing together these two research areas, leading to Temporal Data Warehouses (TDWs), provides the necessary solutions for managing time-varying data in dimensions. In this paper, we introduce temporal extensions for the MultiDimER model, a conceptual multidimensional model. In our model we allow the inclusion of valid and transaction time, which are obtained from source systems, in addition to the data warehouse loading time. Our model allows a conceptual representation of time-varying levels, attributes, and hierarchies. For the latter, we discuss different cases depending on whether the changes in levels affect the relationships between them.
Architectural principles and scheduling strategies for computing agent systems
Authors: Marek Grochowski, Robert Schaefer, Maciej Smołka
Venue: Fundamenta Informaticae (2006)

The paper introduces the formal description of a computing multi-agent system (MAS), its architecture and dynamics (sections 2-4). The optimal scheduling problem for the MAS as well as a way of its verification are presented in terms of such a model (section 5). A brief report of test results published previously in [13, 3, 4, 8] is contained in section 6.
Integration of SQL and XQuery in IBM DB2
Authors: F. Özcan, D. Chamberlin, K. Kulkarni, J.-E. Michels
Venue: IBM Systems Journal (2006)

Relational database systems have dominated the database industry for a quarter century. However, the advent of the Web has led to requirements for storage of new kinds of information in which the order of information is important and data structure can vary over time and from one document to another. These evolving requirements have given rise to Extensible Markup Language (XML) as a widely accepted data format and to XQuery as an emerging standard language for querying XML data sources. A set of extensions to the Structured Query Language (SQL) called SQL/XML enables XML data to be stored in relational databases, taking advantage of the mature infrastructure of relational systems and combining the advantages of SQL and XQuery. However, building a bridge between SQL and XQuery is challenging due to the many syntactic and semantic differences between the two languages. This paper describes how IBM DB2® deals with this challenge and provides users with a flexible system for storing and processing both relational and XML data.
Testing the cluster hypothesis in distributed information retrieval
Authors: Fabio Crestani, Shengli Wu
Venue: Information Processing and Management: an International Journal (2006)

How to merge and organise query results retrieved from different resources is one of the key issues in distributed information retrieval. Some previous research and experiments suggest that cluster-based document browsing is more effective than a single merged list. Cluster-based retrieval results presentation is based on the cluster hypothesis, which states that documents that cluster together have a similar relevance to a given query. However, while this hypothesis has been demonstrated to hold in classical information retrieval environments, it has never been fully tested in heterogeneous distributed information retrieval environments. Heterogeneous document representations, the presence of document duplicates, and disparate qualities of retrieval results, are major features of an heterogeneous distributed information retrieval environment that might disrupt the effectiveness of the cluster hypothesis. In this paper we report on an experimental investigation into the validity and effectiveness of the cluster hypothesis in highly heterogeneous distributed information retrieval environments. The results show that although clustering is affected by different retrieval results representations and quality, the cluster hypothesis still holds and that generating hierarchical clusters in highly heterogeneous distributed information retrieval environments is still a very effective way of presenting retrieval results to users.
HDF5-FastQuery: Accelerating Complex Queries on HDF Datasets using Fast Bitmap Indices
Authors: Luke Gosink, John Shalf, Kurt Stockinger, Kesheng Wu, Wes Bethel
Venue: Proceedings of the 18th International Conference on Scientific and Statistical Database Management (2006)

Large scale scientific data is often stored in scientific data formats such as FITS, netCDF and HDF. These storage formats are of particular interest to the scientific user community since they provide multi-dimensional storage and retrieval. However, one of the drawbacks of these storage formats is that they do not support semantic indexing which is important for interactive data analysis where scientists look for features of interests such as "Find all supernova explosions where energy > 10^5 and temperature > 10^6". In this paper we present a novel approach called HDF5- FastQuery to accelerate the data access of large HDF5 files by introducing multi-dimensional semantic indexing. Our implementation leverages an efficient indexing technology called bitmap indexing that has been widely used in the database community. Bitmap indices are especially well suited for interactive exploration of large-scale readonly data. Storing the bitmap indices into the HDF5 file has the following advantages: a) Significant performance speedup of accessing subsets of multi-dimensional data and b) portability of the indices across multiple computer platforms. We will present an API that simplifies the execution of queries on HDF5 files for general scientific applications and data analysis. The design is flexible enough to accommodate the use of arbitrary indexing technology for semantic range queries. We will also provide a detailed performance analysis of HDF5-FastQuery for both synthetic and scientific data. The results demonstrate that our proposed approach for multi-dimensional queries is up to a factor of 2 faster than HDF5.
ECRbase: database of evolutionary conserved regions, promoters, and transcription factor binding sites in vertebrate genomes
Authors: Gabriela Loots, Ivan Ovcharenko
Venue: Bioinformatics (2007)

Motivation: Evolutionary conservation of DNA sequences provides a tool for the identification of functional elements in genomes. We have created a database of evolutionary conserved regions (ECRs) in vertebrate genomes, entitled ECRbase, which is constructed from a collection of whole-genome alignments produced by the ECR Browser. ECRbase features a database of syntenic blocks that recapitulate the evolution of rearrangements in vertebrates and a comprehensive collection of promoters in all vertebrate genomes generated using multiple sources of gene annotation. The database also contains a collection of annotated transcription factor binding sites (TFBSs) in evolutionary conserved and promoter elements. ECRbase currently includes human, rhesus macaque, dog, opossum, rat, mouse, chicken, frog, zebrafish and fugu genomes. It is freely accessible at http://ecrbase.dcode.org. Contact: ovcharenko1@llnl.gov Supplementary information: Supplementary Data are available at Bioinformatics online.