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4th International Conference on Artificial Immune Systems, ICARIS 2005

作者： Bezerra, George B. Barra, Tiago V. De Castro, Leandro N. Von Zuben, Fernando J. University of Campinas CP: 6101 13083-970 Campinas/SP Brazil Graduate Program on Informatics Catholic University of Santos COPOP R. Dr. Carvalho de Mendonca 144 Vila Mathias Santos/SP Brazil

Many algorithms perform data clustering by compressing the original data into a more compact and interpretable representation, which can be more easily inspected for the presence of clusters. This, however, can be a risky alternative, because the simplified representation may contain distortions mainly related to the density information present in the data, which can considerably act on the clustering results. In order to treat this deficiency, this paper proposes an Adaptive Radius Immune Algorithm (ARIA), which is capable of maximally preserving the density information after compression by implementing an antibody adaptive suppression radius that varies inversely with the local density in the space. ARIA is tested with both artificial and real world problems obtaining a better performance than the aiNet algorithm and showing that preserving the density information leads to refined clustering results. © Springer-Verlag Berlin Heidelberg 2005.

关键词： Algorithms

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Analyzing groupware design by means of usability results

Analyzing groupware design by means of usability results

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International Conference on Computer Supported Cooperative Work in Design

作者： P. Antunes M.R.S. Borges J.A. Pino L. Carrico Department of Informatics Universidade de Lisboa Portugal Graduate Program in Informatics Federal University of Rio de Janeiro Brazil Department of Computer Science Universidad de Chile Chile

GOMS is a well-known model that has been successfully used in predicting the performance of human-computer interaction, identifying usability problems and improving user-interface design. The focus of GOMS on the individual user, however, explains why it has not been applied in the groupware context. We were inspired by GOMS to define a model that describes collaborative tasks in a formal way. We illustrate the application of the model by applying it to the design of a collaborative tool for software engineering requirements negotiation.

关键词： Collaborative software Collaborative work Usability Humans Collaboration Collaborative tools Computer architecture informatics Application software Computer science

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Developing shared context within group stories

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11th International Workshop on Groupware: Design, Implementation, and Use, CRIWG 2005

作者： Santoro, Flávia Maria Brézillon, Patrick Post-Graduate Program in Informatics NCE and IM Universidade Federal do Rio de Janeiro PO Box 2324 CEP 20001-970 Rio de Janeiro Brazil School of Applied Informatics Universidade Federal do Estado do Rio de Janeiro Av. Pasteur 458 Rio de Janeiro Brazil LIP 6 Université Pierre et Marie Curie - Paris VI 8 rue de Capitain Scott Paris France

ISBN: (纸本)3540291105

Eliciting and re-using knowledge within an organization requires a very structured communication process among its employees in order to avoid misunderstanding and confusion. The transfer of knowledge among actors can only be successful if a common interpretative focus and its context are set up. So far, information about the real context that surrounded team's past activities can help their members to better understand situations at hand. In this paper, we argue that a combination of group storytelling technique and a groupware tool can help the elicitation and use of the context shared by a group. Moreover, our main goal is to discuss how groupware can help to structure and formalize the contextual information behind the scenes of a story told by a group, making it easier to understand, interpret and reuse the knowledge intrinsic to it. © Springer-Verlag Berlin Heidelberg 2005.

关键词： Knowledge engineering

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[Symposium of the Process of Fertilization — From Sex Determination to Epigenetics]

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Zoological Science 2005年第12期22卷 1380-1382页

作者： Manabu Yoshida Midori Matsumoto Noritaka Hirohashi Keiichiro Kyozuka Yayoi Obata Qiong Wu Takuya Kumagai Manabu Kawahara Hidehiko Ogawa Tomohiro Kono Yoshiakira Kanai Misaki Marine Biological Station Graduate School of Science The University of Tokyo Department of Biosciences and Informatics Faculty of Science and Technology Keio University Genetic Counseling Program Graduate School of Humanities and Sciences Ochanomizu University Research Center for Marine Biology Asamushi Graduate School of Life Science Tohoku University Department of BioScience Tokyo University of Agriculture / BRAIN Department of Veterinary Anatomy The University of Tokyo

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Handling Data Sparseness in Gene Network Reconstruction

Handling Data Sparseness in Gene Network Reconstruction

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IEEE Symposium on Computational Intelligence and Bioinformatics and Computational Biology (CIBCB)

作者： G.B. Bezerra T.V. Barra F.J. von Zuben L.N. de Castro Laboratory of Bioinformatics and Bio-Inspired Computing (LBiC) Department of Computer Engineering and Industrial Automation State University of Campinas-UNICAMP Sao Paulo Brazil Graduate Program on Informatics Catholic University of Santos Sao Paulo Brazil

One of the main problems related to regulatory network reconstruction from expression data concerns the small size and low quality of the available dataset. When trying to infer a model from little information it is necessary to give much more precedence to generalization, rather than specificity, otherwise, any attempt will be fated to overfitting. In this paper we address this issue by focusing on data sparseness and noisy information, and propose a density estimation technique that achieves regularized curves when data is scarce. We first compare the proposed method with the EM algorithm for mixture models on density estimation problems. Next, we apply the method, together with Bayesian networks, on realistic simulations of static gene networks, and compare the obtained results with the standard discrete Bayesian network model. We intend to demonstrate that adopting a discrete approach is not justifiable when only a small amount of information is available.

关键词： Intelligent networks Bayesian methods Genetics Bioinformatics Computer networks Reverse engineering Cellular networks Noise robustness Laboratories Data engineering

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Learning to plan the collaborative design process

Learning to plan the collaborative design process

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8th International Conference on Computer Supported Cooperative Work in Design I, CSCWD 2004

作者： Santoro, Flávia Maria Borges, Marcos R. S. Santos, Neide Federal University of State of Rio de Janeiro UNIRIO Av. Pasteur 458 CEP 22290-040 Rio de Janeiro Brazil Graduate Program in Informatics Federal University of Rio de Janeiro PO Box 2324 CEP 20001-970 Rio de Janeiro Brazil State University of Rio de Janeiro UERJ Rua São Francisco Xavier 524 CEP 20559-900 Rio de Janeiro Brazil DSIC Polytechnic University of Valencia Spain

ISBN: (纸本)3540294007

A key factor in team collaboration is the process followed by participants. Planning this process helps teams to accomplish their goals. In collaborative design environments, process modeling should be used to make the collaboration explicit. In Computer-Supported Collaborative Learning (CSCL) research, we have observed that most environments do not provide support for the definition of collaborative processes by apprentices and facilitators. This support is very important when the approach is based on project-based learning (PBL). Planning the interactions and the process of a project is a way to stimulate group participants to collaborate, thereby promoting interdependency and commitment between the work and the learning activities. We present a cooperative project-based learning environment that supports facilitators and apprentices in the task of planning their work in order to improve awareness about the "learning-how-to-learn" process. © Springer-Verlag Berlin Heidelberg 2005.

关键词： Computer supported cooperative work

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CaGEDA: A web application for the integrated analysis of global gene expression patterns in cancer

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Applied Bioinformatics 2004年第1期3卷 49-62页

作者： Patel, Satish Lyons-Weiler, James University of Pittsburgh Cancer Institute University of Pittsburgh Medical School Pittsburgh PA United States Department of Pathology University of Pittsburgh Medical School Pittsburgh PA United States Cancer Biomarkers Laboratory University of Pittsburgh Medical School Pittsburgh PA United States Center for Pathology Informatics University of Pittsburgh Medical School Pittsburgh PA United States Benedum Center for Oncology Informatics University of Pittsburgh Medical School Pittsburgh PA United States Center for Biomedical Informatics University of Pittsburgh Medical School Pittsburgh PA United States Interdisciplinary Biomedical Graduate Program University of Pittsburgh Medical School Pittsburgh PA United States UPCI Benedum Oncology Informatics Center 304 Cancer Pavilion Pittsburgh PA 15232 5150 Centre Avenue United States

The explosion of microarray data from pilot studies, basic research and large-scale clinical trials requires the development of integrative computational tools that can not only analyse gene expression patterns but that can also evaluate the methods of analysis adopted and then provide a boost to post-analysis translational interpretation of those patterns. We have developed a web application called caGEDA (cancer gene expression data analyzer) that can: (1) upload gene expression profiles from cDNA or oligonucleotide microarrays;(2) conduct a diverse range of serial linear normalisations;(3) identify differentially expressed genes using a variety of tests - either threshold or permutation tests;(4) produce tables of literature references to papers reporting that specific genes (identified by accession numbers) are up- or down-regulated in specific cancers;(5) estimate the error of sample class prediction using the significant gene set for features;(6) perform low-bias and accurate validated learning using three computational validation techniques (leave-one-out validation, k-fold validation, random resampling validation);and (7) validate a classifier with a randomly selected or user-defined validation set. Significant genes are reported in a table of links to entries in the following databases: LocusLink, Genome View, UCSC, Ensembl, UniGene, dbSNP, AmiGO and OMIM. caGEDA is seamlessly integrated via embedded forms with UCSD's (University of California at San Diego) 2HAPI server (for medical subject heading (MeSH) term exploration) and EZ-Retrieve (to identify common transcription factors located upstream of sets of genes that exhibit similar modes of differential expression). caGEDA offers a variety of previously described and novel tests for differentially expressed genes, most notably the permutation percentile separability test, which is most appropriate for identifying genes that are significantly differentially expressed in a subset of patients. caGEDA, which

关键词： Cancer Genomics Microarray analysis

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A max min ant system applied to the capacitated clustering problem

A max min ant system applied to the capacitated clustering p...

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IEEE Workshop on Machine Learning for Signal Processing

作者： F.O. de Franca F.J. Von Zuben L. Nunes de Castro DCA/FEEC/Unicamp Univ. Estadual de Campinas DCA/FEEC/Unicamp State University of Campinas (Unicamp) Campinas/SP Brazil Research and Graduate Program on Informatics Catholic University of Santos (UniSantos) Santos/SP Brazil

This work introduces a modified max min ant system (MMAS) designed to solve the capacitated clustering problem (CCP). Some improvements on the original MMAS algorithm are proposed, such as the use of a density model on the information heuristic and a local search adapted from the uncapacitated p-medians problem. Also the MMAS ability to deal with large scale instances is improved by means of a new proposal for the pheromone updating rule. Some simulations are performed using instances available from the literature, for benchmarking purposes. As a practical application, given a hypothetical demand proportional to the number of inhabitants of the 186 most populated Brazilian cities, the optimal allocation for a varied number of clustering centers is properly determined by the proposed algorithm, with a superior performance when compared with the original MMAS algorithm

关键词： Clustering algorithms Electronic mail Proposals informatics Large-scale systems Cities and towns Mining industry Data mining Pattern recognition Vehicles

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A rule-based XML access control model

Lecture Notes in Computer Science (including subseries Lectu...

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Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) 2003年 2876卷 35-48页

作者： Anutariya, Chutiporn Chatvichienchai, Somchai Iwiahara, Mizuho Wuwongse, Vilas Kambayashi, Yahiko Computer Science Program Shinawatra University Pathumthani Thailand Department of Social Informatics Graduate School of Informatics Kyoto University Kyoto Japan Computer Science and Information Management Program Asian Institute of Technology Pathumthani Thailand

Due to a widely use of XML language in various application domains, a well-established mechanism for the definition and enforcement of security controls on specific accesses to XML documents is demanded, in order to ensure that only authorized entities can perform certain actions on the protected data. The proposed rule-based, declarative approach supports definition of (possibly implicit and complex) authorization rules on particular nodes within a document as well as enforcement of multiple user-defined policies, specifying selected mechanisms to resolve conflicts or to apply default authorization. Moreover, by founded on both RDF and XDD theory, the developed approach yields a simple yet flexible and interchangeable XML access control model with well-defined declarative semantics. © Springer-Verlag Berlin Heidelberg 2003.

关键词： Access control models

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DCT and wavelet based image compression in satellite images

DCT and wavelet based image compression in satellite images

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International Conference on Recent Advances in Space Technologies, RAST 2003

作者： Hacihaliloglul, Llker Karta, Mesut Satellite Communication and Remote Sensing Graduate Program Advanced Technologies in Engineering Informatics Institute Istanbul Technical University Maslak Istanbul34469 Turkey Electronic and Communication Department Faculty of Electrical and Electronic Engineering Istanbul Technical University Maslak Istanbul34469 Turkey

ISBN: (纸本)0780381424

Synthetic aperture radar (SAR) and SPOT images are becoming increasingly important and abundant in a variety of remote sensing and tactical applications. Thus, there is a strong interest in developing data encoding and decoding algorithms that can obtain higher compression ratios while keeping image quality to an acceptable level. This study aims to compare most of the well-known compression techniques namely discrete cosine transform and discrete wavelet transform. It investigates RADARSAT and SPOT images of different regions of different characteristics. RADARSAT-I fine and standard beam mode images of the different regions in Istanbul are used to test the performance of the compression algorithms. The regions, which have been investigated, were sea areas, forest areas, built environment - residential and industrial areas which define different patterns of urban land use. The studies showed that homogeneous areas like forest and sea gave better compression results compared to heterogeneous areas like industrial and environmental. The second purpose of this study is to compare the two compression algorithms. The discrete wavelet based algorithm gave much better results compared to the discrete cosine transform based algorithm. The results changed according to the quantization process and the transform coding algorithm. © 2003 IEEE.

关键词： Discrete wavelet transforms

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