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A Clustering Algorithm for Planning the Integration Process of a Large Number of Conceptual Schemas

Journal of Computer Science & Technology 2015年第1期30卷 214-224页

作者： Carlo Batini: paola bonizzoni Marco Comerio Riccardo Dondi Yuri Pirola Prancesco Salandra Department of Informatics Systems and Communication University of Milano-Bicocca Milan 20126 Italy Department of Human and Social Sciences University of Bergamo Bergamo 24129 Italy

When tens and even hundreds of schemas are involved in the integration process, criteria are needed for choosing clusters of schemas to be integrated, so as to deal with the integration problem through an efficient iterative process. Schemas in clusters should be chosen according to cohesion and coupling criteria that are based on similarities and dissimilarities among schemas. In this paper, we propose an algorithm for a novel variant of the correlation clustering approach that addresses the problem of assisting a designer in integrating a large number of conceptual schemas. The novel variant introduces upper and lower bounds to the number of schemas in each cluster, in order to avoid too complex and too simple integration contexts respectively. We give a heuristic for solving the problem, being an NP hard combinatorial problem. An experimental activity demonstrates an appreciable increment in the effectiveness of the schema integration process when clusters are computed by means of the proposed algorithm w.r.t, the ones manually defined by an expert.

关键词： conceptual schema schema integration clustering

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Overlap graphs and de Bruijn graphs: data structures for de novo genome assembly in the big data era

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Quantitative Biology 2019年第4期7卷 278-292页

作者： Raffaella Rizzi Stefano Beretta Murray Patterson Yuri Pirola Marco Previtali Gianluca Della Vedova paola bonizzoni Department of Informatics Systems and CommunicationsUniversity of Milan-BicoccaMilanViale Sarca 33620126Italy

Background:De novo genome assembly relies on two kinds of graphs:de Bruijn graphs and overlap *** graphs are the basis for the Celera assembler,while de Bruijn graphs have become the dominant technical device in the last *** two kinds of graphs are collectively called assembly ***:In this review,we discuss the most recent advances in the problem of constructing,representing and navigating assembly graphs,focusing on very large *** will also explore some computational techniques,such as the Bloom filter,to compactly store graphs while keeping all functionalities ***:We complete our analysis with a discussion on the algorithmic issues of assembling from long reads(eg.,PacBio and Oxford Nanopore).Finally,we present some of the most relevant open problems in this field.

关键词： overlap graphs de Bruijn graphs genome assembly long reads string graphs

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Foreword

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Journal of Computer Science & Technology 2004年第1期19卷 1-1页

作者： paola bonizzoni Gianluca Della Vedova Tao Jiang University of Milano-Bicocca Italy University of California-Riverside USA

This special issue of the Journal of Computer Science and Technology is devoted to Bioinformatics. The emerging research field connects classical topics in Computer Science, including the theory of algorithms, databas...

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