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CLUSTER ANALYSIS AND ONTOLOGY GENERATION TECHNIQUES FOR THE DEVELOPMENT OF SCHOLARLY SEMANTIC WEB By Quan Thanh Tho SUBMITTED IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY AT SCHOOL OF COMPUTER ENGINEERING NANYANG TECHNOLOGICAL UNIVERSITY NANYANG AVENUE, SINGAPORE 639798 2005 Table of Contents Table of Contents ii List of Tables viii List of Figures x Abstract xiv Acknowledgements xvi Introduction 1.1 Scholarly Web Information 1.2 Scholarly Information Retrieval 1.3 The Semantic Web 1.4 Semantic Web-based Retrieval Systems 1.5 Objectives 1.6 Major Contributions 1.7 Organization of the Thesis The Semantic Web 2.1 11 Markup Languages 11 2.1.1 Hypertext Markup Language 12 2.1.2 Extensible Markup Language 12 2.1.3 Resource Description Framework 13 2.2 The Semantic Web 14 2.3 Ontology 16 2.4 Ontology Description Languages 17 2.4.1 17 HTML-based Ontology Description Languages ii 2.4.2 XML-based Ontology Description Languages 18 2.4.3 RDF-based Ontology Description Languages 20 Semantic Web Portals 24 2.5.1 Semantic Web Portal Architecture 25 2.5.2 Requirements on Semantic Web Portals 25 2.6 Web Services and Semantic Web Services 27 2.7 Summary 29 2.5 Context-based Cluster Analysis 3.1 3.2 3.3 3.4 31 Clustering Methods 32 3.1.1 Hierarchical Clustering Methods 32 3.1.2 Partitioning Clustering Methods 33 3.1.3 Other Clustering Methods 35 3.1.4 Discussion 37 Context-based Cluster Analysis 38 3.2.1 Cross-Clustering Relation Generation 39 3.2.2 Cross-Clustering Context Generation 51 Performance Evaluation 55 3.3.1 Experiment 55 3.3.2 Evaluation Measures 57 3.3.3 Experimental Results 59 Summary 64 Expert and Expertise Finding 4.1 65 Related Work 65 4.1.1 Expertise Recommender Systems 66 4.1.2 Web Mining for Finding Expertise 66 4.1.3 Author Co-citation Analysis Approach 67 4.1.4 Discussion 68 4.2 CCA-based Expert Finding 68 4.3 Document Clustering 70 4.3.1 Feature Selection 70 4.3.2 Pre-processing 70 4.3.3 Transformation 71 4.3.4 Document Clusters Generation 71 Author Clustering 72 4.4 iii 4.4.1 Creating Author Co-Citation Pairs 72 4.4.2 Creating Raw Co-Citation Matrix 72 4.4.3 Converting into Correlation Matrix 73 4.4.4 Generating Author Clusters 73 4.5 Context-based Cluster Analysis 74 4.6 Expert Information Generation 75 4.6.1 Identifying Researchers’ Research Areas 75 4.6.2 Ranking Expert 76 4.6.3 Retrieving Expert Information 76 Expert Retrieval and Visualization 76 4.7.1 Expert Retrieval 77 4.7.2 Expert Visualization 77 Performance Evaluation 78 4.8.1 Experiment 79 4.8.2 Experimental Results 79 4.8.3 Comparison with Other Approaches 84 Summary 88 4.7 4.8 4.9 Research Trend Detection 5.1 90 Related Work 90 5.1.1 Semi-automatic Approaches 91 5.1.2 Automatic Approaches 92 5.1.3 Discussion 94 5.2 CCA-based Trend Detection 95 5.3 Keyword-based Clustering 96 5.3.1 Document Clustering 97 5.3.2 Publisher Clustering 97 5.3.3 Temporal Clustering 98 5.4 Context-based Cluster Analysis 99 5.5 Trend Information Generation 102 5.5.1 Current Trend Identification 103 5.5.2 Trend Information Extraction 103 5.5.3 Emerging Trend Identification 104 5.6 Trend Retrieval 105 5.7 Performance Evaluation 105 iv 5.8 5.7.1 Experiment 106 5.7.2 Trend Identification 106 5.7.3 Trend Information Extraction and Retrieval 109 5.7.4 Trend Visualization 109 Summary 111 Fuzzy Concept Hierarchy Generation 6.1 112 Related Work 113 6.1.1 Concept Hierarchy Generation 114 6.1.2 Conceptual Clustering 114 6.1.3 Formal Concept Analysis 115 6.1.4 Discussion 116 6.2 Fuzzy Theory 117 6.3 Fuzzy Concept Hierarchy Generation 119 6.4 6.5 6.6 6.7 6.3.1 Fuzzy Formal Concept Analysis 119 6.3.2 Fuzzy Conceptual Clustering 127 6.3.3 Hierarchical Relation Generation 129 Research Concept Hierarchy Generation 132 6.4.1 Fuzzy Formal Concept Analysis 133 6.4.2 Fuzzy Conceptual Clustering 133 6.4.3 Hierarchical Relation Generation 134 6.4.4 Performance Evaluation 135 Machine Faults Concept Hierarchy Generation 142 6.5.1 Fuzzy Formal Concept Analysis 143 6.5.2 Fuzzy Conceptual Clustering 143 6.5.3 Hierarchical Relation Generation 144 6.5.4 Performance Evaluation 145 News Topic Themes Concept Hierarchy Generation 149 6.6.1 Fuzzy Formal Concept Analysis 150 6.6.2 Fuzzy Conceptual Clustering 150 6.6.3 Hierarchical Relation Generation 151 6.6.4 Performance Evaluation 152 Summary 155 v Scholarly Ontology Generation 7.1 7.2 7.3 7.4 157 Related Work 158 7.1.1 Ontology Generation 158 7.1.2 Generating Ontology from Scholarly Knowledge 159 7.1.3 Discussion 160 Fuzzy Ontology Generation 161 7.2.1 The FOGA Approach 161 7.2.2 Incremental Ontology Update 166 7.2.3 Research Hierarchy Ontology Generation 170 Cluster-based Ontology Generation 170 7.3.1 The COGA Approach 171 7.3.2 Experts Ontology Generation 172 7.3.3 Trends Ontology Generation 173 Ontology Integration 174 7.4.1 Ontology Integration Framework 174 7.4.2 Scholarly Ontology Generation 175 7.5 Semantic Web Representation 178 7.6 Browsing Scholarly Ontology 182 7.7 Summary 183 Scholarly Semantic Web 8.1 184 Related Work 184 8.1.1 Citation-based Retrieval 184 8.1.2 Semantic Web-based Information Retrieval 187 8.1.3 Discussion 188 8.2 System Overview of SSWeb 188 8.3 Scholarly Semantic Web Services 189 8.4 8.3.1 Scholarly Service Provider 190 8.3.2 Scholarly Service Requester 192 8.3.3 Matchmaking Agent 193 8.3.4 Scholarly Information Retrieval 194 Summary 197 Conclusions 198 9.1 Summary 198 9.2 Future Work 201 vi 9.2.1 Discovering Other Scholarly Knowledge 201 9.2.2 Fuzzy Semantic Query Languages 201 9.2.3 Automatic Ontology Integration 203 9.2.4 Fuzzy Query Expansion using Fuzzy Concept Hierarchy 204 A List of Publications 205 A.1 Refereed Conferences and Workshops 205 A.2 Book Chapters 206 A.3 Journals 206 B 20 Queries for Performance Evaluation on Expert Finding 207 Bibliography 208 vii List of Tables 3.1 A distance matrix 45 3.2 A cross-table of a document clustering context 52 3.3 A cross-table of an author clustering context 53 3.4 A cross-clustering context from the document and author clustering contexts 55 3.5 Different combinations of clusters mining 57 4.1 An example of the Keyword-Author Cross-Clustering Context 74 4.2 Manually classified experts 79 4.3 Performance results based on the average F-measure 80 5.1 An example of a document clustering context 101 5.2 An example of a topic clustering context 101 5.3 An example of a temporal clustering context 101 5.4 An example of the Keyword-Topic-Temporal Cross-Clustering Context 102 5.5 Manually predefined trends in the Information Retrieval field 106 5.6 Trends identification results using the single link method 107 5.7 Trends identification results using the complete link method 107 5.8 Trends identification results using the average link method 108 5.9 Trends identification results using the Ward’s method 108 5.10 Performance results of trends information extraction 109 6.1 A cross-table of a formal context 120 6.2 A cross-table of a fuzzy formal context 122 6.3 Fuzzy formal context in Table 6.2 with α-cut = 0.5 122 6.4 A cross-table of a L-fuzzy context 125 viii 6.5 Full context of a L-fuzzy context 126 6.6 Number of research clusters using FCHG and LFCA-based conceptual clustering methods based on different similarity thresholds Ts 134 6.7 Runtime (in sec.) required to generate conceptual clusters 134 6.8 Performance results based on precision 137 6.9 Performance results based on recall 137 6.10 Performance results based on F-measure 137 6.11 Performance comparison based on precision 138 6.12 Performance comparison based on precision 138 6.13 Performance comparison based on F-measure 138 6.14 Number of research clusters using FCHG and LFCA-based conceptual clustering methods based on difference confidence thresholds TC 144 6.15 Runtime (in sec.) required to generate conceptual clusters 144 6.16 Retrieval accuracy 149 6.17 Number of research clusters using FCHG and LFCA-based conceptual clustering methods based on difference confidence thresholds TC 151 6.18 Runtime (in sec.) required to generate conceptual clusters 151 6.19 Manually classified themes of Reuters news topics 153 6.20 Performance results based on precision 154 6.21 Performance results based on recall 154 6.22 Performance results based on F-measure 154 B.1 20 queries for performance evaluation on expert finding 207 ix List of Figures 1.1 System architecture of the proposed Scholarly Semantic Web 2.1 Representation of a publication using XML 13 2.2 Another representation of the publication using XML 13 2.3 RDF data model 14 2.4 Representation of a publication using RDF 14 2.5 Architecture of the Semantic Web 15 2.6 Representation of semantic information using SHOE 18 2.7 Representation of semantic information using Ontobroker 19 2.8 Class representation using DAML-ONT 21 2.9 Class representation using OIL 22 2.10 Class representation using DAML+OIL 23 2.11 Class Representation using OWL 24 2.12 Semantic Web Portal 25 2.13 Operational mechanism in Web Services 27 2.14 Technologies used 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Semantic Web, and markup languages Then, the Semantic Web is introduced Next, we discuss ontology, ... (FOGA), Cluster- based Ontology Generation frAmework (COGA) and Ontology Integration Framework (OIF), for ontology generation Chapter 8 presents the proposed system on the Scholarly Semantic Web In this chapter, the distributed architecture of the system is given We then discuss the Scholarly Semantic Web Services that enable the scholarly knowledge understandable, sharable and accessible on the Semantic Web. .. which is adopted for knowledge representation for the Semantic Web, and in particular ontology description languages Finally, we discuss Semantic Web Portals for Semantic Web applications, and Web Services for the delivery of services on the Semantic Web 2.1 Markup Languages The World Wide Web, proposed by Tim Berners-Lee [43], is the universe of networkaccessible information On the Web, information is... investigate the integration of different types of ontologies that are generated from cluster analysis and fuzzy conceptual clustering • Scholarly Semantic Web Services To provide scholarly information retrieval services over the Semantic Web, we will investigate a Semantic Web- based architecture for the delivery of Scholarly Semantic Web Services The proposed architecture should enable the retrieval of scholarly. .. further explored for supporting advanced search functions such as expert finding and trend detection The development of the Semantic Web has provided a very suitable environment for supporting the sharing of scholarly knowledge among different scholarly research communities However, one of the challenges for the development of Semantic Webbased retrieval systems is on the construction of scholarly ontology. .. for expert finding, trend detection and fuzzy document retrieval 1.7 Organization of the Thesis This chapter has discussed the background and motivation of this research work The objectives of the research have been given We have also listed the contributions that have been achieved The rest of the thesis is organized as follows Chapter 2 reviews the Semantic Web and the state -of -the- art Semantic Web. .. scholarly knowledge as ontology, which is distributed on the Semantic Web As such, scholarly information can be managed and refined by the corresponding domain 5 Chapter 1: Introduction Citation Database Cluster Analysis Ontology Generation Scholarly Semantic Web Scholarly Ontology Organization 1 Scholarly Web Services Scholarly Ontology Web Browser User Organization 2 Scholarly Ontology Organization... archives based on the Semantic Web However, one of the major obstacles for developing Semantic Web- based retrieval systems is on the construction of ontology for the corresponding domain In the scholarly domain, the scholarly ontology of the existing Semantic Web- based retrieval systems is constructed mainly based on explicit information from scientific documents (such as titles, authors and abstracts)... technologies, which include ontology, Semantic Web Portals and Semantic Web Services In Chapter 3, we discuss the proposed cluster analysis technique for mining cluster relationships from multiple clustering data The technique, which is known as Contextbased Cluster Analysis, is capable of representing cluster relationships among multiple clusters as mathematical models The performance of the proposed technique... ontology The construction process for scholarly ontology should be easy and preferably automatic rather than manual, which is tedious and time-consuming This research aims to develop a Semantic Web- based system for the sharing and retrieval of scholarly information based on a citation database The proposed system is known as Scholarly Semantic Web (or SSWeb) The proposed SSWeb system will organize scholarly

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