Biomedical data management and graph online querying : VLDB 2015 Workshops, Big-O(Q) and DMAH, Waikoloa, HI, USA, August 31 - September 4, 2015 : revised selected papers

This book constitutes the refereed proceedings of the two International Workshops on Big-Graphs Online Querying, Big-O(Q) 2015, and Data Management and Analytics for Medicine and Healthcare, DMAH 2015, held at Waikoloa, Hawaii, USA on August 31 and September 4, 2015, in conjunction with the 41st International Conference on Very Large Data Bases, VLDB 2015. The 9 revised full papers presented together with 5 invited papers and 1 extended abstract were carefully reviewed and selected from 22 initial submissions. The papers are organized in topical sections on information retrieval and data analytics for electronic medical records; data management and visualization of medical data; biomedical data sharing and integration; medical imaging analytics; and big-graphs online querying. Preface 6 Organization 8 Challenges of Reasoning with Multiple Knowledge Sources in the Context of Drug Induced Liver Injury (Extended Abstract) 10 Contents 13 Information Retrieval and Data Analytics for Electronic Medical Records 15 Vector Space Models for Encoding and Retrieving Longitudinal Medical Record Data 16 Abstract 16 1 Introduction 16 2 Related Work 17 3 Temporal Model 18 4 Methods 19 4.1 Vector Space Models 20 4.2 Similarity Measure and Weighting Schemes 21 5 Experiments and Results 22 5.1 Patient Dataset 22 5.2 Chemotherapy Regimens 23 5.3 VSM Specification 23 5.4 Evaluation Results for Classification 24 5.5 Evaluation Results for Search 25 6 Conclusions 26 7 Future Work 26 References 27 The Study of the Compatibility Rules of Traditional Chinese Medicine Based on Apriori and HMETIS Hypergraph Partitioning Algorithm 29 Abstract 29 1 Introduction 29 1.1 The Value of the Study on the Compatibility of Chinese Herbs 29 1.2 Basic Knowledge About Data Mining 30 1.3 Related Work on the Compatibility Rules of Chinese Herbs Using Data Mining 31 1.4 Our Research 32 2 Data Mining on the Compatibility Rules of Core Herbs with Apriori and Hypergraph Partitioning Algorithm 32 2.1 Apriori Algorithm 32 2.2 Hypergraph and Hypergraph Community Partitioning 33 2.3 The Construction of Hypergraph and the Assessment of Hypergraph Community Partition 36 3 Data and Results 37 3.1 Data Source 37 3.2 Process of the Experiment 39 3.3 Results 40 3.4 Result Assessment 40 4 Conclusion and Outlook 42 4.1 Conclusion 42 4.2 Outlook 42 Acknowledgment 43 References 43 Comparing Small Graph Retrieval Performance for Ontology Concepts in Medical Texts 45 1 Introduction 45 2 Methods 46 2.1 Relational Database 47 2.2 General Graph Database 49 2.3 Triplestore 51 3 Evaluation Methodology 53 4 Results 53 5 Conclusion 56 References 56 Data Management and Visualization of Medical Data 58 Maps of Human Disease: A Web-Based Framework for the Visualization of Human Disease Comorbidity and Clinical Profile Overlay 59 1 Introduction 59 2 Related Work 61 3 Data and Methods 62 3.1 Comorbidity Graph Generation 62 3.2 Base Map Generation 63 3.3 Heat Map Generation 66 3.4 Implementation 67 4 Case Studies 68 5 Conclusions and Future Work 71 References 71 Secure Similarity Queries: Enabling Precision Medicine with Privacy 73 1 Introduction 73 2 Secure Similarity Queries 75 2.1 Secure kNN Queries 75 2.2 Skyline Queries 77 2.3 Problem Statement 77 3 Challenges and Potential Techniques 78 3.1 Challenges 78 3.2 Potential Techniques 79 4 Conclusion 79 References 80 Time-, Energy-, and Monetary Cost-Aware Cache Design for a Mobile-Cloud Database System 83 Abstract 83 1 Introduction 83 2 Background and Related Work 85 3 Proposed Solution 87 3.1 Estimation Computation 88 3.2 Cache Managers 89 3.3 The MOCCAD Cache Algorithm 90 4 Experiments and Results 92 5 Conclusion and Future Work 95 References 96 Biomedical Data Sharing and Integration 98 BiobankCloud: A Platform for the Secure Storage, Sharing, and Processing of Large Biomedical Data Sets 99 1 Introduction 100 2 Related Work 101 3 Architecture 102 4 Security Model 103 4.1 2-Factor Authentication 104 4.2 Role-Based Access Control 104 4.3 Auditing Service 104 5 Hadoop Open Platform-as-a-Service (Hops) 104 6 SAASFEE 106 7 Workflows Implemented in BiobankCloud 108 8 Sharing Data Between Clusters with Charon 110 9 Automated Installation 111 10 Conclusions 113 References 114 Medical Imaging Analytics 116 Three-Dimensional Data Analytics for Pathology Imaging 117 1 Introduction 117 2 3D Data Generation and Analytics 119 2.1 3D Vessel Reconstruction 119 2.2 3D Nucleus Simulation 122 2.3 Distance-Based Query for 3D Vessel and Nucleus 124 3 Experimental Results 127 4 Discussion and Conclusion 129 References 132 Automated Analysis of Muscle X-ray Diffraction Imaging with MCMC 134 1 Motivation 134 2 Prototype 135 2.1 Image Segmentation 136 2.2 Image Modeling with MCMC Processes 138 3 Preliminary Evaluation 138 4 Challenges and Next Steps 139 References 140 SparkGIS: Efficient Comparison and Evaluation of Algorithm Results in Tissue Image Analysis Studies 142 1 Introduction 142 2 Related Work 144 3 SparkGIS Framework 145 3.1 SparkGIS I/O Abstraction Layer 146 3.2 SparkGIS Execution Engine 146 3.3 SparkGIS Based Analysis Results Evaluation Workflow and Heatmap Computations 147 4 Experimental Performance Evaluation 150 4.1 Batch Factor 150 4.2 Execution Performance and Scalability 151 4.3 SparkGIS Versus Hadoop-GIS 152 5 Conclusions 152 References 153 Big-Graphs Online Querying 155 Social Network Analytics: Beyond the Obvious 156 1 The Background 156 2 Viral Marketing 156 3 Event and Story Detection and Tracking 158 4 Conclusions 160 References 160 S2X: Graph-Parallel Querying of RDF with GraphX 162 1 Introduction 162 2 Graph-Parallel Computation with GraphX 163 3 RDF Property Graph Model in S2X 164 4 Query Processing in S2X 165 4.1 Match Candidates and Match Sets 166 4.2 BGP Matching 167 4.3 From Graph-Parallel to Data-Parallel 170 5 Experiments 171 6 Conclusion 174 References 175 The Time Has Come: Traversal and Reachability in Time-Varying Graphs 176 1 Introduction 176 2 Use Cases 178 2.1 Power Grid 178 2.2 Spread of Information 179 3 Temporal Graph Traversals 179 3.1 Time Stable Traversal 181 3.2 Immediate Traversal 182 3.3 Delayed Traversal 183 4 Implementation Details 184 4.1 GRAPHITE 184 4.2 Sparksee 185 4.3 Traversal Types 186 5 Experimental Evaluation 186 5.1 Environmental Setup and Datasets 186 5.2 Experiments 187 6 Related Work 189 7 Conclusion 189 References 190 Robust Cardinality Estimation for Subgraph Isomorphism Queries on Property Graphs 191 1 Introduction 191 2 Related Work 193 2.1 RDF Cardinality Estimation 193 2.2 Cardinality Estimation in DBMS 194 2.3 Graph Cardinality Estimation 194 3 Graph Data Model and Cardinality Estimation 195 3.1 Notation: Attribute Histograms 195 3.2 Topology: Degree Histograms 196 3.3 Cardinality Estimation 196 4 Considering Functional Dependencies Between Attributes 197 5 Handling High-Outdegree Nodes 199 5.1 Discovery of Nodes with a High Outdegree 200 5.2 Processing of High-Outdegree Nodes 200 6 Experimental Evaluation 200 6.1 Correlated Attributes 201 6.2 High-Outdegree Vertices 202 6.3 End-to-End Cardinality Estimation 202 7 Conclusion 203 A Evaluated Queries 204 References 204 Author Index 206 Front Matter....Pages I-XIV Front Matter....Pages 1-1 Vector Space Models for Encoding and Retrieving Longitudinal Medical Record Data....Pages 3-15 The Study of the Compatibility Rules of Traditional Chinese Medicine Based on Apriori and HMETIS Hypergraph Partitioning Algorithm....Pages 16-31 Comparing Small Graph Retrieval Performance for Ontology Concepts in Medical Texts....Pages 32-44 Front Matter....Pages 45-45 Maps of Human Disease: A Web-Based Framework for the Visualization of Human Disease Comorbidity and Clinical Profile Overlay....Pages 47-60 Secure Similarity Queries: Enabling Precision Medicine with Privacy....Pages 61-70 Time-, Energy-, and Monetary Cost-Aware Cache Design for a Mobile-Cloud Database System....Pages 71-85 Front Matter....Pages 87-87 BiobankCloud: A Platform for the Secure Storage, Sharing, and Processing of Large Biomedical Data Sets....Pages 89-105 Front Matter....Pages 107-107 Three-Dimensional Data Analytics for Pathology Imaging....Pages 109-125 Automated Analysis of Muscle X-ray Diffraction Imaging with MCMC....Pages 126-133 SparkGIS: Efficient Comparison and Evaluation of Algorithm Results in Tissue Image Analysis Studies....Pages 134-146 Front Matter....Pages 147-147 Social Network Analytics: Beyond the Obvious....Pages 149-154 S2X: Graph-Parallel Querying of RDF with GraphX....Pages 155-168 The Time Has Come: Traversal and Reachability in Time-Varying Graphs....Pages 169-183 Robust Cardinality Estimation for Subgraph Isomorphism Queries on Property Graphs....Pages 184-198 Back Matter....Pages 199-199