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Big Data in eHealthcare
Challenges and Perspectives
Big Data in eHealthcare
Challenges and Perspectives

Nandini Mukherjee
Sarmistha Neogy
Samiran Chattopadhyay
CRC Press
Taylor & Francis Group
6000 Broken Sound Parkway NW, Suite 300
Boca Raton, FL 33487-2742

© 2019 by Taylor & Francis Group, LLC


CRC Press is an imprint of Taylor & Francis Group, an Informa business

No claim to original U.S. Government works

Printed on acid-free paper


Version Date: 20181122

International Standard Book Number-13: 978-0-8153-9440-2 (Hardback)

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efforts have been made to publish reliable data and information, but the author and publisher cannot
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Trademark Notice: Product or corporate names may be trademarks or registered trademarks, and
are used only for identification and explanation without intent to infringe.

Library of Congress Cataloging-in-Publication Data

Names: Mukherjee, Nandini, author. | Neogy, Sarmistha, author. |


Chattopadhyay, Samiran, author.
Title: Big data in eHealthcare : challenges and perspectives / Nandini
Mukherjee, Sarmistha Neogy, Samiran Chattopadhyay.
Description: Boca Raton, FL : CRC Press/Taylor & Francis Group, 2019. |
Includes bibliographical references and index.
Identifiers: LCCN 2019011925| ISBN 9780815394402 (hardback : acid-free paper)
| ISBN 9781351057790 (ebook)
Subjects: LCSH: Medical informatics. | Medicine--Data processing. | Big data.
| Data mining.
Classification: LCC R858 .M85 2019 | DDC 610.285--dc23
LC record available at https://lccn.loc.gov/2019011925

Visit the Taylor & Francis Web site at


http://www.taylorandfrancis.com
and the CRC Press Web site at
http://www.crcpress.com
To my daughter Shabnam and my husband Biman
— Nandini Mukherjee

To my daughter Roshni and my son-in-law Prince Bose


— Sarmistha Neogy

To my daughter Anwesha and my wife Matangini


— Samiran Chattopadhyay
Contents

List of Figures xiii

Preface xv

Acknowledgements xvii

Authors xix

1 Introduction 1

1.1 What Is eHealth? . . . . . . . . . . . . . . . . . . . . . . . . 2


1.2 eHealth Technologies . . . . . . . . . . . . . . . . . . . . . . 3
1.3 eHealth Applications . . . . . . . . . . . . . . . . . . . . . . 4
1.3.1 Health Informatics . . . . . . . . . . . . . . . . . . . . 5
1.3.2 mHealth . . . . . . . . . . . . . . . . . . . . . . . . . . 5
1.3.3 Telehealth . . . . . . . . . . . . . . . . . . . . . . . . . 6
1.4 eHealth and Big Data . . . . . . . . . . . . . . . . . . . . . . 8
1.5 Issues and Challenges . . . . . . . . . . . . . . . . . . . . . . 9
1.6 Chapter Notes . . . . . . . . . . . . . . . . . . . . . . . . . . 11

References 12

2 Electronic Health Records 13

2.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
2.2 Electronic Health Records . . . . . . . . . . . . . . . . . . . 14
2.3 EHR Standards . . . . . . . . . . . . . . . . . . . . . . . . . 16
2.3.1 ISO 13606 . . . . . . . . . . . . . . . . . . . . . . . . . 17
2.3.2 HL7 . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
2.3.3 OpenEHR . . . . . . . . . . . . . . . . . . . . . . . . . 23
2.4 Adoption of EHR Standards . . . . . . . . . . . . . . . . . . 30
2.5 Ontology-based Approaches . . . . . . . . . . . . . . . . . . . 32
2.5.1 Developing an Ontology . . . . . . . . . . . . . . . . . 33
2.5.2 Ontologies for EHR . . . . . . . . . . . . . . . . . . . 33
2.5.3 Ontologies in Healthcare . . . . . . . . . . . . . . . . . 34
2.6 Chapter Notes . . . . . . . . . . . . . . . . . . . . . . . . . . 35

vii
viii Contents

References 40

3 Big Data: From Hype to Action 43

3.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
3.2 What Is Big Data? . . . . . . . . . . . . . . . . . . . . . . . 44
3.3 Big Data Properties . . . . . . . . . . . . . . . . . . . . . . . 45
3.4 Why Is Big Data Important? . . . . . . . . . . . . . . . . . . 47
3.5 Big Data in the World . . . . . . . . . . . . . . . . . . . . . . 49
3.6 Big Data in Healthcare . . . . . . . . . . . . . . . . . . . . . 50
3.6.1 Is Health Data Big Data? . . . . . . . . . . . . . . . . 51
3.6.2 Big Data: Healthcare Providers . . . . . . . . . . . . . 52
3.7 Other Big Data Applications . . . . . . . . . . . . . . . . . . 54
3.7.1 Banking and Securities . . . . . . . . . . . . . . . . . . 55
3.7.2 Communications, Media, and Entertainment . . . . . 55
3.7.3 Manufacturing and Natural Resources . . . . . . . . . 56
3.7.4 Government . . . . . . . . . . . . . . . . . . . . . . . . 56
3.7.5 Transportation . . . . . . . . . . . . . . . . . . . . . . 56
3.7.6 Education . . . . . . . . . . . . . . . . . . . . . . . . . 56
3.8 Securing Big Data . . . . . . . . . . . . . . . . . . . . . . . . 57
3.8.1 Security Considerations . . . . . . . . . . . . . . . . . 57
3.8.2 Security Requirements . . . . . . . . . . . . . . . . . . 58
3.8.3 Some Observations . . . . . . . . . . . . . . . . . . . . 59
3.9 Big Data Security Framework . . . . . . . . . . . . . . . . . 59
3.10 Chapter Notes . . . . . . . . . . . . . . . . . . . . . . . . . . 61

References 62

4 Acquisition of Big Health Data 65

4.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . 65
4.2 Wireless Body Area Network . . . . . . . . . . . . . . . . . . 66
4.2.1 BAN Design Aspects . . . . . . . . . . . . . . . . . . . 68
4.2.2 WBAN Sensors . . . . . . . . . . . . . . . . . . . . . . 70
4.2.3 Technologies for WBAN . . . . . . . . . . . . . . . . . 70
4.2.3.1 Bluetooth and Bluetooth LE . . . . . . . . . 70
4.2.3.2 ZigBee and WLAN . . . . . . . . . . . . . . 71
4.2.3.3 WBAN standard . . . . . . . . . . . . . . . . 71
4.2.4 Network Layer . . . . . . . . . . . . . . . . . . . . . . 73
4.2.5 Inter-WBAN Interference . . . . . . . . . . . . . . . . 74
4.3 Crowdsourcing . . . . . . . . . . . . . . . . . . . . . . . . . . 76
4.4 Social Network . . . . . . . . . . . . . . . . . . . . . . . . . . 79
4.5 Chapter Notes . . . . . . . . . . . . . . . . . . . . . . . . . . 83

References 84
Contents ix

5 Health Data Analytics 87

5.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . 88
5.2 Artificial Neural Networks . . . . . . . . . . . . . . . . . . . 90
5.2.1 Model of an ANN . . . . . . . . . . . . . . . . . . . . 90
5.2.2 Modes of ANN . . . . . . . . . . . . . . . . . . . . . . 92
5.2.3 Structure of ANNs . . . . . . . . . . . . . . . . . . . . 93
5.2.4 Training a Feedforward Neural Network . . . . . . . . 93
5.2.5 ANN in Medical Domain . . . . . . . . . . . . . . . . 96
5.2.6 Weakness of ANNs . . . . . . . . . . . . . . . . . . . . 97
5.3 Classification and Clustering . . . . . . . . . . . . . . . . . . 98
5.3.1 Clustering via K-Means . . . . . . . . . . . . . . . . . 99
5.3.2 Some Additional Remarks about K-Means . . . . . . . 100
5.4 Statistical Classifier: Bayesian and Naive Classification . . . 102
5.4.1 Experiments with Medical Data . . . . . . . . . . . . 104
5.4.2 Decision Trees . . . . . . . . . . . . . . . . . . . . . . 106
5.4.3 Clasical Indction of Decision Trees . . . . . . . . . . . 108
5.5 Association Rule Mining (ARM) . . . . . . . . . . . . . . . . 111
5.5.1 Simple Approach for Rule Discovery . . . . . . . . . . 112
5.5.2 Processing of Medical Data . . . . . . . . . . . . . . . 113
5.5.3 Association Rule Mining in Health Data . . . . . . . . 113
5.5.4 Issues with Association Rule Mining . . . . . . . . . . 114
5.6 Time Series Analysis . . . . . . . . . . . . . . . . . . . . . . 115
5.6.1 Time Series Regression Models . . . . . . . . . . . . . 116
5.6.2 Linear AR Time Series Models . . . . . . . . . . . . . 117
5.6.3 Application of Time Series . . . . . . . . . . . . . . . 120
5.7 Text Mining . . . . . . . . . . . . . . . . . . . . . . . . . . . 120
5.7.1 Term Frequency and Inverse Document Frequency . . 122
5.7.2 Topic Modeling . . . . . . . . . . . . . . . . . . . . . . 123
5.8 Chapter Notes . . . . . . . . . . . . . . . . . . . . . . . . . . 124

References 126

6 Architecture and Computational Models for Big Data Pro-


cessing 129

6.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . 130


6.2 Performance Issues . . . . . . . . . . . . . . . . . . . . . . . 130
6.3 Parallel Architecture . . . . . . . . . . . . . . . . . . . . . . 135
6.3.1 Distributed Shared Memory . . . . . . . . . . . . . . . 137
6.3.2 Hierarchical Hybrid Architecture . . . . . . . . . . . . 138
6.3.3 Cluster Computing . . . . . . . . . . . . . . . . . . . . 138
6.3.4 Multicore Architecture . . . . . . . . . . . . . . . . . . 139
6.3.5 GPU Computing . . . . . . . . . . . . . . . . . . . . . 140
6.3.6 Recent Advances in Computer Architecture . . . . . . 141
x Contents

6.4 Exploiting Parallelism . . . . . . . . . . . . . . . . . . . . . . 142


6.5 MapReduce Overview . . . . . . . . . . . . . . . . . . . . . . 144
6.5.1 MapReduce Programming Model . . . . . . . . . . . . 146
6.5.2 MapReduce Framework Implementation . . . . . . . . 146
6.6 Hadoop . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 148
6.6.1 Hadoop Architecture . . . . . . . . . . . . . . . . . . . 149
6.6.2 Resource Provisioning Framework . . . . . . . . . . . 149
6.6.3 Hadoop Distributed File System . . . . . . . . . . . . 151
6.6.4 MapReduce Framework . . . . . . . . . . . . . . . . . 152
6.6.5 Hadoop Common . . . . . . . . . . . . . . . . . . . . . 153
6.6.6 Hadoop Performance . . . . . . . . . . . . . . . . . . . 153
6.7 Hadoop Ecosystem . . . . . . . . . . . . . . . . . . . . . . . 153
6.7.1 Apache Spark . . . . . . . . . . . . . . . . . . . . . . . 154
6.7.2 Apache ZooKeeper . . . . . . . . . . . . . . . . . . . . 155
6.8 Streaming Data Processing . . . . . . . . . . . . . . . . . . . 156
6.8.1 Apache Flume . . . . . . . . . . . . . . . . . . . . . . 156
6.8.2 Spark Streaming . . . . . . . . . . . . . . . . . . . . . 158
6.8.3 Amazon Kinesis Streaming Data Platform . . . . . . . 159
6.9 Chapter Notes . . . . . . . . . . . . . . . . . . . . . . . . . . 159

References 161

7 Big Data Storage 163

7.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . 163


7.2 Structured vs. Unstructured Data . . . . . . . . . . . . . . . 164
7.3 Problems with Relational Databases . . . . . . . . . . . . . . 165
7.4 NoSQL Databases . . . . . . . . . . . . . . . . . . . . . . . . 166
7.5 Document-oriented Databases . . . . . . . . . . . . . . . . . 168
7.5.1 MongoDB . . . . . . . . . . . . . . . . . . . . . . . . . 169
7.5.2 Apache CouchDB . . . . . . . . . . . . . . . . . . . . 173
7.6 Column-oriented Databases . . . . . . . . . . . . . . . . . . . 174
7.6.1 Apache Cassandra . . . . . . . . . . . . . . . . . . . . 174
7.6.2 Apache HBase . . . . . . . . . . . . . . . . . . . . . . 179
7.7 Graph Databases . . . . . . . . . . . . . . . . . . . . . . . . 181
7.7.1 Neo4j . . . . . . . . . . . . . . . . . . . . . . . . . . . 181
7.8 Health Data Storage: A Case Study . . . . . . . . . . . . . . 184
7.9 Chapter Notes . . . . . . . . . . . . . . . . . . . . . . . . . . 188

References 189

8 Security and Privacy for Health Data 191

8.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . 192


8.1.1 Security . . . . . . . . . . . . . . . . . . . . . . . . . . 192
8.1.2 Privacy . . . . . . . . . . . . . . . . . . . . . . . . . . 193
Contents xi

8.1.3 Privacy-Preserving Data Management . . . . . . . . . 194


8.1.4 A Few Common Questions . . . . . . . . . . . . . . . 197
8.2 Security and Privacy Issues . . . . . . . . . . . . . . . . . . . 198
8.2.1 Storage . . . . . . . . . . . . . . . . . . . . . . . . . . 199
8.2.2 Security Breach . . . . . . . . . . . . . . . . . . . . . . 199
8.2.3 Data Mingling . . . . . . . . . . . . . . . . . . . . . . 200
8.2.4 Data Sensitivity . . . . . . . . . . . . . . . . . . . . . 200
8.2.5 User . . . . . . . . . . . . . . . . . . . . . . . . . . . . 202
8.2.6 Computations . . . . . . . . . . . . . . . . . . . . . . . 202
8.2.7 Transaction Logs . . . . . . . . . . . . . . . . . . . . . 202
8.2.8 Validation of Input . . . . . . . . . . . . . . . . . . . . 202
8.2.9 Data Mining . . . . . . . . . . . . . . . . . . . . . . . 203
8.2.10 Access Control . . . . . . . . . . . . . . . . . . . . . . 203
8.2.11 Data Audit . . . . . . . . . . . . . . . . . . . . . . . . 204
8.2.12 Data Source . . . . . . . . . . . . . . . . . . . . . . . . 205
8.2.13 Security Best Practices . . . . . . . . . . . . . . . . . 206
8.2.14 Software Security . . . . . . . . . . . . . . . . . . . . . 207
8.2.15 Secure Hardware . . . . . . . . . . . . . . . . . . . . . 207
8.2.16 User Account Management . . . . . . . . . . . . . . . 207
8.2.17 Clustering and Auditing of Databases . . . . . . . . . 208
8.3 Challenges . . . . . . . . . . . . . . . . . . . . . . . . . . . . 208
8.3.1 Malicious User . . . . . . . . . . . . . . . . . . . . . . 208
8.3.2 Identifying Threats . . . . . . . . . . . . . . . . . . . . 209
8.3.3 Risk Mitigation . . . . . . . . . . . . . . . . . . . . . . 209
8.3.4 Real-Time Monitoring . . . . . . . . . . . . . . . . . . 210
8.3.5 Privacy Preservation . . . . . . . . . . . . . . . . . . . 210
8.3.5.1 Health Data Sale . . . . . . . . . . . . . . . . 212
8.3.5.2 Compliance for EHR . . . . . . . . . . . . . 212
8.4 Security of NoSQL Databases . . . . . . . . . . . . . . . . . 213
8.4.1 Reviewing Security in NoSQL databases . . . . . . . . 213
8.4.1.1 Security in Cassandra . . . . . . . . . . . . . 214
8.4.1.2 Security in MongoDB . . . . . . . . . . . . . 215
8.4.1.3 Security in HBase . . . . . . . . . . . . . . . 216
8.4.2 Reviewing Enterprise Approaches towards Security in
NoSQL Databases . . . . . . . . . . . . . . . . . . . . 218
8.5 Integrating Security with Big Data Solutions . . . . . . . . . 219
8.5.1 Big Data Enterprise Security . . . . . . . . . . . . . . 220
8.6 Secured Health Data Delivery: A Case Study . . . . . . . . . 223
8.7 Chapter Notes . . . . . . . . . . . . . . . . . . . . . . . . . . 227

References 228

Index 233
List of Figures

1.1 eHealth sensors and medical IoT development platform . . . 4


1.2 Wearable technology . . . . . . . . . . . . . . . . . . . . . . 4
1.3 Issues in eHealth data . . . . . . . . . . . . . . . . . . . . . 10

2.1 HL7 and OSI layers [Source: [18]] . . . . . . . . . . . . . . . 19


2.2 Core classes of RIM . . . . . . . . . . . . . . . . . . . . . . . 21
2.3 Entity class and its subclasses [Source: [28]] . . . . . . . . . 22
2.4 Role class [Source: [28]] . . . . . . . . . . . . . . . . . . . . . 23
2.5 Participation class and its subclasses [Source: [28]] . . . . . 24
2.6 openEHR - multilevel modeling . . . . . . . . . . . . . . . . 25
2.7 OpenEHR reference model classes . . . . . . . . . . . . . . . 27
2.8 OpenEHR reference model classes — an example . . . . . . 28
2.9 Archetype for blood pressure [Website: https://www.openehr.
org/ckm/] . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
2.10 Hierarchy of different information objects in the ontology for
health data of a remote health framework . . . . . . . . . . 36
2.11 Entities involved during a patient’s visit to a doctor . . . . . 37
2.12 Inheritance of the patient’s history class . . . . . . . . . . . 37
2.13 OWL file describing the inheritance of the history class . . . 38
2.14 OWL file describing the object properties of the treatment
episode class . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
2.15 OWL file describing the data properties of the treatment
episode class . . . . . . . . . . . . . . . . . . . . . . . . . . . 39

4.1 Sensor on human body . . . . . . . . . . . . . . . . . . . . . 66


4.2 Three-tier WBAN architecture . . . . . . . . . . . . . . . . 68
4.3 Inter-WBAN interference . . . . . . . . . . . . . . . . . . . . 75

5.1 Model of an ANN . . . . . . . . . . . . . . . . . . . . . . . . 91


5.2 Structure of an ANN . . . . . . . . . . . . . . . . . . . . . . 93
5.3 Step function . . . . . . . . . . . . . . . . . . . . . . . . . . 94
5.4 Sigmoid function . . . . . . . . . . . . . . . . . . . . . . . . 94
5.5 Hyperbolic tangent function . . . . . . . . . . . . . . . . . . 95
5.6 Architecture of a back propagation network . . . . . . . . . 96
5.7 Set of points in 2D . . . . . . . . . . . . . . . . . . . . . . . 100
5.8 Initialisation of clusters . . . . . . . . . . . . . . . . . . . . . 101

xiii
xiv Big Data in eHealthcare: Challenges and Perspectives

5.9 Assignment of points to clusters . . . . . . . . . . . . . . . . 102


5.10 Assignment of points to clusters . . . . . . . . . . . . . . . . 103
5.11 A part of a decision tree . . . . . . . . . . . . . . . . . . . . 106
5.12 Samples of two classes that cannot be separated by a single
straight line . . . . . . . . . . . . . . . . . . . . . . . . . . . 108
5.13 The sample separated by two lines . . . . . . . . . . . . . . 109
5.14 Annual number of passengers in an airline . . . . . . . . . . 116

6.1 (a) Linear speedup, (b) Super-linear speedup, and (c) Sub-
linear speedup . . . . . . . . . . . . . . . . . . . . . . . . . . 132
6.2 Execution of a parallel code - Amdahl’s law . . . . . . . . . 134
6.3 Shared memory multiprocessors . . . . . . . . . . . . . . . . 136
6.4 Distributed memory multicomputer . . . . . . . . . . . . . . 137
6.5 Distributed shared memory . . . . . . . . . . . . . . . . . . 138
6.6 A hierarchical hybrid architecture . . . . . . . . . . . . . . . 139
6.7 GPU architecture [Source: [10]] . . . . . . . . . . . . . . . . 141
6.8 Memory organization in a GPU architecture [Source: [10]] . 142
6.9 Shared Address Space programming model . . . . . . . . . . 144
6.10 Message Passing programming model . . . . . . . . . . . . . 145
6.11 A workflow of MapReduce program . . . . . . . . . . . . . . 146
6.12 MapReduce execution environment [Source: [6] [7]] . . . . . 148
6.13 Hadoop architecture overview . . . . . . . . . . . . . . . . . 149
6.14 YARN application execution . . . . . . . . . . . . . . . . . . 150
6.15 HDFS architecture . . . . . . . . . . . . . . . . . . . . . . . 151
6.16 Apache Flume data model. [Source: https://flume.apache.org] 157
6.17 Apache Spark Streaming . . . . . . . . . . . . . . . . . . . . 158

7.1 MongoDB referencing relationship between data . . . . . . . 170


7.2 MongoDB embedded documents . . . . . . . . . . . . . . . . 171
7.3 Cassandra column family [Source: [20]] . . . . . . . . . . . . 176
7.4 (a) Structure of a column, (b) Structure of a super column
[Source: [20]) . . . . . . . . . . . . . . . . . . . . . . . . . . 176
7.5 HBase table . . . . . . . . . . . . . . . . . . . . . . . . . . . 179
7.6 Property Graph Model . . . . . . . . . . . . . . . . . . . . . 182
7.7 Neo4j Graph Platform [Source: [6]] . . . . . . . . . . . . . . 183
7.8 A hierarchical data model for health data . . . . . . . . . . 184
Preface

With the advent of cloud computing and related technologies, eHealthcare is


now in the focus of computer scientists and medical experts. According to Jef-
frey P. Harrison, eHealthcare “is an all-encompassing term for the combined
use of electronic information and communication technology in the health
sector”. The above definition assumes that information is transformed into
electronic information, and then communication technology is used to trans-
mit such information. So, health information first has to be converted and
formatted into electronic health records for proper use. The electronic health
information therefore may be made available wherever and whenever required.
At the same time it has to be ensured that the information is reaching the
rightful recipient. Care has to be taken so that it is not put into the wrong
hands. Thus, eHealthcare aims at provisioning quality healthcare through ef-
ficient delivery using information and communication technologies. Wherever
eHealthcare is possible, remote healthcare cannot be far behind. This means
that patients in far off places (possibly remote locations) with negligible med-
ical facilities will get access to doctors from urban areas. This is possible
because of the penetration of communication technologies. Remote access to
healthcare is therefore not a distant dream now, but has become feasible with
the use of advanced communication technologies.
As a result of using eHealthcare, the interesting aspect that has drawn our
attention is the generation of huge amounts of various data. Health data will
contain data of a patient including his/her detailed personal information and
health condition. Information regarding health condition may require X-ray
reports, ECG reports, USG reports, or MRI reports, with other observations
and reports of blood tests, to name a few. Thus, health data contains audio and
video data, images. Health data will also include streaming sensor-generated
data from continuous patient monitoring. This data has characteristics, like
variety, velocity, and veracity, apart from being voluminous. Hence, health
data is essentially, big data, or may be called Big Health Data. Big data is
an evolving term to describe any voluminous amount of structured, semi-
structured, and unstructured data that has the above properties along with
many other properties. With so many properties, big data therefore also has
the potential to be mined for information. It may be righfully observed that
traditional relational databases may not be suitable for storing such big health
data since the data may not always be confined to some structured format.
Hence, NoSQL databases have been evolved to store such types of data. Several
NoSQL database platforms developed and are in use. In order to improve the

xv
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