Biomedical Data Mining for Information Retrieval

BIOMEDICAL DATA MINING FOR INFORMATION RETRIEVAL

THIS BOOK NOT ONLY EMPHASIZES TRADITIONAL COMPUTATIONAL TECHNIQUES, BUT DISCUSSES DATA MINING, BIOMEDICAL IMAGE PROCESSING, INFORMATION RETRIEVAL WITH BROAD COVERAGE OF BASIC SCIENTIFIC APPLICATIONS.Biomedical Data Mining for Information Retrieval comprehensively covers the topic of mining biomedical text, images and visual features towards information retrieval. Biomedical and health informatics is an emerging field of research at the intersection of information science, computer science, and healthcare and brings tremendous opportunities and challenges due to easily available and abundant biomedical data for further analysis. The aim of healthcare informatics is to ensure the high-quality, efficient healthcare, better treatment and quality of life by analyzing biomedical and healthcare data including patient’s data, electronic health records (EHRs) and lifestyle. Previously, it was a common requirement to have a domain expert to develop a model for biomedical or healthcare; however, recent advancements in representation learning algorithms allows us to automatically to develop the model. Biomedical image mining, a novel research area, due to the vast amount of available biomedical images, increasingly generates and stores digitally. These images are mainly in the form of computed tomography (CT), X-ray, nuclear medicine imaging (PET, SPECT), magnetic resonance imaging (MRI) and ultrasound. Patients’ biomedical images can be digitized using data mining techniques and may help in answering several important and critical questions relating to healthcare. Image mining in medicine can help to uncover new relationships between data and reveal new useful information that can be helpful for doctors in treating their patients. AUDIENCEResearchers in various fields including computer science, medical informatics, healthcare IOT, artificial intelligence, machine learning, image processing, clinical big data analytics. SUJATA DASH received her PhD in Computational Modeling from Berhampur University, Orissa, India in 1995. She is an associate professor in P.G. Department of Computer Science & Application, North Orissa University, at Baripada, India. She has published more than 80 technical papers in international journals, conferences, book chapters and has authored 5 books. SUBHENDU KUMAR Pani received his PhD from Utkal University Odisha, India in 2013. He is working as Professor in the Krupajal Computer Academy, BPUT, Odisha, India. S. BALAMURUGAN is the Director-Research and Development, Intelligent Research Consultancy Services(iRCS), Coimbatore, Tamilnadu, India. His PhD is in Infomation Technology and he has published 45 books, 200+ international journals/conferences and 35 patents. AJITH ABRAHAM received PhD in Computer Science from Monash University, Melbourne, Australia in 2001. He is Director of Machine Intelligence Research Labs (MIR Labs) which has members from 100+ countries. Ajith’s research experience includes over 30 years in the industry and academia. He has authored / co-authored over 1300+ publications (with colleagues from nearly 40 countries) and has an h-index of 86+. Preface xv

1 MORTALITY PREDICTION OF ICU PATIENTS USING MACHINE LEARNING TECHNIQUES 1

Babita Majhi, Aarti Kashyap and Ritanjali Majhi

1.1 Introduction 2

1.2 Review of Literature 3

1.3 Materials and Methods 8

1.3.1 Dataset 8

1.3.2 Data Pre-Processing 8

1.3.3 Normalization 8

1.3.4 Mortality Prediction 10

1.3.5 Model Description and Development 11

1.4 Result and Discussion 15

1.5 Conclusion 16

1.6 Future Work 16

References 17

2 ARTIFICIAL INTELLIGENCE IN BIOINFORMATICS 21

V. Samuel Raj, Anjali Priyadarshini, Manoj Kumar Yadav, Ramendra Pati Pandey, Archana Gupta and Arpana Vibhuti

2.1 Introduction 21

2.2 Recent Trends in the Field of AI in Bioinformatics 22

2.2.1 DNA Sequencing and Gene Prediction Using Deep Learning 24

2.3 Data Management and Information Extraction 26

2.4 Gene Expression Analysis 26

2.4.1 Approaches for Analysis of Gene Expression 27

2.4.2 Applications of Gene Expression Analysis 29

2.5 Role of Computation in Protein Structure Prediction 30

2.6 Application in Protein Folding Prediction 31

2.7 Role of Artificial Intelligence in Computer-Aided Drug Design 38

2.8 Conclusions 42

References 43

3 PREDICTIVE ANALYSIS IN HEALTHCARE USING FEATURE SELECTION 53

Aneri Acharya, Jitali Patel and Jigna Patel

3.1 Introduction 54

3.1.1 Overview and Statistics About the Disease 54

3.1.1.1 Diabetes 54

3.1.1.2 Hepatitis 55

3.1.2 Overview of the Experiment Carried Out 56

3.2 Literature Review 58

3.2.1 Summary 58

3.2.2 Comparison of Papers for Diabetes and Hepatitis Dataset 61

3.3 Dataset Description 70

3.3.1 Diabetes Dataset 70

3.3.2 Hepatitis Dataset 71

3.4 Feature Selection 73

3.4.1 Importance of Feature Selection 74

3.4.2 Difference Between Feature Selection, Feature Extraction and Dimensionality Reduction 74

3.4.3 Why Traditional Feature Selection Techniques Still Holds True? 75

3.4.4 Advantages and Disadvantages of Feature Selection Technique 76

3.4.4.1 Advantages 76

3.4.4.2 Disadvantage 76

3.5 Feature Selection Methods 76

3.5.1 Filter Method 76

3.5.1.1 Basic Filter Methods 77

3.5.1.2 Correlation Filter Methods 77

3.5.1.3 Statistical & Ranking Filter Methods 78

3.5.1.4 Advantages and Disadvantages of Filter Method 80

3.5.2 Wrapper Method 80

3.5.2.1 Advantages and Disadvantages of Wrapper Method 82

3.5.2.2 Difference Between Filter Method and Wrapper Method 82

3.6 Methodology 84

3.6.1 Steps Performed 84

3.6.2 Flowchart 84

3.7 Experimental Results and Analysis 85

3.7.1 Task 1—Application of Four Machine Learning Models 85

3.7.2 Task 2—Applying Ensemble Learning Algorithms 86

3.7.3 Task 3—Applying Feature Selection Techniques 87

3.7.4 Task 4—Appling Data Balancing Technique 94

3.8 Conclusion 96

References 99

4 HEALTHCARE 4.0: AN INSIGHT OF ARCHITECTURE, SECURITY REQUIREMENTS, PILLARS AND APPLICATIONS 103

Deepanshu Bajaj, Bharat Bhushan and Divya Yadav

4.1 Introduction 104

4.2 Basic Architecture and Components of e-Health Architecture 105

4.2.1 Front End Layer 106

4.2.2 Communication Layer 107

4.2.3 Back End Layer 107

4.3 Security Requirements in Healthcare 4.0 108

4.3.1 Mutual-Authentications 109

4.3.2 Anonymity 110

4.3.3 Un-Traceability 111

4.3.4 Perfect—Forward—Secrecy 111

4.3.5 Attack Resistance 111

4.3.5.1 Replay Attack 111

4.3.5.2 Spoofing Attack 112

4.3.5.3 Modification Attack 112

4.3.5.4 MITM Attack 112

4.3.5.5 Impersonation Attack 112

4.4 ICT Pillar’s Associated With HC4.0 113

4.4.1 IoT in Healthcare 4.0 114

4.4.2 Cloud Computing (CC) in Healthcare 4.0 115

4.4.3 Fog Computing (FC) in Healthcare 4.0 116

4.4.4 BigData (BD) in Healthcare 4.0 117

4.4.5 Machine Learning (ML) in Healthcare 4.0 118

4.4.6 Blockchain (BC) in Healthcare 4.0 120

4.5 Healthcare 4.0’s Applications-Scenarios 121

4.5.1 Monitor-Physical and Pathological Related Signals 121

4.5.2 Self-Management, and Wellbeing Monitor, and its Precaution 124

4.5.3 Medication Consumption Monitoring and Smart-Pharmaceutics 124

4.5.4 Personalized (or Customized) Healthcare 125

4.5.5 Cloud-Related Medical Information’s Systems 125

4.5.6 Rehabilitation 126

4.6 Conclusion 126

References 127

5 IMPROVED SOCIAL MEDIA DATA MINING FOR ANALYZING MEDICAL TRENDS 131

Minakshi Sharma and Sunil Sharma

5.1 Introduction 132

5.1.1 Data Mining 132

5.1.2 Major Components of Data Mining 132

5.1.3 Social Media Mining 134

5.1.4 Clustering in Data Mining 134

5.2 Literature Survey 136

5.3 Basic Data Mining Clustering Technique 140

5.3.1 Classifier and Their Algorithms in Data Mining 143

5.4 Research Methodology 147

5.5 Results and Discussion 151

5.5.1 Tool Description 151

5.5.2 Implementation Results 152

5.5.3 Comparison Graphs Performance Comparison 156

5.6 Conclusion & Future Scope 157

References 158

6 BIOINFORMATICS: AN IMPORTANT TOOL IN ONCOLOGY 163

Gaganpreet Kaur, Saurabh Gupta, Gagandeep Kaur, Manju Verma and Pawandeep Kaur

6.1 Introduction 164

6.2 Cancer—A Brief Introduction 165

6.2.1 Types of Cancer 166

6.2.2 Development of Cancer 166

6.2.3 Properties of Cancer Cells 166

6.2.4 Causes of Cancer 168

6.3 Bioinformatics—A Brief Introduction 169

6.4 Bioinformatics—A Boon for Cancer Research 170

6.5 Applications of Bioinformatics Approaches in Cancer 174

6.5.1 Biomarkers: A Paramount Tool for Cancer Research 175

6.5.2 Comparative Genomic Hybridization for Cancer Research 177

6.5.3 Next-Generation Sequencing 178

6.5.4 miRNA 179

6.5.5 Microarray Technology 181

6.5.6 Proteomics-Based Bioinformatics Techniques 185

6.5.7 Expressed Sequence Tags (EST) and Serial Analysis of Gene Expression (SAGE) 187

6.6 Bioinformatics: A New Hope for Cancer Therapeutics 188

6.7 Conclusion 191

References 192

7 BIOMEDICAL BIG DATA ANALYTICS USING IOT IN HEALTH INFORMATICS 197

Pawan Singh Gangwar and Yasha Hasija

7.1 Introduction 198

7.2 Biomedical Big Data 200

7.2.1 Big EHR Data 201

7.2.2 Medical Imaging Data 201

7.2.3 Clinical Text Mining Data 201

7.2.4 Big OMICs Data 202

7.3 Healthcare Internet of Things (IoT) 202

7.3.1 IoT Architecture 202

7.3.2 IoT Data Source 204

7.3.2.1 IoT Hardware 204

7.3.2.2 IoT Middleware 205

7.3.2.3 IoT Presentation 205

7.3.2.4 IoT Software 205

7.3.2.5 IoT Protocols 206

7.4 Studies Related to Big Data Analytics in Healthcare IoT 206

7.5 Challenges for Medical IoT & Big Data in Healthcare 209

7.6 Conclusion 210

References 210

8 STATISTICAL IMAGE ANALYSIS OF DRYING BOVINE SERUM ALBUMIN DROPLETS IN PHOSPHATE BUFFERED SALINE 213

Anusuya Pal, Amalesh Gope and Germano S. Iannacchione

8.1 Introduction 214

8.2 Experimental Methods 216

8.3 Results 217

8.3.1 Temporal Study of the Drying Droplets 217

8.3.2 FOS Characterization of the Drying Evolution 219

8.3.3 GLCM Characterization of the Drying Evolution 220

8.4 Discussions 224

8.4.1 Qualitative Analysis of the Drying Droplets and the Dried Films 224

8.4.2 Quantitative Analysis of the Drying Droplets and the Dried Films 227

8.5 Conclusions 231

Acknowledgments 232

References 232

9 INTRODUCTION TO DEEP LEARNING IN HEALTH INFORMATICS 237

Monika Jyotiyana and Nishtha Kesswani

9.1 Introduction 237

9.1.1 Machine Learning v/s Deep Learning 240

9.1.2 Neural Networks and Deep Learning 241

9.1.3 Deep Learning Architecture 242

9.1.3.1 Deep Neural Networks 243

9.1.3.2 Convolutional Neural Networks 243

9.1.3.3 Deep Belief Networks 244

9.1.3.4 Recurrent Neural Networks 244

9.1.3.5 Deep Auto-Encoder 245

9.1.4 Applications 246

9.2 Deep Learning in Health Informatics 246

9.2.1 Medical Imaging 246

9.2.1.1 CNN v/s Medical Imaging 247

9.2.1.2 Tissue Classification 247

9.2.1.3 Cell Clustering 247

9.2.1.4 Tumor Detection 247

9.2.1.5 Brain Tissue Classification 248

9.2.1.6 Organ Segmentation 248

9.2.1.7 Alzheimer’s and Other NDD Diagnosis 248

9.3 Medical Informatics 249

9.3.1 Data Mining 249

9.3.2 Prediction of Disease 249

9.3.3 Human Behavior Monitoring 250

9.4 Bioinformatics 250

9.4.1 Cancer Diagnosis 250

9.4.2 Gene Variants 251

9.4.3 Gene Classification or Gene Selection 251

9.4.4 Compound–Protein Interaction 251

9.4.5 DNA–RNA Sequences 252

9.4.6 Drug Designing 252

9.5 Pervasive Sensing 252

9.5.1 Human Activity Monitoring 253

9.5.2 Anomaly Detection 253

9.5.3 Biological Parameter Monitoring 253

9.5.4 Hand Gesture Recognition 253

9.5.5 Sign Language Recognition 254

9.5.6 Food Intake 254

9.5.7 Energy Expenditure 254

9.5.8 Obstacle Detection 254

9.6 Public Health 255

9.6.1 Lifestyle Diseases 255

9.6.2 Predicting Demographic Information 256

9.6.3 Air Pollutant Prediction 256

9.6.4 Infectious Disease Epidemics 257

9.7 Deep Learning Limitations and Challenges in Health Informatics 257

References 258

10 DATA MINING TECHNIQUES AND ALGORITHMS IN PSYCHIATRIC HEALTH: A SYSTEMATIC REVIEW 263

Shikha Gupta, Nitish Mehndiratta, Swarnim Sinha, Sangana Chaturvedi and Mehak Singla

10.1 Introduction 263

10.2 Techniques and Algorithms Applied 265

10.3 Analysis of Major Health Disorders Through Different Techniques 267

10.3.1 Alzheimer 267

10.3.2 Dementia 268

10.3.3 Depression 274

10.3.4 Schizophrenia and Bipolar Disorders 281

10.4 Conclusion 285

References 286

11 DEEP LEARNING APPLICATIONS IN MEDICAL IMAGE ANALYSIS 293

Ananya Singha, Rini Smita Thakur and Tushar Patel

11.1 Introduction 294

11.1.1 Medical Imaging 295

11.1.2 Artificial Intelligence and Deep Learning 296

11.1.3 Processing in Medical Images 300

11.2 Deep Learning Models and its Classification 303

11.2.1 Supervised Learning 303

11.2.1.1 RNN (Recurrent Neural Network) 303

11.2.2 Unsupervised Learning 304

11.2.2.1 Stacked Auto Encoder (SAE) 304

11.2.2.2 Deep Belief Network (DBN) 306

11.2.2.3 Deep Boltzmann Machine (DBM) 307

11.2.2.4 Generative Adversarial Network (GAN) 308

11.3 Convolutional Neural Networks (CNN)—A Popular Supervised Deep Model 309

11.3.1 Architecture of CNN 310

11.3.2 Learning of CNNs 313

11.3.3 Medical Image Denoising using CNNs 314

11.3.4 Medical Image Classification Using CNN 316

11.4 Deep Learning Advancements—A Biological Overview 317

11.4.1 Sub-Cellular Level 317

11.4.2 Cellular Level 319

11.4.3 Tissue Level 323

11.4.4 Organ Level 326

11.4.4.1 The Brain and Neural System 326

11.4.4.2 Sensory Organs—The Eye and Ear 329

11.4.4.3 Thoracic Cavity 330

11.4.4.4 Abdomen and Gastrointestinal (GI) Track 331

11.4.4.5 Other Miscellaneous Applications 332

11.5 Conclusion and Discussion 335

References 336

12 ROLE OF MEDICAL IMAGE ANALYSIS IN ONCOLOGY 351

Gaganpreet Kaur, Hardik Garg, Kumari Heena, Lakhvir Singh, Navroz Kaur, Shubham Kumar and Shadab Alam

12.1 Introduction 352

12.2 Cancer 353

12.2.1 Types of Cancer 354

12.2.2 Causes of Cancer 355

12.2.3 Stages of Cancer 355

12.2.4 Prognosis 356

12.3 Medical Imaging 357

12.3.1 Anatomical Imaging 357

12.3.2 Functional Imaging 358

12.3.3 Molecular Imaging 358

12.4 Diagnostic Approaches for Cancer 358

12.4.1 Conventional Approaches 358

12.4.1.1 Laboratory Diagnostic Techniques 359

12.4.1.2 Tumor Biopsies 359

12.4.1.3 Endoscopic Exams 360

12.4.2 Modern Approaches 361

12.4.2.1 Image Processing 361

12.4.2.2 Implications of Advanced Techniques 362

12.4.2.3 Imaging Techniques 363

12.5 Conclusion 375

References 376

13 A COMPARATIVE ANALYSIS OF CLASSIFIERS USING PARTICLE SWARM OPTIMIZATION-BASED FEATURE SELECTION 383

Chandra Sekhar Biswal, Subhendu Kumar Pani and Sujata Dash

13.1 Introduction 384

13.2 Feature Selection for Classification 385

13.2.1 An Overview: Data Mining 385

13.2.2 Classification Prediction 387

13.2.3 Dimensionality Reduction 387

13.2.4 Techniques of Feature Selection 388

13.2.5 Feature Selection: A Survey 392

13.2.6 Summary 394

13.3 Use of WEKA Tool 395

13.3.1 WEKA Tool 395

13.3.2 Classifier Selection 395

13.3.3 Feature Selection Algorithms in WEKA 395

13.3.4 Performance Measure 396

13.3.5 Dataset Description 398

13.3.6 Experiment Design 398

13.3.7 Results Analysis 399

13.3.8 Summary 401

13.4 Conclusion and Future Work 401

13.4.1 Summary of the Work 401

13.4.2 Research Challenges 402

13.4.3 Future Work 404

References 404

Index 409