Intelligent Data Analytics for Bioinformatics and Biomedical Systems

Herausgeber: Cengiz, Korhan; Chatterjee, Prasenjit; Sharma, Neha

• Gebundenes Buch

Produktbeschreibung

The book analyzes the combination of intelligent data analytics with the intricacies of biological data that has become a crucial factor for innovation and growth in the fast-changing field of bioinformatics and biomedical systems. Intelligent Data Analytics for Bioinformatics and Biomedical Systems delves into the transformative nature of data analytics for bioinformatics and biomedical research. It offers a thorough examination of advanced techniques, methodologies, and applications that utilize intelligence to improve results in the healthcare sector. With the exponential growth of data in these domains, the book explores how computational intelligence and advanced analytic techniques can be harnessed to extract insights, drive informed decisions, and unlock hidden patterns from vast datasets. From genomic analysis to disease diagnostics and personalized medicine, the book aims to showcase intelligent approaches that enable researchers, clinicians, and data scientists to unravel complex biological processes and make significant strides in understanding human health and diseases. This book is divided into three sections, each focusing on computational intelligence and data sets in biomedical systems. The first section discusses the fundamental concepts of computational intelligence and big data in the context of bioinformatics. This section emphasizes data mining, pattern recognition, and knowledge discovery for bioinformatics applications. The second part talks about computational intelligence and big data in biomedical systems. Based on how these advanced techniques are utilized in the system, this section discusses how personalized medicine and precision healthcare enable treatment based on individual data and genetic profiles. The last section investigates the challenges and future directions of computational intelligence and big data in bioinformatics and biomedical systems. This section concludes with discussions on the potential impact of computational intelligence on addressing global healthcare challenges. Audience Intelligent Data Analytics for Bioinformatics and Biomedical Systems is primarily targeted to professionals and researchers in bioinformatics, genetics, molecular biology, biomedical engineering, and healthcare. The book will also suit academicians, students, and professionals working in pharmaceuticals and interpreting biomedical data.

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Produktdetails

• Verlag: John Wiley & Sons Inc
• Seitenzahl: 432
• Erscheinungstermin: 25. Oktober 2024
• Englisch
• ISBN-13: 9781394270880
• ISBN-10: 1394270887
• Artikelnr.: 71779484

Autorenporträt

Neha Sharma PhD, is an assistant professor in the Department of Computer Science and Engineering, Chitkara University, Rajpura, India. She has more than 60 international publications in reputed peer-reviewed journals. She has also published more than 30 national & international patents under the Intellectual Property Rights of the governments of India and abroad. Her main areas of research are in image processing, machine learning, deep learning, and cybersecurity. Korhan Cengiz, PhD, is an assistant professor at the Department of Information Technologies, Faculty of Informatics and Management, University of Hradec Kralove, Kralove, Czech Republic. He obtained his doctorate in electronics engineering from Kadir Has University, Istanbul, Turkey, in 2016 and has authored more than 40 SCI articles, five international patents, ten chapters in books, and one book. His research interests include wireless sensor networks, wireless communications, statistical signal processing, etc. Prasenjit Chatterjee, PhD, is a professor of mechanical engineering and dean (research and consultancy) at MCKV Institute of Engineering, West Bengal, India. He has authored several books on intelligent decision-making, fuzzy computing, supply chain management, etc. He has over 6850 citations and many research papers in various international journals. Dr. Chatterjee is one of the developers of two multiple-criteria decision-making methods called Measurement of Alternatives and Ranking according to Compromise Solution (MARCOS) and Ranking Alternatives through Functional Mapping of Criterion Sub-Intervals into a Single Interval (RAFSI).

Inhaltsangabe

Preface xix Acknowledgment xxv 1 Advancements in Machine Learning Techniques for Biological Data Analysis 1 S. Kanakaprabha, G. Ganesh Kumar, Y. Padma, Gangavarapu and Venkata Nagaraju Thatha 1.1 Introduction 1 1.1.1 Significance of Advanced Data Analysis in Biology 2 1.2 Literature Survey 3 1.3 Machine Learning Fundamentals 5 1.3.1 Supervised, Unsupervised, and Semi-Supervised Learning 6 1.3.2 Feature Engineering and Selection 6 1.3.3 Deep Learning Architectures for Biological Data 7 1.4 Genomic Sequence Analysis 7 1.4.1 DNA Sequence Classification and Prediction 8 1.4.2 Genomic Variant Analysis with Machine Learning 8 1.4.3 Enhancing Epigenetic Studies through AI 8 1.5 Proteomic Profiling and Structural Prediction 9 1.5.1 Protein Structure Prediction Using Deep Learning 10 1.5.2 Peptide and Protein Identification via Machine Learning 11 1.5.3 Functional Annotation of Proteins 11 1.6 Metabolomics and Pathway Analysis 12 1.6.1 Metabolite Identification and Quantification 14 1.6.2 Metabolic Pathway Reconstruction Using AI 14 1.6.3 Integrative Analysis of Multi-Omics Data 15 1.7 Medical Applications 15 1.7.1 Disease Diagnosis and Biomarker Discovery 15 1.7.2 Personalized Treatment and Drug Discovery 16 1.7.3 Predictive Modeling for Clinical Outcomes 16 1.7.4 Drug Repurposing and Adverse Event Prediction 17 1.7.5 Neuroinformatics and Brain Disorders 17 1.8 Challenges and Future Directions 17 1.8.1 Interpretable Machine Learning in Biology 21 1.8.2 Addressing Data Privacy and Ethics 21 1.8.3 Advancing Quantum Computing in Biological Data Analysis 22 1.8.4 Handling Heterogeneous and Multi-Modal Data 22 1.8.5 Small Data and Imbalanced Datasets 22 1.8.6 Clinical Adoption and Validation 22 1.8.7 Ethical and Societal Implications 23 1.9 Conclusion 23 1.9.1 Synthesis of Key Contributions and Insights 23 1.9.2 Anticipated Transformations in Biological Research 24 References 24 2 Predictive Analytics in Medical Diagnosis 27 Vivek Upadhyaya 2.1 Introduction to Predictive Analytics in Healthcare 28 2.1.1 Definition of Predictive Analytics 28 2.1.2 The Significance of Predictive Analytics in Medical Diagnosis 29 2.2 Overview of the Chapter's Structure 29 2.3 Data Sources and Data Preprocessing 30 2.3.1 Types of Data Sources (Electronic Health Records, Wearable Devices, Genetic Data, etc.) 31 2.4 Data Quality and Cleaning 33 2.4.1 Feature Selection and Engineering 33 2.4.2 Dealing with Missing Data 35 2.5 Predictive Analytics Techniques 36 2.5.1 Regression Analysis 36 2.5.2 Classification Models (e.g., Logistic Regression, Decision Trees, Random Forests) 37 2.5.3 Machine Learning Algorithms (e.g., Support Vector Machines, Neural Networks) 39 2.5.4 Time Series Analysis 40 2.6 Use Cases in Medical Diagnosis 40 2.6.1 Early Detection of Diseases (e.g., Cancer, Diabetes) 42 2.6.2 Risk Assessment and Stratification 42 2.6.3 Personalized Treatment Recommendations 43 2.6.4 Image Analysis and Medical Imaging 43 2.6.5 Disease Progression Tracking 46 2.6.6 Model Interpretability and Explainability 47 2.6.7 The Importance of Model Interpretability in Healthcare 47 2.6.8 Techniques for Making Predictive Models More Interpretable 48 2.6.9 Regulatory Considerations (e.g., GDPR, HIPAA) 49 2.6.10 Ethical and Legal Considerations 50 2.7 Challenges and Limitations 51 2.7.1 Data-Related Challenges (Data Volume, Quality, Interoperability) 53 2.7.2 Overfitting and Model Generalization 53 2.7.3 Addressing Bias and Fairness in Predictive Models 54 2.7.4 Successful Implementation and Case Studies 55 2.7.5 Real-World Examples of Healthcare Institutions Successfully Using Predictive Analytics 56 2.8 Future Trends and Innovations 58 2.8.1 The Role of Artificial Intelligence and Deep Learning 59 2.8.2 Integration with Electronic Health Records and Telemedicine 60 2.8.3 The Potential Impact of Quantum Computing on Medical Diagnosis 60 2.9 Conclusion 62 References 63 3 Skin Disease Detection and Classification 67 M. Aamir Gulzar, Salman Iqbal, Akhtar Jamil, Alaa Ali Hameed and Faezeh Soleimani 3.1 Introduction 68 3.2 Related Work 69 3.3 Data 70 3.4 Methodology 71 3.4.1 Data Pre-Processing 71 3.4.2 Image Enhancement 72 3.4.3 Feature Extraction 73 3.4.4 Machine Learning Algorithm Used 74 3.5 Results 81 3.5.1 Experimental Setup 81 3.5.2 Data Preprocessing, Feature Extraction, and Model Selection 83 3.5.3 Evaluation Metrics 85 3.5.4 Classification and Outcomes 86 3.6 Conclusion 89 3.7 Future Work 90 References 91 4 Computer-Aided Polyp Detection Using Customized Convolutional Neural Network Architecture 93 Palak Handa, Nidhi Goel, S. Indu and Deepak Gunjan 4.1 Introduction 94 4.2 Related Works 96 4.3 Materials and Methods 96 4.3.1 Description of the Used Datasets and Their Preparation 96 4.3.2 Data Augmentation 96 4.3.3 Customized CNN 97 4.4 Results and Discussion 98 4.4.1 CNN Optimizers 99 4.4.2 Kernel Initializers 99 4.4.3 Color Space 100 4.4.4 Image Dimension 101 4.4.5 Kernel Size 101 4.4.6 Sample Maps of the CNN Features 103 4.4.7 Ablation Study 104 4.4.8 Comparison of the Proposed Architecture with Existing Deep-Learning Algorithms in This Field 104 4.5 Conclusion and Future Scope 105 References 106 5 Computational Intelligence Induced Risk in Modern Healthcare: Classical Review and Current Status 109 Nitish Ojha and Shrikant Ojha 5.1 Introduction 110 5.2 People-Based Risk 113 5.3 Doctor-Induced Risk 116 5.4 Patient-Based Risk 120 5.5 Process-Based Risk 121 5.6 Technology-Based Risk 129 5.7 Conclusion 138 References 139 6 A Hybrid Deep Learning Framework to Diagnose Sleep Apnea Using Electrocardiogram Signals for Smart Healthcare 145 Sampoorna Poria, Ahona Ghosh, Biswarup Ganguly and Sriparna Saha 6.1 Introduction 146 6.2 Proposed Methodology 148 6.2.1 Introduction to the Data Acquisition Device 148 6.2.2 Preprocessing Using Discrete Wavelet Transform 148 6.2.3 Feature Extraction Using Auto Encoder 149 6.2.4 Classification Using Bidirectional LSTM 150 6.3 Experiment Results and Discussions 152 6.3.1 Dataset Details 152 6.3.1.1 Preprocessing Outcomes 153 6.3.2 Feature Extraction Outcomes 154 6.3.3 Classification Results 155 6.3.4 Statistical Validation 156 6.3.5 Experimental Setup for Computer Aided Diagnosis System 158 6.3.6 Performance Evaluation 158 6.4 Conclusion and Future Scope 160 Acknowledgments 160 References 160 7 Deep Ensemble Feature Extraction Based Classification of Bleeding Regions Using Wireless Capsule Endoscopy Images 163 Srijita Bandopadhyay, Kyamelia Roy, Sheli Sinha Chaudhuri, Soumen Banerjee and Korhan Cengiz 7.1 Introduction 164 7.2 Related Works 164 7.3 Methodology 166 7.3.1 Dataset 167 7.3.2 Image Processing 168 7.3.3 Histogram Equalizer 169 7.3.4 Denoising 172 7.3.5 Adaptive Filtering 173 7.3.6 Augmentation 173 7.3.7 Data Processing 175 7.3.8 Convolutional Neural Network 175 7.3.8.1 ResNet 50 175 7.3.8.2 Vgg 16 176 7.3.8.3 Inception V 3 177 7.3.9 Feature Extraction 177 7.3.10 Feature Reconstruction 178 7.3.11 Classification 179 7.4 Results and Discussion 180 7.5 Conclusion 189 References 189 8 Advances in Brain Tumor Detection and Localization: A Comprehensive Survey 195 Krishnangshu Paul, Arunima Patra and Prithwineel Paul 8.1 Introduction 195 8.2 Background Study on Various Methods 198 8.2.1 Svm 198 8.2.1.1 Advantages 198 8.2.1.2 Limitations 199 8.2.2 Knn 199 8.2.2.1 Advantages 199 8.2.2.2 Limitations 199 8.2.3 Logistic Regression 200 8.2.3.1 Advantages 200 8.2.3.2 Limitations 200 8.2.4 Cnn 200 8.2.4.1 Advantages 201 8.2.4.2 Limitations 201 8.3 Methodology 202 8.4 Experimentation 205 8.4.1 Dataset 205 8.4.2 Results Achieved 206 8.5 Discussion 210 8.6 Conclusion 210 8.6.1 Future Scope 210 References 211 9 Integrating Apriori Algorithm with Data Mining Classification Techniques for Enhanced Primary Tumor Prediction 213 Khalid Mahboob, Nida Khalil, Fatima Waseem and Abeer Javed Syed 9.1 Overview 214 9.1.1 Feature Selection 216 9.1.2 Hyperparameter Tuning 216 9.1.3 Enhanced Primary Tumor Prediction 217 9.1.4 Continuous Improvement 217 9.1.5 Clinical Integration 217 9.2 Previous Studies on Tumor Prediction Using Data Mining and Apriori Algorithm 218 9.3 Data Mining Process 220 9.3.1 Data Collection and Pre-Processing 221 9.3.1.1 Data Cleaning 221 9.3.1.2 Data Transformation 221 9.3.1.3 Data Reduction 221 9.3.1.4 Data Integration 222 9.3.1.5 Data Discretization 222 9.3.2 Model(s) Selection and Building 222 9.3.2.1 Supervised Learning 222 9.3.2.2 Unsupervised Learning 223 9.3.2.3 Reinforcement Learning 223 9.3.2.4 Ensemble Method 224 9.3.3 Evaluation and Exploratory Data Analysis 224 9.3.3.1 Evaluation Techniques in Data Mining 225 9.4 Data Mining in Bioinformatics 225 9.5 Cancer and Tumor Biology 226 9.6 Data Mining Classification Techniques 228 9.6.1 J48 Decision Tree 229 9.6.2 Naïve Bayes 229 9.6.3 K-Nearest Neighbor 229 9.7 Apriori Algorithm and Association Rule Mining 230 9.8 Conclusion and Future Work 230 References 231 10 Deep Learning in Genomics, Personalized Medicine, and Neurodevelopmental Disorders 235 Ajay Sharma, Shashi Kala, Aman Kumar, Shamneesh Sharma, Gaurav Gupta and Varun Jaiswal 10.1 Introduction 236 10.1.1 Genomics, Genetics, and Personalized-Medicine Genetics 238 10.1.2 The "Omics" Revolution a Bioinformatics Perspective 239 10.2 Machine Learning in Personalized Medicine and Neurogenerative Disorder 241 10.2.1 Machine Learning Using Artificial Deep Neural Networks (DNN) 243 10.2.2 Limitations and Advantages of ML Over Traditional Approaches 245 10.3 Machine Learning in Genomics 246 10.3.1 Multi-Model Data Integration Using Machine Learning 249 10.4 Machine Learning and the Future of Medicine in Healthcare 251 10.4.1 Ethical and Legal Considerations of Precision Medicine 252 10.5 Genomics Technology and Application 255 10.5.1 High-Throughput DNA Sequencing Technology 255 10.5.2 Pharmacogenomics (PGx) 256 10.5.3 The Study of Drug Action is Divided into Different Categories: Pharmacokinetics and Pharmacodynamics 257 10.5.4 Circulating Cell-Free Nucleic Acids 257 10.5.5 Circulating Tumor Cells (CTCs) 258 10.5.6 Mitochondrial DNA (mtDNA) 258 10.6 Artificial Intelligence and Neurodegenerative Disorders 259 10.7 Conclusion 261 Conflict of Interest 261 Acknowledgments 262 References 262 11 Emerging Trends of Big Data in Bioinformatics and Challenges 265 Ajay Sharma, Tarun Pal, Utkarsha Naithani, Gaurav Gupta and Varun Jaiswal 11.1 Introduction 266 11.2 Human Genome 267 11.3 Next-Generation Sequencing 268 11.3.1 Challenges of NGS in Big Data 271 11.4 Bioinformatics Big Data Architecture 272 11.5 Big Data in Immunology 273 11.6 Structural Biology 275 11.7 Computer Science 277 11.8 Healthcare 280 11.8.1 Application of Big Data in Healthcare 282 11.9 Big Data Formats 282 11.9.1 Quantum Computing 284 11.10 Conclusion 285 Conflict of Interest 285 Acknowledgments 285 References 286 12 Wearable Devices and Health Monitoring: Big Data and AI for Remote Patient Care 291 S. Kanakaprabha, G. Ganesh Kumar, Bhargavi Peddi Reddy, Yallapragada Ravi Raju and P. Chandra Mohan Rai 12.1 Introduction 292 12.1.1 Importance of Remote Patient Monitoring 293 12.1.2 Significance of Big Data and AI in Healthcare 294 12.2 Related Work 294 12.3 Wearable Technologies in Healthcare 297 12.3.1 Types of Wearable Devices (Smartwatches, Fitness Trackers, Medical-Grade Wearables, etc.) 297 12.3.2 Applications in Monitoring Vital Signs (Heart Rate, Blood Pressure, Temperature, etc.) 298 12.3.3 Wearables for Tracking Physical Activity and Sleep Patterns 299 12.4 Remote Patient Monitoring 299 12.4.1 Definition and Benefits of Remote Patient Monitoring 300 12.5 Use Cases: Chronic Disease Management, Post
Operative Care, Elderly Care, Etc. 301 12.6 Challenges of Traditional In-Person Care vs. Remote Monitoring 302 12.7 Data Collection and Transmission 303 12.7.1 Sensors and Data Collection Methods in Wearables 303 12.8 Wireless Data Transmission Technologies (Bluetooth, Wi-Fi, Cellular, Etc.) 304 12.8.1 Ensuring Data Security and Privacy 304 12.8.2 Big-Data Analytics in Healthcare 304 12.8.3 Role of Big Data in Healthcare Decision-Making 305 12.8.4 Handling and Processing Large Volumes of Wearable
Generated Data 305 12.8.5 Data Storage, Integration, and Interoperability 305 12.8.6 AI and Machine Learning in Health Monitoring 306 12.9 Introduction to AI and ML Applications in Healthcare 306 12.9.1 Predictive Analytics for Early Disease Detection 307 12.9.2 Real-Time Anomaly Detection and Alerts 307 12.9.3 Clinical Decision Support Systems 307 12.9.4 Integration of AI Insights into Clinical Workflows 308 12.9.5 Enabling Personalized Treatment Plans Based on Wearable Data 308 12.9.6 Enhancing Healthcare Professional Decision-Making 308 12.9.7 Challenges and Ethical Considerations in Using Patient
Generated Data 309 12.10 Future Directions and Trends 309 12.11 Conclusion 310 References 311 13 Disease Biomarker Discovery with Big Data Analysis 313 G. Venu Gopal, Kanakaprabha S., Gangavarapu Moahana Rao, Yallapragada Ravi Raju and G. Ganesh Kumar 13.1 Introduction 314 13.1.1 The Need for Multi-Omics Data Integration in Biomarker Discovery 314 13.1.2 Role of Machine Learning in Multi-Omics Data Analysis 314 13.2 Literature Survey 316 13.3 Challenges in Multi-Omics Data Integration 319 13.3.1 Data Heterogeneity and Integration Challenges 319 13.3.2 Dimensionality Reduction and Feature Selection 319 13.3.3 Feature Representation and Integration Techniques 319 13.3.4 Early Fusion vs. Late Fusion Approaches 320 13.3.5 Network-Based Integration Methods 320 13.4 Deep Learning Architectures for Multi-Omics Data 320 13.4.1 Disease Subtyping and Stratification 321 13.4.2 Identification of Key Regulatory Pathways 322 13.4.3 Predictive Modeling for Treatment Response 322 13.4.4 Cancer Biomarker Discovery Using Multi-Omics Data 322 13.4.5 Neurological Disorder Classification through Integration 322 13.5 Evaluation Metrics and Validation Strategies 323 13.5.1 Cross-Validation Techniques for Multi-Omics Data 324 13.5.2 Assessing Robustness and Generalizability of Biomarker Models 325 13.6 Ethical Considerations in Biomarker Discovery 325 13.6.1 Privacy and Security of Patient Data 325 13.6.2 Bias and Fairness in Machine Learning Models 326 13.6.3 Integration of Single-Cell Omics Data 326 13.6.4 Explainable AI for Biomarker Discovery 327 13.6.5 Personalized Medicine and Biomarker-Based Therapies 327 13.7 Conclusion 328 References 329 14 Real-Time Epilepsy Monitoring and Alerting System Using IoT Devices and Machine Learning Techniques in Blockchain-Based Environment 331 Mohsen Ghorbian and Saeid Ghorbian 14.1 Introduction 332 14.2 Preliminaries 334 14.2.1 Overview of IoT Technology 334 14.2.2 Blockchain Technology 335 14.2.3 Overview of ML Technology 336 14.2.4 Epilepsy Disease 337 14.3 IoT and ML in Healthcare 338 14.3.1 HLF Architectural Framework 338 14.3.2 Epilepsy Detection Procedures 341 14.3.3 Various Approaches to ml 342 14.4 Incorporating ML with IoT in the Blockchain 343 14.5 Intelligent Alert Mechanism in IoT Healthcare 345 14.5.1 Data Gathering, Transmission, and Storage 347 14.5.2 Analyzing Stored Data 348 14.5.3 Sending an Alert Message 349 14.6 Conclusion 351 References 352 15 Integrating Quantum Computing in Bioinformatics and Biomedical Research 357 Prasad Selladurai, Ruby Dahiya, Baskar Kandasamy and Venkateswaran Radhakrishnan 15.1 Introduction 358 15.1.1 Quantum Computing 360 15.1.2 The Role of Quantum Computing in Bioinformatics 361 15.1.3 Application of Quantum Technologies 363 15.1.4 Characteristics of Quantum Computing in Bioinformatics 364 15.1.5 What are the Tools Used in Quantum Computing in Bioinformatics? 366 15.2 Novel Approaches of Quantum Computing in Bioinformatics 367 15.2.1 Quantum Chemistry for Drug Discovery 367 15.2.2 A Quantum Advance in Genetics 369 15.2.3 Hybrid Quantum-Classical Approaches 370 15.2.4 Quantum-Inspired Machine Learning 372 15.2.5 Challenges and Limitations 374 15.3 Conclusion 375 15.4 The Future of Quantum Computing in Bioinformatics and Biomedical Research 376 References 378 16 Future Perspective and Emerging Trends in Computational Intelligence 381 Chander Prabha 16.1 Introduction 382 16.2 Emerging Trends in CI for Bioinformatics 384 16.3 ci Emerging Trends for Biomedical Systems 386 16.4 ci Future Perspective in Bioinformatics 388 16.5 The Future of CI in Biomedical Systems 391 16.6 Conclusion and Future Scope 393 References 394 Index 397