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Rabinarayan Satpathy graduated from the National Institute of Technology - Rourkela. He has received 2 PhDs, one in Computational Mathematics from Utkal University and other in Computer Science Engineering from Fakir Mohan University, as well as a DSc in Computational Fluid Dynamics.
Tanupriya Choudhury earned his PhD in 2016. He has filed 14 patents and received 16 copyrights from MHRD for his own software. He has authored more than 85 research papers. He is also Technical Adviser of Deetya Soft Pvt. Ltd. Noida, IVRGURU Mydigital360, etc.
Suneeta Satpathy, received her PhD from Utkal University, Bhubaneswar, Odisha, in 2015 with Directorate of Forensic Sciences, Her research interests include computer forensics, cyber security, data fusion, data mining, big data analysis, and decision mining. She has edited several books.
Sachi Nandan Mohanty, received his PhD from IIT Kharagpur in 2015. His research areas include data mining, big data analysis, cognitive science, fuzzy decision making, brain-computer interface, and computational intelligence. He has authored 3 books as well as edited four, of which several are with the Wiley-Scrivener imprint.
Xiaobo Zhang received his Master of Computer Science, Doctor of Engineering (Control Theory and Control Engineering) and works in the Department of Automation, Guangdong University of Technology, China. He has published more than 30 papers in academic journals as well as edited three books. He has applied for more than 40 invention patents and obtained 6 software copyrights.
Preface xix
Acknowledgement xxi
Part 1 The Commencement of Machine Learning Solicitation to Bioinformatics 1
1 Introduction to Supervised Learning 3Rajat Verma, Vishal Nagar and Satyasundara Mahapatra
1.1 Introduction 4
1.2 Learning Process & its Methodologies 5
1.3 Classification and its Types 10
1.4 Regression 12
1.5 Random Forest 18
1.6 K-Nearest Neighbor 20
1.7 Decision Trees 21
1.8 Support Vector Machines 22
1.9 Neural Networks 24
1.10 Comparison of Numerical Interpretation 26
1.11 Conclusion & Future Scope 27
References 28
2 Introduction to Unsupervised Learning in Bioinformatics 35Nancy Anurag Parasa, Jaya Vinay Namgiri, Sachi Nandan Mohanty and Jatindra Kumar Dash
2.1 Introduction 36
2.2 Clustering in Unsupervised Learning 37
2.3 Clustering in Bioinformatics-Genetic Data 38
2.4 Conclusion 46
References 47
3 A Critical Review on the Application of Artificial Neural Network in Bioinformatics 51Vrs Jhalia and Tripti Swarnkar
3.1 Introduction 52
3.2 Biological Datasets 57
3.3 Building Computational Model 58
3.4 Literature Review 64
3.5 Critical Analysis 72
3.6 Conclusion 73
References 73
Part 2 Machine Learning and Genomic Technology, Feature Selection and Dimensionality Reduction 77
4 Dimensionality Reduction Techniques: Principles, Benefits, and Limitations 79Hemanta Kumar Palo, Santanu Sahoo and Asit Kumar Subudhi
4.1 Introduction 80
4.2 The Benefits and Limitations of Dimension Reduction Methods 81
4.3 Components of Dimension Reduction 83
4.4 Methods of Dimensionality Reduction 86
4.5 Conclusion 104
References 105
5 Plant Disease Detection Using Machine Learning Tools With an Overview on Dimensionality Reduction 109Saurav Roy, Ratula Ray, Satya Ranjan Dash and Mrunmay Kumar Giri
5.1 Introduction 110
5.2 Flowchart 112
5.3 Machine Learning (ML) in Rapid Stress Phenotyping 113
5.4 Dimensionality Reduction 114
5.5 Literature Survey 116
5.6 Types of Plant Stress 128
5.7 Implementation I: Numerical Dataset 130
5.8 Implementation II: Image Dataset 134
5.9 Conclusion 140
References 141
6 Gene Selection Using Integrative Analysis of Multi-Level Omics Data: A Systematic Review 145S. Mahapatra and T. Swarnkar
6.1 Introduction 146
6.2 Approaches for Gene Selection 147
6.3 Multi-Level Omics Data Integration 152
6.4 Machine Learning Approaches for Multi-Level Data Integration 153
6.5 Critical Observation 165
6.6 Conclusion 166
References 166
7 Random Forest Algorithm in Imbalance Genomics Classification 173Sudhansu Shekhar Patra, Om Praksah Jena, Gaurav Kumar, Sreyashi Pramanik, Chinmaya Misra and Kamakhya Narain Singh
7.1 Introduction 173
7.2 Methodological Issues 175
7.3 Biological Terminologies 181
7.4 Proposed Model 183
7.5 Experimental Analysis 186
7.6 Current and Future Scope of ML in Genomics 188
7.7 Conclusion 189
References 189
8 Feature Selection and Random Forest Classification for Breast Cancer Disease 191Shubham Raj, Swati Singh, Avinash Kumar, Sobhangi Sarkar and Chittaranjan Pradhan
8.1 Introduction 192
8.2 Literature Survey 192
8.3 Machine Learning 196
8.4 Feature Engineering 202
8.5 Methodology 204
8.6 Result Analysis 209
8.7 Conclusion 210
References 210
9 A Comprehensive Study on the Application of Grey Wolf Optimization for Microarray Data 211Swati Sucharita, Barnali Sahu and Tripti Swarnkar
9.1 Introduction 212
9.2 Microarray Data 213
9.3 Grey Wolf Optimization (GWO) Algorithm 214
9.4 Studies on GWO Variants 220
9.5 Application of GWO in Medical Domain 232
9.6 Application of GWO in Microarray Data 232
9.7 Conclusion and Future Work 232
References 243
10 The Cluster Analysis and Feature Selection: Perspective of Machine Learning and Image Processing 249Aradhana Behura
10.1 Introduction 251
10.2 Various Image Segmentation Techniques 254
10.3 How to Deal With Image Dataset 256
10.4 Class Imbalance Problem 264
10.5 Optimization of Hyperparameter 267
10.6 Case Study 270
10.7 Using AI to Detect Coronavirus 273
10.8 Using Artificial Intelligence (AI), CT Scan and X-Ray 274
10.9 Conclusion 276
References 276
Part 3 Machine Learning and Healthcare Applications 281
11 Artificial Intelligence and Machine Learning for Healthcare Solutions 283Ashok Sharma, Parveen Singh and Gowhar Dar
11.1 Introduction 284
11.2 Using Machine Learning Approaches for Different Purposes 284
11.3 Various Resources of Medical Data Set for Research 286
11.4 Deep Learning in Healthcare 287
11.5 Various Projects in Medical Imaging and Diagnostics 288
11.6 Conclusion 289
References 290
12 Forecasting of Novel Corona Virus Disease (Covid-19) Using LSTM and XG Boosting Algorithms 293V. Aakash, S. Sridevi, G. Ananthi and S. Rajaram
12.1 Introduction 294
12.2 Machine Learning Algorithms for Forecasting 296
12.3 Proposed Method 300
12.4 Implementation 304
12.5 Results and Discussion 307
12.6 Conclusion and Future Work 310
References 310
13 An Innovative Machine Learning Approach to Diagnose Cancer at Early Stage 313Poongodi, P., Udayakumar, E., Srihari, K. and Sachi Nandan Mohanty
13.1 Introduction 314
13.2 Related Work 317
13.3 Materials and Methods 320
13.4 System Design 322
13.5 Results and Discussion 331
13.6 Conclusion 335
References 335
14 A Study of Human Sleep Staging Behavior Based on Polysomnography Using Machine Learning Techniques 339Santosh Kumar Satapathy and D. Loganathan
14.1 Introduction 340
14.2 Polysomnography Signal Analysis 341
14.3 Case Study on Automated Sleep Stage Scoring 349
14.4 Summary and Conclusion 356
References 357
15 Detection of Schizophrenia Using EEG Signals 359Shalini Mahato, Laxmi Kumari Pathak and Kajal Kumari
15.1 Introduction 360
15.2 Methodology 367
15.3 Literature Review 372
15.4 Discussion 372
15.5 Conclusion 388
References 388
16 Performance Analysis of Signal Processing Techniques in Bioinformatics for Medical Applications Using Machine Learning Concepts 391G. Aparna, G. Anitha Mary and G. Sumana
16.1 Introduction 392
16.2 Basic Definition of Anatomy and Cell at Micro Level 397
16.3 Signal Processing-Genome Signal Processing 403
16.4 Hotspots Identification Algorithm 414
16.5 Results-Experimental Investigations 416
16.6 Analysis Using Machine Learning Metrics 418
16.7 Conclusion 424
Appendix 424
A.1 Hotspot Identification Code 424
A.2 Performance Metrics Code 425
References 427
17 Survey of Various Statistical Numerical and Machine Learning Ontological Models on Infectious Disease Ontology 431Yuvaraj Natarajan, Srihari Kannan and Sachi Nandan Mohanty
17.1 Introduction 432
17.2 Disease Ontology 432
17.3 Infectious Disease Ontology 433
17.4 Biomedical Ontologies on IDO 434
17.5 Various Methods on IDO 435
17.6 Machine Learning-Based Ontology for IDO 436
17.7 Recommendation or Suggestions for Future Study 437
17.8 Conclusions 438
References 438
18 An Efficient Model for Predicting Liver Disease Using Machine Learning 443Ritesh Choudhary, T. Gopalakrishnan, D. Ruby, A. Gayathri, Vishnu Srinivasa Murthy and Rishabh Shekhar
18.1 Introduction 444
18.2 Related Works 445
18.3 Proposed Model 446
18.4 Results and Analysis 454
18.5 Conclusion 456
References 456
Part 4 Bioinformatics and Market Analysis 459
19 A Novel Approach for Prediction of Stock Market Behavior Using Bioinformatics Techniques 461Prakash Kumar Sarangi, Birendra Kumar Nayak and Sachidananda Dehuri
19.1 Introduction 462
19.2 Literature Review 463
19.3 Proposed Work 466
19.4 Experimental Study 470
19.5 Conclusion and Future Work 482
References 484
20 Stock Market Price Behavior Prediction Using Markov Models: A Bioinformatics Approach 485Prakash Kumar Sarangi, Birendra Kumar Nayak and Sachidananda Dehuri
20.1 Introduction 486
20.2 Literature Survey 487
20.3 Proposed Work 488
20.4 Experimental Work 497
20.5 Conclusions and Future Work 504
References 505
Index 507
Rajat Verma, Vishal Nagar and Satyasundara Mahapatra*
PSIT, Kanpur, Uttar Pradesh, India
Abstract
Artificial Intelligence (AI) has enhanced its importance through machines in the field of present business scenario. AI delineates the intelligence illustrated by machines and performs in a contrasting manner to the natural intelligence signified by all living objects. Today, AI is popular due to its Machine Learning (ML) techniques. In the field of ML, the performance of a machine depend upon the learning performance of that machine. Hence, the improvement of the machine's performance is always proportional to its learning behavior. These Learning behaviors are obtained from the knowledge of living object's intelligence. An introductory aspect of AI through a detailed scenario of ML is presented in this chapter. In the journey of ML's success, data is the only requirement. ML is known because of its execution through its diverse learning approaches. These approaches are known as supervised, unsupervised, and reinforcement. These are performed only on data, as its quintessential element. In Supervised, attempts are done to find the relationship between the independent variables and the dependent variables. The Independent variables are the input attributes whereas the dependent variables are the target attributes. Unsupervised works are contrary to the supervised approach. The former (i.e. unsupervised) deals with the formation of groups or clusters, whereas the latter (i.e. supervised) deals with the relationship between the input and the target attributes. The third aspect (i.e. reinforcement) works through feedback or reward. This Chapter focuses on the importance of ML and its learning techniques in day to day lives with the help of a case study (heart disease) dataset. The numerical interpretation of the learning techniques is explained with the help of graph representation and tabular data representation for easy understanding.
Keywords: Artificial intelligence, machine learning, supervised, unsupervised, reinforcement, knowledge, intelligence
In today's world, businesses are moving towards the implementation of automatic intelligence for decision making. This is only possible with the help of a well-known intelligence technique otherwise known as Artificial Intelligence (AI). This intelligence technique also plays a vital role in the field of research, which is nothing but taking decisions instantly. The dimension of AI is bifurcated into sub-domains such as Machine Learning (ML) and Artificial Neural Networks (ANN) [1]. The term ML is also termed as augmented analytics [2] and depicts the development of machine's performances. This is achieved through the previous experiences obtained by the machines, but the traditional learning (i.e. the intelligence used in the mid-1800s) works not so efficiently if compared with the ML [3]. In traditional learning, the user deals with data and programs as an input attribute and provides the output or results whereas, in the case of ML the user provides the data and output or desired results as an input attribute and produces the program or rules as an output attribute. This means that data is more important rather than the programs. This is so because the business world depends on the accuracy level of the program which is used for decision making. The block diagram of Traditional learning is shown below in Figure 1.1 for easy understanding.
Traditional Learning is a manual process whereas the functioning of ML is an automated one. Due to ML, the accuracy of analytic worthiness is increased in different diversified domains. These domains are utilized for the preparation of data (raw facts and figures), Outlier Detection (Automatic), Natural Language Interfaces (NLI), and Recommendations, etc. [4]. Due to these domains, the bias factor for taking decisions on a business problem is decreased.
Figure 1.1 Traditional learning.
Figure 1.2 Machine learning.
ML is a sub-group of AI and its primary work is allowing systems to learn automatically with the help of data or observations obtained from the environment through different devices [5]. The block-diagram of ML is shown below in Figure 1.2.
ML-based algorithms perform predictions as well as decisions by using mathematical models that are based on some training data [6-8]. Few popular implementations of Machine Learning are Filtering of E-mails [9], Medical Diagnosis [10], Classification [11], Extraction [12], etc. ML works for the growth of the accuracy level of the computer programs. This was done by accessing data from the surrounding, learn the data automatically, and enhancing the capacity of decision making. The main objective of ML is to minimize human intervention and assistance while performing any task. The next section of this chapter highlights the process of learning along with its different methodologies.
In AI, Learning means a process to train a machine in such a way so that the machine can take decisions instantly. Hence, the performance of that machine is upgraded because of its accuracy. When a machine performs in its working environment it may get either success or failure. From these successes or failures machines are gaining experience itself. These newly gained experience, improve the machines through their actions and forms an optimal policy for the working environment. This process is known as learning from experience. This process of learning is possible in an unknown working environment. A general block diagram learning architecture for such a method is presented below in Figure 1.3. This figure tries to present the mechanism of learning a new experience by a machine. The sequence of learning behavior in a stepwise manner is given below.
Step 1. The IoT based sensors received input from the environment.
Step 2. Then, the sensor sends these inputs to the critics for performance evaluation, according to the previously stored performance standards. Simultaneously, the sensor sends the same input to the performance element for checking its effectiveness, if found OK then immediately return the same to the environment through effectors.
Step 3. The Critics provide the feedback to the learning element, if any new feedback occurs then it should be updated in the performance of the element. Then, the updated knowledge comes back to the learning element and send it to the problem generator as a learning goal for evaluating the same through experiments. The updates are sent to the performance of the element for future reference.
Figure 1.3 Learning behavior of a machine.
The learning process of ML is done in three different ways. These are supervised learning, unsupervised learning, and reinforcement learning. These three learning types have their importance in the different fields of bioinformatics research. Hence, they are explained with suitable examples in the next sections.
This is a very common learning mechanism in ML and used by most of the newcomer researchers in their respective fields. This learning mechanism trains the machine by using a labeled dataset in the form of compressed input-output pair as depicted in Refs. [13-15]. These datasets are available in continuous or discrete form. But the important thing is, it needs supervision with an appropriate training model. As supervised learning predicts accurate results [16], hence it is mostly used for Regression analysis and classification purposes. Figure 1.4 shows the execution model of supervised learning.
The figure shows that in supervised learning, a given set of input attributes (i. e. A1, A2, A3, A4 . . Ak) along with their output attributes (i.e. B1, B2, B3, B4 . . . Bk) are kept in a knowledge dataset. The Learning Algorithm takes an input Ai and executes with its model and produces the result Bi as the desired output. Supervised Learning has its importance in the field of Bioinformatics as concerning the heart disease scenario where inputs can be a lot of symptoms of heart diseases such as High Cholesterol, Chest Pain, and Blood Pressure, etc. and the output could be a person suffering from heart disease or not. Now all these inputs are passed on to the learning algorithm where it gets trained and if a new input is passed through the model then the machine gives an expected output. If the expected output's accuracy is not up to the mark then there is a need for modification or up-gradation in the model.
Figure 1.4 Block diagram of supervised learning.
An example of supervised learning could be of a person who felt that he has a high cholesterol level and a chest pain and went to the doctor for a check-up. The Doctor fed the inputs given by the patient to the machine. The Machine predicted and told the doctor that the patient is suffering from a cardiac issue in his heart. It acts as an analogy to the supervised learning as the inputs given by the patient are the independent variables and their corresponding output from the machine acts as the dependent attribute. The Machine acted as a model that predicted and gave a relevant output as it is trained by similar inputs. Supervised Learning is itself a huge subfield of...
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