Genomics at the Nexus of AI, Computer Vision, and Machine Learning

Shilpa Choudhary, PhD, is a postdoctoral fellow at the Singapore Institute of Technology, Singapore. She has authored more than 50 research papers in various national and international journals as well as authored/edited four books. She has been awarded nine patents and was awarded the ‘Gold Medal’ in 2012. Sandeep Kumar, PhD, is a professor in the Department of Computer Science and Engineering, K L Deemed to be University, Vijayawada, Andhra Pradesh, India. He has been granted six patents and has successfully filed another ten. He has published more than 100 research papers in various national and international journals and conferences. Swathi Gowroju, PhD, is an associate professor and deputy head of the Data Science Department, Sretas Institute of Engineering and Technology, Hyderabad, Telangana, India. She has published more than 30 research papers in the fields of image processing and machine learning. Monali Gulhane, PhD, is an assistant professor at the Symbiosis Institute of Technology, Nagpur Campus, Symbiosis International (Deemed University), Pune, India. She received the ‘Young Researcher Award’ in 2022. R. Sri Lakshmi, PhD, is a postdoctoral fellow at the Singapore Institute of Technology, Singapore. She is proficient in machine learning, artificial intelligence, computer design, etc. Most of her research has been published in renowned journals, patents, and book chapters.

Preface xvii 1 Integrating Genomics and Computer Vision: Unravelling Genetic Patterns and Analyzing Genomic Data 1
Neha Tanwar, Sandeep Kumar, Garima Singh and Monika Bhakta

2 Syndrome Detection Unleashed: Computer Vision Applications in Neurogenetic Diagnoses 25
R. Srilakshmi, Shilpa Choudhary, Rohit Raja and Ashish Kumar Luhach

3 Integrating Machine Learning for Personalized Kidney Stone Risk Assessment: A Prospective Validation Using CLDN11 Genetic Data and Clinical Factors 59
Shilpa Choudhary, Monali Gulhane, Sandeep Kumar, Nitin Rakesh, Sudhanshu Maurya and Chanderdeep Tandon

4 Unravelling the Complexities of Genetic Codes Through Advanced Machine Learning Algorithms for DNA Sequencing and Analysis 87
Swathi Gowroju, Mandeep Kumar, Sharvin Vats, Pramadvara Kushwaha and Rohit Raja

5 Deciphering the Complexities of Breast Cancer: Unveiling Resistance Mechanisms 109
Maddula Pallavi, Chirandas Tejaswi, R. Srilakshmi and Chetan Swarup

6 Deciphering the Genetic Terrain: Identifying Genetic Variants in Uncommon Disorders with Pathogenic Effects 133
Nikhila Kathirisetty, Ravula Arun Kumar, G. Suryanarayana, Farhana Begum, C. Padmini and Pravin Tirgar

7 Genome Data-Based Explainable Recommender Systems: A State-of-the-Art Survey 149
V. Lakshmi Chetana and Hari Seetha

8 Optimizing TCGA Data Analysis: Unveiling Crucial Cancer-Related Gene Alterations Through a Fusion Approach QL Gradient 169
Sushma Chowdary Polavarapu, Sri Hari Nallamala, Sudheer Mangalampalli, Brahma Naidu Nalluri, Lalitha Rajeswari Burra and Swarna Lalitha Chukka

9 Leveraging Deep Learning for Genomics Analysis: Advances and Applications 191
Nisarg Gandhewar, Amit Pimpalkar, Anuja Jadhav, Nilesh Shelke and Rashmi Jain

10 Unraveling Biological Complexity: Leveraging Deep Learning Models for Precise Classification and Understanding of Protein Types and Functions 227
Swathi Gowroju, M. Sudhakar, Mohit and Turki Aljrees

11 The Impact of Learning Techniques on Genomics: Revolutionizing Research and Clinical Breast Cancer Application 251
Sumaiya Shaikh, G. Suryanarayana, ShaistaFarhat and LNC Prakash K.

12 Comparison of Machine Learning and Deep Learning Algorithms for Diabetes Prediction Using DNA Sequences 269
Gagandeep Kaur, Poorva Agrawal, Latika Pinjarkar, Rutuja Patil, Suhashini Chaurasia and Seema Patil

13 AI Applications in Analyzing Gene Expression for Cancer Diagnosis: A Comprehensive Review 285
Poorva Agrawal, Gagandeep Kaur, Vansh Gupta, Kruthika Agarwal, Latika Pinjarkar and Seema Patil

14 Optimum Detection of Human Genome Related to Cancer Cells Using Signal Processing 309
Manoranjan Dash and Ritesh Raj

15 Genomics-Driven Strategies for Sustainable Crop Improvement in Agriculture 321
Munish Kumar, Monika Kajal, Mandeep Kumar, Ramesh Kumar and Pramadvara Kushwaha

16 An Efficient Deep Convolutional Neural Networks Model for Genomic Sequence Classification 345
Amit Pimpalkar, Nisarg Gandhewar, Nilesh Shelke, Sachin Patil and Sharda Chhabria

17 Navigating the Genetic Tapestry Using Genetic Analysis on the SLC26A1 Gene Variants in the Detection and Understanding of Kidney Stones for Improved Global Healthcare Management 377
Sandeep Kumar, Monali Gulhane, Nitin Rakesh, Sudhanshu Maurya, Rajni Mohana and Chanderdeep Tandon

18 A Comprehensive Approach for Enhancing Kidney Disease Detection Using Random Forest and Gradient Boosting 395
Mandeep Kumar, Neerav Khare, Soumya Mani, Monika Bhaktaand Gaurab Saha

19 Decoding the Future: COVID-19 RNA Sequence Prediction Through LSTM Transformation 417
M.D. Khaja Shaik, K. Narsimhulu, B.V.N. Praveena,Sarita Dabur and G. Pratyusha

20 Genomics and Machine Learning: ML Approaches, Future Directions and Challenges in Genomics 437
Sunita Gupta, Neha Janu, Meenakshi Nawal and Anjali Goswami

21 Predicting Gene Ontology Annotations from CAFA Using Distance Machine Learning and Transfer Metric Learning 459
Shilpa Choudhary, MD Khaja Shaik, Sivaneasan Bala Krishnan and Sunita Gupta

22 PacMan-RL: A Game-Changing Approach to Drug Development Through Reinforcement Learning 483
Abhishek Goud Amkamgari, Harshita Sharma, Rashmi Verma and Bhawna Kaliraman

23 Genetic Variant Classification Through Decision Tree Analysis for Enhanced Genomic Understanding 505
Prachi Chaudhary and Rajni Mehra

Index 529