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Immunoinformatics of Cancers
Practical Machine Learning Approaches Using R
1st Edition - April 19, 2022
Authors: Nima Rezaei, Parnian Jabbari
Paperback ISBN:9780128224007
9 7 8 - 0 - 1 2 - 8 2 2 4 0 0 - 7
eBook ISBN:9780128224304
9 7 8 - 0 - 1 2 - 8 2 2 4 3 0 - 4
Immunoinformatics of Cancers: Practical Machine Learning Approaches Using R takes a bioinformatics approach to understanding and researching the immunological aspects of… Read more
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Immunoinformatics of Cancers: Practical Machine Learning Approaches Using R takes a bioinformatics approach to understanding and researching the immunological aspects of malignancies. It details biological and computational principles and the current applications of bioinformatic approaches in the study of human malignancies. Three sections cover the role of immunology in cancers and bioinformatics, including databases and tools, R programming and useful packages, and present the foundations of machine learning. The book then gives practical examples to illuminate the application of immunoinformatics to cancer, along with practical details on how computational and biological approaches can best be integrated.This book provides readers with practical computational knowledge and techniques, including programming, and machine learning, enabling them to understand and pursue the immunological aspects of malignancies.
Presents the knowledge researchers need to apply computational techniques to immunodeficiencies
Provides the most practical material for bioinformatics approaches to the immunology of cancers
Gives straightforward and efficient explanations of programming and machine learning approaches in R
Includes details of the most useful databases, tools, programming packages and algorithms for immunoinformatics
Illuminates clear explanations with practical examples of immunoinformatic approaches to cancer
Researchers and graduate students in biological sciences; researchers and graduate students in computational and analytical sciences
Cover image
Title page
Table of Contents
Copyright
Dedication
Preface
Section I: Biological aspects
Chapter 1. Introduction to cancer immunology
Abstract
An introduction to the immune system
Humoral immunity
Cell-mediated immunity
Antigen–major histocompatibility complex binding
Self-tolerance
Immunology of cancers
Immunotherapy of cancers
References
Chapter 2. Introduction to bioinformatics
Abstract
What is bioinformatics?
Immunoinformatics
High-throughput technologies
References
Chapter 3. Practical databases and online tools in immunoinformatics
Abstract
Introduction
ImMunoGeneTics information system
Immune epitope database
Cancer antigenic peptide database
NEPdb: a database of T-cell experimentally-validated neoantigens and pan-cancer predicted neoepitopes for cancer immunotherapy
How do machine learning algorithms treat big data?
Supervised learning
Principles of training the model
Feature selection
Principal component analysis
Accuracy
Performance metrics of regression models
Generalizability of models
References
Chapter 6. Naïve Bayes’ classifiers in R
Abstract
An introduction to Bayes’ theorem
Hands-on Naïve Bayes’ in R
References
Chapter 7. Linear and logistic regressions in R
Abstract
What is regression?
Linear regression
Expected value
Multiple regression
Hands-on linear regression with R
Residual standard error
R-squared
F-statistics
Logistic regression
Binomial logistic regression
Hands-on logistic regression with R
Multinomial logistic regression
Hands-on multinomial logistic regression in R
References
Chapter 8. Linear and quadratic discriminant analysis in R
Abstract
Discriminant-based classifiers
Linear discriminant analysis
Hands-on linear discriminant analysis in R
Hands-on quadratic discriminant analysis in R
References
Chapter 9. Support vector machines in R
Abstract
What is support vector machine?
Mathematics behind support vector machine
Hands-on support vector machine in R
Support vector regression
References
Chapter 10. Decision trees in R
Abstract
Introduction to decision trees
Hands-on decision trees in R
Decision trees for regression
References
Chapter 11. Random forests in R
Abstract
What is a random forest?
Hands-on random forest in R
References
Chapter 12. K-nearest neighbors in R
Abstract
What is K-nearest neighbors?
Hands-on K-nearest neighbors in R
References
Chapter 13. Neural networks in R
Abstract
What are neural networks?
Hands-on neural networks in R
Neural networks for regression problems
Unsupervised neural networks
References
Chapter 14. Practice examples
Abstract
Practice examples for machine learning algorithms
Classification models
Naïve Bayes’ classification
Logistic regression
Linear and quadratic discriminant analysis
Support vector machine
Decision trees
Random forest
K-nearest neighbors
Neural networks
Regression models
Linear regression
Support vector regression
Decision trees for regression
Random forest for regression
K-nearest neighbors for regression
Neural networks for regression
References
Index
No. of pages: 282
Language: English
Published: April 19, 2022
Imprint: Academic Press
Paperback ISBN: 9780128224007
eBook ISBN: 9780128224304
NR
Nima Rezaei
Professor Nima Rezaei gained his medical degree (MD) from Tehran University of Medical Sciences and subsequently obtained an MSc in Molecular and Genetic Medicine and a PhD in Clinical Immunology and Human Genetics from the University of Sheffield, UK. He also spent a short-term fellowship of Pediatric Clinical Immunology and Bone Marrow Transplantation in the Newcastle General Hospital. Professor Rezaei is now the Full Professor of Immunology and Vice Dean of Research, School of Medicine, Tehran University of Medical Sciences, and the co-founder and Head of the Research Center for Immunodeficiencies. He is also the founding President of the Universal Scientific Education and Research Network (USERN). Professor Rezaei has already been the Director of more than 55 research projects and has designed and participated in several international collaborative projects. Professor Rezaei is an editorial assistant or board member for more than 30 international journals. He has edited more than 35 international books, has presented more than 500 lectures/posters in congresses/meetings, and has published more than 1,000 scientific papers in the international journals.
Affiliations and expertise
Professor, Department of Immunology, School of Medicine;
Head, Research Center for Immunodeficiencies, Children’s Medical Center,
Tehran University of Medical Sciences; Founding President,
Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA),
Universal Scientific Education and Research Network (USERN),
Tehran, Iran
PJ
Parnian Jabbari
Parnian Jabbari is a Medical Doctor at Tehran University of Medical Sciences, and a member of the Network of Immunity in Infection, Malignancy & Autoimmunity (NIIMA). She also works with the Universal Scientific Education & Research Network (USERN), based in Tehran, Iran.
Affiliations and expertise
Medical Doctor, Tehran University of Medical Sciences, Tehran, Iran