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Full Description
Machine learning fundamentally learns from the past experiences (seen data) to make predictions about future (unseen data). Predictions in nature are often uncertain. Microbiome data have unique characteristics, including high-dimensionality, over-dispersion, sparsity and zero-inflation, and heterogeneity. Thus, machine learning microbiome data for predicting the outcome of phenotypes is even more uncertain than learning those data from other fields. Machine learning microbiome statistics poses many challenges for evaluating the prediction performance using appropriate metrics and independent data validation.
This unique book aims to address the challenges of machine learning statistics, emphasize the importance of performance valuation by appropriate metrics and independent data, and describe several important concepts of machine learning statistics, such as feature engineering and overfitting. It comprehensively reviews commonly used and newly developed machine learning models for microbiome research. Specifically, this book provides the step-by-step procedures to perform machine learning microbiome data, including feature engineering, algorithm selection and optimization, performance evaluation and model testing. It comments the benefits and limitations of using machine learning for microbiome statistics and clearly remarks on the advantages and disadvantages of each machine learning algorithm.
Presents a thorough overview of machine learning algorithms for microbiome statistics.
Performs step-by-step procedures to perform machine learning microbiome data, using important supervised learning algorithms, including classical, ensemble learning and tree-based models.
Describes important concepts of machine learning, including bias and variance tradeoff, accuracy and precision, overfitting and underfitting, model complexity and interpretability, and feature engineering,
Investigates and applies various cross-validation techniques step-by-step.
Introduces confusion matrix and its derived measures. Comprehensively describes the properties of F1, Matthews' correlation coefficient (MCC), area under the receiver operating characteristic curve (AUC-ROC), and area under the precision-recall curve (AUC-PR), as well as discusses their advantages and disadvantages when using for microbiome data.
Offers all related R codes and the datasets from the authors' first-hand microbiome research and publicly available data.
Contents
Preface Acknowledgements About the Authors Chapter 1 Introduction to Machine Learning Chapter 2 Overview of Machine Learning in Microbiome Research Chapter 3 Accessing Model Accuracy and Goodness of Fit Tests for Normality Chapter 4 Overfitting and Underfitting Chapter 5 Assessing Model Accuracy Using Cross-Validation Chapter 6 Feature Engineering and Model Selection Chapter 7 Logistic Regression Chapter 8 Support Vector Machines Chapter 9 Classification Trees Chapter 10 Random Forest Chapter 11 The Evolution of Tree-Based Algorithms Chapter 12 Extreme Gradient Boosting (XGBoost) Chapter 13 Artificial Neural Networks and Deep Learning Chapter 14 Machine Learning Microbiome with SIAMCAT Chapter 15 Basic Performance Metrics for Machine Learning Models Chapter 16 Matthews Correlation Coefficient Chapter 17 Area Under the Receiver Operating Characteristic Curve (AUC-ROC) Chapter 18 Area Under the Precision-Recall Curve (AUC-PR) Chapter 19 Comparisons of Machine Learning Classification Models with Tidymodels
