R: Unleash Machine Learning Techniques

Table of Contents

R: Unleash Machine Learning Techniques

R: Unleash Machine Learning Techniques

Credits

Preface

What this learning path covers

What you need for this learning path

Who this learning path is for

Reader feedback

Customer support

Downloading the example code

Errata

Piracy

Questions

I. Module 1

1. Getting Started with R and Machine Learning

Delving into the basics of R

Using R as a scientific calculator

Operating on vectors

Special values

Data structures in R

Vectors

Creating vectors

Indexing and naming vectors

Arrays and matrices

Creating arrays and matrices

Names and dimensions

Matrix operations

Lists

Creating and indexing lists

Combining and converting lists

Data frames

Creating data frames

Operating on data frames

Working with functions

Built-in functions

User-defined functions

Passing functions as arguments

Controlling code flow

Working with if, if-else, and ifelse

Working with switch

Loops

Advanced constructs

lapply and sapply

apply

tapply

mapply

Next steps with R

Getting help

Handling packages

Machine learning basics

Machine learning – what does it really mean?

Machine learning – how is it used in the world?

Types of machine learning algorithms

Supervised machine learning algorithms

Unsupervised machine learning algorithms

Popular machine learning packages in R

Summary

2. Let's Help Machines Learn

Understanding machine learning

Algorithms in machine learning

Perceptron

Families of algorithms

Supervised learning algorithms

Linear regression

K-Nearest Neighbors (KNN)

Collecting and exploring data

Normalizing data

Creating training and test data sets

Learning from data/training the model

Evaluating the model

Unsupervised learning algorithms

Apriori algorithm

K-Means

Summary

3. Predicting Customer Shopping Trends with Market Basket Analysis

Detecting and predicting trends

Market basket analysis

What does market basket analysis actually mean?

Core concepts and definitions

Techniques used for analysis

Making data driven decisions

Evaluating a product contingency matrix

Getting the data

Analyzing and visualizing the data

Global recommendations

Advanced contingency matrices

Frequent itemset generation

Getting started

Data retrieval and transformation

Building an itemset association matrix

Creating a frequent itemsets generation workflow

Detecting shopping trends

Association rule mining

Loading dependencies and data

Exploratory analysis

Detecting and predicting shopping trends

Visualizing association rules

Summary

4. Building a Product Recommendation System

Understanding recommendation systems

Issues with recommendation systems

Collaborative filters

Core concepts and definitions

The collaborative filtering algorithm

Predictions

Recommendations

Similarity

Building a recommender engine

Matrix factorization

Implementation

Result interpretation

Production ready recommender engines

Extract, transform, and analyze

Model preparation and prediction

Model evaluation

Summary

5. Credit Risk Detection and Prediction – Descriptive Analytics

Types of analytics

Our next challenge

What is credit risk?

Getting the data

Data preprocessing

Dealing with missing values

Datatype conversions

Data analysis and transformation

Building analysis utilities

Analyzing the dataset

Saving the transformed dataset

Next steps

Feature sets

Machine learning algorithms

Summary

6. Credit Risk Detection and Prediction – Predictive Analytics

Predictive analytics

How to predict credit risk

Important concepts in predictive modeling

Preparing the data

Building predictive models

Evaluating predictive models

Getting the data

Data preprocessing

Feature selection

Modeling using logistic regression

Modeling using support vector machines

Modeling using decision trees

Modeling using random forests

Modeling using neural networks

Model comparison and selection

Summary

7. Social Media Analysis – Analyzing Twitter Data

Social networks (Twitter)

Data mining @social networks

Mining social network data

Data and visualization

Word clouds

Treemaps

Pixel-oriented maps

Other visualizations

Getting started with Twitter APIs

Overview

Registering the application

Connect/authenticate

Extracting sample tweets

Twitter data mining

Frequent words and associations

Popular devices

Hierarchical clustering

Topic modeling

Challenges with social network data mining

References

Summary

8. Sentiment Analysis of Twitter Data

Understanding Sentiment Analysis

Key concepts of sentiment analysis

Subjectivity

Sentiment polarity

Opinion summarization

Feature extraction

Approaches

Applications

Challenges

Sentiment analysis upon Tweets

Polarity analysis

Classification-based algorithms

Labeled dataset

Support Vector Machines

Ensemble methods

Boosting

Cross-validation

Summary

II. Module 2

1. Introducing Machine Learning

The origins of machine learning

Uses and abuses of machine learning

Machine learning successes

The limits of machine learning

Machine learning ethics

How machines learn

Data storage

Abstraction

Generalization

Evaluation

Machine learning in practice

Types of input data

Types of machine learning algorithms

Matching input data to algorithms

Machine learning with R

Installing R packages

Loading and unloading R packages

Summary

2. Managing and Understanding Data

R data structures

Vectors

Factors

Lists

Data frames

Matrixes and arrays

Managing data with R

Saving, loading, and removing R data structures

Importing and saving data from CSV files

Exploring and understanding data

Exploring the structure of data

Exploring numeric variables

Measuring the central tendency – mean and median

Measuring spread – quartiles and the five-number summary

Visualizing numeric variables – boxplots

Visualizing numeric variables – histograms

Understanding numeric data – uniform and normal distributions

Measuring spread – variance and standard deviation

Exploring categorical variables

Measuring the central tendency – the mode

Exploring relationships between variables

Visualizing relationships – scatterplots

Examining relationships – two-way cross-tabulations

Summary

3. Lazy Learning – Classification Using Nearest Neighbors

Understanding nearest neighbor classification

The k-NN algorithm

Measuring similarity with distance

Choosing an appropriate k

Preparing data for use with k-NN

Why is the k-NN algorithm lazy?

Example – diagnosing breast cancer with the k-NN algorithm

Step 1 – collecting data

Step 2 – exploring and preparing the data

Transformation – normalizing numeric data

Data preparation – creating training and test datasets

Step 3 – training a model on the data

Step 4 – evaluating model performance

Step 5 – improving model performance

Transformation – z-score standardization

Testing alternative values of k

Summary

4. Probabilistic Learning – Classification Using Naive Bayes

Understanding Naive Bayes

Basic concepts of Bayesian methods

Understanding probability

Understanding joint probability

Computing conditional probability with Bayes' theorem

The Naive Bayes algorithm

Classification with Naive Bayes

The Laplace estimator

Using numeric features with Naive Bayes

Example – filtering mobile phone spam with the Naive Bayes algorithm

Step 1 – collecting data

Step 2 – exploring and preparing the data

Data preparation – cleaning and standardizing text data

Data preparation – splitting text documents into words

Data preparation – creating training and test datasets

Visualizing text data – word clouds

Data preparation – creating indicator features for frequent words

Step 3 – training a model on the data

Step 4 – evaluating model performance

Step 5 – improving model performance

Summary

5. Divide and Conquer – Classification Using Decision Trees and Rules

Understanding decision trees

Divide and conquer

The C5.0 decision tree algorithm

Choosing the best split

Pruning the decision tree

Example – identifying risky bank loans using C5.0 decision trees

Step 1 – collecting data

Step 2 – exploring and preparing the data

Data preparation – creating random training and test datasets

Step 3 – training a model on the data

Step 4 – evaluating model performance

Step 5 – improving model performance

Boosting the accuracy of decision trees

Making mistakes more costlier than others

Understanding classification rules

Separate and conquer

The 1R algorithm

The RIPPER algorithm

Rules from decision trees

What makes trees and rules greedy?

Example – identifying poisonous mushrooms with rule learners

Step 1 – collecting data

Step 2 – exploring and preparing the data

Step 3 – training a model on the data

Step 4 – evaluating model performance

Step 5 – improving model performance

Summary

6. Forecasting Numeric Data – Regression Methods

Understanding regression

Simple linear regression

Ordinary least squares estimation

Correlations

Multiple linear regression

Example – predicting medical expenses using linear regression

Step 1 – collecting data

Step 2 – exploring and preparing the data

Exploring relationships among features – the correlation matrix

Visualizing relationships among features – the scatterplot matrix

Step 3 – training a model on the data

Step 4 – evaluating model performance

Step 5 – improving model performance

Model specification – adding non-linear relationships

Transformation – converting a numeric variable to a binary indicator

Model specification – adding interaction effects

Putting it all together – an improved regression model

Understanding regression trees and model trees

Adding regression to trees

Example – estimating the quality of wines with regression trees and model trees

Step 1 – collecting data

Step 2 – exploring and preparing the data

Step 3 – training a model on the data

Visualizing decision trees

Step 4 – evaluating model performance

Measuring performance with the mean absolute error

Step 5 – improving model performance

Summary

7. Black Box Methods – Neural Networks and Support Vector Machines

Understanding neural networks

From biological to artificial neurons

Activation functions

Network topology

The number of layers

The direction of information travel

The number of nodes in each layer

Training neural networks with backpropagation

Example – Modeling the strength of concrete with ANNs

Step 1 – collecting data

Step 2 – exploring and preparing the data

Step 3 – training a model on the data

Step 4 – evaluating model performance

Step 5 – improving model performance

Understanding Support Vector Machines

Classification with hyperplanes

The case of linearly separable data

The case of nonlinearly separable data

Using kernels for non-linear spaces

Example – performing OCR with SVMs

Step 1 – collecting data

Step 2 – exploring and preparing the data

Step 3 – training a model on the data

Step 4 – evaluating model performance

Step 5 – improving model performance

Summary

8. Finding Patterns – Market Basket Analysis Using Association Rules

Understanding association rules

The Apriori algorithm for association rule learning

Measuring rule interest – support and confidence

Building a set of rules with the Apriori principle

Example – identifying frequently purchased groceries with association rules

Step 1 – collecting data

Step 2 – exploring and preparing the data

Data preparation – creating a sparse matrix for transaction data

Visualizing item support – item frequency plots

Visualizing the transaction data – plotting the sparse matrix

Step 3 – training a model on the data

Step 4 – evaluating model performance

Step 5 – improving model performance

Sorting the set of association rules

Taking subsets of association rules

Saving association rules to a file or data frame

Summary

9. Finding Groups of Data – Clustering with k-means

Understanding clustering

Clustering as a machine learning task

The k-means clustering algorithm

Using distance to assign and update clusters

Choosing the appropriate number of clusters

Example – finding teen market segments using k-means clustering

Step 1 – collecting data

Step 2 – exploring and preparing the data

Data preparation – dummy coding missing values

Data preparation – imputing the missing values

Step 3 – training a model on the data

Step 4 – evaluating model performance

Step 5 – improving model performance

Summary

10. Evaluating Model Performance

Measuring performance for classification

Working with classification prediction data in R

A closer look at confusion matrices

Using confusion matrices to measure performance

Beyond accuracy – other measures of performance

The kappa statistic

Sensitivity and specificity

Precision and recall

The F-measure

Visualizing performance trade-offs

ROC curves

Estimating future performance

The holdout method

Cross-validation

Bootstrap sampling

Summary

11. Improving Model Performance

Tuning stock models for better performance

Using caret for automated parameter tuning

Creating a simple tuned model

Customizing the tuning process

Improving model performance with meta-learning

Understanding ensembles

Bagging

Boosting

Random forests

Training random forests

Evaluating random forest performance

Summary

12. Specialized Machine Learning Topics

Working with proprietary files and databases

Reading from and writing to Microsoft Excel, SAS, SPSS, and Stata files

Querying data in SQL databases

Working with online data and services

Downloading the complete text of web pages

Scraping data from web pages

Parsing XML documents

Parsing JSON from web APIs

Working with domain-specific data

Analyzing bioinformatics data

Analyzing and visualizing network data

Improving the performance of R

Managing very large datasets

Generalizing tabular data structures with dplyr

Making data frames faster with data.table

Creating disk-based data frames with ff

Using massive matrices with bigmemory

Learning faster with parallel computing

Measuring execution time

Working in parallel with multicore and snow

Taking advantage of parallel with foreach and doParallel

Parallel cloud computing with MapReduce and Hadoop

GPU computing

Deploying optimized learning algorithms

Building bigger regression models with biglm

Growing bigger and faster random forests with bigrf

Training and evaluating models in parallel with caret

Summary

III. Module 3

1. A Process for Success

The process

Business understanding

Identify the business objective

Assess the situation

Determine the analytical goals

Produce a project plan

Data understanding

Data preparation

Modeling

Evaluation

Deployment

Algorithm flowchart

Summary

2. Linear Regression – The Blocking and Tackling of Machine Learning

Univariate linear regression

Business understanding

Multivariate linear regression

Business understanding

Data understanding and preparation

Modeling and evaluation

Other linear model considerations

Qualitative feature

Interaction term

Summary

3. Logistic Regression and Discriminant Analysis

Classification methods and linear regression

Logistic regression

Business understanding

Data understanding and preparation

Modeling and evaluation

The logistic regression model

Logistic regression with cross-validation

Discriminant analysis overview

Discriminant analysis application

Model selection

Summary

4. Advanced Feature Selection in Linear Models

Regularization in a nutshell

Ridge regression

LASSO

Elastic net

Business case

Business understanding

Data understanding and preparation