Java Data Science Cookbook

Table of Contents

Java Data Science Cookbook

Credits

About the Author

About the Reviewer

www.PacktPub.com

Why subscribe?

Customer Feedback

Preface

What this book covers

What you need for this book

Who this book is for

Sections

Getting ready

How to do it...

How it works...

There's more...

See also

Conventions

Reader feedback

Customer support

Downloading the example code

Downloading the color images of this book 

Errata

Piracy

Questions

1. Obtaining and Cleaning Data

Introduction

Retrieving all filenames from hierarchical directories using Java

Getting ready

How to do it...

Retrieving all filenames from hierarchical directories using Apache Commons IO

Getting ready

How to do it...

Reading contents from text files all at once using Java 8

How to do it...

Reading contents from text files all at once using Apache Commons IO

Getting ready

How to do it...

Extracting PDF text using Apache Tika

Getting ready

How to do it...

Cleaning ASCII text files using Regular Expressions

How to do it...

Parsing Comma Separated Value (CSV) Files using Univocity

Getting ready

How to do it...

Parsing Tab Separated Value (TSV) file using Univocity

Getting ready

How to do it...

Parsing XML files using JDOM

Getting ready

How to do it...

Writing JSON files using JSON.simple

Getting ready

How to do it...

Reading JSON files using JSON.simple

Getting ready

How to do it ...

Extracting web data from a URL using JSoup

Getting ready

How to do it...

Extracting web data from a website using Selenium Webdriver

Getting ready

How to do it...

Reading table data from a MySQL database

Getting ready

How to do it...

2. Indexing and Searching Data

Introduction

Indexing data with Apache Lucene

Getting ready

How to do it...

How it works...

Searching indexed data with Apache Lucene

Getting ready

How to do it...

3. Analyzing Data Statistically

Introduction

Generating descriptive statistics

How to do it...

Generating summary statistics

How to do it...

Generating summary statistics from multiple distributions

How to do it...

There's more...

Computing frequency distribution

How to do it...

Counting word frequency in a string

How to do it...

How it works...

Counting word frequency in a string using Java 8

How to do it...

Computing simple regression

How to do it...

Computing ordinary least squares regression

How to do it...

Computing generalized least squares regression

How to do it...

Calculating covariance of two sets of data points

How to do it...

Calculating Pearson's correlation of two sets of data points

How to do it...

Conducting a paired t-test

How to do it...

Conducting a Chi-square test

How to do it...

Conducting the one-way ANOVA test

How to do it...

Conducting a Kolmogorov-Smirnov test

How to do it...

4. Learning from Data - Part 1

Introduction

Creating and saving an Attribute-Relation File Format (ARFF) file

How to do it...

Cross-validating a machine learning model

How to do it...

Classifying unseen test data

Getting ready

How to do it...

Classifying unseen test data with a filtered classifier

How to do it...

Generating linear regression models

How to do it...

Generating logistic regression models

How to do it...

Clustering data points using the KMeans algorithm

How to do it...

Clustering data from classes

How to do it...

Learning association rules from data

Getting ready

How to do it...

Selecting features/attributes using the low-level method, the filtering method, and the meta-classifier method

Getting ready

How to do it...

5. Learning from Data - Part 2

Introduction

Applying machine learning on data using Java Machine Learning (Java-ML) library

Getting ready

How to do it...

Classifying data points using the Stanford classifier

Getting ready

How to do it...

How it works...

Classifying data points using Massive Online Analysis (MOA)

Getting ready

How to do it...

Classifying multilabeled data points using Mulan

Getting ready

How to do it...

6. Retrieving Information from Text Data

Introduction

Detecting tokens (words) using Java

Getting ready

How to do it...

Detecting sentences using Java

Getting ready

How to do it...

Detecting tokens (words) and sentences using OpenNLP

Getting ready

How to do it...

Retrieving lemma, part-of-speech, and recognizing named entities from tokens using Stanford CoreNLP

Getting ready

How to do it...

Measuring text similarity with Cosine Similarity measure using Java 8

Getting ready

How to do it...

Extracting topics from text documents using Mallet

Getting ready

How to do it...

Classifying text documents using Mallet

Getting ready

How to do it...

Classifying text documents using Weka

Getting ready

How to do it...

7. Handling Big Data

Introduction

Training an online logistic regression model using Apache Mahout

Getting ready

How to do it...

Applying an online logistic regression model using Apache Mahout

Getting ready

How to do it...

Solving simple text mining problems with Apache Spark

Getting ready

How to do it...

Clustering using KMeans algorithm with MLib

Getting ready

How to do it...

Creating a linear regression model with MLib

Getting ready

How to do it...

Classifying data points with Random Forest model using MLib

Getting ready

How to do it...

8. Learn Deeply from Data

Introduction

Creating a Word2vec neural net using Deep Learning for Java (DL4j)

How to do it...

How it works...

There's more

Creating a Deep Belief neural net using Deep Learning for Java (DL4j)

How to do it...

How it works...

Creating a deep autoencoder using Deep Learning for Java (DL4j)

How to do it...

How it works...

9. Visualizing Data

Introduction

Plotting a 2D sine graph

Getting ready

How to do it...

Plotting histograms

Getting ready

How to do it...

Plotting a bar chart

Getting ready

How to do it...

Plotting box plots or whisker diagrams

Getting ready

How to do it...

Plotting scatter plots

Getting ready

How to do it...

Plotting donut plots

Getting ready

How to do it...

Plotting area graphs

Getting ready

How to do it...

Java Data Science Cookbook

Java Data Science Cookbook

Copyright © 2017 Packt Publishing

All rights reserved. No part of this book may be reproduced, stored in a retrieval system, or transmitted in any form or by any means, without the prior written permission of the publisher, except in the case of brief quotations embedded in critical articles or reviews.

Every effort has been made in the preparation of this book to ensure the accuracy of the information presented. However, the information contained in this book is sold without warranty, either express or implied. Neither the author, nor Packt Publishing, and its dealers and distributors will be held liable for any damages caused or alleged to be caused directly or indirectly by this book.

Packt Publishing has endeavored to provide trademark information about all of the companies and products mentioned in this book by the appropriate use of capitals. However, Packt Publishing cannot guarantee the accuracy of this information.

First published: March 2017

Production reference: 1240317

Published by Packt Publishing Ltd.

Livery Place

35 Livery Street

Birmingham 

B3 2PB, UK.

ISBN 978-1-78712-253-6

www.packtpub.com

Credits

About the Author

Rushdi Shams has a PhD on application of machine learning in Natural Language Processing (NLP) problem areas from Western University, Canada. Before starting work as a machine learning and NLP specialist in industry, he was engaged in teaching undergrad and grad courses. He has been successfully maintaining his YouTube channel named Learn with Rushdi for learning computer technologies.

I would like to acknowledge the Almighty Allah for giving me the strength, support, and knowledge to finish the book.

I extend my thanks to my family members, friends, and colleagues for continuous support, encouragement, and constructive criticism.

I would also like to thank Ajith and Cheryl from Packt for their continuous and spontaneous collaboration with me. 

About the Reviewer

Prashant Verma started his IT career in 2011 as a Java developer at Ericsson, working in the telecom domain. After a couple of years of Java EE experience, he moved into the big data domain, and has worked on almost all the popular big data technologies such as Hadoop, Spark, Kafka, Flume, Mongo, Cassandra, and so on. He has also worked in Scala and Python. Currently, he works with QA Infotech as Lead Data Engineer, working on solving e-learning domain problems using data analytics and machine learning.

Prashant has also worked on Apache Spark for Java Developers, Packt as a Technical Reviewer.

I want to thank Packt Publishing for giving me the chance to review the book, as well as my employer and my family for their patience while I was busy working on this book.

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To my lovely wife, Mah-Zereen, and adorable daughter, Ruayda.

Preface

Data science is a popular field for specialization nowadays and covers the broad spectrum of artificial intelligence, such as data processing, information retrieval, machine learning, natural language processing, big data, deep neural networks, and data visualization. In this book, we will understand the techniques that are both modern and smart and presented as easy-to-follow recipes for over 70 problems.

Keeping in mind the high demand for quality data scientists, we have compiled recipes using core Java as well as well-known, classic, and state-of-the-art data science libraries written in Java. We start with the data collection and cleaning process. Then we see how the obtained data can be indexed and searched. Afterwards, we cover statistics both descriptive and inferential and their application to data. Then, we have two back-to-back chapters on the application of machine learning on data that can be foundation for building any smart system. Modern information retrieval and natural language processing techniques are also covered. Big data is an emerging field, and a few aspects of this popular field are also covered. We also cover the very basics of deep learning using deep neural networks. Finally, we learn how to represent data and information obtained from data using meaningful visuals or graphs.

The book is aimed at anyone who has an interest in data science and plans to apply data science using Java to understand underlying data better.

What this book covers

Chapter 1, Obtaining and Cleaning Data, covers different ways to read and write data as well as to clean it to get rid of noise. It also familiarizes the readers with different data file types, such as PDF, ASCII, CSV, TSV, XML, and JSON. The chapter also covers recipes for extracting web data.

Chapter 2, Indexing and Searching Data, covers how to index data for fast searching using Apache Lucene. The techniques described in this chapter can be seen as the basis for modern-day search techniques.

Chapter 3, Analyzing Data Statistically, covers the application of Apache Math API to collect and analyze statistics from data. The chapter also covers higher level concepts such as the statistical significance test, which is the standard tool for researchers when they compare their results with benchmarks.

Chapter 4, Learning from Data - Part 1, covers basic classification, clustering, and feature selection exercises using the Weka machine learning Workbench.

Chapter 5, Learning from Data - Part 2, is a follow-up chapter that covers data import and export, classification, and feature selection using another Java library named the Java Machine Learning (Java-ML) Library. The chapter also covers basic classification with the Stanford Classifier and Massive Online Access (MOA).

Chapter 6, Retrieving Information from Text Data, covers the application of data science to text data for information retrieval. It covers the application of core Java as well as popular libraries such as OpenNLP, Stanford CoreNLP, Mallet, and Weka for the application of machine learning to information extraction and retrieval tasks.

Chapter 7, Handling Big Data, covers the application of big data platforms for machine learning, such as Apache Mahout and Spark-MLib.

Chapter 8, Learn Deeply from Data, covers the very basics of deep learning using the Deep Learning for Java (DL4j) library. We cover the word2vec algorithm, belief networks, and auto-encoders.

Chapter 9, Visualizing Data, covers the GRAL package to generate an appealing and informative display based on data. Among the many functionalities of the package, fundamental and basic plots have been selected.

What you need for this book

We have used Java to solve real-world data science problems. Our focus was to deliver content that can be effective for anyone who wants to know how to solve problems with Java. A minimum knowledge of Java is required, such as classes, objects, methods, arguments and parameters, exceptions, and exporting Java Archive (JAR) files. The code is well supported with narrations, information, and tips to help the readers understand the context and purpose. The theories behind the problems solved in this book, on many occasions, are not thoroughly discussed, but references for interested readers are provided whenever necessary.

Who this book is for

The book is for anyone who wants to know how to solve real-world problems related to data science using Java. The book, as it is very comprehensive in terms of coverage, can also be very useful for practitioners already engaged with data science and looking for solving issues in their projects using Java.

Sections

In this book, you will find several headings that appear frequently (Getting ready, How to do it..., How it works..., There's more..., and See also).

To give clear instructions on how to complete a recipe, we use these sections as follows:

Getting ready

This section tells you what to expect in the recipe, and describes how to set up any software or any preliminary settings required for the recipe.

How to do it...

This section contains the steps required to follow the recipe.

How it works...

This section usually consists of a detailed explanation of what happened in the previous section.

There's more...

This section consists of additional information about the recipe in order to make the reader more knowledgeable about the recipe.

See also

This section provides helpful links to other useful information for the recipe.

Conventions

In this book, you will find a number of text styles that distinguish between different kinds of information. Here are some examples of these styles and an explanation of their meaning.

Code words in text, database table names, folder names, filenames, file extensions, pathnames, dummy URLs, user input, and Twitter handles are shown as follows: Among them, you will find a folder named lib, which is the folder of interest.

A block of code is set as follows:

    classVals = new ArrayList();

      for (int i = 0; i < 5; i++){

        classVals.add(class + (i + 1));

    }

Any command-line input or output is written as follows:

@relation MyRelation

@attribute age numeric

@attribute name string

@attribute dob date yyyy-MM-dd

@attribute class {class1,class2,class3,class4,class5}

@data

35,'John Doe',1981-01-20,class3

30,'Harry Potter',1986-07-05,class1

New terms and important words are shown in bold. Words that you see on the screen, for example, in menus or dialog boxes, appear in the text like this: Select System info from the Administration panel.

Note

Warnings or important notes appear in a box like this.

Tip

Tips and tricks appear like this.

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Chapter 1. Obtaining and Cleaning Data

In this chapter, we will cover the following recipes:

Retrieving all file names from hierarchical directories using Java

Retrieving all file names from hierarchical directories using Apache Commons IO

Reading contents from text files all at once using Java 8

Reading contents from text files all at once using Apache Commons IO

Extracting PDF text using Apache Tika

Cleaning ASCII text files using Regular Expressions

Parsing Comma Separated Value files using Univocity

Parsing Tab Separated Value files using Univocity

Parsing XML files using JDOM

Writing JSON files using JSON.simple

Reading JSON files using JSON.simple

Extracting web data from a URL using JSoup

Extracting web data from a website using Selenium Webdriver

Reading table data from MySQL database

Introduction

Every data scientist needs to deal with data that is stored on disks in several formats, such as ASCII text, PDF, XML, JSON, and so on. Also, data can be stored in database tables. The first and foremost task for a data scientist before doing any analysis is to obtain data from these data sources and of these formats, and apply data-cleaning techniques to get rid of noises present in them. In this chapter, we will see recipes to accomplish this important task.

We will be using external Java libraries (Java archive files or simply JAR files) not only for this chapter