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Clever Algorithms Nature Inspired Programming Recipes
1ST Edition Jason Brownlee Digital Instant Download
Author(s): Jason Brownlee
ISBN(s): 9781446785065, 1446785068
Edition: 1ST
File Details: PDF, 2.99 MB
Year: 2011
Language: english
Jason Brownlee

Clever Algorithms
Nature-Inspired Programming Recipes
ii

Jason Brownlee, PhD

Jason Brownlee studied Applied Science at Swinburne University in Melbourne,
Australia, going on to complete a Masters in Information Technology focusing on
Niching Genetic Algorithms, and a PhD in the field of Artificial Immune Systems.
Jason has worked for a number of years as a Consultant and Software Engineer
for a range of Corporate and Government organizations. When not writing books,
Jason likes to compete in Machine Learning competitions.

Cover Image
© Copyright 2011 Jason Brownlee. All Reserved.
Clever Algorithms: Nature-Inspired Programming Recipes
© Copyright 2011 Jason Brownlee. Some Rights Reserved.
First Edition. LuLu. January 2011
ISBN: 978-1-4467-8506-5

This work is licensed under a Creative Commons

Attribution-Noncommercial-Share Alike 2.5 Australia License.
The full terms of the license are located online at
http://creativecommons.org/licenses/by-nc-sa/2.5/au/legalcode

Webpage
Source code and additional resources can be downloaded from the books
companion website online at http://www.CleverAlgorithms.com
Contents

Foreword vii

Preface ix

I Background 1
1 Introduction 3
1.1 What is AI . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
1.2 Problem Domains . . . . . . . . . . . . . . . . . . . . . . . . 9
1.3 Unconventional Optimization . . . . . . . . . . . . . . . . . 13
1.4 Book Organization . . . . . . . . . . . . . . . . . . . . . . . 16
1.5 How to Read this Book . . . . . . . . . . . . . . . . . . . . 19
1.6 Further Reading . . . . . . . . . . . . . . . . . . . . . . . . 20
1.7 Bibliography . . . . . . . . . . . . . . . . . . . . . . . . . . 21

II Algorithms 27
2 Stochastic Algorithms 29
2.1 Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
2.2 Random Search . . . . . . . . . . . . . . . . . . . . . . . . . 30
2.3 Adaptive Random Search . . . . . . . . . . . . . . . . . . . 34
2.4 Stochastic Hill Climbing . . . . . . . . . . . . . . . . . . . . 39
2.5 Iterated Local Search . . . . . . . . . . . . . . . . . . . . . . 43
2.6 Guided Local Search . . . . . . . . . . . . . . . . . . . . . . 49
2.7 Variable Neighborhood Search . . . . . . . . . . . . . . . . . 55
2.8 Greedy Randomized Adaptive Search . . . . . . . . . . . . . 60
2.9 Scatter Search . . . . . . . . . . . . . . . . . . . . . . . . . 66
2.10 Tabu Search . . . . . . . . . . . . . . . . . . . . . . . . . . . 73
2.11 Reactive Tabu Search . . . . . . . . . . . . . . . . . . . . . 79

iii
iv Contents

3 Evolutionary Algorithms 87
3.1 Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87
3.2 Genetic Algorithm . . . . . . . . . . . . . . . . . . . . . . . 92
3.3 Genetic Programming . . . . . . . . . . . . . . . . . . . . . 99
3.4 Evolution Strategies . . . . . . . . . . . . . . . . . . . . . . 108
3.5 Differential Evolution . . . . . . . . . . . . . . . . . . . . . 114
3.6 Evolutionary Programming . . . . . . . . . . . . . . . . . . 120
3.7 Grammatical Evolution . . . . . . . . . . . . . . . . . . . . 126
3.8 Gene Expression Programming . . . . . . . . . . . . . . . . 134
3.9 Learning Classifier System . . . . . . . . . . . . . . . . . . . 141
3.10 Non-dominated Sorting Genetic Algorithm . . . . . . . . . . 152
3.11 Strength Pareto Evolutionary Algorithm . . . . . . . . . . . 160

4 Physical Algorithms 167

4.1 Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . 167
4.2 Simulated Annealing . . . . . . . . . . . . . . . . . . . . . . 169
4.3 Extremal Optimization . . . . . . . . . . . . . . . . . . . . . 175
4.4 Harmony Search . . . . . . . . . . . . . . . . . . . . . . . . 182
4.5 Cultural Algorithm . . . . . . . . . . . . . . . . . . . . . . . 187
4.6 Memetic Algorithm . . . . . . . . . . . . . . . . . . . . . . . 193

5 Probabilistic Algorithms 199

5.1 Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . 199
5.2 Population-Based Incremental Learning . . . . . . . . . . . 203
5.3 Univariate Marginal Distribution Algorithm . . . . . . . . . 208
5.4 Compact Genetic Algorithm . . . . . . . . . . . . . . . . . . 212
5.5 Bayesian Optimization Algorithm . . . . . . . . . . . . . . . 216
5.6 Cross-Entropy Method . . . . . . . . . . . . . . . . . . . . . 224

6 Swarm Algorithms 229

6.1 Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . 229
6.2 Particle Swarm Optimization . . . . . . . . . . . . . . . . . 232
6.3 Ant System . . . . . . . . . . . . . . . . . . . . . . . . . . . 238
6.4 Ant Colony System . . . . . . . . . . . . . . . . . . . . . . . 245
6.5 Bees Algorithm . . . . . . . . . . . . . . . . . . . . . . . . . 252
6.6 Bacterial Foraging Optimization Algorithm . . . . . . . . . 257

7 Immune Algorithms 265

7.1 Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . 265
7.2 Clonal Selection Algorithm . . . . . . . . . . . . . . . . . . 270
7.3 Negative Selection Algorithm . . . . . . . . . . . . . . . . . 277
7.4 Artificial Immune Recognition System . . . . . . . . . . . . 284
7.5 Immune Network Algorithm . . . . . . . . . . . . . . . . . . 292
7.6 Dendritic Cell Algorithm . . . . . . . . . . . . . . . . . . . . 299
 v

8 Neural Algorithms 307

8.1 Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . 307
8.2 Perceptron . . . . . . . . . . . . . . . . . . . . . . . . . . . 311
8.3 Back-propagation . . . . . . . . . . . . . . . . . . . . . . . . 316
8.4 Hopfield Network . . . . . . . . . . . . . . . . . . . . . . . . 324
8.5 Learning Vector Quantization . . . . . . . . . . . . . . . . . 330
8.6 Self-Organizing Map . . . . . . . . . . . . . . . . . . . . . . 336

III Extensions 343

9 Advanced Topics 345
9.1 Programming Paradigms . . . . . . . . . . . . . . . . . . . . 346
9.2 Devising New Algorithms . . . . . . . . . . . . . . . . . . . 356
9.3 Testing Algorithms . . . . . . . . . . . . . . . . . . . . . . . 367
9.4 Visualizing Algorithms . . . . . . . . . . . . . . . . . . . . . 374
9.5 Problem Solving Strategies . . . . . . . . . . . . . . . . . . 386
9.6 Benchmarking Algorithms . . . . . . . . . . . . . . . . . . . 400

IV Appendix 411
A Ruby: Quick-Start Guide 413
A.1 Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . 413
A.2 Language Basics . . . . . . . . . . . . . . . . . . . . . . . . 413
A.3 Ruby Idioms . . . . . . . . . . . . . . . . . . . . . . . . . . 417
A.4 Bibliography . . . . . . . . . . . . . . . . . . . . . . . . . . 419

Index 421
vi Contents
Foreword

I am delighted to write this foreword. This book, a reference where one

can look up the details of most any algorithm to find a clear unambiguous
description, has long been needed and here it finally is. A concise reference
that has taken many hours to write but which has the capacity to save vast
amounts of time previously spent digging out original papers.
I have known the author for several years and have had experience of his
amazing capacity for work and the sheer quality of his output, so this book
comes as no surprise to me. But I hope it will be a surprise and delight to
you, the reader for whom it has been written.
But useful as this book is, it is only a beginning. There are so many
algorithms that no one author could hope to cover them all. So if you know
of an algorithm that is not yet here, how about contributing it using the
same clear and lucid style?

Professor Tim Hendtlass

Complex Intelligent Systems Laboratory
Faculty of Information and Communication Technologies
Swinburne University of Technology

Melbourne, Australia
2010

vii
viii Foreword
Preface

About the book

The need for this project was born of frustration while working towards my
PhD. I was investigating optimization algorithms and was implementing
a large number of them for a software platform called the Optimization
Algorithm Toolkit (OAT)1 . Each algorithm required considerable effort
to locate the relevant source material (from books, papers, articles, and
existing implementations), decipher and interpret the technique, and finally
attempt to piece together a working implementation.
Taking a broader perspective, I realized that the communication of
algorithmic techniques in the field of Artificial Intelligence was clearly a
difficult and outstanding open problem. Generally, algorithm descriptions
are:

ˆ Incomplete: many techniques are ambiguously described, partially

described, or not described at all.

ˆ Inconsistent: a given technique may be described using a variety of

formal and semi-formal methods that vary across different techniques,
limiting the transferability of background skills an audience requires
to read a technique (such as mathematics, pseudocode, program code,
and narratives). An inconsistent representation for techniques means
that the skills used to understand and internalize one technique may
not be transferable to realizing different techniques or even extensions
of the same technique.

ˆ Distributed : the description of data structures, operations, and pa-

rameterization of a given technique may span a collection of papers,
articles, books, and source code published over a number of years, the
access to which may be restricted and difficult to obtain.

For the practitioner, a badly described algorithm may be simply frus-

trating, where the gaps in available information are filled with intuition and
1 OAT located at http://optalgtoolkit.sourceforge.net

ix
x Preface

‘best guess’. At the other end of the spectrum, a badly described algorithm
may be an example of bad science and the failure of the scientific method,
where the inability to understand and implement a technique may prevent
the replication of results, the application, or the investigation and extension
of a technique.
The software I produced provided a first step solution to this problem: a
set of working algorithms implemented in a (somewhat) consistent way and
downloaded from a single location (features likely provided by any library of
artificial intelligence techniques). The next logical step needed to address this
problem is to develop a methodology that anybody can follow. The strategy
to address the open problem of poor algorithm communication is to present
complete algorithm descriptions (rather than just implementations) in a
consistent manner, and in a centralized location. This book is the outcome
of developing such a strategy that not only provides a methodology for
standardized algorithm descriptions, but provides a large corpus of complete
and consistent algorithm descriptions in a single centralized location.
The algorithms described in this work are practical, interesting, and
fun, and the goal of this project was to promote these features by making
algorithms from the field more accessible, usable, and understandable.
This project was developed over a number years through a lot of writing,
discussion, and revision. This book has been released under a permissive
license that encourages the reader to explore new and creative ways of
further communicating its message and content.
I hope that this project has succeeded in some small way and that you
too can enjoy applying, learning, and playing with Clever Algorithms.

Jason Brownlee

Melbourne, Australia
2011
Acknowledgments

This book could not have been completed without the commitment, passion,
and hard work from a large group of editors and supporters.
A special thanks to Steve Dower for his incredible attention to detail
in providing technical and copy edits for large portions of this book, and
for his enthusiasm for the subject area. Also, a special thanks to Daniel
Angus for the discussions around the genesis of the project, his continued
support with the idea of an ‘algorithms atlas’ and for his attention to detail
in providing technical and copy edits for key chapters.
In no particular order, thanks to: Juan Ojeda, Martin Goddard, David
Howden, Sean Luke, David Zappia, Jeremy Wazny, and Andrew Murray.
Thanks to the hundreds of machine learning enthusiasts who voted on
potential covers and helped shape what this book became. You know who
you are!
Finally, I would like to thank my beautiful wife Ying Liu for her unre-
lenting support and patience throughout the project.

xi
xii Acknowledgments
 Part I

Background

1
Chapter 1

Introduction

Welcome to Clever Algorithms! This is a handbook of recipes for com-

putational problem solving techniques from the fields of Computational
Intelligence, Biologically Inspired Computation, and Metaheuristics. Clever
Algorithms are interesting, practical, and fun to learn about and implement.
Research scientists may be interested in browsing algorithm inspirations in
search of an interesting system or process analogs to investigate. Developers
and software engineers may compare various problem solving algorithms
and technique-specific guidelines. Practitioners, students, and interested
amateurs may implement state-of-the-art algorithms to address business or
scientific needs, or simply play with the fascinating systems they represent.
This introductory chapter provides relevant background information on
Artificial Intelligence and Algorithms. The core of the book provides a large
corpus of algorithms presented in a complete and consistent manner. The
final chapter covers some advanced topics to consider once a number of
algorithms have been mastered. This book has been designed as a reference
text, where specific techniques are looked up, or where the algorithms across
whole fields of study can be browsed, rather than being read cover-to-cover.
This book is an algorithm handbook and a technique guidebook, and I hope
you find something useful.

1.1 What is AI
1.1.1 Artificial Intelligence
The field of classical Artificial Intelligence (AI) coalesced in the 1950s
drawing on an understanding of the brain from neuroscience, the new
mathematics of information theory, control theory referred to as cybernetics,
and the dawn of the digital computer. AI is a cross-disciplinary field
of research that is generally concerned with developing and investigating

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