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A Field Guide to Genetic Programming
xiv, 233 p. : il. ; 23 cm.Libro ElectrĂłnicoA Field Guide to Genetic Programming (ISBN 978-1-4092-0073-4) is an introduction to genetic programming (GP). GP is a systematic, domain-independent method for getting computers to solve problems automatically starting from a high-level statement of what needs to be done. Using ideas from natural evolution, GP starts from an ooze of random computer programs, and progressively refines them through processes of mutation and sexual recombination, until solutions emerge. All this without the user having to know or specify the form or structure of solutions in advance. GP has generated a plethora of human-competitive results and applications, including novel scientific discoveries and patentable inventions. The authorsIntroduction --
Representation, initialisation and operators in Tree-based GP --
Getting ready to run genetic programming --
Example genetic programming run --
Alternative initialisations and operators in Tree-based GP --
Modular, grammatical and developmental Tree-based GP --
Linear and graph genetic programming --
Probalistic genetic programming --
Multi-objective genetic programming --
Fast and distributed genetic programming --
GP theory and its applications --
Applications --
Troubleshooting GP --
Conclusions.Contents
xi
1 Introduction
1.1 Genetic Programming in a Nutshell
1.2 Getting Started
1.3 Prerequisites
1.4 Overview of this Field Guide I
Basics
2 Representation, Initialisation and GP
2.1 Representation
2.2 Initialising the Population
2.3 Selection
2.4 Recombination and Mutation Operators in Tree-based
3 Getting Ready to Run Genetic Programming 19
3.1 Step 1: Terminal Set 19
3.2 Step 2: Function Set 20
3.2.1 Closure 21
3.2.2 Sufficiency 23
3.2.3 Evolving Structures other than Programs 23
3.3 Step 3: Fitness Function 24
3.4 Step 4: GP Parameters 26
3.5 Step 5: Termination and solution designation 27
4 Example Genetic Programming Run
4.1 Preparatory Steps 29
4.2 Step-by-Step Sample Run 31
4.2.1 Initialisation 31
4.2.2 Fitness Evaluation Selection, Crossover and Mutation Termination and Solution Designation Advanced Genetic Programming
5 Alternative Initialisations and Operators in
5.1 Constructing the Initial Population
5.1.1 Uniform Initialisation
5.1.2 Initialisation may Affect Bloat
5.1.3 Seeding
5.2 GP Mutation
5.2.1 Is Mutation Necessary?
5.2.2 Mutation Cookbook
5.3 GP Crossover
5.4 Other Techniques 32
5.5 Tree-based GP 39
6 Modular, Grammatical and Developmental Tree-based GP 47
6.1 Evolving Modular and Hierarchical Structures 47
6.1.1 Automatically Defined Functions 48
6.1.2 Program Architecture and Architecture-Altering 50
6.2 Constraining Structures 51
6.2.1 Enforcing Particular Structures 52
6.2.2 Strongly Typed GP 52
6.2.3 Grammar-based Constraints 53
6.2.4 Constraints and Bias 55
6.3 Developmental Genetic Programming 57
6.4 Strongly Typed Autoconstructive GP with PushGP 59
7 Linear and Graph Genetic Programming 61
7.1 Linear Genetic Programming 61
7.1.1 Motivations 61
7.1.2 Linear GP Representations 62
7.1.3 Linear GP Operators 64
7.2 Graph-Based Genetic Programming 65
7.2.1 Parallel Distributed GP (PDGP) 65
7.2.2 PADO 67
7.2.3 Cartesian GP 67
7.2.4 Evolving Parallel Programs using Indirect Encodings 68
8 Probabilistic Genetic Programming
8.1 Estimation of Distribution Algorithms 69
8.2 Pure EDA GP 71
8.3 Mixing Grammars and Probabilities 74
9 Multi-objective Genetic Programming 75
9.1 Combining Multiple Objectives into a Scalar Fitness Function 75
9.2 Keeping the Objectives Separate 76
9.2.1 Multi-objective Bloat and Complexity Control 77
9.2.2 Other Objectives 78
9.2.3 Non-Pareto Criteria 80
9.3 Multiple Objectives via Dynamic and Staged Fitness Functions 80
9.4 Multi-objective Optimisation via Operator Bias 81
10 Fast and Distributed Genetic Programming 83
10.1 Reducing Fitness Evaluations/Increasing their Effectiveness 83
10.2 Reducing Cost of Fitness with Caches 86
10.3 Parallel and Distributed GP are Not Equivalent 88
10.4 Running GP on Parallel Hardware 89
10.4.1 Master–slave GP 89
10.4.2 GP Running on GPUs 90
10.4.3 GP on FPGAs 92
10.4.4 Sub-machine-code GP 93
10.5 Geographically Distributed GP 93
11 GP Theory and its Applications 97
11.1 Mathematical Models 98
11.2 Search Spaces 99
11.3 Bloat 101
11.3.1 Bloat in Theory 101
11.3.2 Bloat Control in Practice 104
III
Practical Genetic Programming
12 Applications
12.1 Where GP has Done Well
12.2 Curve Fitting, Data Modelling and Symbolic Regression
12.3 Human Competitive Results – the Humies
12.4 Image and Signal Processing
12.5 Financial Trading, Time Series, and Economic Modelling
12.6 Industrial Process Control
12.7 Medicine, Biology and Bioinformatics
12.8 GP to Create Searchers and Solvers – Hyper-heuristics xiii
12.9 Entertainment and Computer Games 127
12.10The Arts 127
12.11Compression 128
13 Troubleshooting GP
13.1 Is there a Bug in the Code?
13.2 Can you Trust your Results?
13.3 There are No Silver Bullets
13.4 Small Changes can have Big Effects
13.5 Big Changes can have No Effect
13.6 Study your Populations
13.7 Encourage Diversity
13.8 Embrace Approximation
13.9 Control Bloat
13.10 Checkpoint Results
13.11 Report Well
13.12 Convince your Customers
14 Conclusions
Tricks of the Trade
A Resources
A.1 Key Books
A.2 Key Journals
A.3 Key International Meetings
A.4 GP Implementations
A.5 On-Line Resources 145
B TinyGP 151
B.1 Overview of TinyGP 151
B.2 Input Data Files for TinyGP 153
B.3 Source Code 154
B.4 Compiling and Running TinyGP 162
Bibliography 167
Inde
TensorFlow Enabled Genetic Programming
Genetic Programming, a kind of evolutionary computation and machine learning
algorithm, is shown to benefit significantly from the application of vectorized
data and the TensorFlow numerical computation library on both CPU and GPU
architectures. The open source, Python Karoo GP is employed for a series of 190
tests across 6 platforms, with real-world datasets ranging from 18 to 5.5M data
points. This body of tests demonstrates that datasets measured in tens and
hundreds of data points see 2-15x improvement when moving from the scalar/SymPy
configuration to the vector/TensorFlow configuration, with a single core
performing on par or better than multiple CPU cores and GPUs. A dataset
composed of 90,000 data points demonstrates a single vector/TensorFlow CPU core
performing 875x better than 40 scalar/Sympy CPU cores. And a dataset containing
5.5M data points sees GPU configurations out-performing CPU configurations on
average by 1.3x.Comment: 8 pages, 5 figures; presented at GECCO 2017, Berlin, German
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Artificial intelligence makes computers lazy
This paper looks at the age-old problem of trying to instil some degree of intelligence in computers. Genetic Algorithms (GA) and Genetic Programming (GP) are techniques that are used to evolve a solution to a problem using processes that mimic natural evolution. This paper reflects on the experience gained while conducting research applying GA and GP to two quite different problems: Medical Diagnosis and Robot Path Planning. An observation is made that when these algorithms are not applied correctly the computer seemingly exhibits lazy behaviour, arriving at a suboptimal solutions. Using examples, this paper shows how this 'lazy' behaviour can be overcome
A GPU-Computing Approach to Solar Stokes Profile Inversion
We present a new computational approach to the inversion of solar
photospheric Stokes polarization profiles, under the Milne-Eddington model, for
vector magnetography. Our code, named GENESIS (GENEtic Stokes Inversion
Strategy), employs multi-threaded parallel-processing techniques to harness the
computing power of graphics processing units GPUs, along with algorithms
designed to exploit the inherent parallelism of the Stokes inversion problem.
Using a genetic algorithm (GA) engineered specifically for use with a GPU, we
produce full-disc maps of the photospheric vector magnetic field from polarized
spectral line observations recorded by the Synoptic Optical Long-term
Investigations of the Sun (SOLIS) Vector Spectromagnetograph (VSM) instrument.
We show the advantages of pairing a population-parallel genetic algorithm with
data-parallel GPU-computing techniques, and present an overview of the Stokes
inversion problem, including a description of our adaptation to the
GPU-computing paradigm. Full-disc vector magnetograms derived by this method
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Symbolic regression of generative network models
Networks are a powerful abstraction with applicability to a variety of
scientific fields. Models explaining their morphology and growth processes
permit a wide range of phenomena to be more systematically analysed and
understood. At the same time, creating such models is often challenging and
requires insights that may be counter-intuitive. Yet there currently exists no
general method to arrive at better models. We have developed an approach to
automatically detect realistic decentralised network growth models from
empirical data, employing a machine learning technique inspired by natural
selection and defining a unified formalism to describe such models as computer
programs. As the proposed method is completely general and does not assume any
pre-existing models, it can be applied "out of the box" to any given network.
To validate our approach empirically, we systematically rediscover pre-defined
growth laws underlying several canonical network generation models and credible
laws for diverse real-world networks. We were able to find programs that are
simple enough to lead to an actual understanding of the mechanisms proposed,
namely for a simple brain and a social network
Genetic Programming for Multibiometrics
Biometric systems suffer from some drawbacks: a biometric system can provide
in general good performances except with some individuals as its performance
depends highly on the quality of the capture. One solution to solve some of
these problems is to use multibiometrics where different biometric systems are
combined together (multiple captures of the same biometric modality, multiple
feature extraction algorithms, multiple biometric modalities...). In this
paper, we are interested in score level fusion functions application (i.e., we
use a multibiometric authentication scheme which accept or deny the claimant
for using an application). In the state of the art, the weighted sum of scores
(which is a linear classifier) and the use of an SVM (which is a non linear
classifier) provided by different biometric systems provide one of the best
performances. We present a new method based on the use of genetic programming
giving similar or better performances (depending on the complexity of the
database). We derive a score fusion function by assembling some classical
primitives functions (+, *, -, ...). We have validated the proposed method on
three significant biometric benchmark datasets from the state of the art
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