14,362 research outputs found
Multi-agent evolutionary systems for the generation of complex virtual worlds
Modern films, games and virtual reality applications are dependent on
convincing computer graphics. Highly complex models are a requirement for the
successful delivery of many scenes and environments. While workflows such as
rendering, compositing and animation have been streamlined to accommodate
increasing demands, modelling complex models is still a laborious task. This
paper introduces the computational benefits of an Interactive Genetic Algorithm
(IGA) to computer graphics modelling while compensating the effects of user
fatigue, a common issue with Interactive Evolutionary Computation. An
intelligent agent is used in conjunction with an IGA that offers the potential
to reduce the effects of user fatigue by learning from the choices made by the
human designer and directing the search accordingly. This workflow accelerates
the layout and distribution of basic elements to form complex models. It
captures the designer's intent through interaction, and encourages playful
discovery
A Field Guide to Genetic Programming
xiv, 233 p. : il. ; 23 cm.Libro ElectrónicoA 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
Genetic Optimization Using Derivatives: The rgenoud Package for R
genoud is an R function that combines evolutionary algorithm methods with a derivative-based (quasi-Newton) method to solve difficult optimization problems. genoud may also be used for optimization problems for which derivatives do not exist. genoud solves problems that are nonlinear or perhaps even discontinuous in the parameters of the function to be optimized. When the function to be optimized (for example, a log-likelihood) is nonlinear in the model's parameters, the function will generally not be globally concave and may have irregularities such as saddlepoints or discontinuities. Optimization methods that rely on derivatives of the objective function may be unable to find any optimum at all. Multiple local optima may exist, so that there is no guarantee that a derivative-based method will converge to the global optimum. On the other hand, algorithms that do not use derivative information (such as pure genetic algorithms) are for many problems needlessly poor at local hill climbing. Most statistical problems are regular in a neighborhood of the solution. Therefore, for some portion of the search space, derivative information is useful. The function supports parallel processing on multiple CPUs on a single machine or a cluster of computers.
The impact of cellular characteristics on the evolution of shape homeostasis
The importance of individual cells in a developing multicellular organism is
well known but precisely how the individual cellular characteristics of those
cells collectively drive the emergence of robust, homeostatic structures is
less well understood. For example cell communication via a diffusible factor
allows for information to travel across large distances within the population,
and cell polarisation makes it possible to form structures with a particular
orientation, but how do these processes interact to produce a more robust and
regulated structure? In this study we investigate the ability of cells with
different cellular characteristics to grow and maintain homeostatic structures.
We do this in the context of an individual-based model where cell behaviour is
driven by an intra-cellular network that determines the cell phenotype. More
precisely, we investigated evolution with 96 different permutations of our
model, where cell motility, cell death, long-range growth factor (LGF),
short-range growth factor (SGF) and cell polarisation were either present or
absent. The results show that LGF has the largest positive impact on the
fitness of the evolved solutions. SGF and polarisation also contribute, but all
other capabilities essentially increase the search space, effectively making it
more difficult to achieve a solution. By perturbing the evolved solutions, we
found that they are highly robust to both mutations and wounding. In addition,
we observed that by evolving solutions in more unstable environments they
produce structures that were more robust and adaptive. In conclusion, our
results suggest that robust collective behaviour is most likely to evolve when
cells are endowed with long range communication, cell polarisation, and
selection pressure from an unstable environment
Darwinian Data Structure Selection
Data structure selection and tuning is laborious but can vastly improve an
application's performance and memory footprint. Some data structures share a
common interface and enjoy multiple implementations. We call them Darwinian
Data Structures (DDS), since we can subject their implementations to survival
of the fittest. We introduce ARTEMIS a multi-objective, cloud-based
search-based optimisation framework that automatically finds optimal, tuned DDS
modulo a test suite, then changes an application to use that DDS. ARTEMIS
achieves substantial performance improvements for \emph{every} project in
Java projects from DaCapo benchmark, popular projects and uniformly
sampled projects from GitHub. For execution time, CPU usage, and memory
consumption, ARTEMIS finds at least one solution that improves \emph{all}
measures for () of the projects. The median improvement across
the best solutions is , , for runtime, memory and CPU
usage.
These aggregate results understate ARTEMIS's potential impact. Some of the
benchmarks it improves are libraries or utility functions. Two examples are
gson, a ubiquitous Java serialization framework, and xalan, Apache's XML
transformation tool. ARTEMIS improves gson by \%, and for
memory, runtime, and CPU; ARTEMIS improves xalan's memory consumption by
\%. \emph{Every} client of these projects will benefit from these
performance improvements.Comment: 11 page
Analysis of adaptive walks on NK fitness landscapes with different interaction schemes
Fitness landscapes are genotype to fitness mappings commonly used in
evolutionary biology and computer science which are closely related to spin
glass models. In this paper, we study the NK model for fitness landscapes where
the interaction scheme between genes can be explicitly defined. The focus is on
how this scheme influences the overall shape of the landscape. Our main tool
for the analysis are adaptive walks, an idealized dynamics by which the
population moves uphill in fitness and terminates at a local fitness maximum.
We use three different types of walks and investigate how their length (the
number of steps required to reach a local peak) and height (the fitness at the
endpoint of the walk) depend on the dimensionality and structure of the
landscape. We find that the distribution of local maxima over the landscape is
particularly sensitive to the choice of interaction pattern. Most quantities
that we measure are simply correlated to the rank of the scheme, which is equal
to the number of nonzero coefficients in the expansion of the fitness landscape
in terms of Walsh functions.Comment: 29 pages, 9 figure
A simple algorithm for optimization and model fitting: AGA (asexual genetic algorithm)
Context. Mathematical optimization can be used as a computational tool to
obtain the optimal solution to a given problem in a systematic and efficient
way. For example, in twice-differentiable functions and problems with no
constraints, the optimization consists of finding the points where the gradient
of the objective function is zero and using the Hessian matrix to classify the
type of each point. Sometimes, however it is impossible to compute these
derivatives and other type of techniques must be employed such as the steepest
descent/ascent method and more sophisticated methods such as those based on the
evolutionary algorithms. Aims. We present a simple algorithm based on the idea
of genetic algorithms (GA) for optimization. We refer to this algorithm as AGA
(Asexual Genetic Algorithm) and apply it to two kinds of problems: the
maximization of a function where classical methods fail and model fitting in
astronomy. For the latter case, we minimize the chi-square function to estimate
the parameters in two examples: the orbits of exoplanets by taking a set of
radial velocity data, and the spectral energy distribution (SED) observed
towards a YSO (Young Stellar Object). Methods. The algorithm AGA may also be
called genetic, although it differs from standard genetic algorithms in two
main aspects: a) the initial population is not encoded, and b) the new
generations are constructed by asexual reproduction. Results. Applying our
algorithm in optimizing some complicated functions, we find the global maxima
within a few iterations. For model fitting to the orbits of exoplanets and the
SED of a YSO, we estimate the parameters and their associated errors.Comment: 10 pages, 8 figures, Astronomy and Astrophysics (in press
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