928 research outputs found
Novelty grammar swarms
Tese de mestrado, Engenharia Informática (Sistemas de Informação), Universidade de Lisboa, Faculdade de Ciências, 2015Particle Swarm Optimization (PSO) é um dos métodos de optimização populacionais mais conhecido. Normalmente é aplicado na otimização funções de fitness, que indicam o quão perto o algoritmo está de atingir o objectivo da pesquisa, fazendo com que esta se foque em áreas de fitness mais elevado. Em problemas com muitos ótimos locais, regularmente a pesquisa fica presa em locais com fitness elevado mas que não são o verdadeiro objetivo. Com vista a solucionar este problema em certos domínios, nesta tese é introduzido o Novelty-driven Particle Swarm Optimization (NdPSO). Este algoritmo é inspirado na pesquisa pela novidade (novelty search), um método relativamente recente que guia a pesquisa de forma a encontrar instâncias significativamente diferentes das anteriores. Desta forma, o NdPSO ignora por completo o objetivo perseguindo apenas a novidade, isto torna-o menos susceptivel a ser enganado em problemas com muitos optimos locais. Uma vez que o novelty search mostrou potencial a resolver tarefas no âmbito da programação genética, em particular na evolução gramatical, neste projeto o NdPSO é usado como uma extensão do método de Grammatical Swarm que é uma combinação do PSO com a programação genética. A implementação do NdPSO é testada em três domínios diferentes, representativos daqueles para o qual este algoritmo poderá ser mais vantajoso que os algoritmos guiados pelo objectivo. Isto é, domínios enganadores nos quais seja relativamente intuitivo descrever um comportamento. Em cada um dos domínios testados, o NdPSO supera o aloritmo standard do PSO, uma das suas variantes mais conhecidas (Barebones PSO) e a pesquisa aleatória, mostrando ser uma ferramenta promissora para resolver problemas enganadores. Uma vez que esta é a primeira aplicação da pesquisa por novidade fora do paradigma evolucionário, neste projecto é também efectuado um estudo comparativo do novo algoritmo com a forma mais comum de usar a pesquisa pela novidade (na forma de algoritmo evolucionário).Particle Swarm Optimization (PSO) is a well-known population-based optimization algorithm. Most often it is applied to optimize fitness functions that specify the goal of reaching a desired objective or behavior. As a result, search focuses on higher-fitness areas. In problems with many local optima, search often becomes stuck, and thus can fail to find the intended objective. To remedy this problem in certain kinds of domains, this thesis introduces Novelty-driven Particle Swarm Optimization (NdPSO). Taking motivation from the novelty search algorithm in evolutionary computation, in this method search is driven only towards finding instances significantly different from those found before. In this way, NdPSO completely ignores the objective in its pursuit of novelty, making it less susceptible to deception and local optima. Because novelty search has previously shown potential for solving tasks in Genetic Programming, particularly, in Grammatical Evolution, this paper implements NdPSO as an extension of the Grammatical Swarm method which in effect is a combination of PSO and Genetic Programming.The resulting NdPSO implementation was tested in three different domains representative of those in which it might provide advantage over objective-driven PSO, in particular, those which are deceptive and in which a meaningful high-level description of novel behavior is easy to derive. In each of the tested domains NdPSO outperforms both objective-based PSO and random-search, demonstrating its promise as a tool for solving deceptive problems. Since this is the first application of the search for novelty outside the evolutionary paradigm an empirical comparative study of the new algorithm to a standard novelty search Evolutionary Algorithm is performed
Derivation of Context-free Stochastic L-Grammar Rules for Promoter Sequence Modeling Using Support Vector Machine
Formal grammars can used for describing complex repeatable structures such as DNA sequences. In
this paper, we describe the structural composition of DNA sequences using a context-free stochastic L-grammar.
L-grammars are a special class of parallel grammars that can model the growth of living organisms, e.g. plant
development, and model the morphology of a variety of organisms. We believe that parallel grammars also can
be used for modeling genetic mechanisms and sequences such as promoters. Promoters are short regulatory
DNA sequences located upstream of a gene. Detection of promoters in DNA sequences is important for
successful gene prediction. Promoters can be recognized by certain patterns that are conserved within a species,
but there are many exceptions which makes the promoter recognition a complex problem. We replace the
problem of promoter recognition by induction of context-free stochastic L-grammar rules, which are later used for
the structural analysis of promoter sequences. L-grammar rules are derived automatically from the drosophila and
vertebrate promoter datasets using a genetic programming technique and their fitness is evaluated using a
Support Vector Machine (SVM) classifier. The artificial promoter sequences generated using the derived L-
grammar rules are analyzed and compared with natural promoter sequences
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
Polynomial modeling for time-varying systems based on a particle swarm optimization algorithm
In this paper, an effective particle swarm optimization (PSO) is proposed for polynomial models for time varying systems. The basic operations of the proposed PSO are similar to those of the classical PSO except that elements of particles represent arithmetic operations and variables of time-varying models. The performance of the proposed PSO is evaluated by polynomial modeling based on various sets of time-invariant and time-varying data. Results of polynomial modeling in time-varying systems show that the proposed PSO outperforms commonly used modeling methods which have been developed for solving dynamic optimization problems including genetic programming (GP) and dynamic GP. An analysis of the diversity of individuals of populations in the proposed PSO and GP reveals why the proposed PSO obtains better results than those obtained by GP
Neuroevolution in Deep Neural Networks: Current Trends and Future Challenges
A variety of methods have been applied to the architectural configuration and
learning or training of artificial deep neural networks (DNN). These methods
play a crucial role in the success or failure of the DNN for most problems and
applications. Evolutionary Algorithms (EAs) are gaining momentum as a
computationally feasible method for the automated optimisation and training of
DNNs. Neuroevolution is a term which describes these processes of automated
configuration and training of DNNs using EAs. While many works exist in the
literature, no comprehensive surveys currently exist focusing exclusively on
the strengths and limitations of using neuroevolution approaches in DNNs.
Prolonged absence of such surveys can lead to a disjointed and fragmented field
preventing DNNs researchers potentially adopting neuroevolutionary methods in
their own research, resulting in lost opportunities for improving performance
and wider application within real-world deep learning problems. This paper
presents a comprehensive survey, discussion and evaluation of the
state-of-the-art works on using EAs for architectural configuration and
training of DNNs. Based on this survey, the paper highlights the most pertinent
current issues and challenges in neuroevolution and identifies multiple
promising future research directions.Comment: 20 pages (double column), 2 figures, 3 tables, 157 reference
Automated Design of Metaheuristic Algorithms: A Survey
Metaheuristics have gained great success in academia and practice because
their search logic can be applied to any problem with available solution
representation, solution quality evaluation, and certain notions of locality.
Manually designing metaheuristic algorithms for solving a target problem is
criticized for being laborious, error-prone, and requiring intensive
specialized knowledge. This gives rise to increasing interest in automated
design of metaheuristic algorithms. With computing power to fully explore
potential design choices, the automated design could reach and even surpass
human-level design and could make high-performance algorithms accessible to a
much wider range of researchers and practitioners. This paper presents a broad
picture of automated design of metaheuristic algorithms, by conducting a survey
on the common grounds and representative techniques in terms of design space,
design strategies, performance evaluation strategies, and target problems in
this field
Biomimetic Engineering
Humankind is a privileged animal species for many reasons. A remarkable one is its
ability to conceive and manufacture objects. Human industry is indeed leading the
various winning strategies (along with language and culture) that has permitted this
primate to extraordinarily increase its life expectancy and proliferation rate. (It is indeed
so successful, that it now threatens the whole planet.) The design of this industry kicks
off in the brain, a computing machine particularly good at storing, recognizing and
associating patterns. Even in a time when human beings tend to populate non-natural,
man-made environments, the many forms, colorings, textures and behaviors of nature
continuously excite our senses and blend in our thoughts, even more deeply during
childhood. Then, it would be exaggerated to say that Biomimetics is a brand new
strategy. As long as human creation is based on previously acquired knowledge and
experiences, it is not surprising that engineering, the arts, and any form of expression, is
influenced by nature’s way to some extent.
The design of human industry has evolved from very simple tools, to complex
engineering devices. Nature has always provided us with a rich catalog of excellent
materials and inspiring designs. Now, equipped with new machinery and techniques, we
look again at Nature. We aim at mimicking not only its best products, but also its design
principles.
Organic life, as we know it, is indeed a vast pool of diversity. Living matter inhabits
almost every corner of the terrestrial ecosphere. From warm open-air ecosystems to the
extreme conditions of hot salt ponds, living cells have found ways to metabolize the
sources of energy, and get organized in complex organisms of specialized tissues and organs that adapt themselves to the environment, and can modify the environment to
their own needs as well. Life on Earth has evolved such a diverse portfolio of species
that the number of designs, mechanisms and strategies that can actually be abstracted is
astonishing. As August Krogh put it: "For a large number of problems there will be
some animal of choice, on which it can be most conveniently studied".
The scientific method starts with a meticulous observation of natural phenomena, and
humans are particularly good at that game. In principle, the aim of science is to
understand the physical world, but an observer’s mind can behave either as an engineer
or as a scientist. The minute examination of the many living forms that surround us has
led to the understanding of new organizational principles, some of which can be
imported in our production processes. In practice, bio-inspiration can arise at very
different levels of observation: be it social organization, the shape of an organism, the
structure and functioning of organs, tissular composition, cellular form and behavior, or
the detailed structure of molecules. Our direct experience of the wide portfolio of
species found in nature, and their particular organs, have clearly favored that the initial
models would come from the organism and organ levels. But the development of new
techniques (on one hand to observe the micro- and nanostructure of living beings, and
on the other to simulate the complex behavior of social communities) have significantly
extended the domain of interest
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