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Evolving structure-function mappings in cognitive neuroscience using genetic programming
A challenging goal of psychology and neuroscience is to map cognitive functions onto neuroanatomical structures. This paper shows how computational methods based upon evolutionary algorithms can facilitate the search for satisfactory mappings by efficiently combining constraints from neuroanatomy and physiology (the structures) with constraints from behavioural experiments (the functions). This methodology involves creation of a database coding for known neuroanatomical and physiological constraints, for mental programs made of primitive cognitive functions, and for typical experiments with their behavioural results. The evolutionary algorithms evolve theories mapping structures to functions in order to optimize the fit with the actual data. These theories lead to new, empirically testable predictions. The role of the prefrontal cortex in humans is discussed as an example. This methodology can be applied to the study of structures or functions alone, and can also be used to study other complex systems.
(This article does not exactly replicate the final version published in the Journal of Swiss Psychology. It is not a copy of the original published article and is not suitable for citation.
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
Meta-Genetic Programming: Co-evolving the Operators of Variation
The standard Genetic Programming approach is augmented by co-evolving the genetic operators. To do this the operators are coded as trees of indefinite length. In order for this technique to work, the language that the operators are defined in must be such that it preserves the variation in the base population. This technique can varied by adding further populations of operators and changing which populations act as operators for others, including itself, thus to provide a framework for a whole set of augmented GP techniques. The technique is tested on the parity problem. The pros and cons of the technique are discussed
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
Digital Ecosystems: Ecosystem-Oriented Architectures
We view Digital Ecosystems to be the digital counterparts of biological
ecosystems. Here, we are concerned with the creation of these Digital
Ecosystems, exploiting the self-organising properties of biological ecosystems
to evolve high-level software applications. Therefore, we created the Digital
Ecosystem, a novel optimisation technique inspired by biological ecosystems,
where the optimisation works at two levels: a first optimisation, migration of
agents which are distributed in a decentralised peer-to-peer network, operating
continuously in time; this process feeds a second optimisation based on
evolutionary computing that operates locally on single peers and is aimed at
finding solutions to satisfy locally relevant constraints. The Digital
Ecosystem was then measured experimentally through simulations, with measures
originating from theoretical ecology, evaluating its likeness to biological
ecosystems. This included its responsiveness to requests for applications from
the user base, as a measure of the ecological succession (ecosystem maturity).
Overall, we have advanced the understanding of Digital Ecosystems, creating
Ecosystem-Oriented Architectures where the word ecosystem is more than just a
metaphor.Comment: 39 pages, 26 figures, journa
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An Evolutionary Approach to the Design of Controllable Cellular Automata Structure for Random Number Generation
Cellular Automata (CA) has been used in pseudorandom number generation over a decade. Recent studies show that two-dimensional (2-d) CA Pseudorandom Number Generators (PRNGs) may generate better random sequences than conventional one-dimensional (1-d) CA PRNGs, but they are more complex to implement in hardware than 1-d CA PRNGs. In this paper, we propose a new class of 1-d CA Controllable Cellular Automata (CCA) without much deviation from the structure simplicity of conventional 1-d CA. We give a general definition of CCA first and then introduce two types of CCA – CCA0 and CCA2. Our initial study on them shows that these two CCA PRNGs have better randomness quality than conventional 1-d CA PRNGs but their randomness is affected by their structures. To find good CCA0/CCA2 structures for pseudorandom number generation, we evolve them using the Evolutionary Multi-Objective Optimization (EMOO) techniques. Three different algorithms are presented in this paper. One makes use of an aggregation function; the other two are based on the Vector Evaluated Genetic Algorithm (VEGA). Evolution results show that these three algorithms all perform well. Applying a set of randomness tests on the evolved CCA PRNGs, we demonstrate that their randomness is better than that of 1-d CA PRNGs and can be comparable to that of two-dimensional CA PRNGs
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