Semantically-based crossover in genetic programming: application to real-valued symbolic regression

We investigate the effects of semantically-based crossover operators in genetic programming, applied to real-valued symbolic regression problems. We propose two new relations derived from the semantic distance between subtrees, known as semantic equivalence and semantic similarity. These relations are used to guide variants of the crossover operator, resulting in two new crossover operators—semantics aware crossover (SAC) and semantic similarity-based crossover (SSC). SAC, was introduced and previously studied, is added here for the purpose of comparison and analysis. SSC extends SAC by more closely controlling the semantic distance between subtrees to which crossover may be applied. The new operators were tested on some real-valued symbolic regression problems and compared with standard crossover (SC), context aware crossover (CAC), Soft Brood Selection (SBS), and No Same Mate (NSM) selection. The experimental results show on the problems examined that, with computational effort measured by the number of function node evaluations, only SSC and SBS were significantly better than SC, and SSC was often better than SBS. Further experiments were also conducted to analyse the perfomance sensitivity to the parameter settings for SSC. This analysis leads to a conclusion that SSC is more constructive and has higher locality than SAC, NSM and SC; we believe these are the main reasons for the improved performance of SSC

Comparison of semantic-based local search methods for multiobjective genetic programming

We report a series of experiments that use semantic-based local search within a multiobjective genetic programming (GP) framework. We compare various ways of selecting target subtrees for local search as well as different methods for performing that search; we have also made comparison with the random desired operator of Pawlak et al. using statistical hypothesis testing. We find that a standard steady state or generational GP followed by a carefully-designed single-objective GP implementing semantic-based local search produces models that are mode accurate and with statistically smaller (or equal) tree size than those generated by the corresponding baseline GP algorithms. The depth fair selection strategy of Ito et al. is found to perform best compared with other subtree selection methods in the model refinement

Automatically correcting syntactic and semantic errors in ATL transformations using multi-objective optimization

L’ingénierie dirigée par les modèles (EDM) est un paradigme de développement logiciel qui promeut l’utilisation de modèles en tant qu’artefacts de première plan et de processus automatisés pour en dériver d’autres artefacts tels que le code, la documentation et les cas de test. La transformation de modèle est un élément important de l’EDM puisqu’elle permet de manipuler les représentations abstraites que sont les modèles. Les transformations de modèles, comme d’autres programmes, sont sujettes à la fois à des erreurs syntaxiques et sémantiques. La correction de ces erreurs est difficile et chronophage, car les transformations dépendent du langage de transformation comme ATL et des langages de modélisation dans lesquels sont exprimés les modèles en entrée et en sortie. Les travaux existants sur la réparation des transformations ciblent les erreurs syntaxiques ou sémantiques, une erreur à la fois, et définissent manuellement des patrons de correctifs. L’objectif principal de notre recherche est de proposer un cadre générique pour corriger automatiquement de multiples erreurs syntaxiques et sémantiques. Afin d’atteindre cet objectif, nous reformulons la réparation des transformations de modèles comme un problème d’optimisation multiobjectif et le résolvons au moyen d’algorithmes évolutionnaires. Pour adapter le cadre aux deux catégories d’erreurs, nous utilisons différents types d’objectifs et des stratégies sophistiquées pour guider l’exploration de l’espace des solutions.Model-driven engineering (MDE) is a software development paradigm that promotes the use of models as first-class artifacts and automated processes to derive other artefacts from them such as code, documentation and test cases. Model transformation is an important element of MDE since it allows to manipulate the abstract representations that are models. Model transformations, as other programs are subjects to both syntactic and semantic errors. Fixing those errors is difficult and time consuming as the transformations depend on the transformation language such as ATL, and modeling languages in which input and output models are expressed. Existing work on transformation repair targets either syntactic or semantic errors, one error at a time, and define patch templates manually. The main goal of our research is to propose a generic framework to fix multiple syntactic and semantic errors automatically. In order to achieve this goal, we reformulate the repair of model transformations as a multi-objective optimization problem and solve it by means of evolutionary algorithms. To adapt the framework to the two categories of errors, we use different types of objectives and sophisticated strategies to guide the search

Competent Program Evolution, Doctoral Dissertation, December 2006

Heuristic optimization methods are adaptive when they sample problem solutions based on knowledge of the search space gathered from past sampling. Recently, competent evolutionary optimization methods have been developed that adapt via probabilistic modeling of the search space. However, their effectiveness requires the existence of a compact problem decomposition in terms of prespecified solution parameters. How can we use these techniques to effectively and reliably solve program learning problems, given that program spaces will rarely have compact decompositions? One method is to manually build a problem-specific representation that is more tractable than the general space. But can this process be automated? My thesis is that the properties of programs and program spaces can be leveraged as inductive bias to reduce the burden of manual representation-building, leading to competent program evolution. The central contributions of this dissertation are a synthesis of the requirements for competent program evolution, and the design of a procedure, meta-optimizing semantic evolutionary search (MOSES), that meets these requirements. In support of my thesis, experimental results are provided to analyze and verify the effectiveness of MOSES, demonstrating scalability and real-world applicability

Nonlinear Dynamic System Identification and Model Predictive Control Using Genetic Programming

During the last century, a lot of developments have been made in research of complex nonlinear process control. As a powerful control methodology, model predictive control (MPC) has been extensively applied to chemical industrial applications. Core to MPC is a predictive model of the dynamics of the system being controlled. Most practical systems exhibit complex nonlinear dynamics, which imposes big challenges in system modelling. Being able to automatically evolve both model structure and numeric parameters, Genetic Programming (GP) shows great potential in identifying nonlinear dynamic systems. This thesis is devoted to GP based system identification and model-based control of nonlinear systems. To improve the generalization ability of GP models, a series of experiments that use semantic-based local search within a multiobjective GP framework are reported. The influence of various ways of selecting target subtrees for local search as well as different methods for performing that search were investigated; a comparison with the Random Desired Operator (RDO) of Pawlak et al. was made by statistical hypothesis testing. Compared with the corresponding baseline GP algorithms, models produced by a standard steady state or generational GP followed by a carefully-designed single-objective GP implementing semantic-based local search are statistically more accurate and with smaller (or equal) tree size, compared with the RDO-based GP algorithms. Considering the practical application, how to correctly and efficiently apply an evolved GP model to other larger systems is a critical research concern. Currently, the replication of GP models is normally done by repeating other’s work given the necessary algorithm parameters. However, due to the empirical and stochastic nature of GP, it is difficult to completely reproduce research findings. An XML-based standard file format, named Genetic Programming Markup Language (GPML), is proposed for the interchange of GP trees. A formal definition of this standard and details of implementation are described. GPML provides convenience and modularity for further applications based on GP models. The large-scale adoption of MPC in buildings is not economically viable due to the time and cost involved in designing and adjusting predictive models by expert control engineers. A GP-based control framework is proposed for automatically evolving dynamic nonlinear models for the MPC of buildings. An open-loop system identification was conducted using the data generated by a building simulator, and the obtained GP model was then employed to construct the predictive model for the MPC. The experimental result shows GP is able to produce models that allow the MPC of building to achieve the desired temperature band in a single zone space

Implementing an evolutionary algorithm to optimise fractal patterns and investigate its possible contribution to the design of engineering systems

This is ongoing interdisciplinary research drawing inspiration from the rapidly growing field of evolutionary developmental biology, i.e., the so-called “Evo-Devo” paradigm. We not only aim to investigate the similarities but importantly, also the differences between the synthesis of a biological organism and an engineering system. A bespoke algorithm will be developed using an Evolutionary Algorithm to generate fractal patterns observed in nature. The success of this method will allow us to investigate its possible usage in designing an engineering system

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

Model based test suite minimization using metaheuristics

Software testing is one of the most widely used methods for quality assurance and fault detection purposes. However, it is one of the most expensive, tedious and time consuming activities in software development life cycle. Code-based and specification-based testing has been going on for almost four decades. Model-based testing (MBT) is a relatively new approach to software testing where the software models as opposed to other artifacts (i.e. source code) are used as primary source of test cases. Models are simplified representation of a software system and are cheaper to execute than the original or deployed system. The main objective of the research presented in this thesis is the development of a framework for improving the efficiency and effectiveness of test suites generated from UML models. It focuses on three activities: transformation of Activity Diagram (AD) model into Colored Petri Net (CPN) model, generation and evaluation of AD based test suite and optimization of AD based test suite. Unified Modeling Language (UML) is a de facto standard for software system analysis and design. UML models can be categorized into structural and behavioral models. AD is a behavioral type of UML model and since major revision in UML version 2.x it has a new Petri Nets like semantics. It has wide application scope including embedded, workflow and web-service systems. For this reason this thesis concentrates on AD models. Informal semantics of UML generally and AD specially is a major challenge in the development of UML based verification and validation tools. One solution to this challenge is transforming a UML model into an executable formal model. In the thesis, a three step transformation methodology is proposed for resolving ambiguities in an AD model and then transforming it into a CPN representation which is a well known formal language with extensive tool support. Test case generation is one of the most critical and labor intensive activities in testing processes. The flow oriented semantic of AD suits modeling both sequential and concurrent systems. The thesis presented a novel technique to generate test cases from AD using a stochastic algorithm. In order to determine if the generated test suite is adequate, two test suite adequacy analysis techniques based on structural coverage and mutation have been proposed. In terms of structural coverage, two separate coverage criteria are also proposed to evaluate the adequacy of the test suite from both perspectives, sequential and concurrent. Mutation analysis is a fault-based technique to determine if the test suite is adequate for detecting particular types of faults. Four categories of mutation operators are defined to seed specific faults into the mutant model. Another focus of thesis is to improve the test suite efficiency without compromising its effectiveness. One way of achieving this is identifying and removing the redundant test cases. It has been shown that the test suite minimization by removing redundant test cases is a combinatorial optimization problem. An evolutionary computation based test suite minimization technique is developed to address the test suite minimization problem and its performance is empirically compared with other well known heuristic algorithms. Additionally, statistical analysis is performed to characterize the fitness landscape of test suite minimization problems. The proposed test suite minimization solution is extended to include multi-objective minimization. As the redundancy is contextual, different criteria and their combination can significantly change the solution test suite. Therefore, the last part of the thesis describes an investigation into multi-objective test suite minimization and optimization algorithms. The proposed framework is demonstrated and evaluated using prototype tools and case study models. Empirical results have shown that the techniques developed within the framework are effective in model based test suite generation and optimizatio