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

DOE EPSCoR Initiative in Structural and computational Biology/Bioinformatics

The overall goal of the DOE EPSCoR Initiative in Structural and Computational Biology was to enhance the competiveness of Vermont research in these scientific areas. To develop self-sustaining infrastructure, we increased the critical mass of faculty, developed shared resources that made junior researchers more competitive for federal research grants, implemented programs to train graduate and undergraduate students who participated in these research areas and provided seed money for research projects. During the time period funded by this DOE initiative: (1) four new faculty were recruited to the University of Vermont using DOE resources, three in Computational Biology and one in Structural Biology; (2) technical support was provided for the Computational and Structural Biology facilities; (3) twenty-two graduate students were directly funded by fellowships; (4) fifteen undergraduate students were supported during the summer; and (5) twenty-eight pilot projects were supported. Taken together these dollars resulted in a plethora of published papers, many in high profile journals in the fields and directly impacted competitive extramural funding based on structural or computational biology resulting in 49 million dollars awarded in grants (Appendix I), a 600% return on investment by DOE, the State and University

Visualizing Tree Structures in Genetic Programming

This paper presents methods to visualize the structure of trees that occur in genetic programming. These methods allow for the inspection of structure of entire trees even though several thousands of nodes may be involved. The methods also scale to allow for the inspection of structure for entire populations and for complete trials even though millions of nodes may be involved. Examples are given that demonstrate how this new way of “seeing” can afford a potentially rich way of understanding dynamics that underpin genetic programming. The examples indicate further studies that might be enabled by visualizing structure at these scales.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/45620/1/10710_2005_Article_7621.pd

Evolutionary computation applied to combinatorial optimisation problems

This thesis addresses the issues associated with conventional genetic algorithms (GA) when applied to hard optimisation problems. In particular it examines the problem of selecting and implementing appropriate genetic operators in order to meet the validity constraints for constrained optimisation problems. The problem selected is the travelling salesman problem (TSP), a well known NP-hard problem. Following a review of conventional genetic algorithms, this thesis advocates the use of a repair technique for genetic algorithms: GeneRepair. We evaluate the effectiveness of this operator against a wide range of benchmark problems and compare these results with conventional genetic algorithm approaches. A comparison between GeneRepair and the conventional GA approaches is made in two forms: firstly a handcrafted approach compares GAs without repair against those using GeneRepair. A second automated approach is then presented. This meta-genetic algorithm examines different configurations of operators and parameters. Through the use of a cost/benefit (Quality-Time Tradeoff) function, the user can balance the computational effort against the quality of the solution and thus allow the user to specify exactly what the cost benefit point should be for the search. Results have identified the optimal configuration settings for solving selected TSP problems. These results show that GeneRepair when used consistently generates very good TSP solutions for 50, 70 and 100 city problems. GeneRepair assists in finding TSP solutions in an extremely efficient manner, in both time and number of evaluations required

Utilising restricted for-loops in genetic programming

Genetic programming is an approach that utilises the power of evolution to allow computers to evolve programs. While loops are natural components of most programming languages and appear in every reasonably-sized application, they are rarely used in genetic programming. The work is to investigate a number of restricted looping constructs to determine whether any significant benefits can be obtained in genetic programming. Possible benefits include: Solving problems which cannot be solved without loops, evolving smaller sized solutions which can be more easily understood by human programmers and solving existing problems quicker by using fewer evaluations. In this thesis, a number of explicit restricted loop formats were formulated and tested on the Santa Fe ant problem, a modified ant problem, a sorting problem, a visit-every-square problem and a difficult object classificat ion problem. The experimental results showed that these explicit loops can be successfully used in genetic programming. The evolutionary process can decide when, where and how to use them. Runs with these loops tended to generate smaller sized solutions in fewer evaluations. Solutions with loops were found to some problems that could not be solved without loops. The results and analysis of this thesis have established that there are significant benefits in using loops in genetic programming. Restricted loops can avoid the difficulties of evolving consistent programs and the infinite iterations problem. Researchers and other users of genetic programming should not be afraid of loops

How Fast Can We Play Tetris Greedily With Rectangular Pieces?

Consider a variant of Tetris played on a board of width $w$ and infinite height, where the pieces are axis-aligned rectangles of arbitrary integer dimensions, the pieces can only be moved before letting them drop, and a row does not disappear once it is full. Suppose we want to follow a greedy strategy: let each rectangle fall where it will end up the lowest given the current state of the board. To do so, we want a data structure which can always suggest a greedy move. In other words, we want a data structure which maintains a set of $O(n)$ rectangles, supports queries which return where to drop the rectangle, and updates which insert a rectangle dropped at a certain position and return the height of the highest point in the updated set of rectangles. We show via a reduction to the Multiphase problem [P\u{a}tra\c{s}cu, 2010] that on a board of width $w=\Theta(n)$, if the OMv conjecture [Henzinger et al., 2015] is true, then both operations cannot be supported in time $O(n^{1/2-\epsilon})$ simultaneously. The reduction also implies polynomial bounds from the 3-SUM conjecture and the APSP conjecture. On the other hand, we show that there is a data structure supporting both operations in $O(n^{1/2}\log^{3/2}n)$ time on boards of width $n^{O(1)}$, matching the lower bound up to a $n^{o(1)}$ factor.Comment: Correction of typos and other minor correction

Kernels of Mallows Models under the Hamming Distance for solving the Quadratic Assignment Problem

The Quadratic Assignment Problem (QAP) is a well-known permutation-based combinatorial optimization problem with real applications in industrial and logistics environments. Motivated by the challenge that this NP-hard problem represents, it has captured the attention of the optimization community for decades. As a result, a large number of algorithms have been proposed to tackle this problem. Among these, exact methods are only able to solve instances of size $n<40$. To overcome this limitation, many metaheuristic methods have been applied to the QAP. In this work, we follow this direction by approaching the QAP through Estimation of Distribution Algorithms (EDAs). Particularly, a non-parametric distance-based exponential probabilistic model is used. Based on the analysis of the characteristics of the QAP, and previous work in the area, we introduce Kernels of Mallows Model under the Hamming distance to the context of EDAs. Conducted experiments point out that the performance of the proposed algorithm in the QAP is superior to (i) the classical EDAs adapted to deal with the QAP, and also (ii) to the specific EDAs proposed in the literature to deal with permutation problems.Severo Ochoa SEV-2013-0323 TIN2016-78365-R PID2019-106453GAI00 SVP-2014-068574 TIN2017-82626-