Contents. Preface...VII

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1 Contents Preface...VII 1 An Overview of Evolutionary Computation Examples of Evolutionary Computation Predators Running Backward Wood-Burning Stoves Hyperspectral Data A Little Biology Problems Evolutionary Computation in Detail Representation Evolution and Coevolution A Simple Type of Evolutionary Computation Problems Genetic Programming Problems Designing Simple Evolutionary Algorithms Models of Evolution Problems Types of Crossover Problems Mutation Problems Population Size Problems A Nontrivial String Evolver Problems A Polymodal String Evolver Problems The Many Lives of Roulette Selection... 60

2 XVI Evolutionary Computation for Modeling and Optimization Problems Optimizing Real-Valued Functions The Basic Real Function Optimizer Problems Fitness Landscapes Problems Niche Specialization Problems Path Length: An Extended Example Problems Optimizing a Discrete-Valued Function: Crossing Numbers Problems Sunburn: Coevolving Strings Definition of the Sunburn Model Problems Implementing Sunburn Problems Discussion and Generalizations Problems Other Ways of Getting Burned Problems Small Neural Nets : Symbots Basic Symbot Description Problems Symbot Bodies and Worlds Problems Symbots with Neurons Problems PackSymbots Problems Evolving Finite State Automata Finite State Predictors Problems Prisoner s Dilemma I Prisoner s Dilemma Modeling the Real World Problems Other Games Problems...165

3 Contents XVII 7 Ordered Structures Evolving Permutations Problems The Traveling Salesman Problem Problems Packing Things Problems Costas Arrays Problems Plus-One-Recall-Store Overview of Genetic Programming Problems The PORS Language Problems Seeding Populations Problems Applying Advanced Techniques to PORS Problems Fitting to Data Classical Least Squares Fit Problems Simple Evolutionary Fit Problems Symbolic Regression Problems Automatically Defined Functions Problems Working in Several Dimensions Problems Introns and Bloat Problems Tartarus: Discrete Robotics The Tartarus Environment Problems Tartarus with Genetic Programming Problems Adding Memory to the GP language Problems Tartarus with GP Automata Genetic Operations on GP automata Problems Allocation of Fitness Trials...289

4 XVIII Evolutionary Computation for Modeling and Optimization Problems Evolving Logic Functions Artificial Neural Nets Problems Evolving Logic Functions Problems Selecting the Net Topology Problems GP Logics Problems ISAc List: Alternative Genetic Programming ISAc Lists: Basic Definitions Done? Generating ISAc Lists, Variation Operators Data Vectors and External Objects Problems Tartarus Revisited Problems More Virtual Robotics Problems Return of the String Evolver Problems Graph-Based Evolutionary Algorithms Basic Definitions and Tools Problems Simple Representations Problems More Complex Representations Problems Genetic Programming on Graphs Problems Cellular Encoding Shape Evolution Problems Cellular Encoding of Finite State Automata Problems Cellular Encoding of Graphs Problems Context Free Grammar Genetic Programming Problems...422

5 Contents XIX 15 Application to Bioinformatics Alignment of Transposon Insertion Sequences Problems PCR Primer Design Problems DNA Bar Codes Problems Visualizing DNA Evolvable Fractals Problems Glossary A Example Experiment Report B Probability Theory B.1 Basic Probability Theory B.1.1 Choosing Things and Binomial Probability B.1.2 Choosing Things to Count B.1.3 Two Useful Confidence Intervals B.2 Markov Chains C A Review of Calculus and Vectors C.1 Derivatives in One Variable C.2 Multivariate Derivatives C.3 Lamarckian Mutation with Gradients C.4 The Method of Least Squares D Combinatorial Graphs D.1 Terminology and Examples D.2 Coloring Graphs D.3 Distances in Graphs D.4 Traveling Salesman D.5 Drawings of Graphs References Index...559

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