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From Nature to Natural Computing | |

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Introduction | |

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Motivation | |

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A Small Sample of Ideas | |

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The Philosophy of Natural Computing | |

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The Three Branches: A Brief Overview | |

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Computing Inspried by Nature | |

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The Simulation and Emulation of Nature in Computers | |

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Computing with Natural Materials | |

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When to Use Natural Computing Approaches | |

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Summary | |

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Questions | |

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References | |

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Conceptualization | |

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Introduction | |

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Natural Phenomena, Models, and Metaphors | |

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From Nature to Computing and Back Again | |

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General Concepts | |

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Individuals, Entities, and Agents | |

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Parallelism and Distributivity | |

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Interactivity | |

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Connectivity | |

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Stigmergy | |

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Adaptation | |

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Learning | |

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Evolution | |

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Feedback | |

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Positive Feedback | |

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Negative Feedback | |

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Self-Organization | |

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Characteristics of Self-Organization | |

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Alternatives to Self-Organization | |

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Complexity, Emergence, and Reductionism | |

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Complexity | |

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Emergence | |

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Reductionism | |

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Bottom-up vs. Top-down | |

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Bottom-Up | |

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Top-Down | |

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Determinism, Chaos, and Fractals | |

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Summary | |

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Exercises | |

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Questions | |

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Thought Exercise | |

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Projects and Challenges | |

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References | |

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Computing Inspired by Nature | |

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Evolutionary Computing | |

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Introduction | |

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Problem Solving as a Search Task | |

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Defining a Search Problem | |

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Hill Climbing and Simulated Annealing | |

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Hill Climbing | |

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Simulated Annealing | |

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Basic Principles of Statistical Thermodynamics | |

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The Simulated Annealing Algorithm | |

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From Statistical Thermodynamics to Computing | |

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Example of Application | |

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Evolutionary Biology | |

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On the Theory of Evolution | |

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Darwin's Dangerous Idea | |

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Basic Principles of Genetics | |

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Evolution as an Outcome of Genetic Variation Plus Selection | |

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A Classic Example of Evolution | |

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A Summary of Evolutionary Biology | |

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Evolutionary Computing | |

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Standard Evolutionary Algorithm | |

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Genetic Algorithms | |

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Roulette Wheel Selection | |

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Crossover | |

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Mutation | |

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Examples of Application | |

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A Step by Step Example: Pattern Recognition (Learning) | |

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Numerical Function Optimization | |

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Hill-Climbing, Simulated Annealing, and Genetic Algorithms | |

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The Other Main Evolutionary Algorithms | |

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Evolution Strategies | |

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Selection | |

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Crossover | |

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Mutation | |

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Evolutionary Programming | |

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Selection | |

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Mutation | |

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Genetic Programming | |

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Crossover | |

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Mutation | |

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Selected Applications from the Literature: A Brief Description | |

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ES: Engineering Design | |

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EP: Parameter Optimization | |

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GP: Pattern Classification | |

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From Evolutionary Biology to Computing | |

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Scope of Evolutionary Computing | |

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Summary | |

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The Blind Watchmaker | |

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Exercises | |

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Questions | |

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Computational Exercises | |

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Thought Exercises | |

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Projects and Challenges | |

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References | |

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Neurocomputing | |

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Introduction | |

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The Nervous System | |

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Levels of Organization in the Nervous System | |

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Neurons and Synapses | |

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Networks, Layers, and Maps | |

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Biological and Physical Basis of Learning and Memory | |

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Artificial Neural Networks | |

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Artificial Neurons | |

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The McCulloch and Pitts Neuron | |

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A Basic Integrate-and-Fire Neuron | |

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The Generic Neurocomputing Neuron | |

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Network Architectures | |

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Single-Layer Feedforward Networks | |

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Multi-Layer Feedforward Networks | |

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Recurrent Networks | |

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Learning Approaches | |

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Supervised Learning | |

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Unsupervised Learning | |

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Reinforcement Learning | |

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Typical Anns and Learning Algorithms | |

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Hebbian Learning | |

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Biological Basis of Hebbian Synaptic Modification | |

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Single-Layer Perceptron | |

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Linear Separability | |

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Simple Perceptron for Pattern Classification | |

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Multiple Output Perceptron for Pattern Classification | |

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Examples of Application | |

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Adaline, the LMS Algorithm, and Error Surfaces | |

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LMS Algorithm (Delta Rule) | |

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Error Surfaces | |

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Multi-Layer Perceptron | |

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The Backpropagation Learning Algorithm | |

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Universal Function Approximation | |

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Some Practical Aspects | |

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Biological Plausibility of Backpropagation | |

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Examples of Application | |

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Self-Organizing Maps | |

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Self-Organizing Map Learning Algorithm | |

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Biological Basis and Inspiration for the Self-Organizing Map | |

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Examples of Applications | |

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Discrete Hopfield Network | |

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Recurrent Neural Networks as Nonlinear Dynamical Systems | |

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Discrete Hopfield Network | |

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Spurious Attractors | |

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Example of Application | |

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From Natural to Artificial Neural Networks | |

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Scope of Neurocomputing | |

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Summary | |

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Exercises | |

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Questions | |

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Computational Exercises | |

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Thought Exercises | |

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Projects and Challenges | |

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References | |

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Swarm Intelligence | |

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Introduction | |

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Ant Colonies | |

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Ants at Work: How an Insect Society Is Organized | |

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Ant Foraging Behavior | |

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Stigmergy | |

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Ant Colony Optimization (ACO) | |

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The Simple Ant Colony Optimization Algorithm (S-ACO) | |

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General-Purpose Ant Colony Optimization Algorithm | |

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Selected Applications from the Literature: A Brief Description | |

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Scope of ACO Algorithms | |

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From Natural to Artificial Ants | |

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Clustering of Dead Bodies and Larval Sorting in Ant Colonies | |

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Stigmergy | |

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Ant Clustering Algorithm (ACA) | |

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The Standard Ant Clustering Algorithm (ACA) | |

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Selected Applications from the Literature: A Brief Description | |

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Scope of Ant Clustering Algorithms | |

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From Natural to Artificial Ants | |

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Summary of Swarm Systems Based on Social Insects | |

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Swarm Robotics | |

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Foraging for Food | |

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Clustering of Objects | |

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Collective Prey Retrieval | |

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Cooperative Box Pushing | |

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Recruitment of Nestmates | |

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Scope of Swarm Robotics | |

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Summary of Swarm Robotics | |

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Social Adaptation of Knowledge | |

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Particle Swarm | |

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Selected Applications from the Literature: A Brief Description | |

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Optimization of Neural Network Weights | |

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Numerical Function Optimization | |

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Scope of Particle Swarm Optimization | |

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From Social Systems to Particle Swarm | |

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Summary of Particle Swarm Optimization | |

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Summary | |

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Exercises | |

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Questions | |

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Computational Exercises | |

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Thought Exercises | |

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Projects and Challenges | |

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References | |

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Immunocomputing | |

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Introduction | |

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The Immune System | |

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Physiology and Main Components | |

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Pattern Recognition and Binding | |

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Adaptive Immune Response | |

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Adaptation via Clonal Selection | |

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Clonal Selection and Darwinian Evolution | |

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Self/Nonself Discrimination | |

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The Immune Network Theory | |

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Adaptation and Learning via Immune Network | |

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Danger Theory | |

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A Broader Picture | |

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Artificial Immune Systems | |

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Representation | |

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Evaluating Interactions | |

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Immune Algorithms | |

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Bone Marrow Models | |

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Selected Applications from the Literature: A Brief Description | |

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Evolution of the Genetic Encoding of Antibodies | |

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Antigenic Coverage and Evolution of Antibody Gene Libraries | |

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Generating Antibodies for Job Shop Scheduling | |

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Negative Selection Algorithms | |

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Binary Negative Selection Algorithm | |

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Real-Valued Negative Selection Algorithm | |

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Selected Applications from the Literature: A Brief Description | |

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Network Intrusion Detection | |

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Breast Cancer Diagnosis | |

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Clonal Selection and Affinity Maturation | |

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Forrest's Algorithm | |

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Clonalg | |

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Selected Applications from the Literature: A Brief Description | |

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Pattern Recognition | |

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Multimodal Function Optimization | |

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Artificial Immune Networks | |

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Continuous Immune Networks | |

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Discrete Immune Networks | |

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Selected Applications from the Literature: A Brief Description | |

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A Recommender System | |

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Data Compression and Clustering | |

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From Natural to Artificial Immune Systems | |

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Scope of Artificial Immune Systems | |

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Summary | |

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Exercises | |

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Questions | |

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Computational Exercises | |

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Thought Exercises | |

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Projects and Challenges | |

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References | |

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The Simulation and Emulation of Natural Phenomena in Computers | |

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Fractal Geometry of Nature | |

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Introduction | |

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The Fractal Geometry of Nature | |

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Self-Similarity | |

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Some Pioneering Fractals | |

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Dimension and Fractal Dimension | |

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Scope of Fractal Geometry | |

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Cellular Automata | |

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A Simple One-Dimensional Example | |

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Cellular Automata as Dynamical Systems | |

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Formal Definition | |

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Example of Application | |

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Fractal Patterns | |

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Scope of Cellular Automata | |

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L-Systems | |

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DOL-Systems | |

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Turtle Graphics | |

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Models of Plant Architecture | |

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Scope of L-systems | |

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Iterated Function Systems | |

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Iterated Function Systems (IFS) | |

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Deterministic Iterated Function System (DIFS) | |

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Random Iterated Function System (RIFS) | |

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Creating Fractals with IFS | |

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Self-Similarity Revisited | |

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Scope of IFS | |

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Fractional Brownian Motion | |

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Random Fractals in Nature and Brownian Motion | |

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Fractional Brownian Motion | |

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Scope of fBm | |

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Particle Systems | |

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Principles of Particle Systems | |

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Basic Model of Particle Systems | |

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Particle Generation | |

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Particle Attributes | |

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Particle Extinction | |

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Particle Dynamics | |

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Particle Rendering | |

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Pseudocode and Examples | |

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Scope of Particle Systems | |

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Evolving the Geometry of Nature | |

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Evolving Plant-Like Structures | |

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Scope of Evolutionary Geometry | |

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From Natural to Fractal Geometry | |

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Summary | |

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Exercises | |

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Questions | |

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Computational Exercises | |

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Thought Exercises | |

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Projects and Challenges | |

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References | |

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Artificial Life | |

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Introduction | |

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A Discussion about the Structure of the Chapter | |

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Concepts and Features of Artificial Life Systems | |

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Artificial Life and Computing Inspired by Nature | |

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Life and Artificial Organisms | |

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Artificial Life and Biology | |

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Models and Features of Computer-Based Alife | |

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Alife Systems as Complex (Adaptive) Systems | |

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Examples of Artificial Life Projects | |

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Flocks, Herds, and Schools | |

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Discussion and Applications | |

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Biomorphs | |

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Discussion and Applications | |

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Computer Viruses | |

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Discussion and Applications | |

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Synthesizing Emotional Behavior | |

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Discussion and Applications | |

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AIBO Robot | |

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Discussion and Applications | |

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Wasp Nest Building | |

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Discussion and Applications | |

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Creatures | |

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Discussion and Applications | |

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Artificial Fishes | |

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Discussion and Applications | |

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Turtles, Termites, and Traffic Jams | |

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Predator-Prey Interactions | |

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Termites | |

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Traffic Jams | |

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Slime-Mold | |

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Discussion and Applications | |

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Cellular Automata Simulations | |

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The Game of Life | |

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Langton's Loops | |

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CAFUN | |

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Framsticks | |

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Architecture of the Framsticks and Its Environment | |

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Evolving the Framsticks | |

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Discussion and Applications | |

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Scope of Artificial Life | |

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From Artificial Life to Life-as-We-Know-It | |

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Summary | |

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Exercises | |

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Questions | |

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Computational Exercises | |

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Thought Exercise | |

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Projects and Challenges | |

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References | |

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| |

Computing with New Natural Materials | |

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DNA Computing | |

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Introduction | |

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Motivation | |

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Basic Concepts from Molecular Biology | |

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The DNA Molecule | |

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Manipulating DNA | |

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Filtering Models | |

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Adleman's Experiment | |

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Discussion | |

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Lipton's Solution to the SAT Problem | |

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Discussion | |

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Test Tube Programming Language | |

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The Unrestricted DNA Model | |

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Examples of Application | |

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An Extension of the Unrestricted DNA Model | |

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The DNA Pascal | |

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Formal Models: A Brief Description | |

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Sticker Systems | |

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Splicing Systems | |

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Insertion/Deletion Systems | |

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The PAM Model | |

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Universal DNA Computers | |

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Scope of DNA Computing | |

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From Classical to DNA Computing | |

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Summary and Discussion | |

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Exercises | |

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Questions | |

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Computational Exercises | |

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Thought Exercises | |

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Projects and Challenges | |

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| |

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References | |

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| |

Quantum Computing | |

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Introduction | |

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Motivation | |

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Basic Concepts from Quantum Theory | |

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From Classical to Quantum Mechanics | |

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Wave-Particle Duality | |

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Double-Slit with Bullets | |

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Double-Slit with Water Waves | |

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Double-Slit with Electrons | |

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The Uncertainty Principle | |

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Some Remarks | |

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Principles from Quantum Mechanics | |

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Dirac Notation | |

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Quantum Superposition | |

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Tensor Products | |

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Entanglement | |

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Evolution (Dynamics) | |

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Measurement | |

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No-Cloning Theorem | |

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Quantum Information | |

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Bits and Quantum Bits (Qubits) | |

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Multiple Bits and Qubits | |

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Gates and Quantum Gates | |

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Generalizations of the Hadamard Gate | |

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Quantum Circuits | |

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Quantum Parallelism | |

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| |

Examples of Applications | |

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| |

Dense Coding | |

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| |

Quantum Teleportation | |

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| |

Universal Quantum Computers | |

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| |

Benioff's Computer | |

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| |

Feynman's Computer | |

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Deutsch's Computer | |

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Quantum Algorithms | |

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Deutsch-Jozsa Algorithm | |

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Simon's Algorithm | |

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Shor's Algorithm | |

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Quantum Fourier Transform | |

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Factorization | |

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Grover's Algorithm | |

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Physical Realizations of Quantum Computers: A Brief Description | |

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Ion Traps | |

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Cavity Quantum Electrodynamics (CQED) | |

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Nuclear Magnetic Resonance (NMR) | |

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Quantum Dots | |

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Scope of Quantum Computing | |

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From Classical to Quantum Computing | |

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Summary and Discussion | |

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Exercises | |

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Questions | |

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Exercises | |

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Thought Exercises | |

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Projects and Challenges | |

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References | |

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Afterwords | |

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New Prospects | |

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The Growth of Natural Computing | |

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Some Lessons from Natural Computing | |

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Artificial Intelligence and Natural Computing | |

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The Birth of Artificial Intelligence | |

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The Divorce Between AI and CI | |

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Natural Computing and the Other Nomenclatures | |

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Visions | |

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References | |

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Appendix A | |

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Glossary of Terms | |

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Appendix B | |

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Theoretical Background | |

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Linear Algebra | |

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Sets and Set Operations | |

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Sets | |

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Set Operations | |

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Vectors and Vector Spaces | |

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Scalar | |

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Vector | |

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Linear Vector Space | |

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Linear Vector Subspace | |

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Linear Variety | |

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Convex Set | |

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Linear Combinations, Spanning Sets, and Convex Combinations | |

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Linear Dependence and Independence | |

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Basis and Dimension of a Linear Vector Space | |

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Dot (Inner) Product | |

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Outer Product | |

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Norms, Projections, and Orthogonality | |

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Norms, Semi-Norms and Quasi-Norms | |

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Orthogonal and Orthonormal Vectors | |

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Projecting a Vector along a Given Direction | |

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Orthonormal Vectors Generated from Linearly Independent Vectors | |

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Matrices and Their Properties | |

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Matrix | |

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Basic Operations Involving Vectors and Matrices | |

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Transpose and Square Matrices | |

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Trace | |

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Range and Rank | |

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Symmetry | |

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Inversion | |

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Pseudo-inversion | |

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Cofactor | |

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Determinant | |

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Adjoint | |

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Singularity | |

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Nullity | |

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Eigenvalues and Eigenvectors | |

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Positivity | |

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Complex Numbers and Spaces | |

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Complex Numbers | |

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Complex Conjugate and Absolute Value | |

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Complex Plane | |

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Polar Coordinates | |

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Exponential Form | |

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Complex Matrices | |

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Special Complex Matrices: Self-Adjoint (Hermitian), Unitary | |

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Hilbert Spaces | |

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Tensor Products | |

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Statistics | |

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Elementary Concepts | |

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Population, Sample, Variables | |

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Branches of Statistics | |

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Probability | |

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Event and Sample Space | |

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Probability | |

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Conditional Probability | |

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Bayes Theorem | |

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Counting | |

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Discrete Random Variables | |

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Random Variable | |

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Discrete Random Variable | |

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Probability Distributions | |

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Summary and Association Measures | |

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Central Tendency and Dispersion Measures | |

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Association Measures | |

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Estimation and Sample Sizes | |

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Point and Interval Estimators | |

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Confidence Interval | |

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Theory of Computation and Complexity | |

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Production Systems and Grammars | |

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Universal Turing Machines | |

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Complexity Theory | |

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Other Concepts | |

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Optimization | |

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Logic of Propositions | |

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Theory of Nonlinear Dynamical Systems | |

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Graph Theory | |

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Data Clustering | |

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Affine Transformations | |

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Fourier Transforms | |

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Bibliography | |

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Appendix C | |

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A Quick Guide to the Literature | |

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Introduction | |

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Comments on Selected Bibliography | |

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Main (General) Journals | |

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Main Conferences | |

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Conceptualization | |

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Comments on Selected Bibliography | |

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Evolutionary Computing | |

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Comments on Selected Bibliography | |

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Specific Journals | |

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Specific Conferences | |

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Neurocomputing | |

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Comments on Selected Bibliography | |

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Specific Journals | |

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Specific Conferences | |

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Swarm Intelligence | |

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Comments on Selected Bibliography | |

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Specific Journals | |

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Specific Conferences | |

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Immunocomputing | |

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Comments on Selected Bibliography | |

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Specific Journals | |

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Specific Conferences | |

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Fractal Geometry of Nature | |

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Comments on Selected Bibliography | |

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Specific Journals | |

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Specific Conferences | |

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Artifical Life | |

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Comments on Selected Bibliography | |

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Specific Journals | |

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Specific Conferences | |

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DNA Computing | |

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Comments on Selected Bibliography | |

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Specific Journals | |

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Specific Conferences | |

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Quantum Computing | |

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Comments on Selected Bibliography | |

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Specific Journals | |

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Specific Conferences | |

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Index | |