"Going back to our roots": second generation biocomputing

Researchers in the field of biocomputing have, for many years, successfully "harvested and exploited" the natural world for inspiration in developing systems that are robust, adaptable and capable of generating novel and even "creative" solutions to human-defined problems. However, in this position paper we argue that the time has now come for a reassessment of how we exploit biology to generate new computational systems. Previous solutions (the "first generation" of biocomputing techniques), whilst reasonably effective, are crude analogues of actual biological systems. We believe that a new, inherently inter-disciplinary approach is needed for the development of the emerging "second generation" of bio-inspired methods. This new modus operandi will require much closer interaction between the engineering and life sciences communities, as well as a bidirectional flow of concepts, applications and expertise. We support our argument by examining, in this new light, three existing areas of biocomputing (genetic programming, artificial immune systems and evolvable hardware), as well as an emerging area (natural genetic engineering) which may provide useful pointers as to the way forward.Comment: Submitted to the International Journal of Unconventional Computin

Unimodal optimization using a genetic-programming-based method with periodic boundary conditions

This article describes a new genetic-programming-based optimization method using a multi-gene approach along with a niching strategy and periodic domain constraints. The method is referred to as Niching MG-PMA, where MG refers to multi-gene and PMA to parameter mapping approach. Although it was designed to be a multimodal optimization method, recent tests have revealed its suitability for unimodal optimization. The definition of Niching MG-PMA is provided in a detailed fashion, along with an in-depth explanation of two novelties in our implementation: the feedback of initial parameters and the domain constraints using periodic boundary conditions. These ideas can be potentially useful for other optimization techniques. The method is tested on the basis of the CEC’2015 benchmark functions. Statistical analysis shows that Niching MG-PMA performs similarly to the winners of the competition even without any parametrization towards the benchmark, indicating that the method is robust and applicable to a wide range of problems

Automated Design of Metaheuristic Algorithms: A Survey

Metaheuristics have gained great success in academia and practice because their search logic can be applied to any problem with available solution representation, solution quality evaluation, and certain notions of locality. Manually designing metaheuristic algorithms for solving a target problem is criticized for being laborious, error-prone, and requiring intensive specialized knowledge. This gives rise to increasing interest in automated design of metaheuristic algorithms. With computing power to fully explore potential design choices, the automated design could reach and even surpass human-level design and could make high-performance algorithms accessible to a much wider range of researchers and practitioners. This paper presents a broad picture of automated design of metaheuristic algorithms, by conducting a survey on the common grounds and representative techniques in terms of design space, design strategies, performance evaluation strategies, and target problems in this field

A survey on low-thrust trajectory optimization approaches

In this paper, we provide a survey on available numerical approaches for solving low-thrust trajectory optimization problems. First, a general mathematical framework based on hybrid optimal control will be presented. This formulation and their elements, namely objective function, continuous and discrete state and controls, and discrete and continuous dynamics, will serve as a basis for discussion throughout the whole manuscript. Thereafter, solution approaches for classical continuous optimal control problems will be briefly introduced and their application to low-thrust trajectory optimization will be discussed. A special emphasis will be placed on the extension of the classical techniques to solve hybrid optimal control problems. Finally, an extensive review of traditional and state-of-the art methodologies and tools will be presented. They will be categorized regarding their solution approach, the objective function, the state variables, the dynamical model, and their application to planetocentric or interplanetary transfers

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

Evolutionary Algorithms

Evolutionary algorithms (EAs) are population-based metaheuristics, originally inspired by aspects of natural evolution. Modern varieties incorporate a broad mixture of search mechanisms, and tend to blend inspiration from nature with pragmatic engineering concerns; however, all EAs essentially operate by maintaining a population of potential solutions and in some way artificially 'evolving' that population over time. Particularly well-known categories of EAs include genetic algorithms (GAs), Genetic Programming (GP), and Evolution Strategies (ES). EAs have proven very successful in practical applications, particularly those requiring solutions to combinatorial problems. EAs are highly flexible and can be configured to address any optimization task, without the requirements for reformulation and/or simplification that would be needed for other techniques. However, this flexibility goes hand in hand with a cost: the tailoring of an EA's configuration and parameters, so as to provide robust performance for a given class of tasks, is often a complex and time-consuming process. This tailoring process is one of the many ongoing research areas associated with EAs.Comment: To appear in R. Marti, P. Pardalos, and M. Resende, eds., Handbook of Heuristics, Springe

Evolution-In-Materio: Solving Computational Problems Using Materials

The motivation behind the research is to show that evolutionary algorithms can exploit properties of materials to solve various computational problems without requiring a detailed understanding of such properties. This approach is referred to as evolution-in-materio. In this research, it has been shown that using a purpose-built hardware platform called Mecobo, it is possible to evolve voltages and signals applied to physical materials to solve a number of computational problems. Here it has been demonstrated for the first time that the evolution-in-materio method can be applied to function optimisation, machine learning classification, frequency classification, even parity and bin packing problems. This evolution-in-materio method has also been applied here to discriminate tones and control robots. The physical material used in each of these experiments is a mixture of single-walled carbon nanotubes and a polymer. This is the first time that such material has been used to solve computational problems. The results of all of these experiments indicate that evolution-in-materio has promise and further investigations would be fruitful. Other than the solutions regarding these computational problems, this thesis has also devised and investigated suitable input-output mappings and input signals that allow various computational problems to be solved using the Mecobo platform and the experimental material

Neuroevolution in Deep Neural Networks: Current Trends and Future Challenges

A variety of methods have been applied to the architectural configuration and learning or training of artificial deep neural networks (DNN). These methods play a crucial role in the success or failure of the DNN for most problems and applications. Evolutionary Algorithms (EAs) are gaining momentum as a computationally feasible method for the automated optimisation and training of DNNs. Neuroevolution is a term which describes these processes of automated configuration and training of DNNs using EAs. While many works exist in the literature, no comprehensive surveys currently exist focusing exclusively on the strengths and limitations of using neuroevolution approaches in DNNs. Prolonged absence of such surveys can lead to a disjointed and fragmented field preventing DNNs researchers potentially adopting neuroevolutionary methods in their own research, resulting in lost opportunities for improving performance and wider application within real-world deep learning problems. This paper presents a comprehensive survey, discussion and evaluation of the state-of-the-art works on using EAs for architectural configuration and training of DNNs. Based on this survey, the paper highlights the most pertinent current issues and challenges in neuroevolution and identifies multiple promising future research directions.Comment: 20 pages (double column), 2 figures, 3 tables, 157 reference