d(Tree)-by-dx : automatic and exact differentiation of genetic programming trees

Genetic programming (GP) has developed to the point where it is a credible candidate for the `black box' modeling of real systems. Wider application, however, could greatly benefit from its seamless embedding in conventional optimization schemes, which are most efficiently carried out using gradient-based methods. This paper describes the development of a method to automatically differentiate GP trees using a series of tree transformation rules; the resulting method can be applied an unlimited number of times to obtain higher derivatives of the function approximated by the original, trained GP tree. We demonstrate the utility of our method using a number of illustrative gradient-based optimizations that embed GP models

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

Quantifying the degree of self-nestedness of trees. Application to the structural analysis of plants

17 pagesInternational audienceIn this paper we are interested in the problem of approximating trees by trees with a particular self-nested structure. Self-nested trees are such that all their subtrees of a given height are isomorphic. We show that these trees present remarkable compression properties, with high compression rates. In order to measure how far a tree is from being a self-nested tree, we then study how to quantify the degree of self-nestedness of any tree. For this, we define a measure of the self-nestedness of a tree by constructing a self-nested tree that minimizes the distance of the original tree to the set of self-nested trees that embed the initial tree. We show that this measure can be computed in polynomial time and depict the corresponding algorithm. The distance to this nearest embedding self-nested tree (NEST) is then used to define compression coefficients that reflect the compressibility of a tree. To illustrate this approach, we then apply these notions to the analysis of plant branching structures. Based on a database of simulated theoretical plants in which different levels of noise have been introduced, we evaluate the method and show that the NESTs of such branching structures restore partly or completely the original, noiseless, branching structures. The whole approach is then applied to the analysis of a real plant (a rice panicle) whose topological structure was completely measured. We show that the NEST of this plant may be interpreted in biological terms and may be used to reveal important aspects of the plant growth

Constant optimization and feature standardization in multiobjective genetic programming

This paper extends the numerical tuning of tree constants in genetic programming (GP) to the multiobjective domain. Using ten real-world benchmark regression datasets and employing Bayesian comparison procedures, we first consider the effects of feature standardization (without constant tuning) and conclude that standardization generally produces lower test errors, but, contrary to other recently published work, we find or{blue}{a much less clear trend for} tree sizes. In addition, we consider the effects of constant tuning -- with and without feature standardization -- and observe that i) constant tuning invariably improves test error, and ii) usually decreases tree size. Combined with standardization, constant tuning produces the best test error results; tree sizes, however, are increased. We also examine the effects of applying constant tuning only once at the end a conventional GP run which turns out to be surprisingly promising. Finally, we consider the merits of using numerical procedures to tune tree constants and observe that for around half the datasets evolutionary search alone is superior whereas for the remaining half, parameter tuning is superior. We identify a number of open research questions that arise from this work

Analysis of DNA profiles of ash (Fraxinus excelsior L.) to provide evidence of illegal logging

The present work formed part of a research project supported by the General Directorate of State Forests (Grants BLP-333 and BLP-384). We gratefully acknowledge the Forest Guard staff from Śnieżka Forest District for their efficient cooperation. We also thank Małgorzata Gorzkowska from the Laboratory of Molecular Biology FRI Poland, who assisted with processing of plant material in the laboratory.Peer reviewedPublisher PD

Automated Feature Engineering for Deep Neural Networks with Genetic Programming

Feature engineering is a process that augments the feature vector of a machine learning model with calculated values that are designed to enhance the accuracy of a model’s predictions. Research has shown that the accuracy of models such as deep neural networks, support vector machines, and tree/forest-based algorithms sometimes benefit from feature engineering. Expressions that combine one or more of the original features usually create these engineered features. The choice of the exact structure of an engineered feature is dependent on the type of machine learning model in use. Previous research demonstrated that various model families benefit from different types of engineered feature. Random forests, gradient-boosting machines, or other tree-based models might not see the same accuracy gain that an engineered feature allowed neural networks, generalized linear models, or other dot-product based models to achieve on the same data set. This dissertation presents a genetic programming-based algorithm that automatically engineers features that increase the accuracy of deep neural networks for some data sets. For a genetic programming algorithm to be effective, it must prioritize the search space and efficiently evaluate what it finds. This dissertation algorithm faced a potential search space composed of all possible mathematical combinations of the original feature vector. Five experiments were designed to guide the search process to efficiently evolve good engineered features. The result of this dissertation is an automated feature engineering (AFE) algorithm that is computationally efficient, even though a neural network is used to evaluate each candidate feature. This approach gave the algorithm a greater opportunity to specifically target deep neural networks in its search for engineered features that improve accuracy. Finally, a sixth experiment empirically demonstrated the degree to which this algorithm improved the accuracy of neural networks on data sets augmented by the algorithm’s engineered features

Integration through genetic programming on heterogeneous systems.

Nowadays, numerous applications in various scientific fields require the integration of mathematical functions that, due to some of their characteristics, do not have an analytical expression for their antiderivative. These definite integrals are usually solved by numerical integration methods, which provide an approximation of the numerical value of the integral in the integration range. With this type of solutions, a higher precision of the approximation entails a longer computation time, being necessary a trade-off between both aspects. In this work we present a genetic programming algorithm which provides mathematical expressions that approximate the antiderivative of analytically non-integrable functions. Heterogeneous devices, GPU and multicore CPU, have also been used in the development of the system to accelerate the parts suitable for it. The advantage of obtaining these approximate antiderivatives is the reduction of the computation time necessary to calculate the definite integral of the functions of interest, reducing it to simply evaluating the expression at the beginning and the end of the integration range.<br /

SICLE: A high-throughput tool for extracting evolutionary relationships from phylogenetic trees

We present the phylogeny analysis software SICLE (Sister Clade Extractor), an easy-to-use, high- throughput tool to describe the nearest neighbors to a node of interest in a phylogenetic tree as well as the support value for the relationship. The application is a command line utility that can be embedded into a phylogenetic analysis pipeline or can be used as a subroutine within another C++ program. As a test case, we applied this new tool to the published phylome of Salinibacter ruber, a species of halophilic Bacteriodetes, identifying 13 unique sister relationships to S. ruber across the 4589 gene phylogenies. S. ruber grouped with bacteria, most often other Bacteriodetes, in the majority of phylogenies, but 91 phylogenies showed a branch-supported sister association between S. ruber and Archaea, an evolutionarily intriguing relationship indicative of horizontal gene transfer. This test case demonstrates how SICLE makes it possible to summarize the phylogenetic information produced by automated phylogenetic pipelines to rapidly identify and quantify the possible evolutionary relationships that merit further investigation. SICLE is available for free for noncommercial use at http://eebweb.arizona.edu/sicle/.Comment: 8 pages, 4 figures in journal submission forma

Computation Approaches for Continuous Reinforcement Learning Problems

Optimisation theory is at the heart of any control process, where we seek to control the behaviour of a system through a set of actions. Linear control problems have been extensively studied, and optimal control laws have been identified. But the world around us is highly non-linear and unpredictable. For these dynamic systems, which don’t possess the nice mathematical properties of the linear counterpart, the classic control theory breaks and other methods have to be employed. But nature thrives by optimising non-linear and over-complicated systems. Evolutionary Computing (EC) methods exploit nature’s way by imitating the evolution process and avoid to solve the control problem analytically. Reinforcement Learning (RL) from the other side regards the optimal control problem as a sequential one. In every discrete time step an action is applied. The transition of the system to a new state is accompanied by a sole numerical value, the “reward” that designate the quality of the control action. Even though the amount of feedback information is limited into a sole real number, the introduction of the Temporal Difference method made possible to have accurate predictions of the value-functions. This paved the way to optimise complex structures, like the Neural Networks, which are used to approximate the value functions. In this thesis we investigate the solution of continuous Reinforcement Learning control problems by EC methodologies. The accumulated reward of such problems throughout an episode suffices as information to formulate the required measure, fitness, in order to optimise a population of candidate solutions. Especially, we explore the limits of applicability of a specific branch of EC, that of Genetic Programming (GP). The evolving population in the GP case is comprised from individuals, which are immediately translated to mathematical functions, which can serve as a control law. The major contribution of this thesis is the proposed unification of these disparate Artificial Intelligence paradigms. The provided information from the systems are exploited by a step by step basis from the RL part of the proposed scheme and by an episodic basis from GP. This makes possible to augment the function set of the GP scheme with adaptable Neural Networks. In the quest to achieve stable behaviour of the RL part of the system a modification of the Actor-Critic algorithm has been implemented. Finally we successfully apply the GP method in multi-action control problems extending the spectrum of the problems that this method has been proved to solve. Also we investigated the capability of GP in relation to problems from the food industry. These type of problems exhibit also non-linearity and there is no definite model describing its behaviour