A Study of Dynamic Populations in Geometric Semantic Genetic Programming

Farinati, D., Bakurov, I., & Vanneschi, L. (2023). A Study of Dynamic Populations in Geometric Semantic Genetic Programming. Information Sciences, 648(November), 1-21. [119513]. https://doi.org/10.1016/j.ins.2023.119513 --- This work was supported by national funds through FCT (Fundação para a Ciência e a Tecnologia), under the project - UIDB/04152/2020 - Centro de Investigação em Gestão de Informação (MagIC)/NOVA IMS.Allowing the population size to variate during the evolution can bring advantages to evolutionary algorithms (EAs), retaining computational effort during the evolution process. Dynamic populations use computational resources wisely in several types of EAs, including genetic programming. However, so far, a thorough study on the use of dynamic populations in Geometric Semantic Genetic Programming (GSGP) is missing. Still, GSGP is a resource-greedy algorithm, and the use of dynamic populations seems appropriate. This paper adapts algorithms to GSGP to manage dynamic populations that were successful for other types of EAs and introduces two novel algorithms. The novel algorithms exploit the concept of semantic neighbourhood. These methods are assessed and compared through a set of eight regression problems. The results indicate that the algorithms outperform standard GSGP, confirming the suitability of dynamic populations for GSGP. Interestingly, the novel algorithms that use semantic neighbourhood to manage variation in population size are particularly effective in generating robust models even for the most difficult of the studied test problems.publishersversionpublishe

"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

Search based software engineering: Trends, techniques and applications

© ACM, 2012. This is the author's version of the work. It is posted here by permission of ACM for your personal use. Not for redistribution. The definitive version is available from the link below.In the past five years there has been a dramatic increase in work on Search-Based Software Engineering (SBSE), an approach to Software Engineering (SE) in which Search-Based Optimization (SBO) algorithms are used to address problems in SE. SBSE has been applied to problems throughout the SE lifecycle, from requirements and project planning to maintenance and reengineering. The approach is attractive because it offers a suite of adaptive automated and semiautomated solutions in situations typified by large complex problem spaces with multiple competing and conflicting objectives. This article provides a review and classification of literature on SBSE. The work identifies research trends and relationships between the techniques applied and the applications to which they have been applied and highlights gaps in the literature and avenues for further research.EPSRC and E

Smart Grid Technologies in Europe: An Overview

The old electricity network infrastructure has proven to be inadequate, with respect to modern challenges such as alternative energy sources, electricity demand and energy saving policies. Moreover, Information and Communication Technologies (ICT) seem to have reached an adequate level of reliability and flexibility in order to support a new concept of electricity network—the smart grid. In this work, we will analyse the state-of-the-art of smart grids, in their technical, management, security, and optimization aspects. We will also provide a brief overview of the regulatory aspects involved in the development of a smart grid, mainly from the viewpoint of the European Unio

A Neurogenetic Algorithm Based on Rational Agents

Lately, a lot of research has been conducted on the automatic design of artificial neural networks (ADANNs) using evolutionary algorithms, in the so-called neuro-evolutive algorithms (NEAs). Many of the presented proposals are not biologically inspired and are not able to generate modular, hierarchical and recurrent neural structures, such as those often found in living beings capable of solving intricate survival problems. Bearing in mind the idea that a nervous system's design and organization is a constructive process carried out by genetic information encoded in DNA, this paper proposes a biologically inspired NEA that evolves ANNs using these ideas as computational design techniques. In order to do this, we propose a Lindenmayer System with memory that implements the principles of organization, modularity, repetition (multiple use of the same sub-structure), hierarchy (recursive composition of sub-structures), minimizing the scalability problem of other methods. In our method, the basic neural codification is integrated to a genetic algorithm (GA) that implements the constructive approach found in the evolutionary process, making it closest to biological processes. Thus, the proposed method is a decision-making (DM) process, the fitness function of the NEA rewards economical artificial neural networks (ANNs) that are easily implemented. In other words, the penalty approach implemented through the fitness function automatically rewards the economical ANNs with stronger generalization and extrapolation capacities. Our method was initially tested on a simple, but non-trivial, XOR problem. We also submit our method to two other problems of increasing complexity: time series prediction that represents consumer price index and prediction of the effect of a new drug on breast cancer. In most cases, our NEA outperformed the other methods, delivering the most accurate classification. These superior results are attributed to the improved effectiveness and efficiency of NEA in the decision-making process. The result is an optimized neural network architecture for solving classification problems

Regulatory logic of cellular diversity in the nervous system

During nervous system development, thousands of distinct cell types are generated and assembled into complex circuits that control all aspects of animal cognition and behavior. Understanding what these diverse cells are, how they are generated, and what they do in the context of circuits and behavior form the fundamental efforts of the field of neuroscience. In this thesis, I investigate how the genomic organization of regulatory elements informs specific patterns of gene expression in the nervous system. In particular, I examine how distinct combinations of transcription factors interpret information encoded in the genome to control global gene expression programs in a cell-type-specific manner. In Chapter Two, I describe the establishment of a developmentally inspired transcriptional programming system to generate spinal and cranial motor neurons directly from mouse embryonic stem cells. Programmed motor neurons acquire general characteristics that mirror their in vivo counterparts, providing a robust system for studying cell fate specification in the nervous system. Combinatorial expression of cell-type-specific programming factors informs context-dependent enhancer binding and acquisition of appropriate cell-type-specific molecular and functional properties. In Chapter Three, I take advantage of this robust, experimentally accessible system to probe the chromatin-level organization and regulatory principles controlling specificity of motor neuron gene expression programs. Motor neuron genes are controlled by multiple distantly distributed enhancer constellations stretched across large regulatory domains. Using this motor neuron specification model, I discovered a unique regulatory organization controlling gene expression in the nervous system, whereby neuronal genes are controlled from uniquely complex regulatory domains acting over large distances. In Chapter Four, I extrapolate on the insights gained from studying motor neurons at a single point in time to investigate the dynamics of the regulatory environment during neuronal maturation. We demonstrate that enhancers are highly dynamic even after postmitotic specification. The dynamic nature of enhancers is dependent on combinatorial binding with new transcriptional cofactors. Overall, my results suggest that neuronal gene expression programs within a single cell type are regulated in a highly dynamic fashion by a complex set of enhancers. I propose that during development the immense cellular complexity of the nervous system is established and maintained by correspondingly complex repertoire of enhancers

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

ArrayPlex: distributed, interactive and programmatic access to genome sequence, annotation, ontology, and analytical toolsets

ArrayPlex is a software package that centrally provides a large number of flexible toolsets useful for functional genomics