Speciation dynamics of an agent-based evolution model in phenotype space

This dissertation is an exploration of phase transition behavior and clustering of populations of organisms in an agent-based model of evolutionary dynamics. The agents in the model are organisms, described as branching-coalescing random walkers, which are characterized by their coordinates in a two-dimensional phenotype space. Neutral evolutionary conditions are assumed, such that no organism has a fitness advantage regardless of its phenotype location. Lineages of organisms evolve by limiting the maximum possible offspring distance from their parent(s) (mutability, which is the only heritable trait) along each coordinate in phenotype space. As mutability is varied, a non-equilibrium phase transition is shown to occur for populations reproducing by assortative mating and asexual fission. Furthermore, mutability is also shown to change the clustering behavior of populations. Random mating is shown to destroy both phase transition behavior and clustering. The phase transition behavior is characterized in the asexual fission case. By demonstrating that the populations near criticality collapse to universal scaling functions with appropriate critical exponents, this case is shown to belong to the directed percolation universality class. Finally, lineage behavior is explored for both organisms and clusters. The lineage lifetimes of the initial population of organisms are found to have a power-law probability density which scales with the correlation length exponent near critical mutability. The cluster centroid step-sizes obey a probability density function that is bimodal for all mutability values, and the average displays a linear dependence upon mutability in the supercritical range. Cluster lineage tree structures are shown to have Kingman\u27s coalescent universal tree structure at the directed percolation phase transition despite more complicated lineage structures. --Abstract, page iii

Social Evolution: New Horizons

Cooperation is a widespread natural phenomenon yet current evolutionary thinking is dominated by the paradigm of selfish competition. Recent advanced in many fronts of Biology and Non-linear Physics are helping to bring cooperation to its proper place. In this contribution, the most important controversies and open research avenues in the field of social evolution are reviewed. It is argued that a novel theory of social evolution must integrate the concepts of the science of Complex Systems with those of the Darwinian tradition. Current gene-centric approaches should be reviewed and com- plemented with evidence from multilevel phenomena (group selection), the constrains given by the non-linear nature of biological dynamical systems and the emergent nature of dissipative phenomena.Comment: 16 pages 5 figures, chapter in forthcoming open access book "Frontiers in Ecology, Evolution and Complexity" CopIt-arXives 2014, Mexic

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

Data Analysis Methods for Software Systems

Using statistics, econometrics, machine learning, and functional data analysis methods, we evaluate the consequences of the lockdown during the COVID-19 pandemics for wage inequality and unemployment. We deduce that these two indicators mostly reacted to the first lockdown from March till June 2020. Also, analysing wage inequality, we conduct analysis separately for males and females and different age groups.We noticed that young females were affected mostly by the lockdown.Nevertheless, all the groups reacted to the lockdown at some level

Neural Generative Models and Representation Learning for Information Retrieval

Information Retrieval (IR) concerns about the structure, analysis, organization, storage, and retrieval of information. Among different retrieval models proposed in the past decades, generative retrieval models, especially those under the statistical probabilistic framework, are one of the most popular techniques that have been widely applied to Information Retrieval problems. While they are famous for their well-grounded theory and good empirical performance in text retrieval, their applications in IR are often limited by their complexity and low extendability in the modeling of high-dimensional information. Recently, advances in deep learning techniques provide new opportunities for representation learning and generative models for information retrieval. In contrast to statistical models, neural models have much more flexibility because they model information and data correlation in latent spaces without explicitly relying on any prior knowledge. Previous studies on pattern recognition and natural language processing have shown that semantically meaningful representations of text, images, and many types of information can be acquired with neural models through supervised or unsupervised training. Nonetheless, the effectiveness of neural models for information retrieval is mostly unexplored. In this thesis, we study how to develop new generative models and representation learning frameworks with neural models for information retrieval. Specifically, our contributions include three main components: (1) Theoretical Analysis: We present the first theoretical analysis and adaptation of existing neural embedding models for ad-hoc retrieval tasks; (2) Design Practice: Based on our experience and knowledge, we show how to design an embedding-based neural generative model for practical information retrieval tasks such as personalized product search; And (3) Generic Framework: We further generalize our proposed neural generative framework for complicated heterogeneous information retrieval scenarios that concern text, images, knowledge entities, and their relationships. Empirical results show that the proposed neural generative framework can effectively learn information representations and construct retrieval models that outperform the state-of-the-art systems in a variety of IR tasks

Molecular Epidemiology and Evolution of Corynebacterium diphtheriae and Vibrio cholerae

Molecular Epidemiology and Evolution of Corynebacterium diphtheriae and Vibrio cholerae Robert C. Will The infectious diseases diphtheria and cholera affect thousands of people around the world every year, and are caused by the bacterial species Corynebacterium diphtheriae and Vibrio cholerae respectively. While the two pathogens appear quite different biologically, diphtheria and cholera do share key similarities, including the fact that both diseases are intrinsically linked with poverty, outbreaking rapidly in areas of social turmoil, and during both natural and man-made disasters. Both are also highly treatable and survivable with the right resources available, including antibiotics and antitoxins. Vaccines are also available against both causative agents, although the diphtheria toxoid vaccine is in much wider use than cholera vaccine. In this thesis I have used genomics to investigate the epidemiology and evolution of both pathogens in global and national settings. For C. diphtheriae, we assembled a large collection of sequenced genomes to investigate the evolutionary and population dynamics of the pathogen across the globe. We added a focus on India as the country with the highest number of reported cases in recent years. We identified multiple large phylogenetic clades of the species circulating across geography and time concurrently. Using this collection, we also identified the presence of antimicrobial resistance determinant genes in recently isolated C. diphtheriae. In addition, we categorised a series of variants of the diphtheria toxin gene tox from isolates around the world, several of which were non-synonymous and estimated to have an impact on the 3D structure of the toxin protein. In V. cholerae, we investigated the intriguing population and evolutionary dynamics of cholera in Ghana, presenting a picture of time-separated clades circulating around neighbouring countries in West Africa. We also highlight the increasing presence of AMR in West African V. cholerae, in line with other reports from the ongoing 7th Pandemic. Finally, we present preliminary analysis of a large V. cholerae O139 collection and highlight how rapid AMR development may have caused O139 to so effectively outcompete the existing O1 serogroup, before disappearing almost as quickly due to subsequent loss of AMR. Taken together, these results highlight how much there is still left to understand about both of diseases, which in many parts of the world are believed to be a problem of the past. This dearth of knowledge applies both to the vastly under-researched diphtheria and the more widely researched cholera