Migrating Individuals and Probabilistic Models on DEDAS: a Comparison on Continuous Functions

One of the most promising areas in which probabilistic graphical models have shown an incipient activity is the field of heuristic optimization and, in particular, in the Estimation of Distribution Algorithms (EDAs). EDAs constitute a well-known family of Evolutionary Computation techniques, similar to Genetic Algorithms. Due to their inherent parallelism, different research lines have been studied trying to improve EDAs from the point of view of execution time and/or accuracy. Among these proposals, we focus on the so-called island-based models. This approach defines several islands (EDA instances) running independently and exchanging information with a given frequency. The information sent by the islands can be a set of individuals or a probabilistic model. This paper presents a comparative study of both information exchanging techniques for a univariate EDA (U M DAg) over a wide set of parameters and problems –the standard benchmark developed for the IEEE Workshop on Evolutionary Algorithms and other Metaheuristics for Continuous Optimization Problems of the ISDA 2009 Conference. The study concludes that the configurations based on migrating individuals obtain better result

Distributed Estimation of Distribution Algorithms for continuous optimization: how does the exchanged information influence their behavior?

One of the most promising areas in which probabilistic graphical models have shown an incipient activity is the field of heuristic optimization and, in particular, in Estimation of Distribution Algorithms. Due to their inherent parallelism, different research lines have been studied trying to improve Estimation of Distribution Algorithms from the point of view of execution time and/or accuracy. Among these proposals, we focus on the so-called distributed or island-based models. This approach defines several islands (algorithms instances) running independently and exchanging information with a given frequency. The information sent by the islands can be either a set of individuals or a probabilistic model. This paper presents a comparative study for a distributed univariate Estimation of Distribution Algorithm and a multivariate version, paying special attention to the comparison of two alternative methods for exchanging information, over a wide set of parameters and problems ? the standard benchmark developed for the IEEE Workshop on Evolutionary Algorithms and other Metaheuristics for Continuous Optimization Problems of the ISDA 2009 Conference. Several analyses from different points of view have been conducted to analyze both the influence of the parameters and the relationships between them including a characterization of the configurations according to their behavior on the proposed benchmark

A new initialization procedure for the distributed estimation of distribution algorithms

Estimation of distribution algorithms (EDAs) are one of the most promising paradigms in today’s evolutionary computation. In this field, there has been an incipient activity in the so-called parallel estimation of distribution algorithms (pEDAs). One of these approaches is the distributed estimation of distribution algorithms (dEDAs). This paper introduces a new initialization mechanism for each of the populations of the islands based on the Voronoi cells. To analyze the results, a series of different experiments using the benchmark suite for the special session on Real-parameter Optimization of the IEEE CEC 2005 conference has been carried out. The results obtained suggest that the Voronoi initialization method considerably improves the performance obtained from a traditional uniform initialization

Constrained Optimization with Evolutionary Algorithms: A Comprehensive Review

Global optimization is an essential part of any kind of system. Various algorithms have been proposed that try to imitate the learning and problem solving abilities of the nature up to certain level. The main idea of all nature-inspired algorithms is to generate an interconnected network of individuals, a population. Although most of unconstrained optimization problems can be easily handled with Evolutionary Algorithms (EA), constrained optimization problems (COPs) are very complex. In this paper, a comprehensive literature review will be presented which summarizes the constraint handling techniques for COP

Cooperative Models of Particle Swarm Optimizers

Particle Swarm Optimization (PSO) is one of the most effFective optimization tools, which emerged in the last decade. Although, the original aim was to simulate the behavior of a group of birds or a school of fish looking for food, it was quickly realized that it could be applied in optimization problems. Different directions have been taken to analyze the PSO behavior as well as improving its performance. One approach is the introduction of the concept of cooperation. This thesis focuses on studying this concept in PSO by investigating the different design decisions that influence the cooperative PSO models' performance and introducing new approaches for information exchange. Firstly, a comprehensive survey of all the cooperative PSO models proposed in the literature is compiled and a definition of what is meant by a cooperative PSO model is introduced. A taxonomy for classifying the different surveyed cooperative PSO models is given. This taxonomy classifies the cooperative models based on two different aspects: the approach the model uses for decomposing the problem search space and the method used for placing the particles into the different cooperating swarms. The taxonomy helps in gathering all the proposed models under one roof and understanding the similarities and differences between these models. Secondly, a number of parameters that control the performance of cooperative PSO models are identified. These parameters give answers to the four questions: Which information to share? When to share it? Whom to share it with? and What to do with it? A complete empirical study is conducted on one of the cooperative PSO models in order to understand how the performance changes under the influence of these parameters. Thirdly, a new heterogeneous cooperative PSO model is proposed, which is based on the exchange of probability models rather than the classical migration of particles. The model uses two swarms that combine the ideas of PSO and Estimation of Distribution Algorithms (EDAs) and is considered heterogeneous since the cooperating swarms use different approaches to sample the search space. The model is tested using different PSO models to ensure that the performance is robust against changing the underlying population topology. The experiments show that the model is able to produce better results than its components in many cases. The model also proves to be highly competitive when compared to a number of state-of-the-art cooperative PSO algorithms. Finally, two different versions of the PSO algorithm are applied in the FPGA placement problem. One version is applied entirely in the discrete domain, which is the first attempt to solve this problem in this domain using a discrete PSO (DPSO). Another version is implemented in the continuous domain. The PSO algorithms are applied to several well-known FPGA benchmark problems with increasing dimensionality. The results are compared to those obtained by the academic Versatile Place and Route (VPR) placement tool, which is based on Simulated Annealing (SA). The results show that these methods are competitive for small and medium-sized problems. For higher-sized problems, the methods provide very close results. The work also proposes the use of different cooperative PSO approaches using the two versions and their performances are compared to the single swarm performance

Improvement and evaluation of the mesoscale meteorological model MM5 for air-quality applications in Southern California and the San Joaquin Valley: Final Report

The objective of the Penn State University (PSU) part of the study was to investigate the MM5's ability to simulate wintertime fog in the San Joaquin Valley (SJV) and summertime sea breeze flows in the South Coast Air Basin (SoCAB). For the SJV work the MM5 was configured with four nested grid and an advanced turbulence sub-model. Applied to the event of 7-12 December 1995, observed during the IMS-95 program, the model's innermost domain used 40 vertical layers and a 4-km mesh. Several experiments were performed to improve the turbulence sub-model for saturated conditions and to provide more accurate initial conditions for soil temperature and moisture. Results showed the MM5 correctly predicted the type of visibility obscuration (fog, haze, status or clear) in 14 out of the 18 events. For depth was estimated by the MM5 with a mean absolute error of only 92 m and a mean error of -41 m. Mean errors for both the surface temperature and dew point were within +1C, while the mean absolute errors were ~1.5-2.0 C. As a consequence, the mean error for dew-point depression is very small. Thus, the MM5 was shown to simulate fog and haze in the SJV with considerable accuracy. Extensions of the turbulence sub-model to include saturation effects and the specification of accurate soil temperature and moisture were important for simulating fog characteristics in the case. Additionally, MM5 was able to simulate the light and variable winds in the Sacramento and San Joaquin Valleys that prevailed during this event. Moreover, the winds responded quite well to the slowly changing synoptic-scale weather, as well, as confirmed by the observations. the objective for the San Jose State University (SJSU) work included use of SCOS97 data and MM5 simulations to understand meteorological factors in the formation of high ozone concentrations during 4-7 August 1997. Meteorological data for the case study included observations at 110 SCOS97 surface sites and upper air measurements from 12 rawinsonde and 26 RWP/RASS profilers. the MM5 version contained the PSU Marine Boundary Layer Initialization (MBLI) scheme, quadruple nested grids (horizontal resolutions of 135, 45, 15, and 5 km), 30 vertical layers, minimum sigma level of 46 m, USGS global land-use, GDAS global gridded model analyses and SSTs, analysis nudging, observational nudging, force-restore surface temperature, 1.5 order TKE, one-way continuous nesting, and a MAPS statistical evaluation. Analysis showed the ozone episode resulting from a unique combination of large-scale upper level synoptic forcings that included a weak local coastal 700 mb anticyclone. Its movement around SoCAB rotated the upper level synoptic background flow from its normal westerly onshore direction to a less common offshore easterly flow during the nighttime period preceding the episode. The resulting easterly upper level synoptic background winds influenced surface flow direction at inland sites, so that a surface frontal convergence zone resulted where the easterly flow met the westerly onshore sea breeze flow. The maximum inland penetration of the convergence zone was about to the San Gabriel Mountain peaks, the location of daytime maximum ozone-episode concentrations. The current MM5 simulations reproduced the main qualitative features of the evolution of the diurnal sea breeze cycle in the SoCAB with reasonable accuracy. The position of the sea breeze front during its daytime inland penetration and nighttime retreat could be determined from the simulated wind fields. the accuracy of predicted MM5 surface winds and temperatures over SoCAB were improved by the modifications of its deep-soil temperatures, interpolation of predicted temperatures and winds to SCOS97 observational levels, use of updated urban land-use patterns, and use of corrected input values for ocean and urban surface roughness parameter values.Prepared for the California Air Resources Board and California Environmental Protection AgencySJSU Foundation Subcontract no. 22-1505-7384Approved for public release; distribution is unlimited

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

Bayesian network structure learning using characteristic properties of permutation representations with applications to prostate cancer treatment.

Over the last decades, Bayesian Networks (BNs) have become an increasingly popular technique to model data under presence of uncertainty. BNs are probabilistic models that represent relationships between variables by means of a node structure and a set of parameters. Learning efficiently the structure that models a particular dataset is a NP-hard task that requires substantial computational efforts to be successful. Although there exist many families of techniques for this purpose, this thesis focuses on the study and improvement of search and score methods such as Evolutionary Algorithms (EAs). In the domain of BN structure learning, previous work has investigated the use of permutations to represent variable orderings within EAs. In this thesis, the characteristic properties of permutation representations are analysed and used in order to enhance BN structure learning. The thesis assesses well-established algorithms to provide a detailed analysis of the difficulty of learning BN structures using permutation representations. Using selected benchmarks, rugged and plateaued fitness landscapes are identified that result in a loss of population diversity throughout the search. The thesis proposes two approaches to handle the loss of diversity. First, the benefits of introducing the Island Model (IM) paradigm are studied, showing that diversity loss can be significantly reduced. Second, a novel agent-based metaheuristic is presented in which evolution is based on the use of several mutation operators and the definition of a distance metric in permutation spaces. The latter approach shows that diversity can be maintained throughout the search while exploring efficiently the solution space. In addition, the use of IM is investigated in the context of distributed data, a common property of real-world problems. Experiments prove that privacy can be preserved while learning BNs of high quality. Finally, using UK-wide data related to prostate cancer patients, the thesis assesses the general suitability of BNs alongside the proposed learning approaches for medical data modeling. Following comparisons with tools currently used in clinical settings and with alternative classifiers, it is shown that BNs can improve the predictive power of prostate cancer staging tools, a major concern in the field of urology

Variational Autoencoder Based Estimation Of Distribution Algorithms And Applications To Individual Based Ecosystem Modeling Using EcoSim

Individual based modeling provides a bottom up approach wherein interactions give rise to high-level phenomena in patterns equivalent to those found in nature. This method generates an immense amount of data through artificial simulation and can be made tractable by machine learning where multidimensional data is optimized and transformed. Using individual based modeling platform known as EcoSim, we modeled the abilities of elitist sexual selection and communication of fear. Data received from these experiments was reduced in dimension through use of a novel algorithm proposed by us: Variational Autoencoder based Estimation of Distribution Algorithms with Population Queue and Adaptive Variance Scaling (VAE-EDA-Q AVS). We constructed a novel Estimation of Distribution Algorithm (EDA) by extending generative models known as variational autoencoders (VAE). VAE-EDA-Q, proposed by us, smooths the data generation process using an iteratively updated queue (Q) of populations. Adaptive Variance Scaling (AVS) dynamically updates the variance at which models are sampled based on fitness. The combination of VAE-EDA-Q with AVS demonstrates high computational efficiency and requires few fitness evaluations. We extended VAE-EDA-Q AVS to act as a feature reducing wrapper method in conjunction with C4.5 Decision trees to reduce the dimensionality of data. The relationship between sexual selection, random selection, and speciation is a contested topic. Supporting evidence suggests sexual selection to drive speciation. Opposing evidence contends either a negative or absence of correlation to exist. We utilized EcoSim to model elitist and random mate selection. Our results demonstrated a significantly lower speciation rate, a significantly lower extinction rate, and a significantly higher turnover rate for sexual selection groups. Species diversification was found to display no significant difference. The relationship between communication and foraging behavior similarly features opposing hypotheses in claim of both increases and decreases of foraging behavior in response to alarm communication. Through modeling with EcoSim, we found alarm communication to decrease foraging activity in most cases, yet gradually increase foraging activity in some other cases. Furthermore, we found both outcomes resulting from alarm communication to increase fitness as compared to non-communication