473 research outputs found
Improving the efficiency of Bayesian Network Based EDAs and their application in Bioinformatics
Estimation of distribution algorithms (EDAs) is a relatively new trend of stochastic optimizers which have received a lot of attention during last decade. In each generation, EDAs build probabilistic models of promising solutions of an optimization problem to guide the search process. New sets of solutions are obtained by sampling the corresponding probability distributions. Using this approach, EDAs are able to provide the user a set of models that reveals the dependencies between variables of the optimization problems while solving them. In order to solve a complex problem, it is necessary to use a probabilistic model which is able to capture the dependencies. Bayesian networks are usually used for modeling multiple dependencies between variables. Learning Bayesian networks, especially for large problems with high degree of dependencies among their variables is highly computationally expensive which makes it the bottleneck of EDAs. Therefore introducing efficient Bayesian learning algorithms in EDAs seems necessary in order to use them for large problems. In this dissertation, after comparing several Bayesian network learning algorithms, we propose an algorithm, called CMSS-BOA, which uses a recently introduced heuristic called max-min parent children (MMPC) in order to constrain the model search space. This algorithm does not consider a fixed and small upper bound on the order of interaction between variables and is able solve problems with large numbers of variables efficiently. We compare the efficiency of CMSS-BOA with the standard Bayesian network based EDA for solving several benchmark problems and finally we use it to build a predictor for predicting the glycation sites in mammalian proteins
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Combinatorial optimization and metaheuristics
Today, combinatorial optimization is one of the youngest and most active areas of discrete mathematics. It is a branch of optimization in applied mathematics and computer science, related to operational research, algorithm theory and computational complexity theory. It sits at the intersection of several fields, including artificial intelligence, mathematics and software engineering. Its increasing interest arises for the fact that a large number of scientific and industrial problems can be formulated as abstract combinatorial optimization problems, through graphs and/or (integer) linear programs. Some of these problems have polynomial-time (“efficient”) algorithms, while most of them are NP-hard, i.e. it is not proved that they can be solved in polynomial-time. Mainly, it means that it is not possible to guarantee that an exact solution to the problem can be found and one has to settle for an approximate solution with known performance guarantees. Indeed, the goal of approximate methods is to find “quickly” (reasonable run-times), with “high” probability, provable “good” solutions (low error from the real optimal solution). In the last 20 years, a new kind of algorithm commonly called metaheuristics have emerged in this class, which basically try to combine heuristics in high level frameworks aimed at efficiently and effectively exploring the search space. This report briefly outlines the components, concepts, advantages and disadvantages of different metaheuristic approaches from a conceptual point of view, in order to analyze their similarities and differences. The two very significant forces of intensification and diversification, that mainly determine the behavior of a metaheuristic, will be pointed out. The report concludes by exploring the importance of hybridization and integration methods
Adaptive Estimation of Distribution Algorithms for Low-Thrust Trajectory Optimization
A direct adaptive scheme is presented as an alternative approach for minimum-fuel low-thrust trajectory design in non-coplanar orbit transfers, utilizing fitness landscape analysis (FLA). Spacecraft dynamics is modeled with respect to modified equinoctial elements, considering orbital perturbations. Taking into account the timings of thrust arcs, the discretization nodes for thrust profile, and the solution of multi-impulse orbit transfer, a constrained continuous optimization problem is formed for low-thrust orbital maneuver. An adaptive method within the framework of Estimation of Distribution Algorithms (EDAs) is proposed, which aims at conserving feasibility of the solutions within the search process. Several problem identifiers for low-thrust trajectory optimization are introduced, and the complexity of the solution domain is analyzed by evaluating the landscape feature of the search space via FLA. Two adaptive operators are proposed, which control the search process based on the need for exploration and exploitation of the search domain to achieve optimal transfers. The adaptive operators are implemented in the presented EDA and several perturbed and non-perturbed orbit transfer problems are solved. Results confirm the effectiveness and reliability of the proposed approach in finding optimal low-thrust transfer trajectories.BEAZ Bizkaia, 3/12/DP/2021/00150;
SPRI Group, Ekintzaile Program EK-00112-202
An overview of population-based algorithms for multi-objective optimisation
In this work we present an overview of the most prominent population-based algorithms and the methodologies used to extend them to multiple objective problems. Although not exact in the mathematical sense, it has long been recognised that population-based multi-objective optimisation techniques for real-world applications are immensely valuable and versatile. These techniques are usually employed when exact optimisation methods are not easily applicable or simply when, due to sheer complexity, such techniques could potentially be very costly. Another advantage is that since a population of decision vectors is considered in each generation these algorithms are implicitly parallelisable and can generate an approximation of the entire Pareto front at each iteration. A critique of their capabilities is also provided
On the application of estimation of distribution algorithms to multi-marker tagging SNP selection
This paper presents an algorithm for the automatic selection of a
minimal subset of tagging single nucleotide polymorphisms (SNPs) using an estimation of distribution algorithm (EDA). The EDA stochastically searches the constrained space of possible feasible solutions and takes
advantage of the underlying topological structure defined by the SNP correlations to model the problem interactions. The algorithm is evaluated
across the HapMap reference panel data sets. The introduced algorithm
is effective for the identification of minimal multi-marker SNP sets, which
considerably reduce the dimension of the tagging SNP set in comparison
with single-marker sets. New reduced tagging sets are obtained for all the
HapMap SNP regions considered. We also show that the information extracted from the interaction graph representing the correlations between
the SNPs can help to improve the efficiency of the optimization algorithm.
keywords: SNPs, tagging SNP selection, multi-marker selection, estimation of distribution algorithms, HapMap
A Field Guide to Genetic Programming
xiv, 233 p. : il. ; 23 cm.Libro ElectrĂłnicoA 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
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
A new Taxonomy of Continuous Global Optimization Algorithms
Surrogate-based optimization, nature-inspired metaheuristics, and hybrid
combinations have become state of the art in algorithm design for solving
real-world optimization problems. Still, it is difficult for practitioners to
get an overview that explains their advantages in comparison to a large number
of available methods in the scope of optimization. Available taxonomies lack
the embedding of current approaches in the larger context of this broad field.
This article presents a taxonomy of the field, which explores and matches
algorithm strategies by extracting similarities and differences in their search
strategies. A particular focus lies on algorithms using surrogates,
nature-inspired designs, and those created by design optimization. The
extracted features of components or operators allow us to create a set of
classification indicators to distinguish between a small number of classes. The
features allow a deeper understanding of components of the search strategies
and further indicate the close connections between the different algorithm
designs. We present intuitive analogies to explain the basic principles of the
search algorithms, particularly useful for novices in this research field.
Furthermore, this taxonomy allows recommendations for the applicability of the
corresponding algorithms.Comment: 35 pages total, 28 written pages, 4 figures, 2019 Reworked Versio
Noisy combinatorial optimisation with evolutionary algorithms
The determination of the efficient evolutionary optimisation approaches in solving noisy combinatorial problems is the main focus in this research. Initially, we present an empirical study of a range of evolutionary algorithms applied to various noisy combinatorial optimisation problems. There are four sets of experiments. The first looks at several toy problems, such as OneMax and other linear problems. We find that Univariate Marginal Distribution Algorithm (UMDA) and the Paired-Crossover Evolutionary Algorithm (PCEA) are the only ones able to cope robustly with noise, within a reasonable fixed time budget. In the second stage, UMDA and PCEA are then tested on more complex noisy problems: SubsetSum, Knapsack and SetCover. Both perform well under increasing levels of noise, with UMDA being the better of the two. In the third stage, we consider two noisy multi-objective problems (CountingOnesCountingZeros and a multi-objective formulation of SetCover). We compare several adaptations of UMDA for multi-objective problems with the Simple Evolutionary Multi-objective Optimiser (SEMO) and NSGA-II. In the last stage of empirical analysis, a realistic problem of the path planning for the ground surveillance with Unmanned Aerial Vehicles is considered. We conclude that UMDA, and its variants, can be highly effective on a variety of noisy combinatorial optimisation, outperforming many other evolutionary algorithms.
Next, we study the use of voting mechanisms in populations, and introduce a new Voting algorithm which can solve OneMax and Jump in O(n log n), even for gaps as large as O(n). More significantly, the algorithm solves OneMax with added posterior noise in O(n log n), when the variance of the noise distribution is sigma = O(n) and in O(sigma log n) when the noise variance is greater than this. We assume only that the noise distribution has finite mean and variance and (for the larger noise case) that it is unimodal. Building upon this promising performance, we consider other noise models prevalent in optimisation and learning and show that the Voting algorithm has efficient performance in solving OneMax in presence of these noise variants. We also examine the performance on arbitrary linear and monotonic functions. The Voting algorithm fails on LeadingOnes but we give a variant which can solve the problem in O(n log n). We empirically study the use of voting in population based algorithms (UMDA, PCEA and cGA) and show that this can be effective for large population sizes
Cardinality constraints and dimensionality reduction in optimization problems
Tesis doctoral inédita. Universidad Autónoma de Madrid, Escuela Politécnica Superior, junio de 201
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