A Comparison of Simulated Annealing and Genetic Algorithms for the Genome Mapping Problems


Book Description

The data used for the construction of genome maps is imperfect, therefore the mapping of a physically linear structure must take place in a very uneven feature space. As the number of genes to be ordered grows, it appears to be impractical to use exhaustive search techniques to find the optimal mapping. In this paper we compare genetic algorithms and simulated annealing, two methods that are widely believed to be well-suited to non-smooth feature spaces, and find that the genetic algorithm approach yields superior results. Here we present performance profiles of comparable implementations of both genetic algorithms and simulated annealing. We have translated the problem to a form comparable to the shortest-path problem and found that the ability of a genetic algorithm to combine different partial solutions seems to be responsible for its superiority over the simulated annealing method. This is because in the genome mapping problem, as in the Traveling Salesman Problem, good solutions tend to be rather sparse and because optimal subtours tend to be components of nearly optimal tours.













Masters Theses in the Pure and Applied Sciences


Book Description

Masters Theses in the Pure and Applied Sciences was first conceived, published, and disseminated by the Center for Information and Numerical Data Analysis and Synthesis (CINDAS)* at Purdue University in 1957, starting its coverage of theses with the academic year 1955. Beginning with Volume 13, the printing and dis semination phases of the activity were transferred to University Microfilms/Xerox of Ann Arbor, Michigan, with the thought that such an arrangement would be more beneficial to the academic and general scientific and technical community. After five years of this jOint undertaking we had concluded that it was in the interest of all concerned if the printing and distribution of the volumes were handled by an international publishing house to assure improved service and broader dissemination. Hence, starting with Volume 18, Masters Theses in the Pure and Applied Sciences has been disseminated on a worldwide basis by Plenum Publishing Corporation of New York, and in the same year the coverage was broadened to include Canadian universities. All back issues can also be ordered from Plenum. We have reported in Volume 40 (thesis year 1995) a total of 10,746 thesis titles from 19 Canadian and 144 United States universities. We are sure that this broader base for these titles reported will greatly enhance the value of this impor tant annual reference work. While Volume 40 reports theses submitted in 1995, on occasion, certain uni versities do report theses submitted in previous years but not reported at the time.




Genetic Algorithms with Python


Book Description

Get a hands-on introduction to machine learning with genetic algorithms using Python. Step-by-step tutorials build your skills from Hello World! to optimizing one genetic algorithm with another, and finally genetic programming; thus preparing you to apply genetic algorithms to problems in your own field of expertise. Genetic algorithms are one of the tools you can use to apply machine learning to finding good, sometimes even optimal, solutions to problems that have billions of potential solutions. This book gives you experience making genetic algorithms work for you, using easy-to-follow example projects that you can fall back upon when learning to use other machine learning tools and techniques. Each chapter is a step-by-step tutorial that helps to build your skills at using genetic algorithms to solve problems using Python. Python is a high-level, low ceremony and powerful language whose code can be easily understood even by entry-level programmers. If you have experience with another programming language then you should have no difficulty learning Python by induction. Contents A brief introduction to genetic algorithms Chapter 1: Hello World! - Guess a password given the number of correct letters in the guess. Build a mutation engine. Chapter 2: One Max Problem - Produce an array of bits where all are 1s. Expands the engine to work with any type of gene. Chapter 3: Sorted Numbers - Produce a sorted integer array. Demonstrates handling multiple fitness goals and constraints between genes. Chapter 4: The 8 Queens Puzzle - Find safe Queen positions on an 8x8 board and then expand to NxN. Demonstrates the difference between phenotype and genotype. Chapter 5: Graph Coloring - Color a map of the United States using only 4 colors. Introduces standard data sets and working with files. Also introduces using rules to work with gene constraints. Chapter 6: Card Problem - More gene constraints. Introduces custom mutation, memetic algorithms, and the sum-of-difference technique. Also demonstrates a chromosome where the way a gene is used depends on its position in the gene array. Chapter 7: Knights Problem - Find the minimum number of knights required to attack all positions on a board. Introduces custom genes and gene-array creation. Also demonstrates local minimums and maximums. Chapter 8: Magic Squares - Find squares where all the rows, columns and both diagonals of an NxN matrix have the same sum. Introduces simulated annealing. Chapter 9: Knapsack Problem - Optimize the content of a container for one or more variables. Introduces branch and bound and variable length chromosomes. Chapter 10: Solving Linear Equations - Find the solutions to linear equations with 2, 3 and 4 unknowns. Branch and bound variation. Reinforces genotype flexibility. Chapter 11: Generating Sudoku - A guided exercise in generating Sudoku puzzles. Chapter 12: Traveling Salesman Problem (TSP) - Find the optimal route to visit cities. Introduces crossover and a pool of parents. Chapter 13: Approximating Pi - Find the two 10-bit numbers whose dividend is closest to Pi. Introduces using one genetic algorithm to tune another. Chapter 14: Equation Generation - Find the shortest equation that produces a specific result using addition, subtraction, multiplication, etc. Introduces symbolic genetic programming. Chapter 15: The Lawnmower Problem - Generate a series of instructions that cause a lawnmower to cut a field of grass. Genetic programming with control structures, objects and automatically defined functions (ADFs). Chapter 16: Logic Circuits - Generate circuits that behave like basic gates, gate combinations and finally a 2-bit adder. Introduces tree nodes and hill climbing. Chapter 17: Regular Expressions - Find regular expressions that match wanted strings. Introduces chromosome repair and growth control. Chapter 18: Tic-tac-toe - Create rules for playing the game without losing. Introduces tournament selection.




The Practical Handbook of Genetic Algorithms


Book Description

The mathematics employed by genetic algorithms (GAs)are among the most exciting discoveries of the last few decades. But what exactly is a genetic algorithm? A genetic algorithm is a problem-solving method that uses genetics as its model of problem solving. It applies the rules of reproduction, gene crossover, and mutation to pseudo-organism







Simulated Annealing


Book Description

This book provides the readers with the knowledge of Simulated Annealing and its vast applications in the various branches of engineering. We encourage readers to explore the application of Simulated Annealing in their work for the task of optimization.




Simulated Annealing


Book Description

This book provides the readers with the knowledge of Simulated Annealing and its vast applications in the various branches of engineering. We encourage readers to explore the application of Simulated Annealing in their work for the task of optimization.