Sorting by weighted inversions considering length and symmetry

International audienceLarge-scale mutational events that occur when stretches of DNA sequence move throughout genomes are called genome rearrangements. In bacteria, inversions are one of the most frequently observed rearrangements. In some bacterial families, inversions are biased in favor of symmetry as shown by recent research. In addition, several results suggest that short segment inversions are more frequent in the evolution of microbial genomes. Despite the fact that symmetry and length of the reversed segments seem very important, they have not been considered together in any problem in the genome rearrangement field. Here, we define the problem of sorting genomes (or permutations) using inversions whose costs are assigned based on their lengths and asymmetries. We consider two formulations of the same problem depending on whether we know the orientation of the genes. Several procedures are presented and we assess these procedure performances on a large set of more than 4.4 × 10^9 permutations. The ideas presented in this paper provide insights to solve the problem and set the stage for a proper theoretical analysis

Sorting by Swaps with Noisy Comparisons

We study sorting of permutations by random swaps if each comparison gives the wrong result with some fixed probability $p<1/2$. We use this process as prototype for the behaviour of randomized, comparison-based optimization heuristics in the presence of noisy comparisons. As quality measure, we compute the expected fitness of the stationary distribution. To measure the runtime, we compute the minimal number of steps after which the average fitness approximates the expected fitness of the stationary distribution. We study the process where in each round a random pair of elements at distance at most $r$ are compared. We give theoretical results for the extreme cases $r=1$ and $r=n$, and experimental results for the intermediate cases. We find a trade-off between faster convergence (for large $r$) and better quality of the solution after convergence (for small $r$).Comment: An extended abstract of this paper has been presented at Genetic and Evolutionary Computation Conference (GECCO 2017

Computational Molecular Biology

Computational Biology is a fairly new subject that arose in response to the computational problems posed by the analysis and the processing of biomolecular sequence and structure data. The field was initiated in the late 60's and early 70's largely by pioneers working in the life sciences. Physicists and mathematicians entered the field in the 70's and 80's, while Computer Science became involved with the new biological problems in the late 1980's. Computational problems have gained further importance in molecular biology through the various genome projects which produce enormous amounts of data. For this bibliography we focus on those areas of computational molecular biology that involve discrete algorithms or discrete optimization. We thus neglect several other areas of computational molecular biology, like most of the literature on the protein folding problem, as well as databases for molecular and genetic data, and genetic mapping algorithms. Due to the availability of review papers and a bibliography this bibliography

A Hybrid Lehmer Code Genetic Algorithm and Its Application on Traveling Salesman Problems

Traveling Salesman Problems (TSP) is a widely studied combinatorial optimization problem. The goal of the TSP is to find a tour which begins in a specific city, visits each of the remaining cities once and returns to the initial cities such that the objective functions are optimized, typically involving minimizing functions like total distance traveled, total time used or total cost. Genetic algorithms were first proposed by John Holland (1975). It uses an iterative procedure to find the optimal solutions to optimization problems. This research proposed a hybrid Lehmer code Genetic Algorithm. To compensate for the weaknesses of traditional genetic algorithms in exploitation while not hampering its ability in exploration, this new genetic algorithm will combine genetic algorithm with 2-opt and non-sequential 3-opt heuristics. By using Lehmer code representation, the solutions created by crossover parent solutions are always feasible. The new algorithm was used to solve single objective and multi-objectives Traveling Salesman Problems. A non Pareto-based technique will be used to solve multi-objective TSPs. Specifically we will use the Target Vector Approach. In this research, we used the weighted Tchebycheff function with the ideal points as the reference points as the objective function to evaluate solutions, while the local search heuristics, the 2-opt and non-sequential 3-opt heuristics, were guided by a weighted sum function

CSM429: Abstract Geometric Crossover for the Permutation Representation

Abstract crossover and abstract mutation are representation-independent operators that are well-defined once a notion of distance over the solution space is defined. They were obtained as generalization of genetic operators for binary strings and real vectors. In this paper we explore how the abstract geometric framework applies to the permutation representation. This representation is challenging for various reasons: because of the inherent difference between permutations and the representations that inspired the abstraction; because the whole notion of geometry over permutation spaces radically departs from traditional geometries and it is almost unexplored mathematical territory; because the many notions of distance available and their subtle interconnections make it hard to see the right distance to use, if any; because the various available interpretations of permutations make ambiguous what a permutation represents, hence, how to treat it; because of the existence of various permutation-like representations that are incorrectly confused with permutations; and finally because of the existence of many mutation and recombination operators and their many variations for the same representation. This article shows that the application of our geometric framework naturally clarifies and unifies an important domain,the permutation representation and the related operators, in which there was little or no hope to find order. In addition the abstract geometric framework is used to improve the design of crossover operators for well-known problems naturally connected with the permutation representation

A quasi-Newton proximal splitting method

A new result in convex analysis on the calculation of proximity operators in certain scaled norms is derived. We describe efficient implementations of the proximity calculation for a useful class of functions; the implementations exploit the piece-wise linear nature of the dual problem. The second part of the paper applies the previous result to acceleration of convex minimization problems, and leads to an elegant quasi-Newton method. The optimization method compares favorably against state-of-the-art alternatives. The algorithm has extensive applications including signal processing, sparse recovery and machine learning and classification

Parameterized Complexity Analysis of Randomized Search Heuristics

This chapter compiles a number of results that apply the theory of parameterized algorithmics to the running-time analysis of randomized search heuristics such as evolutionary algorithms. The parameterized approach articulates the running time of algorithms solving combinatorial problems in finer detail than traditional approaches from classical complexity theory. We outline the main results and proof techniques for a collection of randomized search heuristics tasked to solve NP-hard combinatorial optimization problems such as finding a minimum vertex cover in a graph, finding a maximum leaf spanning tree in a graph, and the traveling salesperson problem.Comment: This is a preliminary version of a chapter in the book "Theory of Evolutionary Computation: Recent Developments in Discrete Optimization", edited by Benjamin Doerr and Frank Neumann, published by Springe