A genetic ensemble approach for gene-gene interaction identification

<p>Abstract</p> <p>Background</p> <p>It has now become clear that gene-gene interactions and gene-environment interactions are ubiquitous and fundamental mechanisms for the development of complex diseases. Though a considerable effort has been put into developing statistical models and algorithmic strategies for identifying such interactions, the accurate identification of those genetic interactions has been proven to be very challenging.</p> <p>Methods</p> <p>In this paper, we propose a new approach for identifying such gene-gene and gene-environment interactions underlying complex diseases. This is a hybrid algorithm and it combines genetic algorithm (GA) and an ensemble of classifiers (called genetic ensemble). Using this approach, the original problem of SNP interaction identification is converted into a data mining problem of combinatorial feature selection. By collecting various single nucleotide polymorphisms (SNP) subsets as well as environmental factors generated in multiple GA runs, patterns of gene-gene and gene-environment interactions can be extracted using a simple combinatorial ranking method. Also considered in this study is the idea of combining identification results obtained from multiple algorithms. A novel formula based on pairwise <it>double fault </it>is designed to quantify the degree of complementarity.</p> <p>Conclusions</p> <p>Our simulation study demonstrates that the proposed genetic ensemble algorithm has comparable identification power to Multifactor Dimensionality Reduction (MDR) and is slightly better than Polymorphism Interaction Analysis (PIA), which are the two most popular methods for gene-gene interaction identification. More importantly, the identification results generated by using our genetic ensemble algorithm are highly complementary to those obtained by PIA and MDR. Experimental results from our simulation studies and real world data application also confirm the effectiveness of the proposed genetic ensemble algorithm, as well as the potential benefits of combining identification results from different algorithms.</p

Understanding Algorithm Performance on an Oversubscribed Scheduling Application

The best performing algorithms for a particular oversubscribed scheduling application, Air Force Satellite Control Network (AFSCN) scheduling, appear to have little in common. Yet, through careful experimentation and modeling of performance in real problem instances, we can relate characteristics of the best algorithms to characteristics of the application. In particular, we find that plateaus dominate the search spaces (thus favoring algorithms that make larger changes to solutions) and that some randomization in exploration is critical to good performance (due to the lack of gradient information on the plateaus). Based on our explanations of algorithm performance, we develop a new algorithm that combines characteristics of the best performers; the new algorithms performance is better than the previous best. We show how hypothesis driven experimentation and search modeling can both explain algorithm performance and motivate the design of a new algorithm

Force-imitated particle swarm optimization using the near-neighbor effect for locating multiple optima

Copyright @ Elsevier Inc. All rights reserved.Multimodal optimization problems pose a great challenge of locating multiple optima simultaneously in the search space to the particle swarm optimization (PSO) community. In this paper, the motion principle of particles in PSO is extended by using the near-neighbor effect in mechanical theory, which is a universal phenomenon in nature and society. In the proposed near-neighbor effect based force-imitated PSO (NN-FPSO) algorithm, each particle explores the promising regions where it resides under the composite forces produced by the “near-neighbor attractor” and “near-neighbor repeller”, which are selected from the set of memorized personal best positions and the current swarm based on the principles of “superior-and-nearer” and “inferior-and-nearer”, respectively. These two forces pull and push a particle to search for the nearby optimum. Hence, particles can simultaneously locate multiple optima quickly and precisely. Experiments are carried out to investigate the performance of NN-FPSO in comparison with a number of state-of-the-art PSO algorithms for locating multiple optima over a series of multimodal benchmark test functions. The experimental results indicate that the proposed NN-FPSO algorithm can efficiently locate multiple optima in multimodal fitness landscapes.This work was supported in part by the Key Program of National Natural Science Foundation (NNSF) of China under Grant 70931001, Grant 70771021, and Grant 70721001, the National Natural Science Foundation (NNSF) of China for Youth under Grant 61004121, Grant 70771021, the Science Fund for Creative Research Group of NNSF of China under Grant 60821063, the PhD Programs Foundation of Ministry of Education of China under Grant 200801450008, and in part by the Engineering and Physical Sciences Research Council (EPSRC) of UK under Grant EP/E060722/1 and Grant EP/E060722/2

An experimental comparison of a genetic algorithm and a hill-climber for term selection

Purpose – The term selection problem for selecting query terms in information filtering and routing has been investigated using hill-climbers of various kinds, largely through the Okapi experiments in the TREC series of conferences. Although these are simple deterministic approaches which examine the effect of changing the weight of one term at a time, they have been shown to improve the retrieval effectiveness of filtering queries in these TREC experiments. Hill-climbers are, however, likely to get trapped in local optima, and the use of more sophisticated local search techniques for this problem that attempt to break out of these optima are worth investigating. To this end, we apply a genetic algorithm (GA) to the same problem. Design/Methodology/Approach – We use a standard TREC test collection from the TREC-8 filtering track, recording mean average precision and recall measures to allow comparison between the hillclimber and GA algorithms. We also vary elements of the GA, such as probability of a word being included, probability of mutation and population size in order to measure the effect of these variables. Different strategies such as Elitist and Non-Elitist methods are used, as well as Roulette Wheel and Rank selection GA algorithms. Findings – The results of tests suggest that both techniques are, on average, better than the baseline, but the implemented GA does not match the overall performance of a hill-climber. The Rank selection algorithm does better on average than the Roulette Wheel algorithm. There is no evidence in this study that varying word inclusion probability, mutation probability or Elitist method make much difference to the overall results. Small population sizes do not appear to be as effective as larger population sizes. Research limitations/implications – The evidence provided here would suggest that being stuck in a local optima for the term selection optimization problem does not appear to be detrimental to the overall success of the hill-climber. The evidence from term rank order would appear to provide extra useful evidence which hill-climbers can use efficiently and effectively to narrow the search space. Originality/Value – The paper represents the first attempt to compare hill-climbers with GAs on a problem of this type

Multi-agent evolutionary systems for the generation of complex virtual worlds

Modern films, games and virtual reality applications are dependent on convincing computer graphics. Highly complex models are a requirement for the successful delivery of many scenes and environments. While workflows such as rendering, compositing and animation have been streamlined to accommodate increasing demands, modelling complex models is still a laborious task. This paper introduces the computational benefits of an Interactive Genetic Algorithm (IGA) to computer graphics modelling while compensating the effects of user fatigue, a common issue with Interactive Evolutionary Computation. An intelligent agent is used in conjunction with an IGA that offers the potential to reduce the effects of user fatigue by learning from the choices made by the human designer and directing the search accordingly. This workflow accelerates the layout and distribution of basic elements to form complex models. It captures the designer's intent through interaction, and encourages playful discovery

When Hillclimbers Beat Genetic Algorithms in Multimodal Optimization

It has been shown in the past that a multistart hillclimbing strategy compares favourably to a standard genetic algorithm with respect to solving instances of the multimodal problem generator. We extend that work and verify if the utilization of diversity preservation techniques in the genetic algorithm changes the outcome of the comparison. We do so under two scenarios: (1) when the goal is to find the global optimum, (2) when the goal is to find all optima. A mathematical analysis is performed for the multistart hillclimbing algorithm and a through empirical study is conducted for solving instances of the multimodal problem generator with increasing number of optima, both with the hillclimbing strategy as well as with genetic algorithms with niching. Although niching improves the performance of the genetic algorithm, it is still inferior to the multistart hillclimbing strategy on this class of problems. An idealized niching strategy is also presented and it is argued that its performance should be close to a lower bound of what any evolutionary algorithm can do on this class of problems

Proposal and Comparative Study of Evolutionary Algorithms for Optimum Design of a Gear System

This paper proposes a novel metaheuristic framework using a Differential Evolution (DE) algorithm with the Non-dominated Sorting Genetic Algorithm-II (NSGA-II). Both algorithms are combined employing a collaborative strategy with sequential execution, which is called DE-NSGA-II. The DE-NSGA-II takes advantage of the exploration abilities of the multi-objective evolutionary algorithms strengthened with the ability to search global mono-objective optimum of DE, that enhances the capability of finding those extreme solutions of Pareto Optimal Front (POF) difficult to achieve. Numerous experiments and performance comparisons between different evolutionary algorithms were performed on a referent problem for the mono-objective and multi-objective literature, which consists of the design of a double reduction gear train. A preliminary study of the problem, solved in an exhaustive way, discovers the low density of solutions in the vicinity of the optimal solution (mono-objective case) as well as in some areas of the POF of potential interest to a decision maker (multi-objective case). This characteristic of the problem would explain the considerable difficulties for its resolution when exact methods and/or metaheuristics are used, especially in the multi-objective case. However, the DE-NSGA-II framework exceeds these difficulties and obtains the whole POF which significantly improves the few previous multi-objective studies.Fil: Méndez Babey, Máximo. Universidad de Las Palmas de Gran Canaria; EspañaFil: Rossit, Daniel Alejandro. Universidad Nacional del Sur. Departamento de Ingeniería; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca. Instituto de Matemática Bahía Blanca. Universidad Nacional del Sur. Departamento de Matemática. Instituto de Matemática Bahía Blanca; ArgentinaFil: González, Begoña. Universidad de Las Palmas de Gran Canaria; EspañaFil: Frutos, Mariano. Universidad Nacional del Sur. Departamento de Ingeniería; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca. Instituto de Investigaciones Económicas y Sociales del Sur. Universidad Nacional del Sur. Departamento de Economía. Instituto de Investigaciones Económicas y Sociales del Sur; Argentin