An immune system based genetic algorithm using permutation-based dualism for dynamic traveling salesman problems

Copyright @ Springer-Verlag Berlin Heidelberg 2009.In recent years, optimization in dynamic environments has attracted a growing interest from the genetic algorithm community due to the importance and practicability in real world applications. This paper proposes a new genetic algorithm, based on the inspiration from biological immune systems, to address dynamic traveling salesman problems. Within the proposed algorithm, a permutation-based dualism is introduced in the course of clone process to promote the population diversity. In addition, a memory-based vaccination scheme is presented to further improve its tracking ability in dynamic environments. The experimental results show that the proposed diversification and memory enhancement methods can greatly improve the adaptability of genetic algorithms for dynamic traveling salesman problems.This work was supported by the Key Program of National Natural Science Foundation (NNSF) of China under Grant No. 70431003 and Grant No. 70671020, the Science Fund for Creative Research Group of NNSF of China under GrantNo. 60521003, the National Science and Technology Support Plan of China under Grant No. 2006BAH02A09 and the Engineering and Physical Sciences Research Council (EPSRC) of UK under Grant No. EP/E060722/1

An analysis of the XOR dynamic problem generator based on the dynamical system

This is the post-print version of the article - Copyright @ 2010 Springer-VerlagIn this paper, we use the exact model (or dynamical system approach) to describe the standard evolutionary algorithm (EA) as a discrete dynamical system for dynamic optimization problems (DOPs). Based on this dynamical system model, we analyse the properties of the XOR DOP Generator, which has been widely used by researchers to create DOPs from any binary encoded problem. DOPs generated by this generator are described as DOPs with permutation, where the fitness vector is changed according to a permutation matrix. Some properties of DOPs with permutation are analyzed, which allows explaining some behaviors observed in experimental results. The analysis of the properties of problems created by the XOR DOP Generator is important to understand the results obtained in experiments with this generator and to analyze the similarity of such problems to real world DOPs.This work was supported by Brazil FAPESP under Grant 04/04289-6 and by UK EPSRC under Grant EP/E060722/2

A memetic algorithm with adaptive hill climbing strategy for dynamic optimization problems

Copyright @ Springer-Verlag 2008Dynamic optimization problems challenge traditional evolutionary algorithms seriously since they, once converged, cannot adapt quickly to environmental changes. This paper investigates the application of memetic algorithms, a class of hybrid evolutionary algorithms, for dynamic optimization problems. An adaptive hill climbing method is proposed as the local search technique in the framework of memetic algorithms, which combines the features of greedy crossover-based hill climbing and steepest mutation-based hill climbing. In order to address the convergence problem, two diversity maintaining methods, called adaptive dual mapping and triggered random immigrants, respectively, are also introduced into the proposed memetic algorithm for dynamic optimization problems. Based on a series of dynamic problems generated from several stationary benchmark problems, experiments are carried out to investigate the performance of the proposed memetic algorithm in comparison with some peer evolutionary algorithms. The experimental results show the efficiency of the proposed memetic algorithm in dynamic environments.This work was supported by the National Nature Science Foundation of China (NSFC) under Grant Nos. 70431003 and 70671020, the National Innovation Research Community Science Foundation of China under Grant No. 60521003, and the National Support Plan of China under Grant No. 2006BAH02A09 and the Engineering and Physical Sciences Research Council (EPSRC) of UK under Grant EP/E060722/01

Flux imbalance analysis and the sensitivity of cellular growth to changes in metabolite pools

Stoichiometric models of metabolism, such as flux balance analysis (FBA), are classically applied to predicting steady state rates - or fluxes - of metabolic reactions in genome-scale metabolic networks. Here we revisit the central assumption of FBA, i.e. that intracellular metabolites are at steady state, and show that deviations from flux balance (i.e. flux imbalances) are informative of some features of in vivo metabolite concentrations. Mathematically, the sensitivity of FBA to these flux imbalances is captured by a native feature of linear optimization, the dual problem, and its corresponding variables, known as shadow prices. First, using recently published data on chemostat growth of Saccharomyces cerevisae under different nutrient limitations, we show that shadow prices anticorrelate with experimentally measured degrees of growth limitation of intracellular metabolites. We next hypothesize that metabolites which are limiting for growth (and thus have very negative shadow price) cannot vary dramatically in an uncontrolled way, and must respond rapidly to perturbations. Using a collection of published datasets monitoring the time-dependent metabolomic response of Escherichia coli to carbon and nitrogen perturbations, we test this hypothesis and find that metabolites with negative shadow price indeed show lower temporal variation following a perturbation than metabolites with zero shadow price. Finally, we illustrate the broader applicability of flux imbalance analysis to other constraint-based methods. In particular, we explore the biological significance of shadow prices in a constraint-based method for integrating gene expression data with a stoichiometric model. In this case, shadow prices point to metabolites that should rise or drop in concentration in order to increase consistency between flux predictions and gene expression data. In general, these results suggest that the sensitivity of metabolic optima to violations of the steady state constraints carries biologically significant information on the processes that control intracellular metabolites in the cell.Published versio

Thermodynamic Analysis of Interacting Nucleic Acid Strands

Motivated by the analysis of natural and engineered DNA and RNA systems, we present the first algorithm for calculating the partition function of an unpseudoknotted complex of multiple interacting nucleic acid strands. This dynamic program is based on a rigorous extension of secondary structure models to the multistranded case, addressing representation and distinguishability issues that do not arise for single-stranded structures. We then derive the form of the partition function for a fixed volume containing a dilute solution of nucleic acid complexes. This expression can be evaluated explicitly for small numbers of strands, allowing the calculation of the equilibrium population distribution for each species of complex. Alternatively, for large systems (e.g., a test tube), we show that the unique complex concentrations corresponding to thermodynamic equilibrium can be obtained by solving a convex programming problem. Partition function and concentration information can then be used to calculate equilibrium base-pairing observables. The underlying physics and mathematical formulation of these problems lead to an interesting blend of approaches, including ideas from graph theory, group theory, dynamic programming, combinatorics, convex optimization, and Lagrange duality

A Weight-coded Evolutionary Algorithm for the Multidimensional Knapsack Problem

A revised weight-coded evolutionary algorithm (RWCEA) is proposed for solving multidimensional knapsack problems. This RWCEA uses a new decoding method and incorporates a heuristic method in initialization. Computational results show that the RWCEA performs better than a weight-coded evolutionary algorithm proposed by Raidl (1999) and to some existing benchmarks, it can yield better results than the ones reported in the OR-library.Comment: Submitted to Applied Mathematics and Computation on April 8, 201

An efficient ant colony system based on receding horizon control for the aircraft arrival sequencing and scheduling problem

The aircraft arrival sequencing and scheduling (ASS) problem is a salient problem in air traffic control (ATC), which proves to be nondeterministic polynomial (NP) hard. This paper formulates the ASS problem in the form of a permutation problem and proposes a new solution framework that makes the first attempt at using an ant colony system (ACS) algorithm based on the receding horizon control (RHC) to solve it. The resultant RHC-improved ACS algorithm for the ASS problem (termed the RHC-ACS-ASS algorithm) is robust, effective, and efficient, not only due to that the ACS algorithm has a strong global search ability and has been proven to be suitable for these kinds of NP-hard problems but also due to that the RHC technique can divide the problem with receding time windows to reduce the computational burden and enhance the solution's quality. The RHC-ACS-ASS algorithm is extensively tested on the cases from the literatures and the cases randomly generated. Comprehensive investigations are also made for the evaluation of the influences of ACS and RHC parameters on the performance of the algorithm. Moreover, the proposed algorithm is further enhanced by using a two-opt exchange heuristic local search. Experimental results verify that the proposed RHC-ACS-ASS algorithm generally outperforms ordinary ACS without using the RHC technique and genetic algorithms (GAs) in solving the ASS problems and offers high robustness, effectiveness, and efficienc

A particle swarm optimization based memetic algorithm for dynamic optimization problems

Copyright @ Springer Science + Business Media B.V. 2010.Recently, there has been an increasing concern from the evolutionary computation community on dynamic optimization problems since many real-world optimization problems are dynamic. This paper investigates a particle swarm optimization (PSO) based memetic algorithm that hybridizes PSO with a local search technique for dynamic optimization problems. Within the framework of the proposed algorithm, a local version of PSO with a ring-shape topology structure is used as the global search operator and a fuzzy cognition local search method is proposed as the local search technique. In addition, a self-organized random immigrants scheme is extended into our proposed algorithm in order to further enhance its exploration capacity for new peaks in the search space. Experimental study over the moving peaks benchmark problem shows that the proposed PSO-based memetic algorithm is robust and adaptable in dynamic environments.This work was supported by the National Nature Science Foundation of China (NSFC) under Grant No. 70431003 and Grant No. 70671020, the National Innovation Research Community Science Foundation of China under Grant No. 60521003, the National Support Plan of China under Grant No. 2006BAH02A09 and the Ministry of Education, science, and Technology in Korea through the Second-Phase of Brain Korea 21 Project in 2009, the Engineering and Physical Sciences Research Council (EPSRC) of UK under Grant EP/E060722/01 and the Hong Kong Polytechnic University Research Grants under Grant G-YH60