Ant colony optimization with direct communication for the traveling salesman problem

This article is posted here with permission from IEEE - Copyright @ 2010 IEEEAnts in conventional ant colony optimization (ACO) algorithms use pheromone to communicate. Usually, this indirect communication leads the algorithm to a stagnation behaviour, where the ants follow the same path from early stages. This occurs because high levels of pheromone are developed, which force the ants to follow the same corresponding trails. As a result, the population gets trapped into a local optimum solution which is difficult to escape from it. In this paper, a direct communication (DC) scheme is proposed where ants are able to exchange cities with other ants that belong to their communication range. Experiments show that the DC scheme delays convergence and improves the solution quality of conventional ACO algorithms regarding the traveling salesman problem, since it guides the population towards the global optimum solution. The ACO algorithm with the proposed DC scheme has better performance, especially on large problem instances, even though it increases the computational time in comparison with a conventional ACO algorithm

A memetic ant colony optimization algorithm for the dynamic travelling salesman problem

Copyright @ Springer-Verlag 2010.Ant colony optimization (ACO) has been successfully applied for combinatorial optimization problems, e.g., the travelling salesman problem (TSP), under stationary environments. In this paper, we consider the dynamic TSP (DTSP), where cities are replaced by new ones during the execution of the algorithm. Under such environments, traditional ACO algorithms face a serious challenge: once they converge, they cannot adapt efficiently to environmental changes. To improve the performance of ACO on the DTSP, we investigate a hybridized ACO with local search (LS), called Memetic ACO (M-ACO) algorithm, which is based on the population-based ACO (P-ACO) framework and an adaptive inver-over operator, to solve the DTSP. Moreover, to address premature convergence, we introduce random immigrants to the population of M-ACO when identical ants are stored. The simulation experiments on a series of dynamic environments generated from a set of benchmark TSP instances show that LS is beneficial for ACO algorithms when applied on the DTSP, since it achieves better performance than other traditional ACO and P-ACO algorithms.This work was supported by the Engineering and Physical Sciences Research Council (EPSRC) of UK under Grant EP/E060722/01 and Grant EP/E060722/02

A survey of swarm intelligence for dynamic optimization: algorithms and applications

Swarm intelligence (SI) algorithms, including ant colony optimization, particle swarm optimization, bee-inspired algorithms, bacterial foraging optimization, firefly algorithms, fish swarm optimization and many more, have been proven to be good methods to address difficult optimization problems under stationary environments. Most SI algorithms have been developed to address stationary optimization problems and hence, they can converge on the (near-) optimum solution efficiently. However, many real-world problems have a dynamic environment that changes over time. For such dynamic optimization problems (DOPs), it is difficult for a conventional SI algorithm to track the changing optimum once the algorithm has converged on a solution. In the last two decades, there has been a growing interest of addressing DOPs using SI algorithms due to their adaptation capabilities. This paper presents a broad review on SI dynamic optimization (SIDO) focused on several classes of problems, such as discrete, continuous, constrained, multi-objective and classification problems, and real-world applications. In addition, this paper focuses on the enhancement strategies integrated in SI algorithms to address dynamic changes, the performance measurements and benchmark generators used in SIDO. Finally, some considerations about future directions in the subject are given

Ant Colony Optimization With Local Search for Dynamic Traveling Salesman Problems

For a dynamic traveling salesman problem (DTSP), the weights (or traveling times) between two cities (or nodes) may be subject to changes. Ant colony optimization (ACO) algorithms have proved to be powerful methods to tackle such problems due to their adaptation capabilities. It has been shown that the integration of local search operators can significantly improve the performance of ACO. In this paper, a memetic ACO algorithm, where a local search operator (called unstring and string) is integrated into ACO, is proposed to address DTSPs. The best solution from ACO is passed to the local search operator, which removes and inserts cities in such a way that improves the solution quality. The proposed memetic ACO algorithm is designed to address both symmetric and asymmetric DTSPs. The experimental results show the efficiency of the proposed memetic algorithm for addressing DTSPs in comparison with other state-of-the-art algorithms

Memory-based immigrants for ant colony optimization in changing environments

Copyright @ 2011 SpringerAnt colony optimization (ACO) algorithms have proved that they can adapt to dynamic optimization problems (DOPs) when they are enhanced to maintain diversity. DOPs are important due to their similarities to many real-world applications. Several approaches have been integrated with ACO to improve their performance in DOPs, where memory-based approaches and immigrants schemes have shown good results on different variations of the dynamic travelling salesman problem (DTSP). In this paper, we consider a novel variation of DTSP where traffic jams occur in a cyclic pattern. This means that old environments will re-appear in the future. A hybrid method that combines memory and immigrants schemes is proposed into ACO to address this kind of DTSPs. The memory-based approach is useful to directly move the population to promising areas in the new environment by using solutions stored in the memory. The immigrants scheme is useful to maintain the diversity within the population. The experimental results based on different test cases of the DTSP show that the memory based immigrants scheme enhances the performance of ACO in cyclic dynamic environments.This work was supported by the Engineering and Physical Sciences Research Council (EPSRC) of UK under Grant EP/E060722/2

Ant colony optimization with immigrants schemes for the dynamic railway junction rescheduling problem with multiple delays

Train rescheduling after a perturbation is a challenging task and is an important concern of the railway industry as delayed trains can lead to large fines, disgruntled customers and loss of revenue. Sometimes not just one delay but several unrelated delays can occur in a short space of time which makes the problem even more challenging. In addition, the problem is a dynamic one that changes over time for, as trains are waiting to be rescheduled at the junction, more timetabled trains will be arriving, which will change the nature of the problem. The aim of this research is to investigate the application of several different ant colony optimization (ACO) algorithms to the problem of a dynamic train delay scenario with multiple delays. The algorithms not only resequence the trains at the junction but also resequence the trains at the stations, which is considered to be a first step towards expanding the problem to consider a larger area of the railway network. The results show that, in this dynamic rescheduling problem, ACO algorithms with a memory cope with dynamic changes better than an ACO algorithm that uses only pheromone evaporation to remove redundant pheromone trails. In addition, it has been shown that if the ant solutions in memory become irreparably infeasible it is possible to replace them with elite immigrants, based on the best-so-far ant, and still obtain a good performance

Pre-scheduled colony size variation in dynamic environments

The file attached to this record is the author's final peer reviewed version. The Publisher's final version can be found by following the DOI link.The performance of the MAX -MIN ant system (MMAS) in dynamic optimization problems (DOPs) is sensitive to the colony size. In particular, a large colony size may waste computational resources whereas a small colony size may restrict the searching capabilities of the algorithm. There is a trade off in the behaviour of the algorithm between the early and later stages of the optimization process. A smaller colony size leads to better performance on shorter runs whereas a larger colony size leads to better performance on longer runs. In this paper, pre-scheduling of varying the colony size of MMAS is investigated in dynamic environments

Including metabolite concentrations into flux balance analysis: thermodynamic realizability as a constraint on flux distributions in metabolic networks

<p>Abstract</p> <p>Background</p> <p>In recent years, constrained optimization – usually referred to as flux balance analysis (FBA) – has become a widely applied method for the computation of stationary fluxes in large-scale metabolic networks. The striking advantage of FBA as compared to kinetic modeling is that it basically requires only knowledge of the stoichiometry of the network. On the other hand, results of FBA are to a large degree hypothetical because the method relies on plausible but hardly provable optimality principles that are thought to govern metabolic flux distributions.</p> <p>Results</p> <p>To augment the reliability of FBA-based flux calculations we propose an additional side constraint which assures thermodynamic realizability, i.e. that the flux directions are consistent with the corresponding changes of Gibb's free energies. The latter depend on metabolite levels for which plausible ranges can be inferred from experimental data. Computationally, our method results in the solution of a mixed integer linear optimization problem with quadratic scoring function. An optimal flux distribution together with a metabolite profile is determined which assures thermodynamic realizability with minimal deviations of metabolite levels from their expected values. We applied our novel approach to two exemplary metabolic networks of different complexity, the metabolic core network of erythrocytes (30 reactions) and the metabolic network iJR904 of <it>Escherichia coli </it>(931 reactions). Our calculations show that increasing network complexity entails increasing sensitivity of predicted flux distributions to variations of standard Gibb's free energy changes and metabolite concentration ranges. We demonstrate the usefulness of our method for assessing critical concentrations of external metabolites preventing attainment of a metabolic steady state.</p> <p>Conclusion</p> <p>Our method incorporates the thermodynamic link between flux directions and metabolite concentrations into a practical computational algorithm. The weakness of conventional FBA to rely on intuitive assumptions about the reversibility of biochemical reactions is overcome. This enables the computation of reliable flux distributions even under extreme conditions of the network (e.g. enzyme inhibition, depletion of substrates or accumulation of end products) where metabolite concentrations may be drastically altered.</p

anNET: a tool for network-embedded thermodynamic analysis of quantitative metabolome data

Background: Compared to other omics techniques, quantitative metabolomics is still at its infancy. Complex sample preparation and analytical procedures render exact quantification extremely difficult. Furthermore, not only the actual measurement but also the subsequent interpretation of quantitative metabolome data to obtain mechanistic insights is still lacking behind the current expectations. Recently, the method of network-embedded thermodynamic (NET) analysis was introduced to address some of these open issues. Building upon principles of thermodynamics, this method allows for a quality check of measured metabolite concentrations and enables to spot metabolic reactions where active regulation potentially controls metabolic flux. So far, however, widespread application of NET analysis in metabolomics labs was hindered by the absence of suitable software. Results: We have developed in Matlab a generalized software called 'anNET' that affords a user-friendly implementation of the NET analysis algorithm. anNET supports the analysis of any metabolic network for which a stoichiometric model can be compiled. The model size can span from a single reaction to a complete genome-wide network reconstruction including compartments. anNET can (i) test quantitative data sets for thermodynamic consistency, (ii) predict metabolite concentrations beyond the actually measured data, (iii) identify putative sites of active regulation in the metabolic reaction network, and (iv) help in localizing errors in data sets that were found to be thermodynamically infeasible. We demonstrate the application of anNET with three published Escherichia coli metabolome data sets. Conclusion: Our user-friendly and generalized implementation of the NET analysis method in the software anNET allows users to rapidly integrate quantitative metabolome data obtained from virtually any organism. We envision that use of anNET in labs working on quantitative metabolomics will provide the systems biology and metabolic engineering communities with a mean to proof the quality of metabolome data sets and with all further benefits of the NET analysis approach.