Multiple colony ant algorithm for job-shop scheduling problem

Ant colony optimization (ACO) is a metaheuristic that takes inspiration from the foraging behaviour of a real ant colony to solve the optimization problem. This paper presents a multiple colony ant algorithm to solve the Job-shop Scheduling Problem with the objective that minimizes the makespan. In a multiple colony ant algorithm, ants cooperate to find good solutions by exchanging information among colonies which are stored in a master pheromone matrix that serves the role of global memory. The exploration of the search space in each colony is guided by different heuristic information. Several specific features are introduced in the algorithm in order to improve the efficiency of the search. Among others is the local search method by which the ant can fine-tune their neighbourhood solutions. The proposed algorithm is tested over set of benchmark problems and the computational results demonstrate that the multiple colony ant algorithm performs well on the benchmark problems.     

Ant colony optimisation of decision tree and contingency table models for the discovery of gene–gene interactions

In this study, ant colony optimisation (ACO) algorithm is used to derive near‐optimal interactions between a number of single nucleotide polymorphisms (SNPs). This approach is used to discover small numbers of SNPs that are combined into a decision tree or contingency table model. The ACO algorithm is shown to be very robust as it is proven to be able to find results that are discriminatory from a statistical perspective with logical interactions, decision tree and contingency table models for various numbers of SNPs considered in the interaction. A large number of the SNPs discovered here have been already identified in large genome‐wide association studies to be related to type II diabetes in the literature, lending additional confidence to the results.Inspec keywords: genetics, genomics, DNA, polymorphism, molecular biophysics, molecular configurations, ant colony optimisation, decision trees, bioinformatics, diseasesOther keywords: ant colony optimisation, decision tree, contingency table models, gene‐gene interactions, ACO algorithm, near‐optimal interactions, single nucleotide polymorphisms, SNP, genome‐wide association studies, type II diabetes     

Morphogenesis of an extended phenotype: four-dimensional ant nest architecture

Animals produce a variety of structures to modify their environments adaptively. Such structures represent extended phenotypes whose development is rarely studied. To begin to rectify this, we used micro-computed tomography (CT) scanning and time-series experiments to obtain the first high-resolution dataset on the four-dimensional growth of ant nests. We show that extrinsic features within the environment, such as the presence of planes between layers of sediment, influence the architecture of Lasius flavus nests, with ants excavating horizontal tunnels along such planes. Intrinsically, the dimensions of the tunnels are associated with individual colonies, the dynamics of excavation can be explained by negative feedback and the angular distribution of tunnels is probably a result of local competition among tunnels for miners. The architecture and dynamics of ant nest excavation therefore result from local interactions of ants with one another and templates inherent in the environment. The influence of the environment on the form of structures has been documented across both biotic and abiotic domains. Our study opens up the utility of CT scanning as a technique for observing the morphogenesis of such structures.     

Data-driven modelling of group formation in the fission–fusion dynamics of Bechstein’s bats

Communal roosting in Bechstein’s bat colonies is characterized by the formation of several groups that use different day roosts and that regularly dissolve and re-merge (fission–fusion dynamics). Analysing data from two colonies of different sizes over many years, we find that (i) the number of days that bats stay in the same roost before changing follows an exponential distribution that is independent of the colony size and (ii) the number and size of groups that bats formed for roosting depend on the size of the colony, such that above a critical colony size two to six groups of different sizes are formed. To model these two observations, we propose an agent-based model in which agents make their decisions about roosts based on both random and social influences. For the latter, they copy the roost preference of another agent which models the transfer of the respective information. Our model is able to reproduce both the distribution of stay length in the same roost and the emergence of groups of different sizes dependent on the colony size. Moreover, we are able to predict the critical system size at which the formation of different groups emerges without global coordination. We further comment on dynamics that bridge the roosting decisions on short time scales (less than 1 day) with the social structures observed at long time scales (more than 1 year).     

Social insect colony as a biological regulatory system: modelling information flow in dominance networks

Social insects provide an excellent platform to investigate flow of information in regulatory systems since their successful social organization is essentially achieved by effective information transfer through complex connectivity patterns among the colony members. Network representation of such behavioural interactions offers a powerful tool for structural as well as dynamical analysis of the underlying regulatory systems. In this paper, we focus on the dominance interaction networks in the tropical social wasp Ropalidia marginata—a species where behavioural observations indicate that such interactions are principally responsible for the transfer of information between individuals about their colony needs, resulting in a regulation of their own activities. Our research reveals that the dominance networks of R. marginata are structurally similar to a class of naturally evolved information processing networks, a fact confirmed also by the predominance of a specific substructure—the ‘feed-forward loop’—a key functional component in many other information transfer networks. The dynamical analysis through Boolean modelling confirms that the networks are sufficiently stable under small fluctuations and yet capable of more efficient information transfer compared to their randomized counterparts. Our results suggest the involvement of a common structural design principle in different biological regulatory systems and a possible similarity with respect to the effect of selection on the organization levels of such systems. The findings are also consistent with the hypothesis that dominance behaviour has been shaped by natural selection to co-opt the information transfer process in such social insect species, in addition to its primal function of mediation of reproductive competition in the colony.     

Coupling ant colony and the degraded ceiling algorithm for the redundancy allocation problem of series–parallel systems

The redundancy allocation problem (RAP) is a well known NP-hard problem which involves the selection of elements and redundancy levels to maximize system reliability given various system-level constraints. As telecommunications and internet protocol networks, manufacturing and power systems are becoming more and more complex, while requiring short developments schedules and very high reliability, it is becoming increasingly important to develop efficient solutions to the RAP. This paper presents an efficient algorithm to solve this reliability optimization problem. The idea of a heuristic approach design is inspired from the ant colony meta-heuristic optimization method and the degraded ceiling local search technique. Our hybridization of the ant colony meta-heuristic with the degraded ceiling performs well and is competitive with the best-known heuristics for redundancy allocation. Numerical results for the 33 test problems from previous research are reported and compared. The solutions found by our approach are all better than or are in par with the well-known best solutions.     

Branching instability in expanding bacterial colonies

Self-organization in developing living organisms relies on the capability of cells to duplicate and perform a collective motion inside the surrounding environment. Chemical and mechanical interactions coordinate such a cooperative behaviour, driving the dynamical evolution of the macroscopic system. In this work, we perform an analytical and computational analysis to study pattern formation during the spreading of an initially circular bacterial colony on a Petri dish. The continuous mathematical model addresses the growth and the chemotactic migration of the living monolayer, together with the diffusion and consumption of nutrients in the agar. The governing equations contain four dimensionless parameters, accounting for the interplay among the chemotactic response, the bacteria–substrate interaction and the experimental geometry. The spreading colony is found to be always linearly unstable to perturbations of the interface, whereas branching instability arises in finite-element numerical simulations. The typical length scales of such fingers, which align in the radial direction and later undergo further branching, are controlled by the size parameters of the problem, whereas the emergence of branching is favoured if the diffusion is dominant on the chemotaxis. The model is able to predict the experimental morphologies, confirming that compact (resp. branched) patterns arise for fast (resp. slow) expanding colonies. Such results, while providing new insights into pattern selection in bacterial colonies, may finally have important applications for designing controlled patterns.     

求解集装箱装载问题的混合蚁群模拟退火算法

目的 针对物流行业中存在的大规模、复杂、多规格货物的集装箱装载问题,提出一种基于塔装载启发式算法、二维装载点启发式算法、蚁群模拟退火算法的混合算法。方法 首先,采用塔装载启发式算法将三维待装箱装载成塔集,即将三维装箱问题降为二维装箱问题,有效降低集装箱的装载规模;其次,蚁群算法通过融入信息素选择更新策略,并利用自适应信息素挥发系数来提升算法整体的收敛速度,同时结合模拟退火算法对每代优秀路径集进行局部搜索,避免算法因收敛过快而陷入局部最优;最后,将蚁群模拟退火算法与二维装载点启发式算法相结合,优化每座塔的装载顺序和放置姿态,寻找最优的装载方案。结果 实验证明,在250组算例中,采用混合算法后,集装箱的平均空间利用率为90.92%,优于其他3种对比算法。结论 设计的混合蚁群模拟退火算法适用于解决大规模集装箱装载问题。     

基于蚁群算法的资源均衡优化决策及其MATLAB实现

资源均衡问题已被证明属于组合优化中的NP-hard问题,随着网络计划的复杂化,传统的数学规划法和启发式算法已很难解决该问题。本文以各种资源标准差的加权之和作为衡量资源均衡的评价指标,建立了资源均衡优化决策的数学模型,其次,自行设计蚁群算法步骤,利用Matlab编程进行实现,将蚂蚁随机分布在可行域中,蚂蚁根据转移概率进行全局搜索或局部搜索,经迭代求解资源平衡的全局最优和对应的各工序的开始工作时间,最后使用单资源均衡和多资源均衡两个算例对算法进行了测试,验证了该算法的有效性。     

Probabilistic patterns of interaction: the effects of link-strength variability on food web structure

Patterns of species interactions affect the dynamics of food webs. An important component of species interactions that is rarely considered with respect to food webs is the strengths of interactions, which may affect both structure and dynamics. In natural systems, these strengths are variable, and can be quantified as probability distributions. We examined how variation in strengths of interactions can be described hierarchically, and how this variation impacts the structure of species interactions in predator–prey networks, both of which are important components of ecological food webs. The stable isotope ratios of predator and prey species may be particularly useful for quantifying this variability, and we show how these data can be used to build probabilistic predator–prey networks. Moreover, the distribution of variation in strengths among interactions can be estimated from a limited number of observations. This distribution informs network structure, especially the key role of dietary specialization, which may be useful for predicting structural properties in systems that are difficult to observe. Finally, using three mammalian predator–prey networks (two African and one Canadian) quantified from stable isotope data, we show that exclusion of link-strength variability results in biased estimates of nestedness and modularity within food webs, whereas the inclusion of body size constraints only marginally increases the predictive accuracy of the isotope-based network. We find that modularity is the consequence of strong link-strengths in both African systems, while nestedness is not significantly present in any of the three predator–prey networks.     

Multi-scale modelling of the dynamics of cell colonies: insights into cell-adhesion forces and cancer invasion from in silico simulations

Studying the biophysical interactions between cells is crucial to understanding how normal tissue develops, how it is structured and also when malfunctions occur. Traditional experiments try to infer events at the tissue level after observing the behaviour of and interactions between individual cells. This approach assumes that cells behave in the same biophysical manner in isolated experiments as they do within colonies and tissues. In this paper, we develop a multi-scale multi-compartment mathematical model that accounts for the principal biophysical interactions and adhesion pathways not only at a cell–cell level but also at the level of cell colonies (in contrast to the traditional approach). Our results suggest that adhesion/separation forces between cells may be lower in cell colonies than traditional isolated single-cell experiments infer. As a consequence, isolated single-cell experiments may be insufficient to deduce important biological processes such as single-cell invasion after detachment from a solid tumour. The simulations further show that kinetic rates and cell biophysical characteristics such as pressure-related cell-cycle arrest have a major influence on cell colony patterns and can allow for the development of protrusive cellular structures as seen in invasive cancer cell lines independent of expression levels of pro-invasion molecules.     

Editorial - Selected papers from the 2nd international symposium on optimization and systems biology

One of the major challenges for post-genomic biology is to understand how genes, proteins and small molecules interact to form cellular systems. It has been recognised that a complicated living organism cannot be fully understood by merely analysing individual components, and that interactions of those components or networks are ultimately responsible for an organism?s form and functions. Instead of analysing individual components or aspects of the organism, systems biology is the study of an organism, viewed as a dynamical and interacting network of biomolecules which give rise to a complicated life. With increasingly accumulated data from high-throughput technologies, molecular networks and their dynamics have been studied extensively from various aspects of living organisms. Many mathematical methods have been adopted in computational systems biology; in particular, optimisation and statistics play a key role in analysing and understanding biological mechanisms from system-wide viewpoints.     

Decreasing stochasticity through enhanced seasonality in measles epidemics

Seasonal changes in the environment are known to be important drivers of population dynamics, giving rise to sustained population cycles. However, it is often difficult to measure the strength and shape of seasonal forces affecting populations. In recent years, statistical time-series methods have been applied to the incidence records of childhood infectious diseases in an attempt to estimate seasonal variation in transmission rates, as driven by the pattern of school terms. In turn, school-term forcing was used to show how susceptible influx rates affect the interepidemic period. In this paper, we document the response of measles dynamics to distinct shifts in the parameter regime using previously unexplored records of measles mortality from the early decades of the twentieth century. We describe temporal patterns of measles epidemics using spectral analysis techniques, and point out a marked decrease in birth rates over time. Changes in host demography alone do not, however, suffice to explain epidemiological transitions. By fitting the time-series susceptible–infected–recovered model to measles mortality data, we obtain estimates of seasonal transmission in different eras, and find that seasonality increased over time. This analysis supports theoretical work linking complex population dynamics and the balance between stochastic and deterministic forces as determined by the strength of seasonality.     

Ant colonies with cooperative process applied to the resource allocation problem

Abstract

In this paper, a novel algorithm describing ant colonies, with cooperation, is proposed to solve the resource allocation problem. The resource allocation problem is to allocate resources to activities, with the objective of optimizing the cost function. In our study, we viewed the search in ant colonies as a mechanism providing a main portion of diversity in search space. The cooperative process conducts fine‐tuning for the solution provided by ant colonies, and it has the ability to escape from poor local optima. In this paper, several examples are tested to prove the superiority of our proposed algorithm. From simulation results, the proposed algorithm indeed has remarkable performance.     

求解连续空间优化问题的扩展粒子蚁群算法

扩展蚁群算法是蚁群算法创始人Dorigo提出的一种用于求解连续空间优化问题的最新蚁群算法,但该算法的收敛速度参数和局部搜索参数取值缺乏理论指导,因此其性能受算法参数影响较大.本文提出一种求解连续空间优化的扩展粒子蚁群算法,将粒子群算法嵌入到扩展蚁群算法中用于在线优化扩展蚁群算法参数,减少了参数人为调整的盲目性.从而改善扩展蚁群算法的寻径行为.通过将本文提出的算法与遗传算法、克隆选择算法、蚁群算法、扩展蚁群算法对5种典型测试函数优化的结果对比表明,本文算法在搜索速度和全局搜索能力方面均优于其它算法.     

Reliability optimization using multiobjective ant colony system approaches

The multiobjective ant colony system (ACS) meta-heuristic has been developed to provide solutions for the reliability optimization problem of series-parallel systems. This type of problems involves selection of components with multiple choices and redundancy levels that produce maximum benefits, and is subject to the cost and weight constraints at the system level. These are very common and realistic problems encountered in conceptual design of many engineering systems. It is becoming increasingly important to develop efficient solutions to these problems because many mechanical and electrical systems are becoming more complex, even as development schedules get shorter and reliability requirements become very stringent. The multiobjective ACS algorithm offers distinct advantages to these problems compared with alternative optimization methods, and can be applied to a more diverse problem domain with respect to the type or size of the problems. Through the combination of probabilistic search, multiobjective formulation of local moves and the dynamic penalty method, the multiobjective ACSRAP, allows us to obtain an optimal design solution very frequently and more quickly than with some other heuristic approaches. The proposed algorithm was successfully applied to an engineering design problem of gearbox with multiple stages.     

基于改进蚁群算法的码垛机器人路径规划应用研究

目的为解决蚁群算法在码垛机器人路径规划中存在的收敛速度慢、容易陷入局部最优等问题,提出一种人工势场和蚁群算法相结合的方法。方法首先,根据码垛机器人机械手在人工势场中不同节点所受到的合力,对初始信息素进行不均匀分布,以解决蚁群算法初期由于缺乏信息素导致的无效路径搜索。其次,在启发函数的设计中引入码垛机器人机械手在下一节点所受到的合力,以解决蚁群算法容易陷入局部最优的问题。最后,对信息素的更新策略进行改进。按照寻得路径的长度不同,对每次迭代完成后信息素的增量成比例进行更新,并设置最大、最小值,以解决迭代后期路径上信息素过大而使蚁群算法陷入局部最优的问题。结果改进后的蚁群算法收敛速度提升了约51%,寻找到的最短路径提升了约10%。和其他改进的蚁群算法相比,在综合性能上也有一定程度上的提高。结论改进后的蚁群算法收敛更快,寻找的最优路径更短。     

Beyond contact-based transmission networks: the role of spatial coincidence

Animal societies rely on interactions between group members to effectively communicate and coordinate their actions. To date, the transmission properties of interaction networks formed by direct physical contacts have been extensively studied for many animal societies and in all cases found to inhibit spreading. Such direct interactions do not, however, represent the only viable pathways. When spreading agents can persist in the environment, indirect transmission via ‘same-place, different-time’ spatial coincidences becomes possible. Previous studies have neglected these indirect pathways and their role in transmission. Here, we use rock ant colonies, a model social species whose flat nest geometry, coupled with individually tagged workers, allowed us to build temporally and spatially explicit interaction networks in which edges represent either direct physical contacts or indirect spatial coincidences. We show how the addition of indirect pathways allows the network to enhance or inhibit the spreading of different types of agent. This dual-functionality arises from an interplay between the interaction-strength distribution generated by the ants'' movement and environmental decay characteristics of the spreading agent. These findings offer a general mechanism for understanding how interaction patterns might be tuned in animal societies to control the simultaneous transmission of harmful and beneficial agents.     

Local cost minimization in ant transport networks: from small-scale data to large-scale trade-offs

Transport networks distribute resources and information in many human and biological systems. Their construction requires optimization and balance of conflicting criteria such as robustness against disruptions, transport efficiency and building cost. The colonies of the polydomous Australian meat ant Iridomyrmex purpureus are a striking example of such a decentralized network, consisting of trails that connect spatially separated nests. Here we study the rules that underlie network construction in these ants. We find that a simple model of network growth, which we call the minimum linking model (MLM), is sufficient to explain the growth of real ant colonies. For larger networks, the MLM shows a qualitative similarity with a Euclidean minimum spanning tree, prioritizing cost and efficiency over robustness. We introduce a variant of our model to show that a balance between cost, efficiency and robustness can be also reproduced at larger scales than ant colonies. Remarkably, such a balance is influenced by a parameter reflecting the specific features of the modelled transport system. The extended MLM could thus be a suitable source of inspiration for the construction of cheap and efficient transport networks with non-zero robustness, suggesting possible applications in the design of human-made networks.     

Ant colony optimization system for a multi-quantitative and qualitative objective job-shop parallel-machine-scheduling problem

This paper addresses a multi-stage job-shop parallel-machine-scheduling problem with an ant colony optimization system developed. The problem is practically important and yet more complex, especially when customer order splitting in multiple lots for the reduction of operation times in each workstation is allowed. It also includes the decisions of the numbers of parallel machines in workstations dynamically scheduled. In addition, this paper also addresses the multiple-objectives scheduling. For the practical concern, in addition to the production (or quantitative) objectives, the marketing (strategic or qualitative) criteria are also considered. A soft constraint thus may be realized from a thus-called qualitatively evaluated order sequence. The soft constraint with the ant colony optimization solution constructs a penalty function for the multiple qualitative objectives and the results of scheduling obtained by ant colony optimization. For this problem, the ant colony optimization components (including the network representation, tabu lists, transition probabilities, and pheromone trail updating) are also developed and adapted for the multiple objectives. The experiment results of parameter design and different problem sizes are provided. The results of a genetic algorithm also developed for the present problem under the developed system concept are also provided, since in the literature the genetic algorithm has also not been explored for the present problem with multiple objectives and order splitting. The results of both solution techniques show the potential usefulness of the system and are comparable, but the ant colony optimization provides a more computationally efficient better result.