Active Semi-Supervised Community Detection Based on Must-Link and Cannot-Link Constraints

Community structure detection is of great importance because it can help in discovering the relationship between the function and the topology structure of a network. Many community detection algorithms have been proposed, but how to incorporate the prior knowledge in the detection process remains a challenging problem. In this paper, we propose a semi-supervised community detection algorithm, which makes full utilization of the must-link and cannot-link constraints to guide the process of community detection and thereby extracts high-quality community structures from networks. To acquire the high-quality must-link and cannot-link constraints, we also propose a semi-supervised component generation algorithm based on active learning, which actively selects nodes with maximum utility for the proposed semi-supervised community detection algorithm step by step, and then generates the must-link and cannot-link constraints by accessing a noiseless oracle. Extensive experiments were carried out, and the experimental results show that the introduction of active learning into the problem of community detection makes a success. Our proposed method can extract high-quality community structures from networks, and significantly outperforms other comparison methods.     

Stochastic scheduling for multiclass applications with availability requirements in heterogeneous clusters

High availability plays an important role in heterogeneous clusters, where processors operate at different speeds and are not continuously available for processing. Existing scheduling algorithms designed for heterogeneous clusters do not factor in availability. We address in this paper the stochastic scheduling problem for heterogeneous clusters with availability constraints. Each node in a heterogeneous cluster is modeled by its speed and availability, and different classes of tasks submitted to the cluster are characterized by their execution times and availability requirements. To incorporate availability and heterogeneity into stochastic scheduling, we introduce metrics to quantify availability and heterogeneity in the context of multiclass tasks. A stochastic scheduling algorithm SSAC (stochastic scheduling with availability constraints) is then proposed to improve availability of heterogeneous clusters while reducing average response time of tasks. Experimental results show that our algorithm achieves a good trade-off between availability and responsiveness.

Scheduling unrelated parallel machines in semiconductor manufacturing by problem reduction and local search heuristics

We investigate a difficult scheduling problem in a semiconductor manufacturing process that seeks to minimize the number of tardy jobs and makespan with sequence-dependent setup time, release time, due dates and tool constraints. We propose a mixed integer programming (MIP) formulation which treats tardy jobs as soft constraints so that our objective seeks the minimum weighted sum of makespan and heavily penalized tardy jobs. Although our polynomial-sized MIP formulation can correctly model this scheduling problem, it is so difficult that even a feasible solution can not be calculated efficiently for small-scale problems. We then propose a technique to estimate the upper bound for the number of jobs processed by a machine, and use it to effectively reduce the size of the MIP formulation. In order to handle real-world large-scale scheduling problems, we propose an efficient dispatching rule that assigns a job of the earliest due date to a machine with least recipe changeover (EDDLC) and try to re-optimize the solution by local search heuristics which involves interchange, translocation and transposition between assigned jobs. Our computational experiments indicate that EDDLC and our proposed reoptimization techniques are very efficient and effective. In particular, our method usually gives solutions very close to the exact optimum for smaller scheduling problems, and calculates good solutions for scheduling up to 200 jobs on 40 machines within 10 min.     

Energy and resource efficient workflow scheduling in a virtualized cloud environment

High energy consumption (EC) is one of the leading and interesting issue in the cloud environment. The optimization of EC is generally related to scheduling problem. Optimum scheduling strategy is used to select the resources or tasks in such a way that system performance is not violated while minimizing EC and maximizing resource utilization (RU). This paper presents a task scheduling model for scheduling the tasks on virtual machines (VMs). The objective of the proposed model is to minimize EC, maximize RU, and minimize workflow makespan while preserving the task’s deadline and dependency constraints. An energy and resource efficient workflow scheduling algorithm (ERES) is proposed to schedule the workflow tasks to the VMs and dynamically deploy/un-deploy the VMs based on the workflow task’s requirements. An energy model is presented to compute the EC of the servers. Double threshold policy is used to perceive the server’ status i.e. overloaded/underloaded or normal. To balance the workload on the overloaded/underloaded servers, live VM migration strategy is used. To check the effectiveness of the proposed algorithm, exhaustive simulation experiments are conducted. The proposed algorithm is compared with power efficient scheduling and VM consolidation (PESVMC) algorithm on the accounts of RU, energy efficiency and task makespan. Further, the results are also verified in the real cloud environment. The results demonstrate the effectiveness of the proposed ERES algorithm.

     

Hierarchical genetic-based grid scheduling with energy optimization

An optimization of power and energy consumptions is the important concern for a design of modern-day and future computing and communication systems. Various techniques and high performance technologies have been investigated and developed for an efficient management of such systems. All these technologies should be able to provide good performance and to cope under an increased workload demand in the dynamic environments such as Computational Grids (CGs), clusters and clouds. In this paper we approach the independent batch scheduling in CG as a bi-objective minimization problem with makespan and energy consumption as the scheduling criteria. We use the Dynamic Voltage Scaling (DVS) methodology for scaling and possible reduction of cumulative power energy utilized by the system resources. We develop two implementations of Hierarchical Genetic Strategy-based grid scheduler (Green-HGS-Sched) with elitist and struggle replacement mechanisms. The proposed algorithms were empirically evaluated versus single-population Genetic Algorithms (GAs) and Island GA models for four CG size scenarios in static and dynamic modes. The simulation results show that proposed scheduling methodologies fairly reduce the energy usage and can be easily adapted to the dynamically changing grid states and various scheduling scenarios.     

CECT: computationally efficient congestion-avoidance and traffic engineering in software-defined cloud data centers

The proliferation of cloud data center applications and network function virtualization (NFV) boosts dynamic and QoS dependent traffic into the data centers network. Currently, lots of network routing protocols are requirement agnostic, while other QoS-aware protocols are computationally complex and inefficient for small flows. In this paper, a computationally efficient congestion avoidance scheme, called CECT, for software-defined cloud data centers is proposed. The proposed algorithm, CECT, not only minimizes network congestion but also reallocates the resources based on the flow requirements. To this end, we use a routing architecture to reconfigure the network resources triggered by two events: (1) the elapsing of a predefined time interval, or, (2) the occurrence of congestion. Moreover, a forwarding table entries compression technique is used to reduce the computational complexity of CECT. In this way, we mathematically formulate an optimization problem and define a genetic algorithm to solve the proposed optimization problem. We test the proposed algorithm on real-world network traffic. Our results show that CECT is computationally fast and the solution is feasible in all cases. In order to evaluate our algorithm in term of throughput, CECT is compared with ECMP (where the shortest path algorithm is used as the cost function). Simulation results confirm that the throughput obtained by running CECT is improved up to 3× compared to ECMP while packet loss is decreased up to 2×.     

Efficient scheduling of team truck drivers in the European Union

This paper studies the problem of scheduling working hours of team drivers in European road freight transport where a sequence of ?? locations must be visited within given time windows. Since April 2007 working hours of truck drivers in the European Union must comply with regulation (EC) No 561/2006. These regulations impose standard limits on the daily driving times of truck drivers and extended daily limits that may only be used twice a week for each driver. We present a depth-first-breadth-second search method which can find a feasible schedule complying with standard daily driving time limits in O(??²) time, if such a schedule exists. Furthermore, we show that this method can also be used to find schedules complying with regulation (EC) No 561/2006 if daily driving times may exceed the standard limit.     

A study of nurse scheduling in Japan

Scheduling nurses to staff shifts is a major problem in hospitals. The necessity of maintaining a certain level of service and skill in the makeup of every shift, while balancing the workload among the nurses involved, is incredibly difficult. It is often impossible to develop a schedule which satisfies all the requirements despite the time and resources spent in the effort. This paper summarizes all our published research on nurse scheduling to date. The difficulties realized by our two investigations in Japan are shown first, together with a resulting scheduling problem. The nurse scheduling model based on the results is then described. In this model, all constraints are divided into two essentially different types; that which maintains a certain level of skill for each shift ('shift constraints') and that which concerns the workload for each nurse ('nurse constraints'). By classifying the constraints in this manner, we can determine what is affected by a specific constraint when the constraint is not satisfied. We developed efficient algorithms while taking advantage of the structure of this model. Finally, it is shown that our algorithm can solve this problem for a 2-shift system efficiently.     

PhysarumSpreader: A New Bio-Inspired Methodology for Identifying Influential Spreaders in Complex Networks

Identifying influential spreaders in networks, which contributes to optimizing the use of available resources and efficient spreading of information, is of great theoretical significance and practical value. A random-walk-based algorithm LeaderRank has been shown as an effective and efficient method in recognizing leaders in social network, which even outperforms the well-known PageRank method. As LeaderRank is initially developed for binary directed networks, further extensions should be studied in weighted networks. In this paper, a generalized algorithm PhysarumSpreader is proposed by combining LeaderRank with a positive feedback mechanism inspired from an amoeboid organism called Physarum Polycephalum. By taking edge weights into consideration and adding the positive feedback mechanism, PhysarumSpreader is applicable in both directed and undirected networks with weights. By taking two real networks for examples, the effectiveness of the proposed method is demonstrated by comparing with other standard centrality measures.     

Semi-Supervised Segmentation of Ultrasound Images Based on Patch Representation and Continuous Min Cut

Ultrasound segmentation is a challenging problem due to the inherent speckle and some artifacts like shadows, attenuation and signal dropout. Existing methods need to include strong priors like shape priors or analytical intensity models to succeed in the segmentation. However, such priors tend to limit these methods to a specific target or imaging settings, and they are not always applicable to pathological cases. This work introduces a semi-supervised segmentation framework for ultrasound imaging that alleviates the limitation of fully automatic segmentation, that is, it is applicable to any kind of target and imaging settings. Our methodology uses a graph of image patches to represent the ultrasound image and user-assisted initialization with labels, which acts as soft priors. The segmentation problem is formulated as a continuous minimum cut problem and solved with an efficient optimization algorithm. We validate our segmentation framework on clinical ultrasound imaging (prostate, fetus, and tumors of the liver and eye). We obtain high similarity agreement with the ground truth provided by medical expert delineations in all applications (94% DICE values in average) and the proposed algorithm performs favorably with the literature.     

Deadlock-free scheduling of an automated manufacturing system using an enhanced colored time resource Petri-net model-based evolutionary endosymbiotic learning automata approach

Deadlock-free scheduling of parts is vital for increasing the utilization of an Automated Manufacturing System (AMS). An existing literature survey has identified the role of an effective modeling methodology for AMS in ensuring the appropriate scheduling of the parts on the available resources. In this paper, a new modeling methodology termed as Extended Color Time Net of Set of Simple Sequential Process with Resources (ECTS³PR) has been presented that efficiently handles dynamic behavior of the manufacturing system. The model is subsequently utilized to obtain a deadlock-free schedule with minimized makespan using a new Evolutionary Endosymbiotic Learning Automata (EELA) algorithm. The ECTS³PR model, which can easily handle various relations and structural interactions, proves to be very helpful in measuring and managing system performances. The novel algorithm EELA has the merits of both endosymbiotic systems and learning automata. The proposed algorithm performs better than various benchmark strategies available in the literature. Extensive experiments have been performed to examine the effectiveness of the proposed methodology, and the results obtained over different data sets of varying dimensions authenticate the performance claim. Superiority of the proposed approach has been validated by defining a new performance index termed as the ‘makespan index’ (MI), whereas the ANOVA analysis reveals the robustness of the algorithm.     

A flexible crane scheduling methodology for container terminals

In this paper, we propose a flexible neighbourhood search strategy for quay crane scheduling problems based on the framework of tabu search (TS) algorithm. In the literature, the container workload of a ship is partitioned into a number of fixed jobs to deal with the complexity of the problem. In this paper, we propose flexible jobs which are dynamically changed by TS throughout the search process to eliminate the impact of fixed jobs on the generated schedules. Alternative job sequences are investigated for quay cranes and a new quay crane dispatching policy is developed to generate schedules. Computational experiments conducted with problem instances available in the literature showed that our algorithm is capable of generating quality schedules for quay crane handling operations at reasonable times.     

The train fueling cost minimization problem with fuzzy fuel prices

The train fueling cost minimization problem is to find a scheduling and fueling strategy such that the fueling cost is minimized and no train runs out of fuel. Since fuel prices vary by location and time from month to month, we estimate them by fuzzy variables in this paper. Furthermore, we propose a fuzzy fueling cost minimization model by minimizing the expected fueling cost under the traversing time constraint, maximal allowable speed constraint, tank capacity constraint, and so on. In order to solve the model, we decompose it into a nonlinear scheduling strategy model and a linear fueling strategy model. Based on the Karush–Kuhn–Tucker conditions, we design an iterative algorithm to solve the scheduling strategy model, and furthermore design a numerical algorithm to solve the fuzzy fueling cost minimization model. Finally, some numerical examples are presented for showing the efficiency of the proposed approach on saving fueling cost.     

Near optimal manufacturing flow controller design

Flow control of flexible manufacturing systems (FMSs) addresses an important real-time scheduling requirement of modern manufacturing facilities, which are prone to failures and other controllable or stochastic discrete events affecting production capacity, such as change of setup and maintenance scheduling. Flow controllers are useful both in the coordination of interconnected flexible manufacturing cells through distributed scheduling policies and in the hierarchical decomposition of the planning and scheduling problem of complex manufacturing systems. Optimal flow-control policies are hedging-point policies characterized by a generally intractable system of stochastic partial differential equations. This article proposes a near optimal controller whose design is computationally feasible for realistic-size systems. The design exploits a decomposition of the multiple-part-type problem to many analytically tractable one-part-type problems. The decomposition is achieved by replacing the polyhedra production capacity sets with inscribed hypercubes. Stationary marginal densities of state variables are computed iteratively for successive trial controller designs until the best inscribed hypercubes and the associated optimal hedging points are determined. Computational results are presented for an illustrative example of a failureprone FMS.     

Optimal In Silico Target Gene Deletion through Nonlinear Programming for Genetic Engineering

Background

Optimal selection of multiple regulatory genes, known as targets, for deletion to enhance or suppress the activities of downstream genes or metabolites is an important problem in genetic engineering. Such problems become more feasible to address in silico due to the availability of more realistic dynamical system models of gene regulatory and metabolic networks. The goal of the computational problem is to search for a subset of genes to knock out so that the activity of a downstream gene or a metabolite is optimized.

Methodology/Principal Findings

Based on discrete dynamical system modeling of gene regulatory networks, an integer programming problem is formulated for the optimal in silico target gene deletion problem. In the first result, the integer programming problem is proved to be NP-hard and equivalent to a nonlinear programming problem. In the second result, a heuristic algorithm, called GKONP, is designed to approximate the optimal solution, involving an approach to prune insignificant terms in the objective function, and the parallel differential evolution algorithm. In the third result, the effectiveness of the GKONP algorithm is demonstrated by applying it to a discrete dynamical system model of the yeast pheromone pathways. The empirical accuracy and time efficiency are assessed in comparison to an optimal, but exhaustive search strategy.

Significance

Although the in silico target gene deletion problem has enormous potential applications in genetic engineering, one must overcome the computational challenge due to its NP-hardness. The presented solution, which has been demonstrated to approximate the optimal solution in a practical amount of time, is among the few that address the computational challenge. In the experiment on the yeast pheromone pathways, the identified best subset of genes for deletion showed advantage over genes that were selected empirically. Once validated in vivo, the optimal target genes are expected to achieve higher genetic engineering effectiveness than a trial-and-error procedure.     

StreAM-$$T_g$$: algorithms for analyzing coarse grained RNA dynamics based on Markov models of connectivity-graphs

Background

In this work, we present a new coarse grained representation of RNA dynamics. It is based on adjacency matrices and their interactions patterns obtained from molecular dynamics simulations. RNA molecules are well-suited for this representation due to their composition which is mainly modular and assessable by the secondary structure alone. These interactions can be represented as adjacency matrices of k nucleotides. Based on those, we define transitions between states as changes in the adjacency matrices which form Markovian dynamics. The intense computational demand for deriving the transition probability matrices prompted us to develop StreAM-\(T_g\), a stream-based algorithm for generating such Markov models of k-vertex adjacency matrices representing the RNA.

Results

We benchmark StreAM-\(T_g\) (a) for random and RNA unit sphere dynamic graphs (b) for the robustness of our method against different parameters. Moreover, we address a riboswitch design problem by applying StreAM-\(T_g\) on six long term molecular dynamics simulation of a synthetic tetracycline dependent riboswitch (500 ns) in combination with five different antibiotics.

Conclusions

The proposed algorithm performs well on large simulated as well as real world dynamic graphs. Additionally, StreAM-\(T_g\) provides insights into nucleotide based RNA dynamics in comparison to conventional metrics like the root-mean square fluctuation. In the light of experimental data our results show important design opportunities for the riboswitch.

     

A Classification for Hoist Scheduling Problems

Electroplating lines are totally automated manufacturing systems that are used to cover parts with a coat of metal. They consist of a set of tanks between which the parts to be treated are transported by one or several hoists. Scheduling the movements of these hoists is commonly called a hoist scheduling problem (HSP) in the literature. But the assumptions and constraints that must be taken into account greatly depend on the production environment (physical system, manufacturing specifications, and management policies). Consequently, there exist several classes of HSPs. The systematic frameworks usually used to classify deterministic scheduling problems do not allow distinguishing between these various kinds of HSPs. Therefore, identifying the scope of each published work and comparing the various proposed scheduling methods turn out to be difficult. Thus, this article presents notation for scheduling problems in electroplating systems, to make the specification of problem types and the identification of studied problem instances easier. An associated typology gives a survey of the literature and demonstrates the usefulness of the proposed classification scheme.     

Who Harvests and Why? Characteristics of Guatemalan Households Harvesting Xaté (Chamaedorea ernesti-augusti)1

Who Harvests and Why? Characteristics of Guatemalan Households Harvesting Xaté (Chamaedorea ernesti-augusti). Cultivation of harvested species is frequently proposed as a conservation strategy to reduce wild harvesting pressure and improve local livelihoods. The success of this approach is likely to be influenced by harvesters’ socioeconomic characteristics. Our study focuses on illegal harvesting of a palm species (Chamaedorea ernesti-augusti, locally known as xaté), by Guatemalans in the largely Belizean Greater Maya Mountains. We surveyed 222 households in nine Guatemalan villages close to the Belize/Guatemala border. With this sample we estimated the current intensity of illegal harvesting by Guatemalans in Belize, the characteristics of harvesting households, and their perceptions of the enforcement level of harvesting laws. We estimated that 26 % of households in the study area actively harvest. Harvesting households owned less land than non-harvesting households. Harvesters are aware that harvesting in Belize is illegal and of the sanctions for harvesting. However, incomes from xaté harvesting were favorable compared to alternative available activities and there were few barriers to entry. We conclude that successful conservation interventions promoting cultivation need to take account of existing harvester characteristics and constraints. Lack of secure land tenure means that cultivation is not a feasible alternative for many harvesting households.     

Security-driven scheduling for data-intensive applications on grids

Security-sensitive applications that access and generate large data sets are emerging in various areas including bioinformatics and high energy physics. Data grids provide such data-intensive applications with a large virtual storage framework with unlimited power. However, conventional scheduling algorithms for data grids are unable to meet the security needs of data-intensive applications. In this paper we address the problem of scheduling data-intensive jobs on data grids subject to security constraints. Using a security- and data-aware technique, a dynamic scheduling strategy is proposed to improve quality of security for data-intensive applications running on data grids. To incorporate security into job scheduling, we introduce a new performance metric, degree of security deficiency, to quantitatively measure quality of security provided by a data grid. Results based on a real-world trace confirm that the proposed scheduling strategy significantly improves security and performance over four existing scheduling algorithms by up to 810% and 1478%, respectively.