An Analysis of Some Relations Among Domain Ontologies

* This paper was made according to the program of fundamental scientific research of the Presidium of the Russian Academy of Sciences «Mathematical simulation and intellectual systems», the project "Theoretical foundation of the intellectual systems based on ontologies for intellectual support of scientific researches".

Solving Maximum Clique Problem for Protein Structure Similarity

Computing the similarity between two protein structures is a crucial task in molecular biology, and has been extensively investigated. Many protein structure comparison methods can be modeled as maximum weighted clique problems in specific k-partite graphs, referred here as alignment graphs. In this paper we present both a new integer programming formulation for solving such clique problems and a dedicated branch and bound algorithm for solving the maximum cardinality clique problem. Both approaches have been integrated in VAST, a software for aligning protein 3D structures largely used in the National Center for Biotechnology Information, an original clique solver which uses the well known Bron and Kerbosch algorithm (BK). Our computational results on real protein alignment instances show that our branch and bound algorithm is up to 116 times faster than BK.

Solving the Task Assignment Problem with a Variable Neighborhood Search

In this paper a variable neighborhood search (VNS) approach for the task assignment problem (TAP) is considered. An appropriate neighborhood scheme along with a shaking operator and local search procedure are constructed specifically for this problem. The computational results are presented for the instances from the literature, and compared to optimal solutions obtained by the CPLEX solver and heuristic solutions generated by the genetic algorithm. It can be seen that the proposed VNS approach reaches all optimal solutions in a quite short amount of computational time.

Variable Neighborhood Search for Solving the Capacitated Single Allocation Hub Location Problem

In this paper a Variable Neighborhood Search (VNS) algorithm for solving the Capacitated Single Allocation Hub Location Problem (CSAHLP) is presented. CSAHLP consists of two subproblems; the first is choosing a set of hubs from all nodes in a network, while the other comprises finding the optimal allocation of non-hubs to hubs when a set of hubs is already known. The VNS algorithm was used for the first subproblem, while the CPLEX solver was used for the second. Computational results demonstrate that the proposed algorithm has reached optimal solutions on all 20 test instances for which optimal solutions are known, and this in short computational time.

Highly nonlinear chalcogenide suspended-core fibers for applications in the mid-infrared

Due to their unique dispersion and nonlinear properties, chalcogenide suspended-core fibers, characterized by a few micrometer-sized core suspended between large air-holes by few small glaß struts, are excellent candidates for mid-infrared applications. In the present study the influence of the main croß-section characteristics of the chalcogenide suspended-core fibers on the dispersion curve and on the position of the zero-dispersion wavelength has been thoroughly analyzed with a full-vector modal solver based on the finite element. In particular, the design of suspended-core fibers made of both As2S3 and As2Se3 has been optimized to obtain dispersion properties suitable for the supercontinuum generation in the mid-infrared.

A nettó jelenérték maximalizálása erőforrás-korlátos projektekben - egy új harmóniakereső metaheurisztika (A harmony search metaheuristic for the resourceconstrained project scheduling problem with discounted cash flows)

Ebben a tanulmányban a szerző egy új harmóniakereső metaheurisztikát mutat be, amely a minimális időtartamú erőforrás-korlátos ütemezések halmazán a projekt nettó jelenértékét maximalizálja. Az optimális ütemezés elméletileg két egész értékű (nulla-egy típusú) programozási feladat megoldását jelenti, ahol az első lépésben meghatározzuk a minimális időtartamú erőforrás-korlátos ütemezések időtartamát, majd a második lépésben az optimális időtartamot feltételként kezelve megoldjuk a nettó jelenérték maximalizálási problémát minimális időtartamú erőforrás-korlátos ütemezések halmazán. A probléma NP-hard jellege miatt az egzakt megoldás elfogadható idő alatt csak kisméretű projektek esetében képzelhető el. A bemutatandó metaheurisztika a Csébfalvi (2007) által a minimális időtartamú erőforrás-korlátos ütemezések időtartamának meghatározására és a tevékenységek ennek megfelelő ütemezésére kifejlesztett harmóniakereső metaheurisztika továbbfejlesztése, amely az erőforrás-felhasználási konfliktusokat elsőbbségi kapcsolatok beépítésével oldja fel. Az ajánlott metaheurisztika hatékonyságának és életképességének szemléltetésére számítási eredményeket adunk a jól ismert és népszerű PSPLIB tesztkönyvtár J30 részhalmazán futtatva. Az egzakt megoldás generálásához egy korszerű MILP-szoftvert (CPLEX) alkalmaztunk. _______________ This paper presents a harmony search metaheuristic for the resource-constrained project scheduling problem with discounted cash flows. In the proposed approach, a resource-constrained project is characterized by its „best” schedule, where best means a makespan minimal resource constrained schedule for which the net present value (NPV) measure is maximal. Theoretically the optimal schedule searching process is formulated as a twophase mixed integer linear programming (MILP) problem, which can be solved for small-scale projects in reasonable time. The applied metaheuristic is based on the "conflict repairing" version of the "Sounds of Silence" harmony search metaheuristic developed by Csébfalvi (2007) for the resource-constrained project scheduling problem (RCPSP). In order to illustrate the essence and viability of the proposed harmony search metaheuristic, we present computational results for a J30 subset from the well-known and popular PSPLIB. To generate the exact solutions a state-of-the-art MILP solver (CPLEX) was used.

Készpénz optimalizálás GLPK program használatával (Cash flow management with GLPK software)

A készpénz-optimalizálás az operációkutatás régóta kutatott területe. Ebben a cikkben valós adatokon mutatok be egy banki készpénz-optimalizálást, melyet lineáris programozási feladatok segítségével végeztem el. A cikkben összehasonlítottam a determinisztikus és a sztochasztikus megközelítéseket is. A hagyományos készpénz-optimalizáción két területen léptem túl: egyrészt vizsgáltam a bankfiók valutagazdálkodását is, másrészről a bankfiókok közötti készpénzszállítás lehetőségét is. A vegyes egészértékű lineáris programozási feladatok megoldására a glpk nevű szabad hozzáférésű szoftvert használtam, így a cikkből képet kaphatunk a megoldó (solver) felhasználhatóságáról és korlátairól is. ___________ In recent years both operational research and quantitative ¯nance have paid much attention to cash management issues. In this paper we present a cash management study which is based on real world data and uses a mixed integer linear programming (MILP) model as the main tool. In the paper we compare deterministic and stochastic approaches. The classical cash management problem is extended in two ways: we considered the possibility of bank offices keeping more than one currency and also investigated the opportunity of cash transports between bank offices. The MILP problem was solved with glpk (GNU Linear Programming Kit), a free software. The reader can also get a feel of how to use this solver.

Hatékonyság növelése tervezéssel - avagy: aggregált tervezés alkalmazása egy magyar vállalatnál = Improving efficiency with production planning - Applying aggregate planning at a Hungarian company

A cikk alapvető kérdése, hogy miképpen használható a tervezés a termelési folyamatok, s ezzel a vállalati m}uködés egészének hatékonyságnövelése érdekében. A termeléstervezés szintjei és eszközei közül a középtávú aggregált tervezésre koncentrálunk. Ennek oka elsősorban az, hogy tapasztalatunk szerinte tervezési szint gyakorlati alkalmazása még nem tekinthető elterjedtnek, s ebből következően az eszköz alaposabb ismerete és alkalmazásának elterjedése jelentős tartalékokat tárhat fel a m}uködési hatékonyság növelése terén. A dolgozat a termeléstervezés klasszikusnak tekinthető modelljét alkalmazza egy hazai vállalat esetében. Az elemzés során vizsgáljuk a modell alkalmazhatóságát és a különböző tervezési alternatívák hatását a hatékonyság növelésére. A modell számítógépes megoldását a Microsoft Excel Solver programjával végeztük. _______ The article demonstrates how production planning, especially aggregate production planning can positively influence the competitiveness of production firms. First the structure of production planning, different, but interconnected levels of it are introduced than the aggregate planning is elaborated in more details. Reason for focusing on aggregate planning lies in the fact that according to our experience aggregate planning is an operation planning method applied least of all production planning methods in Hungary. Due to this we are convinced that demonstrating a real case study in this area can help managers to realize that adopting it can significantly influence e±ciency in operation and represent important source of development. We applied a classic aggregate planning model for a Hungarian producing company. We have tested the adaptability of the model and also the effect of different concrete planning scenarios on efficiency. Solution of the mathematical model is calculated using the program of Microsoft Excel Solver.

Hybrid multi-objective optimization and hybridized self-organizing response surface method

Numerical optimization is a technique where a computer is used to explore design parameter combinations to find extremes in performance factors. In multi-objective optimization several performance factors can be optimized simultaneously. The solution to multi-objective optimization problems is not a single design, but a family of optimized designs referred to as the Pareto frontier. The Pareto frontier is a trade-off curve in the objective function space composed of solutions where performance in one objective function is traded for performance in others. A Multi-Objective Hybridized Optimizer (MOHO) was created for the purpose of solving multi-objective optimization problems by utilizing a set of constituent optimization algorithms. MOHO tracks the progress of the Pareto frontier approximation development and automatically switches amongst those constituent evolutionary optimization algorithms to speed the formation of an accurate Pareto frontier approximation. Aerodynamic shape optimization is one of the oldest applications of numerical optimization. MOHO was used to perform shape optimization on a 0.5-inch ballistic penetrator traveling at Mach number 2.5. Two objectives were simultaneously optimized: minimize aerodynamic drag and maximize penetrator volume. This problem was solved twice. The first time the problem was solved by using Modified Newton Impact Theory (MNIT) to determine the pressure drag on the penetrator. In the second solution, a Parabolized Navier-Stokes (PNS) solver that includes viscosity was used to evaluate the drag on the penetrator. The studies show the difference in the optimized penetrator shapes when viscosity is absent and present in the optimization. In modern optimization problems, objective function evaluations may require many hours on a computer cluster to perform these types of analysis. One solution is to create a response surface that models the behavior of the objective function. Once enough data about the behavior of the objective function has been collected, a response surface can be used to represent the actual objective function in the optimization process. The Hybrid Self-Organizing Response Surface Method (HYBSORSM) algorithm was developed and used to make response surfaces of objective functions. HYBSORSM was evaluated using a suite of 295 non-linear functions. These functions involve from 2 to 100 variables demonstrating robustness and accuracy of HYBSORSM.

Customization of the design of antenna using genetic algorithm and finite-difference time-domain technique

Antenna design is an iterative process in which structures are analyzed and changed to comply with certain performance parameters required. The classic approach starts with analyzing a "known" structure, obtaining the value of its performance parameter and changing this structure until the "target" value is achieved. This process relies on having an initial structure, which follows some known or "intuitive" patterns already familiar to the designer. The purpose of this research was to develop a method of designing UWB antennas. What is new in this proposal is that the design process is reversed: the designer will start with the target performance parameter and obtain a structure as the result of the design process. This method provided a new way to replicate and optimize existing performance parameters. The base of the method was the use of a Genetic Algorithm (GA) adapted to the format of the chromosome that will be evaluated by the Electromagnetic (EM) solver. For the electromagnetic study we used XFDTD™ program, based in the Finite-Difference Time-Domain technique. The programming portion of the method was created under the MatLab environment, which serves as the interface for converting chromosomes, file formats and transferring of data between the XFDTD™ and GA. A high level of customization had to be written into the code to work with the specific files generated by the XFDTD™ program. Two types of cost functions were evaluated; the first one seeking broadband performance within the UWB band, and the second one searching for curve replication of a reference geometry. The performance of the method was evaluated considering the speed provided by the computer resources used. Balance between accuracy, data file size and speed of execution was achieved by defining parameters in the GA code as well as changing the internal parameters of the XFDTD™ projects. The results showed that the GA produced geometries that were analyzed by the XFDTD™ program and changed following the search criteria until reaching the target value of the cost function. Results also showed how the parameters can change the search criteria and influence the running of the code to provide a variety of geometries.

Algorithms for scheduling parallel batch processing machines with non-identical job ready times

This research is motivated by a practical application observed at a printed circuit board (PCB) manufacturing facility. After assembly, the PCBs (or jobs) are tested in environmental stress screening (ESS) chambers (or batch processing machines) to detect early failures. Several PCBs can be simultaneously tested as long as the total size of all the PCBs in the batch does not violate the chamber capacity. PCBs from different production lines arrive dynamically to a queue in front of a set of identical ESS chambers, where they are grouped into batches for testing. Each line delivers PCBs that vary in size and require different testing (or processing) times. Once a batch is formed, its processing time is the longest processing time among the PCBs in the batch, and its ready time is given by the PCB arriving last to the batch. ESS chambers are expensive and a bottleneck. Consequently, its makespan has to be minimized. ^ A mixed-integer formulation is proposed for the problem under study and compared to a formulation recently published. The proposed formulation is better in terms of the number of decision variables, linear constraints and run time. A procedure to compute the lower bound is proposed. For sparse problems (i.e. when job ready times are dispersed widely), the lower bounds are close to optimum. ^ The problem under study is NP-hard. Consequently, five heuristics, two metaheuristics (i.e. simulated annealing (SA) and greedy randomized adaptive search procedure (GRASP)), and a decomposition approach (i.e. column generation) are proposed—especially to solve problem instances which require prohibitively long run times when a commercial solver is used. Extensive experimental study was conducted to evaluate the different solution approaches based on the solution quality and run time. ^ The decomposition approach improved the lower bounds (or linear relaxation solution) of the mixed-integer formulation. At least one of the proposed heuristic outperforms the Modified Delay heuristic from the literature. For sparse problems, almost all the heuristics report a solution close to optimum. GRASP outperforms SA at a higher computational cost. The proposed approaches are viable to implement as the run time is very short. ^

Lattice Boltzmann modeling of fluid flow and solute transport in karst aquifers

A novel modeling approach is applied to karst hydrology. Long-standing problems in karst hydrology and solute transport are addressed using Lattice Boltzmann methods (LBMs). These methods contrast with other modeling approaches that have been applied to karst hydrology. The motivation of this dissertation is to develop new computational models for solving ground water hydraulics and transport problems in karst aquifers, which are widespread around the globe. This research tests the viability of the LBM as a robust alternative numerical technique for solving large-scale hydrological problems. The LB models applied in this research are briefly reviewed and there is a discussion of implementation issues. The dissertation focuses on testing the LB models. The LBM is tested for two different types of inlet boundary conditions for solute transport in finite and effectively semi-infinite domains. The LBM solutions are verified against analytical solutions. Zero-diffusion transport and Taylor dispersion in slits are also simulated and compared against analytical solutions. These results demonstrate the LBM’s flexibility as a solute transport solver. The LBM is applied to simulate solute transport and fluid flow in porous media traversed by larger conduits. A LBM-based macroscopic flow solver (Darcy’s law-based) is linked with an anisotropic dispersion solver. Spatial breakthrough curves in one and two dimensions are fitted against the available analytical solutions. This provides a steady flow model with capabilities routinely found in ground water flow and transport models (e.g., the combination of MODFLOW and MT3D). However the new LBM-based model retains the ability to solve inertial flows that are characteristic of karst aquifer conduits. Transient flows in a confined aquifer are solved using two different LBM approaches. The analogy between Fick’s second law (diffusion equation) and the transient ground water flow equation is used to solve the transient head distribution. An altered-velocity flow solver with source/sink term is applied to simulate a drawdown curve. Hydraulic parameters like transmissivity and storage coefficient are linked with LB parameters. These capabilities complete the LBM’s effective treatment of the types of processes that are simulated by standard ground water models. The LB model is verified against field data for drawdown in a confined aquifer.

Makespan minimization in a job shop with a batch processing machine

A job shop with one batch processing and several discrete machines is analyzed. Given a set of jobs, their process routes, processing requirements, and size, the objective is to schedule the jobs such that the makespan is minimized. The batch processing machine can process a batch of jobs as long as the machine capacity is not violated. The batch processing time is equal to the longest processing job in the batch. The problem under study can be represented as Jm:batch:Cmax. If no batches were formed, the scheduling problem under study reduces to the classical job shop scheduling problem (i.e. Jm:: Cmax), which is known to be NP-hard. This research extends the scheduling literature by combining Jm::Cmax with batch processing. The primary contributions are the mathematical formulation, a new network representation and several solution approaches. The problem under study is observed widely in metal working and other industries, but received limited or no attention due to its complexity. A novel network representation of the problem using disjunctive and conjunctive arcs, and a mathematical formulation are proposed to minimize the makespan. Besides that, several algorithms, like batch forming heuristics, dispatching rules, Modified Shifting Bottleneck, Tabu Search (TS) and Simulated Annealing (SA), were developed and implemented. An experimental study was conducted to evaluate the proposed heuristics, and the results were compared to those from a commercial solver (i.e., CPLEX). TS and SA, with the combination of MWKR-FF as the initial solution, gave the best solutions among all the heuristics proposed. Their results were close to CPLEX; and for some larger instances, with total operations greater than 225, they were competitive in terms of solution quality and runtime. For some larger problem instances, CPLEX was unable to report a feasible solution even after running for several hours. Between SA and the experimental study indicated that SA produced a better average Cmax for all instances. The solution approaches proposed will benefit practitioners to schedule a job shop (with both discrete and batch processing machines) more efficiently. The proposed solution approaches are easier to implement and requires short run times to solve large problem instances.

The order selection and lot sizing problem in the make-to-order environment

This research is motivated by the need for considering lot sizing while accepting customer orders in a make-to-order (MTO) environment, in which each customer order must be delivered by its due date. Job shop is the typical operation model used in an MTO operation, where the production planner must make three concurrent decisions; they are order selection, lot size, and job schedule. These decisions are usually treated separately in the literature and are mostly led to heuristic solutions. The first phase of the study is focused on a formal definition of the problem. Mathematical programming techniques are applied to modeling this problem in terms of its objective, decision variables, and constraints. A commercial solver, CPLEX is applied to solve the resulting mixed-integer linear programming model with small instances to validate the mathematical formulation. The computational result shows it is not practical for solving problems of industrial size, using a commercial solver. The second phase of this study is focused on development of an effective solution approach to this problem of large scale. The proposed solution approach is an iterative process involving three sequential decision steps of order selection, lot sizing, and lot scheduling. A range of simple sequencing rules are identified for each of the three subproblems. Using computer simulation as the tool, an experiment is designed to evaluate their performance against a set of system parameters. For order selection, the proposed weighted most profit rule performs the best. The shifting bottleneck and the earliest operation finish time both are the best scheduling rules. For lot sizing, the proposed minimum cost increase heuristic, based on the Dixon-Silver method performs the best, when the demand-to-capacity ratio at the bottleneck machine is high. The proposed minimum cost heuristic, based on the Wagner-Whitin algorithm is the best lot-sizing heuristic for shops of a low demand-to-capacity ratio. The proposed heuristic is applied to an industrial case to further evaluate its performance. The result shows it can improve an average of total profit by 16.62%. This research contributes to the production planning research community with a complete mathematical definition of the problem and an effective solution approach to solving the problem of industry scale.

Minimizing makespan for hybrid flowshops with batch, discrete processing machines and arbitrary job sizes

This research aims at a study of the hybrid flow shop problem which has parallel batch-processing machines in one stage and discrete-processing machines in other stages to process jobs of arbitrary sizes. The objective is to minimize the makespan for a set of jobs. The problem is denoted as: FF: batch1,sj:Cmax. The problem is formulated as a mixed-integer linear program. The commercial solver, AMPL/CPLEX, is used to solve problem instances to their optimality. Experimental results show that AMPL/CPLEX requires considerable time to find the optimal solution for even a small size problem, i.e., a 6-job instance requires 2 hours in average. A bottleneck-first-decomposition heuristic (BFD) is proposed in this study to overcome the computational (time) problem encountered while using the commercial solver. The proposed BFD heuristic is inspired by the shifting bottleneck heuristic. It decomposes the entire problem into three sub-problems, and schedules the sub-problems one by one. The proposed BFD heuristic consists of four major steps: formulating sub-problems, prioritizing sub-problems, solving sub-problems and re-scheduling. For solving the sub-problems, two heuristic algorithms are proposed; one for scheduling a hybrid flow shop with discrete processing machines, and the other for scheduling parallel batching machines (single stage). Both consider job arrival and delivery times. An experiment design is conducted to evaluate the effectiveness of the proposed BFD, which is further evaluated against a set of common heuristics including a randomized greedy heuristic and five dispatching rules. The results show that the proposed BFD heuristic outperforms all these algorithms. To evaluate the quality of the heuristic solution, a procedure is developed to calculate a lower bound of makespan for the problem under study. The lower bound obtained is tighter than other bounds developed for related problems in literature. A meta-search approach based on the Genetic Algorithm concept is developed to evaluate the significance of further improving the solution obtained from the proposed BFD heuristic. The experiment indicates that it reduces the makespan by 1.93 % in average within a negligible time when problem size is less than 50 jobs.