A modified Intelligent Water Drops algorithm and its application to optimization problems

The Intelligent Water Drop (IWD) algorithm is a recent stochastic swarm-based method that is useful for solving combinatorial and function optimization problems. In this paper, we investigate the effectiveness of the selection method in the solution construction phase of the IWD algorithm. Instead of the fitness proportionate selection method in the original IWD algorithm, two ranking-based selection methods, namely linear ranking and exponential ranking, are proposed. Both ranking-based selection methods aim to solve the identified limitations of the fitness proportionate selection method as well as to enable the IWD algorithm to escape from local optima and ensure its search diversity. To evaluate the usefulness of the proposed ranking-based selection methods, a series of experiments pertaining to three combinatorial optimization problems, i.e., rough set feature subset selection, multiple knapsack and travelling salesman problems, is conducted. The results demonstrate that the exponential ranking selection method is able to preserve the search diversity, therefore improving the performance of the IWD algorithm. © 2014 Elsevier Ltd. All rights reserved.

New cutting-planes for the time-and/or precedence-constrained ATSP and directed VRP

In this paper, we introduce five classes of new valid cutting planes for the precedence-constrained (PC) and/or time-window-constrained (TW) Asymmetric Travelling Salesman Problems (ATSPs) and directed Vehicle Routing Problems (VRPs). We show that all five classes of new inequalities are facet-defining for the directed VRP-TW, under reasonable conditions and the assumption that vehicles are identical. Similar proofs can be developed for the VRP-PC. As ATSP-TW and PC-ATSP can be formulated as directed identical-vehicle VRP-TW and PC-VRP, respectively, this provides a link to study the polyhedral combinatorics for the ATSP-TW and PC-ATSP. The first four classes of these new cutting planes are cycle-breaking inequalities that are lifted from the well-known D^-_k and D⁺_k inequalities (see Grötschel and Padberg in Polyhedral theory. The traveling salesman problem: a guided tour of combinatorial optimization, Wiley, New York, 1985). The last class of new cutting planes, the TW ₂ inequalities, are infeasible-path elimination inequalities. Separation of these constraints will also be discussed. We also present prelimanry numerical results to demonstrate the strengh of these new cutting planes.

On the kidney exchange problem: cardinality constrained cycle and chain problems on directed graphs: a survey of integer programming approaches

The Kidney Exchange Problem (KEP) is a combinatorial optimization problem and has attracted the attention from the community of integer programming/combinatorial optimisation in the past few years. Defined on a directed graph, the KEP has two variations: one concerns cycles only, and the other, cycles as well as chains on the same graph. We call the former a Cardinality Constrained Multi-cycle Problem (CCMcP) and the latter a Cardinality Constrained Cycles and Chains Problem (CCCCP). The cardinality for cycles is restricted in both CCMcP and CCCCP. As for chains, some studies in the literature considered cardinality restrictions, whereas others did not. The CCMcP can be viewed as an Asymmetric Travelling Salesman Problem that does allow subtours, however these subtours are constrained by cardinality, and that it is not necessary to visit all vertices. In existing literature of the KEP, the cardinality constraint for cycles is usually considered to be small (to the best of our knowledge, no more than six). In a CCCCP, each vertex on the directed graph can be included in at most one cycle or chain, but not both. The CCMcP and the CCCCP are interesting and challenging combinatorial optimization problems in their own rights, particularly due to their similarities to some travelling salesman- and vehicle routing-family of problems. In this paper, our main focus is to review the existing mathematical programming models and solution methods in the literature, analyse the performance of these models, and identify future research directions. Further, we propose a polynomial-sized and an exponential-sized mixed-integer linear programming model, discuss a number of stronger constraints for cardinality-infeasible-cycle elimination for the latter, and present some preliminary numerical results.

Polyhedral results for the Cardinality Constrained Multi-cycle Problem (CCMcP) and the Cardinality Constrained Cycles and Chains Problem (CCCCP)

In recent years, there has been studies on the cardinality constrained multi-cycle problems on directed graphs, some of which considered chains co-existing on the same digraph whilst others did not. These studies were inspired by the optimal matching of kidneys known as the Kidney Exchange Problem (KEP). In a KEP, a vertex on the digraph represents a donor-patient pair who are related, though the kidney of the donor is incompatible to the patient. When there are multiple such incompatible pairs in the kidney exchange pool, the kidney of the donor of one incompatible pair may in fact be compatible to the patient of another incompatible pair. If Donor A’s kidney is suitable for Patient B, and vice versa, then there will be arcs in both directions between Vertex A to Vertex B. Such exchanges form a 2-cycle. There may also be cycles involving 3 or more vertices. As all exchanges in a kidney exchange cycle must take place simultaneously, (otherwise a donor can drop out from the program once his/her partner has received a kidney from another donor), due to logistic and human resource reasons, only a limited number of kidney exchanges can occur simultaneously, hence the cardinality of these cycles are constrained. In recent years, kidney exchange programs around the world have altruistic donors in the pool. A sequence of exchanges that starts from an altruistic donor forms a chain instead of a cycle. We therefore have two underlying combinatorial optimization problems: Cardinality Constrained Multi-cycle Problem (CCMcP) and the Cardinality Constrained Cycles and Chains Problem (CCCCP). The objective of the KEP is either to maximize the number of kidney matches, or to maximize a certain weighted function of kidney matches. In a CCMcP, a vertex can be in at most one cycle whereas in a CCCCP, a vertex can be part of (but in no more than) a cycle or a chain. The cardinality of the cycles are constrained in all studies. The cardinality of the chains, however, are considered unconstrained in some studies, constrained but larger than that of cycles, or the same as that of cycles in others. Although the CCMcP has some similarities to the ATSP- and VRP-family of problems, there is a major difference: strong subtour elimination constraints are mostly invalid for the CCMcP, as we do allow smaller subtours as long as they do not exceed the size limit. The CCCCP has its distinctive feature that allows chains as well as cycles on the same directed graph. Hence, both the CCMcP and the CCCCP are interesting and challenging combinatorial optimization problems in their own rights. Most existing studies focused on solution methodologies, and as far as we aware, there is no polyhedral studies so far. In this paper, we will study the polyhedral structure of the natural arc-based integer programming models of the CCMcP and the CCCCP, both containing exponentially many constraints. We do so to pave the way for studying strong valid cuts we have found that can be applied in a Lagrangean relaxation-based branch-and-bound framework where at each node of the branch-and-bound tree, we may be able to obtain a relaxation that can be solved in polynomial time, with strong valid cuts dualized into the objective function and the dual multipliers optimised by subgradient optimisation.

Challenges of continuous global optimization in molecular structure prediction

The molecular geometry, the three dimensional arrangement of atoms in space, is a major factor determining the properties and reactivity of molecules, biomolecules and macromolecules. Computation of stable molecular conformations can be done by locating minima on the potential energy surface (PES). This is a very challenging global optimization problem because of extremely large numbers of shallow local minima and complicated landscape of PES. This paper illustrates the mathematical and computational challenges on one important instance of the problem, computation of molecular geometry of oligopeptides, and proposes the use of the Extended Cutting Angle Method (ECAM) to solve this problem.

ECAM is a deterministic global optimization technique, which computes tight lower bounds on the values of the objective function and fathoms those part of the domain where the global minimum cannot reside. As with any domain partitioning scheme, its challenge is an extremely large partition of the domain required for accurate lower bounds. We address this challenge by providing an efficient combinatorial algorithm for calculating the lower bounds, and by combining ECAM with a local optimization method, while preserving the deterministic character of ECAM.

Combinatorial problem arising in chaotic control

An optimization problem arising in the analysis of controllability and stabilization of cycles in discrete time chaotic systems is considered.

Development of combinatorial RNAi transgenes targeting influenza virus

This research investigated the optimization of RNA interference against influenza A viruses. Results obtained in this study increase knowledge of the use of RNA interference in the context of creating antiviral transgenes capable of simultaneously targeting multiple viral genes and preventing the risk of viral escape.

An ensemble of intelligent water drop algorithms and its application to optimization problems

Crown Copyright © 2015 Published by Elsevier Inc. All rights reserved. The Intelligent Water Drop (IWD) algorithm is a recent stochastic swarm-based method that is useful for solving combinatorial and function optimization problems. In this paper, we propose an IWD ensemble known as the Master-River, Multiple-Creek IWD (MRMC-IWD) model, which serves as an extension of the modified IWD algorithm. The MRMC-IWD model aims to improve the exploration capability of the modified IWD algorithm. It comprises a master river which cooperates with multiple independent creeks to undertake optimization problems based on the divide-and-conquer strategy. A technique to decompose the original problem into a number of sub-problems is first devised. Each sub-problem is then assigned to a creek, while the overall solution is handled by the master river. To empower the exploitation capability, a hybrid MRMC-IWD model is introduced. It integrates the iterative improvement local search method with the MRMC-IWD model to allow a local search to be conducted, therefore enhancing the quality of solutions provided by the master river. To evaluate the effectiveness of the proposed models, a series of experiments pertaining to two combinatorial problems, i.e., the travelling salesman problem (TSP) and rough set feature subset selection (RSFS), are conducted. The results indicate that the MRMC-IWD model can satisfactorily solve optimization problems using the divide-and-conquer strategy. By incorporating a local search method, the resulting hybrid MRMC-IWD model not only is able to balance exploration and exploitation, but also to enable convergence towards the optimal solutions, by employing a local search method. In all seven selected TSPLIB problems, the hybrid MRMC-IWD model achieves good results, with an average deviation of 0.021% from the best known optimal tour lengths. Compared with other state-of-the-art methods, the hybrid MRMC-IWD model produces the best results (i.e. the shortest and uniform reducts of 20 runs) for all13 selected RSFS problems.