Using genetic algorithms to solve combinatorial optimization problems

Genetic algorithms are stochastic search techniques based on the mechanics of natural selection and natural genetics. Genetic algorithms differ from traditional analytical methods by using genetic operators and historic cumulative information to prune the search space and generate plausible solutions. Recent research has shown that genetic algorithms have a large range and growing number of applications. The research presented in this thesis is that of using genetic algorithms to solve some typical combinatorial optimization problems, namely the Clique, Vertex Cover and Max Cut problems. All of these are NP-Complete problems. The empirical results show that genetic algorithms can provide efficient search heuristics for solving these combinatorial optimization problems. Genetic algorithms are inherently parallel. The Connection Machine system makes parallel implementation of these inherently parallel algorithms possible. Both sequential genetic algorithms and parallel genetic algorithms for Clique, Vertex Cover and Max Cut problems have been developed and implemented on the SUN4 and the Connection Machine systems respectively

Systems approaches and algorithms for discovery of combinatorial therapies

Effective therapy of complex diseases requires control of highly non-linear complex networks that remain incompletely characterized. In particular, drug intervention can be seen as control of signaling in cellular networks. Identification of control parameters presents an extreme challenge due to the combinatorial explosion of control possibilities in combination therapy and to the incomplete knowledge of the systems biology of cells. In this review paper we describe the main current and proposed approaches to the design of combinatorial therapies, including the empirical methods used now by clinicians and alternative approaches suggested recently by several authors. New approaches for designing combinations arising from systems biology are described. We discuss in special detail the design of algorithms that identify optimal control parameters in cellular networks based on a quantitative characterization of control landscapes, maximizing utilization of incomplete knowledge of the state and structure of intracellular networks. The use of new technology for high-throughput measurements is key to these new approaches to combination therapy and essential for the characterization of control landscapes and implementation of the algorithms. Combinatorial optimization in medical therapy is also compared with the combinatorial optimization of engineering and materials science and similarities and differences are delineated.Comment: 25 page

Biogeography-Based Optimization for Combinatorial Problems and Complex Systems

Biogeography-based optimization (BBO) is a heuristic evolutionary algorithm that has shown good performance on many problems. In this dissertation, three problem1s 1 are researched for BBO: convergence speed and optimal solution convergence of BBO,1 1BBO application to combinatorial problems, and BBO application to complex systems. The first problem is to analyze BBO from two perspectives: how the components of BBO affect its convergence speed and the reason that BBO converges to the optimal solution. For the first perspective, which is convergence speed, we analyze the two essential components of BBO -- population construction and information sharing. For the second perspective, a mathematical BBO model is built to theoretically prove why BBO is capable of reaching the global optimum for any problem. In the second problem addressed by the dissertation, BBO is applied to combinatorial problems. Our research includes the study of migration, local search, population initialization, and greedy methods for combinatorial problems. We conduct a series of simulations based on four benchmarks, the sizes of which vary from small to extra large. The simulation results indicate that when combined with other techniques, the performance of BBO can be significantly improved. Also, a BBO graphical user interface (GUI) is created for combinatorial problems, which is an intuitive way to experiment with BBO algorithms, including hybrid BBO algorithms. The third and final problem addressed in this dissertation is the optimization of complex systems. We invent a new algorithm for complex system optimization based on BBO, which is called BBO/complex. Four real world problems are used to test BBO/Complex and compare with other complex system optimization algorithms, and we obtain encouraging results from BBO/Complex. Then, a Markov model is created for BBO/Complex. Simulation results are provided to confirm the mode

Combinatorial optimization and metaheuristics

Today, combinatorial optimization is one of the youngest and most active areas of discrete mathematics. It is a branch of optimization in applied mathematics and computer science, related to operational research, algorithm theory and computational complexity theory. It sits at the intersection of several fields, including artificial intelligence, mathematics and software engineering. Its increasing interest arises for the fact that a large number of scientific and industrial problems can be formulated as abstract combinatorial optimization problems, through graphs and/or (integer) linear programs. Some of these problems have polynomial-time (“efficient”) algorithms, while most of them are NP-hard, i.e. it is not proved that they can be solved in polynomial-time. Mainly, it means that it is not possible to guarantee that an exact solution to the problem can be found and one has to settle for an approximate solution with known performance guarantees. Indeed, the goal of approximate methods is to find “quickly” (reasonable run-times), with “high” probability, provable “good” solutions (low error from the real optimal solution). In the last 20 years, a new kind of algorithm commonly called metaheuristics have emerged in this class, which basically try to combine heuristics in high level frameworks aimed at efficiently and effectively exploring the search space. This report briefly outlines the components, concepts, advantages and disadvantages of different metaheuristic approaches from a conceptual point of view, in order to analyze their similarities and differences. The two very significant forces of intensification and diversification, that mainly determine the behavior of a metaheuristic, will be pointed out. The report concludes by exploring the importance of hybridization and integration methods