A graph-based gene selection method for medical diagnosis problems using a many-objective PSO algorithm

Background Gene expression data play an important role in bioinformatics applications. Although there may be a large number of features in such data, they mainly tend to contain only a few samples. This can negatively impact the performance of data mining and machine learning algorithms. One of the most effective approaches to alleviate this problem is to use gene selection methods. The aim of gene selection is to reduce the dimensions (features) of gene expression data leading to eliminating irrelevant and redundant genes. Methods This paper presents a hybrid gene selection method based on graph theory and a many-objective particle swarm optimization (PSO) algorithm. To this end, a filter method is first utilized to reduce the initial space of the genes. Then, the gene space is represented as a graph to apply a graph clustering method to group the genes into several clusters. Moreover, the many-objective PSO algorithm is utilized to search an optimal subset of genes according to several criteria, which include classification error, node centrality, specificity, edge centrality, and the number of selected genes. A repair operator is proposed to cover the whole space of the genes and ensure that at least one gene is selected from each cluster. This leads to an increasement in the diversity of the selected genes. Results To evaluate the performance of the proposed method, extensive experiments are conducted based on seven datasets and two evaluation measures. In addition, three classifiers—Decision Tree (DT), Support Vector Machine (SVM), and K-Nearest Neighbors (KNN)—are utilized to compare the effectiveness of the proposed gene selection method with other state-of-the-art methods. The results of these experiments demonstrate that our proposed method not only achieves more accurate classification, but also selects fewer genes than other methods. Conclusion This study shows that the proposed multi-objective PSO algorithm simultaneously removes irrelevant and redundant features using several different criteria. Also, the use of the clustering algorithm and the repair operator has improved the performance of the proposed method by covering the whole space of the problem.

Reliability-Based Robust Design Optimization in Consideration of Manufacturing Tolerance by Multi-Objective Evolutionary Optimization with Repair Algorithm

There are inherently various uncertainties in practical engineering, and reliability-based design optimization (RBDO) and robust design optimization (RDO) are two well-established methodologies when considering the uncertainties. Naturally, reliability-based robust design optimization (RBRDO) is a methodology developed recently by combining RBDO and RDO, in which the tolerances of random design variables are always assumed as constants. However, the tolerance of random design variables is a key factor for the objective robustness and manufacturing cost, and the tolerance allocation is the core problem in mechanical manufacturing. Inspired by the cost–tolerance relationship in mechanical manufacturing, this paper presents an integrated framework to simultaneously find the optimal design variable and the corresponding tolerance in the multi-objective RBRDO, with the trade-off between objective robustness and manufacturing cost. The failure mechanism of the constraint handling strategy of the constrained reference vector-guided evolutionary algorithm (C-RVEA) is discussed to solve the multi-objective optimization formulation. Then the robust repair operator and reliability-based repair operator are proposed to transform unfeasible solutions to the feasible ones under reliability constraints. Numerical results reveal that the proposed repair algorithm is effective. By solving the integrated multi-objective optimization problem, the Pareto front with the compromised solutions between the objective robustness and manufacturing cost could be obtained, from which decision makers can select the satisfying solution conveniently according to the preferred requirements.

A coevolutionary algorithm based on the auxiliary population for constrained large-scale multi-objective supply chain network

<abstract> <p>Supply chain network is important for the enterprise to improve the operation and management, but has become more complicated to optimize in reality. With the consideration of multiple objectives and constraints, this paper proposes a constrained large-scale multi-objective supply chain network (CLMSCN) optimization model. This model is to minimize the total operation cost (including the costs of production, transportation, and inventory) and to maximize the customer satisfaction under the capacity constraints. Besides, a coevolutionary algorithm based on the auxiliary population (CAAP) is proposed, which uses two populations to solve the CLMSCN problem. One population is to solve the original complex problem, and the other population is to solve the problem without any constraints. If the infeasible solutions are generated in the first population, a linear repair operator will be used to improve the feasibility of these solutions. To validate the effectivity of the CAAP algorithm, the experiment is conducted on the randomly generated instances with three different problem scales. The results show that the CAAP algorithm can outperform other compared algorithms, especially on the large-scale instances.</p> </abstract>

Interactive Genetic Algorithms for Optimal Assignment of Blocks into Workspaces of Shipbuilding Industry

In this paper one of the fundamental problems of Shipbuilding Industry known as block assignment problem is modeled and solved. The irregular shape of blocks and the inherent intractability of this problem is the primary motivation to use the interactive genetic algorithms with a specialized chromosome level “repair” operator. Without loss of generality, some domain knowledge has been incorporated during the process of exploration and exploitation of an optimal assignment. Therefore the best attributes of objective and subjective evaluation at system level has been realized. The experimental study confirms that the incorporation of the domain knowledge and a new repair operator in interactive genetic algorithms for assigning blocks in workspaces leads to faster convergence and at the same time it reduces the local optimality.