Identification of full and partial class relevant genes

Multiclass cancer classification on microarray data has provided the feasibility of cancer diagnosis across all of the common malignancies in parallel. Using multiclass cancer feature selection approaches, it is now possible to identify genes relevant to a set of cancer types. However, besides identifying the relevant genes for the set of all cancer types, it is deemed to be more informative to biologists if the relevance of each gene to specific cancer or subset of cancer types could be revealed or pinpointed. In this paper, we introduce two new definitions of multiclass relevancy features, i.e., full class relevant (FCR) and partial class relevant (PCR) features. Particularly, FCR denotes genes that serve as candidate biomarkers for discriminating all cancer types. PCR, on the other hand, are genes that distinguish subsets of cancer types. Subsequently, a Markov blanket embedded memetic algorithm is proposed for the simultaneous identification of both FCR and PCR genes. Results obtained on commonly used synthetic and real-world microarray data sets show that the proposed approach converges to valid FCR and PCR genes that would assist biologists in their research work. The identification of both FCR and PCR genes is found to generate improvement in classification accuracy on many microarray data sets. Further comparison study to existing state-of-the-art feature selection algorithms also reveals the effectiveness and efficiency of the proposed approach.

Evolving cell models for systems and synthetic biology

This paper proposes a new methodology for the automated design of cell models for systems and synthetic biology. Our modelling framework is based on P systems, a discrete, stochastic and modular formal modelling language. The automated design of biological models comprising the optimization of the model structure and its stochastic kinetic constants is performed using an evolutionary algorithm. The evolutionary algorithm evolves model structures by combining different modules taken from a predefined module library and then it fine-tunes the associated stochastic kinetic constants. We investigate four alternative objective functions for the fitness calculation within the evolutionary algorithm: (1) equally weighted sum method, (2) normalization method, (3) randomly weighted sum method, and (4) equally weighted product method. The effectiveness of the methodology is tested on four case studies of increasing complexity including negative and positive autoregulation as well as two gene networks implementing a pulse generator and a bandwidth detector. We provide a systematic analysis of the evolutionary algorithm’s results as well as of the resulting evolved cell models.

Optimal Solutions of Multiproduct Batch Chemical Process Using Multiobjective Genetic Algorithm with Expert Decision System

Optimal design problem are widely known by their multiple performance measures that are often competing with each other. In this paper, an optimal multiproduct batch chemical plant design is presented. The design is firstly formulated as a multiobjective optimization problem, to be solved using the well suited non dominating sorting genetic algorithm (NSGA-II). The NSGA-II have capability to achieve fine tuning of variables in determining a set of non dominating solutions distributed along the Pareto front in a single run of the algorithm. The NSGA-II ability to identify a set of optimal solutions provides the decision-maker DM with a complete picture of the optimal solution space to gain better and appropriate choices. Then an outranking with PROMETHEE II helps the decision-maker to finalize the selection of a best compromise. The effectiveness of NSGA-II method with multiojective optimization problem is illustrated through two carefully referenced examples.

Local search with quadratic approximations into memetic algorithms for optimization with multiple criteria

This paper proposes a local search optimizer that, employed as an additional operator in multiobjective evolutionary techniques, can help to find more precise estimates of the Pareto-optimal surface with a smaller cost of function evaluation. The new operator employs quadratic approximations of the objective functions and constraints, which are built using only the function samples already produced by the usual evolutionary algorithm function evaluations. The local search phase consists of solving the auxiliary multiobjective quadratic optimization problem defined from the quadratic approximations, scalarized via a goal attainment formulation using an LMI solver. As the determination of the new approximated solutions is performed without the need of any additional function evaluation, the proposed methodology is suitable for costly black-box optimization problems.

A hybrid quantum-inspired genetic algorithm for multiobjective flow shop scheduling

This paper proposes a hybrid quantum-inspired genetic algorithm (HQGA) for the multiobjective flow shop scheduling problem (FSSP), which is a typical NP-hard combinatorial optimization problem with strong engineering backgrounds. On the one hand, a quantum-inspired GA (QGA) based on Q-bit representation is applied for exploration in the discrete 0-1 hyperspace by using the updating operator of quantum gate and genetic operators of Q-bit. Moreover, random-key representation is used to convert the Q-bit representation to job permutation for evaluating the objective values of the schedule solution. On the other hand, permutation-based GA (PGA) is applied for both performing exploration in permutation-based scheduling space and stressing exploitation for good schedule solutions. To evaluate solutions in multiobjective sense, a randomly weighted linear-sum function is used in QGA, and a nondominated sorting technique including classification of Pareto fronts and fitness assignment is applied in PGA with regard to both proximity and diversity of solutions. To maintain the diversity of the population, two trimming techniques for population are proposed. The proposed HQGA is tested based on some multiobjective FSSPs. Simulation results and comparisons based on several performance metrics demonstrate the effectiveness of the proposed HQGA.

Multiobjective Optimization and Hybrid Evolutionary Algorithm to Solve Constrained Optimization Problems

This paper presents a novel evolutionary algorithm (EA) for constrained optimization problems, i.e., the hybrid constrained optimization EA (HCOEA). This algorithm effectively combines multiobjective optimization with global and local search models. In performing the global search, a niching genetic algorithm based on tournament selection is proposed. Also, HCOEA has adopted a parallel local search operator that implements a clustering partition of the population and multiparent crossover to generate the offspring population. Then, nondominated individuals in the offspring population are used to replace the dominated individuals in the parent population. Meanwhile, the best infeasible individual replacement scheme is devised for the purpose of rapidly guiding the population toward the feasible region of the search space. During the evolutionary process, the global search model effectively promotes high population diversity, and the local search model remarkably accelerates the convergence speed. HCOEA is tested on 13 well-known benchmark functions, and the experimental results suggest that it is more robust and efficient than other state-of-the-art algorithms from the literature in terms of the selected performance metrics, such as the best, median, mean, and worst objective function values and the standard deviations.

Evolutionary Algorithms Refining a Heuristic: A Hybrid Method for Shared-Path Protections in WDM Networks Under SRLG Constraints

An evolutionary algorithm (EA) can be used to tune the control parameters of a construction heuristic to an optimization problem and generate a nearly optimal solution. This approach is in the spirit of indirect encoding EAs. Its performance relies on both the heuristic and the EA. This paper proposes a three-phase parameterized construction heuristic for the shared-path protection problem in wavelength division multiplexing networks with shared-risk link group constraints and applies an EA for optimizing the control parameters of the proposed heuristics. The experimental results show that the proposed approach is effective on all the tested network instances. It was also demonstrated that an EA with guided mutation performs better than a conventional genetic algorithm for tuning the control parameters, which indicates that a combination of global statistical information extracted from the previous search and location information of the best solutions found so far could improve the performance of an algorithm.

An Effective PSO-Based Memetic Algorithm for Flow Shop Scheduling

This paper proposes an effective particle swarm optimization (PSO)-based memetic algorithm (MA) for the permutation flow shop scheduling problem (PFSSP) with the objective to minimize the maximum completion time, which is a typical non-deterministic polynomial-time (NP) hard combinatorial optimization problem. In the proposed PSO-based MA (PSOMA), both PSO-based searching operators and some special local searching operators are designed to balance the exploration and exploitation abilities. In particular, the PSOMA applies the evolutionary searching mechanism of PSO, which is characterized by individual improvement, population cooperation, and competition to effectively perform exploration. On the other hand, the PSOMA utilizes several adaptive local searches to perform exploitation. First, to make PSO suitable for solving PFSSP, a ranked-order value rule based on random key representation is presented to convert the continuous position values of particles to job permutations. Second, to generate an initial swarm with certain quality and diversity, the famous Nawaz-Enscore-Ham (NEH) heuristic is incorporated into the initialization of population. Third, to balance the exploration and exploitation abilities, after the standard PSO-based searching operation, a new local search technique named NEH_1 insertion is probabilistically applied to some good particles selected by using a roulette wheel mechanism with a specified probability. Fourth, to enrich the searching behaviors and to avoid premature convergence, a simulated annealing (SA)-based local search with multiple different neighborhoods is designed and incorporated into the PSOMA. Meanwhile, an effective adaptive meta-Lamarckian learning strategy is employed to decide which neighborhood to be used in SA-based local search. Finally, to further enhance the exploitation ability, a pairwise-based local search is applied after the SA-based search. Simulation results based on benchmarks demonstrate the effectiveness of the PSOMA. Additionally, the effects of some parameters on optimization performances are also discussed.

A Memetic Algorithm for VLSI Floorplanning

Floorplanning is an important problem in very large scale integrated-circuit (VLSI) design automation as it determines the performance, size, yield, and reliability of VLSI chips. From the computational point of view, VLSI floorplanning is an NP-hard problem. In this paper, a memetic algorithm (MA) for a nonslicing and hard-module VLSI floorplanning problem is presented. This MA is a hybrid genetic algorithm that uses an effective genetic search method to explore the search space and an efficient local search method to exploit information in the search region. The exploration and exploitation are balanced by a novel bias search strategy. The MA has been implemented and tested on popular benchmark problems. Experimental results show that the MA can quickly produce optimal or nearly optimal solutions for all the tested benchmark problems.