A Review of Computational Methods for Clustering Genes with Similar Biological Functions <s> Optimization for Objective Function of Partitioning Clustering Techniques <s> Cellular Robotic Systems are capable of ’intelligent* behavior. The meaning of this intelligence is analyzed in the paper. We define robot intelligence and robot system intelligence in terms of unpredictability of improbable behavior. The concept of unpredictability is analyzed in relation to (1) statistical unpredictability, (2) inaccessibility, (3) undecidability, (4) intractability, and (5) non-representability. We argue that the latter two type of unpredictability, when exhibited by systems capable of producing order, can result in a non-trivial, different form of intelligent behavior (Swarm Intelligence). Engineering problems related to Swarm Intelligence are mentioned in relation to Cellular Robotic Systems which consist of collections of autonomous, non-synchronized, non-intelligent robots cooperating to achieve global tasks. <s> BIB001 </s> A Review of Computational Methods for Clustering Genes with Similar Biological Functions <s> Optimization for Objective Function of Partitioning Clustering Techniques <s> Clustering aims at representing large datasets by a fewer number of prototypes or clusters. It brings simplicity in modeling data and thus plays a central role in the process of knowledge discovery and data mining. Data mining tasks, in these days, require fast and accurate partitioning of huge datasets, which may come with a variety of attributes or features. This, in turn, imposes severe computational requirements on the relevant clustering techniques. A family of bio-inspired algorithms, well-known as Swarm Intelligence (SI) has recently emerged that meets these requirements and has successfully been applied to a number of real world clustering problems. This chapter explores the role of SI in clustering different kinds of datasets. It finally describes a new SI technique for partitioning any dataset into an optimal number of groups through one run of optimization. Computer simulations undertaken in this research have also been provided to demonstrate the effectiveness of the proposed algorithm. <s> BIB002 </s> A Review of Computational Methods for Clustering Genes with Similar Biological Functions <s> Optimization for Objective Function of Partitioning Clustering Techniques <s> Swarm intelligence is an emerging area in the field of optimization and researchers have developed various algorithms by modeling the behaviors of different swarm of animals and insects such as ants, termites, bees, birds, fishes. In 1990s, Ant Colony Optimization based on ant swarm and Particle Swarm Optimization based on bird flocks and fish schools have been introduced and they have been applied to solve optimization problems in various areas within a time of two decade. However, the intelligent behaviors of bee swarm have inspired the researchers especially during the last decade to develop new algorithms. This work presents a survey of the algorithms described based on the intelligence in bee swarms and their applications. <s> BIB003 </s> A Review of Computational Methods for Clustering Genes with Similar Biological Functions <s> Optimization for Objective Function of Partitioning Clustering Techniques <s> In this paper, the algorithmic concepts of the Cuckoo-search (CK), Particle swarm optimization (PSO), Differential evolution (DE) and Artificial bee colony (ABC) algorithms have been analyzed. The numerical optimization problem solving successes of the mentioned algorithms have also been compared statistically by testing over 50 different benchmark functions. Empirical results reveal that the problem solving success of the CK algorithm is very close to the DE algorithm. The run-time complexity and the required function-evaluation number for acquiring global minimizer by the DE algorithm is generally smaller than the comparison algorithms. The performances of the CK and PSO algorithms are statistically closer to the performance of the DE algorithm than the ABC algorithm. The CK and DE algorithms supply more robust and precise results than the PSO and ABC algorithms. <s> BIB004 </s> A Review of Computational Methods for Clustering Genes with Similar Biological Functions <s> Optimization for Objective Function of Partitioning Clustering Techniques <s> In this study, a new metaheuristic optimization algorithm, called cuckoo search (CS), is introduced for solving structural optimization tasks. The new CS algorithm in combination with Levy flights is first verified using a benchmark nonlinear constrained optimization problem. For the validation against structural engineering optimization problems, CS is subsequently applied to 13 design problems reported in the specialized literature. The performance of the CS algorithm is further compared with various algorithms representative of the state of the art in the area. The optimal solutions obtained by CS are mostly far better than the best solutions obtained by the existing methods. The unique search features used in CS and the implications for future research are finally discussed in detail. <s> BIB005 </s> A Review of Computational Methods for Clustering Genes with Similar Biological Functions <s> Optimization for Objective Function of Partitioning Clustering Techniques <s> In this study, we use a new metaheuristic optimization algorithm, called bat algorithm (BA), to solve constraint optimization tasks. BA is verified using several classical benchmark constraint problems. For further validation, BA is applied to three benchmark constraint engineering problems reported in the specialized literature. The performance of the bat algorithm is compared with various existing algorithms. The optimal solutions obtained by BA are found to be better than the best solutions provided by the existing methods. Finally, the unique search features used in BA are analyzed, and their implications for future research are discussed in detail. <s> BIB006 </s> A Review of Computational Methods for Clustering Genes with Similar Biological Functions <s> Optimization for Objective Function of Partitioning Clustering Techniques <s> High power density welding technologies are widely used nowadays in various fields of engineering. However, a computationally efficient and quick predictive tool to select the operating parameters in order to achieve the specified weld attribute is conspicuously missing in the literature. In the present study, a computationally efficient inverse model has been developed using artificial neural networks (ANNs). These ANNs have been trained with the outputs of physics-based phenomenological model using back-propagation (BP) algorithm, genetic algorithm (GA), particle swarm optimization (PSO) algorithm and bat algorithm (BA) separately to develop both the forward and reverse models. Unlike data driven ANN model, such approach is unique and yet based on science. Power, welding speed, beam radius and power distribution factor have been considered as input process parameters, and four weld attributes, such as length of the pool, depth of penetration of the pool, half-width of the pool and cooling time are treated as the responses. The predicted outputs of both the forward and reverse models are found to be in good agreement with the experimental results. The novelty of this study lies with the development and testing of five neural network-based approaches for carrying out both forward and reverse mappings of the electron beam welding process. <s> BIB007 </s> A Review of Computational Methods for Clustering Genes with Similar Biological Functions <s> Optimization for Objective Function of Partitioning Clustering Techniques <s> Kmeans is one of the most-efficient hard-clustering algorithms. It has been successfully applied to a number of problems. However, the efficiency of kmeans is dependent on its initialization of cluster centres. Different swarm intelligence techniques are applied for clustering problem. In this work, we have considered Ant Lion Optimization (ALO) which is a stochastic global optimization models. In this work Kmeans has been integrated with ALO for optimal clustering. The statistical measures of different performance metrics has been calculated and compared. The proposed method performs preferably better than Kmeans and PSO-Kmeans in terms of sum of intracluster distances and F-measure. <s> BIB008 </s> A Review of Computational Methods for Clustering Genes with Similar Biological Functions <s> Optimization for Objective Function of Partitioning Clustering Techniques <s> Abstract K-Means is a popular cluster analysis method which aims to partition a number of data points into K clusters. It has been successfully applied to a number of problems. However, the efficiency of K-Means depends on its initialization of cluster centers. Different swarm intelligence techniques are applied to clustering problem for enhancing the performance. In this work a hybrid clustering approach based on K-means and Ant Lion Optimization has been considered for optimal cluster analysis. Ant Lion Optimization (ALO) is a stochastic global optimization model. The performance of the proposed algorithm is compared against the performance of K-Means, KMeans-PSO, KMeans-FA, DBSCAN and Revised DBSCAN clustering methods based on different performance metrics. Experimentation is performed on eight datasets, for which the statistical analysis is carried out. The obtained results indicate that the hybrid of K-Means and Ant Lion Optimization method performs preferably better than the other three algorithms in terms of sum of intracluster distances and F-measure. <s> BIB009 </s> A Review of Computational Methods for Clustering Genes with Similar Biological Functions <s> Optimization for Objective Function of Partitioning Clustering Techniques <s> Abstract Abandoned areas with substances potentially harmful to the environment or human health have raised numerous concerns around the world. The objective of the present study is to analyze the possibility of building solar power plants capable of capturing solar energy in unproductive areas, both contaminated and uncontaminated. For this purpose, American data from the National Solar Radiation Database (NSRDB) were used, a collection of hourly solar radiation measurements and meteorological data, as well as data from the RE-Powering America's Land project, run by the United States Environmental Protection Agency (EPA). In the analysis, the information about “mapped area”, “distances to the transmission lines”, “solar direct normal irradiance on a utility scale” and “off-grid direct normal irradiance” were considered. To define the best locations, the data were initially pre-processed. A new hybrid fuzzy c-means (HFCM) algorithm was then applied, initialized, comparatively, by three metaheuristics: Differential Evolution (DE), Genetic Algorithm (GA) and Particle Swarm Optimization (PSO), for the data clustering. The number of clusters obtained was validated by three metrics: Calinski-Harabasz Criterion, Davies-Bouldin Criterion and Silhouette Coefficient, with all three unanimously indicating two clusters as the ideal number: one cluster for locations with greater potential for allocating facilities to capture solar energy, and another for locations with a lower potential. With the new approach, an increase of 23.3% in the training velocity of the HFCM algorithm was identified, which required fewer iterations to achieve the same value of the objective function. Else, a round of experiments was conducted with six different datasets (instances from literature) and the results showed that the proposed method can achieve better results (faster convergence and smaller solution cost) than the classic FCM. Visually, the predominance of the allocation of facilities was perceived in states with a greater average incidence of solar radiation. Therefore, this was the predominant factor in the convergence of the algorithm, which is in accordance with expectations for solar energy. Finally, the social, economic and environmental gains were considered with the revitalization of unproductive land with the possibility of implementing solar power plants in these areas. <s> BIB010 </s> A Review of Computational Methods for Clustering Genes with Similar Biological Functions <s> Optimization for Objective Function of Partitioning Clustering Techniques <s> Approximative methods are widely used in the resolution of complex computational problems, since they are able to present significant results regarding the quality of the solution in a satisfactory time in general. This paper addresses the problem of automatic grouping, admittedly NP-difficult. In the context of this problem, non-exact methods, whose complexity is polynomial, are desirable. To solve the problem, the work presents a metaheuristic based on collective intelligence, inspired by the behavior of the ants. The silhouette index was used to measure the quality of the generated clusters. The results obtained by the proposed algorithm were compared with the literature and indicated that the algorithm is able to find clusters that represent well the original distribution of the data. Key words: Ants colony, clustering, metaheuristics. <s> BIB011 </s> A Review of Computational Methods for Clustering Genes with Similar Biological Functions <s> Optimization for Objective Function of Partitioning Clustering Techniques <s> Abstract In this investigation a new optimization algorithm named as interactive search algorithm (ISA) is presented. This method is developed through modifying and hybridizing the affirmative features of recently developed integrated particle swarm optimization (iPSO) algorithm with the pairwise knowledge sharing mechanism of the teaching and learning based optimization (TLBO) method. Proposed ISA provides two different navigation schemes as Tracking and Interacting. Each agent based on its tendency factor can pick one of these two schemes for searching the domain. Additionally, ISA utilizes an improved fly-back technique to handle problem constraints. The proposed method is tested on a set of mathematical and structural optimization benchmark problems with discrete and continuous variables. Numerical results indicate that the new algorithm is competitive with other well-stablished metaheuristic algorithms. <s> BIB012 </s> A Review of Computational Methods for Clustering Genes with Similar Biological Functions <s> Optimization for Objective Function of Partitioning Clustering Techniques <s> Abstract The binarization of Swarm intelligence continuous metaheuristics is an area of great interest in operations research. This interest is mainly due to the application of binarized metaheuristics to combinatorial problems. In this article we propose a general binarization algorithm called K-means Transition Algorithm (KMTA). KMTA uses K-means clustering technique as learning strategy to perform the binarization process. In particular we apply this mechanism to Cuckoo Search and Black Hole metaheuristics to solve the Set Covering Problem (SCP). A methodology is developed to perform the tuning of parameters. We provide necessary experiments to investigate the role of key ingredients of the algorithm. In addition, with the intention of evaluating the behavior of the binarizations while the algorithms are executed, we use the Page's trend test. Finally to demonstrate the efficiency of our proposal, Set Covering benchmark instances of the literature show that KMTA competes clearly with the state-of-the-art algorithms. <s> BIB013
Optimization for objective function can improve the efficiency of partitioning clustering techniques during initialization of the intended cluster number BIB008 BIB009 . Swarm intelligence is widely used as the objective function for a clustering problem. The number of intended clusters can be predicted based on the typical search of the patterns BIB004  . Swarm intelligence can also be applied through maximizing or minimizing the objective function of clustering BIB004 BIB010 BIB012 . In most studies, swarm intelligence has been mostly used in the field of optimization BIB003 BIB013 . Swarm intelligence refers to the collective behavior of decentralized, self-organized systems of living creatures. The swarm intelligence systems consist typically of a population of simple agents or boids interacting locally with one another and with their environment. The inspiration often comes from nature, especially biological systems BIB001 BIB002 . For modeling the behavior of a swarm, the techniques are made up of animals and insects, such as bees, ants, birds, fishes, and so on BIB013 BIB011 . Most recent studies used swarm intelligence to solve problematic real-world problems such as networking, traffic routing, robotics, economics, industry, games, etc. BIB003 BIB013 . Hence, clustering techniques can benefit from swarm intelligence BIB013 . Swarm intelligence can optimize the objective function of clustering based on population and evolution strategies BIB008 BIB009 . This function is usually used to determine the fitness of each particle since the community has a set of particles (known as a swarm), and each particle represents a solution. Table 4 compares the use of optimization in population and evolution strategies. Both optimization strategies are designed to imitate the best features in nature and produce a better quality of solution efficiently BIB006 BIB005 . Previous studies have explored the use of optimization in a generation with more than 1000 populations before the convergence step, but it was not computationally efficient BIB007 . Table 4 . Comparison of the use of optimization between population and evolution strategies.