Multiobjective optimization of cluster measures in Microarray Cancer data using Genetic Algorithm Based Fuzzy Clustering

The field of biological and biomedical research has been changed rapidly with the invention of microarray technology, which facilitates simultaneously monitoring of large number of genes across different experimental conditions. In this report a multi objective genetic algorithm technique called Non-Dominated Sorting Genetic Algorithm (NSGA) - II based approach has been proposed for fuzzy clustering of microarray cancer expression dataset that encodes the cluster modes and simultaneously optimizes the two factors called fuzzy compactness and fuzzy separation of the clusters. The multiobjective technique produces a set of non-dominated solutions. This approach identifies the solution i.e. the individual chromosome which gives the optimal value of the parameters

An unsupervised learning algorithm for membrane computing

This paper focuses on the unsupervised learning problem within membrane computing, and proposes an innovative solution inspired by membrane computing techniques, the fuzzy membrane clustering algorithm. An evolution–communication P system with nested membrane structure is the core component of the algorithm. The feasible cluster centers are represented by means of objects, and three types of membranes are considered: evolution, local store, and global store. Based on the designed membrane structure and the inherent communication mechanism, a modified differential evolution mechanism is developed to evolve the objects in the system. Under the control of the evolution–communication mechanism of the P system, the proposed fuzzy clustering algorithm achieves good fuzzy partitioning for a data set. The proposed fuzzy clustering algorithm is compared to three recently-developed and two classical clustering algorithms for five artificial and five real-life data sets.National Natural Science Foundation of China No 61170030National Natural Science Foundation of China No 61472328Chunhui Project Foundation of the Education Department of China No. Z2012025Chunhui Project Foundation of the Education Department of China No. Z2012031Sichuan Key Technology Research and Development Program No. 2013GZX015

Multiobjective programming for type-2 hierarchical fuzzy inference trees

This paper proposes a design of hierarchical fuzzy inference tree (HFIT). An HFIT produces an optimum tree-like structure. Specifically, a natural hierarchical structure that accommodates simplicity by combining several low-dimensional fuzzy inference systems (FISs). Such a natural hierarchical structure provides a high degree of approximation accuracy. The construction of HFIT takes place in two phases. Firstly, a nondominated sorting based multiobjective genetic programming (MOGP) is applied to obtain a simple tree structure (low model’s complexity) with a high accuracy. Secondly, the differential evolution algorithm is applied to optimize the obtained tree’s parameters. In the obtained tree, each node has a different input’s combination, where the evolutionary process governs the input’s combination. Hence, HFIT nodes are heterogeneous in nature, which leads to a high diversity among the rules generated by the HFIT. Additionally, the HFIT provides an automatic feature selection because it uses MOGP for the tree’s structural optimization that accept inputs only relevant to the knowledge contained in data. The HFIT was studied in the context of both type-1 and type-2 FISs, and its performance was evaluated through six application problems. Moreover, the proposed multiobjective HFIT was compared both theoretically and empirically with recently proposed FISs methods from the literature, such as McIT2FIS, TSCIT2FNN, SIT2FNN, RIT2FNS-WB, eT2FIS, MRIT2NFS, IT2FNN-SVR, etc. From the obtained results, it was found that the HFIT provided less complex and highly accurate models compared to the models produced by most of the other methods. Hence, the proposed HFIT is an efficient and competitive alternative to the other FISs for function approximation and feature selectio

Elastic differential evolution for automatic data clustering

In many practical applications, it is crucial to perform automatic data clustering without knowing the number of clusters in advance. The evolutionary computation paradigm is good at dealing with this task, but the existing algorithms encounter several deficiencies, such as the encoding redundancy and the cross-dimension learning error. In this article, we propose a novel elastic differential evolution algorithm to solve automatic data clustering. Unlike traditional methods, the proposed algorithm considers each clustering layout as a whole and adapts the cluster number and cluster centroids inherently through the variable-length encoding and the evolution operators. The encoding scheme contains no redundancy. To enable the individuals of different lengths to exchange information properly, we develop a subspace crossover and a two-phase mutation operator. The operators employ the basic method of differential evolution and, in addition, they consider the spatial information of cluster layouts to generate offspring solutions. Particularly, each dimension of the parameter vector interacts with its correlated dimensions, which not only adapts the cluster number but also avoids the cross-dimension learning error. The experimental results show that our algorithm outperforms the state-of-the-art algorithms that it is able to identify the correct number of clusters and obtain a good cluster validation value

Adaptive K-means algorithm for overlapped graph clustering

Electronic version of an article published as International Journal of Neural Systems 2, 5, 2012, DOI: 10.1142/S0129065712500189 © 2012 copyright World Scientific Publishing CompanyThe graph clustering problem has become highly relevant due to the growing interest of several research communities in social networks and their possible applications. Overlapped graph clustering algorithms try to find subsets of nodes that can belong to different clusters. In social network-based applications it is quite usual for a node of the network to belong to different groups, or communities, in the graph. Therefore, algorithms trying to discover, or analyze, the behavior of these networks needed to handle this feature, detecting and identifying the overlapped nodes. This paper shows a soft clustering approach based on a genetic algorithm where a new encoding is designed to achieve two main goals: first, the automatic adaptation of the number of communities that can be detected and second, the definition of several fitness functions that guide the searching process using some measures extracted from graph theory. Finally, our approach has been experimentally tested using the Eurovision contest dataset, a well-known social-based data network, to show how overlapped communities can be found using our method.This work has been partly supported by: Spanish Ministry of Science and Education under project TIN2010-19872 and the grant BES-2011-049875 from the same Ministry

A review of quantum-inspired metaheuristic algorithms for automatic clustering

In real-world scenarios, identifying the optimal number of clusters in a dataset is a difficult task due to insufficient knowledge. Therefore, the indispensability of sophisticated automatic clus tering algorithms for this purpose has been contemplated by some researchers. Several automatic clustering algorithms assisted by quantum-inspired metaheuristics have been developed in recent years. However, the literature lacks definitive documentation of the state-of-the-art quantum-inspired metaheuristic algorithms for automatically clustering datasets. This article presents a brief overview of the automatic clustering process to establish the importance of making the clustering process automatic. The fundamental concepts of the quantum computing paradigm are also presented to highlight the utility of quantum-inspired algorithms. This article thoroughly analyses some algo rithms employed to address the automatic clustering of various datasets. The reviewed algorithms were classified according to their main sources of inspiration. In addition, some representative works of each classification were chosen from the existing works. Thirty-six such prominent algorithms were further critically analysed based on their aims, used mechanisms, data specifications, merits and demerits. Comparative results based on the performance and optimal computational time are also presented to critically analyse the reviewed algorithms. As such, this article promises to provide a detailed analysis of the state-of-the-art quantum-inspired metaheuristic algorithms, while highlighting their merits and demerits.Web of Science119art. no. 201

A survey on handling computationally expensive multiobjective optimization problems with evolutionary algorithms

This is the author accepted manuscript. The final version is available from Springer Verlag via the DOI in this record.Evolutionary algorithms are widely used for solving multiobjective optimization problems but are often criticized because of a large number of function evaluations needed. Approximations, especially function approximations, also referred to as surrogates or metamodels are commonly used in the literature to reduce the computation time. This paper presents a survey of 45 different recent algorithms proposed in the literature between 2008 and 2016 to handle computationally expensive multiobjective optimization problems. Several algorithms are discussed based on what kind of an approximation such as problem, function or fitness approximation they use. Most emphasis is given to function approximation-based algorithms. We also compare these algorithms based on different criteria such as metamodeling technique and evolutionary algorithm used, type and dimensions of the problem solved, handling constraints, training time and the type of evolution control. Furthermore, we identify and discuss some promising elements and major issues among algorithms in the literature related to using an approximation and numerical settings used. In addition, we discuss selecting an algorithm to solve a given computationally expensive multiobjective optimization problem based on the dimensions in both objective and decision spaces and the computation budget available.The research of Tinkle Chugh was funded by the COMAS Doctoral Program (at the University of Jyväskylä) and FiDiPro Project DeCoMo (funded by Tekes, the Finnish Funding Agency for Innovation), and the research of Dr. Karthik Sindhya was funded by SIMPRO project funded by Tekes as well as DeCoMo

Improved optimization of numerical association rule mining using hybrid particle swarm optimization and cauchy distribution

Particle Swarm Optimization (PSO) has been applied to solve optimization problems in various fields, such as Association Rule Mining (ARM) of numerical problems. However, PSO often becomes trapped in local optima. Consequently, the results do not represent the overall optimum solutions. To address this limitation, this study aims to combine PSO with the Cauchy distribution (PARCD), which is expected to increase the global optimal value of the expanded search space. Furthermore, this study uses multiple objective functions, i.e., support, confidence, comprehensibility, interestingness and amplitude. In addition, the proposed method was evaluated using benchmark datasets, such as the Quake, Basket ball, Body fat, Pollution, and Bolt datasets. Evaluation results were compared to the results obtained by previous studies. The results indicate that the overall values of the objective functions obtained using the proposed PARCD approach are satisfactory

Multiobjective deep clustering and its applications in single-cell RNA-seq data

The file attached to this record is the author's final peer reviewed version. The Publisher's final version can be found by following the DOI link.Single-cell RNA sequencing is a transformative technology that enables us to study the heterogeneity of the tissue at the cellular level. Clustering is used as the key computational approach to group cells under the transcriptome profiles from single-cell RNA-seq data. However, accurate identification of distinct cell types is facing the challenge of high dimensionality, and it could cause uninformative clusters when clustering is directly applied on the original transcriptome. To address such challenge, an evolutionary multiobjective deep clustering (EMDC) algorithm is proposed to identify single-cell RNA-seq data in this study. First, EMDC removes redundant and irrelevant genes by applying the differential gene expression analysis to identify differentially expressed genes across biological conditions. After that, a deep autoencoder is proposed to project the high-dimensional data into different low-dimensional nonlinear embedding subspaces under different bottleneck layers. Then, the basic clustering algorithm is applied in those nonlinear embedding subspaces to generate some basic clustering results to produce the cluster ensemble. To lessen the unnecessary cost produced by those clusterings in the ensemble, the multiobjective evolutionary optimization is designed to prune the basic clustering results in the ensemble, unleashing its cell type discovery performance under three objective functions. Multiple experiments have been conducted on 30 synthetic single-cell RNA-seq datasets and six real single-cell RNA-seq datasets, which reveal that EMDC outperforms eight other clustering methods and three multiobjective optimization algorithms in cell type identification. In addition, we have conducted extensive comparisons to effectively demonstrate the impact of each component in our proposed EMDC