Clustering Algorithms: Their Application to Gene Expression Data

Gene expression data hide vital information required to understand the biological process that takes place in a particular organism in relation to its environment. Deciphering the hidden patterns in gene expression data proffers a prodigious preference to strengthen the understanding of functional genomics. The complexity of biological networks and the volume of genes present increase the challenges of comprehending and interpretation of the resulting mass of data, which consists of millions of measurements; these data also inhibit vagueness, imprecision, and noise. Therefore, the use of clustering techniques is a first step toward addressing these challenges, which is essential in the data mining process to reveal natural structures and iden-tify interesting patterns in the underlying data. The clustering of gene expression data has been proven to be useful in making known the natural structure inherent in gene expression data, understanding gene functions, cellular processes, and subtypes of cells, mining useful information from noisy data, and understanding gene regulation. The other benefit of clustering gene expression data is the identification of homology, which is very important in vaccine design. This review examines the various clustering algorithms applicable to the gene expression data in order to discover and provide useful knowledge of the appropriate clustering technique that will guarantee stability and high degree of accuracy in its analysis procedure

BigFCM: Fast, Precise and Scalable FCM on Hadoop

Clustering plays an important role in mining big data both as a modeling technique and a preprocessing step in many data mining process implementations. Fuzzy clustering provides more flexibility than non-fuzzy methods by allowing each data record to belong to more than one cluster to some degree. However, a serious challenge in fuzzy clustering is the lack of scalability. Massive datasets in emerging fields such as geosciences, biology and networking do require parallel and distributed computations with high performance to solve real-world problems. Although some clustering methods are already improved to execute on big data platforms, but their execution time is highly increased for large datasets. In this paper, a scalable Fuzzy C-Means (FCM) clustering named BigFCM is proposed and designed for the Hadoop distributed data platform. Based on the map-reduce programming model, it exploits several mechanisms including an efficient caching design to achieve several orders of magnitude reduction in execution time. Extensive evaluation over multi-gigabyte datasets shows that BigFCM is scalable while it preserves the quality of clustering

A review of clustering techniques and developments

© 2017 Elsevier B.V. This paper presents a comprehensive study on clustering: exiting methods and developments made at various times. Clustering is defined as an unsupervised learning where the objects are grouped on the basis of some similarity inherent among them. There are different methods for clustering the objects such as hierarchical, partitional, grid, density based and model based. The approaches used in these methods are discussed with their respective states of art and applicability. The measures of similarity as well as the evaluation criteria, which are the central components of clustering, are also presented in the paper. The applications of clustering in some fields like image segmentation, object and character recognition and data mining are highlighted

Extensive Analysis on Generation and Consensus Mechanisms of Clustering Ensemble: A Survey

Data analysis plays a prominent role in interpreting various phenomena. Data mining is the process to hypothesize useful knowledge from the extensive data. Based upon the classical statistical prototypes the data can be exploited beyond the storage and management of the data. Cluster analysis a primary investigation with little or no prior knowledge, consists of research and development across a wide variety of communities. Cluster ensembles are melange of individual solutions obtained from different clusterings to produce final quality clustering which is required in wider applications. The method arises in the perspective of increasing robustness, scalability and accuracy. This paper gives a brief overview of the generation methods and consensus functions included in cluster ensemble. The survey is to analyze the various techniques and cluster ensemble methods

Improving the accuracy while preserving the interpretability of fuzzy function approximators by means of multi-objective evolutionary algorithms

AbstractThe identification of a model is one of the key issues in the field of fuzzy system modeling and function approximation theory. An important characteristic that distinguishes fuzzy systems from other techniques in this area is their transparency and interpretability. Especially in the construction of a fuzzy system from a set of given training examples, little attention has been paid to the analysis of the trade-off between complexity and accuracy maintaining the interpretability of the final fuzzy system. In this paper a multi-objective evolutionary approach is proposed to determine a Pareto-optimum set of fuzzy systems with different compromises between their accuracy and complexity. In particular, two fundamental and competing objectives concerning fuzzy system modeling are addressed: fuzzy rule parameter optimization and the identification of system structure (i.e. the number of membership functions and fuzzy rules), taking always in mind the transparency of the obtained system. Another key aspect of the algorithm presented in this work is the use of some new expert evolutionary operators, specifically designed for the problem of fuzzy function approximation, that try to avoid the generation of worse solutions in order to accelerate the convergence of the algorithm

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

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

Self learning neuro-fuzzy modeling using hybrid genetic probabilistic approach for engine air/fuel ratio prediction

Machine Learning is concerned in constructing models which can learn and make predictions based on data. Rule extraction from real world data that are usually tainted with noise, ambiguity, and uncertainty, automatically requires feature selection. Neuro-Fuzzy system (NFS) which is known with its prediction performance has the difficulty in determining the proper number of rules and the number of membership functions for each rule. An enhanced hybrid Genetic Algorithm based Fuzzy Bayesian classifier (GA-FBC) was proposed to help the NFS in the rule extraction. Feature selection was performed in the rule level overcoming the problems of the FBC which depends on the frequency of the features leading to ignore the patterns of small classes. As dealing with a real world problem such as the Air/Fuel Ratio (AFR) prediction, a multi-objective problem is adopted. The GA-FBC uses mutual information entropy, which considers the relevance between feature attributes and class attributes. A fitness function is proposed to deal with multi-objective problem without weight using a new composition method. The model was compared to other learning algorithms for NFS such as Fuzzy c-means (FCM) and grid partition algorithm. Predictive accuracy and the complexity of the Fuzzy Rule Base System (FRBS) including number of rules and number of terms in each rule were taken as terms of evaluation. It was also compared to the original GA-FBC depending on the frequency not on Mutual Information (MI). Experimental results using Air/Fuel Ratio (AFR) data sets show that the new model participates in decreasing the average number of attributes in the rule and sometimes in increasing the average performance compared to other models. This work facilitates in achieving a self-generating FRBS from real data. The GA-FBC can be used as a new direction in machine learning research. This research contributes in controlling automobile emissions in helping the reduction of one of the most causes of pollution to produce greener environment

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