Search results for: Modified Pole Clustering

Authors: Fahad Shahbaz Khan, Rao Muhammad Anwer, Olof Torgersson

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The vast amount of information hidden in huge databases has created tremendous interests in the field of data mining. This paper examines the possibility of using data clustering techniques in oral medicine to identify functional relationships between different attributes and classification of similar patient examinations. Commonly used data clustering algorithms have been reviewed and as a result several interesting results have been gathered.

Keywords: Oral Medicine, Cluto, Data Clustering, Data Mining.

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Authors: Semeh Ben Salem, Sami Naouali, Moetez Sallami

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The increasing amount of collected data has limited the performance of the current analyzing algorithms. Thus, developing new cost-effective algorithms in terms of complexity, scalability, and accuracy raised significant interests. In this paper, a modified effective k-means based algorithm is developed and experimented. The new algorithm aims to reduce the computational load without significantly affecting the quality of the clusterings. The algorithm uses the City Block distance and a new stop criterion to guarantee the convergence. Conducted experiments on a real data set show its high performance when compared with the original k-means version.

Keywords: Pattern recognition, partitional clustering, K-means clustering, Manhattan distance, terrorism data analysis.

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Authors: Qin Ding, Jim Gasvoda

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Clustering is the process of subdividing an input data set into a desired number of subgroups so that members of the same subgroup are similar and members of different subgroups have diverse properties. Many heuristic algorithms have been applied to the clustering problem, which is known to be NP Hard. Genetic algorithms have been used in a wide variety of fields to perform clustering, however, the technique normally has a long running time in terms of input set size. This paper proposes an efficient genetic algorithm for clustering on very large data sets, especially on image data sets. The genetic algorithm uses the most time efficient techniques along with preprocessing of the input data set. We test our algorithm on both artificial and real image data sets, both of which are of large size. The experimental results show that our algorithm outperforms the k-means algorithm in terms of running time as well as the quality of the clustering.

Keywords: Clustering, data mining, genetic algorithm, image data.

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Authors: Liping Jing, Michael K. Ng, Xinhua Yang, Joshua Zhexue Huang

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This paper presents a text clustering system developed based on a k-means type subspace clustering algorithm to cluster large, high dimensional and sparse text data. In this algorithm, a new step is added in the k-means clustering process to automatically calculate the weights of keywords in each cluster so that the important words of a cluster can be identified by the weight values. For understanding and interpretation of clustering results, a few keywords that can best represent the semantic topic are extracted from each cluster. Two methods are used to extract the representative words. The candidate words are first selected according to their weights calculated by our new algorithm. Then, the candidates are fed to the WordNet to identify the set of noun words and consolidate the synonymy and hyponymy words. Experimental results have shown that the clustering algorithm is superior to the other subspace clustering algorithms, such as PROCLUS and HARP and kmeans type algorithm, e.g., Bisecting-KMeans. Furthermore, the word extraction method is effective in selection of the words to represent the topics of the clusters.

Keywords: Subspace Clustering, Text Mining, Feature Weighting, Cluster Interpretation, Ontology

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Authors: Mahdi Kiani, Hassan Salarieh, Aria Alasty, S. Mahdi Darbandi

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The design and implementation of the hybrid control method for a three-pole active magnetic bearing (AMB) is proposed in this paper. The system is inherently nonlinear and conventional nonlinear controllers are a little complicated, while the proposed hybrid controller has a piecewise linear form, i.e. linear in each sub-region. A state-feedback hybrid controller is designed in this study, and the unmeasurable states are estimated by an observer. The gains of the hybrid controller are obtained by the Linear Quadratic Regulator (LQR) method in each sub-region. To evaluate the performance, the designed controller is implemented on an experimental setup in static mode. The experimental results show that the proposed method can efficiently stabilize the three-pole AMB system. The simplicity of design, domain of attraction, uncomplicated control law, and computational time are advantages of this method over other nonlinear control strategies in AMB systems.

Keywords: Active magnetic bearing, three pole AMB, hybrid control, Lyapunov function.

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Authors: Sunita Jahirabadkar, Parag Kulkarni

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Many real-world data sets consist of a very high dimensional feature space. Most clustering techniques use the distance or similarity between objects as a measure to build clusters. But in high dimensional spaces, distances between points become relatively uniform. In such cases, density based approaches may give better results. Subspace Clustering algorithms automatically identify lower dimensional subspaces of the higher dimensional feature space in which clusters exist. In this paper, we propose a new clustering algorithm, ISC – Intelligent Subspace Clustering, which tries to overcome three major limitations of the existing state-of-art techniques. ISC determines the input parameter such as є – distance at various levels of Subspace Clustering which helps in finding meaningful clusters. The uniform parameters approach is not suitable for different kind of databases. ISC implements dynamic and adaptive determination of Meaningful clustering parameters based on hierarchical filtering approach. Third and most important feature of ISC is the ability of incremental learning and dynamic inclusion and exclusions of subspaces which lead to better cluster formation.

Keywords: Density based clustering, high dimensional data, subspace clustering, dynamic parameter setting.

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Authors: S. A. Mohamed, A. S. Zayed, O. A. Abolaeha

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A new Feed-Forward/Feedback Generalized Minimum Variance Pole-placement Controller to incorporate the robustness of classical pole-placement into the flexibility of generalized minimum variance self-tuning controller for Single-Input Single-Output (SISO) has been proposed in this paper. The design, which provides the user with an adaptive mechanism, which ensures that the closed loop poles are, located at their pre-specified positions. In addition, the controller design which has a feed-forward/feedback structure overcomes the certain limitations existing in similar poleplacement control designs whilst retaining the simplicity of adaptation mechanisms used in other designs. It tracks set-point changes with the desired speed of response, penalizes excessive control action, and can be applied to non-minimum phase systems. Besides, at steady state, the controller has the ability to regulate the constant load disturbance to zero. Example simulation results using both simulated and real plant models demonstrate the effectiveness of the proposed controller.

Keywords: Pole-placement, Minimum variance control, self-tuning control and feedforward control.

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Authors: Ashanie Guanathillake, Kithsiri Samarasinghe

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Wireless Sensor Networks consist of inexpensive, low power sensor nodes deployed to monitor the environment and collect data. Gathering information in an energy efficient manner is a critical aspect to prolong the network lifetime. Clustering  algorithms have an advantage of enhancing the network lifetime. Current clustering algorithms usually focus on global re-clustering and local re-clustering separately. This paper, proposed a combination of those two reclustering methods to reduce the energy consumption of the network. Furthermore, the proposed algorithm can apply to homogeneous as well as heterogeneous wireless sensor networks. In addition, the cluster head rotation happens, only when its energy drops below a dynamic threshold value computed by the algorithm. The simulation result shows that the proposed algorithm prolong the network lifetime compared to existing algorithms.

Keywords: Energy efficient, Global re-clustering, Local re-clustering, Wireless sensor networks.

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Authors: Cristina G. Dascâlu, Corina Dima Cozma, Elena Carmen Cotrutz

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The medical data statistical analysis often requires the using of some special techniques, because of the particularities of these data. The principal components analysis and the data clustering are two statistical methods for data mining very useful in the medical field, the first one as a method to decrease the number of studied parameters, and the second one as a method to analyze the connections between diagnosis and the data about the patient-s condition. In this paper we investigate the implications obtained from a specific data analysis technique: the data clustering preceded by a selection of the most relevant parameters, made using the principal components analysis. Our assumption was that, using the principal components analysis before data clustering - in order to select and to classify only the most relevant parameters – the accuracy of clustering is improved, but the practical results showed the opposite fact: the clustering accuracy decreases, with a percentage approximately equal with the percentage of information loss reported by the principal components analysis.

Keywords: Data clustering, medical data, principal components analysis.

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Authors: Dharmveer Singh Rajput , P. K. Singh, Mahua Bhattacharya

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Clustering in high dimensional space is a difficult problem which is recurrent in many fields of science and engineering, e.g., bioinformatics, image processing, pattern reorganization and data mining. In high dimensional space some of the dimensions are likely to be irrelevant, thus hiding the possible clustering. In very high dimensions it is common for all the objects in a dataset to be nearly equidistant from each other, completely masking the clusters. Hence, performance of the clustering algorithm decreases. In this paper, we propose an algorithmic framework which combines the (reduct) concept of rough set theory with the k-means algorithm to remove the irrelevant dimensions in a high dimensional space and obtain appropriate clusters. Our experiment on test data shows that this framework increases efficiency of the clustering process and accuracy of the results.

Keywords: High dimensional clustering, sub-space, k-means, rough set, discernibility matrix.

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Authors: Gorazd Karer, Igor Skrjanc, Borut Zupancic

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The complex hybrid and nonlinear nature of many processes that are met in practice causes problems with both structure modelling and parameter identification; therefore, obtaining a model that is suitable for MPC is often a difficult task. The basic idea of this paper is to present an identification method for a piecewise affine (PWA) model based on a fuzzy clustering algorithm. First we introduce the PWA model. Next, we tackle the identification method. We treat the fuzzy clustering algorithm, deal with the projections of the fuzzy clusters into the input space of the PWA model and explain the estimation of the parameters of the PWA model by means of a modified least-squares method. Furthermore, we verify the usability of the proposed identification approach on a hybrid nonlinear batch reactor example. The result suggest that the batch reactor can be efficiently identified and thus formulated as a PWA model, which can eventually be used for model predictive control purposes.

Keywords: Batch reactor, fuzzy clustering, hybrid systems, identification, nonlinear systems, PWA systems.

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Authors: Seo Young Kim, Jae Won Lee, Jong Sung Bae

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Microarray experiments are information rich; however, extensive data mining is required to identify the patterns that characterize the underlying mechanisms of action. For biologists, a key aim when analyzing microarray data is to group genes based on the temporal patterns of their expression levels. In this paper, we used an iterative clustering method to find temporal patterns of gene expression. We evaluated the performance of this method by applying it to real sporulation data and simulated data. The patterns obtained using the iterative clustering were found to be superior to those obtained using existing clustering algorithms.

Keywords: Clustering, microarray experiment, temporal pattern of gene expression data.

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Authors: Mohamed A. Mahfouz, M. A. Ismail

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This paper introduces new algorithms (Fuzzy relative of the CLARANS algorithm FCLARANS and Fuzzy c Medoids based on randomized search FCMRANS) for fuzzy clustering of relational data. Unlike existing fuzzy c-medoids algorithm (FCMdd) in which the within cluster dissimilarity of each cluster is minimized in each iteration by recomputing new medoids given current memberships, FCLARANS minimizes the same objective function minimized by FCMdd by changing current medoids in such away that that the sum of the within cluster dissimilarities is minimized. Computing new medoids may be effected by noise because outliers may join the computation of medoids while the choice of medoids in FCLARANS is dictated by the location of a predominant fraction of points inside a cluster and, therefore, it is less sensitive to the presence of outliers. In FCMRANS the step of computing new medoids in FCMdd is modified to be based on randomized search. Furthermore, a new initialization procedure is developed that add randomness to the initialization procedure used with FCMdd. Both FCLARANS and FCMRANS are compared with the robust and linearized version of fuzzy c-medoids (RFCMdd). Experimental results with different samples of the Reuter-21578, Newsgroups (20NG) and generated datasets with noise show that FCLARANS is more robust than both RFCMdd and FCMRANS. Finally, both FCMRANS and FCLARANS are more efficient and their outputs are almost the same as that of RFCMdd in terms of classification rate.

Keywords: Data Mining, Fuzzy Clustering, Relational Clustering, Medoid-Based Clustering, Cluster Analysis, Unsupervised Learning.

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Authors: Jong-Ian Tsai, Chi-Chuan Chen, Tung-Sheng Zhan, Rong-Ching Wu

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Single-pole switching scheme is widely used in the Extra High Voltage system. However, the substantial negativesequence current injected to the turbine-generators imposes the electromagnetic (E/M) torque of double system- frequency components during the dead time (between single-pole clearing and line reclosing). This would induce supersynchronous resonance (SPSR) torque amplifications on low pressure turbine generator blades and even lead to fatigue damage. This paper proposes the design of a mechanical filter (MF) with natural frequency close to double-system frequency. From the simulation results, it is found that such a filter not only successfully damps the resonant effect, but also has the characteristics of feasibility and compact.

Keywords: Single-pole, Supersynchronous, Blade, Unbalance, filter

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Authors: A. A. Penin, A. S. Sidorenko

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A convenient and physically sound mathematical model of the external or I - V characteristic of solar cells generators is presented in this paper. This model is compared with the traditional model of p-n junction. The direct analytical calculation of load regime leads to a quadratic equation, which is importantly to simplify the calculations in the real time.

Keywords: A solar cell generator, I−V characteristic, activetwo-pole.

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Authors: Gökhan Silahtaroğlu

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Clustering large populations is an important problem when the data contain noise and different shapes. A good clustering algorithm or approach should be efficient enough to detect clusters sensitively. Besides space complexity, time complexity also gains importance as the size grows. Using hierarchies we developed a new algorithm to split attributes according to the values they have and choosing the dimension for splitting so as to divide the database roughly into equal parts as much as possible. At each node we calculate some certain descriptive statistical features of the data which reside and by pruning we generate the natural clusters with a complexity of O(n).

Keywords: Clustering, tree, split, pruning, entropy, gini.

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Authors: S.Aranganayagi, K.Thangavel

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Clustering categorical data is more complicated than the numerical clustering because of its special properties. Scalability and memory constraint is the challenging problem in clustering large data set. This paper presents an incremental algorithm to cluster the categorical data. Frequencies of attribute values contribute much in clustering similar categorical objects. In this paper we propose new similarity measures based on the frequencies of attribute values and its cardinalities. The proposed measures and the algorithm are experimented with the data sets from UCI data repository. Results prove that the proposed method generates better clusters than the existing one.

Keywords: Clustering, Categorical, Incremental, Frequency, Domain

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Authors: S. Sarumathi, N. Shanthi, S. Vidhya, M. Sharmila

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An extensive amount of work has been done in data clustering research under the unsupervised learning technique in Data Mining during the past two decades. Moreover, several approaches and methods have been emerged focusing on clustering diverse data types, features of cluster models and similarity rates of clusters. However, none of the single clustering algorithm exemplifies its best nature in extracting efficient clusters. Consequently, in order to rectify this issue, a new challenging technique called Cluster Ensemble method was bloomed. This new approach tends to be the alternative method for the cluster analysis problem. The main objective of the Cluster Ensemble is to aggregate the diverse clustering solutions in such a way to attain accuracy and also to improve the eminence the individual clustering algorithms. Due to the massive and rapid development of new methods in the globe of data mining, it is highly mandatory to scrutinize a vital analysis of existing techniques and the future novelty. This paper shows the comparative analysis of different cluster ensemble methods along with their methodologies and salient features. Henceforth this unambiguous analysis will be very useful for the society of clustering experts and also helps in deciding the most appropriate one to resolve the problem in hand.

Keywords: Clustering, Cluster Ensemble Methods, Coassociation matrix, Consensus Function, Median Partition.

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Authors: Ouadoudi Zytoune, Youssef Fakhri, Driss Aboutajdine

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This paper focuses on reducing the power consumption of wireless sensor networks. Therefore, a communication protocol named LEACH (Low-Energy Adaptive Clustering Hierarchy) is modified. We extend LEACHs stochastic cluster-head selection algorithm by a modifying the probability of each node to become cluster-head based on its required energy to transmit to the sink. We present an efficient energy aware routing algorithm for the wireless sensor networks. Our contribution consists in rotation selection of clusterheads considering the remoteness of the nodes to the sink, and then, the network nodes residual energy. This choice allows a best distribution of the transmission energy in the network. The cluster-heads selection algorithm is completely decentralized. Simulation results show that the energy is significantly reduced compared with the previous clustering based routing algorithm for the sensor networks.

Keywords: Wireless Sensor Networks, Energy efficiency, WirelessCommunications, Clustering-based algorithm.

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Authors: Maythapolnun Athimethphat, Boontarika Lerteerawong

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There are several approaches for handling multiclass classification. Aside from one-against-one (OAO) and one-against-all (OAA), hierarchical classification technique is also commonly used. A binary classification tree is a hierarchical classification structure that breaks down a k-class problem into binary sub-problems, each solved by a binary classifier. In each node, a set of classes is divided into two subsets. A good class partition should be able to group similar classes together. Many algorithms measure similarity in term of distance between class centroids. Classes are grouped together by a clustering algorithm when distances between their centroids are small. In this paper, we present a binary classification tree with tuned observation-based clustering (BCT-TOB) that finds a class partition by performing clustering on observations instead of class centroids. A merging step is introduced to merge any insignificant class split. The experiment shows that performance of BCT-TOB is comparable to other algorithms.

Keywords: multiclass classification, hierarchical classification, binary classification tree, clustering, observation-based clustering

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Authors: Shuhua Lai, Kairui Chen

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In this paper, we present a fast and efficient mesh coarsening algorithm for 3D triangular meshes. Theis approach can be applied to very complex 3D meshes of arbitrary topology and with millions of vertices. The algorithm is based on the clustering of the input mesh elements, which divides the faces of an input mesh into a given number of clusters for clustering purpose by approximating the Centroidal Voronoi Tessellation of the input mesh. Once a clustering is achieved, it provides us an efficient way to construct uniform tessellations, and therefore leads to good coarsening of polygonal meshes. With proliferation of 3D scanners, this coarsening algorithm is particularly useful for reverse engineering applications of 3D models, which in many cases are dense, non-uniform, irregular and arbitrary topology. Examples demonstrating effectiveness of the new algorithm are also included in the paper.

Keywords: Coarsening, mesh clustering, shape approximation, mesh simplification.

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Authors: Bashar Al-Shboul, Sung-Hyon Myaeng

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K-Means (KM) is considered one of the major algorithms widely used in clustering. However, it still has some problems, and one of them is in its initialization step where it is normally done randomly. Another problem for KM is that it converges to local minima. Genetic algorithms are one of the evolutionary algorithms inspired from nature and utilized in the field of clustering. In this paper, we propose two algorithms to solve the initialization problem, Genetic Algorithm Initializes KM (GAIK) and KM Initializes Genetic Algorithm (KIGA). To show the effectiveness and efficiency of our algorithms, a comparative study was done among GAIK, KIGA, Genetic-based Clustering Algorithm (GCA), and FCM [19].

Keywords: Clustering, Genetic Algorithms, K-means.

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Authors: Sameh H. Ghwanmeh

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In this study a clustering technique has been implemented which is K-Means like with hierarchical initial set (HKM). The goal of this study is to prove that clustering document sets do enhancement precision on information retrieval systems, since it was proved by Bellot & El-Beze on French language. A comparison is made between the traditional information retrieval system and the clustered one. Also the effect of increasing number of clusters on precision is studied. The indexing technique is Term Frequency * Inverse Document Frequency (TF * IDF). It has been found that the effect of Hierarchical K-Means Like clustering (HKM) with 3 clusters over 242 Arabic abstract documents from the Saudi Arabian National Computer Conference has significant results compared with traditional information retrieval system without clustering. Additionally it has been found that it is not necessary to increase the number of clusters to improve precision more.

Keywords: Hierarchical K-mean like clustering (HKM), Kmeans, cluster centroids, initial partition, and document distances

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Authors: Minsoo Lee, Yun-mi Kim, Yearn Jeong Kim, Yoon-kyung Lee, Hyejung Yoon

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Biological data has several characteristics that strongly differentiate it from typical business data. It is much more complex, usually large in size, and continuously changes. Until recently business data has been the main target for discovering trends, patterns or future expectations. However, with the recent rise in biotechnology, the powerful technology that was used for analyzing business data is now being applied to biological data. With the advanced technology at hand, the main trend in biological research is rapidly changing from structural DNA analysis to understanding cellular functions of the DNA sequences. DNA chips are now being used to perform experiments and DNA analysis processes are being used by researchers. Clustering is one of the important processes used for grouping together similar entities. There are many clustering algorithms such as hierarchical clustering, self-organizing maps, K-means clustering and so on. In this paper, we propose a clustering algorithm that imitates the ecosystem taking into account the features of biological data. We implemented the system using an Ant-Colony clustering algorithm. The system decides the number of clusters automatically. The system processes the input biological data, runs the Ant-Colony algorithm, draws the Topic Map, assigns clusters to the genes and displays the output. We tested the algorithm with a test data of 100 to1000 genes and 24 samples and show promising results for applying this algorithm to clustering DNA chip data.

Keywords: Ant colony system, biological data, clustering, DNA chip.

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Authors: S. Sarumathi, N. Shanthi, P. Ranjetha

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Data mining is the procedure of determining interesting patterns from the huge amount of data. With the intention of accessing the data faster the most supporting processes needed is clustering. Clustering is the process of identifying similarity between data according to the individuality present in the data and grouping associated data objects into clusters. Cluster ensemble is the technique to combine various runs of different clustering algorithms to obtain a general partition of the original dataset, aiming for consolidation of outcomes from a collection of individual clustering outcomes. The performances of clustering ensembles are mainly affecting by two principal factors such as diversity and quality. This paper presents the overview about the different cluster ensemble algorithm along with their methods used in cluster ensemble to improve the diversity and quality in the several cluster ensemble related papers and shows the comparative analysis of different cluster ensemble also summarize various cluster ensemble methods. Henceforth this clear analysis will be very useful for the world of clustering experts and also helps in deciding the most appropriate one to determine the problem in hand.

Keywords: Cluster Ensemble, Consensus Function, CSPA, Diversity, HGPA, MCLA.

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Authors: Ioannis P. Panapakidis, Marios N. Moschakis

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With the continuous increment of smart meter installations across the globe, the need for processing of the load data is evident. Clustering-based load profiling is built upon the utilization of unsupervised machine learning tools for the purpose of formulating the typical load curves or load profiles. The most commonly used algorithm in the load profiling literature is the K-means. While the algorithm has been successfully tested in a variety of applications, its drawback is the strong dependence in the initialization phase. This paper proposes a novel modified form of the K-means that addresses the aforementioned problem. Simulation results indicate the superiority of the proposed algorithm compared to the K-means.

Keywords: Clustering, load profiling, load modeling, machine learning, energy efficiency and quality.

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Authors: Pallav Roxy, Durga Toshniwal

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Clustering unstructured text documents is an important issue in data mining community and has a number of applications such as document archive filtering, document organization and topic detection and subject tracing. In the real world, some of the already clustered documents may not be of importance while new documents of more significance may evolve. Most of the work done so far in clustering unstructured text documents overlooks this aspect of clustering. This paper, addresses this issue by using the Fading Function. The unstructured text documents are clustered. And for each cluster a statistics structure called Cluster Profile (CP) is implemented. The cluster profile incorporates the Fading Function. This Fading Function keeps an account of the time-dependent importance of the cluster. The work proposes a novel algorithm Clustering n-ary Merge Algorithm (CnMA) for unstructured text documents, that uses Cluster Profile and Fading Function. Experimental results illustrating the effectiveness of the proposed technique are also included.

Keywords: Clustering, Text Mining, Unstructured TextDocuments, Fading Function.

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Authors: Seo Young Kim, Toshimitsu Hamasaki

Abstract:

Microarrays have become the effective, broadly used tools in biological and medical research to address a wide range of problems, including classification of disease subtypes and tumors. Many statistical methods are available for analyzing and systematizing these complex data into meaningful information, and one of the main goals in analyzing gene expression data is the detection of samples or genes with similar expression patterns. In this paper, we express and compare the performance of several clustering methods based on data preprocessing including strategies of normalization or noise clearness. We also evaluate each of these clustering methods with validation measures for both simulated data and real gene expression data. Consequently, clustering methods which are common used in microarray data analysis are affected by normalization and degree of noise and clearness for datasets.

Keywords: Gene expression, clustering, data preprocessing.

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Authors: A. M. Fahim, G. Saake, A. M. Salem, F. A. Torkey, M. A. Ramadan

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Data clustering is an important data exploration technique with many applications in data mining. We present an enhanced version of the well known single link clustering algorithm. We will refer to this algorithm as DCBOR. The proposed algorithm alleviates the chain effect by removing the outliers from the given dataset. So this algorithm provides outlier detection and data clustering simultaneously. This algorithm does not need to update the distance matrix, since the algorithm depends on merging the most k-nearest objects in one step and the cluster continues grow as long as possible under specified condition. So the algorithm consists of two phases; at the first phase, it removes the outliers from the input dataset. At the second phase, it performs the clustering process. This algorithm discovers clusters of different shapes, sizes, densities and requires only one input parameter; this parameter represents a threshold for outlier points. The value of the input parameter is ranging from 0 to 1. The algorithm supports the user in determining an appropriate value for it. We have tested this algorithm on different datasets contain outlier and connecting clusters by chain of density points, and the algorithm discovers the correct clusters. The results of our experiments demonstrate the effectiveness and the efficiency of DCBOR.

Keywords: Data Clustering, Clustering Algorithms, Handling Noise, Arbitrary Shape of Clusters.

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Authors: Razib M. Othman, Safaai Deris, Rosli M. Illias, Zalmiyah Zakaria, Saberi M. Mohamad

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Nowadays, Gene Ontology has been used widely by many researchers for biological data mining and information retrieval, integration of biological databases, finding genes, and incorporating knowledge in the Gene Ontology for gene clustering. However, the increase in size of the Gene Ontology has caused problems in maintaining and processing them. One way to obtain their accessibility is by clustering them into fragmented groups. Clustering the Gene Ontology is a difficult combinatorial problem and can be modeled as a graph partitioning problem. Additionally, deciding the number k of clusters to use is not easily perceived and is a hard algorithmic problem. Therefore, an approach for solving the automatic clustering of the Gene Ontology is proposed by incorporating cohesion-and-coupling metric into a hybrid algorithm consisting of a genetic algorithm and a split-and-merge algorithm. Experimental results and an example of modularized Gene Ontology in RDF/XML format are given to illustrate the effectiveness of the algorithm.

Keywords: Automatic clustering, cohesion-and-coupling metric, gene ontology; genetic algorithm, split-and-merge algorithm.

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