The emergence of high-dimensional data in various areas has brought new challenges to the ensemble clustering research. To deal with the curse of dimensionality, considerable efforts in ensemble clustering have been made by incorporating various subspace-based techniques. Besides the emphasis on subspaces, rather limited attention has been paid to the potential diversity in similarity dissimilarity metrics. It remains a surprisingly open problem in ensemble clustering how to create and aggregate a large number of diversified metrics, and furthermore, how to jointly exploit the multi-level diversity in the large number of metrics, subspaces, and clusters, in a unified framework. To tackle this problem, this paper proposes a novel multi-diversified ensemble clustering approach. In particular, we create a large number of diversified metrics by randomizing a scaled exponential similarity kernel, which are then coupled with random subspaces to form a large set of metric-subspace pairs. Based on the similarity matrices derived from these metric-subspace pairs, an ensemble of diversified base clusterings can thereby be constructed. Further, an entropy-based criterion is adopted to explore the cluster-wise diversity in ensembles, based on which the consensus function is therefore presented. Experimental results on twenty high-dimensional datasets have confirmed the superiority of our approach over the state-of-the-art.
The pair-wise co-occurrence based methods @cite_17 @cite_27 @cite_13 typically construct a co-association matrix by considering the frequency that two data samples occur in the same cluster among the multiple base clusterings. The co-association matrix is then used as the similarity matrix for the data samples, upon which some clustering algorithms can thereby be performed to obtain the final clustering result. Fred and Jain @cite_17 first introduced the concept of the co-association matrix and proposed the evidence accumulation clustering (EAC) method, which applied a hierarchical agglomerative clustering algorithm @cite_25 on the co-association matrix to build the consensus clustering. To extend the EAC method, @cite_27 took the cluster sizes into consideration and proposed the probability accumulation method. @cite_13 dealt with the uncertain entries in the co-association matrix by first labeling them as unobserved, and then recovering the unobserved entries by the matrix completion technique. @cite_23 proved that the spectral clustering of the co-association matrix is equivalent to a weighted version of @math -means, and proposed the spectral ensemble clustering (SEC) method to effectively and efficiently obtain the consensus result.
@cite_27 @cite_23 @cite_13 @cite_25 @cite_17
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Clustering ensemble methods produce a consensus partition of a set of data points by combining the results of a collection of base clustering algorithms. In the evidence accumulation clustering (EAC) paradigm, the clustering ensemble is transformed into a pairwise co-association matrix, thus avoiding the label correspondence problem, which is intrinsic to other clustering ensemble schemes. In this paper, we propose a consensus clustering approach based on the EAC paradigm, which is not limited to crisp partitions and fully exploits the nature of the co-association matrix. Our solution determines probabilistic assignments of data points to clusters by minimizing a Bregman divergence between the observed co-association frequencies and the corresponding co-occurrence probabilities expressed as functions of the unknown assignments. We additionally propose an optimization algorithm to find a solution under any double-convex Bregman divergence. Experiments on both synthetic and real benchmark data show the effectiveness of the proposed approach. Since a large number of clustering algorithms exist, aggregating different clustered partitions into a single consolidated one to obtain better results has become an important problem. In Fred and Jain's evidence accumulation algorithm, they construct a co-association matrix on original partition labels, and then apply minimum spanning tree to this matrix for the combined clustering. In this paper, we will propose a novel clustering aggregation scheme, probability accumulation. In this algorithm, the construction of correlation matrices takes the cluster sizes of original clusterings into consideration. An alternate improved algorithm with additional pre- and post-processing is also proposed. Experimental results on both synthetic and real data-sets show that the proposed algorithms perform better than evidence accumulation, as well as some other methods. We explore the idea of evidence accumulation (EAC) for combining the results of multiple clusterings. First, a clustering ensemble?a set of object partitions, is produced. Given a data set (n objects or patterns in d dimensions), different ways of producing data partitions are: 1) applying different clustering algorithms and 2) applying the same clustering algorithm with different values of parameters or initializations. Further, combinations of different data representations (feature spaces) and clustering algorithms can also provide a multitude of significantly different data partitionings. We propose a simple framework for extracting a consistent clustering, given the various partitions in a clustering ensemble. According to the EAC concept, each partition is viewed as an independent evidence of data organization, individual data partitions being combined, based on a voting mechanism, to generate a new n n similarity matrix between the n patterns. The final data partition of the n patterns is obtained by applying a hierarchical agglomerative clustering algorithm on this matrix. We have developed a theoretical framework for the analysis of the proposed clustering combination strategy and its evaluation, based on the concept of mutual information between data partitions. Stability of the results is evaluated using bootstrapping techniques. A detailed discussion of an evidence accumulation-based clustering algorithm, using a split and merge strategy based on the K-means clustering algorithm, is presented. Experimental results of the proposed method on several synthetic and real data sets are compared with other combination strategies, and with individual clustering results produced by well-known clustering algorithms. Many stability measures, such as Normalized Mutual Information NMI, have been proposed to validate a set of partitionings. It is highly possible that a set of partitionings may contain one or more high quality clusters but is still adjudged a bad cluster by a stability measure, and as a result, is completely neglected. Inspired by evaluation approaches measuring the efficacy of a set of partitionings, researchers have tried to define new measures for evaluating a cluster. Thus far, the measures defined for assessing a cluster are mostly based on the well-known NMI measure. The drawback of this commonly used approach is discussed in this paper, after which a new asymmetric criterion, called the Alizadeh--Parvin--Moshki--Minaei criterion APMM, is proposed to assess the association between a cluster and a set of partitionings. We show that the APMM criterion overcomes the deficiency in the conventional NMI measure. We also propose a clustering ensemble framework that incorporates the APMM's capabilities in order to find the best performing clusters. The framework uses Average APMM AAPMM as a fitness measure to select a number of clusters instead of using all of the results. Any cluster that satisfies a predefined threshold of the mentioned measure is selected to participate in an elite ensemble. To combine the chosen clusters, a co-association matrix-based consensus function by which the set of resultant partitionings are obtained is used. Because Evidence Accumulation Clustering EAC can not derive the co-association matrix from a subset of clusters appropriately, a new EAC-based method, called Extended EAC EEAC, is employed to construct the co-association matrix from the chosen subset of clusters. Empirical studies show that our proposed approach outperforms other cluster ensemble approaches. Data clustering is an important task and has found applications in numerous real-world problems. Since no single clustering algorithm is able to identify all different types of cluster shapes and structures, ensemble clustering was proposed to combine different partitions of the same data generated by multiple clustering algorithms. The key idea of most ensemble clustering algorithms is to find a partition that is consistent with most of the available partitions of the input data. One problem with these algorithms is their inability to handle uncertain data pairs, i.e. data pairs for which about half of the partitions put them into the same cluster and the other half do the opposite. When the number of uncertain data pairs is large, they can mislead the ensemble clustering algorithm in generating the final partition. To overcome this limitation, we propose an ensemble clustering approach based on the technique of matrix completion. The proposed algorithm constructs a partially observed similarity matrix based on the data pairs whose cluster memberships are agreed upon by most of the clustering algorithms in the ensemble. It then deploys the matrix completion algorithm to complete the similarity matrix. The final data partition is computed by applying an efficient spectral clustering algorithm to the completed matrix. Our empirical studies with multiple real-world datasets show that the proposed algorithm performs significantly better than the state-of-the-art algorithms for ensemble clustering. Co-clustering, or simultaneous clustering of rows and columns of a two-dimensional data matrix, is rapidly becoming a powerful data analysis technique. Co-clustering has enjoyed wide success in varied application domains such as text clustering, gene-microarray analysis, natural language processing and image, speech and video analysis. In this paper, we introduce a partitional co-clustering formulation that is driven by the search for a good matrix approximation---every co-clustering is associated with an approximation of the original data matrix and the quality of co-clustering is determined by the approximation error. We allow the approximation error to be measured using a large class of loss functions called Bregman divergences that include squared Euclidean distance and KL-divergence as special cases. In addition, we permit multiple structurally different co-clustering schemes that preserve various linear statistics of the original data matrix. To accomplish the above tasks, we introduce a new minimum Bregman information (MBI) principle that simultaneously generalizes the maximum entropy and standard least squares principles, and leads to a matrix approximation that is optimal among all generalized additive models in a certain natural parameter space. Analysis based on this principle yields an elegant meta algorithm, special cases of which include most previously known alternate minimization based clustering algorithms such as kmeans and co-clustering algorithms such as information theoretic (, 2003b) and minimum sum-squared residue co-clustering (, 2004). To demonstrate the generality and flexibility of our co-clustering framework, we provide examples and empirical evidence on a variety of problem domains and also describe novel co-clustering applications such as missing value prediction and compression of categorical data matrices. The task of discovering natural groupings of input patterns, or clustering, is an important aspect of machine learning and pattern analysis. In this paper, we study the widely used spectral clustering algorithm which clusters data using eigenvectors of a similarity affinity matrix derived from a data set. In particular, we aim to solve two critical issues in spectral clustering: (1) how to automatically determine the number of clusters, and (2) how to perform effective clustering given noisy and sparse data. An analysis of the characteristics of eigenspace is carried out which shows that (a) not every eigenvectors of a data affinity matrix is informative and relevant for clustering; (b) eigenvector selection is critical because using uninformative irrelevant eigenvectors could lead to poor clustering results; and (c) the corresponding eigenvalues cannot be used for relevant eigenvector selection given a realistic data set. Motivated by the analysis, a novel spectral clustering algorithm is proposed which differs from previous approaches in that only informative relevant eigenvectors are employed for determining the number of clusters and performing clustering. The key element of the proposed algorithm is a simple but effective relevance learning method which measures the relevance of an eigenvector according to how well it can separate the data set into different clusters. Our algorithm was evaluated using synthetic data sets as well as real-world data sets generated from two challenging visual learning problems. The results demonstrated that our algorithm is able to estimate the cluster number correctly and reveal natural grouping of the input data patterns even given sparse and noisy data. Two-dimensional contingency tables or co-occurrence matrices arise frequently in various important applications such as text analysis and web-log mining. As a fundamental research topic, co-clustering aims to generate a meaningful partition of the contingency table to reveal hidden relationships between rows and columns. Traditional co-clustering algorithms usually produce a predefined number of flat partition of both rows and columns, which do not reveal relationship among clusters. To address this limitation, hierarchical co-clustering algorithms have attracted a lot of research interests recently. Although successful in various applications, the existing hierarchical co-clustering algorithms are usually based on certain heuristics and do not have solid theoretical background. In this paper, we present a new co-clustering algorithm, HICC, with solid theoretical background. It simultaneously constructs a hierarchical structure of both row and column clusters, which retains sufficient mutual information between rows and columns of the contingency table. An efficient and effective greedy algorithm is developed, which grows a co-cluster hierarchy by successively performing row-wise or column-wise splits that lead to the maximal mutual information gain. Extensive experiments on both synthetic and real datasets demonstrate that our algorithm can reveal essential relationships of row (and column) clusters and has better clustering precision than existing algorithms. Moreover, the experiments on real dataset show that HICC can effectively reveal hidden relationships between rows and columns in the contingency table. Co-clustering has emerged as an important technique for mining contingency data matrices. However, almost all existing co-clustering algorithms are hard partitioning, assigning each row and column of the data matrix to one cluster. Recently a Bayesian co-clustering approach has been proposed which allows a probability distribution membership in row and column clusters. The approach uses variational inference for parameter estimation. In this work, we modify the Bayesian co-clustering model, and use collapsed Gibbs sampling and collapsed variational inference for parameter estimation. Our empirical evaluation on real data sets shows that both collapsed Gibbs sampling and collapsed variational inference are able to find more accurate likelihood estimates than the standard variational Bayesian co-clustering approach. We present a new method for spectral clustering with paired data based on kernel canonical correlation analysis, called correlational spectral clustering. Paired data are common in real world data sources, such as images with text captions. Traditional spectral clustering algorithms either assume that data can be represented by a single similarity measure, or by co-occurrence matrices that are then used in biclustering. In contrast, the proposed method uses separate similarity measures for each data representation, and allows for projection of previously unseen data that are only observed in one representation (e.g. images but not text). We show that this algorithm generalizes traditional spectral clustering algorithms and show consistent empirical improvement over spectral clustering on a variety of datasets of images with associated text. As a promising way for heterogeneous data analytics, consensus clustering has attracted increasing attention in recent decades. Among various excellent solutions, the co-association matrix based methods form a landmark, which redefines consensus clustering as a graph partition problem. Nevertheless, the relatively high time and space complexities preclude it from wide real-life applications. We, therefore, propose Spectral Ensemble Clustering (SEC) to leverage the advantages of co-association matrix in information integration but run more efficiently. We disclose the theoretical equivalence between SEC and weighted K-means clustering, which dramatically reduces the algorithmic complexity. We also derive the latent consensus function of SEC, which to our best knowledge is the first to bridge co-association matrix based methods to the methods with explicit global objective functions. Further, we prove in theory that SEC holds the robustness, generalizability, and convergence properties. We finally extend SEC to meet the challenge arising from incomplete basic partitions, based on which a row-segmentation scheme for big data clustering is proposed. Experiments on various real-world data sets in both ensemble and multi-view clustering scenarios demonstrate the superiority of SEC to some state-of-the-art methods. In particular, SEC seems to be a promising candidate for big data clustering. We consider the problem of identifying a sparse set of relevant columns and rows in a large data matrix with highly corrupted entries. This problem of identifying groups from a collection of bipartite variables such as proteins and drugs, biological species and gene sequences, malware and signatures, etc is commonly referred to as biclustering or co-clustering. Despite its great practical relevance, and although several ad-hoc methods are available for biclustering, theoretical analysis of the problem is largely non-existent. The problem we consider is also closely related to structured multiple hypothesis testing, an area of statistics that has recently witnessed a flurry of activity. We make the following contributions 1. We prove lower bounds on the minimum signal strength needed for successful recovery of a bicluster as a function of the noise variance, size of the matrix and bicluster of interest. 2. We show that a combinatorial procedure based on the scan statistic achieves this optimal limit. 3. We characterize the SNR required by several computationally tractable procedures for biclustering including element-wise thresholding, column row average thresholding and a convex relaxation approach to sparse singular vector decomposition. We present a new method for clustering based on compression. The method does not use subject-specific features or background knowledge, and works as follows: First, we determine a parameter-free, universal, similarity distance, the normalized compression distance or NCD, computed from the lengths of compressed data files (singly and in pairwise concatenation). Second, we apply a hierarchical clustering method. The NCD is not restricted to a specific application area, and works across application area boundaries. A theoretical precursor, the normalized information distance, co-developed by one of the authors, is provably optimal. However, the optimality comes at the price of using the noncomputable notion of Kolmogorov complexity. We propose axioms to capture the real-world setting, and show that the NCD approximates optimality. To extract a hierarchy of clusters from the distance matrix, we determine a dendrogram (ternary tree) by a new quartet method and a fast heuristic to implement it. The method is implemented and available as public software, and is robust under choice of different compressors. To substantiate our claims of universality and robustness, we report evidence of successful application in areas as diverse as genomics, virology, languages, literature, music, handwritten digits, astronomy, and combinations of objects from completely different domains, using statistical, dictionary, and block sorting compressors. In genomics, we presented new evidence for major questions in Mammalian evolution, based on whole-mitochondrial genomic analysis: the Eutherian orders and the Marsupionta hypothesis against the Theria hypothesis. We present an efficient spectral method for finding consistent correspondences between two sets of features. We build the adjacency matrix M of a graph whose nodes represent the potential correspondences and the weights on the links represent pairwise agreements between potential correspondences. Correct assignments are likely to establish links among each other and thus form a strongly connected cluster. Incorrect correspondences establish links with the other correspondences only accidentally, so they are unlikely to belong to strongly connected clusters. We recover the correct assignments based on how strongly they belong to the main cluster of M, by using the principal eigenvector of M and imposing the mapping constraints required by the overall correspondence mapping (one-to-one or one-to-many). The experimental evaluation shows that our method is robust to outliers, accurate in terms of matching rate, while being much faster than existing methods Co-clustering is a generalization of unsupervised clustering that has recently drawn renewed attention, driven by emerging data mining applications in diverse areas. Whereas clustering groups entire columns of a data matrix, co-clustering groups columns over select rows only, i.e., it simultaneously groups rows and columns. The concept generalizes to data “boxes” and higher-way tensors, for simultaneous grouping along multiple modes. Various co-clustering formulations have been proposed, but no workhorse analogous to K-means has emerged. This paper starts from K-means and shows how co-clustering can be formulated as a constrained multilinear decomposition with sparse latent factors. For three- and higher-way data, uniqueness of the multilinear decomposition implies that, unlike matrix co-clustering, it is possible to unravel a large number of possibly overlapping co-clusters. A basic multi-way co-clustering algorithm is proposed that exploits multilinearity using Lasso-type coordinate updates. Various line search schemes are then introduced to speed up convergence, and suitable modifications are proposed to deal with missing values. The imposition of latent sparsity pays a collateral dividend: it turns out that sequentially extracting one co-cluster at a time is almost optimal, hence the approach scales well for large datasets. The resulting algorithms are benchmarked against the state-of-art in pertinent simulations, and applied to measured data, including the ENRON e-mail corpus. In this paper, we propose a rank minimization method to fuse the predicted confidence scores of multiple models, each of which is obtained based on a certain kind of feature. Specifically, we convert each confidence score vector obtained from one model into a pairwise relationship matrix, in which each entry characterizes the comparative relationship of scores of two test samples. Our hypothesis is that the relative score relations are consistent among component models up to certain sparse deviations, despite the large variations that may exist in the absolute values of the raw scores. Then we formulate the score fusion problem as seeking a shared rank-2 pairwise relationship matrix based on which each original score matrix from individual model can be decomposed into the common rank-2 matrix and sparse deviation errors. A robust score vector is then extracted to fit the recovered low rank score relation matrix. We formulate the problem as a nuclear norm and l 1 norm optimization objective function and employ the Augmented Lagrange Multiplier (ALM) method for the optimization. Our method is isotonic (i.e., scale invariant) to the numeric scales of the scores originated from different models. We experimentally show that the proposed method achieves significant performance gains on various tasks including object categorization and video event detection. The wealth of interaction information provided in biomedical articles motivated the implementation of text mining approaches to automatically extract biomedical relations. This paper presents an unsupervised method based on pattern clustering and sentence parsing to deal with biomedical relation extraction. Pattern clustering algorithm is based on Polynomial Kernel method, which identifies interaction words from unlabeled data; these interaction words are then used in relation extraction between entity pairs. Dependency parsing and phrase structure parsing are combined for relation extraction. Based on the semi-supervised KNN algorithm, we extend the proposed unsupervised approach to a semi-supervised approach by combining pattern clustering, dependency parsing and phrase structure parsing rules. We evaluated the approaches on two different tasks: (1) Protein–protein interactions extraction, and (2) Gene–suicide association extraction. The evaluation of task (1) on the benchmark dataset (AImed corpus) showed that our proposed unsupervised approach outperformed three supervised methods. The three supervised methods are rule based, SVM based, and Kernel based separately. The proposed semi-supervised approach is superior to the existing semi-supervised methods. The evaluation on gene–suicide association extraction on a smaller dataset from Genetic Association Database and a larger dataset from publicly available PubMed showed that the proposed unsupervised and semi-supervised methods achieved much higher F-scores than co-occurrence based method. Clustering ensembles have emerged as a powerful method for improving both the robustness and the stability of unsupervised classification solutions. However, finding a consensus clustering from multiple partitions is a difficult problem that can be approached from graph-based, combinatorial or statistical perspectives. We offer a probabilistic model of consensus using a finite mixture of multinomial distributions in a space of clustering. A combined partition is found as a solution to the corresponding maximum likelihood problem using the GA algorithm. The excellent scalability of this algorithm and comprehensible underlying model are particularly important for clustering of large datasets. This study includes two sections, at the first, calculate correlation matrix. this matrix show correlation between samples and we found the best samples that can be in the center of clusters. In the other section a genetic algorithm is employed to produce the most stable partitions from an evolving ensemble (population) of clustering algorithms along with a special objective function. The objective function evaluates multiple partitions according to changes caused by data perturbations and prefers those clustering that are least susceptible to those perturbations. Based on spectral graph theory, spectral clustering is an optimal graph partition problem. It has been proven that the spectral clustering is equivalent to nonnegative matrix factorization (NMF) under certain conditions. Based on the equivalence, some spectral clustering methods are proposed, but the global discriminative information of the dataset is neglected. In this paper, based on the equivalence between spectral clustering and NMF, we simultaneously maximize the between-class scatter matrix and minimize the within-class scatter matrix to enhance the discriminating power. We integrate the geometrical structure and discriminative structure in a joint framework. With a global discriminative regularization term added into the nonnegative matrix factorization framework, we propose two novel spectral clustering methods, named global discriminative-based nonnegative and spectral clustering (GDBNSC-Ncut and GDBNSC-Rcut) These new spectral clustering algorithms can preserve both the global geometrical structure and global discriminative structure. The intrinsic geometrical information of the dataset is detected, and clustering quality is improved with enhanced discriminating power. In addition, the proposed algorithms also have very good abilities of handling out-of-sample data. Experimental results on real word data demonstrate that the proposed algorithms outperform some state-of-the-art methods with good clustering qualities. We maximize the between-class scatter matrix.Meanwhile, we minimize the within-class scatter matrix.We integrate the geometrical structure and discriminative structure in a framework.A global discriminative regularization term added into the objective functions.The new algorithms can preserve the global geometrical and discriminative structure. Ng-Jordan-Weiss (NJW) method is one of the most widely used spectral clustering algorithms. For a K clustering problem, this method partitions data using the largest K eigenvectors of the normalized affinity matrix derived from the dataset. It has been demonstrated that the spectral relaxation solution of K-way grouping is located on the subspace of the largest K eigenvectors. However, we find from a lot of experiments that the top K eigenvectors cannot always detect the structure of the data for real pattern recognition problems. So it is necessary to select eigenvectors for spectral clustering. We propose an eigenvector selection method based on entropy ranking for spectral clustering (ESBER). In this method, first all the eigenvectors are ranked according to their importance on clustering, and then a suitable eigenvector combination is obtained from the ranking list. In this paper, we propose two strategies to select eigenvectors in the ranking list of eigenvectors. One is directly adopting the first K eigenvectors in the ranking list. Different to the largest K eigenvectors of NJW method, these K eigenvectors are the most important eigenvectors among all the eigenvectors. The other eigenvector selection strategy is to search a suitable eigenvector combination among the first Km (Km>K) eigenvectors in the ranking list. The eigenvector combination obtained by this strategy can reflect the structure of the original data and lead to a satisfying spectral clustering result. Furthermore, we also present computational complexity reduction strategies for ESBER method to deal with large-scale datasets. We have performed experiments on UCI benchmark datasets, MNIST handwritten digits datasets, and Brodatz texture datasets, adopting NJW method for a baseline comparison. The experimental results show that ESBER method is more robust than NJW method. Especially, ESBER method with the latter eigenvector selection strategy can obtain satisfying clustering results in most cases.