StruClus: Scalable Structural Graph Set Clustering with Representative Sampling

Advances made to the traditional clustering algorithms solves the various problems such as curse of dimensionality and sparsity of data for multiple attributes. The traditional H-K clustering algorithm can solve the randomness and apriority of the initial centers of K-means clustering algorithm. But when we apply it to high dimensional data it causes the dimensional disaster problem due to high computational complexity. All the advanced clustering algorithms like subspace and ensemble clustering algorithms improve the performance for clustering high dimension dataset from different aspects in different extent. Still these algorithms will improve the performance form a single perspective. The objective of the proposed model is to improve the performance of traditional H-K clustering and overcome the limitations such as high computational complexity and poor accuracy for high dimensional data by combining the three different approaches of clustering algorithm as subspace clustering algorithm and ensemble clustering algorithm with H-K clustering algorithm.

The development of technology generates huge amounts of non-textual information, such as images. An efficient image annotation and retrieval system is highly desired. Clustering algorithms make it possible to represent visual features of images with finite symbols. Based on this, many statistical models, which analyze correspondence between visual features and words and discover hidden semantics, have been published. These models improve the annotation and retrieval of large image databases. However, image data usually have a large number of dimensions. Traditional clustering algorithms assign equal weights to these dimensions, and become confounded in the process of dealing with these dimensions. In this paper, we propose a top-down, subspace clustering algorithm as a solution to this problem. For a given cluster, we determine relevant features based on histogram analysis and assign greater weight to relevant features as compared to less relevant features. We have implemented four different models to link visual tokens with keywords based on the clustering results of our clustering algorithm and K-means algorithm, and evaluated performance using precision, recall and correspondence accuracy using benchmark dataset. The results show that our algorithm is better than traditional ones for automatic image annotation and retrieval.

Fuzzy weighted C-ordered means clustering algorithm

Recently, many data mining techniques were revisited to cope with the new big data challenges. Nearly all of these algorithms considered the efficiency of the mining algorithm to survive the increasing size of the data. However, as the dimensionality of the data increases, not only the efficiency but also the effectiveness of traditional mining algorithms is compromised. For instance, clusters hidden in some subspaces are hard to be detected using traditional clustering algorithms, as the dimensionality of the data increases. In this paper, we consider both the huge size, and the high dimensionality of big data by providing a novel solution that presents a three-phase model for subspace stream clustering algorithms. Our novel model, overcomes the huge size of the big data in its first phase, by continuously applying a streaming concept over the huge data objects, and summarizing them into micro-clusters. Then, after each certain batch of data, or after upon a user request, the second phase is applied over the data summarized in micro-clusters, to reconstruct the current distribution of the data out of the current summaries. In the third phase, a subspace clustering algorithm is applied to overcome the high dimensionality of the data, and to find hidden clusters within some subspace. An extensive evaluation study over different scenarios that follow our model over a big data set is performed.KeywordsSubspace stream clusteringStreaming big dataReal-time streaming analysis of big data

Generating high-quality gene clusters and identifying the underlying biological mechanism of the gene clusters are the important goals of clustering gene expression analysis. To get high-quality cluster results, most of the current approaches rely on choosing the best cluster algorithm, in which the design biases and assumptions meet the underlying distribution of the dataset. There are two issues for this approach: 1) usually, the underlying data distribution of the gene expression datasets is unknown and 2) there are so many clustering algorithms available and it is very challenging to choose the proper one. To provide a textual summary of the gene clusters, the most explored approach is the extractive approach that essentially builds upon techniques borrowed from the information retrieval, in which the objective is to provide terms to be used for query expansion, and not to act as a stand-alone summary for the entire document sets. Another drawback is that the clustering quality and cluster interpretation are treated as two isolated research problems and are studied separately. In this paper, we design and develop a unified system Gene Expression Miner to address these challenging issues in a principled and general manner by integrating cluster ensemble, text clustering, and multidocument summarization and provide an environment for comprehensive gene expression data analysis. We present a novel cluster ensemble approach to generate high-quality gene cluster. In our text summarization module, given a gene cluster, our expectation-maximization based algorithm can automatically identify subtopics and extract most probable terms for each topic. Then, the extracted top k topical terms from each subtopic are combined to form the biological explanation of each gene cluster. Experimental results demonstrate that our system can obtain high-quality clusters and provide informative key terms for the gene clusters.

Subspace clustering based on latent low rank representation with Frobenius norm minimization

Treatment based on the syndrome differentiation is the key of traditional Chinese medicine (TCM) treating acquired immune deficiency syndrome (AIDS). Syndrome differentiation, where the patients suffering from a western medicine disease are divided into several classes based on their symptoms and signs, is an important diagnostic method and affects the effective use of TCM treatments. Some researches show that the clustering algorithms make it possible to classify the AIDS patients into several syndrome types. These algorithms improve the precision of syndrome differentiation so as to promote the TCM treatment efficacy. However, because of the complexity of AIDS disease, the AIDS clinical data usually have a large number of dimensions. The previous cluster algorithms assign equal weights to these dimensions and become confounded in the process of dealing with these dimensions. In this paper, we use a top-down subspace clustering algorithm as a solution to the syndrome differentiation. For a given cluster, we determine the relevant symptoms based on histogram analysis and assign greater weight to the relevant symptoms as compared to less relevant symptoms. Then, the symptoms with greater weight are used to differentiate the syndrome type of AIDS patients. Finally, the proposed method is compared with the traditional k-means algorithm based on the collected AIDS dataset. We evaluate their performance by the precision and the consistency. The experimental results show that the proposed algorithm is better than the traditional ones for aided TCM syndrome differentiation of AIDS patients.

The sparsity and the problem of the curse of dimensionality of high-dimensional data, which make the most of the traditional clustering algorithm, lose action in high-dimensional space. Therefore, clustering of data in high-dimensional space is becoming the hot research areas. By utilizing the subtractive clustering as initialized method, and combine with the revised clustering validation indices, this paper offers a subspace clustering algorithm for automatically determining the optimal number of clusters on high dimensional data. The experiment results show that the proposed clustering algorithm can get better cluster validation performance than that of conventional indices.

We investigate the use of biased sampling according to the density of the data set to speed up the operation of general data mining tasks, such as clustering and outlier detection in large multidimensional data sets. In density-biased sampling, the probability that a given point will be included in the sample depends on the local density of the data set. We propose a general technique for density-biased sampling that can factor in user requirements to sample for properties of interest and can be tuned for specific data mining tasks. This allows great flexibility and improved accuracy of the results over simple random sampling. We describe our approach in detail, we analytically evaluate it, and show how it can be optimized for approximate clustering and outlier detection. Finally, we present a thorough experimental evaluation of the proposed method, applying density-biased sampling on real and synthetic data sets, and employing clustering and outlier detection algorithms, thus highlighting the utility of our approach.

The text data of the social network platforms take the form of short texts, and the massive text data have high-dimensional and sparse characteristics, which does not make the traditional clustering algorithm perform well. In this paper, a new community detection method based on the sparse subspace clustering (SSC) algorithm is proposed to deal with the problem of sparsity and the high-dimensional characteristic of short texts in online social networks. The main ideal is as follows. First, the structured data including users’ attributions and user behavior and unstructured data such as user reviews are used to construct the vector space for the network. And the similarity of the feature words is calculated by the location relation of the feature words in the synonym word forest. Then, the dimensions of data are deduced based on the principal component analysis in order to improve the clustering accuracy. Further, a new community detection method of social network members based on the SSC is proposed. Finally, experiments on several data sets are performed and compared with the K-means clustering algorithm. Experimental results show that proper dimension reduction for high dimensional data can improve the clustering accuracy and efficiency of the SSC approach. The proposed method can achieve suitable community partition effect on online social network data sets.

This paper presents a new algorithm for subspace clustering for high dimensional data. It is an iterative algorithm based on the minimization of an objective function. A major weakness of subspace clustering algorithms is that almost all of them are developed based on within- class information only or by employing both within-cluster and between- clusters information. The density of cluster is lost. The new function is developed by integrating the separation and compactness of clusters. The density of cluster is introduced also in the compactness term. The experimental results confirm that the proposed algorithm gives good results on different types of images by optimizing the runtime.

To better explore the underlying intrinsic structure of tensorial data, in this Letter, the authors propose a low‐rank approximation‐based tensor decomposition (LRATD) algorithm for subspace clustering. LRATD aims to seek a low‐dimensional intrinsic core tensor representation by projecting the original tensor into a subspace spanned by projection matrices. Different from traditional approaches that impose additional constraints on basis matrices to further eliminate the influence of data noise or corruption, they directly add a low‐rank regulariser on the core tensor to encourage more robust feature representation. Noticeably, they develop an accelerated proximal gradient algorithm to solve the problem of LRATD. Experimental results demonstrate the excellent performance compared with state‐of‐the‐art methods.

Generating high quality gene clusters and identifying the underlying biological mechanism of the gene cluster are the important goals of clustering gene expression analysis. To get high quality cluster results, most of the current approaches rely on choosing the best cluster algorithm whose design biases and assumptions meet the underlying distribution of the data set. There are two issues for this approach: (1) usually the underlying data distribution of the gene expression data sets is unknown, and (2) there are so many clustering algorithms available and it is very challenging to choose the proper one. To provide a textual summary of the gene clusters, the most explored approach is the extractive approach that essentially builds upon techniques borrowed from the information retrieval, in which the objective is to provide terms to be used for query expansion, and not to act as a stand alone summary for the entire document sets. Another drawback is that the clustering quality and cluster interpretation are treated as two isolated research problems and are studied separately. But cluster quality and cluster interpretation are closely related and must be addressed in a coherent and unified way. It is essential to have relatively high quality clusters first, in order to get a correct, informative biological explanation of the gene cluster, otherwise, the biological explanation will be incorrect or misleading, no matter how good or robust the text summarization technique is. Based on this consideration, we design and develop a unified system GE-Miner (gene expression miner) to address these challenging issues in a principled and general manner by integrating cluster ensemble and text summarization and provide an environment for comprehensive gene expression data analysis. Experimental results demonstrate that our system can obtain high quality clusters and provide concise and informative textual summary for the gene clusters.

Dense community detection in multi-valued attributed networks

BackgroundNowadays, it is possible to collect expression levels of a set of genes from a set of biological samples during a series of time points. Such data have three dimensions: gene-sample-time (GST). Thus they are called 3D microarray gene expression data. To take advantage of the 3D data collected, and to fully understand the biological knowledge hidden in the GST data, novel subspace clustering algorithms have to be developed to effectively address the biological problem in the corresponding space.ResultsWe developed a subspace clustering algorithm called Order Preserving Triclustering (OPTricluster), for 3D short time-series data mining. OPTricluster is able to identify 3D clusters with coherent evolution from a given 3D dataset using a combinatorial approach on the sample dimension, and the order preserving (OP) concept on the time dimension. The fusion of the two methodologies allows one to study similarities and differences between samples in terms of their temporal expression profile. OPTricluster has been successfully applied to four case studies: immune response in mice infected by malaria (Plasmodium chabaudi), systemic acquired resistance in Arabidopsis thaliana, similarities and differences between inner and outer cotyledon in Brassica napus during seed development, and to Brassica napus whole seed development. These studies showed that OPTricluster is robust to noise and is able to detect the similarities and differences between biological samples.ConclusionsOur analysis showed that OPTricluster generally outperforms other well known clustering algorithms such as the TRICLUSTER, gTRICLUSTER and K-means; it is robust to noise and can effectively mine the biological knowledge hidden in the 3D short time-series gene expression data.