Multivariate methods using mixtures: Correspondence analysis,scaling and pattern-detection

Matrices of binary or count data are modelled under a unified statistical framework using finite mixtures to group the rows and/or columns. These likelihood-based one-mode and two-mode fuzzy clusterings provide maximum likelihood estimation of parameters and the options of using likelihood ratio tests or information criteria for model comparison. Geometric developments focused on pattern detection give likelihood-based analogues of various techniques in multivariate analysis, including multidimensional scaling, association analysis, ordination, correspondence analysis, and the construction of biplots. Illustrative examples demonstrate the effectiveness of these visualisations for identifying patterns of ecological significance (e.g. abrupt versus slow species turnover).     

Biclustering in data mining

Biclustering consists in simultaneous partitioning of the set of samples and the set of their attributes (features) into subsets (classes). Samples and features classified together are supposed to have a high relevance to each other. In this paper we review the most widely used and successful biclustering techniques and their related applications. This survey is written from a theoretical viewpoint emphasizing mathematical concepts that can be met in existing biclustering techniques.     

采用多样性选择的量子粒子群双向聚类算法

双向聚类已成为分析基因表达数据的一种重要工具,可以同时从基因和条件两个方向寻找具有相同表达波动的簇。但双向聚类是一种多目标优化的局部搜索算法,处理繁杂的基因数据时容易陷入局部最优。为提高算法的全局搜索能力,提出了一种多样性选择的量子粒子群双向聚类算法（Diversify-Optional QPSO,DOQPSO）。算法首先采用DOQPSO处理基因数据,然后用改进的FLOC算法进行贪心迭代寻找双向聚类,以求得更为理想的结果。算法通过实验仿真,并与FLOC算法和QPSO算法进行比较,结果证明DOQPSO双向聚类算法具有更好的全局寻优能力,且聚类效果更佳。     

Stability-based validation of bicluster solutions

Bicluster analysis is an unsupervised learning method to detect homogeneous or uniquely characterized two-way subsets of objects and attributes from a data set. It is useful in finding groups that may not be found by the traditional cluster analysis and in interpreting the groups intuitively, especially for high-dimensional data sets. Because of these advantages, over the last few years, various biclustering algorithms have been developed and applied to bioinformatics and text mining area. However, research into validation of bicluster solutions is rare. We propose a new procedure of validating bicluster solutions by developing a stability index to measure the reproducibility of the solution under variation in the input data set. By generating random resample data sets from the input data set, obtaining bicluster solutions from them, and evaluating the expected agreement of the solutions to the bicluster solution for the original input data set, we quantify the stability of the bicluster solution. Experiments using three artificial data sets and two real gene expression data sets indicate that the proposed method is suitable to validate bicluster solutions.     

BSN: An automatic generation algorithm of social network data

In recent years, there has been considerable interest in the analysis of social network data. In this paper, we propose a novel automatic generation algorithm of social network data - the Biclustering Algorithm for Social Network Data algorithm. The algorithm introduces biclustering to social network analysis for automatic identification of associations among a group of actors and entities. The algorithm is different from existing ones in that it employs a combination of min-max and pattern searching procedures to construct hierarchical biclusters and discover the relationships among these actors, in order to easily interpret social network data. The algorithm is not subject to convexity limitations, and does not need to use derivatives information.     

A new measure for gene expression biclustering based on non-parametric correlation

Background

One of the emerging techniques for performing the analysis of the DNA microarray data known as biclustering is the search of subsets of genes and conditions which are coherently expressed. These subgroups provide clues about the main biological processes. Until now, different approaches to this problem have been proposed. Most of them use the mean squared residue as quality measure but relevant and interesting patterns can not be detected such as shifting, or scaling patterns. Furthermore, recent papers show that there exist new coherence patterns involved in different kinds of cancer and tumors such as inverse relationships between genes which can not be captured.

Results

The proposed measure is called Spearman's biclustering measure (SBM) which performs an estimation of the quality of a bicluster based on the non-linear correlation among genes and conditions simultaneously. The search of biclusters is performed by using a evolutionary technique called estimation of distribution algorithms which uses the SBM measure as fitness function. This approach has been examined from different points of view by using artificial and real microarrays. The assessment process has involved the use of quality indexes, a set of bicluster patterns of reference including new patterns and a set of statistical tests. It has been also examined the performance using real microarrays and comparing to different algorithmic approaches such as Bimax, CC, OPSM, Plaid and xMotifs.

Conclusions

SBM shows several advantages such as the ability to recognize more complex coherence patterns such as shifting, scaling and inversion and the capability to selectively marginalize genes and conditions depending on the statistical significance.     

一种基于粗糙遗传算法的缩放模式双聚类分析方法

研究了基因表达数据的缩放模式发现问题,给出了一种缩放模式双聚类评价函数,并提出了一种基于粗糙遗传算法的双聚类分析方法。该方法先以启发式算法及随机方法生成初始种群,再基于粗糙遗传算法对种群进行迭代,以达到全局优化的目的。在Yeast数据集上进行的测试表明,该算法能对启发式算法的结果进行良好的修正。生物显著性分析表明所发现的缩放模式双聚类具有生物学意义。     

A probabilistic relaxation labeling framework for reducing the noise effect in geometric biclustering of gene expression data

Biclustering is an important method in DNA microarray analysis which can be applied when only a subset of genes is co-expressed in a subset of conditions. Unlike standard clustering analyses, biclustering methodology can perform simultaneous classification on two dimensions of genes and conditions in a microarray data matrix. However, the performance of biclustering algorithms is affected by the inherent noise in data, types of biclusters and computational complexity. In this paper, we present a geometric biclustering method based on the Hough transform and the relaxation labeling technique. Unlike many existing biclustering algorithms, we first consider the biclustering patterns through geometric interpretation. Such a perspective makes it possible to unify the formulation of different types of biclusters as hyperplanes in spatial space and facilitates the use of a generic plane finding algorithm for bicluster detection. In our algorithm, the Hough transform is employed for hyperplane detection in sub-spaces to reduce the computational complexity. Then sub-biclusters are combined into larger ones under the probabilistic relaxation labeling framework. Our simulation studies demonstrate the robustness of the algorithm against noise and outliers. In addition, our method is able to extract biologically meaningful biclusters from real microarray gene expression data.     

Mining permission patterns for contrasting clean and malicious android applications

An Android application uses a permission system to regulate the access to system resources and users’ privacy-relevant information. Existing works have demonstrated several techniques to study the required permissions declared by the developers, but little attention has been paid towards used permissions. Besides, no specific permission combination is identified to be effective for malware detection. To fill these gaps, we have proposed a novel pattern mining algorithm to identify a set of contrast permission patterns that aim to detect the difference between clean and malicious applications. A benchmark malware dataset and a dataset of 1227 clean applications has been collected by us to evaluate the performance of the proposed algorithm. Valuable findings are obtained by analyzing the returned contrast permission patterns.     

Variational algorithms for biclustering models

Biclustering is an important tool in exploratory statistical analysis which can be used to detect latent row and column groups of different response patterns. However, few studies include covariate data directly into their biclustering models to explain these variations. A novel biclustering framework that considers both stochastic block structures and covariate effects is proposed to address this modeling problem. Fast approximation estimation algorithms are also developed to deal with a large number of latent variables and covariate coefficients. These algorithms are derived from the variational generalized expectation–maximization (EM) framework where the goal is to increase, rather than maximize, the likelihood lower bound in both E and M steps. The utility of the proposed biclustering framework is demonstrated through two block modeling applications in model-based collaborative filtering and microarray analysis.