Cluster analysis of genome-wide expression data for feature extraction

Bio-chip data that consists of high-dimensional attributes have more attributes than specimens. Thus, it is difficult to obtain covariance matrix from tens thousands of genes within a number of samples. Feature selection and extraction is critical to remove noisy features and reduce the dimensionality in microarray analysis. This study aims to fill the gap by developing a data mining framework with a proposed algorithm for cluster analysis of gene expression data, in which coefficient correlation is employed to arrange genes. Indeed, cluster analysis of microarray data can find coherent patterns of gene expression. The output is displayed as table list for convenient survey. We adopt the breast cancer microarray dataset to demonstrate practical viability of this approach.     

Microarray-MD: a system for exploratory analysis of microarray gene expression data

In this paper, we present Microarray Medical Data explorer (Microarray-MD), a novel software system that is able to assist in the exploratory analysis of gene expression microarray data. It implements a combination scheme of multiple Support Vector Machines, which integrates a variety of gene selection criteria and allows for the discrimination of multiple diseases or subtypes of a disease. The system can be trained and automatically tune its parameters with the provision of pathologically characterized gene expression data to its input. Given a set of new, uncharacterized, patient's data as input, it outputs a decision on the type or the subtype of a disease. A graphical user interface provides easy access to the system operations and direct adjustment of its parameters. It has been tested on various publicly available datasets. The overall accuracy it achieves was estimated to exceed 90%.     

Cluster analysis using multivariate normal mixture models to detect differential gene expression with microarray data

DNA microarrays make it possible to study simultaneously the expression of thousands of genes in a biological sample. Univariate clustering techniques have been used to discover target genes with differential expression between two experimental conditions. Because of possible loss of information due to use of univariate summary statistics, it may be more effective to use multivariate statistics. We present multivariate normal mixture model based clustering analyses to detect differential gene expression between two conditions.Deviating from the general mixture model and model-based clustering, we propose mixture models with specific mean and covariance structures that account for special features of two-condition microarray experiments. Explicit updating formulas in the EM algorithm for three such models are derived. The methods are applied to a real dataset to compare the expression levels of 1176 genes of rats with and without pneumococcal middle-ear infection to illustrate the performance and usefulness of this approach. About 10 genes and 20 genes are found to be differentially expressed in a six-dimensional modeling and a bivariate modeling, respectively. Two simulation studies are conducted to compare the performance of univariate and multivariate methods. Depending on data, neither method can always dominate the other. The results suggest that multivariate normal mixture models can be useful alternatives to univariate methods to detect differential gene expression in exploratory data analysis.     

Automatic facial expression analysis: a survey

Over the last decade, automatic facial expression analysis has become an active research area that finds potential applications in areas such as more engaging human-computer interfaces, talking heads, image retrieval and human emotion analysis. Facial expressions reflect not only emotions, but other mental activities, social interaction and physiological signals. In this survey, we introduce the most prominent automatic facial expression analysis methods and systems presented in the literature. Facial motion and deformation extraction approaches as well as classification methods are discussed with respect to issues such as face normalization, facial expression dynamics and facial expression intensity, but also with regard to their robustness towards environmental changes.     

An evolutionary clustering algorithm for gene expression microarray data analysis

Clustering is concerned with the discovery of interesting groupings of records in a database. Many algorithms have been developed to tackle clustering problems in a variety of application domains. In particular, some of them have been used in bioinformatics research to uncover inherent clusters in gene expression microarray data. In this paper, we show how some popular clustering algorithms have been used for this purpose. Based on experiments using simulated and real data, we also show that the performance of these algorithms can be further improved. For more effective clustering of gene expression microarray data, which is typically characterized by a lot of noise, we propose a novel evolutionary algorithm called evolutionary clustering (EvoCluster). EvoCluster encodes an entire cluster grouping in a chromosome so that each gene in the chromosome encodes one cluster. Based on such encoding scheme, it makes use of a set of reproduction operators to facilitate the exchange of grouping information between chromosomes. The fitness function that the EvoCluster adopts is able to differentiate between how relevant a feature value is in determining a particular cluster grouping. As such, instead of just local pairwise distances, it also takes into consideration how clusters are arranged globally. Unlike many popular clustering algorithms, EvoCluster does not require the number of clusters to be decided in advance. Also, patterns hidden in each cluster can be explicitly revealed and presented for easy interpretation even by casual users. For performance evaluation, we have tested EvoCluster using both simulated and real data. Experimental results show that it can be very effective and robust even in the presence of noise and missing values. Also, when correlating the gene expression microarray data with DNA sequences, we were able to uncover significant biological binding sites (both previously known and unknown) in each cluster discovered by EvoCluster.     

Multiple-kernel SVM based multiple-task oriented data mining system for gene expression data analysis

Gene expression profiling using DNA microarray technique has been shown as a promising tool to improve the diagnosis and treatment of cancer. Recently, many computational methods have been used to discover maker genes, make class prediction and class discovery based on gene expression data of cancer tissue. However, those techniques fall short on some critical areas. These included (a) interpretation of the solution and extracted knowledge. (b) Integrating various sources data and incorporating the prior knowledge into the system. (c) Giving a global understanding of biological complex systems by a complete knowledge discovery framework. This paper proposes a multiple-kernel SVM based data mining system. Multiple tasks, including feature selection, data fusion, class prediction, decision rule extraction, associated rule extraction and subclass discovery, are incorporated in an integrated framework. ALL-AML Leukemia dataset is used to demonstrate the performance of this system.     

Kernel based nonlinear dimensionality reduction for microarray gene expression data analysis

Accurate recognition of cancers based on microarray gene expressions is very important for doctors to choose a proper treatment. Genomic microarrays are powerful research tools in bioinformatics and modern medicinal research. However, a simple microarray experiment often leads to very high-dimensional data and a huge amount of information, the vast amount of data challenges researchers into extracting the important features and reducing the high dimensionality. This paper proposed the kernel method based locally linear embedding to selecting the optimal number of nearest neighbors, constructing uniform distribution manifold. In this paper, a nonlinear dimensionality reduction kernel method based locally linear embedding is proposed to select the optimal number of nearest neighbors, constructing uniform distribution manifold. In addition, support vector machine which has given rise to the development of a new class of theoretically elegant learning machines will be used to classify and recognise genomic microarray. We demonstrate the application of the techniques to two published DNA microarray data sets. The experimental results and comparisons demonstrate that the proposed method is effective approach.     

Cluster analysis of ultrasonic testing data

The methods of cluster analysis are applied to ultrasonic testing data of welded joints. The methods of principal component analysis, K-means clustering, and support vector machines are considered. The application methodology and the results obtained are presented. The article was translated by the authors.     

Finding groups in data: Cluster analysis with ants

We present in this paper a modification of Lumer and Faieta’s algorithm for data clustering. This approach mimics the clustering behavior observed in real ant colonies. This algorithm discovers automatically clusters in numerical data without prior knowledge of possible number of clusters. In this paper we focus on ant-based clustering algorithms, a particular kind of a swarm intelligent system, and on the effects on the final clustering by using during the classification different metrics of dissimilarity: Euclidean, Cosine, and Gower measures. Clustering with swarm-based algorithms is emerging as an alternative to more conventional clustering methods, such as e.g. k-means, etc. Among the many bio-inspired techniques, ant clustering algorithms have received special attention, especially because they still require much investigation to improve performance, stability and other key features that would make such algorithms mature tools for data mining.As a case study, this paper focus on the behavior of clustering procedures in those new approaches. The proposed algorithm and its modifications are evaluated in a number of well-known benchmark datasets. Empirical results clearly show that ant-based clustering algorithms performs well when compared to another techniques.     

DK-means: a deterministic K-means clustering algorithm for gene expression analysis

Pattern Analysis and Applications - Clustering has been widely applied in interpreting the underlying patterns in microarray gene expression profiles, and many clustering algorithms have been...     

Intelligent data analysis approaches to churn as a business problem: a survey

Globalization processes and market deregulation policies are rapidly changing the competitive environments of many economic sectors. The appearance of new competitors and technologies leads to an increase in competition and, with it, a growing preoccupation among service-providing companies with creating stronger customer bonds. In this context, anticipating the customer’s intention to abandon the provider, a phenomenon known as churn, becomes a competitive advantage. Such anticipation can be the result of the correct application of information-based knowledge extraction in the form of business analytics. In particular, the use of intelligent data analysis, or data mining, for the analysis of market surveyed information can be of great assistance to churn management. In this paper, we provide a detailed survey of recent applications of business analytics to churn, with a focus on computational intelligence methods. This is preceded by an in-depth discussion of churn within the context of customer continuity management. The survey is structured according to the stages identified as basic for the building of the predictive models of churn, as well as according to the different types of predictive methods employed and the business areas of their application.     

Distributed data mining: a survey

Most data mining approaches assume that the data can be provided from a single source. If data was produced from many physically distributed locations like Wal-Mart, these methods require a data center which gathers data from distributed locations. Sometimes, transmitting large amounts of data to a data center is expensive and even impractical. Therefore, distributed and parallel data mining algorithms were developed to solve this problem. In this paper, we survey the-state-of-the-art algorithms and applications in distributed data mining and discuss the future research opportunities.     

基于数据约减的聚类有效性分析

聚类分析中利用有效性指标判断数据集的正确类数极易受到噪声数据、类之间分离性以及聚类算法的影响,所确定类数的正确性难以得到保证.为克服这个问题,以文献[1]中的数据约减方法为基础,对原数据集和约减后的数据集利用有效性指标进行正确类数判别.实验表明:该方法能增大类之间的分离性,有效判断数据集的最优类数.     

Gene-CWGAN: a data enhancement method for gene expression profile based on improved CWGAN-GP

Neural Computing and Applications - Traditional machine learning methods are difficult to obtain good performance in the classification of gene expression data due to its characteristics of high...     

Performance analysis of data intensive cloud systems based on data management and replication: a survey

As we delve deeper into the ‘Digital Age’, we witness an explosive growth in the volume, velocity, and variety of the data available on the Internet. For example, in 2012 about 2.5 quintillion bytes of data was created on a daily basis that originated from myriad of sources and applications including mobile devices, sensors, individual archives, social networks, Internet of Things, enterprises, cameras, software logs, etc. Such ‘Data Explosions’ has led to one of the most challenging research issues of the current Information and Communication Technology era: how to optimally manage (e.g., store, replicated, filter, and the like) such large amount of data and identify new ways to analyze large amounts of data for unlocking information. It is clear that such large data streams cannot be managed by setting up on-premises enterprise database systems as it leads to a large up-front cost in buying and administering the hardware and software systems. Therefore, next generation data management systems must be deployed on cloud. The cloud computing paradigm provides scalable and elastic resources, such as data and services accessible over the Internet Every Cloud Service Provider must assure that data is efficiently processed and distributed in a way that does not compromise end-users’ Quality of Service (QoS) in terms of data availability, data search delay, data analysis delay, and the like. In the aforementioned perspective, data replication is used in the cloud for improving the performance (e.g., read and write delay) of applications that access data. Through replication a data intensive application or system can achieve high availability, better fault tolerance, and data recovery. In this paper, we survey data management and replication approaches (from 2007 to 2011) that are developed by both industrial and research communities. The focus of the survey is to discuss and characterize the existing approaches of data replication and management that tackle the resource usage and QoS provisioning with different levels of efficiencies. Moreover, the breakdown of both influential expressions (data replication and management) to provide different QoS attributes is deliberated. Furthermore, the performance advantages and disadvantages of data replication and management approaches in the cloud computing environments are analyzed. Open issues and future challenges related to data consistency, scalability, load balancing, processing and placement are also reported.