eXamine: a Cytoscape app for exploring annotated modules in networks

Background. Biological networks have growing importance for the interpretation of high-throughput "omics" data. Statistical and combinatorial methods allow to obtain mechanistic insights through the extraction of smaller subnetwork modules. Further enrichment analyses provide set-based annotations of these modules. Results. We present eXamine, a set-oriented visual analysis approach for annotated modules that displays set membership as contours on top of a node-link layout. Our approach extends upon Self Organizing Maps to simultaneously lay out nodes, links, and set contours. Conclusions. We implemented eXamine as a freely available Cytoscape app. Using eXamine we study a module that is activated by the virally-encoded G-protein coupled receptor US28 and formulate a novel hypothesis about its functioning

Information visualization for DNA microarray data analysis: A critical review

Graphical representation may provide effective means of making sense of the complexity and sheer volume of data produced by DNA microarray experiments that monitor the expression patterns of thousands of genes simultaneously. The ability to use ldquoabstractrdquo graphical representation to draw attention to areas of interest, and more in-depth visualizations to answer focused questions, would enable biologists to move from a large amount of data to particular records they are interested in, and therefore, gain deeper insights in understanding the microarray experiment results. This paper starts by providing some background knowledge of microarray experiments, and then, explains how graphical representation can be applied in general to this problem domain, followed by exploring the role of visualization in gene expression data analysis. Having set the problem scene, the paper then examines various multivariate data visualization techniques that have been applied to microarray data analysis. These techniques are critically reviewed so that the strengths and weaknesses of each technique can be tabulated. Finally, several key problem areas as well as possible solutions to them are discussed as being a source for future work

Machine-Part cell formation through visual decipherable clustering of Self Organizing Map

Machine-part cell formation is used in cellular manufacturing in order to process a large variety, quality, lower work in process levels, reducing manufacturing lead-time and customer response time while retaining flexibility for new products. This paper presents a new and novel approach for obtaining machine cells and part families. In the cellular manufacturing the fundamental problem is the formation of part families and machine cells. The present paper deals with the Self Organising Map (SOM) method an unsupervised learning algorithm in Artificial Intelligence, and has been used as a visually decipherable clustering tool of machine-part cell formation. The objective of the paper is to cluster the binary machine-part matrix through visually decipherable cluster of SOM color-coding and labelling via the SOM map nodes in such a way that the part families are processed in that machine cells. The Umatrix, component plane, principal component projection, scatter plot and histogram of SOM have been reported in the present work for the successful visualization of the machine-part cell formation. Computational result with the proposed algorithm on a set of group technology problems available in the literature is also presented. The proposed SOM approach produced solutions with a grouping efficacy that is at least as good as any results earlier reported in the literature and improved the grouping efficacy for 70% of the problems and found immensely useful to both industry practitioners and researchers.Comment: 18 pages,3 table, 4 figure

Detection and Generalization of Spatio-temporal Trajectories for Motion Imagery

In today\u27s world of vast information availability users often confront large unorganized amounts of data with limited tools for managing them. Motion imagery datasets have become increasingly popular means for exposing and disseminating information. Commonly, moving objects are of primary interest in modeling such datasets. Users may require different levels of detail mainly for visualization and further processing purposes according to the application at hand. In this thesis we exploit the geometric attributes of objects for dataset summarization by using a series of image processing and neural network tools. In order to form data summaries we select representative time instances through the segmentation of an object\u27s spatio-temporal trajectory lines. High movement variation instances are selected through a new hybrid self-organizing map (SOM) technique to describe a single spatio-temporal trajectory. Multiple objects move in diverse yet classifiable patterns. In order to group corresponding trajectories we utilize an abstraction mechanism that investigates a vague moving relevance between the data in space and time. Thus, we introduce the spatio-temporal neighborhood unit as a variable generalization surface. By altering the unit\u27s dimensions, scaled generalization is accomplished. Common complications in tracking applications that include occlusion, noise, information gaps and unconnected segments of data sequences are addressed through the hybrid-SOM analysis. Nevertheless, entangled data sequences where no information on which data entry belongs to each corresponding trajectory are frequently evident. A multidimensional classification technique that combines geometric and backpropagation neural network implementation is used to distinguish between trajectory data. Further more, modeling and summarization of two-dimensional phenomena evolving in time brings forward the novel concept of spatio-temporal helixes as compact event representations. The phenomena models are comprised of SOM movement nodes (spines) and cardinality shape-change descriptors (prongs). While we focus on the analysis of MI datasets, the framework can be generalized to function with other types of spatio-temporal datasets. Multiple scale generalization is allowed in a dynamic significance-based scale rather than a constant one. The constructed summaries are not just a visualization product but they support further processing for metadata creation, indexing, and querying. Experimentation, comparisons and error estimations for each technique support the analyses discussed

Exploratory analysis of excitation-emission matrix fluorescence spectra with self-organizing maps as a basis for determination of organic matter removal efficiency at water treatment works

In the paper, the self-organizing map (SOM) was employed for the exploratory analysis of fluorescence excitation-emission data characterizing organic matter removal efficiency at 16 water treatment works in the UK. Fluorescence spectroscopy was used to assess organic matter removal efficiency between raw and partially treated (clarified) water to provide an indication of the potential for disinfection by-products formation. Fluorescence spectroscopy was utilized to evaluate quantitative and qualitative properties of organic matter removal. However, the substantial amount of fluorescence data generated impeded the interpretation process. Therefore a robust SOM technique was used to examine the fluorescence data and to reveal patterns in data distribution and correlations between organic matter properties and fluorescence variables. It was found that the SOM provided a good discrimination between water treatment sites on the base of spectral properties of organic matter. The distances between the units of the SOM map were indicative of the similarity of the fluorescence samples and thus demonstrated the relative changes in organic matter content between raw and clarified water. The higher efficiency of organic matter removal was demonstrated for the larger distances between raw and clarified samples on the map. It was also shown that organic matter removal was highly dependent on the raw water fluorescence properties, with higher efficiencies for higher emission wavelengths in visible and UV humic-like fluorescence centers

Overlap Removal of Dimensionality Reduction Scatterplot Layouts

Dimensionality Reduction (DR) scatterplot layouts have become a ubiquitous visualization tool for analyzing multidimensional data items with presence in different areas. Despite its popularity, scatterplots suffer from occlusion, especially when markers convey information, making it troublesome for users to estimate items' groups' sizes and, more importantly, potentially obfuscating critical items for the analysis under execution. Different strategies have been devised to address this issue, either producing overlap-free layouts, lacking the powerful capabilities of contemporary DR techniques in uncover interesting data patterns, or eliminating overlaps as a post-processing strategy. Despite the good results of post-processing techniques, the best methods typically expand or distort the scatterplot area, thus reducing markers' size (sometimes) to unreadable dimensions, defeating the purpose of removing overlaps. This paper presents a novel post-processing strategy to remove DR layouts' overlaps that faithfully preserves the original layout's characteristics and markers' sizes. We show that the proposed strategy surpasses the state-of-the-art in overlap removal through an extensive comparative evaluation considering multiple different metrics while it is 2 or 3 orders of magnitude faster for large datasets.Comment: 11 pages and 9 figure