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

A Broad Class of Discrete-Time Hypercomplex-Valued Hopfield Neural Networks

In this paper, we address the stability of a broad class of discrete-time hypercomplex-valued Hopfield-type neural networks. To ensure the neural networks belonging to this class always settle down at a stationary state, we introduce novel hypercomplex number systems referred to as real-part associative hypercomplex number systems. Real-part associative hypercomplex number systems generalize the well-known Cayley-Dickson algebras and real Clifford algebras and include the systems of real numbers, complex numbers, dual numbers, hyperbolic numbers, quaternions, tessarines, and octonions as particular instances. Apart from the novel hypercomplex number systems, we introduce a family of hypercomplex-valued activation functions called $\mathcal{B}$-projection functions. Broadly speaking, a $\mathcal{B}$-projection function projects the activation potential onto the set of all possible states of a hypercomplex-valued neuron. Using the theory presented in this paper, we confirm the stability analysis of several discrete-time hypercomplex-valued Hopfield-type neural networks from the literature. Moreover, we introduce and provide the stability analysis of a general class of Hopfield-type neural networks on Cayley-Dickson algebras

O.R.,Statistics,A.I.- the potential for interdisciplinary progress

This paper examines the need for O.R. workers to become more involved in the development of A.I. A brief outline of A.I. is provided noting problems, techniques and objectives similar to those found in O.R. This outline gives an indication of how interdisciplinary development might proceed and indicates the direction in which O.R. training should be progressin

A Regularized Graph Layout Framework for Dynamic Network Visualization

Many real-world networks, including social and information networks, are dynamic structures that evolve over time. Such dynamic networks are typically visualized using a sequence of static graph layouts. In addition to providing a visual representation of the network structure at each time step, the sequence should preserve the mental map between layouts of consecutive time steps to allow a human to interpret the temporal evolution of the network. In this paper, we propose a framework for dynamic network visualization in the on-line setting where only present and past graph snapshots are available to create the present layout. The proposed framework creates regularized graph layouts by augmenting the cost function of a static graph layout algorithm with a grouping penalty, which discourages nodes from deviating too far from other nodes belonging to the same group, and a temporal penalty, which discourages large node movements between consecutive time steps. The penalties increase the stability of the layout sequence, thus preserving the mental map. We introduce two dynamic layout algorithms within the proposed framework, namely dynamic multidimensional scaling (DMDS) and dynamic graph Laplacian layout (DGLL). We apply these algorithms on several data sets to illustrate the importance of both grouping and temporal regularization for producing interpretable visualizations of dynamic networks.Comment: To appear in Data Mining and Knowledge Discovery, supporting material (animations and MATLAB toolbox) available at http://tbayes.eecs.umich.edu/xukevin/visualization_dmkd_201