18,514 research outputs found
A combined measure for quantifying and qualifying the topology preservation of growing self-organizing maps
The Self-OrganizingMap (SOM) is a neural network model that performs an ordered projection of a high dimensional input space in a low-dimensional topological structure. The process in which such mapping is formed is defined by the SOM algorithm, which is a competitive, unsupervised and nonparametric method, since it does not make any assumption about the input data distribution. The feature maps provided by this algorithm have been successfully applied for vector quantization, clustering and high dimensional data visualization processes. However, the initialization of the network topology and the selection of the SOM training parameters are two difficult tasks caused by the unknown distribution of the input signals. A misconfiguration of these parameters can generate a feature map of low-quality, so it is necessary to have some measure of the degree of adaptation of the SOM network to the input data model. The topologypreservation is the most common concept used to implement this measure. Several qualitative and quantitative methods have been proposed for measuring the degree of SOM topologypreservation, particularly using Kohonen's model. In this work, two methods for measuring the topologypreservation of the Growing Cell Structures (GCSs) model are proposed: the topographic function and the topology preserving ma
Principal manifolds and graphs in practice: from molecular biology to dynamical systems
We present several applications of non-linear data modeling, using principal
manifolds and principal graphs constructed using the metaphor of elasticity
(elastic principal graph approach). These approaches are generalizations of the
Kohonen's self-organizing maps, a class of artificial neural networks. On
several examples we show advantages of using non-linear objects for data
approximation in comparison to the linear ones. We propose four numerical
criteria for comparing linear and non-linear mappings of datasets into the
spaces of lower dimension. The examples are taken from comparative political
science, from analysis of high-throughput data in molecular biology, from
analysis of dynamical systems.Comment: 12 pages, 9 figure
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
How to improve robustness in Kohonen maps and display additional information in Factorial Analysis: application to text mining
This article is an extended version of a paper presented in the WSOM'2012
conference [1]. We display a combination of factorial projections, SOM
algorithm and graph techniques applied to a text mining problem. The corpus
contains 8 medieval manuscripts which were used to teach arithmetic techniques
to merchants. Among the techniques for Data Analysis, those used for
Lexicometry (such as Factorial Analysis) highlight the discrepancies between
manuscripts. The reason for this is that they focus on the deviation from the
independence between words and manuscripts. Still, we also want to discover and
characterize the common vocabulary among the whole corpus. Using the properties
of stochastic Kohonen maps, which define neighborhood between inputs in a
non-deterministic way, we highlight the words which seem to play a special role
in the vocabulary. We call them fickle and use them to improve both Kohonen map
robustness and significance of FCA visualization. Finally we use graph
algorithmic to exploit this fickleness for classification of words
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
Context-aware visual exploration of molecular databases
Facilitating the visual exploration of scientific data has
received increasing attention in the past decade or so. Especially
in life science related application areas the amount
of available data has grown at a breath taking pace. In this
paper we describe an approach that allows for visual inspection
of large collections of molecular compounds. In
contrast to classical visualizations of such spaces we incorporate
a specific focus of analysis, for example the outcome
of a biological experiment such as high throughout
screening results. The presented method uses this experimental
data to select molecular fragments of the underlying
molecules that have interesting properties and uses the
resulting space to generate a two dimensional map based
on a singular value decomposition algorithm and a self organizing
map. Experiments on real datasets show that
the resulting visual landscape groups molecules of similar
chemical properties in densely connected regions
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