20,359 research outputs found
Recommended from our members
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
Mining and visualizing uncertain data objects and named data networking traffics by fuzzy self-organizing map
Uncertainty is widely spread in real-world data. Uncertain data-in computer science-is typically found in the area of sensor networks where the sensors sense the environment with certain error. Mining and visualizing uncertain data is one of the new challenges that face uncertain databases. This paper presents a new intelligent hybrid algorithm that applies fuzzy set theory into the context of the Self-Organizing Map to mine and visualize uncertain objects. The algorithm is tested in some benchmark problems and the uncertain traffics in Named Data Networking (NDN). Experimental results indicate that the proposed algorithm is precise and effective in terms of the applied performance criteria.Peer ReviewedPostprint (published version
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
A review of data visualization: opportunities in manufacturing sequence management.
Data visualization now benefits from developments in technologies that offer innovative ways of presenting complex data. Potentially these have widespread application in communicating the complex information domains typical of manufacturing sequence management environments for global enterprises. In this paper the authors review the visualization functionalities, techniques and applications reported in literature, map these to manufacturing sequence information presentation requirements and identify the opportunities available and likely development paths. Current leading-edge practice in dynamic updating and communication with suppliers is not being exploited in manufacturing sequence management; it could provide significant benefits to manufacturing business. In the context of global manufacturing operations and broad-based user communities with differing needs served by common data sets, tool functionality is generally ahead of user application
Batch and median neural gas
Neural Gas (NG) constitutes a very robust clustering algorithm given
euclidian data which does not suffer from the problem of local minima like
simple vector quantization, or topological restrictions like the
self-organizing map. Based on the cost function of NG, we introduce a batch
variant of NG which shows much faster convergence and which can be interpreted
as an optimization of the cost function by the Newton method. This formulation
has the additional benefit that, based on the notion of the generalized median
in analogy to Median SOM, a variant for non-vectorial proximity data can be
introduced. We prove convergence of batch and median versions of NG, SOM, and
k-means in a unified formulation, and we investigate the behavior of the
algorithms in several experiments.Comment: In Special Issue after WSOM 05 Conference, 5-8 september, 2005, Pari
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
- …