Visual analysis of self-organizing maps

In the article, an additional visualization of self-organizing maps (SOM) has been investigated. The main objective of self-organizing maps is data clustering and their graphical presentation. Opportunities of SOM visualization in four systems (NeNet, SOM-Toolbox, Databionic ESOM and Viscovery SOMine) have been investigated. Each system has its additional tools for visualizing SOM. A comparative analysis has been made for two data sets: Fisher’s iris data set and the economic indices of the European Union countries. A new SOM system is also introduced and researched. The system has a specific visualization tool. It is missing in other SOM systems. It helps to see the proportion of neurons, corresponding to the data items, belonging to the different classes, and fallen in the same SOM cell

Tilt Aftereffects in a Self-Organizing Model of the Primary Visual Cortex

RF-LISSOM, a self-organizing model of laterally connected orientation maps in the primary visual cortex, was used to study the psychological phenomenon known as the tilt aftereffect. The same self-organizing processes that are responsible for the long-term development of the map are shown to result in tilt aftereffects over short time scales in the adult. The model permits simultaneous observation of large numbers of neurons and connections, making it possible to relate high-level phenomena to low-level events, which is difficult to do experimentally. The results give detailed computational support for the long-standing conjecture that the direct tilt aftereffect arises from adaptive lateral interactions between feature detectors. They also make a new prediction that the indirect effect results from the normalization of synaptic efficacies during this process. The model thus provides a unified computational explanation of self-organization and both the direct and indirect tilt aftereffect in the primary visual cortex

Fast training of self organizing maps for the visual exploration of molecular compounds

Visual exploration of scientific data in life science area is a growing research field due to the large amount of available data. The Kohonen’s Self Organizing Map (SOM) is a widely used tool for visualization of multidimensional data. In this paper we present a fast learning algorithm for SOMs that uses a simulated annealing method to adapt the learning parameters. The algorithm has been adopted in a data analysis framework for the generation of similarity maps. Such maps provide an effective tool for the visual exploration of large and multi-dimensional input spaces. The approach has been applied to data generated during the High Throughput Screening of molecular compounds; the generated maps allow a visual exploration of molecules with similar topological properties. The experimental analysis on real world data from the National Cancer Institute shows the speed up of the proposed SOM training process in comparison to a traditional approach. The resulting visual landscape groups molecules with similar chemical properties in densely connected regions

Evaluating a Self-Organizing Map for Clustering and Visualizing Optimum Currency Area Criteria

Optimum currency area (OCA) theory attempts to define the geographical region in which it would maximize economic efficiency to have a single currency. In this paper, the focus is on prospective and current members of the Economic and Monetary Union. For this task, a self-organizing neural network, the Self-organizing map (SOM), is combined with hierarchical clustering for a two-level approach to clustering and visualizing OCA criteria. The output of the SOM is a topologically preserved two-dimensional grid. The final models are evaluated based on both clustering tendencies and accuracy measures. Thereafter, the two-dimensional grid of the chosen model is used for visual assessment of the OCA criteria, while its clustering results are projected onto a geographic map.Self-organizing maps, Optimum Currency Area, projection, clustering, geospatial visualization

Visual data mining with self-organizing maps for ''self-monitoring'' data analysis

Data collected in psychological studies are mainly characterized by containing a large number of variables (multidimensional data sets). Analyzing multidimensional data can be a difficult task, especially if only classical approaches are used (hypothesis tests, analyses of variance, linear models, etc.). Regarding multidimensional models, visual techniques play an important role because they can show the relationships among variables in a data set. Parallel coordinates and Chernoff faces are good examples of this. This article presents self-organizing maps (SOM), a multivariate visual data mining technique used to provide global visualizations of all the data. This technique is presented as a tutorial with the aim of showing its capabilities, how it works, and how to interpret its results. Specifically, SOM analysis has been applied to analyze the data collected in a study on the efficacy of a cognitive and behavioral treatment (CBT) for childhood obesity. The objective of the CBT was to modify the eating habits and level of physical activity in a sample of children with overweight and obesity. Children were randomized into two treatment conditions: CBT traditional procedure (face-to-face sessions) and CBT supported by a web platform. In order to analyze their progress in the acquisition of healthier habits, self-register techniques were used to record dietary behavior and physical activity. In the traditional CBT condition, children completed the self-register using a paper-and-pencil procedure, while in the web platform condition, participants completed the self-register using an electronic personal digital assistant. Results showed the potential of SOM for analyzing the large amount of data necessary to study the acquisition of new habits in a childhood obesity treatment. Currently, the high prevalence of childhood obesity points to the need to develop strategies to manage a large number of data in order to design procedures adapted to personal characteristics and increase treatment efficacy

Visual-Interactive Analysis With Self-Organizing Maps - Advances and Research Challenges

Based on the Self-Organizing Map (SOM) algorithm, development of effective solutions for visual analysis and retrieval in complex data is possible. Example application domains include retrieval in multimedia data bases, and analysis in financial, text, and general high-dimensional data sets. While early work defined basic concepts for data representation and visual mappings for SOM-based analysis, recent work contributed advanced visual representations of the output of the SOM algorithm, and explored innovative application concepts

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