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

SOMvisua: Data Clustering and Visualization Based on SOM and GHSOM

Text in web pages is based on expert opinion of a large number of people including the views of authors. These views are based on cultural or community aspects, which make extracting information from text very difficult. Search in text usually finds text similarities between paragraphs in documents. This paper proposes a framework for data clustering and visualization called SOMvisua. SOMvisua is based on a graph representation of data input for Self-Organizing Map (SOM) and Growing Hierarchically Self-Organizing Map (GHSOM) algorithms. In SOMvisua, sentences from an input article are represented as graph model instead of vector space model. SOM and GHSOM clustering algorithms construct knowledge from this article

Exploratory data analysis using self-organising maps defined in up to three dimensions

The SOM is an artificial neural network based on an unsupervised learning process that performs a nonlinear mapping of high dimensional input data onto an ordered and structured array of nodes, designated as the SOM output space. Being simultaneously a quantization algorithm and a projection algorithm, the SOM is able to summarize and map the data, allowing its visualization. Because using the most common visualization methods it is very difficult or even impossible to visualize the SOM defined with more than two dimensions, the SOM output space is generally a regular two dimensional grid of nodes. However, there are no theoretical problems in generating SOMs with higher dimensional output spaces. In this thesis we present evidence that the SOM output space defined in up to three dimensions can be used successfully for the exploratory analysis of spatial data, two-way data and three-way data. Although the differences between the methods that are proposed to visualize each group of data, the approach adopted is commonly based in the projection of colour codes, which are obtained from the output space of 3D SOMs, in some specific bi-dimensional surface, where data can be represented according to its own characteristics. This approach is, in some cases, also complemented with the simultaneous use of SOMs defined in one and two dimensions, so that patterns in data can be properly revealed. The results obtained by using this visualization strategy indicates not only the benefits of using the SOM defined in up to three dimensions but also shows the relevance of the combined and simultaneous use of different models of the SOM in exploratory data analysis

Event-Driven Technologies for Reactive Motion Planning: Neuromorphic Stereo Vision and Robot Path Planning and Their Application on Parallel Hardware

Die Robotik wird immer mehr zu einem Schlüsselfaktor des technischen Aufschwungs. Trotz beeindruckender Fortschritte in den letzten Jahrzehnten, übertreffen Gehirne von Säugetieren in den Bereichen Sehen und Bewegungsplanung noch immer selbst die leistungsfähigsten Maschinen. Industrieroboter sind sehr schnell und präzise, aber ihre Planungsalgorithmen sind in hochdynamischen Umgebungen, wie sie für die Mensch-Roboter-Kollaboration (MRK) erforderlich sind, nicht leistungsfähig genug. Ohne schnelle und adaptive Bewegungsplanung kann sichere MRK nicht garantiert werden. Neuromorphe Technologien, einschließlich visueller Sensoren und Hardware-Chips, arbeiten asynchron und verarbeiten so raum-zeitliche Informationen sehr effizient. Insbesondere ereignisbasierte visuelle Sensoren sind konventionellen, synchronen Kameras bei vielen Anwendungen bereits überlegen. Daher haben ereignisbasierte Methoden ein großes Potenzial, schnellere und energieeffizientere Algorithmen zur Bewegungssteuerung in der MRK zu ermöglichen. In dieser Arbeit wird ein Ansatz zur flexiblen reaktiven Bewegungssteuerung eines Roboterarms vorgestellt. Dabei wird die Exterozeption durch ereignisbasiertes Stereosehen erreicht und die Pfadplanung ist in einer neuronalen Repräsentation des Konfigurationsraums implementiert. Die Multiview-3D-Rekonstruktion wird durch eine qualitative Analyse in Simulation evaluiert und auf ein Stereo-System ereignisbasierter Kameras übertragen. Zur Evaluierung der reaktiven kollisionsfreien Online-Planung wird ein Demonstrator mit einem industriellen Roboter genutzt. Dieser wird auch für eine vergleichende Studie zu sample-basierten Planern verwendet. Ergänzt wird dies durch einen Benchmark von parallelen Hardwarelösungen wozu als Testszenario Bahnplanung in der Robotik gewählt wurde. Die Ergebnisse zeigen, dass die vorgeschlagenen neuronalen Lösungen einen effektiven Weg zur Realisierung einer Robotersteuerung für dynamische Szenarien darstellen. Diese Arbeit schafft eine Grundlage für neuronale Lösungen bei adaptiven Fertigungsprozesse, auch in Zusammenarbeit mit dem Menschen, ohne Einbußen bei Geschwindigkeit und Sicherheit. Damit ebnet sie den Weg für die Integration von dem Gehirn nachempfundener Hardware und Algorithmen in die Industrierobotik und MRK

Spiking neurons in 3D growing self-organising maps

In Kohonen’s Self-Organising Maps (SOM) learning, preserving the map topology to simulate the actual input features appears to be a significant process. Misinterpretation of the training samples can lead to failure in identifying the important features that may affect the outcomes generated by the SOM model. Nonetheless, it is a challenging task as most of the real problems are composed of complex and insufficient data. Spiking Neural Network (SNN) is the third generation of Artificial Neural Network (ANN), in which information can be transferred from one neuron to another using spike, processed, and trigger response as output. This study, hence, embedded spiking neurons for SOM learning in order to enhance the learning process. The proposed method was divided into five main phases. Phase 1 investigated issues related to SOM learning algorithm, while in Phase 2; datasets were collected for analyses carried out in Phase 3, wherein neural coding scheme for data representation process was implemented in the classification task. Next, in Phase 4, the spiking SOM model was designed, developed, and evaluated using classification accuracy rate and quantisation error. The outcomes showed that the proposed model had successfully attained exceptional classification accuracy rate with low quantisation error to preserve the quality of the generated map based on original input data. Lastly, in the final phase, a Spiking 3D Growing SOM is proposed to address the surface reconstruction issue by enhancing the spiking SOM using 3D map structure in SOM algorithm with a growing grid mechanism. The application of spiking neurons to enhance the performance of SOM is relevant in this study due to its ability to spike and to send a reaction when special features are identified based on its learning of the presented datasets. The study outcomes contribute to the enhancement of SOM in learning the patterns of the datasets, as well as in proposing a better tool for data analysis

Mapping Patterns of Multiple Deprivation Using Self-Organising Maps: An Application to EU-SILC Data for Ireland. ESRI WP286. March 2009

The development of conceptual frameworks for the analysis of social exclusion has somewhat out-stripped related methodological developments. This paper seeks to contribute to this process through the application of self-organising maps (SOMs) to the analysis of a detailed set of material deprivation indicators relating to the Irish case. The SOM approach allows us to offer a differentiated and interpretable picture of the structure of multiple deprivation in contemporary Ireland. Employing this approach, we identify 16 clusters characterised by distinct profiles across 42 deprivation indicators. Exploratory analyses demonstrate that position in the income distribution varies systematically by cluster membership. Moreover, in comparison with an analogous latent class approach, the SOM analysis offers considerable additional discriminatory power in relation to individuals’ experience of their economic circumstances. The results suggest that the SOM approach could prove a valuable addition to a ‘methodological platform’ for analysing the shape and form of social exclusion