Self-Organising Networks for Classification: developing Applications to Science Analysis for Astroparticle Physics

Physics analysis in astroparticle experiments requires the capability of recognizing new phenomena; in order to establish what is new, it is important to develop tools for automatic classification, able to compare the final result with data from different detectors. A typical example is the problem of Gamma Ray Burst detection, classification, and possible association to known sources: for this task physicists will need in the next years tools to associate data from optical databases, from satellite experiments (EGRET, GLAST), and from Cherenkov telescopes (MAGIC, HESS, CANGAROO, VERITAS)

Expression cartography of human tissues using self organizing maps

Background: The availability of parallel, high-throughput microarray and sequencing experiments poses a challenge how to best arrange and to analyze the obtained heap of multidimensional data in a concerted way. Self organizing maps (SOM), a machine learning method, enables the parallel sample- and gene-centered view on the data combined with strong visualization and second-level analysis capabilities. The paper addresses aspects of the method with practical impact in the context of expression analysis of complex data sets.
Results: The method was applied to generate a SOM characterizing the whole genome expression profiles of 67 healthy human tissues selected from ten tissue categories (adipose, endocrine, homeostasis, digestion, exocrine, epithelium, sexual reproduction, muscle, immune system and nervous tissues). SOM mapping reduces the dimension of expression data from ten thousands of genes to a few thousands of metagenes where each metagene acts as representative of a minicluster of co-regulated single genes. Tissue-specific and common properties shared between groups of tissues emerge as a handful of localized spots in the tissue maps collecting groups of co-regulated and co-expressed metagenes. The functional context of the spots was discovered using overrepresentation analysis with respect to pre-defined gene sets of known functional impact. We found that tissue related spots typically contain enriched populations of gene sets well corresponding to molecular processes in the respective tissues. Analysis techniques normally used at the gene-level such as two-way hierarchical clustering provide a better signal-to-noise ratio and a better representativeness of the method if applied to the metagenes. Metagene-based clustering analyses aggregate the tissues into essentially three clusters containing nervous, immune system and the remaining tissues. 
Conclusions: The global view on the behavior of a few well-defined modules of correlated and differentially expressed genes is more intuitive and more informative than the separate discovery of the expression levels of hundreds or thousands of individual genes. The metagene approach is less sensitive to a priori selection of genes. It can detect a coordinated expression pattern whose components would not pass single-gene significance thresholds and it is able to extract context-dependent patterns of gene expression in complex data sets.
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Art Neural Networks for Remote Sensing: Vegetation Classification from Landsat TM and Terrain Data

A new methodology for automatic mapping from Landsat Thematic Mapper (TM) and terrain data, based on the fuzzy ARTMAP neural network, is developed. System capabilities are tested on a challenging remote sensing classification problem, using spectral and terrain features for vegetation classification in the Cleveland National Forest. After training at the pixel level, system performance is tested at the stand level, using sites not seen during training. Results are compared to those of maximum likelihood classifiers, as well as back propagation neural networks and K Nearest Neighbor algorithms. ARTMAP dynamics are fast, stable, and scalable, overcoming common limitations of back propagation, which did not give satisfactory performance. Best results are obtained using a hybrid system based on a convex combination of fuzzy ARTMAP and maximum likelihood predictions. A prototype remote sensing example introduces each aspect of data processing and fuzzy ARTMAP classification. The example shows how the network automatically constructs a minimal number of recognition categories to meet accuracy criteria. A voting strategy improves prediction and assigns confidence estimates by training the system several times on different orderings of an input set.National Science Foundation (IRI 94-01659, SBR 93-00633); Office of Naval Research (N00014-95-l-0409, N00014-95-0657

Exploring Human Vision Driven Features for Pedestrian Detection

Motivated by the center-surround mechanism in the human visual attention system, we propose to use average contrast maps for the challenge of pedestrian detection in street scenes due to the observation that pedestrians indeed exhibit discriminative contrast texture. Our main contributions are first to design a local, statistical multi-channel descriptorin order to incorporate both color and gradient information. Second, we introduce a multi-direction and multi-scale contrast scheme based on grid-cells in order to integrate expressive local variations. Contributing to the issue of selecting most discriminative features for assessing and classification, we perform extensive comparisons w.r.t. statistical descriptors, contrast measurements, and scale structures. This way, we obtain reasonable results under various configurations. Empirical findings from applying our optimized detector on the INRIA and Caltech pedestrian datasets show that our features yield state-of-the-art performance in pedestrian detection.Comment: Accepted for publication in IEEE Transactions on Circuits and Systems for Video Technology (TCSVT