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

Methods of Hierarchical Clustering

We survey agglomerative hierarchical clustering algorithms and discuss efficient implementations that are available in R and other software environments. We look at hierarchical self-organizing maps, and mixture models. We review grid-based clustering, focusing on hierarchical density-based approaches. Finally we describe a recently developed very efficient (linear time) hierarchical clustering algorithm, which can also be viewed as a hierarchical grid-based algorithm.Comment: 21 pages, 2 figures, 1 table, 69 reference

A Neural Model for Self Organizing Feature Detectors and Classifiers in a Network Hierarchy

Many models of early cortical processing have shown how local learning rules can produce efficient, sparse-distributed codes in which nodes have responses that are statistically independent and low probability. However, it is not known how to develop a useful hierarchical representation, containing sparse-distributed codes at each level of the hierarchy, that incorporates predictive feedback from the environment. We take a step in that direction by proposing a biologically plausible neural network model that develops receptive fields, and learns to make class predictions, with or without the help of environmental feedback. The model is a new type of predictive adaptive resonance theory network called Receptive Field ARTMAP, or RAM. RAM self organizes internal category nodes that are tuned to activity distributions in topographic input maps. Each receptive field is composed of multiple weight fields that are adapted via local, on-line learning, to form smooth receptive ftelds that reflect; the statistics of the activity distributions in the input maps. When RAM generates incorrect predictions, its vigilance is raised, amplifying subtractive inhibition and sharpening receptive fields until the error is corrected. Evaluation on several classification benchmarks shows that RAM outperforms a related (but neurally implausible) model called Gaussian ARTMAP, as well as several standard neural network and statistical classifters. A topographic version of RAM is proposed, which is capable of self organizing hierarchical representations. Topographic RAM is a model for receptive field development at any level of the cortical hierarchy, and provides explanations for a variety of perceptual learning data.Defense Advanced Research Projects Agency and Office of Naval Research (N00014-95-1-0409

Magnification Control in Self-Organizing Maps and Neural Gas

We consider different ways to control the magnification in self-organizing maps (SOM) and neural gas (NG). Starting from early approaches of magnification control in vector quantization, we then concentrate on different approaches for SOM and NG. We show that three structurally similar approaches can be applied to both algorithms: localized learning, concave-convex learning, and winner relaxing learning. Thereby, the approach of concave-convex learning in SOM is extended to a more general description, whereas the concave-convex learning for NG is new. In general, the control mechanisms generate only slightly different behavior comparing both neural algorithms. However, we emphasize that the NG results are valid for any data dimension, whereas in the SOM case the results hold only for the one-dimensional case.Comment: 24 pages, 4 figure

Medical imaging analysis with artificial neural networks

Given that neural networks have been widely reported in the research community of medical imaging, we provide a focused literature survey on recent neural network developments in computer-aided diagnosis, medical image segmentation and edge detection towards visual content analysis, and medical image registration for its pre-processing and post-processing, with the aims of increasing awareness of how neural networks can be applied to these areas and to provide a foundation for further research and practical development. Representative techniques and algorithms are explained in detail to provide inspiring examples illustrating: (i) how a known neural network with fixed structure and training procedure could be applied to resolve a medical imaging problem; (ii) how medical images could be analysed, processed, and characterised by neural networks; and (iii) how neural networks could be expanded further to resolve problems relevant to medical imaging. In the concluding section, a highlight of comparisons among many neural network applications is included to provide a global view on computational intelligence with neural networks in medical imaging