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

Self-Organizing Time Map: An Abstraction of Temporal Multivariate Patterns

This paper adopts and adapts Kohonen's standard Self-Organizing Map (SOM) for exploratory temporal structure analysis. The Self-Organizing Time Map (SOTM) implements SOM-type learning to one-dimensional arrays for individual time units, preserves the orientation with short-term memory and arranges the arrays in an ascending order of time. The two-dimensional representation of the SOTM attempts thus twofold topology preservation, where the horizontal direction preserves time topology and the vertical direction data topology. This enables discovering the occurrence and exploring the properties of temporal structural changes in data. For representing qualities and properties of SOTMs, we adapt measures and visualizations from the standard SOM paradigm, as well as introduce a measure of temporal structural changes. The functioning of the SOTM, and its visualizations and quality and property measures, are illustrated on artificial toy data. The usefulness of the SOTM in a real-world setting is shown on poverty, welfare and development indicators

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

Batch kernel SOM and related Laplacian methods for social network analysis

Large graphs are natural mathematical models for describing the structure of the data in a wide variety of fields, such as web mining, social networks, information retrieval, biological networks, etc. For all these applications, automatic tools are required to get a synthetic view of the graph and to reach a good understanding of the underlying problem. In particular, discovering groups of tightly connected vertices and understanding the relations between those groups is very important in practice. This paper shows how a kernel version of the batch Self Organizing Map can be used to achieve these goals via kernels derived from the Laplacian matrix of the graph, especially when it is used in conjunction with more classical methods based on the spectral analysis of the graph. The proposed method is used to explore the structure of a medieval social network modeled through a weighted graph that has been directly built from a large corpus of agrarian contracts

Neural Networks for Complex Data

Artificial neural networks are simple and efficient machine learning tools. Defined originally in the traditional setting of simple vector data, neural network models have evolved to address more and more difficulties of complex real world problems, ranging from time evolving data to sophisticated data structures such as graphs and functions. This paper summarizes advances on those themes from the last decade, with a focus on results obtained by members of the SAMM team of Universit\'e Paris

Self-Organizing Maps Algorithm for Parton Distribution Functions Extraction

We describe a new method to extract parton distribution functions from hard scattering processes based on Self-Organizing Maps. The extension to a larger, and more complex class of soft matrix elements, including generalized parton distributions is also discussed.Comment: 6 pages, 3 figures, to be published in the proceedings of ACAT 2011, 14th International Workshop on Advanced Computing and Analysis Techniques in Physics Researc