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

Magnification Control in Winner Relaxing Neural Gas

An important goal in neural map learning, which can conveniently be accomplished by magnification control, is to achieve information optimal coding in the sense of information theory. In the present contribution we consider the winner relaxing approach for the neural gas network. Originally, winner relaxing learning is a slight modification of the self-organizing map learning rule that allows for adjustment of the magnification behavior by an a priori chosen control parameter. We transfer this approach to the neural gas algorithm. The magnification exponent can be calculated analytically for arbitrary dimension from a continuum theory, and the entropy of the resulting map is studied numerically conf irming the theoretical prediction. The influence of a diagonal term, which can be added without impacting the magnification, is studied numerically. This approach to maps of maximal mutual information is interesting for applications as the winner relaxing term only adds computational cost of same order and is easy to implement. In particular, it is not necessary to estimate the generally unknown data probability density as in other magnification control approaches.Comment: 14pages, 2 figure

Winner-relaxing and winner-enhancing Kohonen maps: Maximal mutual information from enhancing the winner

The magnification behaviour of a generalized family of self-organizing feature maps, the Winner Relaxing and Winner Enhancing Kohonen algorithms is analyzed by the magnification law in the one-dimensional case, which can be obtained analytically. The Winner-Enhancing case allows to acheive a magnification exponent of one and therefore provides optimal mapping in the sense of information theory. A numerical verification of the magnification law is included, and the ordering behaviour is analyzed. Compared to the original Self-Organizing Map and some other approaches, the generalized Winner Enforcing Algorithm requires minimal extra computations per learning step and is conveniently easy to implement.Comment: 6 pages, 5 figures. For an extended version refer to cond-mat/0208414 (Neural Computation 17, 996-1009

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

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

Evolutionary Neural Gas (ENG): A Model of Self Organizing Network from Input Categorization

Despite their claimed biological plausibility, most self organizing networks have strict topological constraints and consequently they cannot take into account a wide range of external stimuli. Furthermore their evolution is conditioned by deterministic laws which often are not correlated with the structural parameters and the global status of the network, as it should happen in a real biological system. In nature the environmental inputs are noise affected and fuzzy. Which thing sets the problem to investigate the possibility of emergent behaviour in a not strictly constrained net and subjected to different inputs. It is here presented a new model of Evolutionary Neural Gas (ENG) with any topological constraints, trained by probabilistic laws depending on the local distortion errors and the network dimension. The network is considered as a population of nodes that coexist in an ecosystem sharing local and global resources. Those particular features allow the network to quickly adapt to the environment, according to its dimensions. The ENG model analysis shows that the net evolves as a scale-free graph, and justifies in a deeply physical sense- the term gas here used.Comment: 16 pages, 8 figure

Somoclu: An Efficient Parallel Library for Self-Organizing Maps

Somoclu is a massively parallel tool for training self-organizing maps on large data sets written in C++. It builds on OpenMP for multicore execution, and on MPI for distributing the workload across the nodes in a cluster. It is also able to boost training by using CUDA if graphics processing units are available. A sparse kernel is included, which is useful for high-dimensional but sparse data, such as the vector spaces common in text mining workflows. Python, R and MATLAB interfaces facilitate interactive use. Apart from fast execution, memory use is highly optimized, enabling training large emergent maps even on a single computer.Comment: 26 pages, 9 figures. The code is available at https://peterwittek.github.io/somoclu