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

Integrating Symbolic and Neural Processing in a Self-Organizing Architechture for Pattern Recognition and Prediction

British Petroleum (89A-1204); Defense Advanced Research Projects Agency (N00014-92-J-4015); National Science Foundation (IRI-90-00530); Office of Naval Research (N00014-91-J-4100); Air Force Office of Scientific Research (F49620-92-J-0225

ART and ARTMAP Neural Networks for Applications: Self-Organizing Learning, Recognition, and Prediction

ART and ARTMAP neural networks for adaptive recognition and prediction have been applied to a variety of problems. Applications include parts design retrieval at the Boeing Company, automatic mapping from remote sensing satellite measurements, medical database prediction, and robot vision. This chapter features a self-contained introduction to ART and ARTMAP dynamics and a complete algorithm for applications. Computational properties of these networks are illustrated by means of remote sensing and medical database examples. The basic ART and ARTMAP networks feature winner-take-all (WTA) competitive coding, which groups inputs into discrete recognition categories. WTA coding in these networks enables fast learning, that allows the network to encode important rare cases but that may lead to inefficient category proliferation with noisy training inputs. This problem is partially solved by ART-EMAP, which use WTA coding for learning but distributed category representations for test-set prediction. In medical database prediction problems, which often feature inconsistent training input predictions, the ARTMAP-IC network further improves ARTMAP performance with distributed prediction, category instance counting, and a new search algorithm. A recently developed family of ART models (dART and dARTMAP) retains stable coding, recognition, and prediction, but allows arbitrarily distributed category representation during learning as well as performance.National Science Foundation (IRI 94-01659, SBR 93-00633); Office of Naval Research (N00014-95-1-0409, N00014-95-0657

A binary self-organizing map and its FPGA implementation

A binary Self Organizing Map (SOM) has been designed and implemented on a Field Programmable Gate Array (FPGA) chip. A novel learning algorithm which takes binary inputs and maintains tri-state weights is presented. The binary SOM has the capability of recognizing binary input sequences after training. A novel tri-state rule is used in updating the network weights during the training phase. The rule implementation is highly suited to the FPGA architecture, and allows extremely rapid training. This architecture may be used in real-time for fast pattern clustering and classification of the binary features

Adaptive Resonance Theory: Self-Organizing Networks for Stable Learning, Recognition, and Prediction

Adaptive Resonance Theory (ART) is a neural theory of human and primate information processing and of adaptive pattern recognition and prediction for technology. Biological applications to attentive learning of visual recognition categories by inferotemporal cortex and hippocampal system, medial temporal amnesia, corticogeniculate synchronization, auditory streaming, speech recognition, and eye movement control are noted. ARTMAP systems for technology integrate neural networks, fuzzy logic, and expert production systems to carry out both unsupervised and supervised learning. Fast and slow learning are both stable response to large non stationary databases. Match tracking search conjointly maximizes learned compression while minimizing predictive error. Spatial and temporal evidence accumulation improve accuracy in 3-D object recognition. Other applications are noted.Office of Naval Research (N00014-95-I-0657, N00014-95-1-0409, N00014-92-J-1309, N00014-92-J4015); National Science Foundation (IRI-94-1659

Winner-Relaxing Self-Organizing Maps

A new family of self-organizing maps, the Winner-Relaxing Kohonen Algorithm, is introduced as a generalization of a variant given by Kohonen in 1991. The magnification behaviour is calculated analytically. For the original variant a magnification exponent of 4/7 is derived; the generalized version allows to steer the magnification in the wide range from exponent 1/2 to 1 in the one-dimensional case, thus provides optimal mapping in the sense of information theory. The Winner Relaxing Algorithm requires minimal extra computations per learning step and is conveniently easy to implement.Comment: 14 pages (6 figs included). To appear in Neural Computatio