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.

Reduction of invasive tests in chagasic patients with a modified self-organizing map

The applicability of AI methods to the Chagas' disease diagnosis is carried out by the use of Kohonen's self-organizing feature maps. Electrodiagnosis indicators calculated from ECG records are used as features in input vectors to train the network. Cross-validation results are used to modify the maps, providing an outstanding improvement to the interpretation of the resulting output. As a result, the map might be used to reduce the need for invasive explorations in chronic Chagas' disease.

Self-organising neural networks for adaptive control

Self-organizing neural networks have been implemented in a wide range of application areas such as speech processing, image processing, optimization and robotics. Recent variations to the basic model proposed by the authors enable it to order state space using a subset of the input vector and to apply a local adaptation procedure that does not rely on a predefined test duration limit. Both these variations have been incorporated into a new feature map architecture that forms an integral part of an Hybrid Learning System (HLS) based on a genetic-based classifier system. Problems are represented within HLS as objects characterized by environmental features. Objects controlled by the system have preset targets set against a subset of their features. The system's objective is to achieve these targets by evolving a behavioural repertoire that efficiently explores and exploits the problem environment. Feature maps encode two types of knowledge within HLS — long-term memory traces of useful regularities within the environment and the classifier performance data calibrated against an object's feature states and targets. Self-organization of these networks constitutes non-genetic-based (experience-driven) learning within HLS. This paper presents a description of the HLS architecture and an analysis of the modified feature map implementing associative memory. Initial results are presented that demonstrate the behaviour of the system on a simple control task.

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.

A new linear initialization in SOM for biomolecular data

In the past decade, the amount of data in biological field has become larger and larger; Bio-techniques for analysis of biological data have been developed and new tools have been introduced. Several computational methods are based on unsupervised neural network algorithms that are widely used for multiple purposes including clustering and visualization, i.e. the Self Organizing Maps (SOM). Unfortunately, even though this method is unsupervised, the performances in terms of quality of result and learning speed are strongly dependent from the neuron weights initialization. In this paper we present a new initialization technique based on a totally connected undirected graph, that report relations among some intersting features of data input. Result of experimental tests, where the proposed algorithm is compared to the original initialization techniques, shows that our technique assures faster learning and better performance in terms of quantization error.

Improved SOM learning using simulated annealing

Self-Organizing Map (SOM) algorithm has been extensively used for analysis and classification problems. For this kind of problems, datasets become more and more large and it is necessary to speed up the SOM learning. In this paper we present an application of the Simulated Annealing (SA) procedure to the SOM learning algorithm. The goal of the algorithm is to obtain fast learning and better performance in terms of matching of input data and regularity of the obtained map. An advantage of the proposed technique is that it preserves the simplicity of the basic algorithm. Several tests, carried out on different large datasets, demonstrate the effectiveness of the proposed algorithm in comparison with the original SOM and with some of its modification introduced to speed-up the learning.

Design and evaluation of intelligent classifier based intrusion detection system

We have discovered a novel approach of intrusion detection system using an intelligent data classifier based on a self organizing map (SOM). We have surveyed all other unsupervised intrusion detection methods, different alternative SOM based techniques and KDD winner IDS methods. This paper provides a robust designed and implemented intelligent data classifier technique based on a single large size (30x30) self organizing map (SOM) having the capability to detect all types of attacks given in the DARPA Archive 1999 the lowest false positive rate being 0.04 % and higher detection rate being 99.73% tested using full KDD data sets and 89.54% comparable detection rate and 0.18% lowest false positive rate tested using corrected data sets.

Generative topographic mapping applied to clustering and visualization of motor unit action potentials

The identification and visualization of clusters formed by motor unit action potentials (MUAPs) is an essential step in investigations seeking to explain the control of the neuromuscular system. This work introduces the generative topographic mapping (GTM), a novel machine learning tool, for clustering of MUAPs, and also it extends the GTM technique to provide a way of visualizing MUAPs. The performance of GTM was compared to that of three other clustering methods: the self-organizing map (SOM), a Gaussian mixture model (GMM), and the neural-gas network (NGN). The results, based on the study of experimental MUAPs, showed that the rate of success of both GTM and SOM outperformed that of GMM and NGN, and also that GTM may in practice be used as a principled alternative to the SOM in the study of MUAPs. A visualization tool, which we called GTM grid, was devised for visualization of MUAPs lying in a high-dimensional space. The visualization provided by the GTM grid was compared to that obtained from principal component analysis (PCA). (c) 2005 Elsevier Ireland Ltd. All rights reserved.

Clustering quality and topology preservation in fast learning SOMs

The Self-Organizing Map (SOM) is a popular unsupervised neural network able to provide effective clustering and data visualization for data represented in multidimensional input spaces. In this paper, we describe Fast Learning SOM (FLSOM) which adopts a learning algorithm that improves the performance of the standard SOM with respect to the convergence time in the training phase. We show that FLSOM also improves the quality of the map by providing better clustering quality and topology preservation of multidimensional input data. Several tests have been carried out on different multidimensional datasets, which demonstrate better performances of the algorithm in comparison with the original SOM.

Maximizing revenue in Grid markets using an economically enhanced resource manager

Traditional resource management has had as its main objective the optimization of throughput, based on parameters such as CPU, memory, and network bandwidth. With the appearance of Grid markets, new variables that determine economic expenditure, benefit and opportunity must be taken into account. The Self-organizing ICT Resource Management (SORMA) project aims at allowing resource owners and consumers to exploit market mechanisms to sell and buy resources across the Grid. SORMA's motivation is to achieve efficient resource utilization by maximizing revenue for resource providers and minimizing the cost of resource consumption within a market environment. An overriding factor in Grid markets is the need to ensure that the desired quality of service levels meet the expectations of market participants. This paper explains the proposed use of an economically enhanced resource manager (EERM) for resource provisioning based on economic models. In particular, this paper describes techniques used by the EERM to support revenue maximization across multiple service level agreements and provides an application scenario to demonstrate its usefulness and effectiveness. Copyright © 2008 John Wiley & Sons, Ltd.

Neural networks for power systems alarm handling

A multi-layered architecture of self-organizing neural networks is being developed as part of an intelligent alarm processor to analyse a stream of power grid fault messages and provide a suggested diagnosis of the fault location. Feedback concerning the accuracy of the diagnosis is provided by an object-oriented grid simulator which acts as an external supervisor to the learning system. The utilization of artificial neural networks within this environment should result in a powerful generic alarm processor which will not require extensive training by a human expert to produce accurate results.

Neural network feature maps for Chinese phonemes

It has been shown through a number of experiments that neural networks can be used for a phonetic typewriter. Algorithms can be looked on as producing self-organizing feature maps which correspond to phonemes. In the Chinese language the utterance of a Chinese character consists of a very simple string of Chinese phonemes. With this as a starting point, a neural network feature map for Chinese phonemes can be built up. In this paper, feature map structures for Chinese phonemes are discussed and tested. This research on a Chinese phonetic feature map is important both for Chinese speech recognition and for building a Chinese phonetic typewriter.

Image fusion based on median filters and SOFM neural networks: a three-step scheme

This paper presents a new image data fusion scheme by combining median filtering with self-organizing feature map (SOFM) neural networks. The scheme consists of three steps: (1) pre-processing of the images, where weighted median filtering removes part of the noise components corrupting the image, (2) pixel clustering for each image using self-organizing feature map neural networks, and (3) fusion of the images obtained in Step (2), which suppresses the residual noise components and thus further improves the image quality. It proves that such a three-step combination offers an impressive effectiveness and performance improvement, which is confirmed by simulations involving three image sensors (each of which has a different noise structure).

Simulated annealing technique for fast learning of SOM networks

The Self-Organizing Map (SOM) is a popular unsupervised neural network able to provide effective clustering and data visualization for multidimensional input datasets. In this paper, we present an application of the simulated annealing procedure to the SOM learning algorithm with the aim to obtain a fast learning and better performances in terms of quantization error. The proposed learning algorithm is called Fast Learning Self-Organized Map, and it does not affect the easiness of the basic learning algorithm of the standard SOM. The proposed learning algorithm also improves the quality of resulting maps by providing better clustering quality and topology preservation of input multi-dimensional data. Several experiments are used to compare the proposed approach with the original algorithm and some of its modification and speed-up techniques.