Motivation: We describe a new approach to the analysis of gene expression data coming from DNA array experiments, using an unsupervised neural network. DNA array technologies allow monitoring thousands of genes rapidly and efficiently. One of the interests of these studies is the search for correlated gene expression patterns, and this is usually achieved by clustering them. The Self-Organising Tree Algorithm, (SOTA) (Dopazo,J. and Carazo,J.M. (1997) J. Mol. Evol., 44, 226--233), is a neural network that grows adopting the topology of a binary tree. The result of the algorithm is a hierarchical cluster obtained with the accuracy and robustness of a neural network. Results: SOTA clustering confers several advantages over classical hierarchical clustering methods. SOTA is a divisive method: the clustering process is performed from top to bottom, i.e. the highest hierarchical levels are resolved before going to the details of the lowest levels. The growing can be stopped at the desired hierarchical level. Moreover, a criterion to stop the growing of the tree, based on the approximate distribution of probability obtained by randomisation of the original data set, is provided. By means of this criterion, a statistical support for the definition of clusters is proposed. In addition, obtaining average gene expression patterns is a built-in feature of the algorithm. Different neurons defining the different hierarchical levels represent the averages of the gene expression patterns contained in the clusters. Since SOTA runtimes are approximately linear with the number of items to be classified, it is especially suitable for dealing with huge amounts of data. The method proposed is very general and applies to any data providing that they can be coded as a series of numbers and t...

Finding structures in vast multidimensional data sets, be they measurement data, statistics, or textual documents, is difficult and time-consuming. Interesting, novel relations between the data items may be hidden in the data. The selforganizing map (SOM) algorithm of Kohonen can be used to aid the exploration: the structures in the data sets can be illustrated on special map displays. In this work, the methodology of using SOMs for exploratory data analysis or data mining is reviewed and developed further. The properties of the maps are compared with the properties of related methods intended for visualizing highdimensional multivariate data sets. In a set of case studies the SOM algorithm is applied to analyzing electroencephalograms, to illustrating structures of the standard of living in the world, and to organizing full-text document collections. Measures are proposed for evaluating the quality of different types of maps in representing a given data set, and for measuring the robu...

Neural maps project data given in a (possibly high-dimensional) input space onto a neuron position in a (usually low-dimensional) output space grid. An important property of this projection is the preservation of neighborhoods; neighboring neurons in output space respond to neighboring data points in input space. To achieve this preservation in an optimal way during learning, the topology of the output space has to roughly match the effective structure of the data in the input space. We here present a growth algorithm, called the GSOM, which enhances a widespread map self-organization process, Kohonen's Self-Organizing Feature Map (SOFM), by an adaptation of the output space grid during learning. During the procedure the output space structure is restricted to a general hypercubical shape, with the overall dimensionality of the grid and its extensions along the different directions being subject of the adaptation. This constraint distinguishes the present algorithm from other, less or ...

Abstract—This paper proposes a framework for constructing and training radial basis function (RBF) neural networks. The proposed growing radial basis function (GRBF) network begins with a small number of prototypes, which determine the locations of radial basis functions. In the process of training, the GRBF network grows by splitting one of the prototypes at each growing cycle. Two splitting criteria are proposed to determine which prototype to split in each growing cycle. The proposed hybrid learning scheme provides a framework for incorporating existing algorithms in the training of GRBF networks. These include unsupervised algorithms for clustering and learning vector quantization, as well as learning algorithms for training single-layer linear neural networks. A supervised learning scheme based on the minimization of the localized class-conditional variance is also proposed and tested. GRBF neural networks are evaluated and tested on a variety of data sets with very satisfactory results. Index Terms — Class-conditional variance, network growing, radial basis neural network, radial basis function, splitting criterion,

We present a model of decentralized growth and development for artificial neural networks (ANNs), inspired by developmental biology and the physiology of nervous systems. In this model, each individual artificial neuron is an autonomous unit whose behavior is determined only by the genetic information it harbors and local concentrations of substrates. The chemicals and substrates, in turn, are modeled by a simple artificial chemistry. While the system is designed to allow for the evolution of complex networks, we demonstrate the power of the artificial chemistry by analyzing engineered (handwritten) genomes that lead to the growth of simple networks with behaviors known from physiology. To evolve more complex structures, a Java-based, platform-independent, asynchronous, distributed genetic algorithm (GA) has been implemented that allows users to participate in evolutionary experiments via the World Wide Web.

The ability to grow extra nodes is a potentially useful facility for a self-organising neural network. A network that can add nodes into its map space can approximate the input space more accurately, and often more parsimoniously, than a network with predefined structure and size, such as the Self-Organising Map. In addition, a growing network can deal with dynamic input distributions. Most of the growing networks that have been proposed in the literature add new nodes to support the node that has accumulated the highest error during previous iterations or to support topological structures. This usually means that new nodes are added only when the number of iterations is an integer multiple of some pre-defined constant,

analysis Abstract: Recent development of technologies (e.g. microarray technology) that are capable of producing massive amounts of genetic data has highlighted the need for new pattern recognition techniques that can mine and discover “biologically meaningful ” knowledge in large data sets. Many researchers have begun an endeavor in this direction to devise such datamining techniques. As such, there is a need for survey articles that periodically review and summarize the work that has been done in the area. This article presents one such survey. The first portion of the paper is meant to provide the basic biology (mostly for non-biologists) that is required in such a project. This part is only meant to be a starting point for those experts in the technical fields who wish to embark on this new area of bioinformatics. The second portion of the paper is a survey of various data mining techniques that have been used in mining microarray data for biological knowledge and information (such as sequence information). This survey is not meant to be treated as complete in any form, as the area is currently one of the most active, and the body of research is very large. Furthermore, the applications of the techniques mentioned here are not meant to be taken as the most significant applications of the techniques, but simply as some examples among many. Molecular Genome Biology

The development of mechanisms that enable robot teams to autonomously generate cooperative behaviours is one of the most interesting issues in dis- tributed and autonomous robotic systems. In this paper, the application of reinforcement learning techniques to robot teams is studied, enabling the robot to learn cooperative behaviours based only on local information.

Part I of this paper defines the class of constructive unsupervised on-line learning simplified adaptive resonance theory (SART) clustering networks. Proposed instances of class SART are the symmetric Fuzzy ART (S-Fuzzy ART) and the Gaussian ART (GART) network. In Part II of our work, a third network belonging to class SART, termed fully self-organizing SART (FOSART), is presented and discussed. FOSART is a constructive, soft-to-hard competitive, topology-preserving, minimum-distance-to-means clustering algorithm capable of: 1) generating processing units and lateral connections on an example-driven basis and 2) removing processing units and lateral connections on a minibatch basis. FOSART is compared with Fuzzy ART, S-Fuzzy ART, GART and other well-known clustering techniques (e.g., neural gas and self-organizing map) in several unsupervised learning tasks, such as vector quantization, perceptual grouping and 3-D surface reconstruction. These experiments prove that when compared with other unsupervised learning networks, FOSART provides an interesting balance between easy user interaction, performance accuracy, efficiency, robustness, and flexibility.

We present an efficient approach to forming feature maps. The method involves three stages. In the first stage, we use the-means algorithm to select (i.e., the size of the feature map to be formed) cluster centers from a data set. Then a heuristic assignment strategy is employed to organize the selected data points into an neural array so as to form an initial feature map. If the initial map is not good enough, then it will be fine-tuned by the traditional Kohonen self-organizing feature map (SOM) algorithm under a fast cooling regime in the third stage. By our three-stage method, a topologically ordered feature mapwould be formed very quickly instead of requiring a huge amount of iterations to fine-tune the weights toward the density distribution of the data points, which usually happened in the conventional SOM algorithm. Three data sets are utilized to illustrate the proposed method.