A Semi-Supervised Self-Organizing Map for Clustering and Classification

There has been an increasing interest in semi-supervised learning in the recent years because of the great number of datasets with a large number of unlabeled data but only a few labeled samples. Semi-supervised learning algorithms can work with both types of data, combining them to obtain better performance for both clustering and classification. Also, these datasets commonly have a high number of dimensions. This article presents a new semi-supervised method based on self-organizing maps (SOMs) for clustering and classification, called Semi-Supervised Self-Organizing Map (SS-SOM). The method can dynamically switch between supervised and unsupervised learning during the training according to the availability of the class labels for each pattern. Our results show that the SS-SOM outperforms other semi-supervised methods in conditions in which there is a low amount of labeled samples, also achieving good results when all samples are labeled

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

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

The Parameter-Less Self-Organizing Map algorithm

The Parameter-Less Self-Organizing Map (PLSOM) is a new neural network algorithm based on the Self-Organizing Map (SOM). It eliminates the need for a learning rate and annealing schemes for learning rate and neighbourhood size. We discuss the relative performance of the PLSOM and the SOM and demonstrate some tasks in which the SOM fails but the PLSOM performs satisfactory. Finally we discuss some example applications of the PLSOM and present a proof of ordering under certain limited conditions.Comment: 29 pages, 27 figures. Based on publication in IEEE Trans. on Neural Network