Techniques for clustering gene expression data

Many clustering techniques have been proposed for the analysis of gene expression data obtained from microarray experiments. However, choice of suitable method(s) for a given experimental dataset is not straightforward. Common approaches do not translate well and fail to take account of the data profile. This review paper surveys state of the art applications which recognises these limitations and implements procedures to overcome them. It provides a framework for the evaluation of clustering in gene expression analyses. The nature of microarray data is discussed briefly. Selected examples are presented for the clustering methods considered

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

Data Management and Mining in Astrophysical Databases

We analyse the issues involved in the management and mining of astrophysical data. The traditional approach to data management in the astrophysical field is not able to keep up with the increasing size of the data gathered by modern detectors. An essential role in the astrophysical research will be assumed by automatic tools for information extraction from large datasets, i.e. data mining techniques, such as clustering and classification algorithms. This asks for an approach to data management based on data warehousing, emphasizing the efficiency and simplicity of data access; efficiency is obtained using multidimensional access methods and simplicity is achieved by properly handling metadata. Clustering and classification techniques, on large datasets, pose additional requirements: computational and memory scalability with respect to the data size, interpretability and objectivity of clustering or classification results. In this study we address some possible solutions.Comment: 10 pages, Late

Information visualization for DNA microarray data analysis: A critical review

Graphical representation may provide effective means of making sense of the complexity and sheer volume of data produced by DNA microarray experiments that monitor the expression patterns of thousands of genes simultaneously. The ability to use ldquoabstractrdquo graphical representation to draw attention to areas of interest, and more in-depth visualizations to answer focused questions, would enable biologists to move from a large amount of data to particular records they are interested in, and therefore, gain deeper insights in understanding the microarray experiment results. This paper starts by providing some background knowledge of microarray experiments, and then, explains how graphical representation can be applied in general to this problem domain, followed by exploring the role of visualization in gene expression data analysis. Having set the problem scene, the paper then examines various multivariate data visualization techniques that have been applied to microarray data analysis. These techniques are critically reviewed so that the strengths and weaknesses of each technique can be tabulated. Finally, several key problem areas as well as possible solutions to them are discussed as being a source for future work

APPLICATION OF KOHONEN SELF-ORGANIZING MAP TO SEARCH FOR REGION OF INTEREST IN THE DETECTION OF OBJECTS

Today, there is a serious need to improve the performance of algorithms for detecting objects in images. This process can be accelerated with the help of preliminary processing, having found areas of interest on the images where the probability of object detection is high. To this end, it is proposed to use the algorithm for distinguishing the boundaries of objects using the Sobel operator and Kohonen self-organizing maps, described in this paper and shown by the example of determining zones of interest when searching and recognizing objects in satellite images. The presented algorithm allows 15–100 times reduction in the amount of data arriving at the convolutional neural network, which provides the final recognition. Also, the algorithm can significantly reduce the number of training images, since the size of the parts of the input image supplied to the convolution network is tied to the image scale and equal to the size of the largest recognizable object, and the object is centered in the frame. This allows to accelerate network learning by more than 5 times and increase recognition accuracy by at least 10 %, as well as halve the required minimum number of layers and neurons of the convolutional network, thereby increasing its speed