Hierarchy of protein loop-lock structures: a new server for the decomposition of a protein structure into a set of closed loops

HoPLLS (Hierarchy of protein loop-lock structures) (http://leah.haifa.ac.il/~skogan/Apache/mydata1/main.html) is a web server that identifies closed loops - a structural basis for protein domain hierarchy. The server is based on the loop-and-lock theory for structural organisation of natural proteins. We describe this web server, the algorithms for the decomposition of a 3D protein into loops and the results of scientific investigations into a structural "alphabet" of loops and locks.Comment: 11 pages, 4 figure

An Iterative Projective Clustering Method

AbstractIn this article we offer an algorithm recurrently divides a dataset by search of partitions via one dimensional subspace discovered by means of optimizing of a projected pursuit function. Aiming to assess the model order a resampling technique is employed. For each number of clusters, bounded by a predefined limit, samples from the projected data are drawn and clustered through the EM algorithm. Further, the basis cumulative histogram of the projected data is approximated by means of the GMM histograms constructed using the samples’ partitions. The saturation order of this approximation process, at what time the components’ amount increases, is recognized as the “true” components’ number. Afterward the whole data is clustered and the densest cluster is omitted. The process is repeated while waiting for the true number of clusters equals one. Numerical experiments demonstrate the high ability of the proposed method

A Short-Patterning of the Texts Attributed to Al Ghazali: A “Twitter Look” at the Problem

This article presents an novel approach inspired by the modern exploration of short texts’ patterning to creations prescribed to the outstanding Islamic jurist, theologian, and mystical thinker Abu Hamid Al Ghazali. We treat the task with the general authorship attribution problematics and employ a Convolutional Neural Network (CNN), intended in combination with a balancing procedure to recognize short, concise templates in manuscripts. The proposed system suggests new attitudes make it possible to investigate medieval Arabic documents from a novel computational perspective. An evaluation of the results on a previously tagged collection of books ascribed to Al Ghazali demonstrates the method’s high reliability in recognizing the source authorship. Evaluations of two famous manuscripts, Mishakat al-Anwa and Tahafut al-Falasifa, questioningly attributed to Al Ghazali or co-authored by him, exhibit a significant difference in their overall stylistic style with one inherently assigned to Al Ghazali. This fact can serve as a substantial formal argument in the long-standing dispute about these manuscripts’ authorship. The proposed methodology suggests a new look on the perusal of medieval documents’ inner structures and possible authorship from the short-patterning and signal processing perspectives

On a Minimal Spanning, Tree Approach in the Cluster Validation Problem

In this paper, a method for the study of cluster stability is purposed. We draw pairs of samples from the data, according to two sampling distributions. The first distribution corresponds to the high density zones of data-elements distribution. Thus it is associated with the clusters cores. The second one, associated with file cluster margins, is related to the low density zones. The samples are clustered and the two obtained partitions are compared. The partitions are considered to be consistent if the obtained clusters are similar. The resemblance is measured by the total number of edges, in the clusters minimal spanning trees, connecting points from different samples. We use the Friedman and Rafsky two sample test Statistic. Under the homogeneity hypothesis, this statistic is normally distributed. Thus, it can he expected that the true number of clusters corresponds to the statistic empirical distribution which is closest to normal. Numerical experiments demonstrate the ability of the approach to detect the true number of clusters

Cluster stability using minimal spanning trees

In this paper, a method for the study of cluster stability is purposed. We draw pairs of samples from the data, according to two sampling distributions. The first distribution corresponds to the high density zones of data-elements distribution. It is associated with the clusters cores. The second one, associated with the cluster margins, is related to the low density zones. The samples are clustered and the two obtained partitions are compared. The partitions are considered to be consistent if the obtained clusters are similar. The resemblance is measured by the total number of edges, in the clusters minimal spanning trees, connecting points from different samples. We use the Friedman and Rafsky two sample test statistic. Under the homogeneity hypothesis, this statistic is normally distributed. Thus, it can expected that the true number of clusters corresponds to the statistic empirical distribution which is the closest to normal. Numerical experiments demonstrate the ability of the approach to detect the true number of clusters