Hierarchical classification for multiple, distributed web databases

The proliferation of online information resources increases the importance of effective and efficient distributed searching. Our research aims to provide an alternative hierarchical categorization and search capability based on a Bayesian network learning algorithm. Our proposed approach, which is grounded on automatic textual analysis of subject content of online web databases, attempts to address the database selection problem by first classifying web databases into a hierarchy of topic categories. The experimental results reported demonstrate that such a classification approach not only effectively reduces the class search space, but also helps to significantly improve the accuracy of classification performance

Merging KK-means with hierarchical clustering for identifying general-shaped groups

Clustering partitions a dataset such that observations placed together in a group are similar but different from those in other groups. Hierarchical and $K$-means clustering are two approaches but have different strengths and weaknesses. For instance, hierarchical clustering identifies groups in a tree-like structure but suffers from computational complexity in large datasets while $K$-means clustering is efficient but designed to identify homogeneous spherically-shaped clusters. We present a hybrid non-parametric clustering approach that amalgamates the two methods to identify general-shaped clusters and that can be applied to larger datasets. Specifically, we first partition the dataset into spherical groups using $K$-means. We next merge these groups using hierarchical methods with a data-driven distance measure as a stopping criterion. Our proposal has the potential to reveal groups with general shapes and structure in a dataset. We demonstrate good performance on several simulated and real datasets.Comment: 16 pages, 1 table, 9 figures; accepted for publication in Sta

Fuzzy set methods for object recognition in space applications

Progress on the following tasks is reported: (1) fuzzy set-based decision making methodologies; (2) feature calculation; (3) clustering for curve and surface fitting; and (4) acquisition of images. The general structure for networks based on fuzzy set connectives which are being used for information fusion and decision making in space applications is described. The structure and training techniques for such networks consisting of generalized means and gamma-operators are described. The use of other hybrid operators in multicriteria decision making is currently being examined. Numerous classical features on image regions such as gray level statistics, edge and curve primitives, texture measures from cooccurrance matrix, and size and shape parameters were implemented. Several fractal geometric features which may have a considerable impact on characterizing cluttered background, such as clouds, dense star patterns, or some planetary surfaces, were used. A new approach to a fuzzy C-shell algorithm is addressed. NASA personnel are in the process of acquiring suitable simulation data and hopefully videotaped actual shuttle imagery. Photographs have been digitized to use in the algorithms. Also, a model of the shuttle was assembled and a mechanism to orient this model in 3-D to digitize for experiments on pose estimation is being constructed

Inference of the genetic network regulating lateral root initiation in Arabidopsis thaliana

Regulation of gene expression is crucial for organism growth, and it is one of the challenges in Systems Biology to reconstruct the underlying regulatory biological networks from transcriptomic data. The formation of lateral roots in Arabidopsis thaliana is stimulated by a cascade of regulators of which only the interactions of its initial elements have been identified. Using simulated gene expression data with known network topology, we compare the performance of inference algorithms, based on different approaches, for which ready-to-use software is available. We show that their performance improves with the network size and the inclusion of mutants. We then analyse two sets of genes, whose activity is likely to be relevant to lateral root initiation in Arabidopsis, by integrating sequence analysis with the intersection of the results of the best performing methods on time series and mutants to infer their regulatory network. The methods applied capture known interactions between genes that are candidate regulators at early stages of development. The network inferred from genes significantly expressed during lateral root formation exhibits distinct scale-free, small world and hierarchical properties and the nodes with a high out-degree may warrant further investigation

Variability analysis of the hierarchical clustering algoritms and its implication on consensus clustering

Clustering is one of the most important unsupervised learning tools when no prior knowledge about the data set is available. Clustering algorithms aim to find underlying structure of the data sets taking into account clustering criteria, properties in the data and specific way of data comparison. In the literature many clustering algorithms have been proposed having a common goal which is, given a set of objects, grouping similar objects in the same cluster and dissimilar objects in different clusters. Hierarchical clustering algorithms are of great importance in data analysis providing knowledge about the data structure. Due to the graphical representation of the resultant partitions, through a dendrogram, may give more information than the clustering obtained by non hierarchical clustering algorithms. The use of different clustering methods for the same data set, or the use of the same clustering method but with different initializations (different parameters), can produce different clustering. So several studies have been concerned with validate the resulting clustering analyzing them in terms of stability / variability, and also, there has been an increasing interest on the problem of determining a consensus clustering. This work empirically analyzes the clustering variability delivered by hierarchical algorithms, and some consensus clustering techniques are also investigated. By the variability of hierarchical clustering, we select the most suitable consensus clustering technique existing in literature. Results on a range of synthetic and real data sets reveal significant differences of the variability of hierarchical clustering as well as different performances of the consensus clustering techniques

Towards efficient SimRank computation on large networks

SimRank has been a powerful model for assessing the similarity of pairs of vertices in a graph. It is based on the concept that two vertices are similar if they are referenced by similar vertices. Due to its self-referentiality, fast SimRank computation on large graphs poses significant challenges. The state-of-the-art work [17] exploits partial sums memorization for computing SimRank in O(Kmn) time on a graph with n vertices and m edges, where K is the number of iterations. Partial sums memorizing can reduce repeated calculations by caching part of similarity summations for later reuse. However, we observe that computations among different partial sums may have duplicate redundancy. Besides, for a desired accuracy ϵ, the existing SimRank model requires K = [logC ϵ] iterations [17], where C is a damping factor. Nevertheless, such a geometric rate of convergence is slow in practice if a high accuracy is desirable. In this paper, we address these gaps. (1) We propose an adaptive clustering strategy to eliminate partial sums redundancy (i.e., duplicate computations occurring in partial sums), and devise an efficient algorithm for speeding up the computation of SimRank to 0(Kdn2) time, where d is typically much smaller than the average in-degree of a graph. (2) We also present a new notion of SimRank that is based on a differential equation and can be represented as an exponential sum of transition matrices, as opposed to the geometric sum of the conventional counterpart. This leads to a further speedup in the convergence rate of SimRank iterations. (3) Using real and synthetic data, we empirically verify that our approach of partial sums sharing outperforms the best known algorithm by up to one order of magnitude, and that our revised notion of SimRank further achieves a 5X speedup on large graphs while also fairly preserving the relative order of original SimRank scores