12511265
A Scalable Algorithm for Adjusting Node-Node Overlaps
The node-node overlaps, which occur in drawing of labeled graphs, and more importantly, in the dynamic drawing, have been a problem in graph visualization. Several approaches have recently been proposed to solve such a problem. These approaches, however, lack the scalabilities of dealing with large number of overlapping nodes. Providing a formal description of the problem, this paper presents a scalable version of our previous approach called the force-transfer algorithm. Compared to other methods, our new algorithm is able to achieve the compact adjusted layout of a large graph
5775998
Identification of clusters in the Web graph based on link topology
The Web graph has recently been used to model the link structure of the Web. The studies of such graphs can yield valuable insights into Web algorithms for crawling, searching and discovery of Web communities. This paper proposes a new approach to clustering the Web graph. The proposed algorithm identifies a small subset of the graph as "core" members of clusters, and then incrementally constructs the clusters by a selection criterion. Two qualitative criteria are proposed to measure the quality of graph clustering. We have implemented our algorithm and tested a set of arbitrary graphs with good results. Applications of our approach include graph drawing and Web visualization.
8009887
A Framework of Filtering, Clustering and Dynamic Layout Graphs for Visualization
Many classical graph visualization algorithms have already been developed over the past decades. However, these algorithms face difficulties in practice, such as the overlapping node problem, large graph layout and dynamic graph layout. In order to solve these problems, this paper aims to systematically address algorithmic issues related to a novel framework that describes the process of graph visualization applications. First of all, a framework for graph visualization is described. As the important parts of this framework, we then develop two effective algorithms for filtering and clustering large graphs for the layouts. As for the dynamic graph layout, a new approach to removing overlapping nodes called force-transfer algorithm is developed. The framework has been implemented in a prototype called PGA to demonstrate the performance of the proposed algorithms. Finally, a case study is provided.
6189075
NodeRank: A New Structure Based Approach to Information Filtering
18862916
Clustering graphs for visualization via node similarities
Graph visualization is commonly used to visually model relations in many areas. Examples include Web sites, CASE tools, and knowledge representation. When the amount of information in these graphs becomes too large, users, however, cannot perceive all elements at the same time. A clustered graph can greatly reduce visual complexity by temporarily replacing a set of nodes in clusters with abstract nodes. This paper proposes a new approach to clustering graphs. The approach constructs the node similarity matrix of a graph that is derived from a novel metric of node similarity. The linkage pattern of the graph is thus encoded into the similarity matrix, and then one obtains the hierarchical abstraction of densely linked subgraphs by applying the k-means algorithm to the matrix. A heuristic method is developed to overcome the inherent drawbacks of the k-means algorithm. For clustered graphs we present a multilevel multi-window approach to hierarchically drawing them in different abstract level views with the purpose of improving their readability. The proposed approaches demonstrate good results in our experiments. As application examples, visualization of part of Java class diagrams and Web graphs are provided. We also conducted usability experiments on our algorithm and approach. The results have shown that the hierarchically clustered graph used in our system can improve user performance for certain types of tasks.
17691685
WFMS-based Data Integration for e-Learning
As more and more organisations and institutions are moving towards the e-learning strategy, more and more disparate data are distributed by different e-learning systems. How to effectively use this vast amount of distributed data becomes a big challenge. This paper addresses this challenge and works out a new mechanism to implement data integration for e-learning. A workflow management system based (WFMS-based) data integration model is contributed to the e-learning
9602783
Discovery of interesting association rules from Livelink web log data
We present our experience in mining web usage patterns from a large collection of Livelink log data. Livelink is a web-based product of Open Text, which provides automatic management and retrieval of different types of information objects over an intranet or extranet. We report our experience in preprocessing raw log data and post-processing the mining results for finding interesting rules. In particular we compare and evaluate a number of rule interestingness measures and find that two of the measures that have not been used in association rule learning work very well.
28347745
On global sequence alignment
We present a dynamic programming algorithm for computing a best global alignment of two sequences. The proposed algorithm is robust in identifying any of several global relationships between two sequences. The algorithm delivers a best alignment of two sequences in linear space and quadratic time. We also describe a multiple alignment algorithm based on the pairwise algorithm. Both algorithms have been implemented as portable C programs. Experimental results indicate that for a commonly used set of gap penalties, the new programs produce more satisfactory alignments on sequences of various lengths than some existing pairwise and multiple programs based on the dynamic programming algorithm of Needleman and Wunsch.
37155625
Efficient Parameterized Algorithm for Biopolymer Structure-Sequence Alignment
Computational alignment of a biopolymer sequence (e.g., an RNA or a protein) to a structure is an effective approach to predict and search for the structure of new sequences. To identify the structure of remote homologs, the structure-sequence alignment has to consider not only sequence similarity but also spatially conserved conformations caused by residue interactions, and consequently is computationally intractable. It is difficult to cope with the inefficiency without compromising alignment accuracy, especially for structure search in genomes or large databases. This paper introduces a novel method and a parameterized algorithm for structure-sequence alignment. Both the structure and the sequence are represented as graphs, where in general the graph for a biopolymer structure has a naturally small tree width. The algorithm constructs an optimal alignment by finding in the sequence graph the maximum valued subgraph isomorphic to the structure graph. It has the computational time complexity O(k t N 2) for the structure of N residues and its tree decomposition of width t. The parameter k, small in nature, is determined by a statistical cutoff for the correspondence between the structure and the sequence. The paper demonstrates a successful application of the algorithm to developing a fast program for RNA structural homology search.
3172126
Snapshot density queries on location sensors
Density queries are of practical importance in many mobility related applications. In this paper, we employ the location sensors, which are placed in a geographical area and can only detect the amount of objects moving in vicinity, to estimate the dense regions of objects. Our approach partitions the region of interest into subregions, and deploys in each subregion both location sensors and a processing node that issues and answers density queries. Three algorithms are proposed to process density queries on those processing nodes. Their accuracy and efficiency are empirically evaluated.
37047287
A SoPC Architecture of MIMO Sphere Decoder for Mobile Communications