16444798
Finding Similar Patterns in Microarray Data
In this paper we propose a clustering algorithm called s-Cluster for analysis of gene expression data based on pattern-similarity. The algorithm captures the tight clusters exhibiting strong similar expression patterns in Microarray data,and allows a high level of overlap among discovered clusters without completely grouping all genes like other algorithms. This reflects the biological fact that not all functions are turned on in an experiment, and that many genes are co-expressed in multiple groups in response to different stimuli. The experiments have demonstrated that the proposed algorithm successfully groups the genes with strong similar expression patterns and that the found clusters are interpretable.
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.
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
5703198
On the Structural Algorithm of Filtering Graphs for Layout
When the amount of information in visualization becomes large enough, users can not perceive all elements at the same time. This problem can be solved by removing parts of the information through the process of Filtering. In this paper, we present a novel method for filtering a graph by measuring the important role property of a node. The basic idea of this approach is to quantify the importance of a node as the degree to which it has direct and indirect relationships with the other nodes in a graph. All the nodes are ranked according to their Node Importance Scores, and those less important nodes and their associated edges are then removed or invisible. In comparison with the rule_based approach, our approach is a structure_based one that makes use of the linkage of nodes rather than their semantics. It can therefore be applied to filter any kinds of connected graphs. The examples and applications provided have demonstrated that our approach can effectively reduce the visual complexities.
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
39883279
Identifying Clusters in the Web Graph by Using Local Search
15247747
Clustering Web Surfers with Probabilistic Models in a Real Application
The problem of modeling and predicting a Web surfer's browsing patterns has gained increasing attention in recent years. In this paper we present our experience in clustering Web surfers using a mixture of Markov models with a real application of Livelink log data. We propose different techniques to improve the clustering performance, and evaluate the techniques through experiments.
15090488
The Islands Approach to Nearest Neighbor Querying in Spatial Networks
Much research has recently been devoted to the data management foundations of location-based mobile services. In one important scenario, the service users are constrained to a transportation network. As a result, query processing in spatial road networks is of interest. We propose a versatile approach to k nearest neighbor computation in spatial networks, termed the Islands approach. By offering flexible yet simple means of balancing re-computation and pre-computation, this approach is able to manage the trade-off between query and update performance. The result is a single, efficient, and versatile approach to k nearest neighbor computation that obviates the need for using several k nearest neighbor approaches for supporting a single service scenario. The experimental comparison with the existing techniques uses real-world road network data and considers both I/O and CPU performance, for both queries and updates.
410602
Using self-supervised word segmentation in Chinese information retrieval
We propose a self-supervised word-segmentation technique for Chinese information retrieval. This method combines the advantages of traditional dictionary based approaches with character based approaches, while overcoming many of their shortcomings. Experiments on TREC data show comparable performance to both the dictionary based and the character based approaches. However, our method is language independent and unsupervised, which provides a promising avenue for constructing accurate multilingual information retrieval systems that are flexible and adaptive.
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.