270633
Web document clustering using hyperlink structures
WEB DOCUMENT CLUSTERING USING HYPERLINK STRUCTURES XIAOFENG HE y , HONGYUAN ZHA , CHRIS H.Q. DING y AND HORST D. SIMON y Abstract. With the exponential growth of information on the World Wide Web, there is great demand for developing e cient and e ective methods for organizing and retrieving the information available. Document clustering plays an important role in information retrieval and taxonomy man- agement for the World Wide Web and remains an interesting and challenging problem in the eld of web computing. In this paper we consider document clustering methods exploring textual infor- mation, hyperlink structure and co-citation relations. In particular, we apply the normalized-cut clustering method developed in computer vision to the task of hyperdocument clustering. We also explore some theoretical connections of the normalized-cut method to K-means method. We then experiment with normalized-cut method in the context of clustering query result sets for web search engines. Keywords. World Wide Web, graph partitioning, cheeger constant, clustering method, K-means method, normalized cut method, eigenvalue decomposition, power method. 1. Introduction. Currently the World Wide Web contains billions of documents and it is still growing rapidly. Finding the relevant documents to satisfy a user's infor- mation need is a very important and challenging task. Many commercial search en- gines have been developed and used by millions of people all over the world. However, the relevancy of documents returned in search engine result sets is still lacking, and further research and development is needed to really make search engines a ubiquitous information-seeking tool. The World Wide Web has a rich structure: it contains both textual web documents and the hyperlinks that connect them. The web documents and hyperlinks between them form a directed graph in which the web documents can be viewed as vertices and the hyperlinks as directed edges. Algorithms have been de- veloped utilizing this directed graph to extract information contained in a collection of hyperlinked web documents. Kleinberg proposed HITS algorithm based purely on hyperlink information to retrieve the most relevant information: authority and hub documents for a user query 20]. However, if the hypertext collection consists of sev- eral topics, authority and hub documents may only cover the most popular topics and leave out the less popular ones. One way to remedy this situation is to rst partition the hypertext collection into topical groups, and present the search results as a list of topics to the user. This leads to the need to cluster web documents based on both the textual and hyperlink information. There exists a large literature on clustering methods and algorithms 13, 19]. Gen- erally speaking, the purpose of cluster analysis is to organize the data into meaningful groups: the data objects in the same group are highly similar and those in di erent groups are dissimilar. Judging the e ectiveness of a clustering algorithm is di cult and usually application-dependent. In this paper, we apply a similarity-based cluster- ing method to the problem of clustering web documents. It utilizes a graph-theoretic criterion called normalized cut which has its root in the study of graph isoperimetric Department of Computer Science and Engineering, The Pennsylvania State University, Uni- versity Park, PA 16802, f xhe,zha g @cse.psu.edu . This work was supported in part by NSF grant CCR-9901986. y NERSC Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, CA 94720, f xfhe,chqding,hdsimon g @lbl.gov . Supported by Department of Energy through an LBL LDRD fund.
5650583
Bipartite graph partitioning and data clustering
Many data types arising from data mining applications can be modeled as bipartite graphs, examples include terms and documents in a text corpus, customers and purchasing items in market basket analysis and reviewers and movies in a movie recommender system. In this paper, we propose a new data clustering method based on partitioning the underlying bipartite graph. The partition is constructed by minimizing a normalized sum of edge weights between unmatched pairs of vertices of the bipartite graph. We show that an approximate solution to the minimization problem can be obtained by computing a partial singular value decomposition (SVD) of the associated edge weight matrix of the bipartite graph. We point out the connection of our clustering algorithm to correspondence analysis used in multivariate analysis. We also briefly discuss the issue of assigning data objects to multiple clusters. In the experimental results, we apply our clustering algorithm to the problem of document clustering to illustrate its effectiveness and efficiency.
45840953
Dynamic Cluster Formation Using Level Set Methods
Density-based clustering has the advantages for (i) allowing arbitrary shape of cluster and (ii) not requiring the number of clusters as input. However, when clusters touch each other, both the cluster centers and cluster boundaries (as the peaks and valleys of the density distribution) become fuzzy and difficult to determine. In higher dimension, the boundaries become wiggly and over-fitting often occurs. We introduce the notion of cluster intensity function (CIF) which captures the important characteristics of clusters. When clusters are well-separated, CIFs are similar to density functions. But as clusters touch each other, CIFs still clearly reveal cluster centers, cluster boundaries, and, degree of membership of each data point to the cluster that it belongs. Clustering through bump hunting and valley seeking based on these functions are more robust than that based on kernel density functions which are often oscillatory or over-smoothed. These problems of kernel density estimation are resolved using Level Set Methods and related techniques. Comparisons with two existing density-based methods, valley seeking and DBSCAN, are presented to illustrate the advantages of our approach.
1876538
PSoL: a positive sample only learning algorithm for finding non-coding RNA genes
MOTIVATION
Small non-coding RNA (ncRNA) genes play important regulatory roles in a variety of cellular processes. However, detection of ncRNA genes is a great challenge to both experimental and computational approaches. In this study, we describe a new approach called positive sample only learning (PSoL) to predict ncRNA genes in the Escherichia coli genome. Although PSoL is a machine learning method for classification, it requires no negative training data, which, in general, is hard to define properly and affects the performance of machine learning dramatically. In addition, using the support vector machine (SVM) as the core learning algorithm, PSoL can integrate many different kinds of information to improve the accuracy of prediction. Besides the application of PSoL for predicting ncRNAs, PSoL is applicable to many other bioinformatics problems as well.


RESULTS
The PSoL method is assessed by 5-fold cross-validation experiments which show that PSoL can achieve about 80% accuracy in recovery of known ncRNAs. We compared PSoL predictions with five previously published results. The PSoL method has the highest percentage of predictions overlapping with those from other methods.
4990172
Structure search and stability enhancement of Bayesian networks
Learning Bayesian network structure from large-scale data sets, without any expert-specified ordering of variables, remains a difficult problem. We propose systematic improvements to automatically learn Bayesian network structure from data. (1) We propose a linear parent search method to generate candidate graph. (2) We propose a comprehensive approach to eliminate cycles using minimal likelihood loss, a short cycle first heuristic, and a cut-edge repairing. (3) We propose structure perturbation to assess the stability of the network and a stability-improvement method to refine the network structure. The algorithms are easy to implement and efficient for large networks. Experimental results on two data sets show that our new approach outperforms existing methods.
30201789
Term norm distribution and its effects on Latent Semantic Indexing
Latent Semantic Indexing (LSI) uses the singular value decomposition to reduce noisy dimensions and improve the performance of text retrieval systems. Preliminary results have shown modest improvements in retrieval accuracy and recall, but these have mainly explored small collections. In this paper we investigate text retrieval on a larger document collection (TREC) and focus on distribution of word norm (magnitude). Our results indicate the inadequacy of word representations in LSI space on large collections. We emphasize the query expansion interpretation of LSI and propose an LSI term normalization that achieves better performance on larger collections.
2510063
Software behavior oriented parallelization
Many sequential applications are difficult to parallelize because of unpredictable control flow, indirect data access, and input-dependent parallelism. These difficulties led us to build a software system for behavior oriented parallelization (BOP), which allows a program to be parallelized based on partial information about program behavior, for example, a user reading just part of the source code, or a profiling tool examining merely one or few executions.
 The basis of BOP is programmable software speculation, where a user or an analysis tool marks possibly parallel regions in the code, and the run-time system executes these regions speculatively. It is imperative to protect the entire address space during speculation. The main goal of the paper is to demonstrate that the general protection can be made cost effective by three novel techniques: programmable speculation, critical-path minimization, and value-based correctness checking. On a recently acquired multi-core, multi-processor PC, the BOP system reduced the end-to-end execution time by integer factors for a Lisp interpreter, a data compressor, a language parser, and a scientific library, with no change to the underlying hardware or operating system.
18215853
Study for fusion of different sources to determine relevance
The relevance of a Web document could be measured not only by its text content, but also by some other factors such as the link connectivity and usage patterns. In previous data fusion researches, the text is the only source to determine the relevance, and only the different runs (e.g. by different retrieval models, different query or document representations) on this same source are combined. It is the purpose of this paper to investigate whether the different sources can be combined to determine the relevance with a better accuracy than any single source. We conducted a preliminary experiment to test its feasibility and effectiveness and a positive result was obtained.
19735283
A generalized site ranking model for Web IR
Normally, the unit for a ranking model in a Web IR system is a Web page, which is, sometimes, just an information fragment. A larger unit considering the linkage information may be desired to reduce the cognitive overload for users to identify the complete information from the interconnected Web. We propose a ranking model to measure the relevance of the whole Web site. We take some illustrations to show the idea and provide evidences to indicate its effectiveness.
26301648
Data Integrity Framework and Language Support for Active Web Intermediaries
With the maturity of content adaptation technologies (such as I-CAP and OPES) in web intermediaries and of content personalization in the network, data integrity has already become a key concern when such technologies are deployed. To address this issue, we propose a data integrity framework with the following functionalities: (i) a server can specify its authorizations, (ii) active web intermediaries can provide value-added services in accordance with the server’s intentions, and more importantly, (iii) a client is facilitated to verify the received message with the server’s authorizations and intermediaries’ footprints. With the actual implementation of our data integrity framework in web (content and proxy) servers and clients, we show the feasibility and practicability of our proposed design through its low performance overhead and possible data (re)use.
31782470
Automatic Keyword Extraction by Server Log Analysis
Traditionally, keywords are extracted from full texts of a document. While in the web environment, there are more sources we can use to provide a more complete view of a web page’s contents. In this paper, we propose to analyze web server logs to extract keywords of entry pages from anchor texts and query terms, and propagate these terms along user access paths to other linked pages. The major benefit of this method is that temporal changes could be reflected in extracted terms, and it is more about a user’s viewpoint on page’s contents instead of author’s.