Jingyu Hou

Effectively finding relevant Web pages from linkage information

This paper presents two hyperlink analysis-based algorithms to find relevant pages for a given Web page (URL). The first algorithm comes from the extended cocitation analysis of the Web pages. It is intuitive and easy to implement. The second one takes advantage of linear algebra theories to reveal deeper relationships among the Web pages and to identify relevant pages more precisely and effectively. The experimental results show the feasibility and effectiveness of the algorithms. These algorithms could be used for various Web applications, such as enhancing Web search. The ideas and techniques in this work would be helpful to other Web-related research.

Algorithm for Web Services Matching

UDDI is a standard for publishing and discovery of web services. UDDI registries provide keyword searches for web services. The search functionality is very simple and fails to account for relationships between web services. In this paper, we propose an algorithm which retrieves closely related web services. The proposed algorithm is based on singular value decomposition (SVD) in linear algebra, which reveals semantic relationships among web services. The preliminary evaluation shows the effectiveness and feasibility of the algorithm.

An iterative approach of protein function prediction

BackgroundCurrent approaches of predicting protein functions from a protein-protein interaction (PPI) dataset are based on an assumption that the available functions of the proteins (a.k.a. annotated proteins) will determine the functions of the proteins whose functions are unknown yet at the moment (a.k.a. un-annotated proteins). Therefore, the protein function prediction is a mono-directed and one-off procedure, i.e. from annotated proteins to un-annotated proteins. However, the interactions between proteins are mutual rather than static and mono-directed, although functions of some proteins are unknown for some reasons at present. That means when we use the similarity-based approach to predict functions of un-annotated proteins, the un-annotated proteins, once their functions are predicted, will affect the similarities between proteins, which in turn will affect the prediction results. In other words, the function prediction is a dynamic and mutual procedure. This dynamic feature of protein interactions, however, was not considered in the existing prediction algorithms.ResultsIn this paper, we propose a new prediction approach that predicts protein functions iteratively. This iterative approach incorporates the dynamic and mutual features of PPI interactions, as well as the local and global semantic influence of protein functions, into the prediction. To guarantee predicting functions iteratively, we propose a new protein similarity from protein functions. We adapt new evaluation metrics to evaluate the prediction quality of our algorithm and other similar algorithms. Experiments on real PPI datasets were conducted to evaluate the effectiveness of the proposed approach in predicting unknown protein functions.ConclusionsThe iterative approach is more likely to reflect the real biological nature between proteins when predicting functions. A proper definition of protein similarity from protein functions is the key to predicting functions iteratively. The evaluation results demonstrated that in most cases, the iterative approach outperformed non-iterative ones with higher prediction quality in terms of prediction precision, recall and F-value.

Constructing good quality web page communities

World Wide Web is a rich source of information and continues to expand in size and complexity. To capture the features of the Web at a higher level to realise the information classification and efficient retrieval on the Web is becoming a challenge task. One natural way is to exploit the linkage information among the Web pages. Previous work such as HITS in this area is based on a set of retrieved pages to get a Web community that is a bunch of pages related to the query topics. Since the set of retrieved pages may contain many unrelated pages (noise pages) to the query topics, the obtained Web community sometimes is unsatisfactory. In this paper, we propose an innovative algorithm to eliminate noise pages from set of retrieved pages and improve its quality. This improvement will enable existing community construction algorithms to construct good quality Web page communities. The proposed algorithm reveals and takes advantage of the relationships among concerned Web pages at a deeper level. The numerical experiment results show the effectiveness and feasibility of the algorithm. This algorithm could also be used solely to filter unnecessary Web pages and reduce the management cost and burden of Web-based data management systems. The ideas in the algorithm can also be applied to other hyperlink analysis.

Object-oriented representation for XML data

XML is a new standard for representing and exchanging data on the Internet. How to model XML data for Web applications and data management is a hot topic in the XML research area. The paper presents an object representation model for XML data. A set of transformation rules and steps are established to transform DTDs, as well as XML documents with DTDs, into this model. This model capsulizes elements of XML data and manipulation methods. This pure object oriented model considers the features and usage of XML data and is suitable for Web applications as well as XML data management. DTD-Tree is defined to represent DTD and describe the procedure to use transformation rules. DTD-Tree can also be used as a logical interface for DTD processing.

A neural network based human identification framework using ear images

This paper presents a framework that uses ear images for human identification. The framework makes use of Principal Component Analysis (PCA) for ear image feature extraction and Multilayer Feed Forward Neural Network for classification. Framework are proposed to improve recognition accuracy of human identification. The framework was tested on an ear image database to evaluate its reliability and recognition accuracy. The experimental results showed that our framework achieved higher stable recognition accuracy and over-performed other existing methods. The recognition accuracy stability and computation time with respect to different image sizes and factors were investigated thoroughly as well in the experiments.

Semantic and layered protein function prediction from PPI networks

BACKGROUND The past few years have seen a rapid development in novel high-throughput technologies that have created large-scale data on protein-protein interactions (PPI) across human and most model species. This data is commonly represented as networks, with nodes representing proteins and edges representing the PPIs. A fundamental challenge to bioinformatics is how to interpret this wealth of data to elucidate the interaction of patterns and the biological characteristics of the proteins. One significant purpose of this interpretation is to predict unknown protein functions. Although many approaches have been proposed in recent years, the challenge still remains how to reasonably and precisely measure the functional similarities between proteins to improve the prediction effectiveness. RESULTS We used a Semantic and Layered Protein Function Prediction (SLPFP) framework to more effectively predict unknown protein functions at different functional levels. The framework relies on a new protein similarity measurement and a clustering-based protein function prediction algorithm. The new protein similarity measurement incorporates the topological structure of the PPI network, as well as the proteins semantic information in terms of known protein functions at different functional layers. Experiments on real PPI datasets were conducted to evaluate the effectiveness of the proposed framework in predicting unknown protein functions. CONCLUSION The proposed framework has a higher prediction accuracy compared with other similar approaches. The prediction results are stable even for a large number of proteins. Furthermore, the framework is able to predict unknown functions at different functional layers within the Munich Information Center for Protein Sequence (MIPS) hierarchical functional scheme. The experimental results demonstrated that the new protein similarity measurement reflects more reasonably and precisely relationships between proteins.

Predicting protein functions from PPI networks using functional aggregation

Predicting protein functions computationally from massive protein-protein interaction (PPI) data generated by high-throughput technology is one of the challenges and fundamental problems in the post-genomic era. Although there have been many approaches developed for computationally predicting protein functions, the mutual correlations among proteins in terms of protein functions have not been thoroughly investigated and incorporated into existing prediction methods, especially in voting based prediction methods. In this paper, we propose an innovative method to predict protein functions from PPI data by aggregating the functional correlations among relevant proteins using the Choquet-Integral in fuzzy theory. This functional aggregation measures the real impact of each relevant protein function on the final prediction results, and reduces the impact of repeated functional information on the prediction. Accordingly, a new protein similarity and a new iterative prediction algorithm are proposed in this paper. The experimental evaluations on real PPI datasets demonstrate the effectiveness of our method.

A matrix approach for hierarchical web page clustering based in hyperlinks

This paper proposes a matrix approach for hierarchical web page clustering with two algorithms using hyperlink information among pages.One clustering algorithm clusters web pages without considering cluster overlapping.Another one takes cluster overlapping into account.These algorithms take advantage of intrinsic relationships among the pages, and are independent of the order in which the pages are presented to the algorithms.Furthermore, the proposed algorithms do not require a predefined similarity threshold for clustering.They are easy to be implemented for web applications.The primary evaluations show the effectiveness of the proposed algorithms, as well as a promising application.

Progressive Clustering Based Method for Protein Function Prediction

In recent years, significant effort has been given to predicting protein functions from protein interaction data generated from high throughput techniques. However, predicting protein functions correctly and reliably still remains a challenge. Recently, many computational methods have been proposed for predicting protein functions. Among these methods, clustering based methods are the most promising. The existing methods, however, mainly focus on protein relationship modeling and the prediction algorithms that statically predict functions from the clusters that are related to the unannotated proteins. In fact, the clustering itself is a dynamic process and the function prediction should take this dynamic feature of clustering into consideration. Unfortunately, this dynamic feature of clustering is ignored in the existing prediction methods. In this paper, we propose an innovative progressive clustering based prediction method to trace the functions of relevant annotated proteins across all clusters that are generated through the progressive clustering of proteins. A set of prediction criteria is proposed to predict functions of unannotated proteins from all relevant clusters and traced functions. The method was evaluated on real protein interaction datasets and the results demonstrated the effectiveness of the proposed method compared with representative existing methods.