OntSum: A Semantic Query Routing Scheme in P2P Networks Based on Concise Ontology Indexing
Locating desirable resources is very important for a large distributed system. However, the distributed, heterogeneous, and unstructured nature of the system makes this issue very challenging. The discovering mechanism has to be not only semantically rich, in order to cope with complex queries, but also scalable to handle large numbers of information sources. In this paper, we address these problems by proposing OntSum, an efficient peer-to-peer query routing scheme based on concise ontology indexing. Unlike most existing systems, our system does not assume a global ontology but heterogeneous ontologies. Peers in the system use their own ontologies to describe their resource knowledge and the network topology is adjusted according to peers' ontological properties. A novel indexing strategy enables forwarding queries only to semantically related nodes. The architecture improves interoperability among network participants and aids efficient resource discovery through an expressive query language.

title: Grid Resource Discovery Using Semantic Communities
abstract: Grid technologies enable the sharing and collaborating of a wide variety of resources. To fully utilize these resources, effective resource discovery mechanisms are necessities. However, the complicated and dynamic characteristics of the grid resources make sharing and discovering them a challenging issue. In this paper, we propose a semantic community approach to assisting the efficient resource discovery and query in grids. Semantic community is a natural arrangement of distributed systems. It prunes the searching space and reduces the cost of searching. Moreover, it exhibits many desirable properties, including being fully decentralized and supporting complex queries. Our simulation results show how searching the girds can take advantage of semantic communities to reduce the searching cost and improve the quality of search results.

title: ECSP: An Efficient Cluster Based P2P Architecture

title: FedGrid: An HLA Approach to Federating Grids
abstract: Research on Grids has received considerable attention in recent years. Whereas existing work on connecting the grids primarily focused on grid services, in our work we propose a unified approach, so-called FederationGrid (or FedGrid for short), which integrates both virtual organization (VO) and grid services, thus enabling formation of virtual communities on top of grids. FedGrid is based on the standard High Level Architecture (HLA) that enjoys the advantages of high-level information modeling, including re-usability of software components and real-time performance of the overall systems. In addition, FedGrid is a fractal grid, comprised of hierarchical HLA federations, e.g. Realms and Lobby, which supports well the concept of virtual communities and scalability.

title: An efficient clustered architecture for P2P networks
abstract: Peer-to-peer (P2P) computing offers many attractive features, such as self-organization, load-balancing, availability, fault tolerance, and anonymity. However, it also faces some serious challenges. In this paper, we propose an Efficient Clustered Super-Peer P2P architecture (ECSP) to overcome the scalability and efficiency problems of existing unstructured P2P system. With ECSP, peers are grouped into clusters according to their topological proximity, and super-peers are selected from regular peers to act as cluster leaders and service providers. These super-peers are also connected to each other, forming a backbone overlay network operating as a distinct, yet integrated, application. To maintain the dynamically adaptive overlay network and to manage the routing on it, we propose an application level broadcasting protocol: Efa. Applying only a small amount of information about the topology of a network, Efa is as simple as flooding, a conventional method used in unstructured P2P systems. By eliminating many duplicated messages, Efa is much more efficient and scalable than flooding, and furthermore, it is completely decentralized and self-organized. Our experimental results prove that ESCP architecture, combined with the super-peer backbone protocol, can generate impressive levels of performance and scalability.

title: Efa: an efficient content routing algorithm in large peer-to-peer overlay networks
abstract: An important issue for peer-to-peer application is to locate content within the network. There are many existing solutions to this problem, however, each of them addresses different aspects and each has its deficiencies. We focus on the unstructured peer-to-peer scenario and present a constrained flooding routing algorithm, Efa, which overcomes some of the deficiencies of those existing strategies. Efa performs application level broadcasting in a potentially very large peer-to-peer network overlaid on the Internet. Efa is completely decentralized and self-organized. It is a more scalable alternative to flooding, which is commonly used in unstructured peer-to-peer systems. Utilizing just a small amount of topology info, Efa is almost as simple as flooding, but it is much more efficient and scalable.

title: A framework of integrating gene relations from heterogeneous data sources: an experiment on Arabidopsis thaliana
abstract: One of the most important goals of biological investigation is to uncover gene functional relations. In this study we propose a framework for extraction and integration of gene functional relations from diverse biological data sources, including gene expression data, biological literature and genomic sequence information. We introduce a two-layered Bayesian network approach to integrate relations from multiple sources into a genome-wide functional network. An experimental study was conducted on a test-bed of Arabidopsis thaliana. Evaluation of the integrated network demonstrated that relation integration could improve the reliability of relations by combining evidence from different data sources. Domain expert judgments on the gene functional clusters in the network confirmed the validity of our approach for relation integration and network inference.

title: FIRM: fuzzily integrated region matching for content-based image retrieval
abstract: We propose FIRM (Fuzzily Integrated Region Matching), an efficient and robust similarity measure for region-based image retrieval. Each image in our retrieval system is represented by a set of regions that are characterized by fuzzy sets. The FIRM measure, representing the overall similarity between two images, is defined as the similarity between two families of fuzzy sets. Compared with similarity measures based on individual regions and on all regions with crisp feature representations, our approach greatly reduces the influence of inaccurate segmentation. Experimental results based on a database of about 200,000 general-purpose images demonstrate improved accuracy, robustness, and high speed.

title: Discovery of Binding Motif Pairs from Protein Complex Structural Data and Protein Interaction Sequence Data
abstract: Unravelling the underlying mechanisms of protein interactions requires knowledge about the interactions' binding sites. In this paper, we use a novel concept, binding motif pairs, to describe binding sites. A binding motif pair consists of two motifs each derived from one side of the binding protein sequences. The discovery is a directed approach that uses a combination of two data sources: 3-D structures of protein complexes and sequences of interacting proteins. We first extract maximal contact segment pairs from the protein complexes' structural data. We then use these segment pairs as templates to sub-group the interacting protein sequence dataset, and conduct an iterative refinement to derive significant binding motif pairs. This combination approach is efficient in handling large datasets of protein interactions. From a dataset of 78,390 protein interactions, we have discovered 896 significant binding motif pairs. The discovered motif pairs include many novel motif pairs as well as motifs that agree well with experimentally validated patterns in the literature.

title: RACCOON: a peer-based system for data integration and sharing
abstract: Recent database applications see the emerging need to support data integration in distributed, peer-to-peer environments, in which autonomous peers (sources) connected by a network are willing to exchange data and services with each other. To address related research challenges, we are developing a system called "RACCOON", which allows different sources to integrate and share their data. We use an application to show several important features of the RACCOON system. The system also suggests semantic mappings for the user to choose. We show the two different querying modes, particularly how a query is expanded using the semantic mappings in the extended querying mode to compute as many answers to the query as possible.

title: Probabilistic models for discovering e-communities
abstract: The increasing amount of communication between individuals in e-formats (e.g. email, Instant messaging and the Web) has motivated computational research in social network analysis (SNA). Previous work in SNA has emphasized the social network (SN) topology measured by communication frequencies while ignoring the semantic information in SNs. In this paper, we propose two generative Bayesian models for semantic community discovery in SNs, combining probabilistic modeling with community detection in SNs. To simulate the generative models, an EnF-Gibbs sampling algorithm is proposed to address the efficiency and performance problems of traditional methods. Experimental studies on Enron email corpus show that our approach successfully detects the communities of individuals and in addition provides semantic topic descriptions of these communities.