Expert Finding in a Social Network
This paper addresses the issue of expert finding in a social network. The task of expert finding, as one of the most important research issues in social networks, is aimed at identifying persons with relevant expertise or experience for a given topic. In this paper, we propose a propagation-based approach that takes into consideration of both person local information and network information (e.g. relationships between persons). Experimental results show that our approach can outperform the baseline approach.

title: MicroRNA identification based on sequence and structure alignment
abstract: MicroRNAs (miRNA) are approximately 22 nt long non-coding RNAs that are derived from larger hairpin RNA precursors and play important regulatory roles in both animals and plants. The short length of the miRNA sequences and relatively low conservation of pre-miRNA sequences restrict the conventional sequence-alignment-based methods to finding only relatively close homologs. On the other hand, it has been reported that miRNA genes are more conserved in the secondary structure rather than in primary sequences. Therefore, secondary structural features should be more fully exploited in the homologue search for new miRNA genes.



In this paper, we present a novel genome-wide computational approach to detect miRNAs in animals based on both sequence and structure alignment. Experiments show this approach has higher sensitivity and comparable specificity than other reported homologue searching methods. We applied this method on Anopheles gambiae and detected 59 new miRNA genes.



This program is available at http://bioinfo.au.tsinghua.edu.cn/miralign.



Supplementary information is available at http://bioinfo.au.tsinghua.edu.cn/miralign/supplementary.htm.

title: ArnetMiner: An Expertise Oriented Search System for Web Community
abstract: Expertise Oriented Search aims at providing comprehensive analysis and mining for people from distributed sources. In this paper, we give an overview of the expertise oriented search system (ArnetMiner). The system addresses several key research issues in extraction and mining of a researcher social network. The system is in operation on the internet for more than one year and receives accesses from about 1,500 users per month. Feedbacks from users and system logs indicate that users consider the system can really help people to find and share information in the web community.

title: Computing Exact p-Value for Structured Motif
abstract: Extracting motifs from a set of DNA sequences is important in computational biology. Occurrence probability is a common used statistics to evaluate the statistical significance of a motif. A main problem is how to calculate the occurrence probability of the motif on the random model of DNA sequence efficiently and accurately. In this paper, we are interested in a particular motif model which is useful in transcription process. This motif, which is called structured motif, is composed two motif words on single nucleotide alphabet and with fixed spacers between them. We present an efficient algorithm to calculate the exact occurrence probability of a structured motif on a given sequence. It is the first nontrivial algorithm to calculate the exact p-value for such kind of motifs.

title: ArnetMiner: extraction and mining of academic social networks
abstract: This paper addresses several key issues in the ArnetMiner system, which aims at extracting and mining academic social networks. Specifically, the system focuses on: 1) Extracting researcher profiles automatically from the Web; 2) Integrating the publication data into the network from existing digital libraries; 3) Modeling the entire academic network; and 4) Providing search services for the academic network. So far, 448,470 researcher profiles have been extracted using a unified tagging approach. We integrate publications from online Web databases and propose a probabilistic framework to deal with the name ambiguity problem. Furthermore, we propose a unified modeling approach to simultaneously model topical aspects of papers, authors, and publication venues. Search services such as expertise search and people association search have been provided based on the modeling results. In this paper, we describe the architecture and main features of the system. We also present the empirical evaluation of the proposed methods.

title: htSNPer1.0: software for haplotype block partition and htSNPs selection
abstract: BackgroundThere is recently great interest in haplotype block structure and haplotype tagging SNPs (htSNPs) in the human genome for its implication on htSNPs-based association mapping strategy for complex disease. Different definitions have been used to characterize the haplotype block structure in the human genome, and several different performance criteria and algorithms have been suggested on htSNPs selection. heuristic algorithm, generalized branch-and-bound algorithm, is applied to the searching of minimal set of haplotype tagging SNPs (htSNPs) according to different htSNPs performance criteria. We develop a software htSNPer1.0 to implement the algorithm, and integrate three htSNPs performance criteria and four haplotype block definitions for haplotype block partitioning. It is a software with powerful Graphical User Interface (GUI), which can be used to characterize the haplotype block structure and select htSNPs in the candidate gene or interested genomic regions. It can find the global optimization with only a fraction of the computing time consumed by exhaustive searching algorithm.ConclusionhtSNPer1.0 allows molecular geneticists to perform haplotype block analysis and htSNPs selection using different definitions and performance criteria. The software is a powerful tool for those focusing on association mapping based on strategy of haplotype block and htSNPs.

title: Image Mining: Trends and Developments
abstract: Advances in image acquisition and storage technology have led to tremendous growth in very large and detailed image databases. These images, if analyzed, can reveal useful information to the human users. Image mining deals with the extraction of implicit knowledge, image data relationship, or other patterns not explicitly stored in the images. Image mining is more than just an extension of data mining to image domain. It is an interdisciplinary endeavor that draws upon expertise in computer vision, image processing, image retrieval, data mining, machine learning, database, and artificial intelligence. In this paper, we will examine the research issues in image mining, current developments in image mining, particularly, image mining frameworks, state-of-the-art techniques and systems. We will also identify some future research directions for image mining.

title: Federate Job Mapping Strategy in Grid-Based Virtual Wargame Collaborative Environment
abstract: A crucial issue for grid-based virtual wargame collaborative environment is that of mapping federate jobs to grid nodes efficiently. Because there exits large amount of interactions among federates, it is a challenging work to design an efficient federate mapping strategy. In this paper, we established an objective function for federate job mapping which takes into consideration not only the load of grid nodes, but also network utilization. Experimental results show that the proposed federate job mapping strategy can contribute to load balancing of the virtual wargame collaborative environment.

title: ROI Based Natural Image Retrieval Using Color and Texture Feature
abstract: Region of interest(ROI) plays an important role in image analysis. In this paper, an efficient approach for content based image retrieval combining both color and texture features using three ROIs is proposed. Firstly, segment image to three parts using K-means algorithm. Secondly, select three ROIs from the three parts and then extract color features and texture features of ROIs. The similarity of two images will be determined by the similarities between pairs of ROIs. The experimental results demonstrate that the proposed method is encouraging with a successful retrieval rate.

title: SOA Middleware Support for Service Process Reconfiguration with End-to-End QoS Constraints
abstract: In SOA, services may become volatile and fail to deliver the quality of service as requested by users. In this paper, we present an approach for repairing failed services by replacing them with new services and ensuring the new service process still meets the user specified end-to-end QoS constraints. An iterative structural inspection algorithm is designed to produce reconfiguration regions that include one or more failed service. By reconfiguring only services in the selected regions, the business process will not be affected significantly. The algorithm may also utilize those available QoS constraints to relax the original constraints of a reconfiguration region and to provide more effective reconfiguration solutions. We also present the middleware components to support the service reconfiguration in the LLAMA framework.

title: A Novel Composite Kernel Approach to Chinese Entity Relation Extraction
abstract: Relation extraction is the task of finding semantic relations between two entities from the text. In this paper, we propose a novel composite kernel for Chinese relation extraction. The composite kernel is defined as the combination of two independent kernels. One is the entity kernel built upon the non-content-related features. The other is the string semantic similarity kernel concerning the content information. Three combinations, namely linear combination, semi-polynomial combination and polynomial combination are investigated. When evaluated on the ACE 2005 Chinese data set, the results show that the proposed approach is effective.