Arnetminer: expertise oriented search using social networks
Expertise Oriented Search (EOS) aims at providing comprehensive expertise analysis on data from distributed sources. It is useful in many application domains, for example, finding experts on a given topic, detecting the confliction of interest between researchers, and assigning reviewers to proposals. In this paper, we present the design and implementation of our expertise oriented search system, Arnetminer (http://www.arnetminer.net). Arnetminer has gathered and integrated information about a half-million computer science researchers from the Web, including their profiles and publications. Moreover, Arnetminer constructs a social network among these researchers through their co-authorship, and utilizes this network information as well as the individual profiles to facilitate expertise oriented search tasks. In particular, the co-authorship information is used both in ranking the expertise of individual researchers for a given topic and in searching for associations between researchers. We have conducted initial experiments on Arnetminer. Our results demonstrate that the proposed relevancy propagation expert finding method outperforms the method that only uses person local information, and the proposed two-stage association search on a large-scale social network is order of magnitude faster than the baseline method.

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: 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: 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: 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: 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: The Design of a New Context-Aware Policy Model for Autonomic Networking
abstract: This paper describes a new version of the DEN-ng context model, and how this model in conjunction with the DEN-ng policy model can be used for more effective and flexible context management. Both are part of the FOCALE autonomic network architecture. Context selects policies, which select roles that can be used, which in turn define allowed functionality for that particular context.

title: Transforming Natural Arguments in Araucaria to Formal Arguments in LMA
abstract: Over the last few years, argumentation has been gaining increasing importance in multi-agent systems research. LMA is a Logic of multiple-valued argumentation built on top of EALP (extended annotated logic programming). Araucaria is a software tool for analyzing and diagramming arguments written in natural language. We integrate these two systems involved in argumentation to an easy to use and more user-friendly argumentation system, in which natural arguments can be transformed into formal arguments, in order to lighten users' knowledge burden forced by formal argumentation frameworks, and attain extensive usability of formal argumentation systems. We illustrate the transformation process by translating natural arguments in English to formal arguments in EALP step-by-step, and then how the status of those formal arguments can be determined in LMA, resulting in the status determination of original natural arguments.

title: A Novel Method for Detecting Outlying Subspaces in High-dimensional Databases Using Genetic Algorithm
abstract: Detecting outlying subspaces is a relatively new research problem in outlier-ness analysis for high-dimensional data. An outlying subspace for a given data point p is the sub- space in which p is an outlier. Outlying subspace detection can facilitate a better characterization process for the detected outliers. It can also enable outlier mining for high- dimensional data to be performed more accurately and efficiently. In this paper, we proposed a new method using genetic algorithm paradigm for searching outlying subspaces efficiently. We developed a technique for efficiently computing the lower and upper bounds of the distance between a given point and its kth nearest neighbor in each possible subspace. These bounds are used to speed up the fitness evaluation of the designed genetic algorithm for outlying subspace detection. We also proposed a random sampling technique to further reduce the computation of the genetic algorithm. The optimal number of sampling data is specified to ensure the accuracy of the result. We show that the proposed method is efficient and effective in handling outlying subspace detection problem by a set of experiments conducted on both synthetic and real-life datasets.

title: A Square Root Extended Set Membership Algorithm with Applications to Nonlinear System Estimation
abstract: In this paper, a square root extended set membership (SRESM) state estimation algorithm is proposed to further improve the numerical accuracy and stability of the nonlinear system estimation. In comparison with the existing extended set membership (ESM), the proposed square root ESM using the efficient and stable updating recursions provides much more accurate estimation results. It has improved numerical stability and real time applicability. Simulation results in estimation of mobile robot localization are given to show the effectiveness and robustness of the proposed algorithm.

title: A Novel Approach Using Edge Detection Information for Texture Based Image Retrieval
abstract: Most texture-based image retrieval system just consider an original image of coarseness, contrast and roughness, actually there are many texture information in the edge image. In this paper, a method combining both edge information and gray level co-occurrence matrix properties is proposed to improve the retrieval performance. The proposed method gives encouraging results when comparing its retrieval performance to that of the Yao's method, in the same image database.