Topic-Level Random Walk through Probabilistic Model
In this paper, we study the problem of topic-level random walk, which concerns the random walk at the topic level. Previously, several related works such as topic sensitive page rank have been conducted. However, topics in these methods were predefined, which makes the methods inapplicable to different domains. In this paper, we propose a four-step approach for topic-level random walk. We employ a probabilistic topic model to automatically extract topics from documents. Then we perform the random walk at the topic level. We also propose an approach to model topics of the query and then combine the random walk ranking score with the relevance score based on the modeling results. Experimental results on a real-world data set show that our proposed approach can significantly outperform the baseline methods of using language model and that of using traditional PageRank.

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: 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: 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: 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: Extraction and mining of an academic social network
abstract: This paper addresses several key issues in extraction and mining of an academic social network: 1) extraction of a researcher social network from the existing Web; 2) integration of the publications from existing digital libraries; 3) expertise search on a given topic; and 4) association search between researchers. We developed a social network system, called ArnetMiner, based on proposed methods to the above problems. In total, 448,470 researcher profiles and 981,599 publications were extracted/integrated after the system having been in operation for two years. The paper describes the architecture and main features of the system. It also briefly presents the experimental results of the proposed methods.

title: A dynamic scalable service model for SIP-based video conference
abstract: As an extensible signaling protocol, SIP (session initiation protocol) can be applied in developing video conference system. Traditionally, for SIP-based centralized video conference system, conferencing scale is limited by both the capability of conference server and the availability of bandwidth. The paper focuses on how to keep conferencing when the number of conference users increases. Based on the study of the SIP protocol, we analyze the drawback of the existing video conference model, and propose a dynamic scalable service model for SIP-based video conference. By this model, the extra service requests can be transferred and served in the cooperated conference servers. The paper presents the conferencing control policy of the model in detail. We developed a prototype of video conference system based on the above model. Experimental results show this service model works well.

title: A Pixel-level Statistical Structural Descriptor for Shape Measure and Recognition
abstract: A novel shape descriptor based on the histogram matrix of pixel-level structural features is presented. First, length ratios and angles between the centroid and contour points of a shape are calculated as two structural attributes. Then, the attributes are combined to construct a new histogram matrix in the feature space statistically. The proposed shape descriptor can measure circularity, smoothness, and symmetry of shapes, and be used to recognize shapes. Experimental results demonstrate the effectiveness of our method.

title: A new edge-based text verification approach for video
abstract: In this paper, we propose a new edge-based text verification approach for video. Based on the investigation of the relation between candidate blocks and their neighbor areas, the proposed approach first detects background edges in candidate blocks, then erases them by an edge tracking technique, and finally the candidate blocks containing too few remaining edges are eliminated as false alarms. Three measures for text detection evaluation in video were used to assess the performance of the proposed text verification approach. Experimental results on 50 broadcast news video clips demonstrate the validity of our approach.

title: Information Strategies to Support Full Information Product Pricing: the Role of Trust
abstract: In this paper, we report the importance of trust in the development and operation of distribution networks that attach non-price information to products to mitigate market dynamics introduced by information asymmetries. Often this non-price information is transmitted from producers to consumers through trusting networks or under certifiable labels such as Organic or Fair Trade. We are calling such networks Full Information Product Pricing (FIPP) Networks. This study is part of a larger project aimed at understanding the characteristics of FIPP networks. This initial exploration on four cases in Canada and Latin America indicated that trust, in the forms of institutional trust, calculative trust, and relational trust, plays key roles in FIPP operations and expansion. It is critical for building collaboration, coordinating network activities, and mitigating the risks associated with information asymmetry.

title: High Dependability Design Framework in Real-Time Embedded Control Software
abstract: This paper introduces an abstract high dependability framework for the implementation of embedded control software with hard real-time constraints. The framework specifies time-triggered sensor readings, atomic component invocations, actuator updates, and pattern switches independent of any implementation platform. In order to leverage model continuity, XML-based description of composite component informal description is required, which supports reuse of components and model information interoperability. By separating the platform-independent from the platform-dependent concerns, Consider a quality process control system in steel industry on a distributed real-time embedded environment, we implement a simplified high dependability design framework to prove the feasibility in the validation and synthesis of embedded control component execution.