Name Disambiguation Using Atomic Clusters
Name ambiguity is a critical problem in many applications, in particular in the online bibliography systems, such as DBLP and CiteSeer. Previously, several clustering based methods have been proposed although, the problem still presents to be a big challenge for both research and industry communities. In this paper, we present a complementary study to the problem from another point of view. We propose an approach of finding atomic clusters to improve the performance of existing clustering-based methods. We conducted experiments on a dataset from a real-world system: Arnetminer.org. Experiments results show that significant improvements can be obtained by using the proposed atomic clusters finding approach (about +8% and +27% improvements depending on different clustering methods).

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: 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: 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: Availability-Aware Provisioning Strategies for Differentiated Protection Services in Wavelength-Convertible WDM Mesh Networks
abstract: In an optical WDM mesh network, different protection schemes (such as dedicated or shared protection) can be used to improve the service availability against network failures. However, in order to satisfy a connections service-availability requirement in a cost-effective and resource-efficient manner, we need a systematic mechanism to select a proper protection scheme for each connection request while provisioning the connection. In this paper, we propose to use connection availability as a metric to provide differentiated protection services in a wavelength-convertible WDM mesh network. We develop a mathematical model to analyze the availabilities of connections with different protection modes (i.e., unprotected, dedicated protected, or shared protected). In the shared-protection case, we investigate how a connection's availability is affected by backup resource sharing. The sharing might cause backup resource contention between several connections when multiple simultaneous (or overlapping) failures occur in the network. Using a continuous-time Markov model, we derive the conditional probability for a connection to acquire backup resources in the presence of backup resource contention. Through this model, we show how the availability of a shared-protected connection can be quantitatively computed. Based on the analytical model, we develop provisioning strategies for a given set of connection demands in which an appropriate, possibly different, level of protection is provided to each connection according to its predefined availability requirement, e.g., 0.999, 0.997. We propose integer linear programming (ILP) and heuristic approaches to provision the connections cost effectively while satisfying the connections' availability requirements. The effectiveness of our provisioning approaches is demonstrated through numerical examples. The proposed provisioning strategies inherently facilitate the service differentiation in optical WDM mesh networks.

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.

title: Extraction of Text Objects in Video Documents: Recent Progress
abstract: Text extraction in video documents, as an important research field of content-based information indexing and retrieval, has been developing rapidly since 1990s. This has led to much progress in text extraction, performance evaluation, and related applications. By reviewing the approaches proposed during the past five years, this paper introduces the progress made in this area and discusses promising directions for future research.

title: Simplifying the Reconstruction of 3D Models using Parameter Elimination
abstract: Reconstructing large models from images is a significant challenge for computer vision, computer graphics, and related fields. In this paper, we present an approach for simplifying the reconstruction process by mathematically eliminating external camera parameters. This results in less parameters to estimate and in an overall significantly more robust and accurate reconstruction. We reformulate the problem in such a manner as to be able to identify invariants, eliminate superfluous parameters, and measure the performance of our formulation under various conditions. We compare a two-step camera orientation-free method, where the majority of the points are reconstructed using a linear equation set, and a camera position-and- orientation free method, using a degree-two equation set. Both approaches use a full perspective camera and are applied to synthetic and real-world datasets.

title: Spectral Decomposition Approach for Transient Analysis of Multi-Server Discrete-Time Queues
abstract: Discrete time queueing systems are extensively used in modeling the ATM environment at the cell level. This paper examines the transient behavior of a discrete time FCFS multiple server queue. For the arrival process we assume a general discrete time Markovian batch arrival process, where the batch size distribution of the arrivals in successive slots is governed by a finite state discrete time Markov chain. We show that once the spectral decomposition of the “probability generating matrix” of the arrival process is obtained, the complete solution in the transform domain may be given. Using the complex analysis technique and Cauchy's integral formula, we present an efficient numerical method for the numerical calculation of a few performance measures of interest, namely transient probability of queue being empty, and the mean of the queue length distribution. We also generalize our numerical method in the situations where the superposition of a number of independent arrival sources are fed to the queue. It is shown that the numerical complexity of obtaining the transient solution in this case can be substantially reduced by using the approach based on the Kronecker product. The finite buffer case is also analyzed.