A unified framework for name disambiguation
Name ambiguity problem has been a challenging issue for a long history. In this paper, we intend to make a thorough investigation of the whole problem. Specifically, we formalize the name disambiguation problem in a unified framework. The framework can incorporate both attribute and relationship into a probabilistic model. We explore a dynamic approach for automatically estimating the person number K and employ an adaptive distance measure to estimate the distance between objects. Experimental results show that our proposed framework can significantly outperform the baseline method.

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: 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: 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: Factor analysis based anomaly detection
abstract: We propose a novel anomaly detection algorithm based on factor analysis and Mahalanobis distance. Factor analysis is used to uncover the latent structure (dimensions) of a set of variables. It reduces attribute space from a larger number of variables to a smaller number of factors. The Mahalanobis distance is used to determine the "similarity" of a set of values from an "unknown" sample to a set of values measured from a collection of "known" samples. Combined with factor analysis, Mahalanobis distance is extended to examine whether a given vector is an outlier from a model identified by "factors" based on factor analysis. We present a factor analysis-based network anomaly detection algorithm and apply it to DARPA intrusion detection evaluation data. The experimental results show that the proposed algorithm is able to detect network intrusions with relatively low false alarms.

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: A Multimedia System for Route Sharing and Video-Based Navigation
abstract: Trip planning and in-vehicle navigation are crucial tasks for easier and safer driving. The existing navigation systems are based on machine intelligence without allowing human knowledge incorporation. These systems give turn guidance with abstract visual instruction and have not reached the potential of minimizing driver's cognitive load, which is the amount of mental processing power required. In this paper, we describe the development of a multimedia system that makes driving and navigation safer and easier by offering tools for route sharing in trip planning and video-based route guidance during driving. The system provides a multimodal interface for a user to share his/her route with others by drawing on a digital map, naturally incorporating human knowledge into the trip planning process. The system gives driving instructions by overlaying navigational arrows onto live video and providing synthesized voice to reduce the driver's cognitive load, in addition to presenting landmark images for key maneuvers. We describe our observations which had motivated the development of the system, detailed architecture and user interfaces, and finally discusses our initial test findings in the real-road driving context

title: Automatic detection and recognition of signs from natural scenes
abstract: In this paper, we present an approach to automatic detection and recognition of signs from natural scenes, and its application to a sign translation task. The proposed approach embeds multiresolution and multiscale edge detection, adaptive searching, color analysis, and affine rectification in a hierarchical framework for sign detection, with different emphases at each phase to handle the text in different sizes, orientations, color distributions and backgrounds. We use affine rectification to recover deformation of the text regions caused by an inappropriate camera view angle. The procedure can significantly improve text detection rate and optical character recognition (OCR) accuracy. Instead of using binary information for OCR, we extract features from an intensity image directly. We propose a local intensity normalization method to effectively handle lighting variations, followed by a Gabor transform to obtain local features, and finally a linear discriminant analysis (LDA) method for feature selection. We have applied the approach in developing a Chinese sign translation system, which can automatically detect and recognize Chinese signs as input from a camera, and translate the recognized text into English.

title: A component-oriented software toolkit for patient-specific finite element model generation
abstract: A component-oriented software system, i.BioMech (image-based biomechanical modeling) is proposed for generation of patient-specific finite element model. It applies a systematic software engineering approach to patient/subject-specific meshing and assignment of material properties. The prototype program is based on the component object model (COM), which enables ease of combination of existing mesh generation algorithms and material property assignment schemes, and incorporation of new ones. It also facilitates utilization by other programming languages or platforms. Data input comprises a series of medical images captured from the patient. The output is a patient-specific finite element model for computational analysis using commercially available finite element software. The prototype software system provides a framework to compare the different finite element mesh generation methods as well as schemes for material property assignment. Our focus is on patient/subject-specific modeling of the human vertebrae.