EOS: expertise oriented search using social networks
In this paper, we present the design and implementation of our expertise oriented search system, EOS http://www.arnetminer.net. EOS is a researcher social network system. It has gathered information about a half-million computer science researchers from the Web and constructed a social network among the researchers through their co-authorship. In particular, the relationship in the social network information is used in both ranking experts for a given topic and searching for associations between researchers. Our experimental results demonstrate that the proposed methods for expert finding and association search in a social network are both more effective and efficient than the baseline 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: 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: 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: Application of Immune Classifier Based on Increment of Diversity in the Model Species Genomes Identification
abstract: The model species genomes project has played a very important role in the research of human genomes. By comparing and identifying the genomes' information in the different biological evolution stages with the model species genomes, it is favorable to understand deeply the genomes' structure and function of the advanced species, especially the human being, and to reveal the life's essential law. In the paper, the DNA sequences of three model species including C. elegans, S. cerevisiae and A.thaliana are divided into three types: intron, exon, intergenic DNA at first. The bases of each sequence are given number (1, 2, hellip, N) base by base from the beginning. According to three phases of the codons, we can extract three subsequences which numbers are respectively 3n+1, 3n+2 and 3n+3 (n=0, 1, 2, ...,N/3-1). Calculating respectively the probability of four bases in three subsequence we can attain 12 parameters which are regarded as the state parameters of the diversity sources. Each sequence of intron, exon and intergenic DNA is expressed by a 12-dimension eigenvector. All of these sequences' 12-dimension samples are divided into the training sample set and the testing sample set. Then, according to the immune network theory, a immune classifier based on the diversity increment is constructed, which considers the reciprocal of the diversity increment as affinity function and makes the immune network evolve in the direction of identifying the antigens by submitting unceasingly the antigens one by one, which is a record of the training sample set. Finally, the classifier has high performance and its prediction accuracy is up to 85% by test.

title: Anomaly detection in high-dimensional network data streams: A case study
abstract: In this paper, we study the problem of anomaly detection in high-dimensional network streams. We have developed a new technique, called Stream Projected Outlier deTector (SPOT), to deal with the problem of anomaly detection from high-dimensional data streams. We conduct a case study of SPOT in this paper by deploying it on 1999 KDD Intrusion Detection application. Innovative approaches for training data generation, anomaly classification and false positive reduction are proposed in this paper as well. Experimental results demonstrate that SPOT is effective in detecting anomalies from network data streams and outperforms existing anomaly detection methods.

title: A Task-Based Approach to User Interface Design for a Web-Based Hydrologic Information Systems
abstract: Hydroinformatics is a new and rapidly developing field that integrates knowledge and understanding of water resources with the latest developments in information technology to improve decision-making in many critical applications. It encompasses methods for data capture, storage, processing, analysis and visualization, and the use of advanced modeling, simulation, optimization and knowledge-based tools and systems infrastructure. Three types of hydrological data are most commonly used: flow rate in major rivers and streams, height of water in wells, and precipitation. To get a complete view of the state of water at a given point in space and time, one must analyze many different types of hydrological data together to derive information using an online GIS tool. To help use these disparate data sources more effectively and efficiently, we have built an online interface called the IJEDI WebCenter for Hydroinformatics using a task-based approach. In this design, we first identify the tasks that users perform to study water-related issues, then organize data for each task, and build task-specific tools to present and analyze data and information. In a study involving both novices and experts in hydrology, we found that the both groups performed water-related studies more effectively and efficiently than they would have without the WebCenter.

title: A Novel Approach of Face Detection based on Skin Color Segmentation and PCA
abstract: Nowadays, face detection and recognition have gained importance in security and information access. In this paper, an efficient method of face detection based on skin color segmentation and principal components analysis(PCA) is proposed. Firstly, segmenting image using color model to filter candidate faces roughly; And then Eye-analogue segments at a given scale are discovered by finding regions which are darker than their neighborhoods to filter candidate faces farther; at the end, PCA method is used to extract the relevant information in human faces.

title: Levels of Independence in Aspect-Oriented Modeling
abstract: We are investigating the application of aspect-oriented principles as an aid toward improving the capabilities of domain-specific modeling. The approach, in general, provides transformations by weaving modeling aspects into a base model. The modeling aspects provide variation points within the model and can be used to drive the synthesis of the model into different artifacts. In this brief position paper, we describe how our current and future work improves the capabilities offered in a model-based tool. We highlight several levels of independence that make the approach applicable to numerous modeling situations.