Computing Exact p-Value for Structured Motif
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: A Discriminative Approach to Topic-Based Citation Recommendation
abstract: In this paper, we present a study of a novel problem, i.e. topic-based citation recommendation, which involves recommending papers to be referred to. Traditionally, this problem is usually treated as an engineering issue and dealt with using heuristics. This paper gives a formalization of topic-based citation recommendation and proposes a discriminative approach to this problem. Specifically, it proposes a two-layer Restricted Boltzmann Machine model, called RBM-CS, which can discover topic distributions of paper content and citation relationship simultaneously. Experimental results demonstrate that RBM-CS can significantly outperform baseline methods for citation recommendation.

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: Topic Distributions over Links on Web
abstract: It is well known that Web users create links with different intentions. However, a key question, which is not well studied, is how to categorize the links and how to quantify the strength of the influence of a web page on another if there is a link between the two linked web pages. In this paper, we focus on the problem of link semantics analysis, and propose a novel supervised learning approach to build a model, based on a training link-labeled and link-weighted graph where a link-label represents the category of a link and a link-weight represents the influence of one web page on the other in a link. Based on the model built, we categorize links and quantify the influence of web pages on the others in a large graph in the same application domain. We discuss our proposed approach, namely Pairwise Restricted Boltzmann Machines (PRBMs), and conduct extensive experimental studies to demonstrate the effectiveness of our approach using large real datasets.

title: A Topic Modeling Approach and Its Integration into the Random Walk Framework for Academic Search
abstract: In this paper, we propose a unified topic modeling approach and its integration into the random walk framework for academic search. Specifically, we present a topic model for simultaneously modeling papers, authors, and publication venues. We combine the proposed topic model into the random walk framework. Experimental results show that our proposed approach for academic search significantly outperforms the baseline methods of using BM25 and language model, and those of using the existing topic models (including pLSI, LDA, and the AT model).

title: A Framework for Efficient Association Rule Mining in XML Data
abstract: In this article, we propose a framework, called XAR-Miner, for mining ARs from XML documents efficiently. In XAR-Miner, raw data in the XML document first are preprocessed to transform either to an Indexed XML Tree (IX-tree) or to Multirelational Databases (Multi-DB), depending on the size of the XML document and the memory constraint of the system, for efficient data selection and AR mining. Concepts that are relevant to the AR mining task are generalized to produce generalized metapatterns. A suitable metric is devised for measuring the degree of concept generalization in order to prevent undergeneralization or overgeneralization. Resulting generalized metapatterns are used to generate large ARs that meet the support and confidence levels. A greedy algorithm is also presented in order to integrate data selection and large itemset generation to enhance the efficiency of the AR mining process. The experiments conducted show that XAR-Miner is more efficient in performing a large number of AR mining tasks from XML documents than the state-of-the-art method of repetitively scanning through XML documents in order to perform each of the mining tasks.

title: Spectral Unmixing Technique Based on Flexibly Selected Endmembers
abstract: In traditional spectral unmixing methods of hyperspectral imagery, all endmembers (EMs) take part in the process of each pixel unmixing, and each EM is invariable in the whole processing. This kind of ways discounts unmixing accuracy by introducing some EMs unrelated with mixed pixel to be analyzed, and by the inaccuracy representation of each class by a fixed EM. So the traditional way of spectral unmixing can not get satisfied result. In this case, the paper proposes spectral unmixng ways based on flexibly selected EMs to improve unmixing accuracy. In the first way, partly EMs corresponding to classes of interest are selected to be used in the whole process of spectral unmixing. In the second way, related EMs of a mixed pixel are concluded by utilizing spatial information, then spectral unmixing is done with only related classes considered. In the third way, each class EM is adjusted regionally in each locally divided area. And so, more accuracy EMs are used in spectral unmixing. Experimental results show that spectral unmixing based on flexibly selected EMs can get better performance.

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: Detection of potential positive regulatory motifs of transcription in yeast introns by comparative analysis of oligonucleotide frequencies
abstract: We conducted a comparative statistical analysis of tetra- through hexanucleotide frequencies in two sets of introns of yeast genes. The first set consisted of introns of genes that have transcription rates higher than 30 mRNAs/h while the second set contained introns of genes whose transcription rates were lower than or equal to 10 mRNAs/h. Some oligonucleotides whose occurrence frequencies in the first set of introns are significantly higher than those in the second set of introns were detected. The frequencies of occurrence of most of these detected oligonucleotides are also significantly higher than those in the exons flanking the introns of the first set. Interestingly some of these detected oligonucleotides are the same as well known "signature" sequences of transcriptional regulatory elements. This could imply the existence of potential positive regulatory motifs of transcription in yeast introns.

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.