A Topic Modeling Approach and Its Integration into the Random Walk Framework for Academic Search
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 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: 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 unified framework for name disambiguation
abstract: 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: 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: 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: Weaving Deployment Aspects into Domain-specific Models
abstract: Domain-specific models increase the level of abstraction used to develop large-scale component-based systems. Model-driven development (MDD) approaches (e.g., Model-Integrated Computing and Model-Driven Architecture) emphasize the use of models at all stages of system development. Decomposing problems using MDD approaches may result in a separation of the artifacts in a way that impedes comprehension. For example, a single concern (such as deployment of a distributed system) may crosscut different orthogonal activities (such as component specification, interaction, packaging and planning). To keep track of all entities associated with a component, and to ensure that the constraints for the system as a whole are not violated, a purely model-driven approach imposes extra effort, thereby negating some of the benefits of MDD. This paper provides three contributions to the study of applying aspect-oriented techniques to address the crosscutting challenges of model-driven component-based distributed systems development. First, we identify the sources of crosscutting concerns that typically arise in model-driven development of component-based systems. Second, we describe how aspect-oriented model weaving helps modularize these crosscutting concerns using model transformations. Third, we describe how we have applied model weaving using a tool called the Constraint-Specification Aspect Weaver (C-SAW) in the context of the Platform-Independent Component Modeling Language (PICML), which is a domain-specific modeling language for developing component-based systems. A case study of a joint-emergency response system is presented to express the challenges in modeling a typical distributed system. Our experience shows that model weaving is an effective and scalable technique for dealing with crosscutting aspects of component-based systems development.

title: A Web Service Adapter with Contract-Oriented Methodology
abstract: Loose coupling is a cornerstone for Service-Oriented Architecture (SOA). Service contracts enable loose coupling, because they conceal internal details of services from the outside world behind the facade. However, current works on service oriented analysis and design (SOAD) largely focus on defining processes for developing business processes and services without considering variability in details. In this paper, a Web Service adapter of service-contract oriented is presented in order to enhance the applicability and reusability of such services. We also introduce some critical issues about service contract analysis engine, skeleton code generate engine and web-based WSDL editor in the Web Service adapter. Additionally, the Web Service adapter designed in this paper is compared with related tools, and the results indicate that our methods demonstrate a more desirable interactivity and stability.

title: A Hand-Eye Robotic Model for Total Knee Replacement Surgery
abstract: This paper presents a hand-eye robotic model for total knee replacement (TKR) surgery. Unlike existent robot assisted TKR surgery, the proposed model is a surgical robot that combines with a movable hand-eye navigation system, which would use the full potential of both computer-assisted systems. Without using CT images and landmark pins in the patient's bones, it can directly measure the mechanical axis with high precision. This system provides a new approach of the minimally invasive surgery. Experiment results show that the proposed model is promising in the future application.

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: Performance study of Markov modulated fluid flow models with priority traffic
abstract: The steady-state performance of generic high-speed queuing system with priority traffic is studied, using the Markov modulated fluid models. the focus is on systems with traffic partitioned into two priorities according to a splitting factor alpha , so that low priority traffic can be discarded when congestion occurs. The results are used to further study issues of congestion control with priority traffic. In particular, the expected values, waiting times, variances of the buffer contents, and tail distributions are evaluated. It is found that the waiting time is more sensitive to changes of alpha than the buffer contents. This shows that for time-constrained traffic, the priority assignment is important for properly balancing the tradeoff between packet loss and delays. This model can be considered as a direct extension of the fluid-flow model to include priorities.<<ETX>>