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A Re-Parametrization-Based Bayesian Differential Analysis Algorithm for Gene Regulatory Networks Modeled with Structural Equation Models

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Computer Modeling in engineering & Sciences 2020年第7期124卷 303-313页

作者： Yan Li Dayou Liu Yungang Zhu Jie Liu College of Computer Science and Technology Jilin UniversityChangchun130012China Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education Jilin UniversityChangchun130012China

Under different conditions,gene regulatory networks(GRNs)of the same gene set could be similar but *** differential analysis of GRNs under different conditions is important for understanding condition-specific gene regulatory *** a naive approach,existing GRN inference algorithms can be used to separately estimate two GRNs under different conditions and identify the differences between ***,in this way,the similarities between the pairwise GRNs are not taken into *** joint differential analysis algorithms have been proposed recently,which were proved to outperform the naive approach *** this paper,we model the GRNs under different conditions with structural equation models(SEMs)to integrate gene expression data and genetic perturbations,and re-parameterize the pairwise SEMs to form an integrated model that incorporates the differential ***,a Bayesian inference method is used to make joint differential analysis by solving the integrated *** evaluated the performance of the proposed re-parametrization-based Bayesian differential analysis(ReBDA)algorithm by running simulations on synthetic data with different *** performance of the ReBDA algorithm was demonstrated better than another state-of-the-art joint differential analysis algorithm for SEMs ReDNet *** the end,the ReBDA algorithm was applied to make differential analysis on a real human lung gene data set to illustrate its applicability and practicability.

关键词： Gene regulatory networks structural equation models joint

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Mapping integrity constraint ontology to relational databases

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The Journal of China Universities of Posts and Telecommunications 2010年第6期17卷 113-121页

作者： OUYANG Dan-tong College of Computer Science and Technology Jilin University Changchun 130012 China Key Laboratory of Symbol Computation and Knowledge Engineering Ministry of Education Jilin University Changchun 130012 China

Integrity constraint is a formula that checks whether all necessary information has been explicitly provided. It can be added into ontology to guarantee the data-centric application. In this paper,a set of constraint axioms called IC-mapping axioms are stated. Based on these axioms,a special ontology with integrity constraint,which is adapted to map ontology knowledge to data in relational databases,is defined. It＇s generated through our checking and modification. Making use of the traditional mapping approaches,it can be mapped to relational databases as a normal ontology. Unlike what in the past,a novel mapping approach named IC-based mapping is proposed in accordance with such special ontology. The detailed algorithm is put forward and compared with other existing approaches used in Semantic Web applications. The result shows that our method is advanced to the traditional approaches.

关键词： Semantic Web integrity constraint ontology relational database

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Integrity constraints in OWL ontologies based on grounded circumscription

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Frontiers of Computer Science 2013年第6期7卷 812-821页

作者： Dantong OUYANG College of Computer Science and Technology Jilin University Changchun 130012 China Key Laboratory of Symbolic Computation and Knowledge Engineering Ministry of Education Changchun 130012 China National Engineering Research Center of Geophysics Exploration Instruments Changchun 130026 China

The extensions for logic-based knowledge bases with integrity constraints are rather popular. We put forward an alternative criteria for analysis of integrity constraints in Web ontology language （OWL） ontology under the closed world assumption. According to this criteria, grounded circumscription is applied to define integrity constraints in OWL ontology and the satisfaction of the integrity constraints by minimizing extensions of the predicates in integrity con- straints. According to the semantics of integrity constraints, we provide a modified tableau algorithm which is sound and complete for deciding the consistency of an extended ontol- ogy. Finally, the integrity constraint validation is converted into the corresponding consistency of the extended ontology. Comparing our approach with existing integrity constraint validation approaches, we show that the results of our approach are more in accordance with user requirements than other approaches in certain cases.

关键词： semantic Web description logic ontology integrity constraints grounded circumscription

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SeCCX: Semantics-based fine granular concurrency control for XML data

SeCCX: Semantics-based fine granular concurrency control for...

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1st International Workshop on Graph database, IWGD 2010, 1st International Workshop on Advanced Techniques on XML data Management, XMLDM 2010, 2nd International Workshop on WCMT 2010, Held in Conj. with WAIM 2010

作者： Rong, Chuitian Lu, Wei Zhang, Xiao Liu, Zhen Du, Xiaoyong Key Labs. of Data Engineering and Knowledge Engineering Ministry of Education China School of Information Renmin University of China China

ISBN: (纸本)3642167195

This paper proposes a new locking protocol, SeCCX, for isolation of concurrent transactions on XML data. This protocol adopts the semantics of operations issued by users. Comparing with previous XML locking protocols, SeCCX has some new features, like richer lock modes, finer granular, lower lock confliction and dynamic lock escalation. The importance is that it locks the objects according to the semantics of user's operation and sets different restrictions on different objects. It provides finer granular concurrency control such that the overall system performance can be improved. We prove that the SeCCX protocol is conflict serializability. We also compare it with other protocols to demonstrate the advantages of SeCCX. © 2010 Springer-Verlag.

关键词： Locks (fasteners)

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Distance-based feature selection from probabilistic data

Distance-based feature selection from probabilistic data

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14th International Conference on Web-Age Information Management, WAIM 2013

作者： Zhao, Tingting Pei, Bin Zhao, Suyun Chen, Hong Li, Cuiping Key Lab of Data Engineering and Knowledge Engineering Ministry of Education China Department of Computer Science Renmin University of China China

ISBN: (纸本)9783642385612

Feature selection is a powerful tool of dimension reduction from datasets. In the last decade, more and more researchers have paid attentions on feature selection. Further, some researchers begin to focus on feature selection from probabilistic datasets. However, in the existing method of feature selection from probabilistic data, the distance hidden in probabilistic data is neglected. In this paper, we design a new distance measure to select informative feature from probabilistic databases, in which both the distance and randomness in the data are considered. And then, we propose a feature selection algorithm based on the new distance and develop two accelerative algorithms to boost the computation. Furthermore, we introduce a parameter into the distance to reduce the sensitivity to noise. Finally, the experimental results verify the effectiveness of our algorithms. © 2013 Springer-Verlag Berlin Heidelberg.

关键词： Random processes

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Image Fusion Method Based on NSCT and Adaptive Sparse Representation 4

Image Fusion Method Based on NSCT and Adaptive Sparse Repres...

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4th International Conference on Video and Image Processing, ICVIP 2020

作者： Dong, Zhangyu Wei, Xin Wang, Mengyang School of Computer and Information Hefei University of Technology Key Laboratory of Knowledge Engineering with Big Data Ministry of Education Hefei230009 China

ISBN: (纸本)9781450389075

ABSTRACT: Aiming at the imaging characteristics of multispectral and panchromatic image and the problem that the traditional image fusion methods cannot take into account the spectral quality and spatial resolution of the image at the same time, a novel fusion method based on the Non-subsampled Contourlet Transform (NSCT) domain and adaptive sparse representation (ASR) algorithm is presented in this paper. It combines the advantages of principal component substitution and multi-scale analysis, and uses the ASR model to encode the low-frequency components, which improves the shortcomings of the traditional SR-based approach applications. Firstly, NSCT transform is performed on thefirst principal component of multi-spectral image obtained by PCA transform and panchromatic image,and the low-pass and high-pass coefficients of the source image are obtained. Secondly, the Max-absolute' rule and the ASR model are used to fuse the separated high-pass and low-pass bands respectively. Finally, we obtained the final fused image by the corresponding inverse transformation reconstruction. The results show that the fusion algorithm proposed in this paper performs well in both spatial resolution and spectral performance;it not only improves the subjective visual effect, but also improves the objective evaluation index. © 2020 ACM.

关键词： Image fusion

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Research on Trust Prediction from a Sociological Perspective

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Journal of Computer Science & Technology 2015年第4期30卷 843-858页

作者：王英王鑫左万利 College of Computer Science and Technology Jilin University Changchun 130012 China Key Laboratory of Symbolic Computation and Knowledge Engineering Ministry of Education Changchun 130012 China School of Computer Technology and Engineering Changehun Institute of Technology Changchun 130012 China

Trust, as a major part of human interactions, plays an important role in helping users collect reliable infor-mation and make decisions. However, in reality, user-specified trust relations are often very sparse and follow a power law distribution; hence inferring unknown trust relations attracts increasing attention in recent years. Social theories are frameworks of empirical evidence used to study and interpret social phenomena from a sociological perspective, while social networks reflect the correlations of users in real world; hence, making the principle, rules, ideas and methods of social theories into the analysis of social networks brings new opportunities for trust prediction. In this paper, we investigate how to exploit homophily and social status in trust prediction by modeling social theories. We first give several methods to compute homophily coe？cient and status coe？cient, then provide a principled way to model trust prediction mathe-matically, and propose a novel framework, hsTrust, which incorporates homophily theory and status theory. Experimental results on real-world datasets demonstrate the effectiveness of the proposed framework. Further experiments are conducted to understand the importance of homophily theory and status theory in trust prediction.

关键词： trust prediction homophily coefficient status coefficient social theory matrix factorization

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Combining N-gram retrieval with weights propagation on massive RDF graphs

Combining N-gram retrieval with weights propagation on massi...

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2012 9th International Conference on Fuzzy Systems and knowledge Discovery, FSKD 2012

作者： Hu, He Du, Xiaoyong Key Labs of Data Engineering and Knowledge Engineering Ministry of Education China School of Information Renmin University of China Beijing China

ISBN: (纸本)9781467300223

N-gram approach takes the position information into account additionally and thus can offer higher accuracy in query answering than keyword based approaches and is widely used in IR and NLP. However, in large-scale RDF graphs, URIs instead of documents are the ranking and querying units;URIs are usually much shorter than documents, and different URIs are interlinked into a massive network. One shot n-gram querying is usually not good for the RDF data in many cases. In this paper, we present a hybrid framework which combines the n-gram retrieval with link analysis based weight propagation. The idea is to exploit the link structures in the RDF data graphs and propagate the one shot n-gram score weights along with these links. Large scale experiments using MapReduce on Billion Triples Challenge dataset show the hybrid framework achieves an 80.3% improvement in relevance scores over mere n-gram retrieval. © 2012 IEEE.

关键词： MapReduce

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MFSV: A truthfulness determination approach for fact statements

MFSV: A truthfulness determination approach for fact stateme...

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18th International Conference on database Systems for Advanced Applications, DASFAA 2013

作者： Wang, Teng Zhu, Qing Wang, Shan Key Laboratory of the Ministry of Education for Data Engineering and Knowledge Engineering Renmin University of China Beijing China School of Information Renmin University of China Beijing China

ISBN: (纸本)9783642374494

How to determine the truthfulness of a piece of information becomes an increasingly urgent need for users. In this paper, we propose a method called MFSV, to determine the truthfulness of fact statements. We first calculate the similarity between a piece of related information and the target fact statement and capture the credibility ranking of the related information through combining importance ranking and popularity ranking. Based on these, contributions of a piece of related information to the truthfulness determination is derived. Then we propose two methods to determine the truthfulness of the target fact statement. At last, we run comprehensive experiments to show MFSV's availability and high accuracy. © Springer-Verlag 2013.

关键词： Computers

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Extracting domain-relevant term using wikipedia based on random walk model

Extracting domain-relevant term using wikipedia based on ran...

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7th ChinaGrid Annual Conference, ChinaGrid 2012

作者： Wu, Wenjuan Liu, Tao Hu, He Du, Xiaoyong Key Labs of Data Engineering and Knowledge Engineering Ministry of Education China School of Information Renmin University of China Beijing China

ISBN: (纸本)9780769548166

In this paper we present a new approach for the automatic identification of domain-relevant concepts and entities of a given domain using the category and page structures of the Wikipedia in a language independent way. By applying Markov random walk algorithm on the weighted Wikipedia link graph, our approach can identify large quantities of domain-relevant concepts and entities with very little human effort. Experimental results show that our method achieves high accuracy and acceptable efficiency in domainrelevant term extraction. © 2012 IEEE.

关键词： Markov processes

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