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Reconstruction of Gene Regulatory Networks Based on Two-Stage Bayesian Network Structure Learning Algorithm

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Journal of Bionic Engineering 2009年第1期6卷 86-92页

作者： Gui-xia Liu, Wei Feng, Han Wang, Lei Liu, Chun-guang Zhoucollege of computer science and {3., jilin university, changchun 130012,P.R. china [a]college of computer science and {3. Jilin University Changchun 130012 P. R. China

In the post-genomic biology era,the reconstruction of gene regulatory networks from microarray gene expression data is very important to understand the underlying biological system,and it has been a challenging task in *** Bayesian network model has been used in reconstructing the gene regulatory network for its advantages,but how to determine the network structure and parameters is still important to be *** paper proposes a two-stage structure learning algorithm which integrates immune evolution algorithm to build a Bayesian *** new algorithm is evaluated with the use of both simulated and yeast cell cycle *** experimental results indicate that the proposed algorithm can find many of the known real regulatory relationships from literature and predict the others unknown with high validity and accuracy.

关键词： gene regulatory networks two-stage learning algorithm Bayesian network immune evolutionary algorithm

Deriving all minimal consistency-based diagnosis sets using SAT solvers

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Progress in Natural science:Materials International 2009年第4期19卷 489-494页

作者： Xiangfu Zhao a,b, Liming Zhang a,b, Dantong Ouyang a,b, Yu Jiao a,b a Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, jilin university, changchun 130012, china b School of {3. science and technology, jilin university, changchun 130012, china [a]Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education Jilin University Changchun 130012 China [b]School of Computer Science and Technology Jilin University Changchun 130012 China

In this paper, a novel method is proposed for judging whether a component set is a consistency-based diagnostic set, using SAT solv- ers. Firstly, the model of the system to be diagnosed and all the observations are described with conjunctive normal forms (CNF). Then, all the related clauses in the CNF files to the components other than the considered ones are extracted, to be used for satisfiability checking by SAT solvers. Next, all the minimal consistency-based diagnostic sets are derived by the CSSE-tree or by other similar algorithms. We have implemented four related algorithms, by calling the gold medal SAT solver in SAT07 competition – RSAT. Experimental results show that all the minimal consistency-based diagnostic sets can be quickly computed. Especially our CSSE-tree has the best effciency for the singleor double-fault diagnosis.

关键词： Conjunctive normal form Consistency-based diagnosis Model-based diagnosis SAT solver

Fast bowtie effect elimination for MODIS L1B data

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The Journal of china Universities of Posts and Telecommunications 2010年第1期17卷 120-126页

作者： REN Rui-zhi,GUO Shu-xu,GU Ling-jia college of electronic science and engineering,jilin {3.,changchun 130012,china [a] college of electronic science engineering Jilin University Changchun 130012 China

The bowtie effect refers to geometry distortions for the moderate resolution imaging spectrum-radiometer （MODIS） level 1B （L1 B） data. Till now, to eliminate the bowtie effect, numerous methods are proposed. However, most of them have limitations in computation efficiency. Through a comparative study of existing methods, this article puts forward a fast method to eliminate the bowtie effect using the ephemeris data. In this method, the rough positions of overlapping data are first detected. Because of the influence caused by the instrarnent characters and the earth＇s curvature, the positions of overlapping data need to be rectified to obtain more precise results. The optimal rectification method used in this article is selected by comparing three methods. By using the optimal method, the rectified MODIS data can be obtained. The experiments demonstrate that the bowtie effect can be eliminated in less than 1 s. In contrast, other traditional methods spend at least 3.s, thus the proposed method is faster and more effective.

关键词： bowtie effect MODIS bilinear interpolation overlapping data rectification

Modelling Immune System:Principles,Models,Analysis and Perspectives

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Journal of Bionic Engineering 2009年第1期6卷 77-85页

作者： Xiang-hua Li~1, Zheng-xuan Wang~1, Tian-yang Lu~2, Xiang-jiu Che~11. college of computer science and {3., jilin university, changchun 130012, P. R. china2. college of computer science and {3., Harbin Engineering university, Harbin 150001, P. R. china [a]college of computer science and {3. Jilin University Changchun 130012 P. R. China [b]College of Computer Science and Technology Harbin Engineering University Harbin 150001 P. R. China

The biological immune system is a complex adaptive *** are lots of benefits for building the model of the immune *** biological researchers,they can test some hypotheses about the infection process or simulate the responses of some *** computer researchers,they can build distributed,robust and fault tolerant networks inspired by the functions of the immune *** paper provides a comprehensive survey of the literatures on modelling the immune *** the methodology perspective,the paper compares and analyzes the existing approaches and models,and also demonstrates the focusing research effort on the future immune models in the next few years.

关键词： immune system modelling agent-based simulation complex adaptive system (CAS) HIV

Terrain classification based on adaptive weights with airborne LiDAR data for mining area

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中国有色金属学会会刊：英文版 2011年第S3期21卷 648-653页

作者： LI Hui-ying1, WANG Zhi2, SUN Ya-feng1, LI Wen-hui1 1. college of computer science and {3., jilin university, changchun 130012, china 2. college of Resources and Civil Engineering, Northeastern university, Shenyang 110004, china [a] college of computer science and {3. Jilin University Changchun 130012 China [b] college of Resources and Civil Engineering Northeastern University Shenyang 110004 China

The fast high-efficiency inspection for mining subsidence of mine area is a reliable way for forecasting accident and evaluating losing expense. In order to monitor mining subsidence of exploitation mine efficiently, LiDAR data were used and a novel strip division method was brought forward based on separating-treatment theory, which divided the mass of discrete three-dimensional point cloud data into a series of parallel strips and reduced the dimension in each strip. Polynomial fitting algorithm based on the adaptive weights, which located in the range of the strip, was used for classification complex terrain data of mine-area. The results show that LiDAR datamation can be greatly reduced. In the mean time, the time spending for calculation is shortened, and computational complexity is simplified. Therefore, high-efficiency terrain classification of LiDAR point cloud method can be great beneficial to monitoring environment of mine area.

关键词： mining subsidence airborne LiDAR strip division adaptive weights

A New Clustering Algorithm for Categorical Attributes

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International Journal of Minerals,Metallurgy and Materials 2000年第4期14卷 318-322页

作者： Songfeng Lu, Zhengding Lu (college of computer science and {3., Huazhong university of science and {3., Wuhan 43.074, china) college of computer science and {3. Huazhong University of Science and Technology Wuhan 430074 China

In traditional data clustering, similarity of a cluster of objects is measured by distance between objects. Such measures are not appropriate for categorical data. A new clustering criterion to determine the similarity between points with categorical attributes is pre- sented. Furthermore, a new clustering algorithm for categorical attributes is addressed. A single scan of the dataset yields a good clus- tering, and more additional passes can be used to improve the quality further.

关键词： data mining clustering similarity Information

Simulating the Folding Pathway of RNA Secondary Structure Using the Modified Ant Colony Algorithm

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Journal of Bionic Engineering 2010年第4期7卷 382-389页

作者： Jun Yu~(1,2),Changhai Zhang~(1,2),Yuanning Liu~(1,2),Xin Li~(1,2) 1.college of computer science and {3.,jilin university,changchun 130012,P.R.china 2.Key Laboratory of Symbolic Computation and Knowledge Engineering (Ministry of Education,china) jilin university,changchun 130012,P.R.china [a] college of computer science technology Jilin University Changchun 130012 P. R. China [b] Key Laboratory of Symbolic Computation Knowledge Engineering (Ministry of Education China) Jilin University Changchun 130012 P. R. China

A new method for simulating the folding pathway of RNA secondary structure using the modified ant colony algorithmis *** a given RNA sequence,the set of all possible stems is obtained and the energy of each stem iscalculated and stored at the initial ***,a more realistic formula is used to compute the energy ofmulti-branch loop in the following *** a folding pathway is simulated,including such processes as constructionof the heuristic information,the rule of initializing the pheromone,the mechanism of choosing the initial andnext stem and the strategy of updating the pheromone between two different *** by testing RNA sequences withknown secondary structures from the public databases,we analyze the experimental data to select appropriate values *** measure indexes show that our procedure is more consistent with phylogenetically proven structures thansoftware RNAstructure sometimes and more effective than the standard Genetic Algorithm.

关键词： RNA secondary structure folding pathway ant colony algorithm

Measurement of the linear electro-optic coefficient of a minute cBN sample

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science china(Technological sciences) 2005年第2期48卷 233-340页

作者： DOU Qingping1, , MA Haitao1, JIA Gang1, CHEN Zhanguo1 2 & ZHANG Tiechen3.1. college of Electronic science and Engineering, State Key Laboratory on Integrated Optoelectronics, jilin university, {3. 13.023. china 2. Mudanjiang Normal Institute, Mudanjiang 157012, china 3. State Key Laboratory of Superhard Materials, jilin university, changchun 130012, china 1. college of Electronic science and Engineering State Key Laboratory on Integrated Optoelectronics Jilin University 130023 Changchun China 2. Mudanjiang Normal Institute 157012 Mudanjiang China 3. State Key Laboratory of Superhard Materials Jilin University 130012 Changchun China

Cubic boron nitride (cBN) is a kind of artificial (synthetic) crystal. Transverse electro-optic modulation in a minute cBN sample was carried out. Basing on the practical form of the crystal, we established the theoretical and experimental method according to the sample. For the first time, the linear electro-optic effect was observed in cBN, and half-wave voltage of the cBN sample was measured successfully. Furthermore, its linear electro-optic coefficient was calculated at 1.17×10?14 m/V.

关键词： cBN crystal, linear electro-optic effect, half-wave voltage, linear electro-optic coefficient.

Study of OCDs Reliability Estimation System Based on Bio-Immunology

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Journal of Bionic Engineering 2009年第3期6卷 306-310页

作者： Dan-e Wu~1 Qiu-zhan Zhou~1 Ping-ping Liu~2 He-bin Zhang1.college of Communication Engineering,jilin university,Changehun 13.022,P.R.{3.2.Department of computer science and technology,jilin university,changchun 130012,P.R.{3. [a]college of Communication Engineering Jilin University Changchun 130022 P. R. China [b]Department of Computer Science and Technology Jilin University Changchun 130012 P. R. China

We introduce the relationship between excess noise in Optoelectronic Coupled Devices (OCDs) and their interior defects and explain how low-fiequency noise can be used to estimate their *** concepts from the biological immune system and its process of identifying invaders,we present a system for estimation of the reliability of *** system has expressions for the antigen (excess noise),lymphocyte (criterion) and the role of the lymphocyte eliminating unreliable devices. A genetic algorithm was used to estimate the components parameters of the noise spectrum for estimating the reliability of *** experimental results demonstrated that this method is reliable,adaptable and practical.

关键词： low-frequency noise artificial immunity genetic algonthm device reliability