Leaf image segmentation method based on multifractal detrended fluctuation analysis
作者：
Wang, Fang;Li, Jin-Wei* ;Shi, Wen;Liao, Gui-Ping
期刊：
Journal of Applied Physics ,2013年114(21):214905 ISSN：0021-8979
通讯作者：
Li, Jin-Wei
作者机构：
[Shi, Wen; Wang, Fang] Hunan Agr Univ, Coll Sci, Changsha 410128, Hunan, Peoples R China.;[Liao, Gui-Ping; Li, Jin-Wei; Wang, Fang] Hunan Agr Univ, Agr Informat Inst, Changsha 410128, Hunan, Peoples R China.
通讯机构：
[Li, Jin-Wei] H;Hunan Agr Univ, Agr Informat Inst, Changsha 410128, Hunan, Peoples R China.
关键词：
crops;fuzzy set theory;image segmentation;pattern clustering
摘要：
To identify singular regions of crop leaf affected by diseases, based on multifractal detrended fluctuation analysis (MF-DFA), an image segmentation method is proposed. In the proposed method, first, we defend a new texture descriptor: local generalized Hurst exponent, recorded as LHq based on MF-DFA. And then, box-counting dimension f(LHq) is calculated for sub-images constituted by the LHq of some pixels, which come from a specific region. Consequently, series of f(LHq) of the different regions can be obtained. Finally, the singular regions are segmented according to the corresponding f(LHq). Six kinds of corn diseases leaf's images are tested in our experiments. Both the proposed method and other two segmentation methods—multifractal spectrum based and fuzzy C-means clustering have been compared in the experiments. The comparison results demonstrate that the proposed method can recognize the lesion regions more effectively and provide more robust segmentations.
语种：
英文
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Security improvement for asymmetric cryptosystem based on spherical wave illumination
作者：
Ding, Xiangling;Deng, Xiaopeng* ;Song, Kehui;Chen, Guangyi
期刊：
Applied Optics ,2013年52(3):467-473 ISSN：1559-128X
通讯作者：
Deng, Xiaopeng
作者机构：
[Song, Kehui; Deng, Xiaopeng; Ding, Xiangling] Huaihua Univ, Dept Phys & Informat Engn, Huaihua 418008, Peoples R China.;[Chen, Guangyi] Hunan Agr Univ, Coll Informat Sci & Technol, Changsha 410128, Hunan, Peoples R China.
通讯机构：
[Deng, Xiaopeng] H;Huaihua Univ, Dept Phys & Informat Engn, Huaihua 418008, Peoples R China.
关键词：
Computer simulation;Fourier transforms;Fresnel diffraction;Information processing;Numerical simulation;Optical encryption
摘要：
We propose an improvement method for an asymmetric cryptosystem based on spherical wave illumination. Compared with the phase-truncated Fourier transform-based cryptosystem and the reported improving methods, the encryption process uses a spherical wave to illuminate the encryption system, rather than a uniform plane wave. As a result, the proposed method can avoid various types of the currently existing attacks and maintain the asymmetric characteristic of the cryptosystem. Moreover, due to only changing the illuminating mode, the proposed method can be easily implemented in optics compared with the reported improving methods. Simulation results are presented to demonstrate the feasibility and the security performance of the proposed method. © 2013 Optical Society of America.
语种：
英文
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TSG: A new algorithm for binary and multi-class cancer classification and informative genes selection
作者：
Wang, Haiyan;Zhang, Hongyan;Dai, Zhijun;Chen, Ming-shun;Yuan, Zheming*
期刊：
BMC Medical Genomics ,2013年6(SUPPL.1):1-14 ISSN：1755-8794
通讯作者：
Yuan, Zheming
作者机构：
[Wang, Haiyan] Kansas State Univ, Dept Stat, Manhattan, KS 66506 USA.;[Zhang, Hongyan; Dai, Zhijun; Yuan, Zheming] Hunan Prov Key Lab Crop Germplasm Innovat & Util, Changsha 410128, Hunan, Peoples R China.;[Zhang, Hongyan] Hunan Agr Univ, Coll Informat Sci & Technol, Changsha 410128, Hunan, Peoples R China.;[Zhang, Hongyan; Dai, Zhijun; Yuan, Zheming] Hunan Agr Univ, Coll Bio Safety Sci & Technol, Changsha 410128, Hunan, Peoples R China.;[Chen, Ming-shun] USDA ARS, Manhattan, KS 66506 USA.
通讯机构：
[Yuan, Zheming] H;Hunan Prov Key Lab Crop Germplasm Innovat & Util, Changsha 410128, Hunan, Peoples R China.
会议名称：
International Conference on Bioinformatics and Computational Biology (BIOCOMP)
会议时间：
JUL 18-21, 2011
会议地点：
Las Vegas, NV
会议主办单位：
[Wang, Haiyan] Kansas State Univ, Dept Stat, Manhattan, KS 66506 USA.^[Zhang, Hongyan;Dai, Zhijun;Yuan, Zheming] Hunan Prov Key Lab Crop Germplasm Innovat & Util, Changsha 410128, Hunan, Peoples R China.^[Zhang, Hongyan] Hunan Agr Univ, Coll Informat Sci & Technol, Changsha 410128, Hunan, Peoples R China.^[Zhang, Hongyan;Dai, Zhijun;Yuan, Zheming] Hunan Agr Univ, Coll Bio Safety Sci & Technol, Changsha 410128, Hunan, Peoples R China.^[Chen, Ming-shun] USDA ARS, Manhattan, KS 66506 USA.^[Chen, Ming-shun] Kansas State Univ, Dept Entomol, Manhattan, KS 66506 USA.
关键词：
Support Vector Machine;Chisquare Statistic;Family Classifier;Marker Pair;Informative Gene
摘要：
Background: One of the challenges in classification of cancer tissue samples based on gene expression data is to establish an effective method that can select a parsimonious set of informative genes. The Top Scoring Pair (TSP), k-Top Scoring Pairs (k-TSP), Support Vector Machines (SVM), and prediction analysis of microarrays (PAM) are four popular classifiers that have comparable performance on multiple cancer datasets. SVM and PAM tend to use a large number of genes and TSP, k-TSP always use even number of genes. In addition, the selection of distinct gene pairs in k-TSP simply combined the pairs of top ranking genes without considering the fact that the gene set with best discrimination power may not be the combined pairs. The k-TSP algorithm also needs the user to specify an upper bound for the number of gene pairs. Here we introduce a computational algorithm to address the problems. The algorithm is named Chisquare-statistic-based Top Scoring Genes (Chi-TSG) classifier simplified as TSG. Results: The TSG classifier starts with the top two genes and sequentially adds additional gene into the candidate gene set to perform informative gene selection. The algorithm automatically reports the total number of informative genes selected with cross validation. We provide the algorithm for both binary and multi-class cancer classification. The algorithm was applied to 9 binary and 10 multi-class gene expression datasets involving human cancers. The TSG classifier outperforms TSP family classifiers by a big margin in most of the 19 datasets. In addition to improved accuracy, our classifier shares all the advantages of the TSP family classifiers including easy interpretation, invariant to monotone transformation, often selects a small number of informative genes allowing follow-up studies, resistant to sampling variations due to within sample operations. Conclusions: Redefining the scores for gene set and the classification rules in TSP family classifiers by incorporating the sample size information can lead to better selection of informative genes and classification accuracy. The resulting TSG classifier offers a useful tool for cancer classification based on numerical molecular data. © 2013 Yuan; licensee BioMed Central Ltd.
语种：
英文
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Decentralized group key management for hierarchical access control using multilinear forms
作者：
Zhou, Wei;Xu, Yang;Wang, Guojun*
期刊：
CONCURRENCY AND COMPUTATION-PRACTICE & EXPERIENCE ,2013年28(3):631-645 ISSN：1532-0626
通讯作者：
Wang, Guojun
作者机构：
[Xu, Yang; Zhou, Wei; Wang, Guojun] Cent S Univ, Sch Informat Sci & Engn, Changsha 410083, Hunan, Peoples R China.;[Zhou, Wei] Hunan Agr Univ, Coll Informat Sci & Technol, Changsha 410128, Hunan, Peoples R China.
通讯机构：
[Wang, Guojun] C;Cent S Univ, Sch Informat Sci & Engn, Changsha 410083, Hunan, Peoples R China.
关键词：
multilinear forms;rekeying material;key management;multiprivileged group communications;security
摘要：
Key management becomes more difficult in multiprivileged group communications due to the dynamic membership and the complex relations between users and resources. Because centralized key management schemes have the drawbacks of the single point of failure, and performance bottleneck and distributed key management schemes are not scalable and lack of central control, decentralized key management schemes are proposed as a tradeoff between them. In this paper, we propose a decentralized group key management scheme using multilinear forms for dynamic multiprivileged groups. Once users join/leave the group and change their privileges, the related session keys should be updated. The rekeying in the joining operation is relatively simple because the keys are deduced from the previous keys based on a one-way function. When rekeying for one leaving/switching operation, a uniform rekeying material is negotiated between the related service groups (SGs) by using multilinear forms. Compared with other schemes in which several rounds of negotiations are executed for rekeying in each joining/leaving/switching operation, only one round of negotiation is required in each leaving/switching operation of our decentralized group key management scheme. At last, the affected session keys can be deduced by the related SGs. Our proposed scheme also supports the dynamic formation and decomposition of SGs, which provides good scalability. Security analysis is provided to show that the proposed scheme is secure. The performance analysis and the simulation results show that the proposed scheme reduces the communication cost greatly. Copyright © 2014 John Wiley & Sons, Ltd.
语种：
英文
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The Design of Three-Point Laser Localization System
作者：
Jiang, Ping* ;Luo, Ya-Hui;He, Qing-Hua;Wang, Yi;Hu, Wenwu
期刊：
JOURNAL OF NANOELECTRONICS AND OPTOELECTRONICS ,2012年7(2):144-148 ISSN：1555-130X
通讯作者：
Jiang, Ping
作者机构：
[He, Qing-Hua; Jiang, Ping] Cent S Univ, Coll Mech & Elect Engn, Changsha 410083, Peoples R China.;[Hu, Wenwu; Luo, Ya-Hui; Jiang, Ping] Hunan Agr Univ, Coll Engn, Changsha 410128, Hunan, Peoples R China.;[Wang, Yi] Hunan Agr Univ, Coll Informat Sci & Technol, Changsha 410128, Hunan, Peoples R China.
通讯机构：
[Jiang, Ping] C;Cent S Univ, Coll Mech & Elect Engn, Changsha 410083, Peoples R China.
关键词：
INERTIAL SENSOR;LASER;LOCALIZATION;MOBILE STATION
摘要：
To realize the precise localization of the working machinery in the paddy field, a 3-point laser localization system has been designed based on the experiments of Inertial Localization. This system is composed of the base station with the fixed distance and the moving station fixed on the carrier. The base stations mainly control the laser emission device to trace the corresponding laser receiving device, while the mobile station mainly collects the data of the sensors and calculates the position coordination. The experiment shows that the localization error is less than 10 cm on the test range of 50 meters, and the system is reliable localization.
语种：
英文
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Multi-objective dynamic population shuffled frog-leaping biclustering of microarray data.
作者：
Liu, Junwan;Li, Zhoujun;Hu, Xiaohua* ;Chen, Yiming;Liu, Feifei
期刊：
BMC Genomics ,2012年13(3):1-11 ISSN：1471-2164
通讯作者：
Hu, Xiaohua
作者机构：
[Liu, Junwan] Cent S Univ Forestry & Technol, Sch Comp & Informat Engn, Changsha 410004, Hunan, Peoples R China.;[Hu, Xiaohua] Cent China Normal Univ, Dept Comp Sci, Wuhan 430079, Peoples R China.;[Li, Zhoujun] Beihang Univ, State Key Lab Software Dev Environm, Beijing 100191, Peoples R China.;[Li, Zhoujun] Beihang Univ, Beijing Key Lab Network Technol, Beijing 100191, Peoples R China.;[Hu, Xiaohua] Drexel Univ, Coll Informat Sci, Philadelphia, PA 19104 USA.
通讯机构：
[Hu, Xiaohua] C;Cent China Normal Univ, Dept Comp Sci, Wuhan 430079, Peoples R China.
会议名称：
IEEE International Conference on Bioinformatics and Biomedicine (BIBM)
会议时间：
NOV 12-15, 2011
会议地点：
Atlanta, GA
会议主办单位：
[Hu, Xiaohua] Cent China Normal Univ, Dept Comp Sci, Wuhan 430079, Peoples R China.^[Liu, Junwan] Cent S Univ Forestry & Technol, Sch Comp & Informat Engn, Changsha 410004, Hunan, Peoples R China.^[Li, Zhoujun] Beihang Univ, State Key Lab Software Dev Environm, Beijing 100191, Peoples R China.^[Li, Zhoujun] Beihang Univ, Beijing Key Lab Network Technol, Beijing 100191, Peoples R China.^[Hu, Xiaohua] Drexel Univ, Coll Informat Sci, Philadelphia, PA 19104 USA.^[Chen, Yiming] Hunan Agr Univ, Sch Informat Sci & Technol, Changsha 410128, Hunan, Peoples R China.
关键词：
Particle Swarm Optimization;Pareto Front;Microarray Dataset;MOPSO;Discrete Particle Swarm Optimization
摘要：
Multi-objective optimization (MOO) involves optimization problems with multiple objectives. Generally, theose objectives is used to estimate very different aspects of the solutions, and these aspects are often in conflict with each other. MOO first gets a Pareto set, and then looks for both commonality and systematic variations across the set. For the large-scale data sets, heuristic search algorithms such as EA combined with MOO techniques are ideal. Newly DNA microarray technology may study the transcriptional response of a complete genome to different experimental conditions and yield a lot of large-scale datasets. Biclustering technique can simultaneously cluster rows and columns of a dataset, and hlep to extract more accurate information from those datasets. Biclustering need optimize several conflicting objectives, and can be solved with MOO methods. As a heuristics-based optimization approach, the particle swarm optimization (PSO) simulate the movements of a bird flock finding food. The shuffled frog-leaping algorithm (SFL) is a population-based cooperative search metaphor combining the benefits of the local search of PSO and the global shuffled of information of the complex evolution technique. SFL is used to solve the optimization problems of the large-scale datasets. This paper integrates dynamic population strategy and shuffled frog-leaping algorithm into biclustering of microarray data, and proposes a novel multi-objective dynamic population shuffled frog-leaping biclustering (MODPSFLB) algorithm to mine maximum bicluesters from microarray data. Experimental results show that the proposed MODPSFLB algorithm can effectively find significant biological structures in terms of related biological processes, components and molecular functions. The proposed MODPSFLB algorithm has good diversity and fast convergence of Pareto solutions and will become a powerful systematic functional analysis in genome research.
语种：
英文
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Identification of hierarchical and overlapping functional modules in PPI networks
作者：
Wang, Jianxin* ;Ren, Jun;Li, Min;Wu, Fang-Xiang
期刊：
IEEE Transactions on NanoBioscience ,2012年11(4):386-393 ISSN：1536-1241
通讯作者：
Wang, Jianxin
作者机构：
[Ren, Jun; Li, Min; Wang, Jianxin] Cent South Univ, Sch Informat Sci & Engn, Changsha 410083, Hunan, Peoples R China.;[Ren, Jun] Hunan Agr Univ, Coll Informat Sci & Technol, Changsha 410128, Hunan, Peoples R China.;[Wu, Fang-Xiang] Univ Saskatchewan, Dept Mech Engn, Saskatoon, SK S7N 5A9, Canada.;[Wu, Fang-Xiang] Univ Saskatchewan, Div Biomed Engn, Saskatoon, SK S7N 5A9, Canada.
通讯机构：
[Wang, Jianxin] C;Cent South Univ, Sch Informat Sci & Engn, Changsha 410083, Hunan, Peoples R China.
关键词：
Clustering coefficient;PPI networks;hierarchical clustering algorithm;overlapping and hierarchical module
摘要：
Various evidences have demonstrated that functional modules are overlapping and hierarchically organized in protein-protein interaction (PPI) networks. Up to now, few methods are able to identify both overlapping and hierarchical functional modules in PPI networks. In this paper, a new hierarchical clustering algorithm, called OH-PIN, is proposed based on the overlapping M, λ-module, and a new concept of clustering coefficient between two clusters. By recursively merging two clusters with the maximum clustering coefficient, OH-PIN finally assembles all M into λ-modules. Since M s are overlapping, λ-modules based on them are also overlapping. Thus, OH-PIN can detect a hierarchical organization of overlapping modules by tuning the value of λ. The hierarchical organization is similar to the hierarchical organization of GO annotations and that of the known complexes in MIPS. To compare the performance of OH-PIN and other existing competing algorithms, we apply them to the yeast PPI network. The experimental results show that OH-PIN outperforms the existing algorithms in terms of the functional enrichment and matching with known protein complexes. © 2011 IEEE.
语种：
英文
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Improving accuracy for cancer classification with a new algorithm for genes selection
作者：
Zhang, Hongyan;Wang, Haiyan* ;Dai, Zhijun;Chen, Ming-shun;Yuan, Zheming
期刊：
BMC Bioinformatics ,2012年13(1):298 ISSN：1471-2105
通讯作者：
Wang, Haiyan
作者机构：
[Zhang, Hongyan; Dai, Zhijun; Yuan, Zheming] Hunan Prov Key Lab Crop Germplasm Innovat & Utili, Changsha 410128, Hunan, Peoples R China.;[Zhang, Hongyan; Dai, Zhijun; Yuan, Zheming] Hunan Agr Univ, Coll Biosafety Sci & Technol, Changsha 410128, Hunan, Peoples R China.;[Wang, Haiyan] Kansas State Univ, Dept Stat, Manhattan, KS 66506 USA.;[Chen, Ming-shun] Kansas State Univ, USDA ARS, Manhattan, KS 66506 USA.;[Chen, Ming-shun] Kansas State Univ, Dept Entomol, Manhattan, KS 66506 USA.
通讯机构：
[Wang, Haiyan] K;Kansas State Univ, Dept Stat, Manhattan, KS 66506 USA.
关键词：
Linear Discriminant Analysis;Support Vector Machine Classifier;Feature Subset;Quadratic Discriminant Analysis;Informative Gene
摘要：
Background: Even though the classification of cancer tissue samples based on gene expression data has advanced considerably in recent years, it faces great challenges to improve accuracy. One of the challenges is to establish an effective method that can select a parsimonious set of relevant genes. So far, most methods for gene selection in literature focus on screening individual or pairs of genes without considering the possible interactions among genes. Here we introduce a new computational method named the Binary Matrix Shuffling Filter (BMSF). It not only overcomes the difficulty associated with the search schemes of traditional wrapper methods and overfitting problem in large dimensional search space but also takes potential gene interactions into account during gene selection. This method, coupled with Support Vector Machine (SVM) for implementation, often selects very small number of genes for easy model interpretability.Results: We applied our method to 9 two-class gene expression datasets involving human cancers. During the gene selection process, the set of genes to be kept in the model was recursively refined and repeatedly updated according to the effect of a given gene on the contributions of other genes in reference to their usefulness in cancer classification. The small number of informative genes selected from each dataset leads to significantly improved leave-one-out (LOOCV) classification accuracy across all 9 datasets for multiple classifiers. Our method also exhibits broad generalization in the genes selected since multiple commonly used classifiers achieved either equivalent or much higher LOOCV accuracy than those reported in literature.Conclusions: Evaluation of a gene's contribution to binary cancer classification is better to be considered after adjusting for the joint effect of a large number of other genes. A computationally efficient search scheme was provided to perform effective search in the extensive feature space that includes possible interactions of many genes. Performance of the algorithm applied to 9 datasets suggests that it is possible to improve the accuracy of cancer classification by a big margin when joint effects of many genes are considered. © 2012 Zhang et al.; licensee BioMed Central Ltd.
语种：
英文
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The fractional dimensional theory in Lüroth expansion
作者：
Shen, Luming;Fang, Kui*
期刊：
Czechoslovak Mathematical Journal ,2011年61(3):795-807 ISSN：0011-4642
通讯作者：
Fang, Kui
作者机构：
[Shen, Luming] Huazhong Univ Sci & Technol, Sch Math & Stat, Wuhan 430072, Hubei, Peoples R China.;[Fang, Kui] Hunan Agr Univ, Informat Sci & Technol Coll, Changsha 410128, Hunan, Peoples R China.
通讯机构：
[Fang, Kui] H;Hunan Agr Univ, Informat Sci & Technol Coll, Changsha 410128, Hunan, Peoples R China.
关键词：
Cantor set;Hausdorff dimension;Lüroth series
摘要：
It is well known that every x ∈ (0, 1] can be expanded to an infinite Lüroth series in the form of, where dn(x) ≥ 2 for all n ≥ 1. In this paper, sets of points with some restrictions on the digits in Lüroth series expansions are considered. Mainly, the Hausdorff dimensions of the Cantor sets Fφ ={ x ∈(0,1]:dn(x)≥ φ(n), ∀n ≥1} are completely determined, where φ is an integer-valued function defined on ℕ, and φ(n) → ∞ as n → ∞. © 2011 Institute of Mathematics of the Academy of Sciences of the Czech Republic, Praha, Czech Republic.
语种：
英文
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Identifying differentially expressed genes in cancer patients using a non-parameter Ising model
作者：
Li, Xumeng;Feltus, Frank A.;Sun, Xiaoqian;Wang, James Z.;Luo, Feng*
期刊：
PROTEOMICS ,2011年11(19):3845-3852 ISSN：1615-9853
通讯作者：
Luo, Feng
作者机构：
[Wang, James Z.; Luo, Feng; Li, Xumeng] Clemson Univ, Sch Comp, Clemson, SC 29634 USA.;[Li, Xumeng] Hunan Agr Univ, Dept Informat & Comp Sci, Changsha, Hunan, Peoples R China.;[Feltus, Frank A.] Clemson Univ, Dept Biochem & Genet, Clemson, SC 29634 USA.;[Sun, Xiaoqian] Clemson Univ, Dept Math Sci, Clemson, SC 29634 USA.
通讯机构：
[Luo, Feng] C;Clemson Univ, Sch Comp, Clemson, SC 29634 USA.
关键词：
Bioinformatics;Differentially expressed genes;Ising model;Microarray;Protein interaction network
摘要：
Identification of genes and pathways involved in diseases and physiological conditions is a major task in systems biology. In this study, we developed a novel non-parameter Ising model to integrate protein-protein interaction network and microarray data for identifying differentially expressed (DE) genes. We also proposed a simulated annealing algorithm to find the optimal configuration of the Ising model. The Ising model was applied to two breast cancer microarray data sets. The results showed that more cancer-related DE sub-networks and genes were identified by the Ising model than those by the Markov random field model. Furthermore, cross-validation experiments showed that DE genes identified by Ising model can improve classification performance compared with DE genes identified by Markov random field model. © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
语种：
英文
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Dynamic biclustering of microarray data by multi-objective immune optimization
作者：
Liu, Junwan* ;Li, Zhoujun;Hu, Xiaohua;Chen, Yiming;Park, E. K.
期刊：
BMC Genomics ,2011年12(2):1-7 ISSN：1471-2164
通讯作者：
Liu, Junwan
作者机构：
[Liu, Junwan] Cent S Univ Forestry & Technol, Sch Comp & Informat Engn, Changsha 410004, Hunan, Peoples R China.;[Li, Zhoujun] Beihang Univ, State Key Lab Software Dev Environm, Beijing 100191, Peoples R China.;[Li, Zhoujun] BeiHang Univ, Beijing Key Lab Network Technol, Beijing 100191, Peoples R China.;[Hu, Xiaohua] Drexel Univ, Coll Informat Sci & Technol, Philadelphia, PA 19104 USA.;[Chen, Yiming] Hunan Agr Univ, Sch Informat Sci & Technol, Changsha 410128, Hunan, Peoples R China.
通讯机构：
[Liu, Junwan] C;Cent S Univ Forestry & Technol, Sch Comp & Informat Engn, Changsha 410004, Hunan, Peoples R China.
会议名称：
IEEE International Conference on Bioinformatics and Biomedicine
会议时间：
DEC 18-21, 2010
会议地点：
Hong Kong, PEOPLES R CHINA
会议主办单位：
[Liu, Junwan] Cent S Univ Forestry & Technol, Sch Comp & Informat Engn, Changsha 410004, Hunan, Peoples R China.^[Li, Zhoujun] Beihang Univ, State Key Lab Software Dev Environm, Beijing 100191, Peoples R China.^[Li, Zhoujun] BeiHang Univ, Beijing Key Lab Network Technol, Beijing 100191, Peoples R China.^[Hu, Xiaohua] Drexel Univ, Coll Informat Sci & Technol, Philadelphia, PA 19104 USA.^[Chen, Yiming] Hunan Agr Univ, Sch Informat Sci & Technol, Changsha 410128, Hunan, Peoples R China.^[Park, E. K.] CSI CUNY, Staten Isl, NY USA.
关键词：
Pareto Front;Pareto Optimal Solution;Microarray Dataset;Human Dataset;Yeast Dataset
摘要：
Background: Newly microarray technologies yield large-scale datasets. The microarray datasets are usually presented in 2D matrices, where rows represent genes and columns represent experimental conditions. Systematic analysis of those datasets provides the increasing amount of information, which is urgently needed in the post-genomic era. Biclustering, which is a technique developed to allow simultaneous clustering of rows and columns of a dataset, might be useful to extract more accurate information from those datasets. Biclustering requires the optimization of two conflicting objectives (residue and volume), and a multi-objective artificial immune system capable of performing a multi-population search. As a heuristic search technique, artificial immune systems (AISs) can be considered a new computational paradigm inspired by the immunological system of vertebrates and designed to solve a wide range of optimization problems. During biclustering several objectives in conflict with each other have to be optimized simultaneously, so multi-objective optimization model is suitable for solving biclustering problem.Results: Based on dynamic population, this paper proposes a novel dynamic multi-objective immune optimization biclustering (DMOIOB) algorithm to mine coherent patterns from microarray data. Experimental results on two common and public datasets of gene expression profiles show that our approach can effectively find significant localized structures related to sets of genes that show consistent expression patterns across subsets of experimental conditions. The mined patterns present a significant biological relevance in terms of related biological processes, components and molecular functions in a species-independent manner.Conclusions: The proposed DMOIOB algorithm is an efficient tool to analyze large microarray datasets. It achieves a good diversity and rapid convergence. © 2011 Liu et al; licensee BioMed Central Ltd.
语种：
英文
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A stochastic scheduling algorithm for precedence constrained tasks on Grid
作者：
Tang, Xiaoyong* ;Li, Kenli;Liao, Guiping;Fang, Kui;Wu, Fan
期刊：
Future Generation Computer Systems ,2011年27(8):1083-1091 ISSN：0167-739X
通讯作者：
Tang, Xiaoyong
作者机构：
[Fang, Kui; Liao, Guiping; Tang, Xiaoyong] Hunan Agr Univ, Informat Sci & Technol Coll, Changsha, Hunan, Peoples R China.;[Wu, Fan; Tang, Xiaoyong; Li, Kenli] Hunan Univ, Sch Informat Sci & Engn, Changsha 410082, Hunan, Peoples R China.;[Liao, Guiping] Hunan Agr Univ, Sch Informat Sci & Technol, Changsha, Hunan, Peoples R China.
通讯机构：
[Tang, Xiaoyong] H;Hunan Agr Univ, Informat Sci & Technol Coll, Changsha, Hunan, Peoples R China.
关键词：
Grid;Makespan;Precedence constrained tasks;Stochastic scheduling
摘要：
This paper addresses the problems in scheduling a precedence constrained tasks of parallel application with random tasks processing time and edges communication time on Grid computing systems so as to minimize the makespan in stochastic environment. This is a difficult problem and few efforts have been reported on its solution in the literature. The problem is first formulated in a form of stochastic scheduling model on Grid systems. Then, a stochastic heterogeneous earliest finish time (SHEFT) scheduling algorithm is developed that incorporates the expected value and variance of stochastic processing time into scheduling. Our rigorous performance evaluation study, based on randomly generated stochastic parallel application DAG graphs, shows that our proposed SHEFT scheduling algorithm performs much better than the existing scheduling algorithms in terms of makespan, speedup, and makespan standard deviation. © 2011 Elsevier B.V. All rights reserved.
语种：
英文
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Computer simulation study of nonlinear imaging properties for two phase-typed scatterers
作者：
Xu, Jianbo* ;Hu, Yonghua;Zhuo, Hui
期刊：
JOURNAL OF THE OPTICAL SOCIETY OF AMERICA A-OPTICS IMAGE SCIENCE AND VISION ,2011年28(12):2459-2464 ISSN：1084-7529
通讯作者：
Xu, Jianbo
作者机构：
[Xu, Jianbo; Hu, Yonghua] Hunan Univ Sci & Technol, Sch Comp Sci & Engn, Xiangtan 411201, Peoples R China.;[Zhuo, Hui] Hunan Agr Univ, Informat Sci & Technol Coll, Changsha 410128, Hunan, Peoples R China.
通讯机构：
[Xu, Jianbo] H;Hunan Univ Sci & Technol, Sch Comp Sci & Engn, Xiangtan 411201, Peoples R China.
关键词：
High power lasers;Kerr media;Laser beams;Laser communications;Phase shift;Spatial filtering
摘要：
Nonlinear imaging of two phase-typed scatterers in super-Gaussian laser beams is modeled and its properties obtained by computer simulation are presented. The formations of hot images and second-order hot images are verified. It is found that the in-beam locations of hot images correspond to those of the scatterers, but that there can be only one second-order hot image, which is at the middle point between the in-beam locations of the scatterers. Interestingly, the image intensity can be suppressed and it increases in an oscillating manner with some regularity as the distance between the scatterers increases. Moreover, one more scatterer makes the effect of the B integral and that of the phase shift caused by scatterers quite different from the predictions for singlescatterer case. The variation trend of hot image intensity with the B integral is not in agreement with that described by the analytical result for the single-scatterer case. The variation of phase shift caused by the scatterers can result in two peaks in the variation of hot image intensity with it, and the phase shift corresponding to the larger peak is approximately half the predicted result for the single-scatterer case. These results indicate that the number of scatterers has a significant influence on nonlinear imaging. ©2011 Optical Society of America.
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英文
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Predicting gene function using few positive examples and unlabeled ones
作者：
Chen, Yiming;Li, Zhoujun* ;Wang, Xiaofeng;Feng, Jiali;Hu, Xiaohua
期刊：
BMC Genomics ,2010年11(2):1-9 ISSN：1471-2164
通讯作者：
Li, Zhoujun
作者机构：
[Chen, Yiming] Natl Univ Def Technol, Comp Sch, Changsha, Hunan, Peoples R China.;[Li, Zhoujun] BeiHang Univ, Sch Comp Sci & Engn, Beijing, Peoples R China.;[Chen, Yiming] Hunan Agr Univ, Coll Informat Sci & Technol, Changsha, Hunan, Peoples R China.;[Feng, Jiali; Wang, Xiaofeng] Shanghai Maritime Univ, Coll Informat Engn, Shanghai, Peoples R China.;[Hu, Xiaohua] Drexel Univ, Coll Informat Sci & Technol, Philadelphia, PA 19104 USA.
通讯机构：
[Li, Zhoujun] B;BeiHang Univ, Sch Comp Sci & Engn, Beijing, Peoples R China.
关键词：
Annotate Gene;Unknown Gene;Functional Term;Class Imbalance Problem;Predict Gene Function
摘要：
Background: A large amount of functional genomic data have provided enough knowledge in predicting gene function computationally, which uses known functional annotations and relationship between unknown genes and known ones to map unknown genes to GO functional terms. The prediction procedure is usually formulated as binary classification problem. Training binary classifier needs both positive examples and negative ones that have almost the same size. However, from various annotation database, we can only obtain few positive genes annotation for most offunctional terms, that is, there are only few positive examples for training classifier, which makes predicting directly gene function infeasible.Results: We propose a novel approach SPE_RNE to train classifier for each functional term. Firstly, positive examples set is enlarged by creating synthetic positive examples. Secondly, representative negative examples are selected by training SVM(support vector machine) iteratively to move classification hyperplane to a appropriate place. Lastly, an optimal SVM classifier are trained by using grid search technique. On combined kernel ofYeast protein sequence, microarray expression, protein-protein interaction and GO functional annotation data, we compare SPE_RNE with other three typical methods in three classical performance measures recall R, precise P and their combination F: twoclass considers all unlabeled genes as negative examples, twoclassbal selects randomly same number negative examples from unlabeled gene, PSoL selects a negative examples set that are far from positive examples and far from each other.Conclusions: In test data and unknown genes data, we compute average and variant of measure F. The experiments showthat our approach has better generalized performance and practical prediction capacity. In addition, our method can also be used for other organisms such as human. © 2010 Li et al; licensee BioMed Central Ltd.
语种：
英文
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List scheduling with duplication for heterogeneous computing systems
作者：
Tang, Xiaoyong;Li, Kenli* ;Liao, Guiping;Li, Renfa
期刊：
Journal of Parallel and Distributed Computing ,2010年70(4):323-329 ISSN：0743-7315
通讯作者：
Li, Kenli
作者机构：
[Li, Renfa; Tang, Xiaoyong; Li, Kenli] Hunan Univ, Sch Comp & Commun, Changsha 410082, Hunan, Peoples R China.;[Liao, Guiping; Tang, Xiaoyong] Hunan Agr Univ, Informat Sci & Technol Coll, Changsha 410128, Hunan, Peoples R China.
通讯机构：
[Li, Kenli] H;Hunan Univ, Sch Comp & Commun, Changsha 410082, Hunan, Peoples R China.
关键词：
DAG;Duplication;Heterogeneous computing systems;List scheduling
摘要：
Effective task scheduling is essential for obtaining high performance in heterogeneous computing systems (HCS). However, finding an effective task schedule in HCS, requires the consideration of the heterogeneity of computation and communication. To solve this problem, we present a list scheduling algorithm, called Heterogeneous Earliest Finish with Duplicator (HEFD). As task priority is a key attribute for list scheduling algorithm, this paper presents a new approach for computing their priority which considers the performance difference in target HCS using variance. Another novel idea proposed in this paper is to try to duplicate all parent tasks and get an optimal scheduling solution. The comparison study, based on both randomly generated graphs and the graphs of some real applications, shows that our scheduling algorithm HEFD significantly surpasses other three well-known algorithms.
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英文
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Reconstruction of intersecting curved solids from 2D orthographic views
作者：
Fu, Zi-Gang;Zou, Bei-Ji* ;Chen, Yi-Ming;Wu, Ling;Shen, Yue
期刊：
Computer-Aided Design ,2010年42(9):841-846 ISSN：0010-4485
通讯作者：
Zou, Bei-Ji
作者机构：
[Fu, Zi-Gang; Zou, Bei-Ji] Cent South Univ, Sch Informat Sci & Engn, Changsha 410083, Peoples R China.;[Wu, Ling; Fu, Zi-Gang; Shen, Yue; Chen, Yi-Ming] Hunan Agr Univ, Sch Informat Sci & Technol, Changsha 410128, Hunan, Peoples R China.
通讯机构：
[Zou, Bei-Ji] C;Cent South Univ, Sch Informat Sci & Engn, Changsha 410083, Peoples R China.
关键词：
Intersecting curved solid;Intersection curve;Orthographic views;Reconstruction;Solid reconstruction
摘要：
This paper presents a new approach to reconstruct curved solids composed of elementary volumes intersecting with one another from three-view engineering drawings. Intersection curves arising from two intersecting curved surfaces are mostly higher order spatial curves, which cannot be described exactly by 2D orthographic projections and normally represented as smooth curves passing through several key points or even simplified as arcs or lines. Approximated sketches of higher order intersection curves in 2D views result in the invalidation of existing methods that need the exact projection information as input. Based on some heuristic hints, our method is able to recover the complete and correct half-profiles of the intersecting elementary volumes using the least traces left by them, which ensure the correctness of solution solids constructed finally. Several examples are provided to show the validation of the described method. © 2010 Elsevier Ltd. All rights reserved.
语种：
英文
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Biclustering of microarray data with MOSPO based on crowding distance
作者：
Liu, Junwan* ;Li, Zhoujun;Hu, Xiaohua;Chen, Yiming
期刊：
BMC Bioinformatics ,2009年10(4):1-10 ISSN：1471-2105
通讯作者：
Liu, Junwan
作者机构：
[Li, Zhoujun; Chen, Yiming; Liu, Junwan] Natl Univ Deference Technol, Sch Comp, Changsha, Hunan, Peoples R China.;[Liu, Junwan] Cent S Univ Forestry & Technol, Sch Comp Sci, Changsha, Hunan, Peoples R China.;[Li, Zhoujun] Beihang Univ, Sch Comp Sci & Engn, Beijing, Peoples R China.;[Hu, Xiaohua] Drexel Univ, Coll Informat Sci & Technol, Philadelphia, PA 19104 USA.;[Chen, Yiming] Hunan Agr Univ, Sch Informat Sci & Technol, Changsha, Hunan, Peoples R China.
通讯机构：
[Liu, Junwan] N;Natl Univ Deference Technol, Sch Comp, Changsha, Hunan, Peoples R China.
会议名称：
IEEE International Conference on Bioinformatics and Biomedicine
会议时间：
NOV 03-05, 2008
会议地点：
Philadelphia, PA
会议主办单位：
[Liu, Junwan;Li, Zhoujun;Chen, Yiming] Natl Univ Deference Technol, Sch Comp, Changsha, Hunan, Peoples R China.^[Liu, Junwan] Cent S Univ Forestry & Technol, Sch Comp Sci, Changsha, Hunan, Peoples R China.^[Li, Zhoujun] Beihang Univ, Sch Comp Sci & Engn, Beijing, Peoples R China.^[Hu, Xiaohua] Drexel Univ, Coll Informat Sci & Technol, Philadelphia, PA 19104 USA.^[Chen, Yiming] Hunan Agr Univ, Sch Informat Sci & Technol, Changsha, Hunan, Peoples R China.
关键词：
Gene Ontology;Particle Swarm Optimization;Particle Swarm;Pareto Front;Microarray Dataset
摘要：
Background: High-throughput microarray technologies have generated and accumulated massive amounts of gene expression datasets that contain expression levels of thousands of genes under hundreds of different experimental conditions. The microarray datasets are usually presented in 2D matrices, where rows represent genes and columns represent experimental conditions. The analysis of such datasets can discover local structures composed by sets of genes that show coherent expression patterns under subsets of experimental conditions. It leads to the development of sophisticated algorithms capable of extracting novel and useful knowledge from a biomedical point of view. In the medical domain, these patterns are useful for understanding various diseases, and aid in more accurate diagnosis, prognosis, treatment planning, as well as drug discovery. Results: In this work we present the CMOPSOB (Crowding distance based Multi-objective Particle Swarm Optimization Biclustering), a novel clustering approach for microarray datasets to cluster genes and conditions highly related in sub-portions of the microarray data. The objective of biclustering is to find sub-matrices, i.e. maximal subgroups of genes and subgroups of conditions where the genes exhibit highly correlated activities over a subset of conditions. Since these objectives are mutually conflicting, they become suitable candidates for multi-objective modelling. Our approach CMOPSOB is based on a heuristic search technique, multi-objective particle swarm optimization, which simulates the movements of a flock of birds which aim to find food. In the meantime, the nearest neighbour search strategies based on crowding distance and ε-dominance can rapidly converge to the Pareto front and guarantee diversity of solutions. We compare the potential of this methodology with other biclustering algorithms by analyzing two common and public datasets of gene expression profiles. In all cases our method can find localized structures related to sets of genes that show consistent expression patterns across subsets of experimental conditions. The mined patterns present a significant biological relevance in terms of related biological processes, components and molecular functions in a species-independent manner. Conclusion: The proposed CMOPSOB algorithm is successfully applied to biclustering of microarray dataset. It achieves a good diversity in the obtained Pareto front, and rapid convergence. Therefore, it is a useful tool to analyze large microarray datasets. © 2009 Liu et al; licensee BioMed Central Ltd.
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英文
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Investigation of quasi-steady-state self-focusing in nonlinear left-handed metamaterials
作者：
Hu, Yonghua* ;Zhuo, Hui
期刊：
JOURNAL OF THE OPTICAL SOCIETY OF AMERICA B-OPTICAL PHYSICS ,2009年26(12):B68-B73 ISSN：0740-3224
通讯作者：
Hu, Yonghua
作者机构：
[Hu, Yonghua] Hunan Univ Sci & Technol, Sch Comp Sci & Engn, Xiangtan 411201, Peoples R China.;[Zhuo, Hui] Hunan Agr Univ, Informat Sci & Technol Coll, Changsha 410128, Hunan, Peoples R China.
通讯机构：
[Hu, Yonghua] H;Hunan Univ Sci & Technol, Sch Comp Sci & Engn, Xiangtan 411201, Peoples R China.
关键词：
Laser beams;Light propagation;Negative refraction;Negative refractive index;Nonlinear optics;Split ring resonators
摘要：
We investigate quasi-steady-state (QSS) self-focusing in nonlinear left-handed metamaterials (NL-LHMs) theoretically. We have found that the negative refraction property of LHMs leads to the fact that the changes of the self-focusing distance and the focus appearing time with the spatial-focusing property of the input pulse are contrary to their counterparts for a conventional self-focusing medium. It is further shown that, as the convergence of the input pulse decreases, the first focus appears earlier and corresponds to smaller self-focusing distances, and that the focus moves more slowly at the smallest self-focusing distance, indicating a relatively higher risk of optical damage formation, in sharp contrast with a conventional self-focusing case. Besides, the divergent incidence cases have finite focus moving ranges.
语种：
英文
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Information audit system based on Fuzzy neural networks
作者：
Yu fei* ;Zhang Linfeng;Liao Guiping;Shen Yue
期刊：
2006 Chinese Control Conference Proceedings, CCC 2006 ,2007年:1132-1136
通讯作者：
Yu fei
作者机构：
[Zhang Linfeng; Liao Guiping; Yu fei; Shen Yue] Hunan Agr Univ, Sch Comp & Informat Engn, Changsha 410128, Peoples R China.;[Yu fei] Comp Informat Proc Technol, Provincial Key Lab, Suzhou 2150063, Peoples R China.
通讯机构：
[Yu fei] H;Hunan Agr Univ, Sch Comp & Informat Engn, Changsha 410128, Peoples R China.
会议名称：
25th Chinese Control Conference, CCC 2006
会议时间：
August 7, 2006 - August 11, 2006
会议地点：
Harbin, China
关键词：
information audit;badness information;text character;Fuzzy neural network
摘要：
At Intelligent Methods for information audit system is hot spot in the field of network security, and application of pattern recognition and data mining in information audit system is world widely concerned and worldwide studying. As an important method of pattern recognition, Fuzzy neural network has the capability of self-organization, self-learning and generalization. Application of Fuzzy neural network in information audit system can not only identify the known badness information, but also can detect the new badness information and abnormal event.
语种：
中文
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An information audit system based on Bayes algorithm
作者：
Yu, F* ;Shen, Y;Huang, H;Xu, C;Dai, XP
期刊：
Lecture Notes in Computer Science ,2006年3842:869-876 ISSN：0302-9743
通讯作者：
Yu, F
作者机构：
[Yu, F] Hunan Agr Univ, Sch Comp & Informat Engn, Changsha 410128, Peoples R China.;Chinese Acad Sci, State Key Lab Informat Secur, Grad Sch, Beijing 100049, Peoples R China.;Hunan Univ, Coll Comp & Commun, Changsha 410082, Peoples R China.
通讯机构：
[Yu, F] H;Hunan Agr Univ, Sch Comp & Informat Engn, Changsha 410128, Peoples R China.
摘要：
It is difficult to collect information over Gigabit networks for information audit. In the paper, the information audit system adopts the network processor to collect and analyze the date in the low level of network. Through taking an advanced research on current algorithm, some improvements of the Bayes categorization algorithm have been made as well as the proposal of a text categorization model of the minimal risk Bayes decision. In addition, it considers the risk probability of mistaking the related text for unrelated text during the text categorization. The experiments results show that it promotes the precision of text categorization. ©Springer-Verlag Berlin Heidelberg 2006.
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英文
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