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Whole genome/proteome based phylogeny reconstruction for prokaryotes using higher order Markov model and chaos game representation

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Molecular phylogenetics and evolution 2016年 96卷 102-111页

作者： Wei-Feng Yang Zu-Guo Yu Vo Anh Hunan Key Laboratory for Computation and Simulation in Science and Engineering and Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education Xiangtan University Hunan 411105 PR China Department of Mathematics and Physics Hunan Institute of Engineering Hunan 411104 PR China. Electronic address: yangweifeng09@***. School of Mathematical Sciences Queensland University of Technology GPO Box 2434 Brisbane QLD 4001 Australia. Electronic address: yuzuguo@***. School of Mathematical Sciences Queensland University of Technology GPO Box 2434 Brisbane QLD 4001 Australia. Electronic address: v.anh@qut.edu.au.

UNLABELLED:Traditional methods for sequence comparison and phylogeny reconstruction rely on pair wise and multiple sequence alignments. But alignment could not be directly applied to whole genome/proteome comparison and phylogenomic studies due to their high computational complexity. Hence alignment-free methods became popular in recent years. Here we propose a fast alignment-free method for whole genome/proteome comparison and phylogeny reconstruction using higher order Markov model and chaos game representation. In the present method, we use the transition matrices of higher order Markov models to characterize amino acid or DNA sequences for their comparison. The order of the Markov model is uniquely identified by maximizing the average Shannon entropy of conditional probability distributions. Using one-dimensional chaos game representation and linked list, this method can reduce large memory and time consumption which is due to the large-scale conditional probability distributions. To illustrate the effectiveness of our method, we employ it for fast phylogeny reconstruction based on genome/proteome sequences of two species data sets used in previous published papers. Our results demonstrate that the present method is useful and efficient. AVAILABILITY AND IMPLEMENTATION:The source codes for our algorithm to get the distance matrix and genome/proteome sequences can be downloaded from ftp://121.199.20.25/. The software Phylip and EvolView we used to construct phylogenetic trees can be referred from their websites.

关键词： Alignment-free whole proteome comparison Chaos game representation Higher order Markov model Phylogenetic tree Shannon entropy

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On the encoding complexity of systematic polar codes

On the encoding complexity of systematic polar codes

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IEEE International SOC Conference

作者： Liping Li Wenyi Zhang Key Laboratory of Intelligent Computing and Signal Processing of the Ministry of Education of China Anhui University China Chinese Academy of Sciences and Department of Electronic Engineering and Information Sciences University of Science and Technology of China

Systematic polar codes are proposed by Arikan and are shown to have better BER performance than non-systematic polar codes. From a recursive decomposition of the generator matrix of polar codes, Arikan showed that the encoding complexity of systematic polar codes is also O(N log N) where N is the code block length. But the recursive process involves some additional calculations in transforming the problem instances back and forth. In this paper, by using the sparsity property of the generator matrix, we propose an encoding process which has the same complexity as non-systematic polar codes in the presence of an additional memory array. Without the additional memory elements, the number of additions of the proposed encoding process increases compared with non-systematic polar codes. We also provide an analysis to quantify this additional increase of the complexity.

关键词： Encoding Systematics Complexity theory Decoding Generators Bit error rate Electronic mail

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A saliency detection method based on global contrast

International Journal of Signal Processing, Image Processing...

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International Journal of signal processing, Image processing and Pattern Recognition 2015年第7期8卷 111-122页

作者： Yu, Chun-Yan Zhang, Wei-Shi Wang, Chun-Li Institute of Information and Science Technology Dalian Maritime University China Key Laboratory of Intelligent Computing and Signal Processing Ministry of Education Anhui University No.3 Feixi Road Hefei China

To highlight the saliency object clearly from the foreground, we propose a saliency detection method based on global contrast with cluster. Due to the fact that background pixels usually have similar patches, we use cluster analysis to merge the background regions. By using mean shift filter, the background pixels with similar color level are clustered and the saliency calculation can be decreased a lot. In the method, we use the contrast of color feature with all the other pixels to compute the saliency map. A weight coefficient is utilized to improve the detection accuracy in global contrast differences evaluation. The results of extensive experiments on public dataset show that our method perform well and can highlight the salient object clearly against the other five state-of-the-art methods. Besides, we demonstrate that the applications in image segmentation and fusion with our saliency map can get satisfactory results. © 2015 SERSC.

关键词： Image segmentation

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Numerical Simulation of Infrared Photodetectors with Au Grating by FDFD Method

Numerical Simulation of Infrared Photodetectors with Au Grat...

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Asia-Pacific Microwave Conference

作者： Lulu Cheng Jie Xu Zhixiang Huang Xianliang Wu Key Laboratory of Intelligent Computing and Signal Processing Ministry of Education Anhui University

ISBN: (纸本)9781479987689

Quantum-well infrared photodetectors have been studied extensively due to their night vision, astronomy and environmental monitoring research in recent years. However, responsivity and detectivity are relatively low in these photodetectors without the Au gratings. Therefore, the Au grating will be employed on the surface of photodetector with periodic structure due to the principle of spoof plasmon resonance. The new design mainly aims to enhance the absorption in the QW active region based on the Au grating and can be numerically simulated by using finite-difference frequency-domain method. With optimal grating parameters, the absorption can be enhanced by 250 times compared with that in the reference structure without grating. The theoretical results provide the realistic organic infrared photodetectors with theoretical basis and technical support.

关键词： Au grating Photodetector Finite-difference frequency-domain Plasmon resonance

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Analysis of Periodic Structures at Oblique Incidence by Iterated Finite-Difference Time-Domain Method

Analysis of Periodic Structures at Oblique Incidence by Iter...

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Asia-Pacific Microwave Conference

作者： Chenyang Shen Ming Fang Zhixiang Huang Xianliang Wu Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education Anhui University

ISBN: (纸本)9781479987689

An iterated FDTD method is shown here which can be used for analysis of periodic structures at oblique incidence. The main principle of the algorithm is that the future field for the current iteration is replaced approximately by the field produced in the previous iteration with the time-shifted method. The calculated reflection coefficient of infinite gold plate agrees well with the analytical solution. Furthermore, the method is introduced into the simulation of three dimensional dispersive structure, and the ultra-transmission phenomenon of the structure with nano cylinder on silicon surface is verified theoretically. The results clearly show that the method overcomes the shortcomings compared with traditional method by the limitation of incidence angle, the lack of time domain field evolution procession and the need for large meshes, which provides a new solution for the transmission properties of dispersive periodic structures under oblique incidence conditions.

关键词： oblique incidence Periodic structures Transmission Characteristics Finite difference time domain method TimeDif angle of incidence Reflection coefficient TRADITIONAL METHODS Analysis

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Quantum Electrodynamic Modeling of Quantum Dot Luminescence in Plasmonic Metamaterials

Quantum Electrodynamic Modeling of Quantum Dot Luminescence ...

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IEEE MTT-S International Conference on Numerical Electromagnetic and Multiphysics Modeling and Optimization

作者： Ming Fang Zhixiang Huang Xianliang Wu Key Laboratory of Intelligent Computing and Signal Processing Ministry of Education Anhui University

ISBN: (纸本)9781479968121

We present a self-consistent approach for simulations of metallic metamaterials coupled to the gain materials. An artificial source is introduced to simulate the spontaneous emission process in the quantum dots. Using a four-level gain system, we show numerically the losses of metamaterial can be compensated by the gain, and the hybridizing quantum dots with plasmonic metamaterial can lead to a multi-fold intensity and narrowing of their photoluminescence. The valid method is an essential step for developing and understanding metamaterial system with gain medium inclusion.

关键词： Photoluminescence Quantum dots Plasmonic metamaterial

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A novel algorithm for hand vein enhancement and segmentation based on the retinex method 3

A novel algorithm for hand vein enhancement and segmentation...

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3rd International Workshop on Communication Technology, IWCT 2013

作者： Zhang, Lian-Gang Wu, Yue-Fan Wang, Hua-Bin Zhou, Jian Tao, Liang Key Laboratory of Intelligent Computing and Signal Processing Ministry of Education Anhui University China

ISBN: (纸本)9781845648756

The contrast is low and the venous structure is simple for the hand vein image captured by a near infrared camera. Based on the Retinex method a novel algorithm is presented for human hand dorsal vein image enhancement and segmentation in this paper. First of all, the acquisition device for human hand dorsal vein image is designed based on near infrared imaging. Secondly, the area-of-interest is automatically segmented to reduce the influence of edge and background regions. Thirdly, the Retinex Method based on adaptive filtering is used to enhance the hand dorsal vein image. Finally, the dynamic global threshold method is used to segment the hand vein image, and there are some false hand vein blocks, so the vein block determination criterion is established. The experimental results show the efficiency for the algorithm proposed in this paper. © 2013 WIT Press.

关键词： Adaptive filtering

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Energy efficient feedback design for coordinated multi-point transmission in downlink

International Journal of Signal Processing, Image Processing...

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International Journal of signal processing, Image processing and Pattern Recognition 2015年第6期8卷 155-166页

作者： Wang, Yi Hu, Yanjun Zhou, Yiqing Key Laboratory of Intelligent Computing and Signal Processing Ministry of Education Anhui University Hefei China School of Electronic Science and Technology Anhui University Hefei China Institute of Computing Technology Chinese Academy of Sciences Beijing China

Coordinated multi-point (CoMP) has been raised to increase the average cell throughput and the cell-edge user throughput. However, the energy consumption of mobile stations (MSs) is a key problem restricting the wide application of CoMP systems. Considering the energy consumption of feeding back channel state information (CSI) by MSs and the influence of CSI accuracy on the throughput of system, it is proposed to measure the relationship between feedback energy consumption and throughput with energy efficiency feedback utility (EEFU) function which can adapt to different application scenes by adjusting utilization coefficient. The feedback utilization of two precoders in CoMP systems is analyzed respectively, including the optimization allocation of feedback bits with utility function. The complete EEFU optimized expression and the optimizing flow path satisfying the actual application demands of CoMP systems are then derived. The simulation results illustrate the practicability and necessity of the EEFU function and verify the performance of EEFU with different precoders. © 2015 SERSC.

关键词： Energy efficiency

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An efficient co-evolutionary particle swarm optimizer for solving multi-objective optimization problems

An efficient co-evolutionary particle swarm optimizer for so...

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第27届中国控制与决策会议

作者： Daqing Wu Li Liu Xiang Jian Gong Li Deng Key Laboratory of Intelligent Computing & Signal Processing Ministry of EducationAnhui University Computer Science and Technology Institute University of South China Glorious Sun School of Business and Management Dong Hua University

An efficient co-evolutionary multi-objective particle swarm optimizer named ECMPSO was *** uses dynamic multiple swarms to deal with multiple objectives,taking one objective is optimized by each swarm into account,and maintains diversity of new found non-dominated solutions via adopts a three-level particle swarm optimization(PSO) updating rule wherein the particles learn their experiences based on personal,neighborhood,and external *** prove the validity of the ECMPSO algorithm for solving multi-objective problems,some benchmark problems and one real-life problem are selected to validate the performance of the ECMPSO *** experiment results show that the ECMPSO algorithm is better in terms of search precision and convergence performance than other three algorithms from the literature.

关键词： Multi-objective Optimization,Particle Swarm Optimizer,Neighborhood Best Particle,Dynamic Swarms,Economic Environmental Dispatch

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Uniplanar coupled-feed printed PIFA for LTE/WWAN operation in the laptop computer

Uniplanar coupled-feed printed PIFA for LTE/WWAN operation i...

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2013 International Conference on Communication Technology, ICCT 2013

作者： Zhang, Sai Li, Minquan Rong, Bo Chang, Haixing Peng, Meng Ding, You Key Laboratory of Intelligent Computing and Signal Processing Ministry of Education Anhui University Hefei China

ISBN: (纸本)9781845648633

A new uniplanar printed PIFA with a coupled-feed structure for LTE/WWAN operation is proposed. The PIFA consists of a coupled-feed loop structure and two separated radiators which are able to generate additional bands for the operation. The loop antenna path and the longer radiator can produce a dualresonance generating the required lower band exactly, while three wide bands contributed by the loop path, the loop path with the longer radiator and the loop path with the shorter radiator can form an operating band to cover the (1710-2690 MHz) band. Because of the small size of only 14×70 mm2, the antenna which can cover the required eight bands is therefore very suitable for the modern Ultra-thin laptops. © 2014 WIT Press.

关键词： Radiators

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