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A fast algorithm for Reconstructing Multiple Sequence Alignment and Phylogeny Simultaneously

CURRENT BIOINFORMATICS 2017年第4期12卷 329-348页

作者： Ng, Chi-Tim Li, Chun Fan, Xiaodan Chonnam Natl Univ Dept Stat Fac Nat Sci Gwangju South Korea Chinese Univ Hong Kong Dept Stat Fac Sci Hong Kong Hong Kong Peoples R China Tianjin Univ Technol & Educ Dept Stat Fac Sci Tianjin Peoples R China

Background: There is an increasing need to routinely and quickly compare multiple sequences of, for example, bird flu virus genomes to infer their evolutionary relationship. This entails a fast simultaneous inference of both sequence alignment and phylogeny. Current methods cannot meet the speed requirement though a high phylogeny accuracy is maintained in such scenarios. Objective: We propose a fast algorithm for constructing Multiple sequence Alignment and Phylogeny (FAMAP) from closely related DNA sequences. Method: FAMAP is essentially a sequentially-inputting algorithm and can be implemented in a progressive fashion, i.e., adding a new sequence into an existing tree or multiple sequence alignment. Its time complexity is O[NP(L)] + O(NG) and its space complexity is O(N) + O(G) + O[Q(L)] , where N is the number of sequences, N is the number of mutations on the phylogeny, L is the maximum length of the sequences, and P(L) and Q(L) are the time and space complexity of aligning a pair of sequences of length L, depending on the pairwise alignment algorithm employed. Results: Intensive simulation studies shows that our method is superior in terms of speed over other popular methods and has comparable accuracy of both multiple sequence alignment and the phylogeny. Conclusion: Our new algorithm might be one of the best choices when the user wants to quickly obtain a reliable phylogeny estimation from dozens of closely related long sequences.

关键词： Bioinformatics software fast algorithm multiple sequence alignment phylogenetic tree simultaneous reconstruction tree topology

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A fast algorithm for solving circulant tensor systems

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LINEAR & MULTILINEAR ALGEBRA 2017年第9期65卷 1894-1904页

作者： Xie, Ze-Jia Jin, Xiao-Qing Wei, Yi-Min Univ Macau Dept Math Macau Peoples R China Fudan Univ Sch Math Sci Shanghai Peoples R China Fudan Univ Shanghai Key Lab Contemporary Appl Math Shanghai Peoples R China

A newdefinition for circulant tensors is given, which is a generalization of the one for circulant matrices. Furthermore, we define the generalized circulant tensors which can be diagonalized by the Fourier matrix F and/ or F*. We also consider solving the circulant tensor systems by a fast algorithm based on the fast Fourier transform (FFT). Such algorithm is similar to that for circulant linear systems and it can also be performed in O(n log n).

关键词： Tensor system circulant tensor generalized circulant tensor fast algorithm

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A fast algorithm for prestack Gaussian beam migration adopting the steepest descent approximation

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STUDIA GEOPHYSICA ET GEODAETICA 2017年第3期61卷 575-586页

作者： Gao, Zhenghui Sun, Jianguo Sun, Hui Sun, Xu Yu, Ping Liu, Mingchen Jilin Univ Coll Geoexplorat Sci & Technol Changchun 130026 Jilin Peoples R China Jilin Univ Engn Training Ctr Changchun 130026 Jilin Peoples R China

In the past, prestack Gaussian beam migration adopted the steepest descent approximation to reduce the dimension of the integrals and speed up the computation. However, the simplified formula by the steepest descent approximation was still in the frequency domain, and it had to be evaluated at each frequency. To solve this problem, we present a fast algorithm by changing the order of the integrals. The innermost integral is regarded as a two-dimensional continuous function with respect to the real part and the imaginary part of the total traveltime. A lookup table corresponding to the value of the innermost integral is constructed at the sampling points. The value of the innermost integral at one imaging point can be obtained through interpolation in the constructed lookup table. The accuracy and efficiency of the fast algorithm are validated with the Marmousi dataset. The application to the Sigsbee2A dataset shows a good result.

关键词： prestack Gaussian beam migration steepest descent approximation fast algorithm lookup table

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A fast algorithm of GNSS-R Signal Processing Based on DBZP 8th

A Fast Algorithm of GNSS-R Signal Processing Based on DBZP

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8th China Satellite Navigation Conference (CSNC)

作者： Han, Lin Meng, Yansong Wang, Yanguang Han, Xingyuan Acad Space Elect Informat Technol Inst Satellite Nav & ISL Technol Xian 710100 Shaanxi Peoples R China

ISBN: (纸本)9789811045882;9789811045875

An important observation of GNSS-R is Delay-Doppler mapping (DDM). According to the requirement of GNSS-R signal real-time processing, a fast processing algorithm of GNSS-R signal based on double block zero padding (DBZP) and frequency domain rotation transformation is proposed for DDM generation. The reflected data is blocked and then correlated, which avoids the FFT calculation with too long points. The block and zero padding operations not only guarantee the full search of the pseudo code phase, but also avoid the repetitive calculation. In the frequency domain, the correlation results at different Doppler frequencies are approximated by the rotation transformation method, which avoids a large number of carrier multiplication operations and effectively reduces the computational burden. The computational burden and computational loss of parallel code phase correlation algorithm and fast algorithm are analyzed. Finally, the UK-DMC satellite-borne reflected data are processed by two algorithms and the simulation time-consuming and processing results were compared. The results show that the fast algorithm greatly shortens the DDM generation time and the loss of the processing result is small.

关键词： GNSS-R GNSS reflected signal processing DBZP fast algorithm DDM

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fast algorithm for electromagnetic pulse heating on dispersive medium

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INTERNATIONAL JOURNAL OF APPLIED ELECTROMAGNETICS AND MECHANICS 2016年第2期50卷 275-282页

作者： Liao, Y-H Zhu, H-C Huang, K-M Sichuan Univ Coll Elect & Informat Engn Chengdu 610064 Sichuan Peoples R China

In this paper we present a fast time-domain algorithm to study the electromagnetic pulse heating on dispersive medium. Using the proposed fast algorithm, the long heating process can be compressed by accelerating thermal conduction and scaling the power dissipation density. Comparing with the previous computation of several pulse periods, the proposed algorithm can deal with the heating process up to billions of pulse periods. Besides, employing the proposed algorithm, we study a 2D water post heated by electromagnetic pulses. The results reveal that comparing with continuous microwave heating, pulse heating cannot improve temperature uniformity or enhance heating efficiency.

关键词： Electromagnetic pulse heating fast algorithm temperature uniformity heating efficiency Debye medium

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fast algorithm Based on Rough LCU Minimum Depth Prediction and Early CU Partition Termination for HEVC Intra Coding

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IEICE TRANSACTIONS ON FUNDAMENTALS OF ELECTRONICS COMMUNICATIONS AND COMPUTER SCIENCES 2016年第2期E99A卷 634-638页

作者： Zhang, Mengmeng Zhang, Heng Liu, Zhi North China Univ Technol Beijing Peoples R China

The new generation video standard, i.e., High-efficiency Video Coding (HEVC), shows a significantly improved efficiency relative to the last standard, i.e., H.264. However, the quad tree structured coding units (CUs), which are adopted in HEVC to improve compression efficiency, cause high computational complexity. In this study, a novel fast algorithm is proposed for CU partition in intra coding to reduce the computational complexity. A rough minimum depth prediction of the largest CU method and an early termination method for CU partition based on the total coding bits of the current CU are employed. Many approaches have been proposed to reduce the encoding complexity of HEVC, but these methods do not use the total coding bits of the current CU as the main basis for judgment to judge the CU complexity. Compared with the reference software HM16.6, the proposed algorithm reduces encoding time by 45% on average and achieves an approximately 1.1% increase in Bjntegaard delta bit rate and a negligible peak signal-to-noise ratio loss.

关键词： CU partition fast algorithm depth prediction coding bits

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Robust multiscale analytic sampling approximation to periodic function and fast algorithm

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INTERNATIONAL JOURNAL OF WAVELETS MULTIRESOLUTION AND INFORMATION PROCESSING 2017年第1期15卷 1750006-1750006页

作者： Li, Youfa Shang, Jing Zhang, Gengrong Dang, Pei Guangxi Univ Coll Math & Informat Sci Nanning Peoples R China Anyang Univ Architectural Engn Inst Anyang Peoples R China Macau Univ Sci & Technol Fac Informat Technol Macau Peoples R China

By applying the multiscale method to the Mobius transformation function, we construct the multiscale analytic sampling approximation (MASA) to any function in the Hardy space H-2(T). The approximation error is estimated, and it is proved that the MASA is robust to sample error. We prove that the MASA can be expressed by a Hankel matrix, making use of which, a fast algorithm is established to compute the MASA. Since what we acquire in practice may well be the samples on time domain instead of the analytic ones on the unit disc of the complex plane, we establish a fast algorithm for acquiring analytic samples. Numerical experiments are carried out to demonstrate the efficiency of the MASA.

关键词： Multiscale method analytic sampling approximation Hankel matrix fast algorithm Mobius transformation Hardy space

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fast algorithm for Evaluation of Critical Parameters of Smart Overalls 11

Fast Algorithm for Evaluation of Critical Parameters of Smar...

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ELEKTRO 11th International Conference

作者： Pavlicek, Karel Kotlan, Vaclav Mach, Frantisek Karban, Pavel Dolezel, Ivo Soukup, Radek Kalcik, Jan Univ West Bohemia Pilsen Plzen Czech Republic

ISBN: (纸本)9781467386982

A fast and efficient algorithm is presented allowing a firefighter dressed in a smart firefighter protective suit continuously informing him about the time that he can still safely spend in a burning bidding, which is characterized by an dynamic environment of time-variable temperature. The algorithm starts from precalculated time evolution of temperature at selected places of the overall (mostly along its internal surface) for a number of values of the delivered external heat power that are then approximated by simple exponential functions. The prediction is then based on successive measurements of three or more temperatures in time and finding such a precalculated exponential function that best tits them. This function is important for predicting the maximum time of stay that is still safe for the firefighter in the current conditions.

关键词： smart protective suit fast algorithm forward problem inverse problem numerical analysis

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fast algorithm BASED ON SOLE-AND MULTI-DEPTH MEASUREMENTS FOR HEVC INTRA CODING 23

FAST ALGORITHM BASED ON SOLE-AND MULTI-DEPTH MEASUREMENTS FO...

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23rd IEEE International Conference on Image Processing (ICIP)

作者： He, Gang Hu, Jing Li, Yunsong Yu, Wenxin Xidian Univ Xian Shaanxi Peoples R China Southwest Univ Sci & Technol Mianyang Sichuan Peoples R China

ISBN: (纸本)9781467399616

In High Efficiency Video Coding (HEVC), intra coding plays an important role, but also involves huge computational complexity due to a flexible coding unit (CU) structure and a large number of prediction modes. This paper presents a fast algorithm based on the sole-and multi-depth measurements to reduce the complexity from CU and prediction mode decisions. For the CU decision, evaluation results with sole and multiple depths are utilized to judge if the CU is a heterogeneous, homogeneous, or depth prominent one, where fast CU decisions are made. For the prediction mode decision, the tendencies for different CU sizes are detected based on multiple depths. The number of searching modes is decreased adaptively for the depth with fewer tendencies. Experimental results show the proposed algorithm reduces 61.49% computational complexity, with 0.75% bit-rate increasing, which is more efficient than state-of-the-arts.

关键词： HEVC fast algorithm intra prediction

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A fast algorithm for 2D DOA Estimation Using an Omnidirectional Sensor Array

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SENSORS 2017年第3期17卷 515-515页

作者： Nie, Weike Xu, Kaijie Feng, Dazheng Wu, Chase Qishi Hou, Aiqin Yin, Xiaoyan Northwest Univ Xian Sch Informat Sci & Technol Xian 710127 Peoples R China Xidian Univ Sch Electromech Engn Xian 710071 Peoples R China Xidian Univ Natl Lab Radar Signal Proc Xian 710071 Peoples R China New Jersey Inst Technol Dept Comp Sci Newark NJ 07102 USA

The traditional 2D MUSIC algorithm fixes the azimuth or the elevation, and searches for the other without considering the directions of sources. A spectrum peak diffusion effect phenomenon is observed and may be utilized to detect the approximate directions of sources. Accordingly, a fast 2D MUSIC algorithm, which performs azimuth and elevation simultaneous searches (henceforth referred to as AESS) based on only three rounds of search is proposed. Firstly, AESS searches along a circle to detect the approximate source directions. Then, a subsequent search is launched along several straight lines based on these approximate directions. Finally, the 2D Direction of Arrival (DOA) of each source is derived by searching on several small concentric circles. Unlike the 2D MUSIC algorithm, AESS does not fix any azimuth and elevation parameters. Instead, the adjacent point of each search possesses different azimuth and elevation, i.e., azimuth and elevation are simultaneously searched to ensure that the search path is minimized, and hence the total spectral search over the angular field of view is avoided. Simulation results demonstrate the performance characters of the proposed AESS over some existing algorithms.

关键词： sensor array fast algorithm spectrum peak diffusion effect Direction of Arrival estimation 2D MUSIC

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