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 ...
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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.
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 a...
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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).
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 a...
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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.
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 (D...
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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.
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 ther...
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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.
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),...
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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.
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 estimat...
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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.
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...
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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.
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 p...
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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.
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 utili...
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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.
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