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Integrative cancer genomics： models,d* algorithms and analysis

Frontiers of Computer Science 2017年第3期11卷 392-406页

作者： Jinyu CHEN Shihua ZHANG National Center for Mathematics and Interdisciplinary Sciences Academy of Mathematics and Systems Science Chinese Academy of Sciences Beijing 100190 China

In the past decade, the remarkable development of high-throughput sequencing technology accelerates the generation of large amount of multiple dimensional data such as genomic, epigenomic, transcriptomic and proteomic data. The comprehensive data make it possible to understand the underlying mechanisms of biology and disease such as cancer systematically. It also provides great challenges for computa- tional cancer genomics due to the complexity, scale and noise of data. In this article, we aim to review the recent develop- ments and progresses of computational models,d* algorithms and analysis of complex data in cancer genomics. These topics of this paper include the identification of driver mutations, the genetic heterogeneity analysis, genomic markers discovery of drug response, pan-cancer scale analysis and so on.

关键词： cancer genomics model algorithm data integration bioinformatics computational biology

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Fast Fourier single-pixel imaging based on Sierra–Lite ditheringd* algorithm

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Chinese Physics B 2019年第6期28卷 189-194页

作者： Zhen-Yu Liang Zheng-dong Cheng Yan-Yan Liu Kuai-Kuai Yu Yang-di Hu National University of Defense Technology State Key Laboratory of Pulsed Power Laser TechnologyHefei 230037China Science and Technology on Electro-Optical Information Security Control Laboratory Tianjin 300000China

The single-pixel imaging(SPI) technique is able to capture two-dimensional(2 d) images without conventional array sensors by using a photodiode. As a novel scheme, Fourier single-pixel imaging(FSI) has been proven capable of reconstructing high-quality images. due to the fact that the Fourier basis patterns(also known as grayscale sinusoidal patterns)cannot be well displayed on the digital micromirror device(dMd), a fast FSI system is proposed to solve this problem by binarizing Fourier pattern through a ditheringd* algorithm. However, the traditional ditheringd* algorithm leads to low quality as the extra noise is inevitably induced in the reconstructed images. In this paper, we report a better ditheringd* algorithm to binarize Fourier pattern, which utilizes the Sierra–Lite kernel function by a serpentine scanning method. Numerical simulation and experiment demonstrate that the proposed* algorithm is able to achieve higher quality under different sampling ratios.

关键词： single-pixel imaging binary Fourier basis pattern the dithering algorithm

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New Model and* algorithm for Hardware/Software Partitioning

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Journal of Computer Science & Technology 2008年第4期23卷 644-651页

作者：武继刚 Thambipillai Srikanthan 邹广伟 Centre for High Performance Embedded Systems School of Computer EngineeringNanyang Technological University

This paper focuses on thed* algorithmic aspects for the hardware/software （HW/SW） partitioning which searches a reasonable composition of hardware and software components which not only satisfies the constraint of hardware area but also optimizes the execution time. The computational model is extended so that all possible types of communications can be taken into account for the HW/SW partitioning. Also, a new dynamic programmingd* algorithm is proposed on the basis of the computational model, in which source data, rather than speedup in previous work, of basic scheduling blocks are directly utilized to calculate the optimal solution. The proposed* algorithm runs in O（n·A） for n code fragments and the available hardware area A. Simulation results show that the proposed* algorithm solves the HW/SW partitioning without increase in running time, compared with thed* algorithm cited in the literature.

关键词： algorithm hardware/software partitioning dynamic programming complexity

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Optimal design of steel skeletal structures using the enhanced geneticd* algorithm methodology

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Frontiers of Structural and Civil Engineering 2019年第4期13卷 863-889页

作者： Tugrul TALASLIOGLU Department of Civil Engineering Osmaniye Korkut Ata University Osmaniye 80000 Turkey

This study concerns with the design optimization of steel skeletal structures thereby utilizing both a real-life specification provisions and ready steel profiles named hot-rolled I sections. For this purpose, the enhanced geneticd* algorithm methodology named EGAwMP is utilized as an optimization tool. The evolutionary search mechanism of EGAwMP is constituted on the basis of generational geneticd* algorithm (GGA). The exploration capacity of EGAwMP is improved in a way of dividing an entire population into sub-populations and using of a radial basis neural network for dynamically adjustment of EGAwMP’s genetic operator parameters. In order to improve the exploitation capability of EGAwMP, the proposed neural network implementation is also utilized for prediction of more accurate design variables associating with a new design strategy, design codes of which are based on the provisions of LRFd_AISC V3 specification. EGAwMP is applied to determine the real-life ready steel profiles for the optimal design of skeletal structures with 105, 200, 444, and 942 members. EGAwMP accomplishes to increase the quality degrees of optimum designations Furthermore, the importance of using the real-life steel profiles and design codes is also demonstrated. Consequently, EGAwMP is suggested as a design optimization tool for the real-life steel skeletal structures.

关键词： design optimization genetic algorithm multiple populations neural network

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Two-dimensional self-adapting fast Fourier transformd* algorithm for nanoparticle sizing by ultrafast image-based dynamic light scattering

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Particuology 2018年第6期16卷 74-84页

作者： dechuan Zhang Xiaoshu Cai Wu Zhou Institute of Particle and Two-Phase Flow Measurement University of Shanghai for Sdence and TechnologyShanghai Key Laboratory of Multiphase Flow and Heat Transfer in Power Engineering (University of Shanghai for Sdence and Technology)Shanghai 200093China

In nanoparticle sizing using the ultrafast image-based dynamic light scattering (UIdLS)method,larger impurities and dark noise from the complementary metal-oxide-semiconductor (CMOS)detector affect measurement *** solve this problem,a two-dimensional self-adapting fast Fourier transform (2d-SAFFT)algorithm is proposed for *** light scattering images of nanoparticles are processed using 2d fast Fourier transforms,and a high-frequency threshold and a low-frequency threshold are then set using the self-adaptingd* algorithm to eliminate the effects of the dark noise of the CMOS detector and the *** signals caused by the dark noise of the CMOS detector and the impurities are cut off using the high-frequency threshold and the low-frequency *** signals without the high- and low-frequency components are then processed again using an inverse Fourier transform to obtain new images without the dark noise and impurities *** mean diameters of the measured nanoparticles can be obtained from images obtained using *** standard latex nanoparticles (46,100, 203,508,994nm)and commercial nanoparticles (antimony-doped tin oxide,indium tin oxide,TWEEN- 80,nano-Fe,and nano-Al2O3)were measured using this new *** show that 2d-SAFFT can effectively eliminate the effects of dark noise from the CMOS detector and the impurities.

关键词： dynamic light scattering Nanoparticle size Fast Fourier transform algorithm Spectrum segmentation

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Accurate real-time truck simulation via semirecursive formulation and Adams-Bashforth-Moultond* algorithm

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Acta Mechanica Sinica 2019年第3期35卷 641-652页

作者： Yongjun Pan Yansong He Aki Mikkola School of Automotive Engineering Chongqing UniversityChongqing 400044China Department of Mechanical Engineering Lappeenranta University of Technology53850 LappeenrantaFinland

In this paper, a tailored four-step Adams-Bashforth-Moulton (ABM)d* algorithm is applied to a semirecursive formulation to perform a real-time simulation of a semitrailer truck. In the ABMd* algorithm, each integration step involves two function evaluations, namely predictor and corrector. This is fundamentally different when compared to the classic fourth-order Runge-Kutta (RK) integrator approach that contains four function evaluations. A semitrailer truck under investigation is modeled in term of a semirecursive method and simulated by using the presented ABMd* algorithm. The results show that the four-step ABM method can reduce CPU time almost 50% for solving the truck dynamics with very similar accuracy, in comparison to the fourth-order RK method. The presented ABMd* algorithm could be used in the semirecursive formulation to carry out accurate real-time simulation of medium-large vehicle systems.

关键词： Numerical algorithm Semirecursive formulation Vehicle dynamics Computational efficiency

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A Locating Method for Reliability-Critical Gates with a Parallel-Structured Geneticd* algorithm

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Journal of Computer Science & Technology 2019年第5期34卷 1136-1151页

作者： Jie Xiao Zhan-Hui Shi Jian-Hui Jiang Xu-Hua Yang Yu-Jiao Huang Hai-Gen Hu College of Computer Science and Technology Zhejiang University of TechnologyHangzhou 310023China School of Software Engineering Tongji UniversityShanghai 201804China

The reliability allowance of circuits tends to decrease with the increase of circuit integration and the application of new technology and materials, and the hardening strategy oriented toward gates is an effective technology for improving the circuit reliability of the current situations. Therefore, a parallel-structured geneticd* algorithm (GA), PGA, is proposed in this paper to locate reliability-critical gates to successfully perform targeted hardening. Firstly, we design a binary coding method for reliability-critical gates and build an ordered initial population consisting of dominant individuals to improve the quality of the initial population. Secondly, we construct an embedded parallel operation loop for directional crossover and directional mutation to compensate for the deficiency of the poor local search of the GA. Thirdly, for combination with a diversity protection strategy for the population, we design an elitism retention based selection method to boost the convergence speed and avoid being trapped by a local optimum. Finally, we present an ordered identification method oriented toward reliability-critical gates using a scoring mechanism to retain the potential optimal solutions in each round to improve the robustness of the proposed locating method. The simulation results on benchmark circuits show that the proposed method PGA is an efficient locating method for reliability-critical gates in terms of accuracy and convergence speed.

关键词： gate-level circuit reliability locating reliability-critical gate parallel-structured genetic algorithm directing strategy scoring mechanism

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design of task priority model and* algorithm for imaging observation problem

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Journal of Systems Engineering and Electronics 2020年第2期31卷 321-334页

作者： WU Jian LU Fang ZHANG Jiawei YANG Jinghui XING Lining College of Systems Engineering National University of Defense TechnologyChangsha 410073China College of Logistics and Transportation Central South University of Forestry and TechnologyChangsha 410004China College of Information and Communication National University of Defense TechnologyXi’an 710106China College of Engineering Shanghai Polytechnic UniversityShanghai 201209China

In the imaging observation system, imaging task scheduling is an important topic. Most scholars study the imaging task scheduling from the perspective of static priority, and only a few from the perspective of dynamic priority. However,the priority of the imaging task is dynamic in actual engineering. To supplement the research on imaging observation, this paper proposes the task priority model, dynamic scheduling strategy and Heuristicd* algorithm. At first, this paper analyzes the relevant theoretical basis of imaging observation, decomposes the task priority into four parts, including target priority, imaging task priority, track, telemetry & control(TT&C)requirement priority and data transmission requirement priority, summarizes the attribute factors that affect the above four types of priority in detail, and designs the corresponding priority model. Then, this paper takes the emergency tasks scheduling problem as the background, proposes the dynamic scheduling strategy and heuristicd* algorithm. Finally, the task priority model,dynamic scheduling strategy and heuristicd* algorithm are verified by experiments.

关键词： imaging observation system imaging task priority task priority model dynamic scheduling strategy heuristic algorithm

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An active method suppressing rolling mill vibration: disturbance estimation and compensationd* algorithm

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Journal of Iron and Steel Research International 2019年第7期26卷 697-703页

作者： Xiao-qiang Yan Jie-bin Qi Xin-xin Wang School of Mechanical Engineering University of Science and Technology Beijing Beijing 100083 China

The rolling mill vibration not only seriously causes the strip thickness heterogeneity, but also damages the rolling mill equipment and its electrical components. Existing vibration suppression methods are passive and mainly tune mechanical, hydraulic, electrical and rolling process parameters. A new active vibration suppression method was thus proposed using the disturbance estimation and compensationd* algorithm. Firstly, the hydraulic-mechanical coupling model of the rolling mill vibration was established, and an active vibration suppressor was designed based on the extended state observer. Then, through the numerical simulation, it is found that the vibration energy is reduced by 35.3% using the vibration suppressor, and the vibration suppressor is valid when the vibration frequency is lower than 60 Hz Finally, the vibration suppressor was applied to the in-site manufacturing, and the expected vibration suppression was obtained. The method makes the produced steel strip have more uniform thickness and further significantly increases the finished product ratio.

关键词： Rolling mill vibration Active vibration suppression disturbance estimation Compensation algorithm Extended state observer

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An improved arctangentd* algorithm based on phase-locked loop for heterodyne detection system

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Chinese Physics B 2019年第3期28卷 141-148页

作者： Chun-Hui Yan Ting-Feng Wang Yuan-Yang Li Tao Lv Shi-Song Wu State Key Laboratory of Laser Interaction with Matter Changchun Institute of OpticsFine Mechanics and PhysicsChinese Academy of SciencesChangchun 130033China University of Chinese Academy of Sciences Beijing 100049China

We present an ameliorated arctangentd* algorithm based on phase-locked loop for digital doppler signal processing,utilized within the heterodyne detection system. We define the error gain factor given by the approximation of Taylor expansion by means of a comparison of the measured values and true values. Exact expressions are derived for the amplitude error of two in-phase & quadrature signals and the frequency error of the acousto-optic modulator. Numerical simulation results and experimental results make it clear that the dynamic instability of the intermediate frequency signals leads to cumulative errors, which will spiral upward. An improved arctangentd* algorithm for the heterodyne detection is proposed to eliminate the cumulative errors and harmonic components. depending on the narrow-band filter, our experiments were performed to realize the detectable displacement of 20 nm at a detection distance of 20 m. The aim of this paper is the demonstration of the optimized arctangentd* algorithm as a powerful approach to the demodulationd* algorithm, which will advance the signal-to-noise ratio and measurement accuracy of the heterodyne detection system.

关键词： heterodyne detection laser applications arctangent algorithm phase-locked loop

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