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SW-DDFT: Parallel Optimization of the Dynamical Density Functional Theory Algorithm Based on Sunway Bluelight II Supercomputer 认领 引用
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作者 Xiaoguang Lv Tao Liu +5 位作者 Han Qin Ying Guo Jingshan Pan Dawei Zhao Xiaoming Wu Meihong Yang 《Computers, Materials & Continua》 SCIE EI 2025年第7期1417-1436,共20页
The Dynamical Density Functional Theory(DDFT)algorithm,derived by associating classical Density Functional Theory(DFT)with the fundamental Smoluchowski dynamical equation,describes the evolution of inhomo-geneous flui... The Dynamical Density Functional Theory(DDFT)algorithm,derived by associating classical Density Functional Theory(DFT)with the fundamental Smoluchowski dynamical equation,describes the evolution of inhomo-geneous fluid density distributions over time.It plays a significant role in studying the evolution of density distributions over time in inhomogeneous systems.The Sunway Bluelight II supercomputer,as a new generation of China’s developed supercomputer,possesses powerful computational capabilities.Porting and optimizing industrial software on this platform holds significant importance.For the optimization of the DDFT algorithm,based on the Sunway Bluelight II supercomputer and the unique hardware architecture of the SW39000 processor,this work proposes three acceleration strategies to enhance computational efficiency and performance,including direct parallel optimization,local-memory constrained optimization for CPEs,and multi-core groups collaboration and communication optimization.This method combines the characteristics of the program’s algorithm with the unique hardware architecture of the Sunway Bluelight II supercomputer,optimizing the storage and transmission structures to achieve a closer integration of software and hardware.For the first time,this paper presents Sunway-Dynamical Density Functional Theory(SW-DDFT).Experimental results show that SW-DDFT achieves a speedup of 6.67 times within a single-core group compared to the original DDFT implementation,with six core groups(a total of 384 CPEs),the maximum speedup can reach 28.64 times,and parallel efficiency can reach 71%,demonstrating excellent acceleration performance. 展开更多
关键词 Sunway supercomputer high-performance computing dynamical density functional theory parallel optimization
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A Comprehensive Review of Parallel Optimization Algorithms for High-Dimensional and Incomplete Matrix Factorization 认领 引用
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作者 Qicong Hu Hao Wu Xin Luo 《IEEE/CAA Journal of Automatica Sinica》 SCIE EI CSCD 2025年第12期2399-2426,共28页
High-dimensional and incomplete(HDI) matrices are commonly encountered in various big data-related applications for illustrating the complex interactions among numerous entities, like the user-item interactions in a c... High-dimensional and incomplete(HDI) matrices are commonly encountered in various big data-related applications for illustrating the complex interactions among numerous entities, like the user-item interactions in a commercial recommender system or the user-user interactions in a social network services system. The factorization of such an HDI matrix can embed the involved entities into the low-dimensional feature space for acquiring their principal representation, which is a vital task in various application scenes and is often established through the Latent Factor Analysis(LFA). Nevertheless, an HDI matrix can be huge when the corresponding application explodes to involve millions of users, items, or other interactive nodes. In this case, a parallel optimization algorithm is desired for raising the scalability and time efficiency of an LFA model. This paper provides a comprehensive review of the existing parallel optimization algorithms for the LFA model. Specifically, it performs: 1) discussion and summary of these algorithms based on computing architecture and mode, 2) empirical studies of representative models, and3) summary of the current challenges and future directions in this domain. This survey aims to offer an exhaustive review of Parallel Optimization Algorithms for High-Dimensional and Incomplete Matrix Factorization, thereby fostering further research in this field. 展开更多
关键词 Data-related application high-dimensional and incomplete(HDI)data high-performance computing latent feature analysis(LFA) matrix factorization parallel optimization algorithm
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Data Analyses and Parallel Optimization of the Regional Marine Ecological Model 认领 引用
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作者 Yanqiang Wang Jingjing Zheng +2 位作者 Tianyu Zhang Peng Liang Bo Lin 《国际计算机前沿大会会议论文集》 2023年第2期213-224,共12页
Under the joint influence of high-intensity human activities and cli-mate change,the coastal ecological environment is deteriorating,and the ecologi-cal environment security and the sustainable development of the marin... Under the joint influence of high-intensity human activities and cli-mate change,the coastal ecological environment is deteriorating,and the ecologi-cal environment security and the sustainable development of the marine economy are seriously threatened.Therefore,it is of great significance to establish a high-resolution ecological environment operational forecasting system.To meet the run time requirements of the ecological operational forecasting system,a vari-ety of parallel optimization methods were proposed to improve the operation efficiency of the model.First,based on the National Marine Environmental Fore-casting Center’s Lenovo cluster,the ROMS benchmark experiment was expanded to the 4000 Processes scale.A good speedup was obtained by the experiment.The ROMS model was analysed with strong scalability.Second,in the hydrodynamic-ecological simulation experiment of the Bohai Sea-Yellow Sea-East China Sea,by optimizing Vector,InfiniBand,and Parallel I/O,the performance of the model can be improved by 270%while maintaining the same computing resources.That computing resources were more reasonably used lay the foundation for the operational forecast. 展开更多
关键词 marine ecological model ROMS high-performance computing parallel optimization
Parallel discrete lion swarm optimization algorithm for solving traveling salesman problem 认领 引用 被引量：4
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作者 ZHANG Daoqing JIANG Mingyan 《Journal of Systems Engineering and Electronics》 SCIE CSCD 2020年第4期751-760,共10页
As a typical representative of the NP-complete problem, the traveling salesman problem(TSP) is widely utilized in computer networks, logistics distribution, and other fields. In this paper, a discrete lion swarm optim... As a typical representative of the NP-complete problem, the traveling salesman problem(TSP) is widely utilized in computer networks, logistics distribution, and other fields. In this paper, a discrete lion swarm optimization(DLSO) algorithm is proposed to solve the TSP. Firstly, we introduce discrete coding and order crossover operators in DLSO. Secondly, we use the complete 2-opt(C2-opt) algorithm to enhance the local search ability.Then in order to enhance the efficiency of the algorithm, a parallel discrete lion swarm optimization(PDLSO) algorithm is proposed.The PDLSO has multiple populations, and each sub-population independently runs the DLSO algorithm in parallel. We use the ring topology to transfer information between sub-populations. Experiments on some benchmarks TSP problems show that the DLSO algorithm has a better accuracy than other algorithms, and the PDLSO algorithm can effectively shorten the running time. 展开更多
关键词 discrete lion swarm optimization(DLSO)algorithm complete 2-opt(C2-opt)algorithm parallel discrete lion swarm optimization(PDLSO)algorithm traveling salesman problem(TSP)
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Parallel implementation and optimization of LMS adaptive filtering algorithms based on vector DSP 认领 引用
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作者 Yonghua Hu Linyun Deng +1 位作者 Xiangyu Gao Zhezhuo Zhao 《CCF Transactions on High Performance Computing》 EI CSCD 2026年第2期180-195,共16页
The Least Mean Square(LMS)adaptive filtering algorithm is a significant filtering algorithm widely used in noise processing and other fields that automatically adjusts the values of filter coefficients according to th... The Least Mean Square(LMS)adaptive filtering algorithm is a significant filtering algorithm widely used in noise processing and other fields that automatically adjusts the values of filter coefficients according to the results,aimed at optimizing the filtered results.Based on a basic serial LMS adaptive filtering algorithm,we propose a vectorized parallel processing scheme for the LMS adaptive filtering algorithm in this work.By combining the characteristics of the algorithm processing flow and those of the parallel technologies used in vector Digital Signal Processes(DSPs),the optimizations such as loop fusion,double-word accessing,and vector shuffling of the LMS algorithm are studied in depth,and the loop unrolling optimization method is used to accelerate the calculation of the algorithm further.Experimental research was conducted on the high-performance FT-M7002 DSP platform in this paper.The results show that,compared with the running performance of the LMS adaptive filtering algorithm in Texas Instruments(TI)’s dsplib library on the TMS320C6678 processor,the optimization effect of the proposed optimization algorithm in this paper can achieve a maximum speed-up ratio of up to 6.9×for medium-scale data.The merged memory access optimization implemented on the GPU platform achieves an average 1.5x speedup compared to the basic parallel scheme. 展开更多
关键词 Vector DSP High-performance computing Parallel optimization LMS adaptive filtering algorithm
Research on Grid Planning of Dual Power Distribution Network Based on Parallel Ant Colony Optimization Algorithm 认领 引用
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作者 Shuaixiang Wang 《Journal of Electronic Research and Application》 2023年第1期32-41,共10页
A distribution network plays an extremely important role in the safe and efficient operation of a power grid.As the core part of a power grid’s operation,a distribution network will have a significant impact on the s... A distribution network plays an extremely important role in the safe and efficient operation of a power grid.As the core part of a power grid’s operation,a distribution network will have a significant impact on the safety and reliability of residential electricity consumption.it is necessary to actively plan and modify the distribution network’s structure in the power grid,improve the quality of the distribution network,and optimize the planning of the distribution network,so that the network can be fully utilized to meet the needs of electricity consumption.In this paper,a distribution network grid planning algorithm based on the reliability of electricity consumption was completed using ant colony algorithm.For the distribution network structure planning of dual power sources,the parallel ant colony algorithm was used to prove that the premise of parallelism is the interactive process of ant colonies,and the dual power distribution network structure model is established based on the principle of the lowest cost.The artificial ants in the algorithm were compared with real ants in nature,and the basic steps and working principle of the ant colony optimization algorithm was studied with the help of the travelling salesman problem(TSP).Then,the limitations of the ant colony algorithm were analyzed,and an improvement strategy was proposed by using python for digital simulation.The results demonstrated the reliability of model-building and algorithm improvement. 展开更多
关键词 Parallel ant colony optimization algorithm Dual power sources Distribution network Grid planning
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Optimal Design of a 3-Leg 6-DOF Parallel Manipulator for a Specific Workspace 认领 引用 被引量：17
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作者 FU Jianxun GAO Feng 《Chinese Journal of Mechanical Engineering》 SCIE EI CAS CSCD 2016年第4期659-668,共10页
Researchers seldom study optimum design of a six-degree-of-freedom（DOF） parallel manipulator with three legs based upon the given workspace.An optimal design method of a novel three-leg six-DOF parallel manipulator... Researchers seldom study optimum design of a six-degree-of-freedom（DOF） parallel manipulator with three legs based upon the given workspace.An optimal design method of a novel three-leg six-DOF parallel manipulator（TLPM） is presented.The mechanical structure of this robot is introduced,with this structure the kinematic constrain equations is decoupled.Analytical solutions of the forward kinematics are worked out,one configuration of this robot,including position and orientation of the end-effector are graphically displayed.Then,on the basis of several extreme positions of the kinematic performances,the task workspace is given.An algorithm of optimal designing is introduced to find the smallest dimensional parameters of the proposed robot.Examples illustrate the design results,and a design stability index is introduced,which ensures that the robot remains a safe distance from the boundary of sits actual workspace.Finally,one prototype of the robot is developed based on this method.This method can easily find appropriate kinematic parameters that can size a robot having the smallest workspace enclosing a predefined task workspace.It improves the design efficiency,ensures that the robot has a small mechanical size possesses a large given workspace volume,and meets the lightweight design requirements. 展开更多
关键词 parallel robot optimal design workspace three legs
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Application of Evolution Sequential Number Theoretic Optimization in Global Optimization 认领 引用
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作者 刘洪谦 袁希钢 方开泰 《Transactions of Tianjin University》 CAS 2002年第4期221-225,共5页
Synthesis of chemical processes is of non-convex and multi-modal. Deterministic strategies often fail to find global optimum within reasonable time scales. Stochastic methodologies generally approach global solution i... Synthesis of chemical processes is of non-convex and multi-modal. Deterministic strategies often fail to find global optimum within reasonable time scales. Stochastic methodologies generally approach global solution in probability. In recogniting the state of art status in the discipline, a new approach for global optimization of processes, based on sequential number theoretic optimization (SNTO), is proposed. In this approach, subspaces and feasible points are derived from uniformly scattered points, and iterations over passing the corner of local optimum are enhanced via parallel strategy. The efficiency of the approach proposed is verified by results obtained from various case studies. 展开更多
关键词 global optimization sequential number theoretic optimization parallel optimization
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A novel hybrid estimation of distribution algorithm for solving hybrid flowshop scheduling problem with unrelated parallel machine 认领 引用 被引量：9
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作者 孙泽文 顾幸生 《Journal of Central South University》 SCIE EI CAS CSCD 2017年第8期1779-1788,共10页
The hybrid flow shop scheduling problem with unrelated parallel machine is a typical NP-hard combinatorial optimization problem, and it exists widely in chemical, manufacturing and pharmaceutical industry. In this wor... The hybrid flow shop scheduling problem with unrelated parallel machine is a typical NP-hard combinatorial optimization problem, and it exists widely in chemical, manufacturing and pharmaceutical industry. In this work, a novel mathematic model for the hybrid flow shop scheduling problem with unrelated parallel machine(HFSPUPM) was proposed. Additionally, an effective hybrid estimation of distribution algorithm was proposed to solve the HFSPUPM, taking advantage of the features in the mathematic model. In the optimization algorithm, a new individual representation method was adopted. The(EDA) structure was used for global search while the teaching learning based optimization(TLBO) strategy was used for local search. Based on the structure of the HFSPUPM, this work presents a series of discrete operations. Simulation results show the effectiveness of the proposed hybrid algorithm compared with other algorithms. 展开更多
关键词 hybrid estimation of distribution algorithm teaching learning based optimization strategy hybrid flow shop unrelated parallel machine scheduling
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Rule-based scheduling of multi-stage multi-product batch plants with parallel units 认领 引用 被引量：2
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作者 Bin Shi Xinrui Qian +1 位作者 Shanshan Sun Liexiang Yan 《Chinese Journal of Chemical Engineering》 SCIE EI CAS CSCD 2017年第8期1022-1036,共15页
A novel rule-based model for multi-stage multi-product scheduling problem(MMSP)in batch plants with parallel units is proposed.The scheduling problem is decomposed into two sub-problems of order assignment and order s... A novel rule-based model for multi-stage multi-product scheduling problem(MMSP)in batch plants with parallel units is proposed.The scheduling problem is decomposed into two sub-problems of order assignment and order sequencing.Firstly,hierarchical scheduling strategy is presented for solving the former sub-problem,where the multi-stage multi-product batch process is divided into multiple sequentially connected single process stages,and then the production of orders are arranged in each single stage by using forward order assignment strategy and backward order assignment strategy respectively according to the feature of scheduling objective.Line-up competition algorithm(LCA)is presented to find out optimal order sequence and order assignment rule,which can minimize total flow time or maximize total weighted process time.Computational results show that the proposed approach can obtain better solutions than those of the literature for all scheduling problems with more than 10 orders.Moreover,with the problem size increasing,the solutions obtained by the proposed approach are improved remarkably.The proposed approach has the potential to solve large size MMSP. 展开更多
关键词 Line-up competition algorithm Order assignment role Multi-stage multi-product Parallel unit Scheduling optimization
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Reconstruction method of irregular seismic data with adaptive thresholds based on different sparse transform bases 认领 引用 被引量：5
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作者 Zhao Hu Yang Tun +4 位作者 Ni Yu-Dong Liu Xing-Gang Xu Yin-Po Zhang Yi-Lei Zhang Guang-Rong 《Applied Geophysics》 SCIE CSCD 2021年第3期345-360,432,共16页
Oil and gas seismic exploration have to adopt irregular seismic acquisition due to the increasingly complex exploration conditions to adapt to complex geological conditions and environments.However,the irregular seism... Oil and gas seismic exploration have to adopt irregular seismic acquisition due to the increasingly complex exploration conditions to adapt to complex geological conditions and environments.However,the irregular seismic acquisition is accompanied by the lack of acquisition data,which requires high-precision regularization.The sparse signal feature in the transform domain in compressed sensing theory is used in this paper to recover the missing signal,involving sparse transform base optimization and threshold modeling.First,this paper analyzes and compares the effects of six sparse transformation bases on the reconstruction accuracy and efficiency of irregular seismic data and establishes the quantitative relationship between sparse transformation and reconstruction accuracy and efficiency.Second,an adaptive threshold modeling method based on sparse coefficient is provided to improve the reconstruction accuracy.Test results show that the method has good adaptability to different seismic data and sparse transform bases.The f-x domain reconstruction method of effective frequency samples is studied to address the problem of low computational efficiency.The parallel computing strategy of curvelet transform combined with OpenMP is further proposed,which substantially improves the computational efficiency under the premise of ensuring the reconstruction accuracy.Finally,the actual acquisition data are used to verify the proposed method.The results indicate that the proposed method strategy can solve the regularization problem of irregular seismic data in production and improve the imaging quality of the target layer economically and efficiently. 展开更多
关键词 irregular acquisition seismic data reconstruction adaptive threshold f-x domain OpenMP parallel optimization sparse transformation
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A parallel algorithm for an Ocean General Circulation Model based on a unified dynamics framework 认领 引用
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作者 Yaxin Li Xuebin Chi +7 位作者 Jinrong Jiang Run Guo Lian Zhao Chen Li Yidi Bai Junlin Wei Xiang Han Guangqing Zhou 《CCF Transactions on High Performance Computing》 EI CSCD 2025年第6期537-555,共19页
Ocean General Circulation Model(OGCM)is a computer simulation tool based on physical principles and mathematical equations,aiming at studying global ocean circulation and its impact on the climate system.Its diverse r... Ocean General Circulation Model(OGCM)is a computer simulation tool based on physical principles and mathematical equations,aiming at studying global ocean circulation and its impact on the climate system.Its diverse resolutions and large computational data make parallel optimization a research hotspot.In the present study,we redesign the OGCM under a unified dynamic framework of serial versions(based on an unstructured grid)for the first time with a MPI parallel algorithm.Specifically,our work mainly consists of the following two parts:(1)we first change the model from a raw serial program to a parallel program that supports communication between multiple CPU cores.(2)In response to the problem of a sharp decrease in parallel efficiency as the number of CPU cores increases in the parallel optimized mode,we optimize the grid coding of the original model and proposed a new boundary communication scheme.We conduct single-node and multi-node experiments on a multi-CPU cluster to evaluate the proposed approach.Using the original OGCM-initially limited to serial execution-as a baseline,we achieve a 175.91×speedup on 640 cores.Afterwards,we extend the parallel version to multiple nodes,with strong scaling parallel efficiency of 42.2%on 8 nodes using 320 cores. 展开更多
关键词 Ocean General Circulation Model Parallel optimization Unstructured grid High performance computing
Hierarchical Bulk Synchronous Parallel Model and Performance Optimization 认领 引用
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作者 黄林鹏 孙永强 袁伟 《Journal of Computer Science & Technology》 SCIE EI 1999年第3期224-233,共10页
Based on the framework of BSP, a Hierarchical Bulk Synchronous Parallel (HBSP) performance model is introduced in this paper to capture the per formance optimization problem for various stages in parallel program deve... Based on the framework of BSP, a Hierarchical Bulk Synchronous Parallel (HBSP) performance model is introduced in this paper to capture the per formance optimization problem for various stages in parallel program development and to accurately predict the performance of a parallel program by considering fac tors causing variance at local computation and global communication. The related methodology has been applied to several real applications and the results show that HBSP is a suitable model for optimizing parallel programs. 展开更多
关键词 parallel programming bulk synchronous parallel model,perfor mance optimization
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Enhancing Design of Visual-Servo Delayed System 认领 引用 被引量：3
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作者 Zhi-Ren Tsai Yau-Zen Chang 《Journal of Electronic Science and Technology》 EI CAS CSCD 2018年第3期232-240,共9页
A robust adaptive predictor is proposed to solve the time-varying and delay control problem of an overhead crane system with a stereo-vision servo. The predictor is based on the use of a recurrent neural network(RNN) ... A robust adaptive predictor is proposed to solve the time-varying and delay control problem of an overhead crane system with a stereo-vision servo. The predictor is based on the use of a recurrent neural network(RNN) with tapped delays, and is used to supply the real-time signal of the swing angle. There are two types of discrete-time controllers under investigation, i.e., the proportional-integral-derivative(PID) controller and the sliding controller. Firstly, a design principle of the neural predictor is developed to guarantee the convergence of its swing angle estimation. Then, an improved version of the particle swarm optimization algorithm, the parallel particle swarm optimization(PPSO) method is used to optimize the control parameters of these two types of controllers. Finally, a homemade overhead crane system equipped with the Kinect sensor for the visual servo is used to verify the proposed scheme. Experimental results demonstrate the effectiveness of the approach, which also show the parameter convergence in the predictor. 展开更多
关键词 Parallel particle swarm optimization robust adaptive predictor stereo-vision servo time-varying delay
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The uncoupled microbial fed-batch fermentation optimization based on state-dependent switched system 认领 引用 被引量：2
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作者 Teng Niu Jingang Zhai +2 位作者 Hongchao Yin Enmin Feng Chongyang Liu 《International Journal of Biomathematics》 SCIE 2021年第4期189-210,共22页
In the actual microbial fermentation process,excessive or insufficient substrate can produce inhibitory effects on cells growth.The artificial substrate feeding rules by past experiences have great blindness to keep s... In the actual microbial fermentation process,excessive or insufficient substrate can produce inhibitory effects on cells growth.The artificial substrate feeding rules by past experiences have great blindness to keep substrate concentration in a given appropriate range.This paper considers that alkali feed depends on pH value of the solution and glycerol feed depends on glycerol concentration of the solution in the uncoupled microbial fed-hatch fermentation process,and establishes a state-dependent switched system in which the flow rates of glycerol and alkali,the number of mode switches,the mode sequence and the switching times are prior unknown.To maximize the yield of target product 1,3-Propanediol(1,3-PD),we formulate a switching optimal control problem with the flow rates of glycerol and alkali,the number of mode switches,the mode sequence and the switching times as decision variables,which is a mixed-integer dynamic programming problem.For solving the mixed-integer dynamic programming problem,the control parametrization technique,the time scaling transformation and the embedded system technology are used to obtain an approximate parameter optimization problem.By using a parallel optimization algorithm,we obtain the optimal control strategies.Under the obtained optimal control strategies,the 1,3-PD yield at the terminal time is increased significantly compared with the previous results. 展开更多
关键词 Uncoupled fed-batch fermentation state-dependent switched system switching optimal control embedded system parallel optimization
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Optimized design of parallel beam-splitting prism 认领 引用 被引量：1
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作者 赵培涛 李国华 《Chinese Optics Letters》 EI CAS 2004年第10期615-617,共3页
A large lateral shearing distance of parallel beam-splitting prism is often needed in laser modulation and polarization interference. In this letter, we present an optimized design of parallel beam-splitting prism and... A large lateral shearing distance of parallel beam-splitting prism is often needed in laser modulation and polarization interference. In this letter, we present an optimized design of parallel beam-splitting prism and list some different cases in detail. The optimized design widens the use range of parallel beam-splitting prism. At the wavelength of 632.8 nm, the law that the enlargement ratio changes with the refractive index and the apex angle is verified. 展开更多
关键词 Optimized design of parallel beam-splitting prism Figure
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Optimized Parallel Execution of Declarative Programs on Distributed Memory Multiprocessors 认领 引用
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作者 沈美明 田新民 +2 位作者 王鼎兴 郑纬民 温冬婵 《Journal of Computer Science & Technology》 SCIE EI 1993年第3期233-242,共10页
In this paper,we focus on the compiling implementation of parallel logic language PARLOG and functional language ML on distributed memory multiprocessors.Under the graph rewriting framework, a Heterogeneous Parallel G... In this paper,we focus on the compiling implementation of parallel logic language PARLOG and functional language ML on distributed memory multiprocessors.Under the graph rewriting framework, a Heterogeneous Parallel Graph Rewriting Execution Model(HPGREM)is presented firstly.Then based on HPGREM,a parallel abstract machine PAM/TGR is described.Furthermore,several optimizing compilation schemes for executing declarative programs on transputer array are proposed. The performance statistics on a transputer array demonstrate the effectiveness of our model,parallel ab- stract machine,optimizing compilation strategies and compiler. 展开更多
关键词 Declarative language parallel graph rewriting execution model optimized parallel compiler distributed memory multiprocessors parallel abstract machine
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Research on the Optimal Parallel Algorithms of Broadcast-Class Problems 认领 引用
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作者 李晓峰 寿标 郑世荣 《Journal of Computer Science & Technology》 SCIE EI 1998年第5期455-463,共9页
Speedup is considered as the criterion of determining whether a parallel algorithm is optimal. But broadcast-class problems, existing only on parallel computer system, have no sequential algorithms at all. Speedup sta... Speedup is considered as the criterion of determining whether a parallel algorithm is optimal. But broadcast-class problems, existing only on parallel computer system, have no sequential algorithms at all. Speedup standard becomes invalid here. Through this research on broadcast algorithms under several typical parallel computation models,a model-independent evaluation standard min C2 is developed, which can be not only used to determine an optimal broadcasting algorithm, but also normalized to apply to any parallel algorithm. As a new idea, min C2 will lead to a new way in this field. 展开更多
关键词 Optimal parallel algorithm broadcast-class problem parallel computation model min C^2
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EDISON-WMW: Exact Dynamic Programing Solution of the Wilcoxon–Mann–Whitney Test 认领 引用 被引量：4
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作者 Alexander Marx Christina Backes +2 位作者 Eckart Meese Hans-Peter Lenhof Andreas Keller 《Genomics, Proteomics & Bioinformatics》 SCIE CAS CSCD 2016年第1期55-61,共7页
In many research disciplines, hypothesis tests are applied to evaluate whether findings are statistically significant or could be explained by chance. The Wilcoxon-Mann-Whitney （WMW） test is among the most popular h... In many research disciplines, hypothesis tests are applied to evaluate whether findings are statistically significant or could be explained by chance. The Wilcoxon-Mann-Whitney （WMW） test is among the most popular hypothesis tests in medicine and life science to analyze if two groups of samples are equally distributed. This nonparametric statistical homogeneity test is commonly applied in molecular diagnosis. Generally, the solution of the WMW test takes a high combinatorial effort for large sample cohorts containing a significant number of ties. Hence, P value is frequently approximated by a normal distribution. We developed EDISON-WMW, a new approach to calcu- late the exact permutation of the two-tailed unpaired WMW test without any corrections required and allowing for ties. The method relies on dynamic programing to solve the combinatorial problem of the WMW test efficiently. Beyond a straightforward implementation of the algorithm, we pre- sented different optimization strategies and developed a parallel solution. Using our program, the exact P value for large cohorts containing more than 1000 samples with ties can be calculated within minutes. We demonstrate the performance of this novel approach on randomly-generated data, benchmark it against 13 other commonly-applied approaches and moreover evaluate molec- ular biomarkers for lung carcinoma and chronic obstructive pulmonary disease （COPD）. We foundthat approximated P values were generally higher than the exact solution provided by EDISON- WMW. Importantly, the algorithm can also be applied to high-throughput omics datasets, where hundreds or thousands of features are included. To provide easy access to the multi-threaded version of EDISON-WMW, a web-based solution of our algorithm is freely available at http：// www.ccb.uni-saarland.de/software/wtest/. 展开更多
关键词 Wilcoxon-Mann-Whitneytest：Wilcoxon rank-sum test Dynamic programing Exact permutation Parallel optimization
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