Wu Jigang, Thambipillai Srikanthan · 2006
www.elsevier.com/locate/ipl A low-complex algorithm is proposed for the hardware/software partitioning. The proposed algorithm employs dynamic programming principles while accounting for communication delays. It is shown that the time complexity of the latest algorithm has been reduced from O(n2 · A) to O(n · A), without increase in space complexity, for n code fragments and hardware area A. © 2005 Elsevier B.V. All rights reserved.
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2008
Abstract. Multiple sequence alignment (MSA) is one of the most basic and central tasks for many studies in modern biology. In this paper, we present a new progressive alignment algorithm for this very difficult problem. Given two groups A and B of aligned sequences, this algorithm uses Dynamic Programming and the sum-of-pairs objective function to determine an optimal alignment C of A and B. The proposed algorithm has a much lower time complexity compared with a previously published algorithm for the same task [11]. Its performance is extensively assessed on the well-known BAliBase benchmarks and compared with several state-of-the-art MSA tools.
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Wei‐Kuo Chiang, Yun-Fan Huang, Fengming Chen · Future Generation Computer Systems · 2025
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Zhexue Wei, Daming Zhu, Lusheng Wang · Journal of Computational Biology · 2015
The exemplar breakpoint distance problem is motivated by finding conserved sets of genes between two genomes. It asks to find respective exemplars in two genomes to minimize the breakpoint distance between them. If one genome has no repeated gene (called trivial genome) and the other has genes repeating at most twice, it is referred to as the (1, 2)-exemplar breakpoint distance problem, EBD(1, 2) for short. Little has been done on algorithm design for this problem by now. In this article, we propose a parameter to describe the maximum physical span between two copies of a gene in a genome, and based on it, design a fixed-parameter algorithm for EBD(1, 2). Using a dynamic programming approach, our algorithm can take O(4(s)n(2)) time and O(4(s)n) space to solve an EBD(1, 2) instance that has two genomes of n genes where the second genome has each two copies of a gene spanning at most s copies of the genes. Our algorithm can also be used to compute the maximum adjacencies between two genomes. The algorithm has been implemented in C++. Simulations on randomly generated data have verified the effectiveness of our algorithm. The software package is available from the authors.
Cited by 3
Shou‐Hsuan Stephen Huang, Hongfei Liu, Venkatraman Viswanathan · Theoretical Computer Science · 1992
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Paulo R. Zanjácomo, Carlos Humes Júnior · 1992
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Ji Wei, Shu Chun Yu, Wen Dong et al. · Advanced materials research · 2014
A stereo matching algorithm was proposed based on pyramid algorithm and dynamic programming. High and low resolution images was computed by pyramid algorithm, and then candidate control points were stroke on low-resolution image, and final control points were stroke on the high-resolution images. Finally, final control points were used in directing stereo matching based on dynamic programming. Since the striking of candidate control points on low-resolution image, the time is greatly reduced. Experiments show that the proposed method has a high matching precision.
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Tomi Silander, Tze-Yun Leong · Lecture notes in computer science · 2013
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Wenbo Dai, Yabo Hao, Shenggang Liu et al. · Lecture notes in electrical engineering · 2025
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Jiajia Li, Guangming Tan, Mingyu Chen · 2010
As the complexity of current computer architecture increases, domain-specific program generators are extensively used to implement performance portable libraries. Dynamic programming is a performance-critical kernel in many applications including engineering operations and bioinformatics. In this paper, we propose an Automatically Tuned Dynamic Programming (ATDP) to optimize performance of dynamic programming algorithm across various architectures. First, an algorithm-by-blocks for dynamic programming is designed to facilitate optimizing with well-known techniques including cache and register tiling. Further, the parameterized algorithm-by-blocks is cooperative with an auto-tuning framework and leverages a hill climbing algorithm to search the possible best program on a given platform. The experiments on two ×86 processors demonstrate that (i) the generated scalar programs improve performance by over 10 times, (ii) the vector programs further speedup the scalar ones by a factor of 4 and 2 for single-precision and double-precision, respectively.
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Moshe Sniedovich · ACM SIGAPL APL Quote Quad · 1993
The travelling salesman problem (TSP) is considered "...the most prominent unsolved combinatorial optimization problems .._" [1, p. 2]. And to be sure, the best that existing solution methods can do is to handle relatively small TSPs or large problems with special structures.
Cited by 8Open access
S.D. Bond, B. Fox · IEE Proceedings C Generation Transmission and Distribution · 1986
The economic scheduling of power generation is considered, and an improved algorithm based on a combination of mixed integer-linear and dynamic programming presented. Mixed integer-linear programming is used to determine feasible combinations of units at each scheduling point, while a novel dynamic programming approach identifies promising scheduling routes in the time domain. The algorithm obtains the same solutions as mixed integer-linear programming, but with significant savings in the solution times required and the amount of computer memory used.
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Dongna Zhang · 2022 IEEE 2nd International Conference on Mobile Networks and Wireless Communications (ICMNWC) · 2022
With the development of global economic integration, international exchanges become more and more frequent, and the language commonly used in communication is gradually recognized and popularized. If the use and popularity of a language reach a monopoly degree, there will be a strong language. There is no denying that English has developed into the most powerful language in the world. Not only a large number of people and countries use it as their mother tongue, but also more countries and people use it as a second language. No other language can compare it in terms of the number of speakers, the wide geographical distribution and the wide range of applications. Therefore, its status as a “world lingua franca” has become increasingly prominent. The status of English is not only an inevitability of historical development, but also a manifestation of powerful languages in the language field. This phenomenon not only greatly destroys the fairness of the language environment worldwide, but also causes many languages or dialects in the world to be excluded or even gradually perish or become extinct, resulting in serious imbalance of language development. Such decay and extinction of language is not a normal phenomenon of language development and change, but an important part of the current world ecological crisis. This paper studies the literature language system based on dynamic programming algorithm, and expounds the basic principles of literature language system. The data show that the research of literary language system based on dynamic programming algorithm has an obvious scientific guiding effect on the development of literary language and effectively promotes the planning of literary language.
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Gang Sheng, Yanguang Sun, Xiaodong Hao et al. · 2024
Regarding the gas scheduling issue in the coal gas systems of steel enterprises, a gas scheduling optimization model is proposed based on the multi-input and multi-output characteristics of the gas system. This model combines knowledge-based and dynamic programming approaches, utilizing production experience to establish scheduling knowledge. The model calculates the scheduling results under two scenarios: non-optimized and optimized, across various time dimensions (1 minute, 15 minutes, 30 minutes) and different production conditions (with and without blast furnace maintenance). The results from simulation experiments with field data demonstrate the model's timeliness and practicality, providing a reasonable guide for developing gas system schemes. This model is particularly suitable for steel production enterprises with no gas holders and significant pipeline pressure fluctuations, offering a scientific and effective guidance method. This research can be applied to solve energy optimization problems in complex production systems and scenarios.
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束鑫, Wu Jun -, 潘磊 et al. · Journal of Image and Graphics · 2011
用形状轮廓上点的坐标位置相对于形状重心位置的分布关系描述形状，提出一种极坐标下形状轮廓点分布直方图描述符(contour points distribution histogram)，该描述符不仅符合人眼的视觉直观感受、计算简单，而且其本质上具有缩放和平移不变性。用动态规划算法(dynamic programming algorithm)来度量轮廓点分布直方图之间的距离，部分解决了轮廓点分布直方图对于旋转不变性的要求。在多个形状图像数据库中的实验结果表明，该方法在单目标封闭轮廓的形状图像检索中取得了良好效果。
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Ferreira, C.E., Freire, A. S., Giuseppe Diego Puglia · HAL (Le Centre pour la Communication Scientifique Directe) · 2011
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Olivier Beaumont, Lionel Eyraud‐Dubois, Alena Shilova · SPIRE - Sciences Po Institutional REpository · 2022
The training phase in Deep Neural Networks (DNNs) is very computationally intensive and is nowadays often performed on parallel computing platforms, ranging from a few GPUs to several thousand GPUs. The strategy of choice for the parallelization of training is the so-called data parallel approach, based of the parallel training of the different inputs (typically images) and a the aggregation of network weights with collective communications (AllReduce). The scalability of this approach is limited both by the memory available on each node and the networking capacities for collective operations. Recently, a parallel model approach, in which the network weights are distributed and images are trained in a pipeline/stream manner over the computational nodes has been proposed (Pipedream, Gpipe). In this paper, we formalize in detail the optimization problem associated with the placement of DNN layers onto computation resources when using pipelined model parallelism, and we derive a dynamic programming based heuristic, MadPipe, that allows to significantly improve the performance of the parallel model approach compared to the literature.
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Silander T.,, Tze-Yun LEONG, · Institutional Knowledge (InK) - Institutional Knowledge at Singapore Management University (Singapore Management University) · 2013
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Hal Berghel, David Roach · ACM Transactions on Information Systems · 1996
We describe an improvement on Ukkonen's Enhanced Dynamic Programming (EHD) approximate string-matching algorithm for unit-penalty four-edit comparisons. The new algorithm has an asymptotic complexity similar to that of Ukkonen's but is significantly faster due to a decrease in the number of array cell calculations. A 42% speedup was achieved in an application involving name comparisons. Even greater improvements are possible when comparing longer and more dissimilar strings. Although the speed of the algorithm under consideration is comparable to other fast ASM algorithms, it has greater effectiveness in text-processing applications because it supports all four basic Damerau-type editing operations.
Cited by 26Open access
Yu-Yen Mo, Chris Chu · IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems · 2001
We present an algorithm for delay minimization of interconnect trees by simultaneous buffer insertion/sizing and wire sizing in this paper. Both wire widths and buffer sizes are chosen from user-defined discrete sets. Our algorithm integrates the quadratic programming approach for handling a wire branch into the dynamic programming (DP) framework. Our experimental results show that our hybrid dynamic/quadratic programming algorithm is faster, more accurate, and uses considerably less memory than the pure DP approach.
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