• Title/Summary/Keyword: Approximate Dynamic Programming

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A Practical Approximate Sub-Sequence Search Method for DNA Sequence Databases (DNA 시퀀스 데이타베이스를 위한 실용적인 유사 서브 시퀀스 검색 기법)

  • Won, Jung-Im;Hong, Sang-Kyoon;Yoon, Jee-Hee;Park, Sang-Hyun;Kim, Sang-Wook
    • Journal of KIISE:Databases
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    • v.34 no.2
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    • pp.119-132
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    • 2007
  • In molecular biology, approximate subsequence search is one of the most important operations. In this paper, we propose an accurate and efficient method for approximate subsequence search in large DNA databases. The proposed method basically adopts a binary trie as its primary structure and stores all the window subsequences extracted from a DNA sequence. For approximate subsequence search, it traverses the binary trie in a breadth-first fashion and retrieves all the matched subsequences from the traversed path within the trie by a dynamic programming technique. However, the proposed method stores only window subsequences of the pre-determined length, and thus suffers from large post-processing time in case of long query sequences. To overcome this problem, we divide a query sequence into shorter pieces, perform searching for those subsequences, and then merge their results. To verify the superiority of the proposed method, we conducted performance evaluation via a series of experiments. The results reveal that the proposed method, which requires smaller storage space, achieves 4 to 17 times improvement in performance over the suffix tree based method. Even when the length of a query sequence is large, our method is more than an order of magnitude faster than the suffix tree based method and the Smith-Waterman algorithm.

Extensions of Histogram Construction Algorithms for Interval Data (구간 데이타에 대한 히스토그램 구축 알고리즘의 확장)

  • Lee, Ho-Seok;Shim, Kyu-Seok;Yi, Byoung-Kee
    • Journal of KIISE:Databases
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    • v.34 no.4
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    • pp.369-377
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    • 2007
  • Histogram is one of tools that efficiently summarize data, and it is widely used for selectivity estimation and approximate query answering. Existing histogram construction algorithms are applicable to point data represented by a set of values. As often as point data, we can meet interval data such as daily temperature and daily stock prices. In this paper, we thus propose the histogram construction algorithms for interval data by extending several methods used in existing histogram construction algorithms. Our experiment results, using synthetic data, show our algorithms outperform naive extension of existing algorithms.

Parallel Computation for Extended Edit Distances Using the Shared Memory on GPU (GPU의 공유메모리를 활용한 확장편집거리 병렬계산)

  • Kim, Youngho;Na, Joong Chae;Sim, Jeong Seop
    • KIPS Transactions on Computer and Communication Systems
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    • v.4 no.7
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    • pp.213-218
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    • 2015
  • Given two strings X and Y (|X|=m, |Y|=n) over an alphabet ${\Sigma}$, the extended edit distance between X and Y can be computed using dynamic programming in O(mn) time and space. Recently, a parallel algorithm that takes O(m+n) time and O(mn) space using m threads to compute the extended edit distance between X and Y was presented. In this paper, we present an improved parallel algorithm using the shared memory on GPU. The experimental results show that our parallel algorithm runs about 19~25 times faster than the previous parallel algorithm.

Parallel Computation For The Edit Distance Based On The Four-Russians' Algorithm (4-러시안 알고리즘 기반의 편집거리 병렬계산)

  • Kim, Young Ho;Jeong, Ju-Hui;Kang, Dae Woong;Sim, Jeong Seop
    • KIPS Transactions on Computer and Communication Systems
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    • v.2 no.2
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    • pp.67-74
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    • 2013
  • Approximate string matching problems have been studied in diverse fields. Recently, fast approximate string matching algorithms are being used to reduce the time and costs for the next generation sequencing. To measure the amounts of errors between two strings, we use a distance function such as the edit distance. Given two strings X(|X| = m) and Y(|Y| = n) over an alphabet ${\Sigma}$, the edit distance between X and Y is the minimum number of edit operations to convert X into Y. The edit distance between X and Y can be computed using the well-known dynamic programming technique in O(mn) time and space. The edit distance also can be computed using the Four-Russians' algorithm whose preprocessing step runs in $O((3{\mid}{\Sigma}{\mid})^{2t}t^2)$ time and $O((3{\mid}{\Sigma}{\mid})^{2t}t)$ space and the computation step runs in O(mn/t) time and O(mn) space where t represents the size of the block. In this paper, we present a parallelized version of the computation step of the Four-Russians' algorithm. Our algorithm computes the edit distance between X and Y in O(m+n) time using m/t threads. Then we implemented both the sequential version and our parallelized version of the Four-Russians' algorithm using CUDA to compare the execution times. When t = 1 and t = 2, our algorithm runs about 10 times and 3 times faster than the sequential algorithm, respectively.

Development of Intelligent ATP System Using Genetic Algorithm (유전 알고리듬을 적용한 지능형 ATP 시스템 개발)

  • Kim, Tai-Young
    • Journal of Intelligence and Information Systems
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    • v.16 no.4
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    • pp.131-145
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    • 2010
  • The framework for making a coordinated decision for large-scale facilities has become an important issue in supply chain(SC) management research. The competitive business environment requires companies to continuously search for the ways to achieve high efficiency and lower operational costs. In the areas of production/distribution planning, many researchers and practitioners have developedand evaluated the deterministic models to coordinate important and interrelated logistic decisions such as capacity management, inventory allocation, and vehicle routing. They initially have investigated the various process of SC separately and later become more interested in such problems encompassing the whole SC system. The accurate quotation of ATP(Available-To-Promise) plays a very important role in enhancing customer satisfaction and fill rate maximization. The complexity for intelligent manufacturing system, which includes all the linkages among procurement, production, and distribution, makes the accurate quotation of ATP be a quite difficult job. In addition to, many researchers assumed ATP model with integer time. However, in industry practices, integer times are very rare and the model developed using integer times is therefore approximating the real system. Various alternative models for an ATP system with time lags have been developed and evaluated. In most cases, these models have assumed that the time lags are integer multiples of a unit time grid. However, integer time lags are very rare in practices, and therefore models developed using integer time lags only approximate real systems. The differences occurring by this approximation frequently result in significant accuracy degradations. To introduce the ATP model with time lags, we first introduce the dynamic production function. Hackman and Leachman's dynamic production function in initiated research directly related to the topic of this paper. They propose a modeling framework for a system with non-integer time lags and show how to apply the framework to a variety of systems including continues time series, manufacturing resource planning and critical path method. Their formulation requires no additional variables or constraints and is capable of representing real world systems more accurately. Previously, to cope with non-integer time lags, they usually model a concerned system either by rounding lags to the nearest integers or by subdividing the time grid to make the lags become integer multiples of the grid. But each approach has a critical weakness: the first approach underestimates, potentially leading to infeasibilities or overestimates lead times, potentially resulting in excessive work-inprocesses. The second approach drastically inflates the problem size. We consider an optimized ATP system with non-integer time lag in supply chain management. We focus on a worldwide headquarter, distribution centers, and manufacturing facilities are globally networked. We develop a mixed integer programming(MIP) model for ATP process, which has the definition of required data flow. The illustrative ATP module shows the proposed system is largely affected inSCM. The system we are concerned is composed of a multiple production facility with multiple products, multiple distribution centers and multiple customers. For the system, we consider an ATP scheduling and capacity allocationproblem. In this study, we proposed the model for the ATP system in SCM using the dynamic production function considering the non-integer time lags. The model is developed under the framework suitable for the non-integer lags and, therefore, is more accurate than the models we usually encounter. We developed intelligent ATP System for this model using genetic algorithm. We focus on a capacitated production planning and capacity allocation problem, develop a mixed integer programming model, and propose an efficient heuristic procedure using an evolutionary system to solve it efficiently. This method makes it possible for the population to reach the approximate solution easily. Moreover, we designed and utilized a representation scheme that allows the proposed models to represent real variables. The proposed regeneration procedures, which evaluate each infeasible chromosome, makes the solutions converge to the optimum quickly.

Facial Expression Control of 3D Avatar using Motion Data (모션 데이터를 이용한 3차원 아바타 얼굴 표정 제어)

  • Kim Sung-Ho;Jung Moon-Ryul
    • The KIPS Transactions:PartA
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    • v.11A no.5
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    • pp.383-390
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    • 2004
  • This paper propose a method that controls facial expression of 3D avatar by having the user select a sequence of facial expressions in the space of facial expressions. And we setup its system. The space of expression is created from about 2400 frames consist of motion captured data of facial expressions. To represent the state of each expression, we use the distance matrix that represents the distances between pairs of feature points on the face. The set of distance matrices is used as the space of expressions. But this space is not such a space where one state can go to another state via the straight trajectory between them. We derive trajectories between two states from the captured set of expressions in an approximate manner. First, two states are regarded adjacent if the distance between their distance matrices is below a given threshold. Any two states are considered to have a trajectory between them If there is a sequence of adjacent states between them. It is assumed . that one states goes to another state via the shortest trajectory between them. The shortest trajectories are found by dynamic programming. The space of facial expressions, as the set of distance matrices, is multidimensional. Facial expression of 3D avatar Is controled in real time as the user navigates the space. To help this process, we visualized the space of expressions in 2D space by using the multidimensional scaling(MDS). To see how effective this system is, we had users control facial expressions of 3D avatar by using the system. As a result of that, users estimate that system is very useful to control facial expression of 3D avatar in real-time.