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Balanced Multi-process Parallel Algorithm for Chemical Compound Inference with Given Path Frequencies

  • Conference paper
Algorithms and Architectures for Parallel Processing (ICA3PP 2010)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 6082))

Abstract

To enumerate chemical compounds with given path frequencies is a fundamental procedure in Chemo- and Bio-informatics. The applications include structure determination, novel molecular development, etc. The problem complexity has been proven as NP-hard. Many methods have been proposed to solve this problem. However, most of them are heuristic algorithms. Fujiwara et al. propose a sequential branch-and-bound algorithm. Although it reaches all solutions and avoids exhaustive searching, the computation time still increases significantly when the number of atoms increases. Hence, in this paper, a parallel algorithm is presented for solving this problem. The experimental results showed that computation time was reduced even when more processes were launched. Moreover, the speed-up ratio for most of the test cases was satisfactory and, furthermore, it showed potential for use in drug design.

This work is partially supported by Nation Science Council. (NSC98-2221-E-216-023 and NSC97-2221-E-216-020).

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Author information

Authors and Affiliations

  1. Department of Computer Science, National Tsing Hua University, Hsinchu, 300, Taiwan

    Jiayi Zhou, Kuei-Chung Shih & Chuan Yi Tang

  2. Department of Computer Science and Information Engineering, Chung Hua University, Hsinchu, 300, Taiwan

    Kun-Ming Yu

  3. Department of Computer Science and Information Engineering, Chang Gung University, Taoyuan, 333, Taiwan

    Chun Yuan Lin

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  1. Jiayi Zhou
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  2. Kun-Ming Yu
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  3. Chun Yuan Lin
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  4. Kuei-Chung Shih
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  5. Chuan Yi Tang
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Editor information

Editors and Affiliations

  1. Department of Computer Science and Information Engineering, Chung Hua University, 300, Hsinchu, Taiwan, China

    Ching-Hsien Hsu

  2. Department of Computer Science, St. Francis Xavier University, B2G 2W5, Antigonish, NS, Canada

    Laurence T. Yang

  3. Department of Computer Science ad Engineering, Seoul National University of Technology, 172 Gongreund 2-dong, Nowon-gou, 139-742, Seoul, Korea

    Jong Hyuk Park

  4. Division of Computer Engineering, Mokwon University, 302-729, Daejeon, Korea

    Sang-Soo Yeo

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© 2010 Springer-Verlag Berlin Heidelberg

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Zhou, J., Yu, KM., Lin, C.Y., Shih, KC., Tang, C.Y. (2010). Balanced Multi-process Parallel Algorithm for Chemical Compound Inference with Given Path Frequencies. In: Hsu, CH., Yang, L.T., Park, J.H., Yeo, SS. (eds) Algorithms and Architectures for Parallel Processing. ICA3PP 2010. Lecture Notes in Computer Science, vol 6082. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-13136-3_18

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  • DOI: https://doi.org/10.1007/978-3-642-13136-3_18

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-13135-6

  • Online ISBN: 978-3-642-13136-3

  • eBook Packages: Computer ScienceComputer Science (R0)

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