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Parallelization of Enumerating Tree-like Chemical Compounds by Breadth-first Search Order
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- Morihiro Hayashida
- Bioinformatics Center, Institute for Chemical Research, Kyoto University
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- Jira Jindalertudomdee
- Bioinformatics Center, Institute for Chemical Research, Kyoto University
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- Yang Zhao
- Bioinformatics Center, Institute for Chemical Research, Kyoto University
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- Tatsuya Akutsu
- Bioinformatics Center, Institute for Chemical Research, Kyoto University
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Description
Enumerating chemical compounds greatly assists designing drugs and determining chemical structures from mass spectrometry. In our previous study, we developed efficient algorithms, BfsSimEnum and BfsMulEnum for enumerating tree-like chemical compounds without and with multiple bonds, respectively. In this technical report, we develop a parallelized algorithm BfsEnumP by modifying BfsSimEnum in a simple manner to further reduce execution time. BfsSimEnum constructs a family tree in which each node denotes a molecular tree. BfsEnumP divides the family tree at some depth, and each subtree to be constructed is assigned to a processor. For evaluation, we perform experiments for several instances with varying the division depth and the number of processors, and show that it achieves about 80% parallelization efficiency.
Journal
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- IPSJ SIG Notes
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IPSJ SIG Notes 2014 (23), 1-2, 2014-02-24
Information Processing Society of Japan (IPSJ)
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Keywords
Details 詳細情報について
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- CRID
- 1572261552743193088
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- NII Article ID
- 110009673895
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- NII Book ID
- AN10505667
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- ISSN
- 09196072
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- Text Lang
- en
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- Data Source
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- CiNii Articles