Kernel Methods for Chemical Compounds : From Classification to Design

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著者

    • AKUTSU Tatsuya
    • Bioinformatics Center, Institute for Chemical Research, Kyoto University
    • NAGAMOCHI Hiroshi
    • the Department of Applied Mathematics and Physics, Graduate School of Informatics, Kyoto University

抄録

In this paper, we briefly review kernel methods for analysis of chemical compounds with focusing on the authors' works. We begin with a brief review of existing kernel functions that are used for classification of chemical compounds and prediction of their activities. Then, we focus on the pre-image problem for chemical compounds, which is to infer a chemical structure that is mapped to a given feature vector, and has a potential application to design of novel chemical compounds. In particular, we consider the pre-image problem for feature vectors consisting of frequencies of labeled paths of length at most K. We present several time complexity results that include: NP-hardness result for a general case, polynomial time algorithm for tree structured compounds with fixed K, and polynomial time algorithm for K=1 based on graph detachment. Then we review practical algorithms for the pre-image problem, which are based on enumeration of chemical structures satisfying given constraints. We also briefly review related results which include efficient enumeration of stereoisomers of tree-like chemical compounds and efficient enumeration of outerplanar graphs.

In this paper, we briefly review kernel methods for analysis of chemical compounds with focusing on the authors' works. We begin with a brief review of existing kernel functions that are used for classification of chemical compounds and prediction of their activities. Then, we focus on the pre-image problem for chemical compounds, which is to infer a chemical structure that is mapped to a given feature vector, and has a potential application to design of novel chemical compounds. In particular, we consider the pre-image problem for feature vectors consisting of frequencies of labeled paths of length at most <i>K</i>. We present several time complexity results that include: NP-hardness result for a general case, polynomial time algorithm for tree structured compounds with fixed <i>K</i>, and polynomial time algorithm for <i>K</i>=1 based on graph detachment. Then we review practical algorithms for the pre-image problem, which are based on enumeration of chemical structures satisfying given constraints. We also briefly review related results which include efficient enumeration of stereoisomers of tree-like chemical compounds and efficient enumeration of outerplanar graphs.

収録刊行物

  • IEICE transactions on information and systems

    IEICE transactions on information and systems 94(10), 1846-1853, 2011-10-01

    IEICE(電子情報通信学会)

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各種コード

  • NII論文ID(NAID)
    10030193064
  • NII書誌ID(NCID)
    AA10826272
  • 本文言語コード
    ENG
  • 資料種別
    ART
  • ISSN
    09168532
  • データ提供元
    CJP書誌  IR  J-STAGE 
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