Graph of Words Embedding for Molecular Structure-Activity Relationship Analysis

  • Jaume Gibert
  • Ernest Valveny
  • Horst Bunke
Part of the Lecture Notes in Computer Science book series (LNCS, volume 6419)


Structure-Activity relationship analysis aims at discovering chemical activity of molecular compounds based on their structure. In this article we make use of a particular graph representation of molecules and propose a new graph embedding procedure to solve the problem of structure-activity relationship analysis. The embedding is essentially an arrangement of a molecule in the form of a vector by considering frequencies of appearing atoms and frequencies of covalent bonds between them. Results on two benchmark databases show the effectiveness of the proposed technique in terms of recognition accuracy while avoiding high operational costs in the transformation.


Feature Vector Adjacency Matrix Graph Match Pattern Recognition Letter Edge Attribute 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


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Copyright information

© Springer-Verlag Berlin Heidelberg 2010

Authors and Affiliations

  • Jaume Gibert
    • 1
  • Ernest Valveny
    • 1
  • Horst Bunke
    • 2
  1. 1.Computer Vision CenterUniversitat Autònoma de BarcelonaBellaterraSpain
  2. 2.Institute for Computer Science and Applied MathematicsUniversity of BernBernSwitzerland

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