Graph of words embedding for molecular structure-activity relationship analysis

Authors:
Jaume Gibert;Ernest Valveny;Horst Bunke
Affiliations:
Computer Vision Center, Universitat Autònoma de Barcelona, Bellaterra, Spain;Computer Vision Center, Universitat Autònoma de Barcelona, Bellaterra, Spain;Institute for Computer Science and Applied Mathematics, University of Bern, Bern, Switzerland
Venue:
CIARP'10 Proceedings of the 15th Iberoamerican congress conference on Progress in pattern recognition, image analysis, computer vision, and applications
Year:
2010

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Abstract

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.