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Frequent Subgraph Retrieval in Geometric Graph Databases


Technical Report


Discovery of knowledge from geometric graph databases is of particular importance in chemistry and biology, because chemical compounds and proteins are represented as graphs with 3D geometric coordinates. In such applications, scientists are not interested in the statistics of the whole database. Instead they need information about a novel drug candidate or protein at hand, represented as a query graph. We propose a polynomial-delay algorithm for geometric frequent subgraph retrieval. It enumerates all subgraphs of a single given query graph which are frequent geometric epsilon-subgraphs under the entire class of rigid geometric transformations in a database. By using geometric epsilon-subgraphs, we achieve tolerance against variations in geometry. We compare the proposed algorithm to gSpan on chemical compound data, and we show that for a given minimum support the total number of frequent patterns is substantially limited by requiring geometric matching. Although the computation time per pattern is larger than for non-geometric graph mining, the total time is within a reasonable level even for small minimum support.

Author(s): Nowozin, S. and Tsuda, K.
Number (issue): 180
Year: 2008
Month: November
Day: 0

Department(s): Empirical Inference
Bibtex Type: Technical Report (techreport)

Institution: Max-Planck Institute for Biological Cybernetics, Tübingen, Germany

Digital: 0
Language: en
Organization: Max-Planck-Gesellschaft
School: Biologische Kybernetik

Links: PDF


  title = {Frequent Subgraph Retrieval in Geometric Graph Databases},
  author = {Nowozin, S. and Tsuda, K.},
  number = {180},
  organization = {Max-Planck-Gesellschaft},
  institution = {Max-Planck Institute for Biological Cybernetics, Tübingen, Germany},
  school = {Biologische Kybernetik},
  month = nov,
  year = {2008},
  month_numeric = {11}