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GPD: A Graph Pattern Diffusion Kernel for Accurate Graph Classification with Applications in Cheminformatics
April-June 2010 (vol. 7 no. 2)
pp. 197-207
Aaron Smalter, University of Kansas, Lawrence
Jun (Luke) Huan, University of Kansas, Lawrence
Yi Jia, University of Kansas, Lawrence
Gerald Lushington, University of Kansas, Lawrence
Graph data mining is an active research area. Graphs are general modeling tools to organize information from heterogeneous sources and have been applied in many scientific, engineering, and business fields. With the fast accumulation of graph data, building highly accurate predictive models for graph data emerges as a new challenge that has not been fully explored in the data mining community. In this paper, we demonstrate a novel technique called graph pattern diffusion (GPD) kernel. Our idea is to leverage existing frequent pattern discovery methods and to explore the application of kernel classifier (e.g., support vector machine) in building highly accurate graph classification. In our method, we first identify all frequent patterns from a graph database. We then map subgraphs to graphs in the graph database and use a process we call "pattern diffusion” to label nodes in the graphs. Finally, we designed a graph alignment algorithm to compute the inner product of two graphs. We have tested our algorithm using a number of chemical structure data. The experimental results demonstrate that our method is significantly better than competing methods such as those kernel functions based on paths, cycles, and subgraphs.

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Index Terms:
Graph classification, graph alignment, frequent subgraph mining.
Aaron Smalter, Jun (Luke) Huan, Yi Jia, Gerald Lushington, "GPD: A Graph Pattern Diffusion Kernel for Accurate Graph Classification with Applications in Cheminformatics," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 7, no. 2, pp. 197-207, April-June 2010, doi:10.1109/TCBB.2009.80
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