Graph kernel - Wikipedia https://en.wikipedia.

org/wiki/Graph_kernel

Graph kernel
In structure mining, a domain of learning on structured data objects in machine learning, a graph
kernel is a kernel function that computes an inner product on graphs.[1] Graph kernels can be
intuitively understood as functions measuring the similarity of pairs of graphs. They allow kernelized
learning algorithms such as support vector machines to work directly on graphs, without having to do
feature extraction to transform them to fixed-length, real-valued feature vectors. They find
applications in bioinformatics, in chemoinformatics (as a type of molecule kernels[2]), and in social
network analysis.[1]

Concepts of graph kernels have been around since the 1999, when D. Haussler[3] introduced
convolutional kernels on discrete structures. The term graph kernels was more officially coined in
2002 by R. I. Kondor and John Lafferty[4] as kernels on graphs, i.e. similarity functions between the
nodes of a single graph, with the World Wide Web hyperlink graph as a suggested application. In
2003, Gaertner et al.[5] and Kashima et al.[6] defined kernels between graphs. In 2010, Vishwanathan
et al. gave their unified framework.[1] In 2018, Ghosh et al. [7] described the history of graph kernels
and their evolution over two decades.

An example of a kernel between graphs is the random walk kernel[5][6], which conceptually
performs random walks on two graphs simultaneously, then counts the number of paths that were
produced by both walks. This is equivalent to doing random walks on the direct product of the pair of
graphs, and from this, a kernel can be derived that can be efficiently computed.[1]

Applications
The marginalized graph kernel has been shown to allow accurate predictions of the atomization
energy of small organic molecules[8].

References
1. S.V. N. Vishwanathan; Nicol N. Schraudolph; Risi Kondor; Karsten M. Borgwardt (2010). "Graph
kernels" (http://jmlr.csail.mit.edu/papers/volume11/vishwanathan10a/vishwanathan10a.pdf) (PDF).
Journal of Machine Learning Research. 11: 1201–1242.
2. L. Ralaivola; S. J. Swamidass; H. Saigo; P. Baldi (2005). "Graph kernels for chemical informatics".
Neural Networks. 18 (8): 1093–1110. doi:10.1016/j.neunet.2005.07.009 (https://doi.org/10.1016%
2Fj.neunet.2005.07.009). PMID 16157471 (https://pubmed.ncbi.nlm.nih.gov/16157471).
3. Haussler, David (1999). Convolution Kernels on Discrete Structures. CiteSeerX 10.1.1.110.638 (ht
tps://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.110.638).
4. Risi Imre Kondor; John Lafferty (2002). Diffusion Kernels on Graphs and Other Discrete Input
Spaces (http://people.cs.uchicago.edu/~risi/papers/diffusion-kernels.pdf) (PDF). Proc. Int'l Conf.
on Machine Learning (ICML).
5. Thomas Gaertner; Peter Flach; Stefan Wrobel (2003). On graph kernels: Hardness results and
efficient alternatives. Proc. the 16th Annual Conference on Computational Learning Theory
(COLT) and the 7th Kernel Workshop. doi:10.1007/978-3-540-45167-9_11 (https://doi.org/10.100

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Graph kernel - Wikipedia https://en.wikipedia.org/wiki/Graph_kernel

7%2F978-3-540-45167-9_11).
6. Hisashi Kashima; Koji Tsuda; Akihiro Inokuchi (2003). Marginalized kernels between labeled
graphs (http://www.aaai.org/Papers/ICML/2003/ICML03-044.pdf) (PDF). Proc. the 20th
International Conference on Machine Learning (ICML).
7. Ghosh, Swarnendu; Das, Nibaran; Gonçalves, Teresa; Quaresma, Paulo; Kundu, Mahantapas
(2018). "The journey of graph kernels through two decades". Computer Science Review. 27:
88–111. doi:10.1016/j.cosrev.2017.11.002 (https://doi.org/10.1016%2Fj.cosrev.2017.11.002).
8. Yu-Hang Tang; Wibe A. de Jong (2019). "Prediction of atomization energy using graph kernel and
active learning". The Journal of Chemical Physics. 150 (4): 044107. arXiv:1810.07310 (https://arxi
v.org/abs/1810.07310). Bibcode:2019JChPh.150d4107T (https://ui.adsabs.harvard.edu/abs/2019J
ChPh.150d4107T). doi:10.1063/1.5078640 (https://doi.org/10.1063%2F1.5078640).
PMID 30709286 (https://pubmed.ncbi.nlm.nih.gov/30709286).

See also
Tree kernel, as special case of non-cyclic graphs
Molecule mining, as special case of small multi-label graphs

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