skip to main content
10.1145/3447548.3467442acmconferencesArticle/Chapter ViewAbstractPublication PageskddConference Proceedingsconference-collections
research-article
Open Access

Filtration Curves for Graph Representation

Authors Info & Claims
Published:14 August 2021Publication History

ABSTRACT

The two predominant approaches to graph comparison in recent years are based on (i) enumerating matching subgraphs or (ii) comparing neighborhoods of nodes. In this work, we complement these two perspectives with a third way of representing graphs: using filtration curves from topological data analysis that capture both edge weight information and global graph structure. Filtration curves are highly efficient to compute and lead to expressive representations of graphs, which we demonstrate on graph classification benchmark datasets. Our work opens the door to a new form of graph representation in data mining.

Skip Supplemental Material Section

Supplemental Material

filtration_curves_for_graph_representation-leslie_obray-bastian_rieck-38958016-yqAO.mp4

mp4

120.8 MB

References

  1. Kubilay Atasu and Thomas Mittelholzer. 2019. Linear-Complexity Data-Parallel Earth Mover's Distance Approximations. In ICML, Vol. 97. PMLR, 364--373.Google ScholarGoogle Scholar
  2. Serguei A. Barannikov. 1994. The Framed Morse Complex and its Invariants. Advances in Soviet Mathematics, Vol. 21 (1994), 93--115.Google ScholarGoogle Scholar
  3. Eric Berry, Yen-Chi Chen, Jessi Cisewski-Kehe, and Brittany Terese Fasy. 2018. Functional Summaries of Persistence Diagrams. arXiv e-prints, Article arXiv:1804.01618 (2018), arXiv:1804.01618 pages.arxiv: 1804.01618 [stat.ME]Google ScholarGoogle Scholar
  4. Karsten Borgwardt, Elisabetta Ghisu, Felipe Llinares-López, Leslie O'Bray, and Bastian Rieck. 2020. Graph Kernels: State-of-the-Art and Future Challenges. Foundations and Trends® in Machine Learning, Vol. 13, 5--6 (2020), 531--712.Google ScholarGoogle ScholarCross RefCross Ref
  5. Karsten Borgwardt and Hans-Peter Kriegel. 2005. Shortest-path kernels on graphs. In Proceedings of the Fifth IEEE International Conference on Data Mining. IEEE Computer Society, Washington, DC, USA, 74--81.Google ScholarGoogle ScholarDigital LibraryDigital Library
  6. Karsten M. Borgwardt, Cheng Soon Ong, Stefan Schönauer, S. V. N. Vishwanathan, Alex J. Smola, and Hans-Peter Kriegel. 2005. Protein function prediction via graph kernels. Bioinformatics, Vol. 21, suppl 1 (2005), i47--i56.Google ScholarGoogle ScholarDigital LibraryDigital Library
  7. Horst Bunke and Kaspar Riesen. 2007. A Family of Novel Graph Kernels for Structural Pattern Recognition. In Progress in Pattern Recognition, Image Analysis and Applications. Springer, Heidelberg, Germany, 20--31.Google ScholarGoogle Scholar
  8. Mathieu Carrière, Frédéric Chazal, Yuichi Ike, Théo Lacombe, Martin Royer, and Yuhei Umeda. 2020. PersLay: A Neural Network Layer for Persistence Diagrams and New Graph Topological Signatures. In Proceedings of the 23rd International Conference on Artificial Intelligence and Statistics, Vol. 108. PMLR, 2786--2796.Google ScholarGoogle Scholar
  9. Deli Chen, Yankai Lin, Wei Li, Peng Li, Jie Zhou, and Xu Sun. 2020. Measuring and Relieving the Over-Smoothing Problem for Graph Neural Networks from the Topological View. Proceedings of the AAAI Conference on Artificial Intelligence, Vol. 34, 4 (2020), 3438--3445.Google ScholarGoogle ScholarCross RefCross Ref
  10. Ilya Chevyrev, Vidit Nanda, and Harald Oberhauser. 2020. Persistence Paths and Signature Features in Topological Data Analysis. IEEE Transactions on Pattern Analysis and Machine Intelligence, Vol. 42, 1 (2020), 192--202.Google ScholarGoogle ScholarDigital LibraryDigital Library
  11. Herbert Edelsbrunner, David Letscher, and Afra Zomorodian. 2002. Topological Persistence and Simplification. Discrete & Computational Geometry, Vol. 28, 4 (2002), 511--533.Google ScholarGoogle ScholarDigital LibraryDigital Library
  12. Federico Errica, Marco Podda, Davide Bacciu, and Alessio Micheli. 2020. A Fair Comparison of Graph Neural Networks for Graph Classification. In ICLR .Google ScholarGoogle Scholar
  13. Justin Gilmer, Samuel S Schoenholz, Patrick F Riley, Oriol Vinyals, and George E Dahl. 2017. Neural message passing for quantum chemistry. In ICML. PMLR, 1263--1272.Google ScholarGoogle Scholar
  14. Robert Glem, Andreas Bender, Catrin Hasselgren, Lars Carlsson, Scott Boyer, and James Smith. 2006. Circular fingerprints: Flexible molecular descriptors with applications from physical chemistry to ADME. IDrugs : The Investigational Drugs Journal, Vol. 9 (2006), 199--204.Google ScholarGoogle Scholar
  15. Alexander Grigor'yan. 2009. Heat Kernel and Analysis on Manifolds .American Mathematical Society.Google ScholarGoogle Scholar
  16. Christoph Hofer, Roland Kwitt, Marc Niethammer, and Andreas Uhl. 2017. Deep Learning with Topological Signatures. In NeurIPS, I. Guyon, U. V. Luxburg, S. Bengio, H. Wallach, R. Fergus, S. Vishwanathan, and R. Garnett (Eds.). Curran Associates, Inc., 1634--1644.Google ScholarGoogle Scholar
  17. Christoph D. Hofer, Florian Graf, Bastian Rieck, Marc Niethammer, and Roland Kwitt. 2020. Graph Filtration Learning. In ICML, Hal Daumé III and Aarti Singh (Eds.), Vol. 119. PMLR, 4314----4323.Google ScholarGoogle Scholar
  18. Thomas N. Kipf and Max Welling. 2017. Semi-Supervised Classification with Graph Convolutional Networks. In ICLR .Google ScholarGoogle Scholar
  19. Risi Kondor and Horace Pan. 2016. The Multiscale Laplacian Graph Kernel. In NeurIPS, D. D. Lee, M. Sugiyama, U. V. Luxburg, I. Guyon, and R. Garnett (Eds.). Curran Associates, Inc., 2990--2998.Google ScholarGoogle Scholar
  20. Nils Kriege and Petra Mutzel. 2012. Subgraph Matching Kernels for Attributed Graphs. In ICML .Google ScholarGoogle Scholar
  21. Nils M. Kriege, Pierre-Louis Giscard, and Richard C. Wilson. 2016. On Valid Optimal Assignment Kernels and Applications to Graph Classification. In NeurIPS. 1623--1631.Google ScholarGoogle Scholar
  22. Nils M. Kriege, Fredrik D. Johansson, and Christopher Morris. 2020. A Survey on Graph Kernels. Applied Network Science, Vol. 5, 1 (2020), 6.Google ScholarGoogle ScholarCross RefCross Ref
  23. Yong Lin, Linyuan Lu, and Shing-Tung Yau. 2011. Ricci curvature of graphs. Tohoku Mathematical Journal, Second Series, Vol. 63, 4 (2011), 605--627.Google ScholarGoogle ScholarCross RefCross Ref
  24. H. Ling and K. Okada. 2007. An Efficient Earth Mover's Distance Algorithm for Robust Histogram Comparison. IEEE Transactions on Pattern Analysis and Machine Intelligence, Vol. 29, 5 (2007), 840--853.Google ScholarGoogle ScholarDigital LibraryDigital Library
  25. Christopher Morris, Nils M. Kriege, Kristian Kersting, and Petra Mutzel. 2016. Faster Kernels for Graphs with Continuous Attributes via Hashing. In Proceedings of the 16th IEEE International Conference on Data Mining. 1095--1100.Google ScholarGoogle ScholarCross RefCross Ref
  26. T. Ramraj and R. Prabhakar. 2015. Frequent Subgraph Mining Algorithms -- A Survey. Procedia Computer Science, Vol. 47 (2015), 197--204. Graph Algorithms, High Performance Implementations and Its Applications ( ICGHIA 2014 ).Google ScholarGoogle ScholarCross RefCross Ref
  27. Bastian Rieck, Christian Bock, and Karsten Borgwardt. 2019. A Persistent Weisfeiler--Lehman Procedure for Graph Classification. In ICML. PMLR, 5448--5458.Google ScholarGoogle Scholar
  28. Bastian Rieck, Filip Sadlo, and Heike Leitte. 2020. Topological Machine Learning with Persistence Indicator Functions. In Topological Methods in Data Analysis and Visualization V, Hamish Carr, Issei Fujishiro, Filip Sadlo, and Shigeo Takahashi (Eds.). Springer, 87--101.Google ScholarGoogle Scholar
  29. Kaspar Riesen. 2015. Graph Edit Distance. In Structural Pattern Recognition with Graph Edit Distance: Approximation Algorithms and Applications. Springer, Chapter 2, 29--44.Google ScholarGoogle Scholar
  30. Nino Shervashidze and Karsten Borgwardt. 2009. Fast subtree kernels on graphs. In NeurIPS. 1660--1668.Google ScholarGoogle Scholar
  31. N. Shervashidze, P. Schweitzer, E. Jan van Leeuwen, K. Mehlhorn, and K. M. Borgwardt. 2011. Weisfeiler--Lehman Graph Kernels. Journal of Machine Learning Research 12 (2011), 2539--2561.Google ScholarGoogle ScholarDigital LibraryDigital Library
  32. Martin Simonovsky and Nikos Komodakis. 2017. Dynamic edge-conditioned filters in convolutional neural networks on graphs. In Proceedings of the IEEE Conference on Computer Vision and Pattern Recognition. 3693--3702.Google ScholarGoogle ScholarCross RefCross Ref
  33. Jeffrey J. Sutherland, Lee A. O'Brien, and Donald F. Weaver. 2003. Spline-fitting with a genetic algorithm: a method for developing classification structure-activity relationships. Journal of Chemical Information and Computer Sciences, Vol. 43, 6 (2003), 1906--1915.Google ScholarGoogle ScholarCross RefCross Ref
  34. Matteo Togninalli, Elisabetta Ghisu, Felipe Llinares-López, Bastian Rieck, and Karsten Borgwardt. 2019. Wasserstein Weisfeiler--Lehman Graph Kernels. In NeurIPS, H. Wallach, H. Larochelle, A. Beygelzimer, F. d'Alché Buc, E. Fox, and R. Garnett (Eds.). Curran Associates, Inc., 6436--6446.Google ScholarGoogle Scholar
  35. Anton Tsitsulin, Davide Mottin, Panagiotis Karras, Alexander Bronstein, and Emmanuel Müller. 2018. NetLSD: Hearing the Shape of a Graph. In Proceedings of the 24th ACM SIGKDD International Conference on Knowledge Discovery & Data Mining. 2347--2356.Google ScholarGoogle ScholarDigital LibraryDigital Library
  36. Yuhei Umeda. 2017. Time Series Classification via Topological Data Analysis. Transactions of the Japanese Society for Artificial Intelligence, Vol. 32, 3 (2017), D--G72_1--12.Google ScholarGoogle ScholarCross RefCross Ref
  37. Zonghan Wu, Shirui Pan, Fengwen Chen, Guodong Long, Chengqi Zhang, and Philip S. Yu. 2021. A Comprehensive Survey on Graph Neural Networks. IEEE Transactions on Neural Networks and Learning Systems, Vol. 32, 1 (2021), 4--24.Google ScholarGoogle Scholar
  38. Keyulu Xu, Weihua Hu, Jure Leskovec, and Stefanie Jegelka. 2019. How Powerful are Graph Neural Networks?. In ICLR .Google ScholarGoogle Scholar
  39. Ze Ye, Kin Sum Liu, Tengfei Ma, Jie Gao, and Chao Chen. 2020. Curvature Graph Network. In ICLR .Google ScholarGoogle Scholar
  40. Qi Zhao and Yusu Wang. 2019. Learning metrics for persistence-based summaries and applications for graph classification. In NeurIPS. 9855--9866.Google ScholarGoogle Scholar

Index Terms

  1. Filtration Curves for Graph Representation

      Recommendations

      Comments

      Login options

      Check if you have access through your login credentials or your institution to get full access on this article.

      Sign in

      PDF Format

      View or Download as a PDF file.

      PDF

      eReader

      View online with eReader.

      eReader