skip to main content
10.1145/3555776.3578600acmconferencesArticle/Chapter ViewAbstractPublication PagessacConference Proceedingsconference-collections
research-article

Quasi-CliquePool: Hierarchical Graph Pooling for Graph Classification

Authors Info & Claims
Published:07 June 2023Publication History

ABSTRACT

Graph Neural Networks (GNNs) have revolutionized graph learning through efficiently learned node embeddings and achieved promising results in various graph-related tasks such as node and graph classification. Within GNNs, a pooling operation reduces the size of the input graph by grouping nodes that share commonalities intending to generate more robust and expressive latent representations. For this reason, pooling is a critical operation that significantly affects downstream tasks. Existing global pooling methods mostly use readout functions like max or sum to perform the pooling operations, but these methods neglect the hierarchical information of graphs. Clique-based hierarchical pooling methods have recently been developed to overcome global pooling issues. Such clique pooling methods perform a hard partition between nodes, which destroys the topological structural relationship of nodes, assuming that a node should belong to a single cluster. However, overlapping clusters widely exist in many real-world networks since a node can belong to more than one cluster. Here we introduce a new hierarchical graph pooling method to address this issue. Our pooling method, named Quasi-CliquePool, builds on the concept of a quasi-clique, which generalizes the notion of cliques to extract dense incomplete subgraphs of a graph. We also introduce a soft peel-off strategy to find the overlapping cluster nodes to keep the topological structural relationship of nodes. For a fair comparison, we follow the same procedure and training settings used by state-of-the-art pooling techniques. Our experiments demonstrate that combining the Quasi-Clique Pool with existing GNN architectures yields an average improvement of 2% accuracy on four out of six graph classification benchmarks compared to other existing pooling methods.

References

  1. Davide Bacciu, Alessio Conte, Roberto Grossi, Francesco Landolfi, and Andrea Marino. 2021. K-plex cover pooling for graph neural networks. Data Mining and Knowledge Discovery 35, 5 (2021), 2200--2220.Google ScholarGoogle ScholarDigital LibraryDigital Library
  2. Filippo Maria Bianchi, Daniele Grattarola, and Cesare Alippi. 2020. Spectral clustering with graph neural networks for graph pooling. In International Conference on Machine Learning. PMLR, 874--883.Google ScholarGoogle Scholar
  3. Karsten M Borgwardt, Cheng Soon Ong, Stefan Schönauer, SVN Vishwanathan, Alex J Smola, and Hans-Peter Kriegel. 2005. Protein function prediction via graph kernels. Bioinformatics 21, suppl_1 (2005), i47--i56.Google ScholarGoogle ScholarDigital LibraryDigital Library
  4. Michael M Bronstein, Joan Bruna, Yann LeCun, Arthur Szlam, and Pierre Vandergheynst. 2017. Geometric deep learning: going beyond euclidean data. IEEE Signal Processing Magazine 34, 4 (2017), 18--42.Google ScholarGoogle ScholarCross RefCross Ref
  5. Lei Cai, Jundong Li, Jie Wang, and Shuiwang Ji. 2021. Line graph neural networks for link prediction. IEEE Transactions on Pattern Analysis and Machine Intelligence (2021).Google ScholarGoogle ScholarCross RefCross Ref
  6. Michaël Defferrard, Xavier Bresson, and Pierre Vandergheynst. 2016. Convolutional neural networks on graphs with fast localized spectral filtering. Advances in neural information processing systems 29 (2016).Google ScholarGoogle Scholar
  7. Inderjit S Dhillon, Yuqiang Guan, and Brian Kulis. 2007. Weighted graph cuts without eigenvectors a multilevel approach. IEEE transactions on pattern analysis and machine intelligence 29, 11 (2007), 1944--1957.Google ScholarGoogle ScholarDigital LibraryDigital Library
  8. Paul D Dobson and Andrew J Doig. 2003. Distinguishing enzyme structures from non-enzymes without alignments. Journal of molecular biology 330, 4 (2003), 771--783.Google ScholarGoogle ScholarCross RefCross Ref
  9. Aasa Feragen, Niklas Kasenburg, Jens Petersen, Marleen de Bruijne, and Karsten Borgwardt. 2013. Scalable kernels for graphs with continuous attributes. Advances in neural information processing systems 26 (2013).Google ScholarGoogle Scholar
  10. Hongyang Gao and Shuiwang Ji. 2019. Graph u-nets. In international conference on machine learning. PMLR, 2083--2092.Google ScholarGoogle Scholar
  11. Justin Gilmer, Samuel S Schoenholz, Patrick F Riley, Oriol Vinyals, and George E Dahl. 2017. Neural message passing for quantum chemistry. In International conference on machine learning. PMLR, 1263--1272.Google ScholarGoogle Scholar
  12. Arousha Haghighian Roudsari, Jafar Afshar, Wookey Lee, and Suan Lee. 2022. PatentNet: multi-label classification of patent documents using deep learning based language understanding. Scientometrics 127, 1 (2022), 207--231.Google ScholarGoogle ScholarDigital LibraryDigital Library
  13. Will Hamilton, Zhitao Ying, and Jure Leskovec. 2017. Inductive representation learning on large graphs. Advances in neural information processing systems 30 (2017).Google ScholarGoogle Scholar
  14. William L Hamilton, Rex Ying, and Jure Leskovec. 2017. Representation learning on graphs: Methods and applications. arXiv preprint arXiv:1709.05584 (2017).Google ScholarGoogle Scholar
  15. Kristian Kersting, Nils M Kriege, Christopher Morris, Petra Mutzel, and Marion Neumann. 2016. Benchmark data sets for graph kernels. (2016).Google ScholarGoogle Scholar
  16. Thomas N Kipf and Max Welling. 2016. Semi-supervised classification with graph convolutional networks. arXiv preprint arXiv:1609.02907 (2016).Google ScholarGoogle Scholar
  17. Kamran Kowsari, Donald E Brown, Mojtaba Heidarysafa, Kiana Jafari Meimandi, Matthew S Gerber, and Laura E Barnes. 2017. Hdltex: Hierarchical deep learning for text classification. In 2017 16th IEEE international conference on machine learning and applications (ICMLA). IEEE, 364--371.Google ScholarGoogle ScholarCross RefCross Ref
  18. Junhyun Lee, Inyeop Lee, and Jaewoo Kang. 2019. Self-attention graph pooling. In International conference on machine learning. PMLR, 3734--3743.Google ScholarGoogle Scholar
  19. Xinyu Lei, Hongguang Pan, and Xiangdong Huang. 2019. A dilated CNN model for image classification. IEEE Access 7 (2019), 124087--124095.Google ScholarGoogle ScholarCross RefCross Ref
  20. Guohao Li, Matthias Muller, Ali Thabet, and Bernard Ghanem. 2019. Deep-gcns: Can gcns go as deep as cnns?. In Proceedings of the IEEE/CVF international conference on computer vision. 9267--9276.Google ScholarGoogle ScholarCross RefCross Ref
  21. Y Li, D Tarlow, M Brockschmidt, and R Zemel. 2016. Gated graph sequence neural networks In: International Conference on Learning Representations. San Juan (2016).Google ScholarGoogle Scholar
  22. Enxhell Luzhnica, Ben Day, and Pietro Lio. 2019. Clique pooling for graph classification. arXiv preprint arXiv:1904.00374 (2019).Google ScholarGoogle Scholar
  23. Yao Ma, Suhang Wang, Charu C Aggarwal, and Jiliang Tang. 2019. Graph convolutional networks with eigenpooling. In Proceedings of the 25th ACM SIGKDD international conference on knowledge discovery & data mining. 723--731.Google ScholarGoogle ScholarDigital LibraryDigital Library
  24. Shervin Minaee, Yuri Y Boykov, Fatih Porikli, Antonio J Plaza, Nasser Kehtarnavaz, and Demetri Terzopoulos. 2021. Image segmentation using deep learning: A survey. IEEE transactions on pattern analysis and machine intelligence (2021).Google ScholarGoogle ScholarCross RefCross Ref
  25. Christopher Morris, Nils M Kriege, Franka Bause, Kristian Kersting, Petra Mutzel, and Marion Neumann. 2020. Tudataset: A collection of benchmark datasets for learning with graphs. arXiv preprint arXiv:2007.08663 (2020).Google ScholarGoogle Scholar
  26. Christopher Morris, Martin Ritzert, Matthias Fey, William L Hamilton, Jan Eric Lenssen, Gaurav Rattan, and Martin Grohe. 2019. Weisfeiler and leman go neural: Higher-order graph neural networks. In Proceedings of the AAAI conference on artificial intelligence, Vol. 33. 4602--4609.Google ScholarGoogle ScholarDigital LibraryDigital Library
  27. Marcello Pelillo and Andrea Torsello. 2006. Payoff-monotonic game dynamics and the maximum clique problem. Neural Computation 18, 5 (2006), 1215--1258.Google ScholarGoogle ScholarDigital LibraryDigital Library
  28. Sungmin Rhee, Seokjun Seo, and Sun Kim. 2017. Hybrid approach of relation network and localized graph convolutional filtering for breast cancer subtype classification. arXiv preprint arXiv:1711.05859 (2017).Google ScholarGoogle Scholar
  29. Kaspar Riesen and Horst Bunke. 2008. IAM graph database repository for graph based pattern recognition and machine learning. In Joint IAPR International Workshops on Statistical Techniques in Pattern Recognition (SPR) and Structural and Syntactic Pattern Recognition (SSPR). Springer, 287--297.Google ScholarGoogle ScholarDigital LibraryDigital Library
  30. Franco Scarselli, Marco Gori, Ah Chung Tsoi, Markus Hagenbuchner, and Gabriele Monfardini. 2008. The graph neural network model. IEEE transactions on neural networks 20, 1 (2008), 61--80.Google ScholarGoogle ScholarDigital LibraryDigital Library
  31. 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
  32. Petar Velickovic, Guillem Cucurull, Arantxa Casanova, Adriana Romero, Pietro Lio, and Yoshua Bengio. 2017. Graph attention networks. stat 1050 (2017), 20.Google ScholarGoogle Scholar
  33. Nikil Wale, Ian A Watson, and George Karypis. 2008. Comparison of descriptor spaces for chemical compound retrieval and classification. Knowledge and Information Systems 14, 3 (2008), 347--375.Google ScholarGoogle ScholarDigital LibraryDigital Library
  34. Xiang Wang, Buyue Qian, and Ian Davidson. 2014. On constrained spectral clustering and its applications. Data Mining and Knowledge Discovery 28, 1 (2014), 1--30.Google ScholarGoogle ScholarDigital LibraryDigital Library
  35. Zhengyang Wang and Shuiwang Ji. 2020. Second-order pooling for graph neural networks. IEEE Transactions on Pattern Analysis and Machine Intelligence (2020).Google ScholarGoogle ScholarDigital LibraryDigital Library
  36. Max Welling and Thomas N Kipf. 2016. Semi-supervised classification with graph convolutional networks. In J. International Conference on Learning Representations (ICLR 2017).Google ScholarGoogle Scholar
  37. Keyulu Xu, Weihua Hu, Jure Leskovec, and Stefanie Jegelka. 2018. How powerful are graph neural networks? arXiv preprint arXiv:1810.00826 (2018).Google ScholarGoogle Scholar
  38. Zhitao Ying, Jiaxuan You, Christopher Morris, Xiang Ren, Will Hamilton, and Jure Leskovec. 2018. Hierarchical graph representation learning with differentiable pooling. Advances in neural information processing systems 31 (2018).Google ScholarGoogle Scholar
  39. Lihi Zelnik-Manor and Pietro Perona. 2004. Self-tuning spectral clustering. Advances in neural information processing systems 17 (2004).Google ScholarGoogle Scholar
  40. Muhan Zhang, Zhicheng Cui, Marion Neumann, and Yixin Chen. 2018. An end-to-end deep learning architecture for graph classification. In Proceedings of the AAAI conference on artificial intelligence, Vol. 32.Google ScholarGoogle ScholarCross RefCross Ref
  41. Zhen Zhang, Jiajun Bu, Martin Ester, Jianfeng Zhang, Chengwei Yao, Zhi Yu, and Can Wang. 2019. Hierarchical graph pooling with structure learning. arXiv preprint arXiv:1911.05954 (2019).Google ScholarGoogle Scholar
  42. Zhen Zhang, Hongxia Yang, Jiajun Bu, Sheng Zhou, Pinggang Yu, Jianwei Zhang, Martin Ester, and Can Wang. 2018. ANRL: attributed network representation learning via deep neural networks.. In Ijcai, Vol. 18. 3155--3161.Google ScholarGoogle Scholar

Index Terms

  1. Quasi-CliquePool: Hierarchical Graph Pooling for Graph Classification
          Index terms have been assigned to the content through auto-classification.

          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
          • Published in

            cover image ACM Conferences
            SAC '23: Proceedings of the 38th ACM/SIGAPP Symposium on Applied Computing
            March 2023
            1932 pages
            ISBN:9781450395175
            DOI:10.1145/3555776

            Copyright © 2023 ACM

            Permission to make digital or hard copies of all or part of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. Copyrights for components of this work owned by others than ACM must be honored. Abstracting with credit is permitted. To copy otherwise, or republish, to post on servers or to redistribute to lists, requires prior specific permission and/or a fee. Request permissions from [email protected].

            Publisher

            Association for Computing Machinery

            New York, NY, United States

            Publication History

            • Published: 7 June 2023

            Permissions

            Request permissions about this article.

            Request Permissions

            Check for updates

            Qualifiers

            • research-article

            Acceptance Rates

            Overall Acceptance Rate1,650of6,669submissions,25%
          • Article Metrics

            • Downloads (Last 12 months)81
            • Downloads (Last 6 weeks)6

            Other Metrics

          PDF Format

          View or Download as a PDF file.

          PDF

          eReader

          View online with eReader.

          eReader