skip to main content
10.1145/3543507.3583386acmconferencesArticle/Chapter ViewAbstractPublication PageswwwConference Proceedingsconference-collections
research-article
Open Access

GraphPrompt: Unifying Pre-Training and Downstream Tasks for Graph Neural Networks

Published:30 April 2023Publication History

ABSTRACT

Graphs can model complex relationships between objects, enabling a myriad of Web applications such as online page/article classification and social recommendation. While graph neural networks (GNNs) have emerged as a powerful tool for graph representation learning, in an end-to-end supervised setting, their performance heavily relies on a large amount of task-specific supervision. To reduce labeling requirement, the “pre-train, fine-tune” and “pre-train, prompt” paradigms have become increasingly common. In particular, prompting is a popular alternative to fine-tuning in natural language processing, which is designed to narrow the gap between pre-training and downstream objectives in a task-specific manner. However, existing study of prompting on graphs is still limited, lacking a universal treatment to appeal to different downstream tasks. In this paper, we propose GraphPrompt, a novel pre-training and prompting framework on graphs. GraphPrompt not only unifies pre-training and downstream tasks into a common task template, but also employs a learnable prompt to assist a downstream task in locating the most relevant knowledge from the pre-trained model in a task-specific manner. Finally, we conduct extensive experiments on five public datasets to evaluate and analyze GraphPrompt.

References

  1. Hangbo Bao, Li Dong, Songhao Piao, and Furu Wei. 2022. BEiT: BERT Pre-Training of Image Transformers. In International Conference on Learning Representations.Google ScholarGoogle Scholar
  2. Iz Beltagy, Kyle Lo, and Arman Cohan. 2019. SciBERT: A Pretrained Language Model for Scientific Text. In Conference on Empirical Methods in Natural Language Processing and the International Joint Conference on Natural Language Processing. 3615–3620.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. Tom Brown, Benjamin Mann, Nick Ryder, Melanie Subbiah, Jared D Kaplan, Prafulla Dhariwal, Arvind Neelakantan, Pranav Shyam, Girish Sastry, Amanda Askell, 2020. Language models are few-shot learners. Advances in Neural Information Processing Systems 33 (2020), 1877–1901.Google ScholarGoogle Scholar
  5. Hongyun Cai, Vincent W Zheng, and Kevin Chen-Chuan Chang. 2018. A comprehensive survey of graph embedding: Problems, techniques, and applications. IEEE Transactions on Knowledge and Data Engineering 30, 9 (2018), 1616–1637.Google ScholarGoogle ScholarDigital LibraryDigital Library
  6. 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. In AAAI Conference on Artificial Intelligence. 3438–3445.Google ScholarGoogle ScholarCross RefCross Ref
  7. Li Dong, Nan Yang, Wenhui Wang, Furu Wei, Xiaodong Liu, Yu Wang, Jianfeng Gao, Ming Zhou, and Hsiao-Wuen Hon. 2019. Unified language model pre-training for natural language understanding and generation. Advances in Neural Information Processing Systems 32 (2019).Google ScholarGoogle Scholar
  8. David K Duvenaud, Dougal Maclaurin, Jorge Iparraguirre, Rafael Bombarell, Timothy Hirzel, Alán Aspuru-Guzik, and Ryan P Adams. 2015. Convolutional networks on graphs for learning molecular fingerprints. Advances in Neural Information Processing Systems 28 (2015).Google ScholarGoogle Scholar
  9. Chelsea Finn, Pieter Abbeel, and Sergey Levine. 2017. Model-agnostic meta-learning for fast adaptation of deep networks. In International Conference on Machine Learning. 1126–1135.Google ScholarGoogle Scholar
  10. Hongyang Gao and Shuiwang Ji. 2019. Graph u-nets. In International Conference on Machine Learning. 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. 1263–1272.Google ScholarGoogle Scholar
  12. Aditya Grover and Jure Leskovec. 2016. node2vec: Scalable feature learning for networks. In ACM SIGKDD International Conference on Knowledge Discovery and Data Mining. 855–864.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), 1025–1035.Google ScholarGoogle Scholar
  14. Kaveh Hassani and Amir Hosein Khasahmadi. 2020. Contrastive multi-view representation learning on graphs. In International Conference on Machine Learning. 4116–4126.Google ScholarGoogle Scholar
  15. Weihua Hu, Bowen Liu, Joseph Gomes, Marinka Zitnik, Percy Liang, Vijay Pande, and Jure Leskovec. 2020. Strategies for Pre-training Graph Neural Networks. In International Conference on Learning Representations.Google ScholarGoogle Scholar
  16. Ziniu Hu, Yuxiao Dong, Kuansan Wang, Kai-Wei Chang, and Yizhou Sun. 2020. GPT-GNN: Generative pre-training of graph neural networks. In ACM SIGKDD International Conference on Knowledge Discovery and Data Mining. 1857–1867.Google ScholarGoogle ScholarDigital LibraryDigital Library
  17. Kexin Huang and Marinka Zitnik. 2020. Graph meta learning via local subgraphs. Advances in Neural Information Processing Systems 33 (2020), 5862–5874.Google ScholarGoogle Scholar
  18. Dasol Hwang, Jinyoung Park, Sunyoung Kwon, KyungMin Kim, Jung-Woo Ha, and Hyunwoo J Kim. 2020. Self-supervised auxiliary learning with meta-paths for heterogeneous graphs. Advances in Neural Information Processing Systems 33 (2020), 10294–10305.Google ScholarGoogle Scholar
  19. Thomas N Kipf and Max Welling. 2016. Variational graph auto-encoders. In Bayesian Deep Learning Workshop.Google ScholarGoogle Scholar
  20. Thomas N Kipf and Max Welling. 2017. Semi-supervised classification with graph convolutional networks. In International Conference on Learning Representations.Google ScholarGoogle Scholar
  21. Junhyun Lee, Inyeop Lee, and Jaewoo Kang. 2019. Self-attention graph pooling. In International Conference on Machine Learning. 3734–3743.Google ScholarGoogle Scholar
  22. Brian Lester, Rami Al-Rfou, and Noah Constant. 2021. The Power of Scale for Parameter-Efficient Prompt Tuning. In Conference on Empirical Methods in Natural Language Processing. 3045–3059.Google ScholarGoogle Scholar
  23. Pengfei Liu, Weizhe Yuan, Jinlan Fu, Zhengbao Jiang, Hiroaki Hayashi, and Graham Neubig. 2021. Pre-train, prompt, and predict: A systematic survey of prompting methods in natural language processing. arXiv preprint arXiv:2107.13586 (2021).Google ScholarGoogle ScholarDigital LibraryDigital Library
  24. Xiao Liu, Yanan Zheng, Zhengxiao Du, Ming Ding, Yujie Qian, Zhilin Yang, and Jie Tang. 2021. GPT understands, too. arXiv preprint arXiv:2103.10385 (2021).Google ScholarGoogle Scholar
  25. Zemin Liu, Yuan Fang, Chenghao Liu, and Steven C.H. Hoi. 2021. Node-wise Localization of Graph Neural Networks. In International Joint Conference on Artificial Intelligence. 1520–1526.Google ScholarGoogle Scholar
  26. Zemin Liu, Yuan Fang, Chenghao Liu, and Steven CH Hoi. 2021. Relative and absolute location embedding for few-shot node classification on graph. In AAAI Conference on Artificial Intelligence. 4267–4275.Google ScholarGoogle ScholarCross RefCross Ref
  27. Zemin Liu, Trung-Kien Nguyen, and Yuan Fang. 2021. Tail-GNN: Tail-Node Graph Neural Networks. In ACM SIGKDD Conference on Knowledge Discovery and Data Mining. 1109–1119.Google ScholarGoogle ScholarDigital LibraryDigital Library
  28. Zemin Liu, Wentao Zhang, Yuan Fang, Xinming Zhang, and Steven C. H. Hoi. 2020. Towards Locality-Aware Meta-Learning of Tail Node Embeddings on Networks. In Conference on Information and Knowledge Management. 975–984.Google ScholarGoogle Scholar
  29. Jiasen Lu, Dhruv Batra, Devi Parikh, and Stefan Lee. 2019. ViLBERT: Pretraining task-agnostic visiolinguistic representations for vision-and-language tasks. Advances in Neural Information Processing Systems 32 (2019).Google ScholarGoogle Scholar
  30. Yuanfu Lu, Xunqiang Jiang, Yuan Fang, and Chuan Shi. 2021. Learning to pre-train graph neural networks. In AAAI Conference on Artificial Intelligence. 4276–4284.Google ScholarGoogle ScholarCross RefCross Ref
  31. Yao Ma, Suhang Wang, Charu C Aggarwal, and Jiliang Tang. 2019. Graph convolutional networks with eigenpooling. In ACM SIGKDD International Conference on Knowledge Discovery and Data Mining. 723–731.Google ScholarGoogle ScholarDigital LibraryDigital Library
  32. Zhen Peng, Wenbing Huang, Minnan Luo, Qinghua Zheng, Yu Rong, Tingyang Xu, and Junzhou Huang. 2020. Graph representation learning via graphical mutual information maximization. In The Web Conference. 259–270.Google ScholarGoogle ScholarDigital LibraryDigital Library
  33. Bryan Perozzi, Rami Al-Rfou, and Steven Skiena. 2014. DeepWalk: Online learning of social representations. In ACM SIGKDD International Conference on Knowledge Discovery and Data Mining. 701–710.Google ScholarGoogle ScholarDigital LibraryDigital Library
  34. Jiezhong Qiu, Qibin Chen, Yuxiao Dong, Jing Zhang, Hongxia Yang, Ming Ding, Kuansan Wang, and Jie Tang. 2020. GCC: Graph contrastive coding for graph neural network pre-training. In ACM SIGKDD International Conference on Knowledge Discovery and Data Mining. 1150–1160.Google ScholarGoogle ScholarDigital LibraryDigital Library
  35. Ryan A. Rossi and Nesreen K. Ahmed. 2015. The Network Data Repository with Interactive Graph Analytics and Visualization. In AAAI Conference on Artificial Intelligence. 4292–4293.Google ScholarGoogle Scholar
  36. Nino Shervashidze, Pascal Schweitzer, Erik Jan Van Leeuwen, Kurt Mehlhorn, and Karsten M Borgwardt. 2011. Weisfeiler-lehman graph kernels.Journal of Machine Learning Research 12, 9 (2011).Google ScholarGoogle Scholar
  37. Fan-Yun Sun, Jordan Hoffman, Vikas Verma, and Jian Tang. 2020. InfoGraph: Unsupervised and Semi-supervised Graph-Level Representation Learning via Mutual Information Maximization. In International Conference on Learning Representations.Google ScholarGoogle Scholar
  38. Fan-Yun Sun, Jordan Hoffmann, Vikas Verma, and Jian Tang. 2020. InfoGraph: Unsupervised and semi-supervised graph-level representation learning via mutual information maximization. In International Conference on Learning Representations.Google ScholarGoogle Scholar
  39. Mingchen Sun, Kaixiong Zhou, Xin He, Ying Wang, and Xin Wang. 2022. GPPT: Graph Pre-training and Prompt Tuning to Generalize Graph Neural Networks. In ACM SIGKDD Conference on Knowledge Discovery and Data Mining. 1717–1727.Google ScholarGoogle ScholarDigital LibraryDigital Library
  40. Susheel Suresh, Pan Li, Cong Hao, and Jennifer Neville. 2021. Adversarial graph augmentation to improve graph contrastive learning. Advances in Neural Information Processing Systems 34 (2021), 15920–15933.Google ScholarGoogle Scholar
  41. Jian Tang, Meng Qu, Mingzhe Wang, Ming Zhang, Jun Yan, and Qiaozhu Mei. 2015. LINE: Large-scale information network embedding. In The Web Conference. 1067–1077.Google ScholarGoogle ScholarDigital LibraryDigital Library
  42. Matteo Togninalli, Elisabetta Ghisu, Felipe Llinares-López, Bastian Rieck, and Karsten Borgwardt. 2019. Wasserstein weisfeiler-lehman graph kernels. Advances in Neural Information Processing Systems 32 (2019).Google ScholarGoogle Scholar
  43. Petar Veličković, Guillem Cucurull, Arantxa Casanova, Adriana Romero, Pietro Lio, and Yoshua Bengio. 2018. Graph attention networks. In International Conference on Learning Representations.Google ScholarGoogle Scholar
  44. Petar Velickovic, William Fedus, William L Hamilton, Pietro Liò, Yoshua Bengio, and R Devon Hjelm. 2019. Deep Graph Infomax. In International Conference on Learning Representations.Google ScholarGoogle Scholar
  45. Ning Wang, Minnan Luo, Kaize Ding, Lingling Zhang, Jundong Li, and Qinghua Zheng. 2020. Graph few-shot learning with attribute matching. In ACM International Conference on Information and Knowledge Management. 1545–1554.Google ScholarGoogle ScholarDigital LibraryDigital Library
  46. Song Wang, Yushun Dong, Xiao Huang, Chen Chen, and Jundong Li. 2022. FAITH: Few-Shot Graph Classification with Hierarchical Task Graphs. In International Joint Conference on Artificial Intelligence.Google ScholarGoogle Scholar
  47. Zhihao Wen, Yuan Fang, and Zemin Liu. 2021. Meta-inductive node classification across graphs. In International ACM SIGIR Conference on Research and Development in Information Retrieval. 1219–1228.Google ScholarGoogle ScholarDigital LibraryDigital Library
  48. Zonghan Wu, Shirui Pan, Fengwen Chen, Guodong Long, Chengqi Zhang, and S Yu Philip. 2020. A comprehensive survey on graph neural networks. IEEE Transactions on Neural Networks and Learning Systems 32, 1 (2020), 4–24.Google ScholarGoogle ScholarCross RefCross Ref
  49. Jun Xia, Yanqiao Zhu, Yuanqi Du, and Stan Z Li. 2022. A survey of pretraining on graphs: Taxonomy, methods, and applications. arXiv preprint arXiv:2202.07893 (2022).Google ScholarGoogle Scholar
  50. Keyulu Xu, Weihua Hu, Jure Leskovec, and Stefanie Jegelka. 2019. How powerful are graph neural networks¿. In International Conference on Learning Representations.Google ScholarGoogle Scholar
  51. 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), 4805–4815.Google ScholarGoogle Scholar
  52. Yuning You, Tianlong Chen, Yang Shen, and Zhangyang Wang. 2021. Graph contrastive learning automated. In International Conference on Machine Learning. 12121–12132.Google ScholarGoogle Scholar
  53. Yuning You, Tianlong Chen, Yongduo Sui, Ting Chen, Zhangyang Wang, and Yang Shen. 2020. Graph contrastive learning with augmentations. Advances in Neural Information Processing Systems 33 (2020), 5812–5823.Google ScholarGoogle Scholar
  54. Jiayou Zhang, Zhirui Wang, Shizhuo Zhang, Megh Manoj Bhalerao, Yucong Liu, Dawei Zhu, and Sheng Wang. 2021. GraphPrompt: Biomedical Entity Normalization Using Graph-based Prompt Templates. arXiv preprint arXiv:2112.03002 (2021).Google ScholarGoogle Scholar
  55. Muhan Zhang and Yixin Chen. 2018. Link prediction based on graph neural networks. Advances in Neural Information Processing Systems 31 (2018).Google ScholarGoogle Scholar
  56. Muhan Zhang, Zhicheng Cui, Marion Neumann, and Yixin Chen. 2018. An end-to-end deep learning architecture for graph classification. In AAAI conference on artificial intelligence, Vol. 32.Google ScholarGoogle ScholarCross RefCross Ref
  57. Fan Zhou, Chengtai Cao, Kunpeng Zhang, Goce Trajcevski, Ting Zhong, and Ji Geng. 2019. Meta-GNN: On few-shot node classification in graph meta-learning. In ACM International Conference on Information and Knowledge Management. 2357–2360.Google ScholarGoogle ScholarDigital LibraryDigital Library

Index Terms

  1. GraphPrompt: Unifying Pre-Training and Downstream Tasks for Graph Neural Networks

      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

      HTML Format

      View this article in HTML Format .

      View HTML Format