Neural Bellman-Ford Networks: A General Graph Neural Network Framework for Link Prediction
Paper · 2021 · Zhaocheng Zhu, Zuobai Zhang, Louis-Pascal Xhonneux et al.
Summary
Link prediction methods tend to fall into two camps. Classic path heuristics such as Katz index, personalized PageRank and graph distance transfer to unseen graphs and are easy to interpret, but they rely on hand-designed scores. GNN-based models are more expressive, but they are usually transductive, hard to explain, or, like SEAL and GraIL, expensive to run. The authors connect these camps by representing a node pair as a generalized "sum" over every path between the two nodes, where each path is a generalized "product" of its edge representations. Many classic heuristics turn out to be special cases of this formulation, and it can be computed efficiently with the generalized Bellman-Ford algorithm. NBFNet then replaces the fixed operators with three learned components: INDICATOR (the initial boundary condition), MESSAGE (multiplication, which can be built from KG-embedding relation operators such as TransE) and AGGREGATE (summation). In experiments on knowledge graphs as well as homogeneous graphs, covering transductive and inductive settings alike, NBFNet reports state-of-the-art results. It stays scalable and explains its predictions through high-importance paths.
Key points
- The authors report an average relative improvement of 18% in HITS@1 on knowledge graph completion and 22% in HITS@10 on inductive relation prediction over previous methods.
- On the FB15k-237 test set, NBFNet takes about 4.0 minutes of wall time. The estimate for GraIL is roughly one month, while the transductive VGAE/RGCN take 18 seconds.
- Predictions are explained by the top-k paths, ranked by gradient-based edge importance. Examples from FB15k-237 include soft rule chaining and analogical reasoning.
- The framework recovers rule-learning methods such as NeuralLP and DRUM as special cases. The theory assumes the operators form a semiring, which no longer holds once non-linear activations are used.
- The paper was published at NeurIPS 2021, and the code is available at github.com/DeepGraphLearning/NBFNet.
Institutions
Fields, topics and concepts
📚 Shelves 5The field of science this work belongs to (OpenAlex fields).Computer Science · 18,614 worksArtificial Intelligence · 17,965 worksComputer Vision and Pattern Recognition · 3,486 worksPhysics and Astronomy · 52 worksStatistical and Nonlinear Physics · 47 works
Cite
Cite as Zhaocheng Zhu, Zuobai Zhang, Louis-Pascal Xhonneux and Jian Tang. 2021. Neural Bellman-Ford Networks: A General Graph Neural Network Framework for Link Prediction. arXiv:2106.06935.
@misc{zhu2021neural,
title = {{Neural Bellman-Ford Networks: A General Graph Neural Network Framework for Link Prediction}},
author = {Zhaocheng Zhu, Zuobai Zhang, Louis-Pascal Xhonneux and Jian Tang},
year = {2021},
doi = {10.48550/arxiv.2106.06935},
eprint = {2106.06935},
archivePrefix = {arXiv},
url = {https://doi.org/10.48550/arxiv.2106.06935}
}References
- Saadullah Amin, Stalin Varanasi, Katherine Ann Dunfield, and Günter Neumann. Lowfer: Low-rank bilinear pooling for link prediction. In International Conference on Machine Learning, pages 257–268. PMLR, 2020. find
- Jimmy Lei Ba, Jamie Ryan Kiros, and Geoffrey E Hinton. Layer normalization. arXiv preprint arXiv:1607.06450, 2016.
- David Baehrens, Timon Schroeter, Stefan Harmeling, Motoaki Kawanabe, Katja Hansen, and Klaus-Robert Müller. How to explain individual classification decisions. The Journal of Machine Learning Research, 11:1803–1831, 2010. find
- John S Baras and George Theodorakopoulos. Path problems in networks. Synthesis Lectures on Communication Networks, 3(1):1–77, 2010. find
- Richard Bellman. On a routing problem. Quarterly of applied mathematics, 16(1):87–90, 1958. find
- Antoine Bordes, Nicolas Usunier, Alberto Garcia-Duran, Jason Weston, and Oksana Yakhnenko. Translating embeddings for modeling multi-relational data. In Advances in Neural Information Processing Systems, pages 1–9, 2013.
- Linlin Chao, Jianshan He, Taifeng Wang, and Wei Chu. PairRE: Knowledge graph embeddings via paired relation vectors. In Proceedings of the 59th Annual Meeting of the Association for Computational Linguistics and the 11th International Joint Conference on Natural Language Processing (Volume 1: Long P… find
- Wenhu Chen, Wenhan Xiong, Xifeng Yan, and William Yang Wang. Variational knowledge graph reasoning. In Proceedings of the 2018 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies, Volume 1 (Long Papers), pages 1823–1832, 2018. find
- Gabriele Corso, Luca Cavalleri, Dominique Beaini, Pietro Liò, and Petar Veličković. Principal neighbourhood aggregation for graph nets. volume 33, 2020. find
- Rajarshi Das, Shehzaad Dhuliawala, Manzil Zaheer, Luke Vilnis, Ishan Durugkar, Akshay Krishnamurthy, Alex Smola, and Andrew McCallum. Go for a walk and arrive at the answer: Reasoning over paths in knowledge bases using reinforcement learning. In International Conference on Learning Representations,… find
- Rajarshi Das, Arvind Neelakantan, David Belanger, and Andrew McCallum. Chains of reasoning over entities, relations, and text using recurrent neural networks. In Proceedings of the 15th Conference of the European Chapter of the Association for Computational Linguistics: Volume 1, Long Papers, pages… find
- Tim R Davidson, Luca Falorsi, Nicola De Cao, Thomas Kipf, and Jakub M Tomczak. Hyperspherical variational auto-encoders. 2018. find
- Tim Dettmers, Pasquale Minervini, Pontus Stenetorp, and Sebastian Riedel. Convolutional 2d knowledge graph embeddings. In Proceedings of the AAAI Conference on Artificial Intelligence, volume 32, 2018. find
- Luis Antonio Galárraga, Christina Teflioudi, Katja Hose, and Fabian Suchanek. Amie: association rule mining under incomplete evidence in ontological knowledge bases. In Proceedings of the 22nd international conference on World Wide Web, pages 413–422, 2013. find
- Matt Gardner and Tom Mitchell. Efficient and expressive knowledge base completion using subgraph feature extraction. In Proceedings of the 2015 Conference on Empirical Methods in Natural Language Processing, pages 1488–1498, 2015. find
- Justin Gilmer, Samuel S Schoenholz, Patrick F Riley, Oriol Vinyals, and George E Dahl. Neural message passing for quantum chemistry. In International Conference on Machine Learning, pages 1263–1272. PMLR, 2017.
- Aditya Grover and Jure Leskovec. node2vec: Scalable feature learning for networks. In Proceedings of the 22nd ACM SIGKDD international conference on Knowledge discovery and data mining, pages 855–864, 2016. find
- William L Hamilton, Payal Bajaj, Marinka Zitnik, Dan Jurafsky, and Jure Leskovec. Embedding logical queries on knowledge graphs. In Advances in Neural Information Processing Systems, pages 2030–2041, 2018. find
- William L Hamilton, Rex Ying, and Jure Leskovec. Inductive representation learning on large graphs. In Advances in Neural Information Processing Systems, pages 1025–1035, 2017.
- Zhen Han, Peng Chen, Yunpu Ma, and Volker Tresp. xerte: Explainable reasoning on temporal knowledge graphs for forecasting future links. 2021. find
- Udo Hebisch and Hanns Joachim Weinert. Semirings: algebraic theory and applications in computer science, volume 5. World Scientific, 1998. find
- Marcel Hildebrandt, Jorge Andres Quintero Serna, Yunpu Ma, Martin Ringsquandl, Mitchell Joblin, and Volker Tresp. Reasoning on knowledge graphs with debate dynamics. In Proceedings of the AAAI Conference on Artificial Intelligence, volume 34, pages 4123–4131, 2020. find
- Sepp Hochreiter and Jürgen Schmidhuber. Long short-term memory. Neural computation, 9(8):1735–1780, 1997. find
- Weihua Hu, Matthias Fey, Hongyu Ren, Maho Nakata, Yuxiao Dong, and Jure Leskovec. Ogb-lsc: A large-scale challenge for machine learning on graphs. arXiv preprint arXiv:2103.09430, 2021. find
- Weihua Hu, Matthias Fey, Marinka Zitnik, Yuxiao Dong, Hongyu Ren, Bowen Liu, Michele Catasta, and Jure Leskovec. Open graph benchmark: Datasets for machine learning on graphs. arXiv preprint arXiv:2005.00687, 2020. find
- Guyue Huang, Guohao Dai, Yu Wang, and Huazhong Yang. Ge-spmm: General-purpose sparse matrix-matrix multiplication on gpus for graph neural networks. In SC20: International Conference for High Performance Computing, Networking, Storage and Analysis, pages 1–12. IEEE, 2020. find
- Vassilis N Ioannidis, Da Zheng, and George Karypis. Few-shot link prediction via graph neural networks for covid-19 drug-repurposing. arXiv preprint arXiv:2007.10261, 2020. — [arXiv:2007.10261](https://arxiv.org/abs/2007.10261) find
- Glen Jeh and Jennifer Widom. Simrank: a measure of structural-context similarity. In Proceedings of the eighth ACM SIGKDD international conference on Knowledge discovery and data mining, pages 538–543, 2002. find
- Glen Jeh and Jennifer Widom. Scaling personalized web search. In Proceedings of the 12th international conference on World Wide Web, pages 271–279, 2003. find
- Leo Katz. A new status index derived from sociometric analysis. Psychometrika, 18(1):39–43, 1953. find
- Seyed Mehran Kazemi and David Poole. Simple embedding for link prediction in knowledge graphs. In Advances in Neural Information Processing Systems, pages 4289–4300, 2018. find
- Thomas N Kipf and Max Welling. arXiv:1611.07308, 2016. find
- Thomas N Kipf and Max Welling. Semi-supervised classification with graph convolutional networks. In International Conference on Learning Representations, 2017.
- Yehuda Koren, Robert Bell, and Chris Volinsky. Matrix factorization techniques for recommender systems. Computer, 42(8):30–37, 2009. find
- Ni Lao and William W Cohen. Relational retrieval using a combination of path-constrained random walks. Machine learning, 81(1):53–67, 2010. find
- Qimai Li, Zhichao Han, and Xiao-Ming Wu. Deeper insights into graph convolutional networks for semi-supervised learning. In Proceedings of the AAAI Conference on Artificial Intelligence, volume 32, 2018. find
- David Liben-Nowell and Jon Kleinberg. The link-prediction problem for social networks. Journal of the American society for information science and technology, 58(7):1019–1031, 2007. find
- Xi Victoria Lin, Richard Socher, and Caiming Xiong. Multi-hop knowledge graph reasoning with reward shaping. In Proceedings of the 2018 Conference on Empirical Methods in Natural Language Processing, EMNLP 2018, Brussels, Belgium, October 31-November 4, 2018, 2018. Variational graph auto-encoders. a… find
- Christian Meilicke, Manuel Fink, Yanjie Wang, Daniel Ruffinelli, Rainer Gemulla, and Heiner Stuckenschmidt. Fine-grained evaluation of rule-and embedding-based systems for knowledge graph completion. In International Semantic Web Conference, pages 3–20. Springer, 2018. find
- Arvind Neelakantan, Benjamin Roth, and Andrew McCallum. Compositional vector space models for knowledge base completion. In Proceedings of the 53rd Annual Meeting of the Association for Computational Linguistics and the 7th International Joint Conference on Natural Language Processing (Volume 1: Lon…
- Maximilian Nickel, Kevin Murphy, Volker Tresp, and Evgeniy Gabrilovich. A review of relational machine learning for knowledge graphs. Proceedings of the IEEE, 104(1):11–33, 2015. find
- Lawrence Page, Sergey Brin, Rajeev Motwani, and Terry Winograd. The pagerank citation ranking: Bringing order to the web. Technical report, Stanford InfoLab, 1999.
- Bryan Perozzi, Rami Al-Rfou, and Steven Skiena. Deepwalk: Online learning of social representations. In Proceedings of the 20th ACM SIGKDD international conference on Knowledge discovery and data mining, pages 701–710, 2014. find
- Meng Qu, Junkun Chen, Louis-Pascal Xhonneux, Yoshua Bengio, and Jian Tang. Rnnlogic: Learning logic rules for reasoning on knowledge graphs. In International Conference on Learning Representations, 2021. find
- H Ren, W Hu, and J Leskovec. Query2box: Reasoning over knowledge graphs in vector space using box embeddings. In International Conference on Learning Representations, 2020. find
- Ali Sadeghian, Mohammadreza Armandpour, Patrick Ding, and Daisy Zhe Wang. Drum: End-to-end differentiable rule mining on knowledge graphs. volume 32, pages 15347–15357, 2019. find
- Franco Scarselli, Marco Gori, Ah Chung Tsoi, Markus Hagenbuchner, and Gabriele Monfardini. The graph neural network model. IEEE transactions on neural networks, 20(1):61–80, 2008. find
- Michael Schlichtkrull, Thomas N Kipf, Peter Bloem, Rianne Van Den Berg, Ivan Titov, and Max Welling. Modeling relational data with graph convolutional networks. In European semantic web conference, pages 593–607. Springer, 2018. find
- Prithviraj Sen, Galileo Namata, Mustafa Bilgic, Lise Getoor, Brian Galligher, and Tina Eliassi-Rad. Collective classification in network data. AI magazine, 29(3):93–93, 2008.
- Yelong Shen, Jianshu Chen, Po-Sen Huang, Yuqing Guo, and Jianfeng Gao. M-walk: learning to walk over graphs using monte carlo tree search. In Advances in Neural Information Processing Systems, pages 6787–6798, 2018. find
- Yizhou Sun, Jiawei Han, Xifeng Yan, Philip S Yu, and Tianyi Wu. Pathsim: Meta path-based top-k similarity search in heterogeneous information networks. volume 4, pages 992–1003. VLDB Endowment, 2011. find
- Zhiqing Sun, Zhi-Hong Deng, Jian-Yun Nie, and Jian Tang. Rotate: Knowledge graph embedding by relational rotation in complex space. In International Conference on Learning Representations, 2019.
- Jian Tang, Meng Qu, Mingzhe Wang, Ming Zhang, Jun Yan, and Qiaozhu Mei. Line: Large-scale information network embedding. In Proceedings of the 24th international conference on World Wide Web, pages 1067–1077, 2015. find
- Yun Tang, Jing Huang, Guangtao Wang, Xiaodong He, and Bowen Zhou. Orthogonal relation transforms with graph context modeling for knowledge graph embedding. In Proceedings of the 58th Annual Meeting of the Association for Computational Linguistics, pages 2713–2722, 2020. find
- Komal Teru, Etienne Denis, and Will Hamilton. Inductive relation prediction by subgraph reasoning. In International Conference on Machine Learning, pages 9448–9457. PMLR, 2020. find
- Kristina Toutanova and Danqi Chen. Observed versus latent features for knowledge base and text inference. In Proceedings of the 3rd workshop on continuous vector space models and their compositionality, pages 57–66, 2015.
- Kristina Toutanova, Xi Victoria Lin, Wen-tau Yih, Hoifung Poon, and Chris Quirk. Compositional learning of embeddings for relation paths in knowledge base and text. In Proceedings of the 54th Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers), pages 1434–1444, 20… find
- Théo Trouillon, Johannes Welbl, Sebastian Riedel, Éric Gaussier, and Guillaume Bouchard. Complex embeddings for simple link prediction. In International Conference on Machine Learning, pages 2071–2080. PMLR, 2016.
- Shikhar Vashishth, Soumya Sanyal, Vikram Nitin, and Partha Talukdar. Composition-based multi-relational graph convolutional networks. In International Conference on Learning Representations, 2020. find
- Petar Veličković, Guillem Cucurull, Arantxa Casanova, Adriana Romero, Pietro Liò, and Yoshua Bengio. Graph attention networks. In International Conference on Learning Representations, 2018. find
- Andrew Viterbi. Error bounds for convolutional codes and an asymptotically optimum decoding algorithm. IEEE transactions on Information Theory, 13(2):260–269, 1967. find
- Hongwei Wang, Hongyu Ren, and Jure Leskovec. Relational message passing for knowledge graph completion. In Proceedings of the 27th ACM SIGKDD Conference on Knowledge Discovery & Data Mining, pages 1697–1707, 2021. find
- Zhen Wang, Jianwen Zhang, Jianlin Feng, and Zheng Chen. Knowledge graph embedding by translating on hyperplanes. In Proceedings of the AAAI Conference on Artificial Intelligence, volume 28, 2014. find
- Wenhan Xiong, Thien Hoang, and William Yang Wang. Deeppath: A reinforcement learning method for knowledge graph reasoning. In Proceedings of the 2017 Conference on Empirical Methods in Natural Language Processing (EMNLP 2017), Copenhagen, Denmark, September 2017. ACL. find
- Keyulu Xu, Weihua Hu, Jure Leskovec, and Stefanie Jegelka. How powerful are graph neural networks? In International Conference on Learning Representations, 2019.
- Xiaoran Xu, Wei Feng, Yunsheng Jiang, Xiaohui Xie, Zhiqing Sun, and Zhi-Hong Deng. Dynamically pruned message passing networks for large-scale knowledge graph reasoning. In International Conference on Learning Representations, 2019. find
- Zuoyu Yan, Tengfei Ma, Liangcai Gao, Zhi Tang, and Chao Chen. Link prediction with persistent homology: An interactive view. In International Conference on Machine Learning, pages 11659–11669. PMLR, 2021. find
- Bishan Yang, Wen-tau Yih, Xiaodong He, Jianfeng Gao, and Li Deng. Embedding entities and relations for learning and inference in knowledge bases. In International Conference on Learning Representations, 2015.
- Fan Yang, Zhilin Yang, and William W Cohen. Differentiable learning of logical rules for knowledge base reasoning. In Advances in Neural Information Processing Systems, pages 2316–2325, 2017. find
- Jiaxuan You, Jonathan M Gomes-Selman, Rex Ying, and Jure Leskovec. Identity-aware graph neural networks. In Proceedings of the AAAI Conference on Artificial Intelligence, volume 35, pages 10737–10745, 2021. find
- Manzil Zaheer, Satwik Kottur, Siamak Ravanbakhsh, Barnabas Poczos, Russ R Salakhutdinov, and Alexander J Smola. Deep sets. volume 30, 2017. find
- Matthew D Zeiler and Rob Fergus. Visualizing and understanding convolutional networks. In European conference on computer vision, pages 818–833. Springer, 2014.
- Muhan Zhang and Yixin Chen. Link prediction based on graph neural networks. volume 31, pages 5165–5175, 2018. find
- Muhan Zhang, Pan Li, Yinglong Xia, Kai Wang, and Long Jin. Revisiting graph neural networks for link prediction. arXiv preprint arXiv:2010.16103, 2020. — [arXiv:2010.16103](https://arxiv.org/abs/2010.16103) find
- Yongqi Zhang, Quanming Yao, Wenyuan Dai, and Lei Chen. Autosf: Searching scoring functions for knowledge graph embedding. In 2020 IEEE 36th International Conference on Data Engineering (ICDE), pages 433–444. IEEE, 2020. find
- Zhanqiu Zhang, Jianyu Cai, Yongdong Zhang, and Jie Wang. Learning hierarchy-aware knowledge graph embeddings for link prediction. In Proceedings of the AAAI Conference on Artificial Intelligence, volume 34, pages 3065–3072, 2020. find
- Lingxiao Zhao and Leman Akoglu. Pairnorm: Tackling oversmoothing in gnns. In International Conference on Learning Representations, 2019. find
- Zhaocheng Zhu, Shizhen Xu, Meng Qu, and Jian Tang. Graphvite: A high-performance cpu-gpu hybrid system for node embedding. In The World Wide Web Conference, pages 2494–2504, 2019. find
Updated
This page in Markdown → https://md.research.elamur.ai/free/en/papers/zhu-2021-neural-bellman-ford-networks-general/