Biography
Muhan is a tenure-track assistant professor and PhD advisor in the Institute for Artificial Intelligence of Peking University . Before coming back to China, he was a research scientist in Facebook AI (now Meta AI) working on large-scale graph learning systems and problems (2019-2021). He received his PhD degree in computer science from Washington University in St. Louis (2015-2019), advised by Prof. Yixin Chen. Before WashU, he obtained a bachelor degree from Shanghai Jiao Tong University as a member of the IEEE pilot class, where he worked with Prof. Ya Zhang and Prof. Wenjun Zhang.
Research Interests
Graph machine learning. Many real-world problems are inherently graph-structured, e.g., social networks, biological networks, World Wide Web, molecules, circuits, brain, road networks, knowledge graphs. Many machine learning algorithms are also defined on graphs, such as neural networks and graphical models. In this field, I develop algorithms and theories for learning over graphs, and apply them to problems like link prediction, graph classification, graph structure optimization, and knowledge graph reasoning. I am also interested in practical applications of graph neural networks, including brain modeling, drug discovery, circuit design, and healthcare applications.
Large language models reasoning. Compared to machine, human posesses extreme flexibility in handling unseen tasks in a few-shot/zero-shot way, much of which is attributed to human's system-II intelligence for complex logical reasoning, task planning, causal reasoning, and inductive generalization. Recently, large language models (LLMs) show promising improvement on such abilities, while also demonstrating insufficiency in some simplest cases and are ultimately still unreliable. For example, state-of-the-art LLMs cannot accurately add two large integers without resorting to external tools. In this field, we aim to understand and improve LLMs' reasoning ability, with means like graphs, code, rules, fine-tuning, etc. Ultimately, we want to build machines with human-like reasoning ability which are flexible, intepretable, and reliable, and enable machines to master top human general intelligence like induction, math, coding, and scientific discovery.
Prospective Students
I am looking for highly motivated PhD/undergraduate students who are interested in doing graph ML
research with me.
Please shoot me an email if you meet at least three of the following criteria:
1) creativity and passion for research,
2) solid math skills,
3) solid coding skills,
4) good English (writing and speaking).
I will do my best to provide support for your success, including detailed guidance, plenty of
computation resources, and research freedom for senior PhDs. You are especially welcome if you have
interdisciplinary backgrounds (such as maths/physics/chemistry/biology) while proficient in coding.
For students in Peking University, you can schedule one on one chats with me at my office.
Due to the large number of applicants, the competition is intense every year and I may not be able
to
respond to every email. Hope you understand!
For potential PhD students: I am mainly affiliated with the Insitute for AI (人工智能研究院), which is
based in the main campus (燕园) of PKU. Your office will also be there and you don't need to go to
the Changping (昌平) campus.
News
Publications
- [NeurIPS-24] F. Meng, Z. Wang and M. Zhang, PiSSA: Principal Singular Values and Singular Vectors Adaptation of Large Language Models , Advances in Neural Information Processing Systems (NeurIPS-24), spotlight presentation, 2024. (PDF)
- [NeurIPS-24] C. Zhou, X. Wang and M. Zhang, Latent Graph Diffusion: A Unified Framework for Generation and Prediction on Graphs , Advances in Neural Information Processing Systems (NeurIPS-24), 2024. (PDF)
- [NeurIPS-24-Benchmark] X. Tang, J. Li, Y. Liang, S. C. Zhu, M. Zhang# and Z. Zheng#, Mars: Situated Inductive Reasoning in an Open-World Environment , Advances in Neural Information Processing Systems, D&B Track (NeurIPS-24-Benchmark), 2024. (PDF)
- [NeurIPS-24-Benchmark] 4DBInfer: A 4D Benchmarking Toolbox for Graph-Centric Predictive Modeling on Relational DBs , Advances in Neural Information Processing Systems, D&B Track (NeurIPS-24-Benchmark), 2024. (PDF)
- [KDD-24] Z. Yan, J. Zhou, L. Gao#, Z. Tang and M. Zhang#, An Efficient Subgraph GNN with Provable Substructure Counting Power , Proc. ACM SIGKDD Conference on Knowledge Discovery and Data Mining (KDD-24), 2024. (PDF)
- [ACL-24] J. Li, M. Wang, Z. Zheng and M. Zhang, LooGLE: Can Long-Context Language Models Understand Long Contexts?, The 62nd Annual Meeting of the Association for Computational Linguistics (ACL-24), 2024. (PDF) (Source code)
- [ACL-24] X. Tang, S. C. Zhu, Y. Liang and M. Zhang, RulE: Knowledge Graph Reasoning with Rule Embedding, Findings of the 62nd Annual Meeting of the Association for Computational Linguistics (ACL-24), 2024. (PDF) (Source code)
- [TNNLS-24] Z. Liu, F. Ji, J. Yang, X. Cao, M. Zhang, H. Chen and Y. Chang, Refining Euclidean Obfuscatory Nodes Helps: A Joint-Space Graph Learning Method for Graph Neural Networks, IEEE Transactions on Neural Networks and Learning Systems (TNNLS) , 2024.
- [iScience-24] X. Meng, X. Yan, K. Zhang, D. Liu, X. Cui, Y. Yang, M. Zhang, ..., and Y. Tang, The application of large language models in medicine: A scoping review , iScience, Volumn 27, Issue 5, May 2024. (PDF)
- [JACT-24] C. Wan, M. Zhang, P. Dang, W. Hao, S. Cao, P. Li and C. Zhang Ambiguities in neural-network-based hyperedge prediction, Journal of Applied and Computational Topology, May 2024. (PDF) (Source code)
- [ICML-24] Y. Hu, X. Tang, H. Yang and M. Zhang, Case-Based or Rule-Based: How Do Transformers Do the Math?, Proc. International Conference on Machine Learning (ICML-24), 2024. (PDF) (Source code)
- [ICML-24] X. Wang, P. Li and M. Zhang, Graph As Point Set, Proc. International Conference on Machine Learning (ICML-24), 2024. (PDF)
- [ICML-24] Y. Wang and M. Zhang, An Empirical Study of Realized GNN Expressiveness, Proc. International Conference on Machine Learning (ICML-24), 2024. (PDF) (Source code)
- [WWW-24] H. Liu, J. Feng, L. Kong, D. Tao, Y. Chen and M. Zhang, Graph Contrastive Learning Meets Graph Meta Learning: A Unified Method for Few-shot Node Tasks, The Web Conference (WWW-24), 2024. (PDF) (Source code)
- [ICLR-24] H. Liu, J. Feng, L. Kong, N. Liang, D. Tao, Y. Chen and M. Zhang, One For All: Towards Training One Graph Model For All Classification Tasks, International Conference on Learning Representations (ICLR-24), spotlight presentation, (4.96% acceptance rate), 2024. (PDF) (Source code)
- [ICLR-24] X. Wang, H. Yang and M. Zhang, Neural Common Neighbor with Completion for Link Prediction, International Conference on Learning Representations (ICLR-24), 2024. (PDF) (Source code)
- [ICLR-24] Y. Huang, W. Lu, J. Robinson, Y. Yang, M. Zhang, S. Jegelka and P. Li, On the Stability of Expressive Positional Encodings for Graph Neural Networks, International Conference on Learning Representations (ICLR-24), 2024. (PDF) (Source code)
- [ICLR-24] Z. Dong, M. Zhang, P. Payne, M. Province, C. Cruchaga, T. Zhao, F. Li, Y. Chen, Rethinking the Power of Graph Canonization in Graph Representation Learning with Stability, International Conference on Learning Representations (ICLR-24), 2024. (PDF)
- [ICLR-24] L. Yang, Y. Tian, M. Xu, Z. Liu, S. Hong, W. Qu, W. Zhang, B. Cui, M. Zhang# and J. Leskovec, VQGraph: Rethinking Graph Representation Space for Bridging GNNs and MLPs, International Conference on Learning Representations (ICLR-24), 2024. (PDF) (Source code)
- [NeurIPS-23] J. Zhou, J. Feng, X. Wang and M. Zhang, Distance-Restricted Folklore Weisfeiler-Lehman GNNs with Provable Cycle Counting Power, Advances in Neural Information Processing Systems (NeurIPS-23), spotlight presentation (3.06% acceptance rate), 2023. (PDF)
- [NeurIPS-23] Z. Li, X. Wang, Y. Huang and M. Zhang, Is Distance Matrix Enough for Geometric Deep Learning?, Advances in Neural Information Processing Systems (NeurIPS-23), 2023. (PDF)
- [NeurIPS-23] L. Kong, J. Feng, H. Liu, D. Tao, Y. Chen and M. Zhang, MAG-GNN: Reinforcement Learning Boosted Graph Neural Network, Advances in Neural Information Processing Systems (NeurIPS-23), 2023. (PDF)
- [NeurIPS-23] J. Feng, L. Kong, H. Liu, D. Tao, F. Li, M. Zhang and Y. Chen, Extending the Design Space of Graph Neural Networks by Rethinking Folklore Weisfeiler-Lehman, Advances in Neural Information Processing Systems (NeurIPS-23), 2023. (PDF)
- [NeurIPS-23] C. Zhou, X. Wang and M. Zhang, Facilitating Graph Neural Networks with Random Walk on Simplicial Complexes, Advances in Neural Information Processing Systems (NeurIPS-23), 2023. (PDF)
- [VLDB-23] H. Yin, M. Zhang, J. Wang and P. Li, SUREL+: Moving from Walks to Sets for Scalable Subgraph-based Graph Representation Learning, Proc. of the VLDB Endowment (VLDB-23), volume 16, 2023. (PDF) (Source code)
- [ICML-23] C. Zhou, X. Wang and M. Zhang, From Relational Pooling to Subgraph GNNs: A Universal Framework for More Expressive Graph Neural Networks, Proc. International Conference on Machine Learning (ICML-23), 2023. (PDF)
- [ICLR-23] Y. Huang, X. Peng, J. Ma, M. Zhang, Boosting the Cycle Counting Power of Graph Neural Networks with I2-GNNs, International Conference on Learning Representations (ICLR-23), 2023. (PDF) (Source code)
- [ICLR-23] Z. Dong, W. Cao, M. Zhang, D. Tao, Y. Chen, X. Zhang, CktGNN: Circuit Graph Neural Network for Electronic Design Automation, International Conference on Learning Representations (ICLR-23), 2023. (PDF)
- [ASP-DAC-23] Y. Chen, J. Mai, X. Gao, M. Zhang and Y. Lin, MacroRank: Ranking Macro Placement Solutions Leveraging Translation Equivariancy, 28th Asia and South Pacific Design Automation Conference (ASP-DAC-23), 2023. (PDF)
- [LoG-22] X. Wang and M. Zhang, Graph Neural Network with Local Frame for Molecular Potential Energy Surface, The First Learning on Graphs Conference (LoG-22), 2022. (PDF)(Source code)
- [LoG-22] Z. Wang, Q. Cao, H. Shen#, B. Xu, M. Zhang# and X. Cheng, Towards Efficient and Expressive GNNs for Graph Classification via Subgraph-aware Weisfeiler-Lehman, The First Learning on Graphs Conference (LoG-22), 2022. (#corresponding author)(PDF)
- [NeurIPS-22] H. Yang, Z. Lin and M. Zhang, Rethinking Knowledge Graph Evaluation Under the Open-World Assumption, Advances in Neural Information Processing Systems (NeurIPS-22), oral presentation (1.7% acceptance rate), 2022. (PDF)(Source code)
- [NeurIPS-22] J. Feng, Y. Chen, F. Li, A. Sarkar and M. Zhang, How Powerful are K-hop Message Passing Graph Neural Networks, Advances in Neural Information Processing Systems (NeurIPS-22), 2022. (PDF)(Source code)
- [NeurIPS-22] L. Kong, Y. Chen, M. Zhang, Geodesic Graph Neural Network for Efficient Graph Representation Learning, Advances in Neural Information Processing Systems (NeurIPS-22), 2022. (PDF)(Source code)
- [ICML-22-DyNN] Y. Yang, Y. Liang and M. Zhang, PA-GNN: Parameter-Adaptive Graph Neural Networks , Workshop on Dynamic Neural Networks in International Conference on Machine Learning (ICML-22-DyNN-Workshop), oral presentation, 2022. (PDF)
- [VLDB-22] H. Yin, M. Zhang, Y. Wang, J. Wang and P. Li, Algorithm and System Co-design for Efficient Subgraph-based Graph Representation Learning , Proc. of the VLDB Endowment (VLDB-22), volume 15, 2022. (PDF)(Source code)
- [ICML-22] Y. Huang, X. Peng, J. Ma, and M. Zhang, 3DLinker: An E(3) Equivariant Variational Autoencoder for Molecular Linker Design, Proc. International Conference on Machine Learning (ICML-22), long presentation, 2022. (Only 118 out of 5630 submissions are accepted as long presentations) (PDF)(Source code)
- [ICML-22] X. Wang and M. Zhang, How Powerful are Spectral Graph Neural Networks, Proc. International Conference on Machine Learning (ICML-22), 2022. (PDF)(Source code)
- [ICML-22] Z. Dong*, M. Zhang*, F. Li, and Y. Chen, PACE: A Parallelizable Computation Encoder for Directed Acyclic Graphs, Proc. International Conference on Machine Learning (ICML-22), 2022. (*co-first author) (PDF)(Source code)
- [ICLR-22] X. Wang and M. Zhang, GLASS: GNN with Labeling Tricks for Subgraph Representation Learning, International Conference on Learning Representations (ICLR-22), 2022. (PDF)(Source code)
- [ICLR-22] H. Wang, H. Yin, M. Zhang, and P. Li, Equivariant and Stable Positional Encoding for More Powerful Graph Neural Networks, International Conference on Learning Representations (ICLR-22), 2022. (PDF)(Source code)
- [MIA-21] X. Li, Y. Zhou, N. Dvornek, M. Zhang, S. Gao, J. Zhuang, D. Scheinost, LH Staib, P. Ventola and JS Duncan, Braingnn: Interpretable brain graph neural network for fmri analysis, Medical Image Analysis (MIA-21), 2021. (PDF)
- [NeurIPS-21] M. Zhang, P. Li, Y. Xia, K. Wang, and L. Jin, Labeling Trick: A Theory of Using Graph Neural Networks for Multi-Node Representation Learning, Advances in Neural Information Processing Systems (NeurIPS-21), 2021. (PDF)(Source code)
- [NeurIPS-21] M. Zhang and P. Li, Nested Graph Neural Networks, Advances in Neural Information Processing Systems (NeurIPS-21), 2021. (PDF) (Source code)
- [NeurIPS-21] H. Zeng, M. Zhang#, Y. Xia, A. Srivastava, A. Malevich, R. Kannan, V. Prasanna, L. Jin, and R. Chen, Decoupling the Depth and Scope of Graph Neural Networks, Advances in Neural Information Processing Systems (NeurIPS-21), 2021. (#corresponding author) (PDF)(Source code)
- [ICLR-20] M. Zhang and Y. Chen, Inductive Matrix Completion Based on Graph Neural Networks, International Conference on Learning Representations (ICLR-20), spotlight presentation (4.16% acceptance rate), 2020. (PDF)(Source code)
- [KDD-20] M. Zhang, C. King, M. Avidan, and Y. Chen, Hierarchical Attention Propagation for Healthcare Representation Learning, Proc. ACM SIGKDD Conference on Knowledge Discovery and Data Mining (KDD-20), 2020. (PDF)(Source code)
- [MICCAI-20] X. Li, Y. Zhou, N. Dvornek, M. Zhang, J. Zhuang, P. Ventola, and J. Duncan, Pooling Regularized Graph Neural Network for fMRI Biomarker Analysis, Proc. International Conference on Medical Image Computing and Computer-Assisted Intervention. (MICCAI-20), 2020. (PDF)
- [NeurIPS-19] M. Zhang, S. Jiang, Z. Cui, R. Garnett, and Y. Chen, D-VAE: A Variational Autoencoder for Directed Acyclic Graphs, Advances in Neural Information Processing Systems (NeurIPS-19), 2019. (PDF)(Source code)
- [BJA-19] B. Fritz, Z. Cui, M. Zhang, Y. He, Y. Chen, A. Kronzer, A. Ben Abdallah, C. King, M. Avidan, A Deep Learning Model for Predicting 30-day Postoperative Mortalit, British Journal of Anaesthesia (BJA-19), 2019. (PDF)
- [NeurIPS-18] M. Zhang and Y. Chen, Link Prediction Based on Graph Neural Networks, Advances in Neural Information Processing Systems (NeurIPS-18), spotlight presentation, 2018. (Only 168 out of 4856 submissions are accepted as spotlight presentations) (PDF)(Source code)(Website)(Video)
- [AAAI-18] M. Zhang, Z. Cui, M. Neumann, and Y. Chen, An End-to-End Deep Learning Architecture for Graph Classification, Proc. AAAI Conference on Artificial Intelligence (AAAI-18), 2018. (PDF)(Supplement)(Source code)
- [AAAI-18] M. Zhang, Z. Cui, S. Jiang, and Y. Chen, Beyond Link Prediction: Predicting Hyperlinks in Adjacency Space, Proc. AAAI Conference on Artificial Intelligence (AAAI-18), 2018. (PDF)(Source code)
- [ICBK-18] Z. Cui, M. Zhang, and Y. Chen, Deep Embedding Logistic Regression, Proc. IEEE International Conference on Big Knowledge (ICBK-18), 2018. (PDF)
- [KDD-17] M. Zhang and Y. Chen, Weisfeiler-Lehman Neural Machine for Link Prediction, Proc. ACM SIGKDD Conference on Knowledge Discovery and Data Mining (KDD-17), oral presentation, 2017. (Only 64 out of 748 submissions are accepted as oral presentations) (PDF)(Video)(Slides)(Source code)
- [Bioinformatics-17] T. Oyetunde*, M. Zhang*, Y. Chen, Y. Tang, and C. Lo, BoostGAPFILL: Improving the fidelity of metabolic network reconstructions through integrated constraint and pattern-based methods, Bioinformatics, 33(4):608-611, 2017. (*co-first author) (PDF)
- [BMC Bioinformatics-16] L. He, S. Wu, M. Zhang, Y. Chen, and Y. Tang, WUFlux: an open-source platform for 13C metabolic flux analysis of bacterial metabolism, BMC Bioinformatics, 17.1 (2016): 444. (PDF)
-
[TNNLS-16]
W. Cai, M. Zhang, and Y. Zhang, Batch Mode Active Learning for
Regression With Expected Model Change, IEEE Transactions on Neural
Networks
and Learning Systems (TNNLS) , (2016): 1-14. (PDF)
2015
- [IRJ-15] W. Cai, M. Zhang, and Y. Zhang, Active learning for ranking with sample density, Information Retrieval Journal , 18.2 (2015): 123-144. (PDF)
- [TWEB-15] W. Cai, M. Zhang, and Y. Zhang, Active learning for Web search ranking via noise injection, ACM Transactions on the Web (TWEB), 9.1 (2015): 3. (PDF)
2024
2023
2022
2021
2020
2019
2018
2017
2016
Group
Haotong Yang, PhD Student, PKU 2021 (co-advised with Zhouchen Lin)
Xiyuan Wang, PhD Student, PKU 2022
Fanxu Meng, PhD Student, PKU 2022
Xiaojuan Tang, PhD Student, PKU 2022 (co-advised with Song-Chun Zhu)
Zian Li, PhD Student, PKU 2023
Yanbo Wang, PhD Student, PKU 2023
Lecheng Kong, PhD Student, WashU
Jiarui Feng, PhD Student, WashU
Zehao Dong, PhD Student, WashU
Hao Liu, PhD Student, WashU
Xingang Peng, PhD Student, PKU
Zuoyu Yan, PhD Student, PKU
Junru Zhou, Undergraduate, PKU
Yuran Xiang, Undergraduate, PKU
Cai Zhou, Undergraduate, THU
Yi Hu, Undergraduate, PKU
Alumni
Yinan Huang, Research Intern, BIGAI
Yang Hu, Research Intern, PKU
Yuxin Yang, Research Intern, BIGAI
Zhaohui Wang, PhD Student, ICT-CAS
Software
IGMC (Inductive Graph-based Matrix Completion)
D-VAE (DAG Variational Autoencoder)
SEAL (learning from Subgraphs, Embeddings, and Attributes for Link prediction)
WLNM (Weisfeiler-Lehman Neural Machine)