Publications

You can find my recent and full list of publications on my Google Scholar profile.

Preprints

• Efficient Evolutionary Search over Chemical Space with Large Language Models.
  Haorui Wang*, Marta Skreta*, …, Yuanqi Du†, Alán Aspuru-Guzik†, Kirill Neklyudov†, Chao Zhang†.
  In arXiv preprint arXiv:2406.16976.
• Doob’s Lagrangian: A Sample-Efficient Variational Approach to Transition Path Sampling.
  Yuanqi Du*, Michael Plainer*, Rob Brekelmans*, Chenru Duan, Frank Noe, Carla P. Gomes, Alán Aspuru-Guzik, Kirill Neklyudov.
  Available soon.
• Large Language Models are Catalyzing Chemistry Education.
  Yuanqi Du*, Chenru Duan*, Andres Bran*, Anna Sotnikova, Yi Qu, Heather Kulik, Antoine Bosselut, Jinjia Xu, Philippe Schwaller.
  In ChemRxiv 10.26434/chemrxiv-2024-h722v.
• React-OT: Optimal Transport for Generating Transition State in Chemical Reactions.
  Chenru Duan*, Guan-Horng Liu*, Yuanqi Du*, Tianrong Chen, Qiyuan Zhao, Haojun Jia, Carla P. Gomes, Evangelos A. Theodorou, Heather J. Kulik.
  In arXiv preprint arXiv:2404.13430.
• Diffusion Models as Constrained Samplers for Optimization with Unknown Constraints.
  Yuanqi Du*, Lingkai Kong*, Wenhao Mu*, Kirill Neklyudov, Valentin De Bortol, Haorui Wang, Dongxia Wu, Aaron Ferber, Yi-An Ma, Carla P. Gomes, Chao Zhang.
  In arXiv preprint arXiv:2402.18012.
• Navigating Chemical Space with Latent Flows. Check out our Demo!
  Guanghao Wei*, Yining Huang*, Chenru Duan, Yue Song†, Yuanqi Du†.
  In arXiv preprint arXiv:2405.03987.

Selected Publications

• Machine Learning-Aided Generative Molecular Design.
  Yuanqi Du*, Arian R. Jamasb*, Jeff Guo*, Tianfan Fu, Charles Harris, Yingheng Wang, Chenru Duan, Pietro Lio, Philippe Schwaller, Tom L. Blundell.
  In Nature Machine Intelligence 2024.
• Accurate Transition State Generation with an Object-aware Equivariant Elementary Reaction Diffusion Model.
  Chenru Duan, Yuanqi Du, Haojun Jia, Heather J. Kulik.
  In Nature Computational Science 2023. (Cover Story)
• A New Perspective on Building Efficient and Expressive 3D Equivariant Graph Neural Networks.
  Weitao Du*, Yuanqi Du*, Limei Wang*, Dieqiao Feng, Guifeng Wang, Shuiwang Ji, Carla P. Gomes, Zhi-Ming Ma.
  In Neural Information Processing Systems (NeurIPS) 2023. In TAG in ML workshop ICML 2023. (Oral)
• Path Integral Stochastic Optimal Control for Sampling Transition Paths.
  Lars Holdijk*, Yuanqi Du*, Priyank Jaini, Ferry Hooft, Bernd Ensing, Max Welling.
  In Neural Information Processing Systems (NeurIPS) 2023. In Machine Learning for Physical Sciences workshop NeurIPS 2022.
• M²Hub: Unlocking the Potential of Machine Learning for Materials Discovery.
  Yuanqi Du*, Yingheng Wang*, Yining Huang, Jianan Canal Li, Yanqiao Zhu, Tian Xie, Chenru Duan, John M. Gregoire, Carla P. Gomes.
  In Neural Information Processing Systems (NeurIPS) 2023 Datasets and Benchmarks track.
• A Flexible Diffusion Model.
  Weitao Du, Tao Yang, He Zhang, Yuanqi Du.
  In International Conference on Machine Learning (ICML) 2023.
• Scientific Discovery in the Age of Artificial Intelligence.
  Hanchen Wang*, Tianfan Fu*, Yuanqi Du*, Wenhao Gao+, Kexin Huang+, Ziming Liu+, …, Max Welling, Linfeng Zhang, Connor Coley, Yoshua Bengio, Marinka Zitnik.
  In Nature 2023.
• ChemSpacE: Interpretable and Interactive Chemical Space Exploration.
  Yuanqi Du, Xian Liu, Shengchao Liu, Jieyu Zhang, Bolei Zhou.
  In Transactions on Machine Learning Research (TMLR) 2023. In ELLIS ML4Molecules workshop 2021. (Oral)
• Structure-based Drug Design with Equivariant Diffusion Models.
  Arne Schneuing*, Yuanqi Du*, Charles Harris, Arian Jamasb, Ilia Igashov, Weitao Du, Tom Blundell, Pietro Lió, Carla P. Gomes, Max Welling, Michael Bronstein, Bruno Correia.
  In arXiv preprint arXiv:2210.13695 (2022). In Machine Learning for Structural Biology workshop NeurIPS 2022.
• A Survey on Deep Graph Generation: Methods and Applications.
  Yuanqi Du*, Yanqiao Zhu*, Yinkai Wang*, Jieyu Zhang, Qiang Liu, Shu Wu.
  In First Learning on Graphs conference (LoG) 2022.
• Equivariant Graph Neural Networks with Complete Local Frames.
  Weitao Du*, He Zhang*, Yuanqi Du, Qi Meng, Wei Chen, Tie-Yan Liu, Nanning Zheng, Bin Shao.
  In Thirty-ninth International Conference on Machine Learning (ICML) 2022.
• Disentangled Spatiotemporal Graph Generative Models.
  Yuanqi Du*, Xiaojie Guo*, Hengning Cao, Yanfang Ye, Liang Zhao.
  In AAAI Conference on Artificial Intelligence (AAAI) 2022. (Oral)
• GraphGT: Machine Learning Datasets for Graph Generation and Transformation.
  Yuanqi Du*, Shiyu Wang*, Xiaojie Guo, Hengning Cao, Shujie Hu, Junji Jiang, Aishwarya Varala, Abhinav Angirekula, Liang Zhao.
  In Neural Information Processing Systems (NeurIPS) 2021 Datasets and Benchmarks track.
• Deep Generative Model for Spatial Networks.
  Xiaojie Guo*, Yuanqi Du*, Liang Zhao.
  In ACM SIGKDD Conference on Knowledge Discovery and Data Mining (KDD) 2021.