Du, Yuanqi

64 publications

FnTML 2025 Artificial Intelligence for Science in Quantum, Atomistic, and Continuum Systems Xuan Zhang, Limei Wang, Jacob Helwig, Youzhi Luo, Cong Fu, Yaochen Xie, Meng Liu, Yuchao Lin, Zhao Xu, Keqiang Yan, Keir Adams, Maurice Weiler, Xiner Li, Tianfan Fu, Yucheng Wang, Alex Strasser, Haiyang Yu, Yuqing Xie, Xiang Fu, Shenglong Xu, Yi Liu, Yuanqi Du, Alexandra Saxton, Hongyi Ling, Hannah Lawrence, Hannes Stärk, Shurui Gui, Carl Edwards, Nicholas Gao, Adriana Ladera, Tailin Wu, Elyssa F. Hofgard, Aria Mansouri Tehrani, Rui Wang, Ameya Daigavane, Montgomery Bohde, Jerry Kurtin, Qian Huang, Tuong Phung, Minkai Xu, Chaitanya K. Joshi, Simon V. Mathis, Kamyar Azizzadenesheli, Ada Fang, Alán Aspuru-Guzik, Erik J. Bekkers, Michael M. Bronstein, Marinka Zitnik, Anima Anandkumar, Stefano Ermon, Pietro Liò, Rose Yu, Stephan Günnemann, Jure Leskovec, Heng Ji, Jimeng Sun, Regina Barzilay, Tommi S. Jaakkola, Connor W. Coley, Xiaoning Qian, Xiaofeng Qian, Tess E. Smidt, Shuiwang Ji

AISTATS 2025 Diffusion Models as Constrained Samplers for Optimization with Unknown Constraints Lingkai Kong, Yuanqi Du, Wenhao Mu, Kirill Neklyudov, Valentin De Bortoli, Dongxia Wu, Haorui Wang, Aaron M Ferber, Yian Ma, Carla P Gomes, Chao Zhang

ICLR 2025 Efficient Evolutionary Search over Chemical Space with Large Language Models Haorui Wang, Marta Skreta, Cher Tian Ser, Wenhao Gao, Lingkai Kong, Felix Strieth-Kalthoff, Chenru Duan, Yuchen Zhuang, Yue Yu, Yanqiao Zhu, Yuanqi Du, Alan Aspuru-Guzik, Kirill Neklyudov, Chao Zhang

NeurIPS 2025 FEAT: Free Energy Estimators with Adaptive Transport Yuanqi Du, Jiajun He, Francisco Vargas, Yuanqing Wang, Carla P Gomes, José Miguel Hernández-Lobato, Eric Vanden-Eijnden

ICML 2025 Graph Generative Pre-Trained Transformer Xiaohui Chen, Yinkai Wang, Jiaxing He, Yuanqi Du, Soha Hassoun, Xiaolin Xu, Liping Liu

ICLRW 2025 Graph Generative Pre-Trained Transformer Xiaohui Chen, Yinkai Wang, Jiaxing He, Yuanqi Du, Soha Hassoun, Xiaolin Xu, Liping Liu

ICML 2025 LLM-Augmented Chemical Synthesis and Design Decision Programs Haorui Wang, Jeff Guo, Lingkai Kong, Rampi Ramprasad, Philippe Schwaller, Yuanqi Du, Chao Zhang

ICLRW 2025 LLM-Augmented Chemical Synthesis and Design Decision Programs Haorui Wang, Jeff Guo, Lingkai Kong, Rampi Ramprasad, Philippe Schwaller, Yuanqi Du, Chao Zhang

ICLRW 2025 Large Language Model Is Secretly a Protein Sequence Optimizer Yinkai Wang, Jiaxing He, Yuanqi Du, Xiaohui Chen, Jianan Canal Li, Liping Liu, Xiaolin Xu, Soha Hassoun

ICLRW 2025 Large Language Models Are Innate Crystal Structure Generators Jingru Gan, Peichen Zhong, Yuanqi Du, Yanqiao Zhu, Chenru Duan, Haorui Wang, Daniel Schwalbe-Koda, Carla P Gomes, Kristin Persson, Wei Wang

ICLRW 2025 No Trick, No Treat: Pursuits and Challenges Towards Simulation-Free Training of Neural Samplers Jiajun He, Yuanqi Du, Francisco Vargas, Dinghuai Zhang, Shreyas Padhy, RuiKang OuYang, Carla P Gomes, José Miguel Hernández-Lobato

ICLRW 2025 Scaling Deep Learning Solutions for Transition Path Sampling Jungyoon Lee, Michael Plainer, Yuanqi Du, Lars Holdijk, Rob Brekelmans, Dominique Beaini, Kirill Neklyudov

ICLRW 2025 Scaling Deep Learning Solutions for Transition Path Sampling Jungyoon Lee, Michael Plainer, Yuanqi Du, Lars Holdijk, Rob Brekelmans, Carla P Gomes, Dominique Beaini, Kirill Neklyudov

NeurIPS 2025 Trust Region Constrained Measure Transport in Path Space for Stochastic Optimal Control and Inference Denis Blessing, Julius Berner, Lorenz Richter, Carles Domingo-Enrich, Yuanqi Du, Arash Vahdat, Gerhard Neumann

NeurIPS 2024 Aligning Large Language Models with Representation Editing: A Control Perspective Lingkai Kong, Haorui Wang, Wenhao Mu, Yuanqi Du, Yuchen Zhuang, Yifei Zhou, Yue Song, Rongzhi Zhang, Kai Wang, Chao Zhang

ICMLW 2024 Aligning Large Language Models with Representation Editing: A Control Perspective Lingkai Kong, Haorui Wang, Wenhao Mu, Yuanqi Du, Yuchen Zhuang, Yifei Zhou, Yue Song, Rongzhi Zhang, Kai Wang, Chao Zhang

NeurIPS 2024 Doob's Lagrangian: A Sample-Efficient Variational Approach to Transition Path Sampling Yuanqi Du, Michael Plainer, Rob Brekelmans, Chenru Duan, Frank Noé, Carla P. Gomes, Alán Aspuru-Guzik, Kirill Neklyudov

ICMLW 2024 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, Alan Aspuru-Guzik, Kirill Neklyudov

ICMLW 2024 Efficient Evolutionary Search over Chemical Space with Large Language Models Haorui Wang, Marta Skreta, Yuanqi Du, Wenhao Gao, Lingkai Kong, Cher Tian Ser, Felix Strieth-Kalthoff, Chenru Duan, Yuchen Zhuang, Yue Yu, Yanqiao Zhu, Alan Aspuru-Guzik, Kirill Neklyudov, Chao Zhang

NeurIPSW 2024 Generalized Flow Matching for Transition Dynamics Modeling Haibo Wang, Yuxuan Qiu, Yanze Wang, Rob Brekelmans, Yuanqi Du

ICLR 2024 Learning over Molecular Conformer Ensembles: Datasets and Benchmarks Yanqiao Zhu, Jeehyun Hwang, Keir Adams, Zhen Liu, Bozhao Nan, Brock Stenfors, Yuanqi Du, Jatin Chauhan, Olaf Wiest, Olexandr Isayev, Connor W. Coley, Yizhou Sun, Wei Wang

TMLR 2024 MUBen: Benchmarking the Uncertainty of Molecular Representation Models Yinghao Li, Lingkai Kong, Yuanqi Du, Yue Yu, Yuchen Zhuang, Wenhao Mu, Chao Zhang

NeurIPS 2024 Navigating Chemical Space with Latent Flows Guanghao Wei, Yining Huang, Chenru Duan, Yue Song, Yuanqi Du

ICMLW 2024 Navigating Chemical Space with Latent Flows Guanghao Wei, Yining Huang, Chenru Duan, Yue Song, Yuanqi Du

ICLRW 2024 Traversing Chemical Space with Latent Potential Flows Guanghao Wei, Yining Huang, Chenru Duan, Yue Song, Yuanqi Du

ICML 2023 A Flexible Diffusion Model Weitao Du, He Zhang, Tao Yang, Yuanqi Du

ICMLW 2023 A Flexible Diffusion Model Weitao Du, He Zhang, Tao Yang, Yuanqi Du

NeurIPS 2023 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

IJCAI 2023 A Systematic Survey of Chemical Pre-Trained Models Jun Xia, Yanqiao Zhu, Yuanqi Du, Stan Z. Li

TMLR 2023 ChemSpacE: Interpretable and Interactive Chemical Space Exploration Yuanqi Du, Xian Liu, Nilay Mahesh Shah, Shengchao Liu, Jieyu Zhang, Bolei Zhou

ICLRW 2023 Flexible Small-Molecule Design and Optimization with Equivariant Diffusion Models Charles Harris, Kieran Didi, Arne Schneuing, Yuanqi Du, Arian Rokkum Jamasb, Michael M. Bronstein, Bruno Correia, Pietro Lio, Tom Leon Blundell

NeurIPS 2023 GAUCHE: A Library for Gaussian Processes in Chemistry Ryan-Rhys Griffiths, Leo Klarner, Henry Moss, Aditya Ravuri, Sang Truong, Yuanqi Du, Samuel Stanton, Gary Tom, Bojana Rankovic, Arian Jamasb, Aryan Deshwal, Julius Schwartz, Austin Tripp, Gregory Kell, Simon Frieder, Anthony Bourached, Alex Chan, Jacob Moss, Chengzhi Guo, Johannes Peter Dürholt, Saudamini Chaurasia, Ji Won Park, Felix Strieth-Kalthoff, Alpha Lee, Bingqing Cheng, Alan Aspuru-Guzik, Philippe Schwaller, Jian Tang

NeurIPSW 2023 Learning over Molecular Conformer Ensembles: Datasets and Benchmarks Yanqiao Zhu, Jeehyun Hwang, Keir Adams, Zhen Liu, Bozhao Nan, Brock Stenfors, Yuanqi Du, Jatin Chauhan, Olaf Wiest, Olexandr Isayev, Connor Coley, Yizhou Sun, Wei Wang

NeurIPS 2023 M$^2$Hub: 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 Gregoire, Carla P. Gomes

NeurIPSW 2023 MUBen: Benchmarking the Uncertainty of Molecular Representation Models Yinghao Li, Lingkai Kong, Yuanqi Du, Yue Yu, Yuchen Zhuang, Wenhao Mu, Chao Zhang

NeurIPS 2023 On Separate Normalization in Self-Supervised Transformers Xiaohui Chen, Yinkai Wang, Yuanqi Du, Soha Hassoun, Liping Liu

WACV 2023 Pik-Fix: Restoring and Colorizing Old Photos Runsheng Xu, Zhengzhong Tu, Yuanqi Du, Xiaoyu Dong, Jinlong Li, Zibo Meng, Jiaqi Ma, Alan Bovik, Hongkai Yu

NeurIPS 2023 Stochastic Optimal Control for Collective Variable Free Sampling of Molecular Transition Paths Lars Holdijk, Yuanqi Du, Ferry Hooft, Priyank Jaini, Berend Ensing, Max Welling

LoG 2023 The Second Learning on Graphs Conference: Preface Soledad Villar, Benjamin Chamberlain, Yuanqi Du, Hannes St"ark, Chaitanya K. Joshi, Andreea Deac, Iulia Duta, Joshua Robinson, Yanqiao Zhu, Kexin Huang, Michelle Li, Sofia Bourhim, Ilia Igashov, Alexandre Duval, Mathieu Alain, Dominique Beaini, Xinyu Yuan

NeurIPS 2023 Uncovering Neural Scaling Laws in Molecular Representation Learning Dingshuo Chen, Yanqiao Zhu, Jieyu Zhang, Yuanqi Du, Zhixun Li, Qiang Liu, Shu Wu, Liang Wang

ICML 2023 Weighted Sampling Without Replacement for Deep Top-$k$ Classification Dieqiao Feng, Yuanqi Du, Carla P Gomes, Bart Selman

LoG 2022 A Survey on Deep Graph Generation: Methods and Applications Yanqiao Zhu, Yuanqi Du, Yinkai Wang, Yichen Xu, Jieyu Zhang, Qiang Liu, Shu Wu

NeurIPS 2022 Audio-Driven Co-Speech Gesture Video Generation Xian Liu, Qianyi Wu, Hang Zhou, Yuanqi Du, Wayne Wu, Dahua Lin, Ziwei Liu

ICLRW 2022 ChemSpacE: Toward Steerable and Interpretable Chemical Space Exploration Yuanqi Du, Xian Liu, Shengchao Liu, Jieyu Zhang, Bolei Zhou

AAAI 2022 Disentangled Spatiotemporal Graph Generative Models Yuanqi Du, Xiaojie Guo, Hengning Cao, Yanfang Ye, Liang Zhao

ICMLW 2022 Featurizations Matter: A Multiview Contrastive Learning Approach to Molecular Pretraining Yanqiao Zhu, Dingshuo Chen, Yuanqi Du, Yingze Wang, Qiang Liu, Shu Wu

ICMLW 2022 GAUCHE: A Library for Gaussian Processes in Chemistry Ryan-Rhys Griffiths, Leo Klarner, Henry Moss, Aditya Ravuri, Sang T. Truong, Bojana Rankovic, Yuanqi Du, Arian Rokkum Jamasb, Julius Schwartz, Austin Tripp, Gregory Kell, Anthony Bourached, Alex Chan, Jacob Moss, Chengzhi Guo, Alpha Lee, Philippe Schwaller, Jian Tang

NeurIPS 2022 Graphein - A Python Library for Geometric Deep Learning and Network Analysis on Biomolecular Structures and Interaction Networks Arian Jamasb, Ramon Viñas Torné, Eric Ma, Yuanqi Du, Charles Harris, Kexin Huang, Dominic Hall, Pietro Lió, Tom Blundell

ICMLW 2022 Graphein - A Python Library for Geometric Deep Learning and Network Analysis on Biomolecular Structures and Interaction Networks Arian Rokkum Jamasb, Ramon Viñas Torné, Eric J Ma, Yuanqi Du, Charles Harris, Kexin Huang, Dominic Hall, Pietro Lio, Tom Leon Blundell

NeurIPS 2022 Multi-Objective Deep Data Generation with Correlated Property Control Shiyu Wang, Xiaojie Guo, Xuanyang Lin, Bo Pan, Yuanqi Du, Yinkai Wang, Yanfang Ye, Ashley Petersen, Austin Leitgeb, Saleh Alkhalifa, Kevin Minbiole, William M. Wuest, Amarda Shehu, Liang Zhao

ICMLW 2022 Path Integral Stochastic Optimal Control for Sampling Transition Paths Lars Holdijk, Yuanqi Du, Priyank Jaini, Ferry Hooft, Bernd Ensing, Max Welling

ICMLW 2022 Pre-Training Graph Neural Networks for Molecular Representations: Retrospect and Prospect Jun Xia, Yanqiao Zhu, Yuanqi Du, Stan Z. Li

ICML 2022 SE(3) Equivariant Graph Neural Networks with Complete Local Frames Weitao Du, He Zhang, Yuanqi Du, Qi Meng, Wei Chen, Nanning Zheng, Bin Shao, Tie-Yan Liu

NeurIPSW 2022 Structural Causal Model for Molecular Dynamics Simulation Qi Liu, Yuanqi Du, Fan Feng, Qiwei Ye, Jie Fu

LoG 2022 The First Learning on Graphs Conference: Preface Bastian Rieck, Razvan Pascanu, Yuanqi Du, Hannes Stärk, Derek Lim, Chaitanya K. Joshi, Andreea Deac, Iulia Duta, Joshua Robinson, Gabriele Corso, Leonardo Cotta, Yanqiao Zhu, Kexin Huang, Michelle Li, Sofia Bourhim, Ilia Igashov

NeurIPSW 2022 Xtal2DoS: Attention-Based Crystal to Sequence Learning for Density of States Prediction Junwen Bai, Yuanqi Du, Yingheng Wang, Shufeng Kong, John Gregoire, Carla P Gomes

NeurIPSW 2021 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

NeurIPSW 2021 Learning Disentangled Representation for Spatiotemporal Graph Generation Yuanqi Du, Xiaojie Guo, Hengning Cao, Yanfang Ye, Liang Zhao

NeurIPSW 2021 Physics-Augmented Learning: A New Paradigm Beyond Physics-Informed Learning Ziming Liu, Yuanqi Du, Yunyue Chen, Max Tegmark

ICLR 2021 Property Controllable Variational Autoencoder via Invertible Mutual Dependence Xiaojie Guo, Yuanqi Du, Liang Zhao

AAAI 2020 American Sign Language Recognition Using an FMCW Wireless Sensor (Student Abstract) Yuanqi Du, Nguyen Dang, Riley Wilkerson, Parth H. Pathak, Huzefa Rangwala, Jana Kosecka