Yuanqi Du

Publication Activity (10 Years)

Years Active: 2020-2024
Publications (10 Years): 76

Top Topics

American Sign Language

Machine Learning

Diffusion Models

Top Venues

Publications

Shiyu Wang, Yuanqi Du, Xiaojie Guo, Bo Pan, Zhaohui S. Qin, Liang Zhao
Controllable Data Generation by Deep Learning: A Review. ACM Comput. Surv. 56 (9) (2024)
Chenru Duan, Guan-Horng Liu, Yuanqi Du, Tianrong Chen, Qiyuan Zhao, Haojun Jia, Carla P. Gomes, Evangelos A. Theodorou, Heather J. Kulik
React-OT: Optimal Transport for Generating Transition State in Chemical Reactions. CoRR (2024)
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
Learning Over Molecular Conformer Ensembles: Datasets and Benchmarks. ICLR (2024)
Lingkai Kong, Haorui Wang, Wenhao Mu, Yuanqi Du, Yuchen Zhuang, Yifei Zhou, Yue Song, Rongzhi Zhang, Kai Wang, Chao Zhang
Aligning Large Language Models with Representation Editing: A Control Perspective. CoRR (2024)
Yanqiao Zhu, Dingshuo Chen, Yuanqi Du, Yingze Wang, Qiang Liu, Shu Wu
Molecular Contrastive Pretraining with Collaborative Featurizations. J. Chem. Inf. Model. 64 (4) (2024)
Lingkai Kong, Yuanqi Du, Wenhao Mu, Kirill Neklyudov, Valentin De Bortol, Haorui Wang, Dongxia Wu, Aaron Ferber, Yi-An Ma, Carla P. Gomes, Chao Zhang
Diffusion Models as Constrained Samplers for Optimization with Unknown Constraints. CoRR (2024)
Guanghao Wei, Yining Huang, Chenru Duan, Yue Song, Yuanqi Du
Navigating Chemical Space with Latent Flows. CoRR (2024)
Haorui Wang, Marta Skreta, Cher-Tian Ser, Wenhao Gao, Lingkai Kong, Felix Streith-Kalthoff, Chenru Duan, Yuchen Zhuang, Yue Yu, Yanqiao Zhu, Yuanqi Du, Alán Aspuru-Guzik, Kirill Neklyudov, Chao Zhang
Efficient Evolutionary Search Over Chemical Space with Large Language Models. CoRR (2024)
Yuanqi Du, Arian R. Jamasb, Jeff Guo, Tianfan Fu, Charles Harris, Yingheng Wang, Chenru Duan, Pietro Liò, Philippe Schwaller, Tom L. Blundell
Machine learning-aided generative molecular design. Nat. Mac. Intell. 6 (6) (2024)
Yinghao Li, Lingkai Kong, Yuanqi Du, Yue Yu, Yuchen Zhuang, Wenhao Mu, Chao Zhang
MUBen: Benchmarking the Uncertainty of Molecular Representation Models. Trans. Mach. Learn. Res. 2024 (2024)
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
Learning Over Molecular Conformer Ensembles: Datasets and Benchmarks. CoRR (2023)
Weitao Du, He Zhang, Tao Yang, Yuanqi Du
A Flexible Diffusion Model. ICML (2023)
Weitao Du, Yuanqi Du, Limei Wang, Dieqiao Feng, Guifeng Wang, Shuiwang Ji, Carla Gomes, Zhi-Ming Ma
A new perspective on building efficient and expressive 3D equivariant graph neural networks. CoRR (2023)
Yuanqi Du, Yingheng Wang, Yining Huang, Jianan Canal Li, Yanqiao Zhu, Tian Xie, Chenru Duan, John M. Gregoire, Carla P. Gomes
Hub: Unlocking the Potential of Machine Learning for Materials Discovery. CoRR (2023)
Junwen Bai, Yuanqi Du, Yingheng Wang, Shufeng Kong, John M. Gregoire, Carla Gomes
Xtal2DoS: Attention-based Crystal to Sequence Learning for Density of States Prediction. CoRR (2023)
Chenru Duan, Yuanqi Du, Haojun Jia, Heather J. Kulik
Accurate transition state generation with an object-aware equivariant elementary reaction diffusion model. Nat. Comput. Sci. 3 (12) (2023)
Jun Xia, Yanqiao Zhu, Yuanqi Du, Stan Z. Li
A Systematic Survey of Chemical Pre-trained Models. IJCAI (2023)
Xiaohui Chen, Yinkai Wang, Yuanqi Du, Soha Hassoun, Li-Ping Liu
On Separate Normalization in Self-supervised Transformers. CoRR (2023)
Xiaohui Chen, Yinkai Wang, Yuanqi Du, Soha Hassoun, Liping Liu
On Separate Normalization in Self-supervised Transformers. NeurIPS (2023)
Dieqiao Feng, Yuanqi Du, Carla P. Gomes, Bart Selman
Weighted Sampling without Replacement for Deep Top-k Classification. ICML (2023)
Ryan-Rhys Griffiths, Leo Klarner, Henry B. Moss, Aditya Ravuri, Sang Truong, Yuanqi Du, Samuel Stanton, Gary Tom, Bojana Rankovic, Arian Rokkum 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 A. Lee, Bingqing Cheng, Alán Aspuru-Guzik, Philippe Schwaller, Jian Tang
GAUCHE: A Library for Gaussian Processes in Chemistry. NeurIPS (2023)
Yinghao Li, Lingkai Kong, Yuanqi Du, Yue Yu, Yuchen Zhuang, Wenhao Mu, Chao Zhang
MUBen: Benchmarking the Uncertainty of Pre-Trained Models for Molecular Property Prediction. CoRR (2023)
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, Haiyang Yu, Yuqing Xie, Xiang Fu, Alex Strasser, 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 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
Artificial Intelligence for Science in Quantum, Atomistic, and Continuum Systems. CoRR (2023)
Hanchen Wang, Tianfan Fu, Yuanqi Du, Wenhao Gao, Kexin Huang, Ziming Liu, Payal Chandak, Shengchao Liu, Peter Van Katwyk, Andreea Deac, Anima Anandkumar, Karianne Bergen, Carla P. Gomes, Shirley Ho, Pushmeet Kohli, Joan Lasenby, Jure Leskovec, Tie-Yan Liu, Arjun Manrai, Debora S. Marks, Bharath Ramsundar, Le Song, Jimeng Sun, Jian Tang, Petar Velickovic, Max Welling, Linfeng Zhang, Connor W. Coley, Yoshua Bengio, Marinka Zitnik
Scientific discovery in the age of artificial intelligence. Nat. 620 (7972) (2023)
Yuanqi Du, Xian Liu, Nilay Mahesh Shah, Shengchao Liu, Jieyu Zhang, Bolei Zhou
ChemSpacE: Interpretable and Interactive Chemical Space Exploration. Trans. Mach. Learn. Res. 2023 (2023)
Soledad Villar, Benjamin Paul Chamberlain, Yuanqi Du, Hannes Stärk, Chaitanya K. Joshi, Andreea Deac, Iulia Duta, Joshua Robinson, Yanqiao Zhu, Kexin Huang, Michelle M. Li, Sofia Bourhim, Ilia Igashov, Alexandre Duval, Mathieu Alain, Dominique Beaini, Xinyu Yuan
The Second Learning on Graphs Conference: Preface. LoG (2023)
Runsheng Xu, Zhengzhong Tu, Yuanqi Du, Xiaoyu Dong, Jinlong Li, Zibo Meng, Jiaqi Ma, Alan C. Bovik, Hongkai Yu
Pik-Fix: Restoring and Colorizing Old Photos. WACV (2023)
Dingshuo Chen, Yanqiao Zhu, Jieyu Zhang, Yuanqi Du, Zhixun Li, Qiang Liu, Shu Wu, Liang Wang
Uncovering Neural Scaling Laws in Molecular Representation Learning. NeurIPS (2023)
Lars Holdijk, Yuanqi Du, Ferry Hooft, Priyank Jaini, Bernd Ensing, Max Welling
Stochastic Optimal Control for Collective Variable Free Sampling of Molecular Transition Paths. NeurIPS (2023)
Chenru Duan, Yuanqi Du, Haojun Jia, Heather J. Kulik
Accurate transition state generation with an object-aware equivariant elementary reaction diffusion model. CoRR (2023)
Dingshuo Chen, Yanqiao Zhu, Jieyu Zhang, Yuanqi Du, Zhixun Li, Qiang Liu, Shu Wu, Liang Wang
Uncovering Neural Scaling Laws in Molecular Representation Learning. CoRR (2023)
Yuanqi Du, Yingheng Wang, Yining Huang, Jianan Canal Li, Yanqiao Zhu, Tian Xie, Chenru Duan, John M. Gregoire, Carla Pedro Gomes
Hub: Unlocking the Potential of Machine Learning for Materials Discovery. NeurIPS (2023)
Weitao Du, Yuanqi Du, Limei Wang, Dieqiao Feng, Guifeng Wang, Shuiwang Ji, Carla P. Gomes, Zhi-Ming Ma
A new perspective on building efficient and expressive 3D equivariant graph neural networks. NeurIPS (2023)
Shiyu Wang, Xiaojie Guo, Xuanyang Lin, Bo Pan, Yuanqi Du, Yinkai Wang, Yanfang Ye, Ashley Ann Petersen, Austin Leitgeb, Saleh AlKhalifa, Kevin Minbiole, William Wuest, Amarda Shehu, Liang Zhao
Multi-objective Deep Data Generation with Correlated Property Control. CoRR (2022)
Shiyu Wang, Yuanqi Du, Xiaojie Guo, Bo Pan, Liang Zhao
Controllable Data Generation by Deep Learning: A Review. CoRR (2022)
Xian Liu, Qianyi Wu, Hang Zhou, Yuanqi Du, Wayne Wu, Dahua Lin, Ziwei Liu
Audio-Driven Co-Speech Gesture Video Generation. CoRR (2022)
Arne Schneuing, Yuanqi Du, Charles Harris, Arian R. Jamasb, Ilia Igashov, Weitao Du, Tom L. Blundell, Pietro Lió, Carla Gomes, Max Welling, Michael M. Bronstein, Bruno E. Correia
Structure-based Drug Design with Equivariant Diffusion Models. CoRR (2022)
Lars Holdijk, Yuanqi Du, Ferry Hooft, Priyank Jaini, Bernd Ensing, Max Welling
Path Integral Stochastic Optimal Control for Sampling Transition Paths. CoRR (2022)
Yuanqi Du, Xiaojie Guo, Amarda Shehu, Liang Zhao
Interpretable Molecular Graph Generation via Monotonic Constraints. CoRR (2022)
Ryan-Rhys Griffiths, Leo Klarner, Henry B. Moss, Aditya Ravuri, Sang Truong, Bojana Rankovic, Yuanqi Du, Arian Jamasb, Julius Schwartz, Austin Tripp, Gregory Kell, Anthony Bourached, Alex Chan, Jacob Moss, Chengzhi Guo, Alpha A. Lee, Philippe Schwaller, Jian Tang
GAUCHE: A Library for Gaussian Processes in Chemistry. CoRR (2022)
Yuanqi Du, Xiaojie Guo, Hengning Cao, Yanfang Ye, Liang Zhao
Disentangled Spatiotemporal Graph Generative Models. AAAI (2022)
Yanqiao Zhu, Dingshuo Chen, Yuanqi Du, Yingze Wang, Qiang Liu, Shu Wu
Improving Molecular Pretraining with Complementary Featurizations. CoRR (2022)
Yuanqi Du, Xiaojie Guo, Amarda Shehu, Liang Zhao
Interpretable Molecular Graph Generation via Monotonic Constraints. SDM (2022)
Yuanqi Du, Xiaojie Guo, Hengning Cao, Yanfang Ye, Liang Zhao
Disentangled Spatiotemporal Graph Generative Models. CoRR (2022)
Jun Xia, Yanqiao Zhu, Yuanqi Du, Stan Z. Li
A Survey of Pretraining on Graphs: Taxonomy, Methods, and Applications. CoRR (2022)
Runsheng Xu, Zhengzhong Tu, Yuanqi Du, Xiaoyu Dong, Jinlong Li, Zibo Meng, Jiaqi Ma, Hongkai Yu
ROMNet: Renovate the Old Memories. CoRR (2022)
Yuanqi Du, Tianfan Fu, Jimeng Sun, Shengchao Liu
MolGenSurvey: A Systematic Survey in Machine Learning Models for Molecule Design. CoRR (2022)
Bo Pan, Yinkai Wang, Xuanyang Lin, Muran Qin, Yuanqi Du, Shiva Ghaemi, Aowei Ding, Shiyu Wang, Saleh AlKhalifa, Kevin Minbiole, William Wuest, Ashley Ann Petersen, Austin Leitgeb, Amarda Shehu, Liang Zhao
Property-Controllable Generation of Quaternary Ammonium Compounds. BIBM (2022)
Weitao Du, Tao Yang, He Zhang, Yuanqi Du
A Flexible Diffusion Model. CoRR (2022)
Xian Liu, Qianyi Wu, Hang Zhou, Yuanqi Du, Wayne Wu, Dahua Lin, Ziwei Liu
Audio-Driven Co-Speech Gesture Video Generation. NeurIPS (2022)
Arian R. Jamasb, Ramón Viñas Torné, Eric Ma, Yuanqi Du, Charles Harris, Kexin Huang, Dominic Hall, Pietro Lió, Tom L. Blundell
Graphein - a Python Library for Geometric Deep Learning and Network Analysis on Biomolecular Structures and Interaction Networks. NeurIPS (2022)
Yanqiao Zhu, Yuanqi Du, Yinkai Wang, Yichen Xu, Jieyu Zhang, Qiang Liu, Shu Wu
A Survey on Deep Graph Generation: Methods and Applications. CoRR (2022)
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 M. Li, Sofia Bourhim, Ilia Igashov
The First Learning on Graphs Conference: Preface. LoG (2022)
Yuanqi Du, Xiaojie Guo, Yinkai Wang, Amarda Shehu, Liang Zhao
Small molecule generation via disentangled representation learning. Bioinform. 38 (12) (2022)
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
Multi-objective Deep Data Generation with Correlated Property Control. NeurIPS (2022)
Yuanqi Du, Quan Quan, Hu Han, S. Kevin Zhou
Semi-Supervised Pseudo-Healthy Image Synthesis via Confidence Augmentation. ISBI (2022)
Quan Quan, Qiyuan Wang, Yuanqi Du, Liu Li, S. Kevin Zhou
Recovering medical images from CT film photos. CoRR (2022)
Runsheng Xu, Zhengzhong Tu, Yuanqi Du, Xiaoyu Dong, Jinlong Li, Zibo Meng, Jiaqi Ma, Alan C. Bovik, Hongkai Yu
Pik-Fix: Restoring and Colorizing Old Photos. CoRR (2022)
Weitao Du, He Zhang, Yuanqi Du, Qi Meng, Wei Chen, Nanning Zheng, Bin Shao, Tie-Yan Liu
SE(3) Equivariant Graph Neural Networks with Complete Local Frames. ICML (2022)
Yanqiao Zhu, Yuanqi Du, Yinkai Wang, Yichen Xu, Jieyu Zhang, Qiang Liu, Shu Wu
A Survey on Deep Graph Generation: Methods and Applications. LoG (2022)
Jun Xia, Yanqiao Zhu, Yuanqi Du, Yue Liu, Stan Z. Li
A Systematic Survey of Molecular Pre-trained Models. CoRR (2022)
Xiaojie Guo, Yuanqi Du, Liang Zhao
Deep Generative Models for Spatial Networks. KDD (2021)
Pengbo Liu, Hu Han, Yuanqi Du, Heqin Zhu, Yinhao Li, Feng Gu, Honghu Xiao, Jun Li, Chunpeng Zhao, Li Xiao, Xinbao Wu, S. Kevin Zhou
Deep learning to segment pelvic bones: large-scale CT datasets and baseline models. Int. J. Comput. Assist. Radiol. Surg. 16 (5) (2021)
Yinkai Wang, Aowei Ding, Kaiyi Guan, Yuanqi Du
Ensemble Machine Learning System for Student AcademicPerformance Prediction. EDM (Workshops) (2021)
Weitao Du, He Zhang, Yuanqi Du, Qi Meng, Wei Chen, Bin Shao, Tie-Yan Liu
Equivariant vector field network for many-body system modeling. CoRR (2021)
Yuanqi Du, Yinkai Wang, Fardina Fathmiul Alam, Yuanjie Lu, Xiaojie Guo, Liang Zhao, Amarda Shehu
Deep Latent-Variable Models for Controllable Molecule Generation. BIBM (2021)
Yuanqi Du, Shiyu Wang, Xiaojie Guo, Hengning Cao, Shujie Hu, Junji Jiang, Aishwarya Varala, Abhinav Angirekula, Liang Zhao
GraphGT: Machine Learning Datasets for Graph Generation and Transformation. NeurIPS Datasets and Benchmarks (2021)
Yuanqi Du, Quan Quan, Hu Han, S. Kevin Zhou
Where is the disease? Semi-supervised pseudo-normality synthesis from an abnormal image. CoRR (2021)
Yinkai Wang, Aowei Ding, Kaiyi Guan, Shixi Wu, Yuanqi Du
Graph-based Ensemble Machine Learning for Student Performance Prediction. CoRR (2021)
Taseef Rahman, Yuanqi Du, Amarda Shehu
Graph Representation Learning for Protein Conformation Sampling. ICCABS (2021)
Ziming Liu, Yunyue Chen, Yuanqi Du, Max Tegmark
Physics-Augmented Learning: A New Paradigm Beyond Physics-Informed Learning. CoRR (2021)
Xiaojie Guo, Yuanqi Du, Liang Zhao
Property Controllable Variational Autoencoder via Invertible Mutual Dependence. ICLR (2021)
Pengbo Liu, Hu Han, Yuanqi Du, Heqin Zhu, Yinhao Li, Feng Gu, Honghu Xiao, Jun Li, Chunpeng Zhao, Li Xiao, Xinbao Wu, S. Kevin Zhou
Deep Learning to Segment Pelvic Bones: Large-scale CT Datasets and Baseline Models. CoRR (2020)
Yuanqi Du, Nguyen Dang, Riley Wilkerson, Parth H. Pathak, Huzefa Rangwala, Jana Kosecka
American Sign Language Recognition Using an FMCW Wireless Sensor (Student Abstract). AAAI (2020)
Quan Quan, Qiyuan Wang, Liu Li, Yuanqi Du, S. Kevin Zhou
CT Film Recovery via Disentangling Geometric Deformation and Illumination Variation: Simulated Datasets and Deep Models. CoRR (2020)
Panneer Selvam Santhalingam, Yuanqi Du, Riley Wilkerson, Al Amin Hosain, Ding Zhang, Parth H. Pathak, Huzefa Rangwala, Raja S. Kushalnagar
Expressive ASL Recognition using Millimeter-wave Wireless Signals. SECON (2020)