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Du, Yuanqi

  1. Structure-based Drug Design with Equivariant Diffusion Models
    2022/10/24 by Arne Schneuing, Charles B. Harris, Schneuing, Arne +22 · 49 citations
    Computer Science · Medicine · Biochemistry, Genetics and Molecular Biology · #Computational Drug Discovery Methods #Monoclonal and Polyclonal Antibodies Research #Cancer-related gene regulation
  2. Evaluating Large Language Models in Scientific Discovery
    2025/12/17 by Zhangde Song, Jieyu Lu, Song, Zhangde +109 · 18 voices · 2 citations
    Materials Science · Medicine · Social Sciences · #Machine Learning in Materials Science #Artificial Intelligence in Healthcare and Education #Computational and Text Analysis Methods
  3. Artificial Intelligence for Science in Quantum, Atomistic, and Continuum Systems
    2023/07/17 by Xuan Zhang, Zhang, Xuan, Limei Wang +123 · 1 voice · 21 citations
    #cs.LG #physics.comp-ph
  4. Audio-Driven Co-Speech Gesture Video Generation
    2022/12/05 by Xian Liu, Liu, Xian, Qianyi Wu +11 · 10 citations
    Engineering · Computer Science · #Human Motion and Animation #Human Pose and Action Recognition #Multimodal Machine Learning Applications
  5. Stochastic Optimal Control for Collective Variable Free Sampling of Molecular Transition Paths
    2022/06/27 by Lars Holdijk, Yuanqi Du, Holdijk, Lars +9 · 9 citations
    Biochemistry, Genetics and Molecular Biology · Chemistry · #Biomolecules (q-bio.BM) #Chemical Physics (physics.chem-ph) #FOS: Biological sciences #FOS: Computer and information sciences #FOS: Physical sciences #Gene Regulatory Network Analysis #Machine Learning (cs.LG) #Mass Spectrometry Techniques and Applications #Receptor Mechanisms and Signaling
  6. Aligning Large Language Models with Representation Editing: A Control Perspective
    2024/06/10 by Lingkai Kong, Haorui Wang, Kong, Lingkai +17 · 14 citations
    Computer Science · #Artificial Intelligence (cs.AI) #FOS: Computer and information sciences #FOS: Electrical engineering #Machine Learning (cs.LG) #Natural Language Processing Techniques #Systems and Control (eess.SY) #Topic Modeling #electronic engineering #information engineering
  7. Accurate transition state generation with an object-aware equivariant elementary reaction diffusion model
    2023/04/12 by Duan, Chenru, Du, Yuanqi, Jia, Haojun +1 · 9 citations
    #Chemical Physics (physics.chem-ph) #FOS: Computer and information sciences #FOS: Physical sciences #Machine Learning (cs.LG)
  8. Doob's Lagrangian: A Sample-Efficient Variational Approach to Transition Path Sampling
    2024/10/10 by Yuanqi Du, Du, Yuanqi, Michael Plainer +13 · 1 voice · 11 citations
    Decision Sciences · #Probabilistic and Robust Engineering Design
  9. GAUCHE: A Library for Gaussian Processes in Chemistry
    2022/12/06 by Griffiths, Ryan-Rhys, Klarner, Leo, Moss, Henry B. +24 · 7 citations
    #Chemical Physics (physics.chem-ph) #FOS: Computer and information sciences #FOS: Physical sciences #Machine Learning (cs.LG) #Materials Science (cond-mat.mtrl-sci)
  10. A Survey on Graph Structure Learning: Progress and Opportunities
    2021/03/04 by Zhu, Yanqiao, Xu, Weizhi, Zhang, Jinghao +5 · 5 citations
    #FOS: Computer and information sciences #Machine Learning (cs.LG) #Social and Information Networks (cs.SI)
  11. Efficient Evolutionary Search Over Chemical Space with Large Language Models
    2024/06/23 by Haorui Wang, Wang, Haorui, Marta Skreta +24 · 10 citations
    Computer Science · Biochemistry, Genetics and Molecular Biology · #Evolutionary Algorithms and Applications #Metaheuristic Optimization Algorithms Research #DNA and Biological Computing
  12. A Survey on Deep Graph Generation: Methods and Applications
    2022/03/13 by Yanqiao Zhu, Zhu, Yanqiao, Yuanqi Du +11 · 5 citations
    Computer Science · #Advanced Graph Neural Networks #FOS: Biological sciences #FOS: Computer and information sciences #Machine Learning (cs.LG) #Molecular Networks (q-bio.MN) #Social and Information Networks (cs.SI) #Text and Document Classification Technologies #Topic Modeling
  13. Diffusion Models as Constrained Samplers for Optimization with Unknown Constraints
    2024/02/28 by Lingkai Kong, Yuanqi Du, Kong, Lingkai +19 · 8 citations
    Engineering · #Advanced Control Systems Optimization #Artificial Intelligence (cs.AI) #FOS: Computer and information sciences #Machine Learning (cs.LG)
  14. Deep Learning to Segment Pelvic Bones: Large-scale CT Datasets and Baseline Models
    2020/12/16 by Liu, Pengbo, Han, Hu, Du, Yuanqi +9 · 4 citations
    #Computer Vision and Pattern Recognition (cs.CV) #FOS: Computer and information sciences
  15. A new perspective on building efficient and expressive 3D equivariant graph neural networks
    2023/04/07 by Weitao Du, Yuanqi Du, Du, Weitao +13 · 5 citations
    Computer Science · Materials Science · #Advanced Graph Neural Networks #Artificial Intelligence (cs.AI) #FOS: Computer and information sciences #Graph Theory and Algorithms #Machine Learning (cs.LG) #Machine Learning in Materials Science
  16. SE(3) Equivariant Graph Neural Networks with Complete Local Frames
    2021/10/26 by Du, Weitao, Zhang, He, Du, Yuanqi +4 · 4 citations
    #Applied Physics (physics.app-ph) #Artificial Intelligence (cs.AI) #Computational Engineering #Differential Geometry (math.DG) #FOS: Computer and information sciences #FOS: Mathematics #FOS: Physical sciences #Finance #Machine Learning (cs.LG) #and Science (cs.CE)
  17. No Trick, No Treat: Pursuits and Challenges Towards Simulation-free Training of Neural Samplers
    2025/02/10 by Jiajun He, Yuanqi Du, He, Jiajun +13 · 9 citations
    Computer Science · Medicine · #Neural Networks and Applications #Explainable Artificial Intelligence (XAI) #Artificial Intelligence in Healthcare and Education
  18. Learning Over Molecular Conformer Ensembles: Datasets and Benchmarks
    2023/09/29 by Yanqiao Zhu, Zhu, Yanqiao, JeeHyun Hwang +23 · 2 citations
    Materials Science · Computer Science · Chemistry · #Machine Learning in Materials Science #Computational Drug Discovery Methods #Various Chemistry Research Topics
  19. Uncovering Neural Scaling Laws in Molecular Representation Learning
    2023/09/15 by Chen, Dingshuo, Zhu, Yanqiao, Zhang, Jieyu +5 · 2 citations
    #Chemical Physics (physics.chem-ph) #FOS: Computer and information sciences #FOS: Physical sciences #Machine Learning (cs.LG)
  20. LLM-Augmented Chemical Synthesis and Design Decision Programs
    2025/05/11 by Haorui Wang, Jeff Guo, Wang, Haorui +11 · 6 citations
    Materials Science · Computer Science · Environmental Science · #Machine Learning in Materials Science #Computational Drug Discovery Methods #Chemistry and Chemical Engineering
  21. Graph Generative Pre-trained Transformer
    2025/01/02 by Yinkai Wang, Chen, Xiaohui, Jiaxing He +10 · 4 citations
    Computer Science · Health Professions · #Advanced Graph Neural Networks #Neural Networks and Applications #Artificial Intelligence in Healthcare
  22. Navigating Chemical Space with Latent Flows
    2024/05/07 by Guanghao Wei, Wei, Guanghao, Yining Huang +7 · 2 citations
    Decision Sciences · #Chemical Physics (physics.chem-ph) #FOS: Computer and information sciences #FOS: Physical sciences #Machine Learning (cs.LG) #Scientific Computing and Data Management
  23. FEAT: Free energy Estimators with Adaptive Transport
    2025/04/15 by Jiajun He, He, Jiajun, Yuanqi Du +12 · 1 voice · 4 citations
    Materials Science · Physics and Astronomy · #Advanced Thermodynamics and Statistical Mechanics #Machine Learning in Materials Science #Quantum many-body systems #cs.LG #physics.chem-ph #physics.comp-ph #stat.ML
  24. Recovering medical images from CT film photos
    2022/03/10 by Quan, Quan, Wang, Qiyuan, Du, Yuanqi +2 · 1 citation
    #Computer Vision and Pattern Recognition (cs.CV) #FOS: Computer and information sciences #FOS: Electrical engineering #Image and Video Processing (eess.IV) #electronic engineering #information engineering
  25. Interpretable Molecular Graph Generation via Monotonic Constraints
    2022/02/28 by Du, Yuanqi, Guo, Xiaojie, Shehu, Amarda +1 · 1 citation
    #Artificial Intelligence (cs.AI) #FOS: Computer and information sciences #Machine Learning (cs.LG)
  26. A Systematic Survey of Chemical Pre-trained Models
    2022/10/29 by Jun Xia, Yanqiao Zhu, Xia, Jun +5 · 1 citation
    Biochemistry, Genetics and Molecular Biology · Computer Science · Materials Science · #Artificial Intelligence (cs.AI) #Chemical Synthesis and Analysis #Computational Drug Discovery Methods #FOS: Computer and information sciences #Machine Learning (cs.LG) #Machine Learning in Materials Science
  27. AlphaNet: Scaling Up Local-frame-based Atomistic Interatomic Potential
    2025/01/13 by Yin, Bangchen, Wang, Jiaao, Du, Weitao +9 · 3 citations
    #FOS: Computer and information sciences #Machine Learning (cs.LG)
  28. Trust Region Constrained Measure Transport in Path Space for Stochastic Optimal Control and Inference
    2025/08/17 by Denis Blessing, Julius Berner, Blessing, Denis +11 · 8 citations
    Computer Science · Engineering · #Advanced Control Systems Optimization #FOS: Computer and information sciences #Machine Learning (cs.LG) #Stochastic Gradient Optimization Techniques
  29. On Separate Normalization in Self-supervised Transformers
    2023/09/22 by Chen, Xiaohui, Wang, Yinkai, Du, Yuanqi +2 · 1 citation
    #Artificial Intelligence (cs.AI) #Computation and Language (cs.CL) #FOS: Computer and information sciences #Machine Learning (cs.LG)
  30. Generalized Flow Matching for Transition Dynamics Modeling
    2024/10/19 by Haibo Wang, Yuxuan Qiu, Wang, Haibo +7 · 1 voice · 1 citation
    Engineering · #Artificial Intelligence (cs.AI) #Biological Physics (physics.bio-ph) #Chemical Physics (physics.chem-ph) #FOS: Computer and information sciences #FOS: Physical sciences #Fluid Dynamics and Turbulent Flows #Machine Learning (cs.LG)
  31. Accelerated Parallel Tempering via Neural Transports
    2025/02/14 by Leo Yu Zhang, Zhang, Leo, Peter Potaptchik +10 · 3 citations
    Biochemistry, Genetics and Molecular Biology · Computer Science · Engineering · #Algorithms and Data Compression #DNA and Biological Computing #FOS: Computer and information sciences #Machine Learning (cs.LG) #Machine Learning (stat.ML) #Modular Robots and Swarm Intelligence
  32. Generating Tertiary Protein Structures via an Interpretative Variational Autoencoder
    2020/04/08 by Xiaojie Guo, Guo, Xiaojie, Sivani Tadepalli +6 · 1 citation
    Biochemistry, Genetics and Molecular Biology · Materials Science · #Protein Structure and Dynamics #Bioinformatics and Genomic Networks #Machine Learning in Materials Science
  33. Building-Block Aware Generative Modeling for 3D Crystals of Metal Organic Frameworks
    2025/05/13 by Duan, Chenru, Nandy, Aditya, Liu, Sizhan +5 · 2 citations
    #Chemical Physics (physics.chem-ph) #FOS: Computer and information sciences #FOS: Physical sciences #Machine Learning (cs.LG) #Materials Science (cond-mat.mtrl-sci)
  34. The Rise of Generative AI for Metal-Organic Framework Design and Synthesis
    2025/08/15 by Duan, Chenru, Nandy, Aditya, Pal, Shyam Chand +17 · 4 citations
    #Artificial Intelligence (cs.AI) #FOS: Computer and information sciences #FOS: Physical sciences #Materials Science (cond-mat.mtrl-sci)