YD

Yuanqi Du

0000-0003-2988-0374

cs.LGcs.AIphysics.chem-phcs.CVcond-mat.mtrl-sciphysics.comp-phq-bio.BMstat.MLcs.SIeess.IV

On Valency

published · living versions

Science Prediction Universe

with Zengji Tu, Xiang Liu, Jiarui Sun, Ruoyu Wu +31

1 version

W_xgqyup7dv1 · current

MoLRSI: A Recursive Self-Improving AI agent for Molecular Discovery

W_ka3rjr2vv1

Preprints & journals

55 papers in the corpus · 2020–2026

Measuring AI Scientists: From Exams to Discovery

Yuanqi Du, Steven Dillmann, Jon Laurent et al.

0 citations

10.26434/chemrxiv.15007582/v12026ChemRxiv

Assessing generative modeling approaches for free energy estimates in condensed matter.

Schebek, Maximilian, He, Jiajun, Hoffmann, Emil et al.

2 citations

421176502026The Journal of chemical physics. 2026;164(18)

A unified perspective on fine-tuning and sampling with diffusion and flow models

Carles Domingo-Enrich, Yuanqi Du, Michael S. Albergo

0 citations

2605.00229v12026arXiv

Accelerating Scientific Discovery with Autonomous Goal-evolving Agents

Yuanqi Du, Botao Yu, Tianyu Liu et al.

1 citation

2512.21782v22025arXiv

CREPE: Controlling Diffusion with Replica Exchange

Jiajun He, Paul Jeha, Peter Potaptchik et al.

0 citations

2509.23265v22025arXiv

Trust Region Constrained Measure Transport in Path Space for Stochastic Optimal Control and Inference

Denis Blessing, Julius Berner, Lorenz Richter et al.

0 citations

2508.12511v22025arXiv

The Rise of Generative AI for Metal-Organic Framework Design and Synthesis

Chenru Duan, Aditya Nandy, Shyam Chand Pal et al.

22 citations

2508.13197v12025arXiv

Generative Design of Functional Metal Complexes Utilizing the Internal Knowledge and Reasoning Capability of Large Language Models.

Lu, Jieyu, Song, Zhangde, Zhao, Qiyuan et al.

24 citations

406079902025Journal of the American Chemical Society. 2025;147(36):32377-32388

RNE: plug-and-play diffusion inference-time control and energy-based training

Jiajun He, Jos'e Miguel Hern'andez-Lobato, Yuanqi Du et al.

1 citation

2506.05668v62025arXiv

FEAT: Free energy Estimators with Adaptive Transport

Jiajun He, Yuanqi Du, Francisco Vargas et al.

2 citations

2504.11516v42025arXiv

No Trick, No Treat: Pursuits and Challenges Towards Simulation-free Training of Neural Samplers

Jiajun He, Yuanqi Du, Francisco Vargas et al.

2 citations

2502.06685v22025arXiv

Large Language Model is Secretly a Protein Sequence Optimizer

Yinkai Wang, Jiaxing He, Yuanqi Du et al.

1 citation

2501.09274v22025arXiv

Graph Generative Pre-trained Transformer

Xiaohui Chen, Yinkai Wang, Jiaxing He et al.

1 citation

2501.01073v22025arXiv

Structure-based drug design with equivariant diffusion models.

Schneuing, Arne, Harris, Charles, Du, Yuanqi et al.

324 citations

396538462024Nature computational science. 2024;4(12):899-909

Generative Design of Functional Metal Complexes Utilizing the Internal Knowledge of Large Language Models

Jieyu Lu, Zhangde Song, Qiyuan Zhao et al.

6 citations

2410.18136v12024arXiv

Generalized Flow Matching for Transition Dynamics Modeling

Haibo Wang, Yuxuan Qiu, Yanze Wang et al.

1 citation

2410.15128v12024arXiv

Doob's Lagrangian: A Sample-Efficient Variational Approach to Transition Path Sampling

Yuanqi Du, Michael Plainer, Rob Brekelmans et al.

2 citations

2410.07974v42024arXiv

Large Language Models are Catalyzing Chemistry Education

Yuanqi Du, Chenru Duan, Andres Bran et al.

10 citations

10.26434/chemrxiv-2024-h722v2024ChemRxiv

Aligning Large Language Models with Representation Editing: A Control Perspective

Lingkai Kong, Haorui Wang, Wenhao Mu et al.

3 citations

2406.05954v32024arXiv

React-OT: Optimal Transport for Generating Transition State in Chemical Reactions

Chenru Duan, Guan-Horng Liu, Yuanqi Du et al.

4 citations

2404.13430v22024arXiv

Diffusion Models as Constrained Samplers for Optimization with Unknown Constraints

Lingkai Kong, Yuanqi Du, Wenhao Mu et al.

0 citations

2402.18012v42024arXiv

Molecular Contrastive Pretraining with Collaborative Featurizations.

Zhu, Yanqiao, Chen, Dingshuo, Du, Yuanqi et al.

7 citations

383150022024Journal of chemical information and modeling. 2024;64(4):1112-1122

Accurate transition state generation with an object-aware equivariant elementary reaction diffusion model.

Duan, Chenru, Du, Yuanqi, Jia, Haojun et al.

90 citations

381777242024Nature computational science. 2023;3(12):1045-1055

Learning Over Molecular Conformer Ensembles: Datasets and Benchmarks

Yanqiao Zhu, Jeehyun Hwang, Keir Adams et al.

5 citations

2310.00115v22023arXiv

Uncovering Neural Scaling Laws in Molecular Representation Learning

Dingshuo Chen, Yanqiao Zhu, Jieyu Zhang et al.

5 citations

2309.15123v22023arXiv

Publisher Correction: Scientific discovery in the age of artificial intelligence.

Wang, Hanchen, Fu, Tianfan, Du, Yuanqi et al.

19 citations

376488712025Nature. 2023;621(7978):E33

Scientific discovery in the age of artificial intelligence.

Wang, Hanchen, Fu, Tianfan, Du, Yuanqi et al.

1,804 citations

375328112023Nature. 2023;620(7972):47-60

Artificial Intelligence for Science in Quantum, Atomistic, and Continuum Systems

Xuan Zhang, Limei Wang, Jacob Helwig et al.

74 citations

2307.08423v62023Foundations and Trends in Machine Learning: Vol. 18: No. 4, pp 385-912 (2025)

MUBen: Benchmarking the Uncertainty of Molecular Representation Models

Yinghao Li, Lingkai Kong, Yuanqi Du et al.

6 citations

2306.10060v42023arXiv

M $^2$ Hub: Unlocking the Potential of Machine Learning for Materials Discovery

Yuanqi Du, Yingheng Wang, Yining Huang et al.

6 citations

2307.05378v12023arXiv

Xtal2DoS: Attention-based Crystal to Sequence Learning for Density of States Prediction

Junwen Bai, Yuanqi Du, Yingheng Wang et al.

2 citations

2302.01486v12023arXiv

GAUCHE: A Library for Gaussian Processes in Chemistry

Ryan-Rhys Griffiths, Leo Klarner, Henry B. Moss et al.

29 citations

2212.04450v22022arXiv

A Systematic Survey of Chemical Pre-trained Models

Jun Xia, Yanqiao Zhu, Yuanqi Du et al.

61 citations

2210.16484v32022arXiv

Improving Molecular Pretraining with Complementary Featurizations

Yanqiao Zhu, Dingshuo Chen, Yuanqi Du et al.

1 citation

2209.15101v12022arXiv

Controllable Data Generation by Deep Learning: A Review

Shiyu Wang, Yuanqi Du, Xiaojie Guo et al.

31 citations

2207.09542v62022arXiv

ChemSpacE: Interpretable and Interactive Chemical Space Exploration

Yuanqi Du, Xian Liu, Nilay Shah et al.

7 citations

10.26434/chemrxiv-2022-x49mh-v32022ChemRxiv

A Flexible Diffusion Model

Weitao Du, Tao Yang, He Zhang et al.

3 citations

2206.10365v12022arXiv

Small molecule generation via disentangled representation learning.

Du, Yuanqi, Guo, Xiaojie, Wang, Yinkai et al.

16 citations

355111252022Bioinformatics (Oxford, England). 2022;38(12):3200-3208

Pik-Fix: Restoring and Colorizing Old Photos

Runsheng Xu, Zhengzhong Tu, Yuanqi Du et al.

27 citations

2205.01902v32022arXiv

MolGenSurvey: A Systematic Survey in Machine Learning Models for Molecule Design

Yuanqi Du, Tianfan Fu, Jimeng Sun et al.

26 citations

2203.14500v12022arXiv

A Survey on Deep Graph Generation: Methods and Applications

Yanqiao Zhu, Yuanqi Du, Yinkai Wang et al.

29 citations

2203.06714v32022arXiv

Recovering medical images from CT film photos

Quan Quan, Qiyuan Wang, Yuanqi Du et al.

0 citations

2203.05567v12022arXiv

Disentangled Spatiotemporal Graph Generative Models

Yuanqi Du, Xiaojie Guo, Hengning Cao et al.

18 citations

2203.00411v12022arXiv

Interpretable Molecular Graph Generation via Monotonic Constraints

Yuanqi Du, Xiaojie Guo, Amarda Shehu et al.

17 citations

2203.00412v12022arXiv

A Survey of Pretraining on Graphs: Taxonomy, Methods, and Applications

Jun Xia, Yanqiao Zhu, Yuanqi Du et al.

28 citations

2202.07893v22022arXiv

ROMNet: Renovate the Old Memories

Runsheng Xu, Zhengzhong Tu, Yuanqi Du et al.

2 citations

2202.02606v22022arXiv

Graph-based Ensemble Machine Learning for Student Performance Prediction

Yinkai Wang, Aowei Ding, Kaiyi Guan et al.

3 citations

2112.07893v32021arXiv

Generating tertiary protein structures via interpretable graph variational autoencoders.

Guo, Xiaojie, Du, Yuanqi, Tadepalli, Sivani et al.

31 citations

367001102023Bioinformatics advances. 2021;1(1):vbab036

SE(3) Equivariant Graph Neural Networks with Complete Local Frames

Weitao Du, He Zhang, Yuanqi Du et al.

20 citations

2110.14811v22021arXiv

Physics-Augmented Learning: A New Paradigm Beyond Physics-Informed Learning

Ziming Liu, Yunyue Chen, Yuanqi Du et al.

14 citations

2109.13901v12021arXiv

Career total: 77 works. 55 are in this corpus.Showing the 50 most recent.

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