BibTeX records: Tianfan Fu

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@article{DBLP:journals/qmi/ZhengFL26,
  author       = {Kangyu Zheng and
                  Tianfan Fu and
                  Zhiding Liang},
  title        = {{QCS-ADME:} Quantum circuit search for drug property prediction with
                  imbalanced data and regression adaptation},
  journal      = {Quantum Mach. Intell.},
  volume       = {8},
  number       = {1},
  pages        = {23},
  year         = {2026},
  url          = {https://doi.org/10.1007/s42484-026-00369-6},
  doi          = {10.1007/S42484-026-00369-6},
  timestamp    = {Thu, 19 Mar 2026 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/qmi/ZhengFL26.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tmlr/ZhengZTCLZSZFL26,
  author       = {Kangyu Zheng and
                  Kai Zhang and
                  Jiale Tan and
                  Xuehan Chen and
                  Yingzhou Lu and
                  Zaixi Zhang and
                  Lichao Sun and
                  Marinka Zitnik and
                  Tianfan Fu and
                  Zhiding Liang},
  title        = {Beyond Affinity: {A} Benchmark of 1D, 2D, and 3D Methods Reveals Critical
                  Trade-offs in Structure-Based Drug Design},
  journal      = {Trans. Mach. Learn. Res.},
  volume       = {2026},
  year         = {2026},
  url          = {https://openreview.net/forum?id=gaTwx1rzCw},
  timestamp    = {Mon, 09 Feb 2026 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/tmlr/ZhengZTCLZSZFL26.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2601-00290,
  author       = {Sixue Xing and
                  Xuanye Xia and
                  Kerui Wu and
                  Meng Jiang and
                  Jintai Chen and
                  Tianfan Fu},
  title        = {ClinicalReTrial: {A} Self-Evolving {AI} Agent for Clinical Trial Protocol
                  Optimization},
  journal      = {CoRR},
  volume       = {abs/2601.00290},
  year         = {2026},
  url          = {https://doi.org/10.48550/arXiv.2601.00290},
  doi          = {10.48550/ARXIV.2601.00290},
  eprinttype   = {arXiv},
  eprint       = {2601.00290},
  timestamp    = {Mon, 09 Feb 2026 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/corr/abs-2601-00290.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2601-02213,
  author       = {Haoyu Zhou and
                  Ping Xue and
                  Tianfan Fu and
                  Hao Zhang},
  title        = {Quantized SO(3)-Equivariant Graph Neural Networks for Efficient Molecular
                  Property Prediction},
  journal      = {CoRR},
  volume       = {abs/2601.02213},
  year         = {2026},
  url          = {https://doi.org/10.48550/arXiv.2601.02213},
  doi          = {10.48550/ARXIV.2601.02213},
  eprinttype   = {arXiv},
  eprint       = {2601.02213},
  timestamp    = {Mon, 02 Mar 2026 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/corr/abs-2601-02213.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2601-14283,
  author       = {Kangyu Zheng and
                  Kai Zhang and
                  Jiale Tan and
                  Xuehan Chen and
                  Yingzhou Lu and
                  Zaixi Zhang and
                  Lichao Sun and
                  Marinka Zitnik and
                  Tianfan Fu and
                  Zhiding Liang},
  title        = {Beyond Affinity: {A} Benchmark of 1D, 2D, and 3D Methods Reveals Critical
                  Trade-offs in Structure-Based Drug Design},
  journal      = {CoRR},
  volume       = {abs/2601.14283},
  year         = {2026},
  url          = {https://doi.org/10.48550/arXiv.2601.14283},
  doi          = {10.48550/ARXIV.2601.14283},
  eprinttype   = {arXiv},
  eprint       = {2601.14283},
  timestamp    = {Mon, 16 Feb 2026 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/corr/abs-2601-14283.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2601-19205,
  author       = {Zefeng Lin and
                  Zhihang Zhang and
                  Weirong Zhu and
                  Tongchang Han and
                  Xianyong Fang and
                  Tianfan Fu and
                  Xiaohua Xu},
  title        = {EnzyPGM: Pocket-conditioned Generative Model for Substrate-specific
                  Enzyme Design},
  journal      = {CoRR},
  volume       = {abs/2601.19205},
  year         = {2026},
  url          = {https://doi.org/10.48550/arXiv.2601.19205},
  doi          = {10.48550/ARXIV.2601.19205},
  eprinttype   = {arXiv},
  eprint       = {2601.19205},
  timestamp    = {Thu, 26 Feb 2026 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/corr/abs-2601-19205.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2602-10158,
  author       = {Liujia Yang and
                  Zhuo Yang and
                  Jiaqing Xie and
                  Yubin Wang and
                  Ben Gao and
                  Tianfan Fu and
                  Xingjian Wei and
                  Jiaxing Sun and
                  Jiang Wu and
                  Conghui He and
                  Yuqiang Li and
                  Qinying Gu},
  title        = {NMRTrans: Structure Elucidation from Experimental {NMR} Spectra via
                  Set Transformers},
  journal      = {CoRR},
  volume       = {abs/2602.10158},
  year         = {2026},
  url          = {https://doi.org/10.48550/arXiv.2602.10158},
  doi          = {10.48550/ARXIV.2602.10158},
  eprinttype   = {arXiv},
  eprint       = {2602.10158},
  timestamp    = {Tue, 31 Mar 2026 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/corr/abs-2602-10158.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2602-10422,
  author       = {Srinivas Anumasa and
                  Barath Chandran. C and
                  Tingting Chen and
                  Nuwaisir Mohammad Rahman and
                  Yingtao Zhu and
                  Rushi Shah and
                  Hongyu He and
                  Peisong Zhang and
                  Yizhen Liao and
                  Yiming Tang and
                  Yong Shen and
                  Tianfan Fu and
                  Rui Qing and
                  Xiao Li and
                  Sebastian Maurer{-}Stroh and
                  Xinyi Su and
                  Zhizhuo Zhang and
                  Dianbo Liu},
  title        = {Navigating heterogeneous protein landscapes through geometry-aware
                  smoothing},
  journal      = {CoRR},
  volume       = {abs/2602.10422},
  year         = {2026},
  url          = {https://doi.org/10.48550/arXiv.2602.10422},
  doi          = {10.48550/ARXIV.2602.10422},
  eprinttype   = {arXiv},
  eprint       = {2602.10422},
  timestamp    = {Wed, 25 Mar 2026 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/corr/abs-2602-10422.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2603-05343,
  author       = {Haoyu Zhou and
                  Ping Xue and
                  Hao Zhang and
                  Tianfan Fu},
  title        = {Preserving Continuous Symmetry in Discrete Spaces: Geometric-Aware
                  Quantization for SO(3)-Equivariant GNNs},
  journal      = {CoRR},
  volume       = {abs/2603.05343},
  year         = {2026},
  url          = {https://doi.org/10.48550/arXiv.2603.05343},
  doi          = {10.48550/ARXIV.2603.05343},
  eprinttype   = {arXiv},
  eprint       = {2603.05343},
  timestamp    = {Wed, 08 Apr 2026 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/corr/abs-2603-05343.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2603-09715,
  author       = {Peng Sun and
                  Huawen Shen and
                  Yi Ban and
                  Tianfan Fu and
                  Yanbo Wang and
                  Yuqiang Li},
  title        = {Does the Question Really Matter? Training-Free Data Selection for
                  Vision-Language {SFT}},
  journal      = {CoRR},
  volume       = {abs/2603.09715},
  year         = {2026},
  url          = {https://doi.org/10.48550/arXiv.2603.09715},
  doi          = {10.48550/ARXIV.2603.09715},
  eprinttype   = {arXiv},
  eprint       = {2603.09715},
  timestamp    = {Thu, 09 Apr 2026 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/corr/abs-2603-09715.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2603-19636,
  author       = {Zhou Zhang and
                  Hanqun Cao and
                  Cheng Tan and
                  Fang Wu and
                  Pheng{-}Ann Heng and
                  Tianfan Fu},
  title        = {RiboSphere: Learning Unified and Efficient Representations of {RNA}
                  Structures},
  journal      = {CoRR},
  volume       = {abs/2603.19636},
  year         = {2026},
  url          = {https://doi.org/10.48550/arXiv.2603.19636},
  doi          = {10.48550/ARXIV.2603.19636},
  eprinttype   = {arXiv},
  eprint       = {2603.19636},
  timestamp    = {Thu, 16 Apr 2026 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/corr/abs-2603-19636.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/XieLF25,
  author       = {Jiaqing Xie and
                  Yuqiang Li and
                  Tianfan Fu},
  title        = {DeepProtein: deep learning library and benchmark for protein sequence
                  learning},
  journal      = {Bioinform.},
  volume       = {41},
  number       = {10},
  year         = {2025},
  url          = {https://doi.org/10.1093/bioinformatics/btaf165},
  doi          = {10.1093/BIOINFORMATICS/BTAF165},
  timestamp    = {Sat, 15 Nov 2025 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/bioinformatics/XieLF25.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ftml/ZhangWHLFXLLXYAWLFWSYXF25,
  author       = {Xuan Zhang and
                  Limei Wang and
                  Jacob Helwig and
                  Youzhi Luo and
                  Cong Fu and
                  Yaochen Xie and
                  Meng Liu and
                  Yuchao Lin and
                  Zhao Xu and
                  Keqiang Yan and
                  Keir Adams and
                  Maurice Weiler and
                  Xiner Li and
                  Tianfan Fu and
                  Yucheng Wang and
                  Alex Strasser and
                  Haiyang Yu and
                  Yuqing Xie and
                  Xiang Fu and
                  Shenglong Xu and
                  Yi Liu and
                  Yuanqi Du and
                  Alexandra Saxton and
                  Hongyi Ling and
                  Hannah Lawrence and
                  Hannes St{\"{a}}rk and
                  Shurui Gui and
                  Carl Edwards and
                  Nicholas Gao and
                  Adriana Ladera and
                  Tailin Wu and
                  Elyssa F. Hofgard and
                  Aria Mansouri Tehrani and
                  Rui Wang and
                  Ameya Daigavane and
                  Montgomery Bohde and
                  Jerry Kurtin and
                  Qian Huang and
                  Tuong Phung and
                  Minkai Xu and
                  Chaitanya K. Joshi and
                  Simon V. Mathis and
                  Kamyar Azizzadenesheli and
                  Ada Fang and
                  Al{\'{a}}n Aspuru{-}Guzik and
                  Erik J. Bekkers and
                  Michael M. Bronstein and
                  Marinka Zitnik and
                  Anima Anandkumar and
                  Stefano Ermon and
                  Pietro Li{\`{o}} and
                  Rose Yu and
                  Stephan G{\"{u}}nnemann and
                  Jure Leskovec and
                  Heng Ji and
                  Jimeng Sun and
                  Regina Barzilay and
                  Tommi S. Jaakkola and
                  Connor W. Coley and
                  Xiaoning Qian and
                  Xiaofeng Qian and
                  Tess E. Smidt and
                  Shuiwang Ji},
  title        = {Artificial Intelligence for Science in Quantum, Atomistic, and Continuum
                  Systems},
  journal      = {Found. Trends Mach. Learn.},
  volume       = {18},
  number       = {4},
  pages        = {385--912},
  year         = {2025},
  url          = {https://doi.org/10.1561/2200000115},
  doi          = {10.1561/2200000115},
  timestamp    = {Thu, 07 May 2026 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/ftml/ZhangWHLFXLLXYAWLFWSYXF25.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jbi/CuiLXWMYYKLZQHFMHWY25,
  author       = {Hejie Cui and
                  Jiaying Lu and
                  Ran Xu and
                  Shiyu Wang and
                  Wenjing Ma and
                  Yue Yu and
                  Shaojun Yu and
                  Xuan Kan and
                  Chen Ling and
                  Liang Zhao and
                  Zhaohui S. Qin and
                  Joyce C. Ho and
                  Tianfan Fu and
                  Jing Ma and
                  Mengdi Huai and
                  Fei Wang and
                  Carl Yang},
  title        = {A review on knowledge graphs for healthcare: Resources, applications,
                  and promises},
  journal      = {J. Biomed. Informatics},
  volume       = {169},
  pages        = {104861},
  year         = {2025},
  url          = {https://doi.org/10.1016/j.jbi.2025.104861},
  doi          = {10.1016/J.JBI.2025.104861},
  timestamp    = {Thu, 25 Dec 2025 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/jbi/CuiLXWMYYKLZQHFMHWY25.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/XieWGYWZFL25,
  author       = {Jiaqing Xie and
                  Weida Wang and
                  Ben Gao and
                  Zhuo Yang and
                  Haiyuan Wang and
                  Shufei Zhang and
                  Tianfan Fu and
                  Yuqiang Li},
  title        = {QCBench: Evaluating Large Language Models on Domain-Specific Quantitative
                  Chemistry},
  journal      = {J. Chem. Inf. Model.},
  volume       = {65},
  number       = {22},
  pages        = {12268--12278},
  year         = {2025},
  url          = {https://doi.org/10.1021/acs.jcim.5c02033},
  doi          = {10.1021/ACS.JCIM.5C02033},
  timestamp    = {Tue, 24 Mar 2026 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/jcisd/XieWGYWZFL25.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tmlr/MukherjeeZLFZ25,
  author       = {Debadyuti Mukherjee and
                  Chris Zhuang and
                  Yingzhou Lu and
                  Tianfan Fu and
                  Ruqi Zhang},
  title        = {Gradient {GA:} Gradient Genetic Algorithm For Drug Molecular Design},
  journal      = {Trans. Mach. Learn. Res.},
  volume       = {2025},
  year         = {2025},
  url          = {https://openreview.net/forum?id=kFKcktAeEG},
  timestamp    = {Mon, 22 Dec 2025 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/tmlr/MukherjeeZLFZ25.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/aaai/JiangXFBK0025,
  author       = {Pengcheng Jiang and
                  Cao Xiao and
                  Tianfan Fu and
                  Parminder Bhatia and
                  Taha A. Kass{-}Hout and
                  Jimeng Sun and
                  Jiawei Han},
  editor       = {Toby Walsh and
                  Julie Shah and
                  Zico Kolter},
  title        = {Bi-level Contrastive Learning for Knowledge-Enhanced Molecule Representations},
  booktitle    = {Thirty-Ninth {AAAI} Conference on Artificial Intelligence, Thirty-Seventh
                  Conference on Innovative Applications of Artificial Intelligence,
                  Fifteenth Symposium on Educational Advances in Artificial Intelligence,
                  {AAAI} 2025, Philadelphia, PA, USA, February 25 - March 4, 2025},
  pages        = {352--360},
  publisher    = {{AAAI} Press},
  year         = {2025},
  url          = {https://doi.org/10.1609/aaai.v39i1.32013},
  doi          = {10.1609/AAAI.V39I1.32013},
  timestamp    = {Wed, 18 Mar 2026 17:07:12 +0100},
  biburl       = {https://dblp.org/rec/conf/aaai/JiangXFBK0025.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/emnlp/ZhengWPXLZFY25,
  author       = {Wenhao Zheng and
                  Liaoyaqi Wang and
                  Dongsheng Peng and
                  Hongxia Xu and
                  Yun Li and
                  Hongtu Zhu and
                  Tianfan Fu and
                  Huaxiu Yao},
  editor       = {Christos Christodoulopoulos and
                  Tanmoy Chakraborty and
                  Carolyn Rose and
                  Violet Peng},
  title        = {{LIFTED:} Multimodal Clinical Trial Outcome Prediction via Large Language
                  Models and Mixture-of-Experts},
  booktitle    = {Findings of the Association for Computational Linguistics: {EMNLP}
                  2025, Suzhou, China, November 4-9, 2025},
  pages        = {7503--7517},
  publisher    = {Association for Computational Linguistics},
  year         = {2025},
  url          = {https://aclanthology.org/2025.findings-emnlp.396/},
  timestamp    = {Thu, 19 Feb 2026 17:28:40 +0100},
  biburl       = {https://dblp.org/rec/conf/emnlp/ZhengWPXLZFY25.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2501-16509,
  author       = {Zhiyuan Wang and
                  Chunlin Feng and
                  Christopher Poon and
                  Lijian Huang and
                  Xingjian Zhao and
                  Yao Ma and
                  Tianfan Fu and
                  Xiao{-}Yang Liu},
  title        = {Reinforcement Learning for Quantum Circuit Design: Using Matrix Representations},
  journal      = {CoRR},
  volume       = {abs/2501.16509},
  year         = {2025},
  url          = {https://doi.org/10.48550/arXiv.2501.16509},
  doi          = {10.48550/ARXIV.2501.16509},
  eprinttype   = {arXiv},
  eprint       = {2501.16509},
  timestamp    = {Tue, 01 Apr 2025 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/corr/abs-2501-16509.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2502-09860,
  author       = {Chris Zhuang and
                  Debadyuti Mukherjee and
                  Yingzhou Lu and
                  Tianfan Fu and
                  Ruqi Zhang},
  title        = {Gradient {GA:} Gradient Genetic Algorithm for Drug Molecular Design},
  journal      = {CoRR},
  volume       = {abs/2502.09860},
  year         = {2025},
  url          = {https://doi.org/10.48550/arXiv.2502.09860},
  doi          = {10.48550/ARXIV.2502.09860},
  eprinttype   = {arXiv},
  eprint       = {2502.09860},
  timestamp    = {Wed, 26 Mar 2025 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/corr/abs-2502-09860.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2503-01927,
  author       = {Kangyu Zheng and
                  Tianfan Fu and
                  Zhiding Liang},
  title        = {{QCS-ADME:} Quantum Circuit Search for Drug Property Prediction with
                  Imbalanced Data and Regression Adaptation},
  journal      = {CoRR},
  volume       = {abs/2503.01927},
  year         = {2025},
  url          = {https://doi.org/10.48550/arXiv.2503.01927},
  doi          = {10.48550/ARXIV.2503.01927},
  eprinttype   = {arXiv},
  eprint       = {2503.01927},
  timestamp    = {Mon, 21 Apr 2025 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/corr/abs-2503-01927.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2503-02104,
  author       = {Xiangrui Liu and
                  Yuanyuan Zhang and
                  Yingzhou Lu and
                  Changchang Yin and
                  Xiaoling Hu and
                  Xiaoou Liu and
                  Lulu Chen and
                  Sheng Wang and
                  Alexander Rodriguez and
                  Huaxiu Yao and
                  Yezhou Yang and
                  Ping Zhang and
                  Jintai Chen and
                  Tianfan Fu and
                  Xiao Wang},
  title        = {Biomedical Foundation Model: {A} Survey},
  journal      = {CoRR},
  volume       = {abs/2503.02104},
  year         = {2025},
  url          = {https://doi.org/10.48550/arXiv.2503.02104},
  doi          = {10.48550/ARXIV.2503.02104},
  eprinttype   = {arXiv},
  eprint       = {2503.02104},
  timestamp    = {Tue, 07 Oct 2025 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/corr/abs-2503-02104.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2504-05454,
  author       = {Yoshitaka Inoue and
                  Tianfan Fu and
                  Augustin Luna},
  title        = {GraphPINE: Graph Importance Propagation for Interpretable Drug Response
                  Prediction},
  journal      = {CoRR},
  volume       = {abs/2504.05454},
  year         = {2025},
  url          = {https://doi.org/10.48550/arXiv.2504.05454},
  doi          = {10.48550/ARXIV.2504.05454},
  eprinttype   = {arXiv},
  eprint       = {2504.05454},
  timestamp    = {Mon, 19 May 2025 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/corr/abs-2504-05454.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2505-01700,
  author       = {Yize Jiang and
                  Xinze Li and
                  Yuanyuan Zhang and
                  Jin Han and
                  Youjun Xu and
                  Ayush Pandit and
                  Zaixi Zhang and
                  Mengdi Wang and
                  Mengyang Wang and
                  Chong Liu and
                  Guang Yang and
                  Yejin Choi and
                  Wu{-}Jun Li and
                  Tianfan Fu and
                  Fang Wu and
                  Junhong Liu},
  title        = {PoseX: {AI} Defeats Physics Approaches on Protein-Ligand Cross Docking},
  journal      = {CoRR},
  volume       = {abs/2505.01700},
  year         = {2025},
  url          = {https://doi.org/10.48550/arXiv.2505.01700},
  doi          = {10.48550/ARXIV.2505.01700},
  eprinttype   = {arXiv},
  eprint       = {2505.01700},
  timestamp    = {Fri, 12 Dec 2025 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/corr/abs-2505-01700.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2505-12833,
  author       = {Zhuo Yang and
                  Lingli Ge and
                  Dong Han and
                  Tianfan Fu and
                  Yuqiang Li},
  title        = {Reasoning {BO:} Enhancing Bayesian Optimization with Long-Context
                  Reasoning Power of LLMs},
  journal      = {CoRR},
  volume       = {abs/2505.12833},
  year         = {2025},
  url          = {https://doi.org/10.48550/arXiv.2505.12833},
  doi          = {10.48550/ARXIV.2505.12833},
  eprinttype   = {arXiv},
  eprint       = {2505.12833},
  timestamp    = {Wed, 25 Jun 2025 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/corr/abs-2505-12833.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2505-16326,
  author       = {Qian Tan and
                  Dongzhan Zhou and
                  Peng Xia and
                  Wanhao Liu and
                  Wanli Ouyang and
                  Lei Bai and
                  Yuqiang Li and
                  Tianfan Fu},
  title        = {ChemMLLM: Chemical Multimodal Large Language Model},
  journal      = {CoRR},
  volume       = {abs/2505.16326},
  year         = {2025},
  url          = {https://doi.org/10.48550/arXiv.2505.16326},
  doi          = {10.48550/ARXIV.2505.16326},
  eprinttype   = {arXiv},
  eprint       = {2505.16326},
  timestamp    = {Wed, 25 Jun 2025 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/corr/abs-2505-16326.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2506-10521,
  author       = {Yuhao Zhou and
                  Yiheng Wang and
                  Xuming He and
                  Ruoyao Xiao and
                  Zhiwei Li and
                  Qiantai Feng and
                  Zijie Guo and
                  Yuejin Yang and
                  Hao Wu and
                  Wenxuan Huang and
                  Jiaqi Wei and
                  Dan Si and
                  Xiuqi Yao and
                  Jia Bu and
                  Haiwen Huang and
                  Tianfan Fu and
                  Shixiang Tang and
                  Ben Fei and
                  Dongzhan Zhou and
                  Fenghua Ling and
                  Yan Lu and
                  Siqi Sun and
                  Chenhui Li and
                  Guanjie Zheng and
                  Jiancheng Lv and
                  Wenlong Zhang and
                  Lei Bai},
  title        = {Scientists' First Exam: Probing Cognitive Abilities of {MLLM} via
                  Perception, Understanding, and Reasoning},
  journal      = {CoRR},
  volume       = {abs/2506.10521},
  year         = {2025},
  url          = {https://doi.org/10.48550/arXiv.2506.10521},
  doi          = {10.48550/ARXIV.2506.10521},
  eprinttype   = {arXiv},
  eprint       = {2506.10521},
  timestamp    = {Thu, 29 Jan 2026 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/corr/abs-2506-10521.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2506-19613,
  author       = {Sha Zhang and
                  Suorong Yang and
                  Tong Xie and
                  Xiangyuan Xue and
                  Zixuan Hu and
                  Rui Li and
                  Wenxi Qu and
                  Zhenfei Yin and
                  Tianfan Fu and
                  Di Hu and
                  Andres M. Bran and
                  Nian Ran and
                  Bram Hoex and
                  Wangmeng Zuo and
                  Philippe Schwaller and
                  Wanli Ouyang and
                  Lei Bai and
                  Yanyong Zhang and
                  Lingyu Duan and
                  Shixiang Tang and
                  Dongzhan Zhou},
  title        = {Position: Intelligent Science Laboratory Requires the Integration
                  of Cognitive and Embodied {AI}},
  journal      = {CoRR},
  volume       = {abs/2506.19613},
  year         = {2025},
  url          = {https://doi.org/10.48550/arXiv.2506.19613},
  doi          = {10.48550/ARXIV.2506.19613},
  eprinttype   = {arXiv},
  eprint       = {2506.19613},
  timestamp    = {Thu, 26 Feb 2026 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/corr/abs-2506-19613.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2508-01188,
  author       = {Zhuo Yang and
                  Jiaqing Xie and
                  Shuaike Shen and
                  Daolang Wang and
                  Yeyun Chen and
                  Ben Gao and
                  Shuzhou Sun and
                  Biqing Qi and
                  Dongzhan Zhou and
                  Lei Bai and
                  Linjiang Chen and
                  Shufei Zhang and
                  Jun Jiang and
                  Tianfan Fu and
                  Yuqiang Li},
  title        = {SpectrumWorld: Artificial Intelligence Foundation for Spectroscopy},
  journal      = {CoRR},
  volume       = {abs/2508.01188},
  year         = {2025},
  url          = {https://doi.org/10.48550/arXiv.2508.01188},
  doi          = {10.48550/ARXIV.2508.01188},
  eprinttype   = {arXiv},
  eprint       = {2508.01188},
  timestamp    = {Thu, 11 Sep 2025 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/corr/abs-2508-01188.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2508-01670,
  author       = {Jiaqing Xie and
                  Weida Wang and
                  Ben Gao and
                  Zhuo Yang and
                  Haiyuan Wang and
                  Shufei Zhang and
                  Tianfan Fu and
                  Yuqiang Li},
  title        = {QCBench: Evaluating Large Language Models on Domain-Specific Quantitative
                  Chemistry},
  journal      = {CoRR},
  volume       = {abs/2508.01670},
  year         = {2025},
  url          = {https://doi.org/10.48550/arXiv.2508.01670},
  doi          = {10.48550/ARXIV.2508.01670},
  eprinttype   = {arXiv},
  eprint       = {2508.01670},
  timestamp    = {Wed, 10 Sep 2025 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/corr/abs-2508-01670.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2508-10696,
  author       = {Lei Jiang and
                  Shuzhou Sun and
                  Biqing Qi and
                  Yuchen Fu and
                  Xiaohua Xu and
                  Yuqiang Li and
                  Dongzhan Zhou and
                  Tianfan Fu},
  title        = {Chem3DLLM: 3D Multimodal Large Language Models for Chemistry},
  journal      = {CoRR},
  volume       = {abs/2508.10696},
  year         = {2025},
  url          = {https://doi.org/10.48550/arXiv.2508.10696},
  doi          = {10.48550/ARXIV.2508.10696},
  eprinttype   = {arXiv},
  eprint       = {2508.10696},
  timestamp    = {Mon, 15 Sep 2025 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/corr/abs-2508-10696.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2508-15379,
  author       = {Jinliang Yu and
                  Mingduo Xie and
                  Yue Wang and
                  Tianfan Fu and
                  Xianglai Xu and
                  Jiajun Wang},
  title        = {Bladder Cancer Diagnosis with Deep Learning: {A} Multi-Task Framework
                  and Online Platform},
  journal      = {CoRR},
  volume       = {abs/2508.15379},
  year         = {2025},
  url          = {https://doi.org/10.48550/arXiv.2508.15379},
  doi          = {10.48550/ARXIV.2508.15379},
  eprinttype   = {arXiv},
  eprint       = {2508.15379},
  timestamp    = {Wed, 24 Sep 2025 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/corr/abs-2508-15379.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2508-21148,
  author       = {Ming Hu and
                  Chenglong Ma and
                  Wei Li and
                  Wanghan Xu and
                  Jiamin Wu and
                  Jucheng Hu and
                  Tianbin Li and
                  Guohang Zhuang and
                  Jiaqi Liu and
                  Yingzhou Lu and
                  Ying Chen and
                  Chaoyang Zhang and
                  Cheng Tan and
                  Jie Ying and
                  Guocheng Wu and
                  Shujian Gao and
                  Pengcheng Chen and
                  Jiashi Lin and
                  Haitao Wu and
                  Lulu Chen and
                  Fengxiang Wang and
                  Yuanyuan Zhang and
                  Xiangyu Zhao and
                  Feilong Tang and
                  Encheng Su and
                  Junzhi Ning and
                  Xinyao Liu and
                  Ye Du and
                  Changkai Ji and
                  Cheng Tang and
                  Huihui Xu and
                  Ziyang Chen and
                  Ziyan Huang and
                  Jiyao Liu and
                  Pengfei Jiang and
                  Yizhou Wang and
                  Chen Tang and
                  Jianyu Wu and
                  Yuchen Ren and
                  Siyuan Yan and
                  Zhonghua Wang and
                  Zhongxing Xu and
                  Shiyan Su and
                  Shangquan Sun and
                  Runkai Zhao and
                  Zhisheng Zhang and
                  Yu Liu and
                  Fudi Wang and
                  Yuanfeng Ji and
                  Yanzhou Su and
                  Hongming Shan and
                  Chun{-}Mei Feng and
                  Jiahao Xu and
                  Jiangtao Yan and
                  Wenhao Tang and
                  Diping Song and
                  Lihao Liu and
                  Yanyan Huang and
                  Lequan Yu and
                  Bin Fu and
                  Shujun Wang and
                  Xiaomeng Li and
                  Xiaowei Hu and
                  Yun Gu and
                  Ben Fei and
                  Zhongying Deng and
                  Benyou Wang and
                  Yuewen Cao and
                  Minjie Shen and
                  Haodong Duan and
                  Jie Xu and
                  Yirong Chen and
                  Fang Yan and
                  Hongxia Hao and
                  Jielan Li and
                  Jiajun Du and
                  Yanbo Wang and
                  Imran Razzak and
                  Chi Zhang and
                  Lijun Wu and
                  Conghui He and
                  Zhaohui Lu and
                  Jinhai Huang and
                  Yihao Liu and
                  Fenghua Ling and
                  Yuqiang Li and
                  Aoran Wang and
                  Qihao Zheng and
                  Nanqing Dong and
                  Tianfan Fu and
                  Dongzhan Zhou and
                  Yan Lu and
                  Wenlong Zhang and
                  Jin Ye and
                  Jianfei Cai and
                  Wanli Ouyang and
                  Yu Qiao and
                  Zongyuan Ge and
                  Shixiang Tang and
                  Junjun He},
  title        = {A Survey of Scientific Large Language Models: From Data Foundations
                  to Agent Frontiers},
  journal      = {CoRR},
  volume       = {abs/2508.21148},
  year         = {2025},
  url          = {https://doi.org/10.48550/arXiv.2508.21148},
  doi          = {10.48550/ARXIV.2508.21148},
  eprinttype   = {arXiv},
  eprint       = {2508.21148},
  timestamp    = {Thu, 26 Mar 2026 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/corr/abs-2508-21148.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2509-21861,
  author       = {Shuaike Shen and
                  Jiaqing Xie and
                  Zhuo Yang and
                  Antong Zhang and
                  Shuzhou Sun and
                  Ben Gao and
                  Tianfan Fu and
                  Biqing Qi and
                  Yuqiang Li},
  title        = {MolSpectLLM: {A} Molecular Foundation Model Bridging Spectroscopy,
                  Molecule Elucidation, and 3D Structure Generation},
  journal      = {CoRR},
  volume       = {abs/2509.21861},
  year         = {2025},
  url          = {https://doi.org/10.48550/arXiv.2509.21861},
  doi          = {10.48550/ARXIV.2509.21861},
  eprinttype   = {arXiv},
  eprint       = {2509.21861},
  timestamp    = {Mon, 20 Oct 2025 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/corr/abs-2509-21861.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2510-01571,
  author       = {Hanqun Cao and
                  Hongrui Zhang and
                  Junde Xu and
                  Zhou Zhang and
                  Lingdong Shen and
                  Minghao Sun and
                  Ge Liu and
                  Jinbo Xu and
                  Wu{-}Jun Li and
                  Jinren Ni and
                  Cesar de la Fuente{-}Nunez and
                  Tianfan Fu and
                  Yejin Choi and
                  Pheng{-}Ann Heng and
                  Fang Wu},
  title        = {From Supervision to Exploration: What Does Protein Language Model
                  Learn During Reinforcement Learning?},
  journal      = {CoRR},
  volume       = {abs/2510.01571},
  year         = {2025},
  url          = {https://doi.org/10.48550/arXiv.2510.01571},
  doi          = {10.48550/ARXIV.2510.01571},
  eprinttype   = {arXiv},
  eprint       = {2510.01571},
  timestamp    = {Fri, 12 Dec 2025 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/corr/abs-2510-01571.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2510-16880,
  author       = {Weida Wang and
                  Benteng Chen and
                  Di Zhang and
                  Wanhao Liu and
                  Shuchen Pu and
                  Ben Gao and
                  Jin Zeng and
                  Xiaoyong Wei and
                  Tianshu Yu and
                  Shuzhou Sun and
                  Tianfan Fu and
                  Wanli Ouyang and
                  Lei Bai and
                  Jiatong Li and
                  Zifu Wang and
                  Yuqiang Li and
                  Shufei Zhang},
  title        = {Chem-R: Learning to Reason as a Chemist},
  journal      = {CoRR},
  volume       = {abs/2510.16880},
  year         = {2025},
  url          = {https://doi.org/10.48550/arXiv.2510.16880},
  doi          = {10.48550/ARXIV.2510.16880},
  eprinttype   = {arXiv},
  eprint       = {2510.16880},
  timestamp    = {Sat, 09 May 2026 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/corr/abs-2510-16880.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2511-14366,
  author       = {Hongwei Liu and
                  Junnan Liu and
                  Shudong Liu and
                  Haodong Duan and
                  Yuqiang Li and
                  Mao Su and
                  Xiaohong Liu and
                  Guangtao Zhai and
                  Xinyu Fang and
                  Qianhong Ma and
                  Taolin Zhang and
                  Zihan Ma and
                  Yufeng Zhao and
                  Peiheng Zhou and
                  Linchen Xiao and
                  Wenlong Zhang and
                  Shijie Zhou and
                  Xingjian Ma and
                  Siqi Sun and
                  Jiaye Ge and
                  Meng Li and
                  Yuhong Liu and
                  Jianxin Dong and
                  Jiaying Li and
                  Hui Wu and
                  Hanwen Liang and
                  Jintai Lin and
                  Yanting Wang and
                  Jie Dong and
                  Tong Zhu and
                  Tianfan Fu and
                  Conghui He and
                  Qi Zhang and
                  Songyang Zhang and
                  Lei Bai and
                  Kai Chen},
  title        = {{ATLAS:} {A} High-Difficulty, Multidisciplinary Benchmark for Frontier
                  Scientific Reasoning},
  journal      = {CoRR},
  volume       = {abs/2511.14366},
  year         = {2025},
  url          = {https://doi.org/10.48550/arXiv.2511.14366},
  doi          = {10.48550/ARXIV.2511.14366},
  eprinttype   = {arXiv},
  eprint       = {2511.14366},
  timestamp    = {Fri, 16 Jan 2026 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/corr/abs-2511-14366.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2512-00126,
  author       = {Jin Han and
                  Tianfan Fu and
                  Wu{-}Jun Li},
  title        = {RadDiff: Retrieval-Augmented Denoising Diffusion for Protein Inverse
                  Folding},
  journal      = {CoRR},
  volume       = {abs/2512.00126},
  year         = {2025},
  url          = {https://doi.org/10.48550/arXiv.2512.00126},
  doi          = {10.48550/ARXIV.2512.00126},
  eprinttype   = {arXiv},
  eprint       = {2512.00126},
  timestamp    = {Mon, 26 Jan 2026 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/corr/abs-2512-00126.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2512-20135,
  author       = {Zhuo Yang and
                  Yeyun Chen and
                  Jiaqing Xie and
                  Ben Gao and
                  Shuaike Shen and
                  Wanhao Liu and
                  Liujia Yang and
                  Beilun Wang and
                  Tianfan Fu and
                  Yuqiang Li},
  title        = {MolAct: An Agentic {RL} Framework for Molecular Editing and Property
                  Optimization},
  journal      = {CoRR},
  volume       = {abs/2512.20135},
  year         = {2025},
  url          = {https://doi.org/10.48550/arXiv.2512.20135},
  doi          = {10.48550/ARXIV.2512.20135},
  eprinttype   = {arXiv},
  eprint       = {2512.20135},
  timestamp    = {Mon, 26 Jan 2026 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/corr/abs-2512-20135.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/natmi/DuJGFHWDLSB24,
  author       = {Yuanqi Du and
                  Arian R. Jamasb and
                  Jeff Guo and
                  Tianfan Fu and
                  Charles Harris and
                  Yingheng Wang and
                  Chenru Duan and
                  Pietro Li{\`{o}} and
                  Philippe Schwaller and
                  Tom L. Blundell},
  title        = {Machine learning-aided generative molecular design},
  journal      = {Nat. Mac. Intell.},
  volume       = {6},
  number       = {6},
  pages        = {589--604},
  year         = {2024},
  url          = {https://doi.org/10.1038/s42256-024-00843-5},
  doi          = {10.1038/S42256-024-00843-5},
  timestamp    = {Fri, 02 Aug 2024 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/natmi/DuJGFHWDLSB24.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bcb/YueXCF24,
  author       = {Ling Yue and
                  Sixue Xing and
                  Jintai Chen and
                  Tianfan Fu},
  title        = {ClinicalAgent: Clinical Trial Multi-Agent System with Large Language
                  Model-based Reasoning},
  booktitle    = {Proceedings of the 15th {ACM} International Conference on Bioinformatics,
                  Computational Biology and Health Informatics, {BCB} 2024, Shenzhen,
                  China, November 22-25, 2024},
  pages        = {11:1--11:10},
  publisher    = {{ACM}},
  year         = {2024},
  url          = {https://doi.org/10.1145/3698587.3701359},
  doi          = {10.1145/3698587.3701359},
  timestamp    = {Sun, 22 Dec 2024 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/conf/bcb/YueXCF24.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bcb/YueXCF24a,
  author       = {Ling Yue and
                  Sixue Xing and
                  Jintai Chen and
                  Tianfan Fu},
  title        = {TrialEnroll: Predicting Clinical Trial Enrollment Success with Deep
                  {\&} Cross Network and Large Language Models},
  booktitle    = {Proceedings of the 15th {ACM} International Conference on Bioinformatics,
                  Computational Biology and Health Informatics, {BCB} 2024, Shenzhen,
                  China, November 22-25, 2024},
  pages        = {43:1--43:9},
  publisher    = {{ACM}},
  year         = {2024},
  url          = {https://doi.org/10.1145/3698587.3701375},
  doi          = {10.1145/3698587.3701375},
  timestamp    = {Sun, 22 Dec 2024 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/conf/bcb/YueXCF24a.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bcb/YueX0IXCF24,
  author       = {Ling Yue and
                  Sixue Xing and
                  Jonathan Li and
                  Md. Zabirul Islam and
                  Bolun Xia and
                  Jintai Chen and
                  Tianfan Fu},
  title        = {TrialDura: Hierarchical Attention Transformer for Interpretable Clinical
                  Trial Duration Prediction},
  booktitle    = {Proceedings of the 15th {ACM} International Conference on Bioinformatics,
                  Computational Biology and Health Informatics, {BCB} 2024, Shenzhen,
                  China, November 22-25, 2024},
  pages        = {85:1},
  publisher    = {{ACM}},
  year         = {2024},
  url          = {https://doi.org/10.1145/3698587.3701434},
  doi          = {10.1145/3698587.3701434},
  timestamp    = {Sun, 22 Dec 2024 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/conf/bcb/YueX0IXCF24.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icml/LiuCF0ZW24,
  author       = {Songtao Liu and
                  Jinghui Chen and
                  Tianfan Fu and
                  Lu Lin and
                  Marinka Zitnik and
                  Dinghao Wu},
  editor       = {Ruslan Salakhutdinov and
                  Zico Kolter and
                  Katherine A. Heller and
                  Adrian Weller and
                  Nuria Oliver and
                  Jonathan Scarlett and
                  Felix Berkenkamp},
  title        = {Graph Adversarial Diffusion Convolution},
  booktitle    = {Forty-first International Conference on Machine Learning, {ICML} 2024,
                  Vienna, Austria, July 21-27, 2024},
  series       = {Proceedings of Machine Learning Research},
  pages        = {30789--30806},
  publisher    = {{PMLR} / OpenReview.net},
  year         = {2024},
  url          = {https://proceedings.mlr.press/v235/liu24h.html},
  timestamp    = {Mon, 09 Feb 2026 15:35:36 +0100},
  biburl       = {https://dblp.org/rec/conf/icml/LiuCF0ZW24.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/kdd/HongYTFMGFWYWLZ24,
  author       = {Shenda Hong and
                  Daoxin Yin and
                  Gongzheng Tang and
                  Tianfan Fu and
                  Liantao Ma and
                  Junyi Gao and
                  Mengling Feng and
                  Mai Wang and
                  Yu Yang and
                  Fei Wang and
                  Hongfang Liu and
                  Luxia Zhang},
  editor       = {Ricardo Baeza{-}Yates and
                  Francesco Bonchi},
  title        = {Artificial Intelligence and Data Science for Healthcare: Bridging
                  Data-Centric {AI} and People-Centric Healthcare},
  booktitle    = {Proceedings of the 30th {ACM} {SIGKDD} Conference on Knowledge Discovery
                  and Data Mining, {KDD} 2024, Barcelona, Spain, August 25-29, 2024},
  pages        = {6720--6721},
  publisher    = {{ACM}},
  year         = {2024},
  url          = {https://doi.org/10.1145/3637528.3671497},
  doi          = {10.1145/3637528.3671497},
  timestamp    = {Sun, 02 Nov 2025 21:27:16 +0100},
  biburl       = {https://dblp.org/rec/conf/kdd/HongYTFMGFWYWLZ24.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2402-06512,
  author       = {Wenhao Zheng and
                  Dongsheng Peng and
                  Hongxia Xu and
                  Hongtu Zhu and
                  Tianfan Fu and
                  Huaxiu Yao},
  title        = {Multimodal Clinical Trial Outcome Prediction with Large Language Models},
  journal      = {CoRR},
  volume       = {abs/2402.06512},
  year         = {2024},
  url          = {https://doi.org/10.48550/arXiv.2402.06512},
  doi          = {10.48550/ARXIV.2402.06512},
  eprinttype   = {arXiv},
  eprint       = {2402.06512},
  timestamp    = {Fri, 16 Feb 2024 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/corr/abs-2402-06512.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2404-02003,
  author       = {Xinze Li and
                  Penglei Wang and
                  Tianfan Fu and
                  Wenhao Gao and
                  Chengtao Li and
                  Leilei Shi and
                  Junhong Liu},
  title        = {{AUTODIFF:} Autoregressive Diffusion Modeling for Structure-based
                  Drug Design},
  journal      = {CoRR},
  volume       = {abs/2404.02003},
  year         = {2024},
  url          = {https://doi.org/10.48550/arXiv.2404.02003},
  doi          = {10.48550/ARXIV.2404.02003},
  eprinttype   = {arXiv},
  eprint       = {2404.02003},
  timestamp    = {Tue, 14 May 2024 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/corr/abs-2404-02003.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2404-13235,
  author       = {Ling Yue and
                  Jonathan Li and
                  Md. Zabirul Islam and
                  Bolun Xia and
                  Tianfan Fu and
                  Jintai Chen},
  title        = {TrialDura: Hierarchical Attention Transformer for Interpretable Clinical
                  Trial Duration Prediction},
  journal      = {CoRR},
  volume       = {abs/2404.13235},
  year         = {2024},
  url          = {https://doi.org/10.48550/arXiv.2404.13235},
  doi          = {10.48550/ARXIV.2404.13235},
  eprinttype   = {arXiv},
  eprint       = {2404.13235},
  timestamp    = {Wed, 25 Feb 2026 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/corr/abs-2404-13235.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2404-14777,
  author       = {Ling Yue and
                  Tianfan Fu},
  title        = {CT-Agent: Clinical Trial Multi-Agent with Large Language Model-based
                  Reasoning},
  journal      = {CoRR},
  volume       = {abs/2404.14777},
  year         = {2024},
  url          = {https://doi.org/10.48550/arXiv.2404.14777},
  doi          = {10.48550/ARXIV.2404.14777},
  eprinttype   = {arXiv},
  eprint       = {2404.14777},
  timestamp    = {Sat, 25 May 2024 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/corr/abs-2404-14777.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2405-06662,
  author       = {Chufan Gao and
                  Tianfan Fu and
                  Jimeng Sun},
  title        = {Language Interaction Network for Clinical Trial Approval Estimation},
  journal      = {CoRR},
  volume       = {abs/2405.06662},
  year         = {2024},
  url          = {https://doi.org/10.48550/arXiv.2405.06662},
  doi          = {10.48550/ARXIV.2405.06662},
  eprinttype   = {arXiv},
  eprint       = {2405.06662},
  timestamp    = {Mon, 24 Jun 2024 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/corr/abs-2405-06662.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2405-08979,
  author       = {Yoshitaka Inoue and
                  Hunmin Lee and
                  Tianfan Fu and
                  Augustin Luna},
  title        = {drGAT: Attention-Guided Gene Assessment of Drug Response Utilizing
                  a Drug-Cell-Gene Heterogeneous Network},
  journal      = {CoRR},
  volume       = {abs/2405.08979},
  year         = {2024},
  url          = {https://doi.org/10.48550/arXiv.2405.08979},
  doi          = {10.48550/ARXIV.2405.08979},
  eprinttype   = {arXiv},
  eprint       = {2405.08979},
  timestamp    = {Sat, 15 Jun 2024 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/corr/abs-2405-08979.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2406-02059,
  author       = {Songtao Liu and
                  Jinghui Chen and
                  Tianfan Fu and
                  Lu Lin and
                  Marinka Zitnik and
                  Dinghao Wu},
  title        = {Graph Adversarial Diffusion Convolution},
  journal      = {CoRR},
  volume       = {abs/2406.02059},
  year         = {2024},
  url          = {https://doi.org/10.48550/arXiv.2406.02059},
  doi          = {10.48550/ARXIV.2406.02059},
  eprinttype   = {arXiv},
  eprint       = {2406.02059},
  timestamp    = {Wed, 14 Aug 2024 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/corr/abs-2406-02059.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2406-03403,
  author       = {Kangyu Zheng and
                  Yingzhou Lu and
                  Zaixi Zhang and
                  Zhongwei Wan and
                  Yao Ma and
                  Marinka Zitnik and
                  Tianfan Fu},
  title        = {Structure-based Drug Design Benchmark: Do 3D Methods Really Dominate?},
  journal      = {CoRR},
  volume       = {abs/2406.03403},
  year         = {2024},
  url          = {https://doi.org/10.48550/arXiv.2406.03403},
  doi          = {10.48550/ARXIV.2406.03403},
  eprinttype   = {arXiv},
  eprint       = {2406.03403},
  timestamp    = {Fri, 05 Jul 2024 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/corr/abs-2406-03403.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2407-00631,
  author       = {Jintai Chen and
                  Yaojun Hu and
                  Yue Wang and
                  Yingzhou Lu and
                  Xu Cao and
                  Miao Lin and
                  Hongxia Xu and
                  Jian Wu and
                  Cao Xiao and
                  Jimeng Sun and
                  Lucas Glass and
                  Kexin Huang and
                  Marinka Zitnik and
                  Tianfan Fu},
  title        = {TrialBench: Multi-Modal Artificial Intelligence-Ready Clinical Trial
                  Datasets},
  journal      = {CoRR},
  volume       = {abs/2407.00631},
  year         = {2024},
  url          = {https://doi.org/10.48550/arXiv.2407.00631},
  doi          = {10.48550/ARXIV.2407.00631},
  eprinttype   = {arXiv},
  eprint       = {2407.00631},
  timestamp    = {Fri, 09 Aug 2024 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/corr/abs-2407-00631.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2407-13115,
  author       = {Ling Yue and
                  Sixue Xing and
                  Jintai Chen and
                  Tianfan Fu},
  title        = {TrialEnroll: Predicting Clinical Trial Enrollment Success with Deep
                  {\&} Cross Network and Large Language Models},
  journal      = {CoRR},
  volume       = {abs/2407.13115},
  year         = {2024},
  url          = {https://doi.org/10.48550/arXiv.2407.13115},
  doi          = {10.48550/ARXIV.2407.13115},
  eprinttype   = {arXiv},
  eprint       = {2407.13115},
  timestamp    = {Thu, 22 Aug 2024 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/corr/abs-2407-13115.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2408-02600,
  author       = {Ling Yue and
                  Sixue Xing and
                  Yingzhou Lu and
                  Tianfan Fu},
  title        = {BioMamba: {A} Pre-trained Biomedical Language Representation Model
                  Leveraging Mamba},
  journal      = {CoRR},
  volume       = {abs/2408.02600},
  year         = {2024},
  url          = {https://doi.org/10.48550/arXiv.2408.02600},
  doi          = {10.48550/ARXIV.2408.02600},
  eprinttype   = {arXiv},
  eprint       = {2408.02600},
  timestamp    = {Thu, 12 Sep 2024 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/corr/abs-2408-02600.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2408-05696,
  author       = {Bohao Xu and
                  Yingzhou Lu and
                  Chenhao Li and
                  Ling Yue and
                  Xiao Wang and
                  Nan Hao and
                  Tianfan Fu and
                  Jim Chen},
  title        = {SMILES-Mamba: Chemical Mamba Foundation Models for Drug {ADMET} Prediction},
  journal      = {CoRR},
  volume       = {abs/2408.05696},
  year         = {2024},
  url          = {https://doi.org/10.48550/arXiv.2408.05696},
  doi          = {10.48550/ARXIV.2408.05696},
  eprinttype   = {arXiv},
  eprint       = {2408.05696},
  timestamp    = {Tue, 17 Sep 2024 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/corr/abs-2408-05696.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2408-13378,
  author       = {Yoshitaka Inoue and
                  Tianci Song and
                  Tianfan Fu},
  title        = {DrugAgent: Explainable Drug Repurposing Agent with Large Language
                  Model-based Reasoning},
  journal      = {CoRR},
  volume       = {abs/2408.13378},
  year         = {2024},
  url          = {https://doi.org/10.48550/arXiv.2408.13378},
  doi          = {10.48550/ARXIV.2408.13378},
  eprinttype   = {arXiv},
  eprint       = {2408.13378},
  timestamp    = {Sat, 28 Sep 2024 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/corr/abs-2408-13378.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2408-13479,
  author       = {Yidong Zhou and
                  Jintai Chen and
                  Jinglei Cheng and
                  Gopal Karemore and
                  Marinka Zitnik and
                  Frederic T. Chong and
                  Junyu Liu and
                  Tianfan Fu and
                  Zhiding Liang},
  title        = {Quantum-machine-assisted Drug Discovery: Survey and Perspective},
  journal      = {CoRR},
  volume       = {abs/2408.13479},
  year         = {2024},
  url          = {https://doi.org/10.48550/arXiv.2408.13479},
  doi          = {10.48550/ARXIV.2408.13479},
  eprinttype   = {arXiv},
  eprint       = {2408.13479},
  timestamp    = {Mon, 03 Mar 2025 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/corr/abs-2408-13479.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2409-09183,
  author       = {Dannong Wang and
                  Jintai Chen and
                  Zhiding Liang and
                  Tianfan Fu and
                  Xiao{-}Yang Liu},
  title        = {Quantum-inspired Reinforcement Learning for Synthesizable Drug Design},
  journal      = {CoRR},
  volume       = {abs/2409.09183},
  year         = {2024},
  url          = {https://doi.org/10.48550/arXiv.2409.09183},
  doi          = {10.48550/ARXIV.2409.09183},
  eprinttype   = {arXiv},
  eprint       = {2409.09183},
  timestamp    = {Sat, 12 Oct 2024 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/corr/abs-2409-09183.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2409-14617,
  author       = {Bohao Xu and
                  Yingzhou Lu and
                  Yoshitaka Inoue and
                  Namkyeong Lee and
                  Tianfan Fu and
                  Jintai Chen},
  title        = {Protein-Mamba: Biological Mamba Models for Protein Function Prediction},
  journal      = {CoRR},
  volume       = {abs/2409.14617},
  year         = {2024},
  url          = {https://doi.org/10.48550/arXiv.2409.14617},
  doi          = {10.48550/ARXIV.2409.14617},
  eprinttype   = {arXiv},
  eprint       = {2409.14617},
  timestamp    = {Tue, 15 Oct 2024 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/corr/abs-2409-14617.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2410-02023,
  author       = {Jiaqing Xie and
                  Yue Zhao and
                  Tianfan Fu},
  title        = {DeepProtein: Deep Learning Library and Benchmark for Protein Sequence
                  Learning},
  journal      = {CoRR},
  volume       = {abs/2410.02023},
  year         = {2024},
  url          = {https://doi.org/10.48550/arXiv.2410.02023},
  doi          = {10.48550/ARXIV.2410.02023},
  eprinttype   = {arXiv},
  eprint       = {2410.02023},
  timestamp    = {Fri, 08 Nov 2024 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/corr/abs-2410-02023.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2410-12476,
  author       = {Zerui Xu and
                  Fang Wu and
                  Tianfan Fu and
                  Yue Zhao},
  title        = {Retrieval-Reasoning Large Language Model-based Synthetic Clinical
                  Trial Generation},
  journal      = {CoRR},
  volume       = {abs/2410.12476},
  year         = {2024},
  url          = {https://doi.org/10.48550/arXiv.2410.12476},
  doi          = {10.48550/ARXIV.2410.12476},
  eprinttype   = {arXiv},
  eprint       = {2410.12476},
  timestamp    = {Tue, 10 Feb 2026 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/corr/abs-2410-12476.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2411-15692,
  author       = {Sizhe Liu and
                  Yizhou Lu and
                  Siyu Chen and
                  Xiyang Hu and
                  Jieyu Zhao and
                  Tianfan Fu and
                  Yue Zhao},
  title        = {DrugAgent: Automating AI-aided Drug Discovery Programming through
                  {LLM} Multi-Agent Collaboration},
  journal      = {CoRR},
  volume       = {abs/2411.15692},
  year         = {2024},
  url          = {https://doi.org/10.48550/arXiv.2411.15692},
  doi          = {10.48550/ARXIV.2411.15692},
  eprinttype   = {arXiv},
  eprint       = {2411.15692},
  timestamp    = {Thu, 07 Aug 2025 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/corr/abs-2411-15692.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2412-02957,
  author       = {Namkyeong Lee and
                  Yunhak Oh and
                  Heewoong Noh and
                  Gyoung S. Na and
                  Minkai Xu and
                  Hanchen Wang and
                  Tianfan Fu and
                  Chanyoung Park},
  title        = {3D Interaction Geometric Pre-training for Molecular Relational Learning},
  journal      = {CoRR},
  volume       = {abs/2412.02957},
  year         = {2024},
  url          = {https://doi.org/10.48550/arXiv.2412.02957},
  doi          = {10.48550/ARXIV.2412.02957},
  eprinttype   = {arXiv},
  eprint       = {2412.02957},
  timestamp    = {Mon, 24 Feb 2025 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/corr/abs-2412-02957.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2412-06864,
  author       = {Lincan Li and
                  Jiaqi Li and
                  Catherine Chen and
                  Fred Gui and
                  Hongjia Yang and
                  Chenxiao Yu and
                  Zhengguang Wang and
                  Jianing Cai and
                  Junlong Aaron Zhou and
                  Bolin Shen and
                  Alex Qian and
                  Weixin Chen and
                  Zhongkai Xue and
                  Lichao Sun and
                  Lifang He and
                  Hanjie Chen and
                  Kaize Ding and
                  Zijian Du and
                  Fangzhou Mu and
                  Jiaxin Pei and
                  Jieyu Zhao and
                  Swabha Swayamdipta and
                  Willie Neiswanger and
                  Hua Wei and
                  Xiyang Hu and
                  Shixiang Zhu and
                  Tianlong Chen and
                  Yingzhou Lu and
                  Yang Shi and
                  Lianhui Qin and
                  Tianfan Fu and
                  Zhengzhong Tu and
                  Yuzhe Yang and
                  Jaemin Yoo and
                  Jiaheng Zhang and
                  Ryan A. Rossi and
                  Liang Zhan and
                  Liang Zhao and
                  Emilio Ferrara and
                  Yan Liu and
                  Furong Huang and
                  Xiangliang Zhang and
                  Lawrence Rothenberg and
                  Shuiwang Ji and
                  Philip S. Yu and
                  Yue Zhao and
                  Yushun Dong},
  title        = {Political-LLM: Large Language Models in Political Science},
  journal      = {CoRR},
  volume       = {abs/2412.06864},
  year         = {2024},
  url          = {https://doi.org/10.48550/arXiv.2412.06864},
  doi          = {10.48550/ARXIV.2412.06864},
  eprinttype   = {arXiv},
  eprint       = {2412.06864},
  timestamp    = {Thu, 07 May 2026 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/corr/abs-2412-06864.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2412-11378,
  author       = {Dannong Wang and
                  Daniel Kim and
                  Bo Jin and
                  Xingjian Zhao and
                  Tianfan Fu and
                  Steve Yang and
                  Xiao{-}Yang Liu},
  title        = {FinLoRA: Finetuning Quantized Financial Large Language Models Using
                  Low-Rank Adaptation},
  journal      = {CoRR},
  volume       = {abs/2412.11378},
  year         = {2024},
  url          = {https://doi.org/10.48550/arXiv.2412.11378},
  doi          = {10.48550/ARXIV.2412.11378},
  eprinttype   = {arXiv},
  eprint       = {2412.11378},
  timestamp    = {Tue, 21 Jan 2025 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/corr/abs-2412-11378.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@phdthesis{DBLP:phd/basesearch/Fu23a,
  author       = {Tianfan Fu},
  title        = {Deep Generative Models for Drug Design},
  school       = {Georgia Institute of Technology, Atlanta, GA, {USA}},
  year         = {2023},
  url          = {https://hdl.handle.net/1853/72001},
  timestamp    = {Tue, 29 Apr 2025 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/phd/basesearch/Fu23a.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nature/WangFD0HLCLKDAB23,
  author       = {Hanchen Wang and
                  Tianfan Fu and
                  Yuanqi Du and
                  Wenhao Gao and
                  Kexin Huang and
                  Ziming Liu and
                  Payal Chandak and
                  Shengchao Liu and
                  Peter Van Katwyk and
                  Andreea Deac and
                  Anima Anandkumar and
                  Karianne Bergen and
                  Carla P. Gomes and
                  Shirley Ho and
                  Pushmeet Kohli and
                  Joan Lasenby and
                  Jure Leskovec and
                  Tie{-}Yan Liu and
                  Arjun K. Manrai and
                  Debora S. Marks and
                  Bharath Ramsundar and
                  Le Song and
                  Jimeng Sun and
                  Jian Tang and
                  Petar Velickovic and
                  Max Welling and
                  Linfeng Zhang and
                  Connor W. Coley and
                  Yoshua Bengio and
                  Marinka Zitnik},
  title        = {Scientific discovery in the age of artificial intelligence},
  journal      = {Nat.},
  volume       = {620},
  number       = {7972},
  pages        = {47--60},
  year         = {2023},
  url          = {https://doi.org/10.1038/s41586-023-06221-2},
  doi          = {10.1038/S41586-023-06221-2},
  timestamp    = {Thu, 04 Dec 2025 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/nature/WangFD0HLCLKDAB23.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2306-04018,
  author       = {Zifeng Wang and
                  Brandon Theodorou and
                  Tianfan Fu and
                  Cao Xiao and
                  Jimeng Sun},
  title        = {PyTrial: {A} Comprehensive Platform for Artificial Intelligence for
                  Drug Development},
  journal      = {CoRR},
  volume       = {abs/2306.04018},
  year         = {2023},
  url          = {https://doi.org/10.48550/arXiv.2306.04018},
  doi          = {10.48550/ARXIV.2306.04018},
  eprinttype   = {arXiv},
  eprint       = {2306.04018},
  timestamp    = {Fri, 06 Dec 2024 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/corr/abs-2306-04018.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2307-08423,
  author       = {Xuan Zhang and
                  Limei Wang and
                  Jacob Helwig and
                  Youzhi Luo and
                  Cong Fu and
                  Yaochen Xie and
                  Meng Liu and
                  Yuchao Lin and
                  Zhao Xu and
                  Keqiang Yan and
                  Keir Adams and
                  Maurice Weiler and
                  Xiner Li and
                  Tianfan Fu and
                  Yucheng Wang and
                  Haiyang Yu and
                  Yuqing Xie and
                  Xiang Fu and
                  Alex Strasser and
                  Shenglong Xu and
                  Yi Liu and
                  Yuanqi Du and
                  Alexandra Saxton and
                  Hongyi Ling and
                  Hannah Lawrence and
                  Hannes St{\"{a}}rk and
                  Shurui Gui and
                  Carl Edwards and
                  Nicholas Gao and
                  Adriana Ladera and
                  Tailin Wu and
                  Elyssa F. Hofgard and
                  Aria Mansouri Tehrani and
                  Rui Wang and
                  Ameya Daigavane and
                  Montgomery Bohde and
                  Jerry Kurtin and
                  Qian Huang and
                  Tuong Phung and
                  Minkai Xu and
                  Chaitanya K. Joshi and
                  Simon V. Mathis and
                  Kamyar Azizzadenesheli and
                  Ada Fang and
                  Al{\'{a}}n Aspuru{-}Guzik and
                  Erik J. Bekkers and
                  Michael M. Bronstein and
                  Marinka Zitnik and
                  Anima Anandkumar and
                  Stefano Ermon and
                  Pietro Li{\`{o}} and
                  Rose Yu and
                  Stephan G{\"{u}}nnemann and
                  Jure Leskovec and
                  Heng Ji and
                  Jimeng Sun and
                  Regina Barzilay and
                  Tommi S. Jaakkola and
                  Connor W. Coley and
                  Xiaoning Qian and
                  Xiaofeng Qian and
                  Tess E. Smidt and
                  Shuiwang Ji},
  title        = {Artificial Intelligence for Science in Quantum, Atomistic, and Continuum
                  Systems},
  journal      = {CoRR},
  volume       = {abs/2307.08423},
  year         = {2023},
  url          = {https://doi.org/10.48550/arXiv.2307.08423},
  doi          = {10.48550/ARXIV.2307.08423},
  eprinttype   = {arXiv},
  eprint       = {2307.08423},
  timestamp    = {Sat, 31 May 2025 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/corr/abs-2307-08423.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2310-05365,
  author       = {Tao Feng and
                  Pengcheng Xu and
                  Tianfan Fu and
                  Siddhartha Laghuvarapu and
                  Jimeng Sun},
  title        = {Molecular De Novo Design through Transformer-based Reinforcement Learning},
  journal      = {CoRR},
  volume       = {abs/2310.05365},
  year         = {2023},
  url          = {https://doi.org/10.48550/arXiv.2310.05365},
  doi          = {10.48550/ARXIV.2310.05365},
  eprinttype   = {arXiv},
  eprint       = {2310.05365},
  timestamp    = {Sat, 21 Oct 2023 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/corr/abs-2310-05365.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2312-13289,
  author       = {Namkyeong Lee and
                  Heewoong Noh and
                  Gyoung S. Na and
                  Tianfan Fu and
                  Jimeng Sun and
                  Chanyoung Park},
  title        = {Stoichiometry Representation Learning with Polymorphic Crystal Structures},
  journal      = {CoRR},
  volume       = {abs/2312.13289},
  year         = {2023},
  url          = {https://doi.org/10.48550/arXiv.2312.13289},
  doi          = {10.48550/ARXIV.2312.13289},
  eprinttype   = {arXiv},
  eprint       = {2312.13289},
  timestamp    = {Mon, 03 Feb 2025 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/corr/abs-2312-13289.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/patterns/FuHXGS22,
  author       = {Tianfan Fu and
                  Kexin Huang and
                  Cao Xiao and
                  Lucas M. Glass and
                  Jimeng Sun},
  title        = {{HINT:} Hierarchical interaction network for clinical-trial-outcome
                  predictions},
  journal      = {Patterns},
  volume       = {3},
  number       = {4},
  pages        = {100445},
  year         = {2022},
  url          = {https://doi.org/10.1016/j.patter.2022.100445},
  doi          = {10.1016/J.PATTER.2022.100445},
  timestamp    = {Mon, 28 Aug 2023 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/patterns/FuHXGS22.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tkde/FuXGS22,
  author       = {Tianfan Fu and
                  Cao Xiao and
                  Lucas M. Glass and
                  Jimeng Sun},
  title        = {{MOLER:} Incorporate Molecule-Level Reward to Enhance Deep Generative
                  Model for Molecule Optimization},
  journal      = {{IEEE} Trans. Knowl. Data Eng.},
  volume       = {34},
  number       = {11},
  pages        = {5459--5471},
  year         = {2022},
  url          = {https://doi.org/10.1109/TKDE.2021.3052150},
  doi          = {10.1109/TKDE.2021.3052150},
  timestamp    = {Mon, 28 Aug 2023 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/tkde/FuXGS22.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/iclr/FuGXYCS22,
  author       = {Tianfan Fu and
                  Wenhao Gao and
                  Cao Xiao and
                  Jacob Yasonik and
                  Connor W. Coley and
                  Jimeng Sun},
  title        = {Differentiable Scaffolding Tree for Molecule Optimization},
  booktitle    = {The Tenth International Conference on Learning Representations, {ICLR}
                  2022, Virtual Event, April 25-29, 2022},
  publisher    = {OpenReview.net},
  year         = {2022},
  url          = {https://openreview.net/forum?id=w\_drCosT76},
  timestamp    = {Mon, 28 Aug 2023 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/conf/iclr/FuGXYCS22.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/kdd/FuS22,
  author       = {Tianfan Fu and
                  Jimeng Sun},
  editor       = {Aidong Zhang and
                  Huzefa Rangwala},
  title        = {{SIPF:} Sampling Method for Inverse Protein Folding},
  booktitle    = {{KDD} '22: The 28th {ACM} {SIGKDD} Conference on Knowledge Discovery
                  and Data Mining, Washington, DC, USA, August 14 - 18, 2022},
  pages        = {378--388},
  publisher    = {{ACM}},
  year         = {2022},
  url          = {https://doi.org/10.1145/3534678.3539284},
  doi          = {10.1145/3534678.3539284},
  timestamp    = {Mon, 28 Aug 2023 21:17:29 +0200},
  biburl       = {https://dblp.org/rec/conf/kdd/FuS22.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/kdd/FuS22a,
  author       = {Tianfan Fu and
                  Jimeng Sun},
  editor       = {Aidong Zhang and
                  Huzefa Rangwala},
  title        = {Antibody Complementarity Determining Regions (CDRs) design using Constrained
                  Energy Model},
  booktitle    = {{KDD} '22: The 28th {ACM} {SIGKDD} Conference on Knowledge Discovery
                  and Data Mining, Washington, DC, USA, August 14 - 18, 2022},
  pages        = {389--399},
  publisher    = {{ACM}},
  year         = {2022},
  url          = {https://doi.org/10.1145/3534678.3539285},
  doi          = {10.1145/3534678.3539285},
  timestamp    = {Mon, 28 Aug 2023 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/conf/kdd/FuS22a.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/nips/0001F0C22,
  author       = {Wenhao Gao and
                  Tianfan Fu and
                  Jimeng Sun and
                  Connor W. Coley},
  editor       = {Sanmi Koyejo and
                  S. Mohamed and
                  A. Agarwal and
                  Danielle Belgrave and
                  K. Cho and
                  A. Oh},
  title        = {Sample Efficiency Matters: {A} Benchmark for Practical Molecular Optimization},
  booktitle    = {Advances in Neural Information Processing Systems 35: Annual Conference
                  on Neural Information Processing Systems 2022, NeurIPS 2022, New Orleans,
                  LA, USA, November 28 - December 9, 2022},
  year         = {2022},
  url          = {http://papers.nips.cc/paper\_files/paper/2022/hash/8644353f7d307baaf29bc1e56fe8e0ec-Abstract-Datasets\_and\_Benchmarks.html},
  timestamp    = {Mon, 08 Jan 2024 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/conf/nips/0001F0C22.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/nips/Fu0C022,
  author       = {Tianfan Fu and
                  Wenhao Gao and
                  Connor W. Coley and
                  Jimeng Sun},
  editor       = {Sanmi Koyejo and
                  S. Mohamed and
                  A. Agarwal and
                  Danielle Belgrave and
                  K. Cho and
                  A. Oh},
  title        = {Reinforced Genetic Algorithm for Structure-based Drug Design},
  booktitle    = {Advances in Neural Information Processing Systems 35: Annual Conference
                  on Neural Information Processing Systems 2022, NeurIPS 2022, New Orleans,
                  LA, USA, November 28 - December 9, 2022},
  year         = {2022},
  url          = {http://papers.nips.cc/paper\_files/paper/2022/hash/4fe1859112230a032c7143a9adc3be78-Abstract-Conference.html},
  timestamp    = {Mon, 08 Jan 2024 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/conf/nips/Fu0C022.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2203-14500,
  author       = {Yuanqi Du and
                  Tianfan Fu and
                  Jimeng Sun and
                  Shengchao Liu},
  title        = {MolGenSurvey: {A} Systematic Survey in Machine Learning Models for
                  Molecule Design},
  journal      = {CoRR},
  volume       = {abs/2203.14500},
  year         = {2022},
  url          = {https://doi.org/10.48550/arXiv.2203.14500},
  doi          = {10.48550/ARXIV.2203.14500},
  eprinttype   = {arXiv},
  eprint       = {2203.14500},
  timestamp    = {Mon, 28 Aug 2023 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/corr/abs-2203-14500.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2206-12411,
  author       = {Wenhao Gao and
                  Tianfan Fu and
                  Jimeng Sun and
                  Connor W. Coley},
  title        = {Sample Efficiency Matters: {A} Benchmark for Practical Molecular Optimization},
  journal      = {CoRR},
  volume       = {abs/2206.12411},
  year         = {2022},
  url          = {https://doi.org/10.48550/arXiv.2206.12411},
  doi          = {10.48550/ARXIV.2206.12411},
  eprinttype   = {arXiv},
  eprint       = {2206.12411},
  timestamp    = {Mon, 28 Aug 2023 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/corr/abs-2206-12411.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2211-16508,
  author       = {Tianfan Fu and
                  Wenhao Gao and
                  Connor W. Coley and
                  Jimeng Sun},
  title        = {Reinforced Genetic Algorithm for Structure-based Drug Design},
  journal      = {CoRR},
  volume       = {abs/2211.16508},
  year         = {2022},
  url          = {https://doi.org/10.48550/arXiv.2211.16508},
  doi          = {10.48550/ARXIV.2211.16508},
  eprinttype   = {arXiv},
  eprint       = {2211.16508},
  timestamp    = {Mon, 28 Aug 2023 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/corr/abs-2211-16508.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HuangFGZXS21,
  author       = {Kexin Huang and
                  Tianfan Fu and
                  Lucas M. Glass and
                  Marinka Zitnik and
                  Cao Xiao and
                  Jimeng Sun},
  title        = {DeepPurpose: a deep learning library for drug-target interaction prediction},
  journal      = {Bioinform.},
  volume       = {36},
  number       = {22-23},
  pages        = {5545--5547},
  year         = {2021},
  url          = {https://doi.org/10.1093/bioinformatics/btaa1005},
  doi          = {10.1093/BIOINFORMATICS/BTAA1005},
  timestamp    = {Mon, 28 Aug 2023 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/bioinformatics/HuangFGZXS21.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/aaai/FuXLGS21,
  author       = {Tianfan Fu and
                  Cao Xiao and
                  Xinhao Li and
                  Lucas M. Glass and
                  Jimeng Sun},
  title        = {{MIMOSA:} Multi-constraint Molecule Sampling for Molecule Optimization},
  booktitle    = {Thirty-Fifth {AAAI} Conference on Artificial Intelligence, {AAAI}
                  2021, Thirty-Third Conference on Innovative Applications of Artificial
                  Intelligence, {IAAI} 2021, The Eleventh Symposium on Educational Advances
                  in Artificial Intelligence, {EAAI} 2021, Virtual Event, February 2-9,
                  2021},
  pages        = {125--133},
  publisher    = {{AAAI} Press},
  year         = {2021},
  url          = {https://doi.org/10.1609/aaai.v35i1.16085},
  doi          = {10.1609/AAAI.V35I1.16085},
  timestamp    = {Wed, 18 Mar 2026 17:07:12 +0100},
  biburl       = {https://dblp.org/rec/conf/aaai/FuXLGS21.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bcb/FuXHGS21,
  author       = {Tianfan Fu and
                  Cao Xiao and
                  Kexin Huang and
                  Lucas M. Glass and
                  Jimeng Sun},
  editor       = {Hongmei Jiang and
                  Xiuzhen Huang and
                  Jiajie Zhang},
  title        = {{SPEAR:} self-supervised post-training enhancer for molecule optimization},
  booktitle    = {{BCB} '21: 12th {ACM} International Conference on Bioinformatics,
                  Computational Biology and Health Informatics, Gainesville, Florida,
                  USA, August 1-4, 2021},
  pages        = {27:1--27:10},
  publisher    = {{ACM}},
  year         = {2021},
  url          = {https://doi.org/10.1145/3459930.3469530},
  doi          = {10.1145/3459930.3469530},
  timestamp    = {Mon, 28 Aug 2023 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/conf/bcb/FuXHGS21.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/kdd/FuX0GS21,
  author       = {Tianfan Fu and
                  Cao Xiao and
                  Cheng Qian and
                  Lucas M. Glass and
                  Jimeng Sun},
  editor       = {Feida Zhu and
                  Beng Chin Ooi and
                  Chunyan Miao},
  title        = {Probabilistic and Dynamic Molecule-Disease Interaction Modeling for
                  Drug Discovery},
  booktitle    = {{KDD} '21: The 27th {ACM} {SIGKDD} Conference on Knowledge Discovery
                  and Data Mining, Virtual Event, Singapore, August 14-18, 2021},
  pages        = {404--414},
  publisher    = {{ACM}},
  year         = {2021},
  url          = {https://doi.org/10.1145/3447548.3467286},
  doi          = {10.1145/3447548.3467286},
  timestamp    = {Mon, 28 Aug 2023 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/conf/kdd/FuX0GS21.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/nips/HuangFG0RLCXSZ21,
  author       = {Kexin Huang and
                  Tianfan Fu and
                  Wenhao Gao and
                  Yue Zhao and
                  Yusuf H. Roohani and
                  Jure Leskovec and
                  Connor W. Coley and
                  Cao Xiao and
                  Jimeng Sun and
                  Marinka Zitnik},
  editor       = {Joaquin Vanschoren and
                  Sai{-}Kit Yeung},
  title        = {Therapeutics Data Commons: Machine Learning Datasets and Tasks for
                  Drug Discovery and Development},
  booktitle    = {Proceedings of the Neural Information Processing Systems Track on
                  Datasets and Benchmarks 1, NeurIPS Datasets and Benchmarks 2021, December
                  2021, virtual},
  year         = {2021},
  url          = {https://datasets-benchmarks-proceedings.neurips.cc/paper/2021/hash/4c56ff4ce4aaf9573aa5dff913df997a-Abstract-round1.html},
  timestamp    = {Mon, 23 Dec 2024 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/conf/nips/HuangFG0RLCXSZ21.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2102-04252,
  author       = {Tianfan Fu and
                  Kexin Huang and
                  Cao Xiao and
                  Lucas M. Glass and
                  Jimeng Sun},
  title        = {{HINT:} Hierarchical Interaction Network for Trial Outcome Prediction
                  Leveraging Web Data},
  journal      = {CoRR},
  volume       = {abs/2102.04252},
  year         = {2021},
  url          = {https://arxiv.org/abs/2102.04252},
  eprinttype   = {arXiv},
  eprint       = {2102.04252},
  timestamp    = {Mon, 28 Aug 2023 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/corr/abs-2102-04252.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2102-09548,
  author       = {Kexin Huang and
                  Tianfan Fu and
                  Wenhao Gao and
                  Yue Zhao and
                  Yusuf H. Roohani and
                  Jure Leskovec and
                  Connor W. Coley and
                  Cao Xiao and
                  Jimeng Sun and
                  Marinka Zitnik},
  title        = {Therapeutics Data Commons: Machine Learning Datasets and Tasks for
                  Therapeutics},
  journal      = {CoRR},
  volume       = {abs/2102.09548},
  year         = {2021},
  url          = {https://arxiv.org/abs/2102.09548},
  eprinttype   = {arXiv},
  eprint       = {2102.09548},
  timestamp    = {Mon, 23 Dec 2024 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/corr/abs-2102-09548.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2109-10469,
  author       = {Tianfan Fu and
                  Wenhao Gao and
                  Cao Xiao and
                  Jacob Yasonik and
                  Connor W. Coley and
                  Jimeng Sun},
  title        = {Differentiable Scaffolding Tree for Molecular Optimization},
  journal      = {CoRR},
  volume       = {abs/2109.10469},
  year         = {2021},
  url          = {https://arxiv.org/abs/2109.10469},
  eprinttype   = {arXiv},
  eprint       = {2109.10469},
  timestamp    = {Mon, 28 Aug 2023 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/corr/abs-2109-10469.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/aaai/FuXS20,
  author       = {Tianfan Fu and
                  Cao Xiao and
                  Jimeng Sun},
  title        = {{CORE:} Automatic Molecule Optimization Using Copy {\&} Refine
                  Strategy},
  booktitle    = {The Thirty-Fourth {AAAI} Conference on Artificial Intelligence, {AAAI}
                  2020, The Thirty-Second Innovative Applications of Artificial Intelligence
                  Conference, {IAAI} 2020, The Tenth {AAAI} Symposium on Educational
                  Advances in Artificial Intelligence, {EAAI} 2020, New York, NY, USA,
                  February 7-12, 2020},
  pages        = {638--645},
  publisher    = {{AAAI} Press},
  year         = {2020},
  url          = {https://doi.org/10.1609/aaai.v34i01.5404},
  doi          = {10.1609/AAAI.V34I01.5404},
  timestamp    = {Wed, 18 Mar 2026 17:07:12 +0100},
  biburl       = {https://dblp.org/rec/conf/aaai/FuXS20.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bibm/FuXGS20,
  author       = {Tianfan Fu and
                  Cao Xiao and
                  Lucas M. Glass and
                  Jimeng Sun},
  editor       = {Taesung Park and
                  Young{-}Rae Cho and
                  Xiaohua Hu and
                  Illhoi Yoo and
                  Hyun Goo Woo and
                  Jianxin Wang and
                  Julio C. Facelli and
                  Seungyoon Nam and
                  Mingon Kang},
  title        = {{\(\alpha\)}-MOP: Molecule optimization with {\(\alpha\)}-divergence},
  booktitle    = {{IEEE} International Conference on Bioinformatics and Biomedicine,
                  {BIBM} 2020, Virtual Event, South Korea, December 16-19, 2020},
  pages        = {240--244},
  publisher    = {{IEEE}},
  year         = {2020},
  url          = {https://doi.org/10.1109/BIBM49941.2020.9313409},
  doi          = {10.1109/BIBM49941.2020.9313409},
  timestamp    = {Mon, 28 Aug 2023 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/conf/bibm/FuXGS20.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2004-08919,
  author       = {Kexin Huang and
                  Tianfan Fu and
                  Cao Xiao and
                  Lucas Glass and
                  Jimeng Sun},
  title        = {DeepPurpose: a Deep Learning Based Drug Repurposing Toolkit},
  journal      = {CoRR},
  volume       = {abs/2004.08919},
  year         = {2020},
  url          = {https://arxiv.org/abs/2004.08919},
  eprinttype   = {arXiv},
  eprint       = {2004.08919},
  timestamp    = {Mon, 28 Aug 2023 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/corr/abs-2004-08919.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2010-02318,
  author       = {Tianfan Fu and
                  Cao Xiao and
                  Xinhao Li and
                  Lucas M. Glass and
                  Jimeng Sun},
  title        = {{MIMOSA:} Multi-constraint Molecule Sampling for Molecule Optimization},
  journal      = {CoRR},
  volume       = {abs/2010.02318},
  year         = {2020},
  url          = {https://arxiv.org/abs/2010.02318},
  eprinttype   = {arXiv},
  eprint       = {2010.02318},
  timestamp    = {Mon, 28 Aug 2023 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/corr/abs-2010-02318.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2010-03951,
  author       = {Kexin Huang and
                  Tianfan Fu and
                  Dawood Khan and
                  Ali Abid and
                  Ali Abdalla and
                  Abubakar Abid and
                  Lucas M. Glass and
                  Marinka Zitnik and
                  Cao Xiao and
                  Jimeng Sun},
  title        = {MolDesigner: Interactive Design of Efficacious Drugs with Deep Learning},
  journal      = {CoRR},
  volume       = {abs/2010.03951},
  year         = {2020},
  url          = {https://arxiv.org/abs/2010.03951},
  eprinttype   = {arXiv},
  eprint       = {2010.03951},
  timestamp    = {Mon, 28 Aug 2023 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/corr/abs-2010-03951.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bcb/FuGXMS19,
  author       = {Tianfan Fu and
                  Tian Gao and
                  Cao Xiao and
                  Tengfei Ma and
                  Jimeng Sun},
  editor       = {Xinghua Mindy Shi and
                  Michael Buck and
                  Jian Ma and
                  Pierangelo Veltri},
  title        = {{PEARL:} Prototype Learning via Rule Learning},
  booktitle    = {Proceedings of the 10th {ACM} International Conference on Bioinformatics,
                  Computational Biology and Health Informatics, {BCB} 2019, Niagara
                  Falls, NY, USA, September 7-10, 2019},
  pages        = {223--232},
  publisher    = {{ACM}},
  year         = {2019},
  url          = {https://doi.org/10.1145/3307339.3342159},
  doi          = {10.1145/3307339.3342159},
  timestamp    = {Tue, 02 Dec 2025 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/conf/bcb/FuGXMS19.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bcb/FuGXMS19a,
  author       = {Tianfan Fu and
                  Tian Gao and
                  Cao Xiao and
                  Tengfei Ma and
                  Jimeng Sun},
  editor       = {Xinghua Mindy Shi and
                  Michael Buck and
                  Jian Ma and
                  Pierangelo Veltri},
  title        = {{PEARL:} Prototype Learning via Rule Learning},
  booktitle    = {Proceedings of the 10th {ACM} International Conference on Bioinformatics,
                  Computational Biology and Health Informatics, {BCB} 2019, Niagara
                  Falls, NY, USA, September 7-10, 2019},
  pages        = {542},
  publisher    = {{ACM}},
  year         = {2019},
  url          = {https://doi.org/10.1145/3307339.3343250},
  doi          = {10.1145/3307339.3343250},
  timestamp    = {Tue, 02 Dec 2025 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/conf/bcb/FuGXMS19a.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ijcai/FuHXS19,
  author       = {Tianfan Fu and
                  Trong Nghia Hoang and
                  Cao Xiao and
                  Jimeng Sun},
  editor       = {Sarit Kraus},
  title        = {{DDL:} Deep Dictionary Learning for Predictive Phenotyping},
  booktitle    = {Proceedings of the Twenty-Eighth International Joint Conference on
                  Artificial Intelligence, {IJCAI} 2019, Macao, China, August 10-16,
                  2019},
  pages        = {5857--5863},
  publisher    = {ijcai.org},
  year         = {2019},
  url          = {https://doi.org/10.24963/ijcai.2019/812},
  doi          = {10.24963/IJCAI.2019/812},
  timestamp    = {Sun, 02 Nov 2025 21:27:16 +0100},
  biburl       = {https://dblp.org/rec/conf/ijcai/FuHXS19.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-1912-05910,
  author       = {Tianfan Fu and
                  Cao Xiao and
                  Jimeng Sun},
  title        = {{CORE:} Automatic Molecule Optimization Using Copy {\&} Refine
                  Strategy},
  journal      = {CoRR},
  volume       = {abs/1912.05910},
  year         = {2019},
  url          = {http://arxiv.org/abs/1912.05910},
  eprinttype   = {arXiv},
  eprint       = {1912.05910},
  timestamp    = {Mon, 28 Aug 2023 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/corr/abs-1912-05910.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/conll/FuZM18,
  author       = {Tianfan Fu and
                  Cheng Zhang and
                  Stephan Mandt},
  editor       = {Anna Korhonen and
                  Ivan Titov},
  title        = {Continuous Word Embedding Fusion via Spectral Decomposition},
  booktitle    = {Proceedings of the 22nd Conference on Computational Natural Language
                  Learning, CoNLL 2018, Brussels, Belgium, October 31 - November 1,
                  2018},
  pages        = {11--20},
  publisher    = {Association for Computational Linguistics},
  year         = {2018},
  url          = {https://doi.org/10.18653/v1/k18-1002},
  doi          = {10.18653/V1/K18-1002},
  timestamp    = {Thu, 07 Aug 2025 09:17:40 +0200},
  biburl       = {https://dblp.org/rec/conf/conll/FuZM18.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/aistats/FuZ17,
  author       = {Tianfan Fu and
                  Zhihua Zhang},
  editor       = {Aarti Singh and
                  Xiaojin (Jerry) Zhu},
  title        = {{CPSG-MCMC:} Clustering-Based Preprocessing method for Stochastic
                  Gradient {MCMC}},
  booktitle    = {Proceedings of the 20th International Conference on Artificial Intelligence
                  and Statistics, {AISTATS} 2017, 20-22 April 2017, Fort Lauderdale,
                  FL, {USA}},
  series       = {Proceedings of Machine Learning Research},
  pages        = {841--850},
  publisher    = {{PMLR}},
  year         = {2017},
  url          = {http://proceedings.mlr.press/v54/fu17a.html},
  timestamp    = {Wed, 29 May 2019 08:41:44 +0200},
  biburl       = {https://dblp.org/rec/conf/aistats/FuZ17.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/speech/LiFYZC16,
  author       = {Wei Li and
                  Tianfan Fu and
                  Hanxu You and
                  Jie Zhu and
                  Ning Chen},
  title        = {Feature sparsity analysis for i-vector based speaker verification},
  journal      = {Speech Commun.},
  volume       = {80},
  pages        = {60--70},
  year         = {2016},
  url          = {https://doi.org/10.1016/j.specom.2016.02.008},
  doi          = {10.1016/J.SPECOM.2016.02.008},
  timestamp    = {Fri, 24 Apr 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/speech/LiFYZC16.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/uai/FuLZ16,
  author       = {Tianfan Fu and
                  Luo Luo and
                  Zhihua Zhang},
  editor       = {Alexander Ihler and
                  Dominik Janzing},
  title        = {Quasi-Newton Hamiltonian Monte Carlo},
  booktitle    = {Proceedings of the Thirty-Second Conference on Uncertainty in Artificial
                  Intelligence, {UAI} 2016, June 25-29, 2016, New York City, NY, {USA}},
  publisher    = {{AUAI} Press},
  year         = {2016},
  url          = {http://auai.org/uai2016/proceedings/papers/102.pdf},
  timestamp    = {Wed, 19 Mar 2025 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/conf/uai/FuLZ16.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ejasmp/LiFZ15,
  author       = {Wei Li and
                  Tianfan Fu and
                  Jie Zhu},
  title        = {An improved i-vector extraction algorithm for speaker verification},
  journal      = {{EURASIP} J. Audio Speech Music. Process.},
  volume       = {2015},
  pages        = {18},
  year         = {2015},
  url          = {https://doi.org/10.1186/s13636-015-0061-x},
  doi          = {10.1186/S13636-015-0061-X},
  timestamp    = {Tue, 29 Sep 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/ejasmp/LiFZ15.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/speech/LiuQCFZY15,
  author       = {Yuan Liu and
                  Yanmin Qian and
                  Nanxin Chen and
                  Tianfan Fu and
                  Ya Zhang and
                  Kai Yu},
  title        = {Deep feature for text-dependent speaker verification},
  journal      = {Speech Commun.},
  volume       = {73},
  pages        = {1--13},
  year         = {2015},
  url          = {https://doi.org/10.1016/j.specom.2015.07.003},
  doi          = {10.1016/J.SPECOM.2015.07.003},
  timestamp    = {Tue, 07 May 2024 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/speech/LiuQCFZY15.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/specom/LiFZC15,
  author       = {Wei Li and
                  Tianfan Fu and
                  Jie Zhu and
                  Ning Chen},
  editor       = {Andrey Ronzhin and
                  Rodmonga Potapova and
                  Nikos Fakotakis},
  title        = {Sparsity Analysis and Compensation for i-Vector Based Speaker Verification},
  booktitle    = {Speech and Computer - 17th International Conference, {SPECOM} 2015,
                  Athens, Greece, September 20-24, 2015, Proceedings},
  series       = {Lecture Notes in Computer Science},
  pages        = {381--388},
  publisher    = {Springer},
  year         = {2015},
  url          = {https://doi.org/10.1007/978-3-319-23132-7\_47},
  doi          = {10.1007/978-3-319-23132-7\_47},
  timestamp    = {Fri, 24 Apr 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/conf/specom/LiFZC15.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icassp/DengQFFY14,
  author       = {Wei Deng and
                  Yanmin Qian and
                  Yuchen Fan and
                  Tianfan Fu and
                  Kai Yu},
  title        = {Stochastic data sweeping for fast {DNN} training},
  booktitle    = {{IEEE} International Conference on Acoustics, Speech and Signal Processing,
                  {ICASSP} 2014, Florence, Italy, May 4-9, 2014},
  pages        = {240--244},
  publisher    = {{IEEE}},
  year         = {2014},
  url          = {https://doi.org/10.1109/ICASSP.2014.6853594},
  doi          = {10.1109/ICASSP.2014.6853594},
  timestamp    = {Tue, 25 Nov 2025 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/conf/icassp/DengQFFY14.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ijcnn/LiuFFQY14,
  author       = {Yuan Liu and
                  Tianfan Fu and
                  Yuchen Fan and
                  Yanmin Qian and
                  Kai Yu},
  title        = {Speaker verification with deep features},
  booktitle    = {2014 International Joint Conference on Neural Networks, {IJCNN} 2014,
                  Beijing, China, July 6-11, 2014},
  pages        = {747--753},
  publisher    = {{IEEE}},
  year         = {2014},
  url          = {https://doi.org/10.1109/IJCNN.2014.6889708},
  doi          = {10.1109/IJCNN.2014.6889708},
  timestamp    = {Tue, 25 Nov 2025 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/conf/ijcnn/LiuFFQY14.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/interspeech/FuQLY14,
  author       = {Tianfan Fu and
                  Yanmin Qian and
                  Yuan Liu and
                  Kai Yu},
  editor       = {Haizhou Li and
                  Helen M. Meng and
                  Bin Ma and
                  Engsiong Chng and
                  Lei Xie},
  title        = {Tandem deep features for text-dependent speaker verification},
  booktitle    = {15th Annual Conference of the International Speech Communication Association,
                  {INTERSPEECH} 2014, Singapore, September 14-18, 2014},
  pages        = {1327--1331},
  publisher    = {{ISCA}},
  year         = {2014},
  url          = {https://doi.org/10.21437/Interspeech.2014-329},
  doi          = {10.21437/INTERSPEECH.2014-329},
  timestamp    = {Tue, 11 Jun 2024 16:45:43 +0200},
  biburl       = {https://dblp.org/rec/conf/interspeech/FuQLY14.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}