| 孙思琦 青年研究员 博士生导师 复旦大学 智能复杂体系基础理论与关键技术实验室 青年研究员 E-mail: siqisun AT fudan.edu.cn URL: https://intersun.github.io/ 招生招聘：诚聘博士生/实习生/全职研究员，详情发邮件垂询，并附个人简历及成绩单。 课题组主页：BEAM LAB |
个人简介
本科毕业于复旦大学数学系（2011），博士毕业于TTIC研究院（2017），师从许锦波教授本科毕业于复旦大学数学系（2011），博士毕业于TTIC研究院（2017），师从许锦波教授。2018-2022年继续在微软研究院开展研究，2022至今复旦大学智能复杂体系基础理论与关键技术实验室担任青年研究员。致力于深度学习在生命科学和自然语言处理等交叉学科中的应用研究,并侧重于提高模型的精度和速度，解决模型在实践落地中的具体问题。在Science、Nature Biotechnology、Nature Methods、Nature Communications、PLOS Computational Biology、Nucleic Acids Research、ACL、EMNLP、NAACL、NeurIPS、ICML等国际顶级刊物和会议上发表多篇论文,总引用超9000次（据谷歌学术统计）。
研究兴趣
深度学习，自然语言处理，计算生物学
近期成果
期刊论文
Liu Wang*, Jiahao Xie*, Tao Gong*, Hao Wu*, Yifan Tu*, Xin Peng*, Sitong Shang*, Xinyu Jia, Haiyun Ma, Jian Zou, Sheng Xu, Xin Zheng, Dong Zhang, Yang Liu, Chong Zhang, Yongbo Luo, Zirui Huang, Bin Shao, Binwu Ying, Yu Cheng, Siqi Sun#, Xuedong Zhou#, Zhaoming Su#. Cryo-EM reveals mechanisms of natural RNA multivalency. Science. 2025 May;388(6746):545-550.
Xiang Zhang*, Tianze Ling*, Zhi Jin*, Sheng Xu*, Zhiqiang Gao, Boyan Sun, Zijie Qiu, Jiaqi Wei, Nanqing Dong, Guangshuai Wang, Guibin Wang, Leyuan Li, Muhammad Abdul-Mageed, Laks V.S. Lakshmanan, Fuchu He, Wanli Ouyang#, Cheng Chang#, Siqi Sun#. π-PrimeNovo: an accurate and efficient non-autoregressive deep learning model for de novo peptide sequencing. Nat Commun. 2025 Jan 2;16(1):267.
Sheng Xu*, Qiantai Feng*, Lifeng Qiao, Hao Wu, Tao Shen, Yu Cheng#, Shuangjia Zheng#, Siqi Sun#. Benchmarking all-atom biomolecular structure prediction with FoldBench. Nat Commun. 2025 Dec 4;17(1):442.
Tao Shen*, Zhihang Hu*, Siqi Sun*,#, Di Liu, Felix Wong, Jiuming Wang, Jiayang Chen, Yixuan Wang, Liang Hong, Jin Xiao, Mark Gerstein, Yu Li#. Accurate RNA 3D structure prediction using a language model-based deep learning approach. Nat Methods. 2024 Dec;21(12):2287-2298.
Liang Hong*, Zhihang Hu*, Siqi Sun*,#, Xiangru Tang, Jiuming Wang, Qingxiong Tan, Liangzhen Zheng, Sheng Wang, Sheng Xu, Irwin King, Mark Gerstein#, Yu Li#. Fast, sensitive detection of protein homologs using deep dense retrieval. Nat Biotechnol. 2024 Aug;43(6):983-995.
会议论文
Xiang Zhang*, Jiaqi Wei*, Zijie Qiu, Sheng Xu, Zhi Jin, ZhiQiang Gao, Nanqing Dong, Siqi Sun#.Bidirectional Representations Augmented Autoregressive Biological Sequence Generation, NeurIPS 2025.
Jiaqi Wei*, Hao Zhou*, Xiang Zhang*, Di Zhang, Zijie Qiu, Noah Wei, Jinzhe Li, Wanli Ouyang, Siqi Sun#.Retrieval is Not Enough: Enhancing RAG through Test-Time Critique and Optimization, NeurIPS 2025.
Zijie Qiu*, Jiaqi Wei*, Xiang Zhang*, Sheng Xu, Kai Zou, Zhi Jin, Zhiqiang Gao, Nanqing Dong, Siqi Sun#.Universal Biological Sequence Reranking for Improved De Novo Peptide Sequencing, ICML 2025.
Xiang Zhang*, Jiaqi Wei*, Zijie Qiu, Sheng Xu, Nanqing Dong, Zhiqiang Gao, Siqi Sun#.Curriculum Learning for Biological Sequence Prediction, ICML 2025.
Le Zhang*, Jiayang Chen, Tao Shen, Yu Li, Siqi Sun# .MSA Generation with Seqs2Seqs Pretraining: Advancing Protein Structure Predictions, NeurIPS 2024.
Zhi Jin*, Sheng Xu*, Xiang Zhang*, Tianze Ling, Nanqing Dong, Wanli Ouyang, Zhiqiang Gao, Cheng Chang#, Siqi Sun#. ContraNovo: a contrastive learning approach to enhance de novo peptide sequencing, AAAI 2024.
