Associate Professor (tenured), Research Institute of Intelligent Complex Systems, Fudan University. (2024.12-now)
Assistant Professor (tenure track), Research Institute of Intelligent Complex Systems, Fudan University. (2022.5-2024.12)
Researcher, Shanghai Artificial Intelligence Laboratory. (2023.4-2024.6)
Project Researcher, International Research Center for Neurointelligence (IRCN), The University of Tokyo Institutes for Advanced Study, The University of Tokyo.(2020.4-2022.3)
Project Researcher, Institute of Industrial Science (IIS), the University of Tokyo. (2018.4-2020.3)
PhD degree of Computational Mathematics, School of Mathematical Sciences, Peking University.
Bachelor degree of Information and Computing Science, School of Mathematical Sciences, Peking University.
Doctoral supervisor for Complex Systems Science and Engineering.
Stochastic modeling, algorithms and their applications; Mathematical theory in biology and life sciences.
Complex systems: modeling and network inference, constructing undirected/directed networks, quantifying dynamical causality, inferring gene regulations etc.
Critical phenomena analysis: critical transition, tipping point, early-warning signal etc.
Biological data modeling and analysis: scRNA-seq, multi-omics data, EEG/fMRI data etc.
《动力学刻画的数据科学理论和方法》, 陈洛南、刘锐、马欢飞、史际帆. 科学出版社, 北京, 2024. ISBN 978-7-5088-6449-5. [专著]
Dynamics Characterized Data Science: Theory and Methods. Luonan Chen, Rui Liu, Huanfei Ma, and Jifan Shi. Science Press, Beijing, Oct 2024, ISBN 978-7-5088-6449-5.
《基于理工信的医学数据采集与分析》, 沈百荣、杨恩策主编. 编写组成员. 北京大学医学出版社, 北京, 2024. ISBN 978-7-5659-3198-7. [“101计划” 核心教材]
Medical Data Collection and Analysis Based on Science, Engineering and Information Technology. Bairong Shen, and Ence Yang. Editorial board member. Peking University Medical Press, Beijing, Jul 2024, ISBN 978-7-5659-3198-7.
Integrative cross-sample alignment and spatially differential gene analysis for spatial transcriptomics. Yecheng Tan, Zezhou Wang, Ai Wang, Yan Yan, Wei Lin*, Qing Nie*, and Jifan Shi*. BioRxiv, https://doi.org/10.1101/2025.06.05.653933. In submission.
Dynamical causality under invisible confounders for biological network reconstruction. Jinling Yan#, Shao-Wu Zhang*, Chihao Zhang#, Weitian Huang, Jifan Shi, and Luonan Chen*. ArXiv, https://arxiv.org/abs/2408.05584. In submission.
Deciphering interventional dynamical causality from non-intervention complex systems. Jifan Shi*, Yang Li, Juan Zhao, Siyang Leng, Rui Bao, Kazuyuki Aihara*, Luonan Chen*, and Wei Lin*. ArXiv, https://arxiv.org/abs/2407.01621v2. In submission.
Kolmogorov-Arnold autoencoder for conditional mutual information estimation. Yiqiao Chen, Jifan Shi*, Siyang Leng. Journal of Fudan University (Natural Science), 64(4), 2025. (In Chinese, selected as the Cover Article).
Machine learning prediction of short cervix in mid-pregnancy based on multimodal data from the first-trimester screening period: An observational study in a high-risk population. Shengyu Wu#, Jiaqi Dong#, Jifan Shi, Xiaoxian Qu, Yirong Bao, Xiaoyuan Mao, Mu Lv, Xuan Chen, and Hao Ying*. Biomedicines, 13(9), 2025.
Utilizing causal network markers to identify tipping points ahead of critical transition. Shirui Bian#, Zezhou Wang#, Siyang Leng, Wei Lin, Jifan Shi*. Accepted by Advanced Science, 2025.
Reservoir cross mapping as a nonlinear framework for detecting dynamical causality. Ren Cao, Jintong Zhao, Chun Guan, Huanfei Ma*, Jifan Shi*, and Siyang Leng*. Cell Reports Physical Science, 6(7): 102683, 2025.
diffMIN: Reconstructing sample-specific differential gene regulatory networks based on mutual information. Songwei Ai, Yiwei Zhou, Wenkui Zou, Emeli Chatterjee, Guoping Li, Jifan Shi*, Junjie Xiao*, and Juan Zhao*. IEEE Transactions on Computational Biology and Bioinformatics, https://doi.org/10.1109/TCBBIO.2025.3576169, 2025.
Transfer learning of multicellular organization via single-cell and spatial transcriptomics. Yecheng Tan#, Ai Wang#, Zezhou Wang, Wei Lin*, Yan Yan*, Qing Nie*, Jifan Shi*. PLoS Computational Biology 21(4): e1012991, 2025.
A deep learning approach of artificial neural network with attention mechanism to predicting marine biogeochemistry data. Mingzhi Liu, Yipeng Wang, Guoqiang Zhong, Yongxin Liu, Xiaoqing Liu, Jifan Shi, Yangli Che, and Rui Bao*. Journal of Geophysical Research-Biogeosciences, 130(3): e2024JG008386, 2025.
Unveiling the mechanism of compound Ku-Shen injection in liver cancer treatment through ingredient-target network analysis. Wenkui Zou, Jiazhen Liu, Zexin Wei, Chunhua Peng, Ying Zhao, Yue Ding, Jifan Shi*, and Juan Zhao*. Genes 15(10): 1278, 2024.
Detecting dynamical causality via intervened reservoir computing. Jintong Zhao, Zhongxue Gan*, Ruixi Huang, Chun Guan, Jifan Shi*, and Siyang Leng*. Communications Physics 7: 232, 2024.
Detecting dynamical causality by intersection cardinal concavity. Peng Tao#, Qifan Wang#, Jifan Shi#, Xiaohu Hao, Xiaoping Liu, Bin Min, Yiheng Zhang, Chenyang Li, He Cui*, and Luonan Chen*. Fundamental Research, https://doi.org/10.1016/j.fmre.2023.01.007, 2023.
Energy landscape decomposition for cell differentiation with proliferation effect. Jifan Shi, Kazuyuki Aihara*, Tiejun Li*, and Luonan Chen*. National Science Review 9: nwac116, DOI: 10.1093/nsr/nwac116, 2022. (Preprint, SI, IICSnews, NSRnews).
Mean-field analysis of Stuart-Landau oscillator networks with symmetric coupling and dynamical noise. Yang Li*, Jifan Shi, and Kazuyuki Aihara. Chaos 32: 063114, 2022. (Preprint)
Embedding entropy: a nonlinear measure of dynamical causality. Jifan Shi*, Luonan Chen*, and Kazuyuki Aihara*. Journal of the Royal Society Interface. 19: 20210766, 2022. (Preprint, SI, code)
Criticality in the healthy brain. Jifan Shi*, Kenji Kirihara, Mariko Tada, Mao Fujioka, Kaori Usui, Daisuke Koshiyama, Tsuyoshi Araki, Luonan Chen, Kiyoto Kasai*, and Kazuyuki Aihara*. Frontiers in Network Physiology, section Networks of Dynamical Systems. 1: 755685, 2022. (SI)
Dynamics-based data science in biology. Jifan Shi, Kazuyuki Aihara, and Luonan Chen*. Natl Sci Rev. 8(5): nwab029, 2021. (a brief news report).
On the Mathematics of RNA Velocity I: Theoretical Analysis. Tiejun Li*, Jifan Shi*, Yichong Wu*, and Peijie Zhou*. CSIAM Trans. Appl. Math. 2(1): 1-55, 2021. (pdf)
Quantifying pluripotency landscape of cell differentiation from scRNA-seq data by continuous birth-death process. Jifan Shi, Tiejun Li*, Luonan Chen*, and Kazuyuki Aihara*. PLoS Comput. Biol. 15(11): e1007488, 2019. (SI, code)
Quantifying Waddington’s epigenetic landscape: a comparison of single-cell potency measures. Jifan Shi, Andrew E Teschendorff*, Weiyan Chen, Luonan Chen*, and Tiejun Li*. Brief. in Bioinformatics. 21(1): 248-261, 2020. (SI, code)
关于临界现象和强相关网络推断的多尺度建模与分析 (Multiscale modeling and analysis of critical transitions and network inference with strong connections). Jifan Shi. 北京大学博士学位论文(PhD thesis, in Chinese), 2018. (pdf)
Quantifying direct dependencies in biological networks by multiscale association analysis. Jifan Shi, Juan Zhao, Xiaoping Liu, Luonan Chen*, and Tiejun Li*. IEEE/ACM Trans. Comp. Biol. Bioinfo. 17(2): 449-458, 2020. (pdf, SI, code).
Detecting direct associations in a network by information theoretic approaches. Jifan Shi#, Juan Zhao#, Tiejun Li*, and Luonan Chen*. Sci. China Math. 62(5): 823-838, 2019.
Towards a critical transition theory under different temporal scales and noise strengths. Jifan Shi, Tiejun Li*, and Luonan Chen*. Phys. Rev. E 93(3): 032137, 2016.
一种基于互信息的单样本调控网络构建方法. 史际帆, 赵娟, 艾凇玮, 邹文葵, 柳家振, 孙毅, 杨伟, 林伟. 国家知识产权局. 申请号202411593970.7.
National Natural Science Foundation of China (NSFC), No. 42450192. 2025/01 --- 2027/12. PI. Ongoing.
Shanghai Data Bureau. 2024/06 --- 2026/05. Participants. Ongoing.
AI for Science Foundation of Fudan University, FudanX24AI041. 2024/07 --- 2025/12. PI. Ongoing.
Fudan AI4S Foundation for Brain Science. 2023/11 --- 2024/10. Participants. Finished.
National Natural Science Foundation of China (NSFC), No. 12301620. 2024/01 --- 2026/12. PI. Ongoing.
National Key R&D, 2022YFC2704600/2022YFC2704604. Ministry of science and technology (MOST). 2022/12 --- 2025/11. Sub-project Core Member. Ongoing.
Comprehensive Mathematical Understanding of the Complex Control System between Organs and Challenge for Ultra-Early Precision Medicine. Japan Science and Technology Agency (JST). Moonshot Research & Development Program, JPMJMS2021. 2020/12 --- 2025/11, direct costs 1,530,100,000 yen. Participants. Finished.
Research and Development on Next-generation AI and its Key Technology Based on Nonlinear Dynamics. Japan Agency for Medical Research and Development (AMED). Strategic Research Program for Brain Sciences, JP21dm0307009. 2018/06 --- 2024/03, direct costs 94,500,000 yen. Participants. Finished.
Establishing Theoretical Foundations for Mathematical Modeling of Pathological Biosystems and its Applications to Personalized Medicine. Japan Society for the Promotion of Science (JSPS). Grant-in-Aid for Scientific Research (S), JP15H05707. 2015/05 --- 2020/03, direct costs 148,000,000 yen. Participants. Finished.
Chinese Mathematical Society (CMS)
China Society for Industrial and Applied Mathematics (CSIAM)
Operations Research Society of China (ORSC)
Shanghai Society of Nonlinear Sciences
Shanghai Society for Bioinformatics
Academy Editor for PLOS Computational Biology
Editorial Board Member for Emerging Science and Technology
Reviewer for over ten journals
Complex systems: theory, algorithms, and applications (复杂系统理论、算法与应用). Course Lecturer at FDU. (CSSE40003, 2025 Autumn)
Advanced Mathematics A(I) (高等数学 A (上)). Course Lecturer at FDU. (MATH10015, 2025 Autumn)
Complex systems: theory, algorithms, and applications (复杂系统理论、算法与应用). Course Lecturer at FDU. (IICS737004, 2024 Autumn)
Time series analysis and causal modeling (时间序列分析与因果建模). Course Lecturer at FDU. (IICS737002, 2024 Autumn)
Intelligent algorithms for complex systems analysis (复杂系统分析的智能算法). Course Lecturer at FDU. (AIS531011, 2024 Autumn)
Graduate Fundamental and Advanced Course. Course Lecturer at NPU. (2023/03-2023/04, 2024/03-2024/04, 2025/05)
TA at Peking University. (2012/09-2013/01, 2013/02-2013/06, 2013/09-2014/01, 2015/02-2015/06, 2015/09-2016/01, 2016/02-2016/06, 2016/09-2017/02)
PhD candidates: 4
Undergraduates: 2
The 4th Mathematical Life Science Conference (MLS2025), Aug. 8-10, 2025, Tongzhou, China.
The 3rd Annual Meeting of the Causal Inference Branch of Chinese Association for Applied Statistics, Jul. 26-29, 2025, Urumqi, China.
† Joint Conference of Asian Conference on Mathematical Biology and Annual Meeting of Japanese Society for Mathematical Biology(ACMB-JSMB2025), Jul. 7-11, 2025, Kyoto, Japan.
The 9th China Systems Science Conference (CSSC2025), May 16-18, 2025, Kunming, China.
*† The First Symposium of “Emotion and Cognition with Focus on Give up, Perseverance and Strategic behavior”, Apr. 9-11, 2025, Fudan University, China.
† The 22nd Annual Meeting of China Society for Industrial and Applied Mathematics (CSIAM2024), Oct. 24-27, 2024, Nanjing, China.
† The 10th Annual Conference of Biomathematics Committee of Chinese Mathematical Society, Jul. 15-19, 2024, Harbin, China.
The 5th International Conference on Biomathematical Modelling and Stochastic Analysis, Apr. 18-21, 2024, Huai’an, China.
The Annual Meeting of Chinese Mathematical Society (CMS2023), Dec. 22-26, 2023, Dalian, China.
The 3rd Mathematical Life Science Conference (MLS2023), Oct. 20-22, 2023, Wuxi, China.
The 21st Annual Meeting of China Society for Industrial and Applied Mathematics (CSIAM2023), Oct. 12-15, 2023, Kunming, China.
The 10th International Congress on Industrial and Applied Mathematics (ICIAM2023), Aug. 20-25, 2023, Waseda University, Tokyo, Japan.
*† The 9th Shanghai International Symposium on Nonlinear Sciences and Applications (Shanghai NSA’23), July 23-28, 2023, Zhangye, Gansu Province, China.
The 342nd Shuangqing Forum of NSFC, July 9-11, 2023, Peking, China.
† The 7th China System Science Conference (CSSC2023), May 19-21, 2023, Chongqing, China.
The 4th International Conference on Biomathematical Modelling and Stochastic Analysis, Apr. 28-30, 2023, Xuzhou, China.
The 1st Yangtze River Delta Academic Conference of Bioinformatics, Apr. 14-16, 2023, Huzhou, China.
*† Symposium on Biological Mathematics and Computational Systems Biology 2022, held by IICS Fudan, Dec. 17-18, 2022, Online.
The 20th Annual Meeting of China Society for Industrial and Applied Mathematics (CSIAM2022), Nov. 17-20, 2022, Online.
NetSci2022, NetBioMed2022 Satellite, July 18-19, 2022, Online.
Workshop of Collective Dynamics and Networks, June 10-12, 2022, Online.
The 10th International Conference on Bioinformatics and Computational Biology (ICBCB2022), May 13-15, 2022, Online.
The 2nd CSIAM Conference of Mathematics and Life Science, Aug. 28-29, 2021, Online.
The 13th International Conference on Computational Systems Biology (ISB2020), Sep.18-21, 2020, Online.
The 12th International Conference on Computational Systems Biology (ISB2018), Aug.18-21, 2018, Guiyang, China.
The 11th International Conference on Computational Systems Biology (ISB2017), Aug.18-21, 2017, Shenzhen, China.
The 11th Annual Meeting of Chinese Computational Mathematical Society, July 21-23, 2017, Xi'an, China.
SIAM Conference on the Life Sciences (LS16), July 11-14, 2016, Boston, Massachusetts, USA.
The 9th International Conference on Systems Biology (ISB2015), Aug.21-24, 2015, Luoyang, China.
The 8th International Congress on Industrial and Applied Mathematics (ICIAM 2015), Aug. 10-14, 2015, Beijing, China.
The 12th annual meeting for CompMath in Chinese Universities, Oct. 19-23, 2013, Changsha.
*As an organizer. †As a session convenor.
Since Autumn 2023 to now, serve for Fudan-High School project, providing interest development and career planning for middle school students.
Nov 2023, served as the keynote speaker at “FDU Complex Systems Science for the Future - Interdisciplinary and Fusion” for undergraduates and young researchers.
Prof. Tiejun Li, Prof. Luonan Chen, Prof. Wei Lin, Dr. Yang Li, Dr. Juan Zhao.
scRNA-seq:
Analysis of single cell RNA-seq data. A course by Hemberg-lab, with codes on github.
Datasets: Single Cell Expression Atlas, Single Cell Portal, Human Cell Atlas, SC2disease, CancerSEA, JingleBells, SpatialDB
EEG:
Database: OpenNeuro, EPR Core, European Epilepsy Database, Kaggle Seizure, TUH EEG, others(1, 2)
Others:
Deep learning tutorials: (i) Deep learning tutorial (Hung-yi Lee's ppt); (ii) MorvanZhou's programming; (iii) Tensorflow; (iv) Pytorch.
*Last Modified: Jul. 2025.