Publications

See also my Google Scholar profile.

2026

• Yongkai Chen, Samuel W. K. Wong, S. C. Kou (2026). Classifying Metamorphic versus Single-Fold Proteins with Statistical Learning and AlphaFold2. Annals of Applied Statistics, accepted.

• Yongkai Chen, Wenxuan Zhong, Ping Ma (2026). Wahkon: A Statistically Principled Deep RKHS Superposition Network. The First Conference on Statistics and Trustworthy AI for Cross (X)-Domain. (Best Paper Award) [code]

• Huimin Cheng*, Yongkai Chen*, Ping Ma, Wenxuan Zhong (2026). Graphon Cross-Validation: Assessing Models on Network Data. International Conference on Learning Representations (ICLR). (* joint first authors)

• Jiazhang Cai, Yongkai Chen, Luyang Fang, Wenxuan Zhong, Guo-Cheng Yuan, Ping Ma (2026). SpaDiff: Denoising for Sequence-based Spatial Transcriptomics via Diffusion Process. Cell Reports Methods.

• Luyang Fang, Haoran Lu, Yongkai Chen, Wenxuan Zhong, Ping Ma (2026). Knowledge Cascade: Reverse Knowledge Distillation on Nonparametric Multivariate Functional Estimation. Journal of Machine Learning Research, 27(54), 1–38.

• Da Wang, Jun S. Liu, Yongkai Chen, Yuyao Wang, Huimin Cheng (2026). Network Perturbation Aggregation for Graphon Estimation. Statistical Learning and Data Science, 100005.

• Luyang Fang, Xiaowei Yu, Jiazhang Cai, Yongkai Chen, Shushan Wu, Zhengliang Liu, Zhenyuan Yang, Haoran Lu, Xilin Gong, Yufang Liu, and others (2026). Knowledge Distillation and Dataset Distillation of Large Language Models: Emerging Trends, Challenges, and Future Directions. Artificial Intelligence Review, 59(1), 17.

• Yongkai Chen, Ping Ma, Wenxuan Zhong (2026). Quantum Statistical Bootstrap. arXiv: 2604.00951. [code]

• Luyang Fang, Yongkai Chen, Jiazhang Cai, Ping Ma, Wenxuan Zhong (2026). Multi-Teacher Knowledge Distillation via Teacher-Informed Mixture Priors. arXiv: 2605.27967.

2025

• Yongkai Chen, Shushan Wu, Ping Ma, Wenxuan Zhong (2025). Fluid Correlation: A Novel Nonparametric Metric to Assess the Dynamic Association. Journal of Computational and Graphical Statistics, 34(4), 1331–1343.

• Yongkai Chen, Samuel W. K. Wong, S. C. Kou (2025). Uncovering Distinct Protein Conformations Using Coevolutionary Information and AlphaFold. bioRxiv: 2025.10.08.681198. [code]

• Xilin Gong, Yongkai Chen, Shushan Wu, Fang Wang, Ping Ma, Wenxuan Zhong (2025). S2MNet: Speckle-To-Mesh Net for Three-Dimensional Cardiac Morphology Reconstruction via Echocardiogram. arXiv: 2505.06105.

• Bo Zheng, Yaokun Liu, Jingyi Zhang, Terry T. Ma, Yun Zhou, Yongkai Chen, Ying Yang, Wei Ma, Fangfang Fan, Jia Jia, and others (2025). A Machine Learning Model Using Echocardiographic Myocardial Strain to Detect Myocardial Ischemia. Internal and Emergency Medicine, 20(5), 1425–1436.

• Haoran Lu, Luyang Fang, Ruidong Zhang, Xinliang Li, Jiazhang Cai, Huimin Cheng, Lin Tang, Ziyu Liu, Zeliang Sun, Tao Wang, Yongkai Chen, and others (2025). Alignment and Safety in Large Language Models: Safety Mechanisms, Training Paradigms, and Emerging Challenges. arXiv: 2507.19672.

2024

• Ping Ma*, Yongkai Chen*, Haoran Lu, Wenxuan Zhong (2024). Bisection Grover’s Search Algorithm and Its Application in Analyzing CITE-seq Data. Journal of the American Statistical Association, Applications and Case Studies, 1–12. (* joint first authors) [code]

• Luyang Fang*, Yongkai Chen*, Wenxuan Zhong, Ping Ma (2024). Bayesian Knowledge Distillation: A Bayesian Perspective of Distillation with Uncertainty Quantification. Proceedings of the Forty-first International Conference on Machine Learning (ICML). (* joint first authors)

• Yufang Liu*, Yongkai Chen*, Haoran Lu, Wenxuan Zhong, Guo-Cheng Yuan, Ping Ma (2024). Orthogonal Multimodality Integration and Clustering in Single-Cell Data. BMC Bioinformatics, 25(1), 164. (* joint first authors)

• Yang Liu*, Yongkai Chen*, Carly R. Duffy*, Ariel J. VanLeuven, John Branson Byers, Hannah C. Schriever, Rebecca E. Ball, Jessica M. Carpenter, Chelsea E. Gunderson, Nikolay M. Filipov, and others (2024). Decreased GABA Levels During Development Result in Increased Connectivity in the Larval Zebrafish Tectum. bioRxiv. (* joint first authors) [code]

2023

• Mengrui Zhang*, Yongkai Chen*, Dingyi Yu, Wenxuan Zhong, Jingyi Zhang, Ping Ma (2023). Elucidating Dynamic Cell Lineages and Gene Networks in Time-Course Single Cell Differentiation. Artificial Intelligence in the Life Sciences, 3, 100068. (* joint first authors)

2022

• Ping Ma, Yongkai Chen, Xinlian Zhang, Xin Xing, Jingyi Ma, Michael W. Mahoney (2022). Asymptotic Analysis of Sampling Estimators for Randomized Numerical Linear Algebra Algorithms. Journal of Machine Learning Research, 23, 1–45.

• Cheng Meng, Jun Yu, Yongkai Chen, Wenxuan Zhong, Ping Ma (2022). Smoothing Splines Approximation Using Hilbert Curve Basis Selection. Journal of Computational and Graphical Statistics, 31(3), 802–812.

2021

• Jingyi Zhang, Huolan Zhu, Yongkai Chen, Chenguang Yang, Huimin Cheng, Yi Li, Wenxuan Zhong, Fang Wang (2021). Ensemble Machine Learning Approach for Screening of Coronary Heart Disease Based on Echocardiography and Risk Factors. BMC Medical Informatics and Decision Making, 21(1), 187.

• Logan Ganzen, Mee Jung Ko, Mengrui Zhang, Rui Xie, Yongkai Chen, Liyun Zhang, Rebecca James, Jeff Mumm, Richard M. van Rijn, Wenxuan Zhong, and others (2021). Drug Screening with Zebrafish Visual Behavior Identifies Carvedilol as a Potential Treatment for an Autosomal Dominant Form of Retinitis Pigmentosa. Scientific Reports, 11(1), 11432.