Functional Gradient Flows for Constrained Sampling
Shiyue Zhang*, Longlin Yu*, Ziheng Cheng*, Cheng Zhang
In Proceedings of the 38th Neural Information Processing Systems (NeurIPS 2024)

Improved Tree Probability Estimation with Stochastic Optimization and Variance Reduction
Tianyu Xie*, Musu Yuan*, Minghua Deng, Cheng Zhang
Statistics and Computing, 34(186), 2024

Variational Supertrees for Bayesian Phylogenetics
Michael Karcher, Cheng Zhang, Frederick A. Matsen IV.
Bulletin of Mathematical Biology, 86(114), 2024

A Variational Approach to Bayesian Phylogenetic Inference
Cheng Zhang, Frederick A. Matsen IV.
Journal of Machine Learning Research, 25(145), 2024, pp. 1-56

Kernel Semi-Implicit Variational Inference
Ziheng Cheng*, Longlin Yu*, Tianyu Xie, Shiyue Zhang, Cheng Zhang
In Proceedings of the 41st International Conference on Machine Learning (ICML 2024)

Reflected Flow Matching
Tianyu Xie*, Yu Zhu*, Longlin Yu*, Tong Yang, Ziheng Cheng, Shiyue Zhang, Xiangyu Zhang, Cheng Zhang
In Proceedings of the 41st International Conference on Machine Learning (ICML 2024)

Reduced-order Model-based Variational Inference with Normalizing Flows for Bayesian Elliptic Inverse Problems
Zhizhang Wu, Cheng Zhang, Zhiwen Zhang
Journal of Computational and Applied Mathematics, 441, 2024

Particle-based Variational Inference with Generalized Wasserstein Gradient Flow
Ziheng Cheng*, Shiyue Zhang*, Longlin Yu, Cheng Zhang
In Proceedings of the 37th Neural Information Processing Systems (NeurIPS 2023)
[code]

Hierarchical Semi-Implicit Variational Inference with Application to Diffusion Model Acceleration
Longlin Yu*, Tianyu Xie*, Yu Zhu*, Tong Yang, Xiangyu Zhang, Cheng Zhang
In Proceedings of the 37th Neural Information Processing Systems (NeurIPS 2023)
[code]

ARTree: A Deep Autoregressive Model for Phylogenetic Inference
Tianyu Xie, Cheng Zhang
In Proceedings of the 37th Neural Information Processing Systems (NeurIPS 2023, spotlight presentation)
[code]

A Topology-marginal Composite Likelihood via a Generalized Phylogenetic Pruning Algorithm
Seong-Hwan Jun, Hassan Nasif, Chris Jennings-Shaffer, David H Rich, Anna Kooperberg, Mathieu Fourment, Cheng Zhang, Marc A. Suchard, Frederick A. Matsen IV
Algorithms for Molecular Biology, 18(10), 2023

A Data-driven and Model-based Accelerated Hamiltonian Monte Carlo Method for Bayesian Elliptic Inverse Problems
Sijing Li, Cheng Zhang, Zhiwen Zhang, Hongkai Zhao
Statistics and Computing, 33(90), 2023
[code]

Learnable Topological Features for Phylogenetic Inference via Graph Neural Networks
Cheng Zhang
In Proceedings of the 11th International Conference on Learning Representations (ICLR 2023)
[code]

Semi-Implicit Variational Inference via Score Matching
Longlin Yu, Cheng Zhang
In Proceedings of the 11th International Conference on Learning Representations (ICLR 2023, spotlight presentation)
[code]

Non-bifurcating Phylogenetic Tree Inference via The Adaptive LASSO
Cheng Zhang*, Vu Dinh*, Frederick A. Matsen IV
Journal of the American Statistical Association, 116(534), 2021, pp. 858-873

Improved Variational Bayesian Phylogenetic Inference with Normalizing Flows
Cheng Zhang
In Proceedings of the 34th Neural Information Processing Systems (NeurIPS 2020, oral presentation)
[code] [poster]

Variational Bayesian Phylogenetic Inference
Cheng Zhang, Frederick A. Matsen IV.
In Proceedings of the 7th International Conference on Learning Representations (ICLR 2019)
[poster]

Generalizing Tree Probability Estimation via Bayesian Networks
Cheng Zhang, Frederick A. Matsen IV
In Proceedings of the 32th Neural Information Processing Systems (NeurIPS 2018, spotlight presentation)
[code] [poster]

Variational Hamiltonian Monte Carlo via Score Matching
Cheng Zhang, Babak Shahbaba, Hongkai Zhao
Bayesian Analysis, 13(2), 2018, pp. 486-506

Hamiltonian Monte Carlo Acceleration Using Surrogate Functions with Random Bases
Cheng Zhang, Babak Shahbaba, Hongkai Zhao
Statistics and Computing, 27(6), 2017, pp. 1473-1490
[code]

Precomputing Strategy for Hamiltonian Monte Carlo Methods Based on Regularity in Parameter Space
Cheng Zhang, Babak Shahbaba, Hongkai Zhao
Computational Statistics, 32(1), 2017, pp. 253-279

Probabilistic Path Hamiltonian Monte Carlo
Vu Dinh*, Arman Bilge*, Cheng Zhang*, Frederick A. Matsen IV
In Proceedings of the 34th International Conference on Machine Learning (ICML 2017)
[code] [poster]