PhyloVAE: Unsupervise Learning of Phylogenetic Trees via Variational Autoencoders
Tianyu Xie, Harry Richman, Jiansi Gao, Frederick A. Matsen IV, Cheng Zhang
In Proceedings of the 13th International Conference on Learning Representations (ICLR 2025)

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]