ARTree: A Deep Autoregressive Model for Phylogenetic Inference. - Tianyu Xie 001; Cheng Zhang (NeurIPS, 2023)

Hierarchical Semi-Implicit Variational Inference with Application to Diffusion Model Acceleration. - Longlin Yu; Tianyu Xie 001; Yu Zhu 004; Tong Yang; Xiangyu Zhang; Cheng Zhang (NeurIPS, 2023)

Reflected Flow Matching. - Tianyu Xie 001; Yu Zhu 004; Longlin Yu; Tong Yang; Ziheng Cheng; Shiyue Zhang 002; Xiangyu Zhang; Cheng Zhang (ICML, 2024)

Kernel Semi-Implicit Variational Inference. - Ziheng Cheng; Longlin Yu; Tianyu Xie 001; Shiyue Zhang 002; Cheng Zhang (ICML, 2024)

Variational Bayesian Phylogenetic Inference with Semi-implicit Branch Length Distributions. - Tianyu Xie 001; Frederick A. Matsen IV; Marc A. Suchard; Cheng Zhang (CoRR, 2024)

Diffusion-PINN Sampler. - Zhekun Shi; Longlin Yu; Tianyu Xie 001; Cheng Zhang (CoRR, 2024)

Improving tree probability estimation with stochastic optimization and variance reduction. - Tianyu Xie 001; Musu Yuan; Minghua Deng; Cheng Zhang (Stat. Comput., 2024)

PhyloVAE: Unsupervised Learning of Phylogenetic Trees via Variational Autoencoders. - Tianyu Xie 001; Harry Richman; Jiansi Gao; Frederick A. Matsen IV; Cheng Zhang (ICLR, 2025)

Provable Sample-Efficient Transfer Learning Conditional Diffusion Models via Representation Learning. - Ziheng Cheng; Tianyu Xie 001; Shiyue Zhang 002; Cheng Zhang (CoRR, 2025)

Variational Autoencoding Discrete Diffusion with Enhanced Dimensional Correlations Modeling. - Tianyu Xie 001; Shuchen Xue; Zijin Feng; Tianyang Hu; Jiacheng Sun; Zhenguo Li; Cheng Zhang (CoRR, 2025)

Continuous Semi-Implicit Models. - Longlin Yu; Jiajun Zha; Tong Yang; Tianyu Xie 001; Xiangyu Zhang; S.-H. Gary Chan; Cheng Zhang (CoRR, 2025)

Any-Order GPT as Masked Diffusion Model: Decoupling Formulation and Architecture. - Shuchen Xue; Tianyu Xie 001; Tianyang Hu; Zijin Feng; Jiacheng Sun; Kenji Kawaguchi; Zhenguo Li; Zhi-Ming Ma (CoRR, 2025)