Tianyu Xie

Tianyu Xie, Frederick A. Matsen, Marc A. Suchard et al. · pku

Reconstructing the evolutionary history relating a collection of molecular sequences is the main subject of modern Bayesian phylogenetic inference. However, the commonly used Markov chain Monte Carlo methods can be inefficient due to the complicated space of phylogenetic trees, especially when the number of sequences is large. An alternative approach is variational Bayesian phylogenetic inference (VBPI) which transforms the inference problem into an optimization problem. While effective, the default diagonal lognormal approximation for the branch lengths of the tree used in VBPI is often insufficient to capture the complexity of the exact posterior. In this work, we propose a more flexible family of branch length variational posteriors based on semi-implicit hierarchical distributions using graph neural networks. We show that this semi-implicit construction emits straightforward permutation equivariant distributions, and therefore can handle the non-Euclidean branch length space across different tree topologies with ease. To deal with the intractable marginal probability of semi-implicit variational distributions, we develop several alternative lower bounds for stochastic optimization. We demonstrate the effectiveness of our proposed method over baseline methods on benchmark data examples, in terms of both marginal likelihood estimation and branch length posterior approximation.

Longlin Yu, Tianyu Xie, Yu Zhu et al. · pku

Semi-implicit variational inference (SIVI) has been introduced to expand the analytical variational families by defining expressive semi-implicit distributions in a hierarchical manner. However, the single-layer architecture commonly used in current SIVI methods can be insufficient when the target posterior has complicated structures. In this paper, we propose hierarchical semi-implicit variational inference, called HSIVI, which generalizes SIVI to allow more expressive multi-layer construction of semi-implicit distributions. By introducing auxiliary distributions that interpolate between a simple base distribution and the target distribution, the conditional layers can be trained by progressively matching these auxiliary distributions one layer after another. Moreover, given pre-trained score networks, HSIVI can be used to accelerate the sampling process of diffusion models with the score matching objective. We show that HSIVI significantly enhances the expressiveness of SIVI on several Bayesian inference problems with complicated target distributions. When used for diffusion model acceleration, we show that HSIVI can produce high quality samples comparable to or better than the existing fast diffusion model based samplers with a small number of function evaluations on various datasets.

Tianyu Xie, Cheng Zhang · pku

Designing flexible probabilistic models over tree topologies is important for developing efficient phylogenetic inference methods. To do that, previous works often leverage the similarity of tree topologies via hand-engineered heuristic features which would require pre-sampled tree topologies and may suffer from limited approximation capability. In this paper, we propose a deep autoregressive model for phylogenetic inference based on graph neural networks (GNNs), called ARTree. By decomposing a tree topology into a sequence of leaf node addition operations and modeling the involved conditional distributions based on learnable topological features via GNNs, ARTree can provide a rich family of distributions over the entire tree topology space that have simple sampling algorithms and density estimation procedures, without using heuristic features. We demonstrate the effectiveness and efficiency of our method on a benchmark of challenging real data tree topology density estimation and variational Bayesian phylogenetic inference problems.

Shuchen Xue, Tianyu Xie, Tianyang Hu et al. · pku

Large language models (LLMs) predominantly use autoregressive (AR) approaches, but masked diffusion models (MDMs) are emerging as viable alternatives. A key challenge in comparing AR and MDM paradigms is their typical architectural difference: AR models are often decoder-only, while MDMs have largely been encoder-only. This practice of changing both the modeling paradigm and architecture simultaneously makes direct comparisons unfair, as it's hard to distinguish whether observed differences stem from the paradigm itself or the architectural shift. This research evaluates MDMs within a decoder-only framework to: (1) equitably compare MDM (as Any-Order AR, or AO-AR) and standard AR paradigms. Our investigation suggests that the standard AO-AR objective, which averages over all token permutations, may benefit from refinement, as many permutations appear less informative compared to the language's inherent left-to-right structure. (2) Investigate architectural influences (decoder-only vs. encoder-only) within MDMs. We demonstrate that while encoder-only MDMs model a simpler conditional probability space, decoder-only MDMs can achieve dramatic generation speedups ($\sim25\times$) and comparable perplexity with temperature annealing despite modeling a vastly larger space, highlighting key trade-offs. This work thus decouples core paradigm differences from architectural influences, offering insights for future model design. Code is available at https://github.com/scxue/AO-GPT-MDM.

Tianyu Xie, Harry Richman, Jiansi Gao et al. · pku

Learning informative representations of phylogenetic tree structures is essential for analyzing evolutionary relationships. Classical distance-based methods have been widely used to project phylogenetic trees into Euclidean space, but they are often sensitive to the choice of distance metric and may lack sufficient resolution. In this paper, we introduce phylogenetic variational autoencoders (PhyloVAEs), an unsupervised learning framework designed for representation learning and generative modeling of tree topologies. Leveraging an efficient encoding mechanism inspired by autoregressive tree topology generation, we develop a deep latent-variable generative model that facilitates fast, parallelized topology generation. PhyloVAE combines this generative model with a collaborative inference model based on learnable topological features, allowing for high-resolution representations of phylogenetic tree samples. Extensive experiments demonstrate PhyloVAE's robust representation learning capabilities and fast generation of phylogenetic tree topologies.

Ziheng Cheng, Tianyu Xie, Shiyue Zhang et al. · pku

While conditional diffusion models have achieved remarkable success in various applications, they require abundant data to train from scratch, which is often infeasible in practice. To address this issue, transfer learning has emerged as an essential paradigm in small data regimes. Despite its empirical success, the theoretical underpinnings of transfer learning conditional diffusion models remain unexplored. In this paper, we take the first step towards understanding the sample efficiency of transfer learning conditional diffusion models through the lens of representation learning. Inspired by practical training procedures, we assume that there exists a low-dimensional representation of conditions shared across all tasks. Our analysis shows that with a well-learned representation from source tasks, the samplecomplexity of target tasks can be reduced substantially. In addition, we investigate the practical implications of our theoretical results in several real-world applications of conditional diffusion models. Numerical experiments are also conducted to verify our results.

Zhekun Shi, Longlin Yu, Tianyu Xie et al. · pku

Recent success of diffusion models has inspired a surge of interest in developing sampling techniques using reverse diffusion processes. However, accurately estimating the drift term in the reverse stochastic differential equation (SDE) solely from the unnormalized target density poses significant challenges, hindering existing methods from achieving state-of-the-art performance. In this paper, we introduce the Diffusion-PINN Sampler (DPS), a novel diffusion-based sampling algorithm that estimates the drift term by solving the governing partial differential equation of the log-density of the underlying SDE marginals via physics-informed neural networks (PINN). We prove that the error of log-density approximation can be controlled by the PINN residual loss, enabling us to establish convergence guarantees of DPS. Experiments on a variety of sampling tasks demonstrate the effectiveness of our approach, particularly in accurately identifying mixing proportions when the target contains isolated components.

Ling Feng, Tianyu Xie, Wei Ma et al.

The modernization of smart farming is a way to improve agricultural production efficiency, and improve the agricultural production environment. Although many large models have achieved high accuracy in the task of object recognition and segmentation, they cannot really be put into use in the farming industry due to their own poor interpretability and limitations in computational volume. In this paper, we built AnYue Shelduck Dateset, which contains a total of 1951 Shelduck datasets, and performed target detection and segmentation annotation with the help of professional annotators. Based on AnYue ShelduckDateset, this paper describes DuckProcessing, an efficient and powerful module for duck identification based on real shelduckfarms. First of all, using the YOLOv8 module designed to divide the mahjong between them, Precision reached 98.10%, Recall reached 96.53% and F1 score reached 0.95 on the test set. Again using the DuckSegmentation segmentation model, DuckSegmentation reached 96.43% mIoU. Finally, the excellent DuckSegmentation was used as the teacher model, and through knowledge distillation, Deeplabv3 r50 was used as the student model, and the final student model achieved 94.49% mIoU on the test set. The method provides a new way of thinking in practical sisal duck smart farming.