arXiv subjects

Hongteng Xu

Publications and source records attributed to Hongteng Xu.

At least 37 records · Page 2Linked to original sources

arXiv2025

ReQFlow: Rectified Quaternion Flow for Efficient and High-Quality Protein Backbone Generation

Protein backbone generation plays a central role in de novo protein design and is significant for many biological and medical applications. Although diffusion and flow-based generative models provide potential solutions to this challenging task, they often generate proteins with undesired designability and suffer computational inefficiency. In this study, we propose a novel rectified quaternion flow (ReQFlow) matching method for fast and high-quality protein backbone generation. In particular, our method generates a local translation and a 3D rotation from random noise for each residue in a protein chain, which represents each 3D rotation as a unit quaternion and constructs its flow by spherical linear interpolation (SLERP) in an exponential format. We train the model by quaternion flow (QFlow) matching with guaranteed numerical stability and rectify the QFlow model to accelerate its inference and improve the designability of generated protein backbones, leading to the proposed ReQFlow model. Experiments show that ReQFlow achieves on-par performance in protein backbone generation while requiring much fewer sampling steps and significantly less inference time (e.g., being 37x faster than RFDiffusion and 63x faster than Genie2 when generating a backbone of length 300), demonstrating its effectiveness and efficiency. The code is available at https://github.com/AngxiaoYue/ReQFlow.

cs.LG↗

arXiv2025

WGFormer: An SE(3)-Transformer Driven by Wasserstein Gradient Flows for Molecular Ground-State Conformation Prediction

Predicting molecular ground-state conformation (i.e., energy-minimized conformation) is crucial for many chemical applications such as molecular docking and property prediction. Classic energy-based simulation is time-consuming when solving this problem, while existing learning-based methods have advantages in computational efficiency but sacrifice accuracy and interpretability. In this work, we propose a novel and effective method to bridge the energy-based simulation and the learning-based strategy, which designs and learns a Wasserstein gradient flow-driven SE(3)-Transformer, called WGFormer, for ground-state conformation prediction. Specifically, our method tackles this task within an auto-encoding framework, which encodes low-quality conformations by the proposed WGFormer and decodes corresponding ground-state conformations by an MLP. The architecture of WGFormer corresponds to Wasserstein gradient flows -- it optimizes conformations by minimizing an energy function defined on the latent mixture models of atoms, thereby significantly improving performance and interpretability. Extensive experiments demonstrate that our method consistently outperforms state-of-the-art competitors, providing a new and insightful paradigm to predict ground-state conformation.

q-bio.BM↗

arXiv2025

PolyConf: Unlocking Polymer Conformation Generation through Hierarchical Generative Models

Polymer conformation generation is a critical task that enables atomic-level studies of diverse polymer materials. While significant advances have been made in designing conformation generation methods for small molecules and proteins, these methods struggle to generate polymer conformations due to their unique structural characteristics. Meanwhile, the scarcity of polymer conformation datasets further limits the progress, making this important area largely unexplored. In this work, we propose PolyConf, a pioneering tailored polymer conformation generation method that leverages hierarchical generative models to unlock new possibilities. Specifically, we decompose the polymer conformation into a series of local conformations (i.e., the conformations of its repeating units), generating these local conformations through an autoregressive model, and then generating their orientation transformations via a diffusion model to assemble them into the complete polymer conformation. Moreover, we develop the first benchmark with a high-quality polymer conformation dataset derived from molecular dynamics simulations to boost related research in this area. The comprehensive evaluation demonstrates that PolyConf consistently outperforms existing conformation generation methods, thus facilitating advancements in polymer modeling and simulation.

cond-mat.soft↗

arXiv2025

Learning Structure-enhanced Temporal Point Processes with Gromov-Wasserstein Regularization

Real-world event sequences are often generated by different temporal point processes (TPPs) and thus have clustering structures. Nonetheless, in the modeling and prediction of event sequences, most existing TPPs ignore the inherent clustering structures of the event sequences, leading to the models with unsatisfactory interpretability. In this study, we learn structure-enhanced TPPs with the help of Gromov-Wasserstein (GW) regularization, which imposes clustering structures on the sequence-level embeddings of the TPPs in the maximum likelihood estimation framework.In the training phase, the proposed method leverages a nonparametric TPP kernel to regularize the similarity matrix derived based on the sequence embeddings. In large-scale applications, we sample the kernel matrix and implement the regularization as a Gromov-Wasserstein (GW) discrepancy term, which achieves a trade-off between regularity and computational efficiency.The TPPs learned through this method result in clustered sequence embeddings and demonstrate competitive predictive and clustering performance, significantly improving the model interpretability without compromising prediction accuracy.

cs.LG↗

arXiv2025

A Plug-and-Play Bregman ADMM Module for Inferring Event Branches in Temporal Point Processes

An event sequence generated by a temporal point process is often associated with a hidden and structured event branching process that captures the triggering relations between its historical and current events. In this study, we design a new plug-and-play module based on the Bregman ADMM (BADMM) algorithm, which infers event branches associated with event sequences in the maximum likelihood estimation framework of temporal point processes (TPPs). Specifically, we formulate the inference of event branches as an optimization problem for the event transition matrix under sparse and low-rank constraints, which is embedded in existing TPP models or their learning paradigms. We can implement this optimization problem based on subspace clustering and sparse group-lasso, respectively, and solve it using the Bregman ADMM algorithm, whose unrolling leads to the proposed BADMM module. When learning a classic TPP (e.g., Hawkes process) by the expectation-maximization algorithm, the BADMM module helps derive structured responsibility matrices in the E-step. Similarly, the BADMM module helps derive low-rank and sparse attention maps for the neural TPPs with self-attention layers. The structured responsibility matrices and attention maps, which work as learned event transition matrices, indicate event branches, e.g., inferring isolated events and those key events triggering many subsequent events. Experiments on both synthetic and real-world data show that plugging our BADMM module into existing TPP models and learning paradigms can improve model performance and provide us with interpretable structured event branches. The code is available at \url{https://github.com/qingmeiwangdaily/BADMM_TPP}.

cs.LG↗

arXiv2025

Conservation-informed Graph Learning for Spatiotemporal Dynamics Prediction

Data-centric methods have shown great potential in understanding and predicting spatiotemporal dynamics, enabling better design and control of the object system. However, deep learning models often lack interpretability, fail to obey intrinsic physics, and struggle to cope with the various domains. While geometry-based methods, e.g., graph neural networks (GNNs), have been proposed to further tackle these challenges, they still need to find the implicit physical laws from large datasets and rely excessively on rich labeled data. In this paper, we herein introduce the conservation-informed GNN (CiGNN), an end-to-end explainable learning framework, to learn spatiotemporal dynamics based on limited training data. The network is designed to conform to the general conservation law via symmetry, where conservative and non-conservative information passes over a multiscale space enhanced by a latent temporal marching strategy. The efficacy of our model has been verified in various spatiotemporal systems based on synthetic and real-world datasets, showing superiority over baseline models. Results demonstrate that CiGNN exhibits remarkable accuracy and generalizability, and is readily applicable to learning for prediction of various spatiotemporal dynamics in a spatial domain with complex geometry.

cs.LG↗

arXiv2024

Efficient Video Face Enhancement with Enhanced Spatial-Temporal Consistency

As a very common type of video, face videos often appear in movies, talk shows, live broadcasts, and other scenes. Real-world online videos are often plagued by degradations such as blurring and quantization noise, due to the high compression ratio caused by high communication costs and limited transmission bandwidth. These degradations have a particularly serious impact on face videos because the human visual system is highly sensitive to facial details. Despite the significant advancement in video face enhancement, current methods still suffer from $i)$ long processing time and $ii)$ inconsistent spatial-temporal visual effects (e.g., flickering). This study proposes a novel and efficient blind video face enhancement method to overcome the above two challenges, restoring high-quality videos from their compressed low-quality versions with an effective de-flickering mechanism. In particular, the proposed method develops upon a 3D-VQGAN backbone associated with spatial-temporal codebooks recording high-quality portrait features and residual-based temporal information. We develop a two-stage learning framework for the model. In Stage \Rmnum{1}, we learn the model with a regularizer mitigating the codebook collapse problem. In Stage \Rmnum{2}, we learn two transformers to lookup code from the codebooks and further update the encoder of low-quality videos. Experiments conducted on the VFHQ-Test dataset demonstrate that our method surpasses the current state-of-the-art blind face video restoration and de-flickering methods on both efficiency and effectiveness. Code is available at \url{https://github.com/Dixin-Lab/BFVR-STC}.

cs.CV↗

arXiv2024

Bridging The Gap between Low-rank and Orthogonal Adaptation via Householder Reflection Adaptation

While following different technical routes, both low-rank and orthogonal adaptation techniques can efficiently adapt large-scale pre-training models in specific tasks or domains based on a small piece of trainable parameters. In this study, we bridge the gap between these two techniques, proposing a simple but effective adaptation method based on Householder reflections. Given a pre-trained model, our method fine-tunes its layers by multiplying each frozen weight matrix with an orthogonal matrix constructed by a chain of learnable Householder reflections (HRs). This HR-based orthogonal fine-tuning is equivalent to an adaptive low-rank adaptation. Moreover, we show that the orthogonality of the reflection planes corresponding to the HRs impacts the model capacity and regularity. The analysis motivates us to regularize the orthogonality of the HRs, leading to different implementations of the proposed Householder reflection adaptation (HRA) method. Compared with state-of-the-art methods, HRA achieves superior performance with fewer learnable parameters when adapting large language models and conditional image generators. The code of the experiments is available at \url{https://github.com/DaShenZi721/HRA}, and the method has been merged into the \href{https://github.com/huggingface/peft}{PEFT} package.

cs.LG↗

arXiv2024

A Bayesian Mixture Model of Temporal Point Processes with Determinantal Point Process Prior

Asynchronous event sequence clustering aims to group similar event sequences in an unsupervised manner. Mixture models of temporal point processes have been proposed to solve this problem, but they often suffer from overfitting, leading to excessive cluster generation with a lack of diversity. To overcome these limitations, we propose a Bayesian mixture model of Temporal Point Processes with Determinantal Point Process prior (TP$^2$DP$^2$) and accordingly an efficient posterior inference algorithm based on conditional Gibbs sampling. Our work provides a flexible learning framework for event sequence clustering, enabling automatic identification of the potential number of clusters and accurate grouping of sequences with similar features. It is applicable to a wide range of parametric temporal point processes, including neural network-based models. Experimental results on both synthetic and real-world data suggest that our framework could produce moderately fewer yet more diverse mixture components, and achieve outstanding results across multiple evaluation metrics.

cs.LG↗

arXiv2024

Towards Better Multi-head Attention via Channel-wise Sample Permutation

Transformer plays a central role in many fundamental deep learning models, e.g., the ViT in computer vision and the BERT and GPT in natural language processing, whose effectiveness is mainly attributed to its multi-head attention (MHA) mechanism. In this study, we propose a simple and novel channel-wise sample permutation (CSP) operator, achieving a new structured MHA with fewer parameters and lower complexity. Given an input matrix, CSP circularly shifts the samples of different channels with various steps and then sorts grouped samples of each channel. This operator is equivalent to implicitly implementing cross-channel attention maps as permutation matrices, which achieves linear complexity and suppresses the risk of rank collapse when representing data. We replace the MHA of some representative models with CSP and test the CSP-based models in several discriminative tasks, including image classification and long sequence analysis. Experiments show that the CSP-based models achieve comparable or better performance with fewer parameters and lower computational costs than the classic Transformer and its state-of-the-art variants. The code is available at https://github.com/DaShenZi721/CSP.

cs.LG↗

arXiv2024

Robust Graph Matching Using An Unbalanced Hierarchical Optimal Transport Framework

Graph matching is one of the most significant graph analytic tasks, which aims to find the node correspondence across different graphs. Most existing graph matching approaches mainly rely on topological information, whose performances are often sub-optimal and sensitive to data noise because of not fully leveraging the multi-modal information hidden in graphs, such as node attributes, subgraph structures, etc. In this study, we propose a novel and robust graph matching method based on an unbalanced hierarchical optimal transport (UHOT) framework, which, to our knowledge, makes the first attempt to exploit cross-modal alignment in graph matching. In principle, applying multi-layer message passing, we represent each graph as layer-wise node embeddings corresponding to different modalities. Given two graphs, we align their node embeddings within the same modality and across different modalities, respectively. Then, we infer the node correspondence by the weighted average of all the alignment results. This method is implemented as computing the UHOT distance between the two graphs -- each alignment is achieved by a node-level optimal transport plan between two sets of node embeddings, and the weights of all alignment results correspond to an unbalanced modality-level optimal transport plan. Experiments on various graph matching tasks demonstrate the superiority and robustness of our method compared to state-of-the-art approaches. Our implementation is available at https://github.com/Dixin-Lab/UHOT-GM.

cs.AI↗

arXiv2024

An Inverse Partial Optimal Transport Framework for Music-guided Movie Trailer Generation

Trailer generation is a challenging video clipping task that aims to select highlighting shots from long videos like movies and re-organize them in an attractive way. In this study, we propose an inverse partial optimal transport (IPOT) framework to achieve music-guided movie trailer generation. In particular, we formulate the trailer generation task as selecting and sorting key movie shots based on audio shots, which involves matching the latent representations across visual and acoustic modalities. We learn a multi-modal latent representation model in the proposed IPOT framework to achieve this aim. In this framework, a two-tower encoder derives the latent representations of movie and music shots, respectively, and an attention-assisted Sinkhorn matching network parameterizes the grounding distance between the shots' latent representations and the distribution of the movie shots. Taking the correspondence between the movie shots and its trailer music shots as the observed optimal transport plan defined on the grounding distances, we learn the model by solving an inverse partial optimal transport problem, leading to a bi-level optimization strategy. We collect real-world movies and their trailers to construct a dataset with abundant label information called CMTD and, accordingly, train and evaluate various automatic trailer generators. Compared with state-of-the-art methods, our IPOT method consistently shows superiority in subjective visual effects and objective quantitative measurements.

cs.MM↗

arXiv2024

MMPolymer: A Multimodal Multitask Pretraining Framework for Polymer Property Prediction

Polymers are high-molecular-weight compounds constructed by the covalent bonding of numerous identical or similar monomers so that their 3D structures are complex yet exhibit unignorable regularity. Typically, the properties of a polymer, such as plasticity, conductivity, bio-compatibility, and so on, are highly correlated with its 3D structure. However, existing polymer property prediction methods heavily rely on the information learned from polymer SMILES sequences (P-SMILES strings) while ignoring crucial 3D structural information, resulting in sub-optimal performance. In this work, we propose MMPolymer, a novel multimodal multitask pretraining framework incorporating polymer 1D sequential and 3D structural information to encourage downstream polymer property prediction tasks. Besides, considering the scarcity of polymer 3D data, we further introduce the "Star Substitution" strategy to extract 3D structural information effectively. During pretraining, in addition to predicting masked tokens and recovering clear 3D coordinates, MMPolymer achieves the cross-modal alignment of latent representations. Then we further fine-tune the pretrained MMPolymer for downstream polymer property prediction tasks in the supervised learning paradigm. Experiments show that MMPolymer achieves state-of-the-art performance in downstream property prediction tasks. Moreover, given the pretrained MMPolymer, utilizing merely a single modality in the fine-tuning phase can also outperform existing methods, showcasing the exceptional capability of MMPolymer in polymer feature extraction and utilization.

cs.LG↗

arXiv2024

Decentralized Entropic Optimal Transport for Distributed Distribution Comparison

Distributed distribution comparison aims to measure the distance between the distributions whose data are scattered across different agents in a distributed system and cannot even be shared directly among the agents. In this study, we propose a novel decentralized entropic optimal transport (DEOT) method, which provides a communication-efficient and privacy-preserving solution to this problem with theoretical guarantees. In particular, we design a mini-batch randomized block-coordinate descent (MRBCD) scheme to optimize the DEOT distance in its dual form. The dual variables are scattered across different agents and updated locally and iteratively with limited communications among partial agents. The kernel matrix involved in the gradients of the dual variables is estimated by a decentralized kernel approximation method, in which each agent only needs to approximate and store a sub-kernel matrix by one-shot communication and without sharing raw data. Besides computing entropic Wasserstein distance, we show that the proposed MRBCD scheme and kernel approximation method also apply to entropic Gromov-Wasserstein distance. We analyze our method's communication complexity and, under mild assumptions, provide a theoretical bound for the approximation error caused by the convergence error, the estimated kernel, and the mismatch between the storage and communication protocols. In addition, we discuss the trade-off between the precision of the EOT distance and the strength of privacy protection when implementing our method. Experiments on synthetic data and real-world distributed domain adaptation tasks demonstrate the effectiveness of our method.

cs.LG↗

arXiv2024

Revisiting Counterfactual Regression through the Lens of Gromov-Wasserstein Information Bottleneck

As a promising individualized treatment effect (ITE) estimation method, counterfactual regression (CFR) maps individuals' covariates to a latent space and predicts their counterfactual outcomes. However, the selection bias between control and treatment groups often imbalances the two groups' latent distributions and negatively impacts this method's performance. In this study, we revisit counterfactual regression through the lens of information bottleneck and propose a novel learning paradigm called Gromov-Wasserstein information bottleneck (GWIB). In this paradigm, we learn CFR by maximizing the mutual information between covariates' latent representations and outcomes while penalizing the kernelized mutual information between the latent representations and the covariates. We demonstrate that the upper bound of the penalty term can be implemented as a new regularizer consisting of $i)$ the fused Gromov-Wasserstein distance between the latent representations of different groups and $ii)$ the gap between the transport cost generated by the model and the cross-group Gromov-Wasserstein distance between the latent representations and the covariates. GWIB effectively learns the CFR model through alternating optimization, suppressing selection bias while avoiding trivial latent distributions. Experiments on ITE estimation tasks show that GWIB consistently outperforms state-of-the-art CFR methods. To promote the research community, we release our project at https://github.com/peteryang1031/Causal-GWIB.

cs.LG↗

arXiv2024

Generalizable Face Landmarking Guided by Conditional Face Warping

As a significant step for human face modeling, editing, and generation, face landmarking aims at extracting facial keypoints from images. A generalizable face landmarker is required in practice because real-world facial images, e.g., the avatars in animations and games, are often stylized in various ways. However, achieving generalizable face landmarking is challenging due to the diversity of facial styles and the scarcity of labeled stylized faces. In this study, we propose a simple but effective paradigm to learn a generalizable face landmarker based on labeled real human faces and unlabeled stylized faces. Our method learns the face landmarker as the key module of a conditional face warper. Given a pair of real and stylized facial images, the conditional face warper predicts a warping field from the real face to the stylized one, in which the face landmarker predicts the ending points of the warping field and provides us with high-quality pseudo landmarks for the corresponding stylized facial images. Applying an alternating optimization strategy, we learn the face landmarker to minimize $i)$ the discrepancy between the stylized faces and the warped real ones and $ii)$ the prediction errors of both real and pseudo landmarks. Experiments on various datasets show that our method outperforms existing state-of-the-art domain adaptation methods in face landmarking tasks, leading to a face landmarker with better generalizability. Code is available at https://plustwo0.github.io/project-face-landmarker.

cs.CV↗

arXiv2024

To Search or to Recommend: Predicting Open-App Motivation with Neural Hawkes Process

Incorporating Search and Recommendation (S&R) services within a singular application is prevalent in online platforms, leading to a new task termed open-app motivation prediction, which aims to predict whether users initiate the application with the specific intent of information searching, or to explore recommended content for entertainment. Studies have shown that predicting users' motivation to open an app can help to improve user engagement and enhance performance in various downstream tasks. However, accurately predicting open-app motivation is not trivial, as it is influenced by user-specific factors, search queries, clicked items, as well as their temporal occurrences. Furthermore, these activities occur sequentially and exhibit intricate temporal dependencies. Inspired by the success of the Neural Hawkes Process (NHP) in modeling temporal dependencies in sequences, this paper proposes a novel neural Hawkes process model to capture the temporal dependencies between historical user browsing and querying actions. The model, referred to as Neural Hawkes Process-based Open-App Motivation prediction model (NHP-OAM), employs a hierarchical transformer and a novel intensity function to encode multiple factors, and open-app motivation prediction layer to integrate time and user-specific information for predicting users' open-app motivations. To demonstrate the superiority of our NHP-OAM model and construct a benchmark for the Open-App Motivation Prediction task, we not only extend the public S&R dataset ZhihuRec but also construct a new real-world Open-App Motivation Dataset (OAMD). Experiments on these two datasets validate NHP-OAM's superiority over baseline models. Further downstream application experiments demonstrate NHP-OAM's effectiveness in predicting users' Open-App Motivation, highlighting the immense application value of NHP-OAM.

cs.IR↗

arXiv2024

A Quasi-Wasserstein Loss for Learning Graph Neural Networks

When learning graph neural networks (GNNs) in node-level prediction tasks, most existing loss functions are applied for each node independently, even if node embeddings and their labels are non-i.i.d. because of their graph structures. To eliminate such inconsistency, in this study we propose a novel Quasi-Wasserstein (QW) loss with the help of the optimal transport defined on graphs, leading to new learning and prediction paradigms of GNNs. In particular, we design a ``Quasi-Wasserstein'' distance between the observed multi-dimensional node labels and their estimations, optimizing the label transport defined on graph edges. The estimations are parameterized by a GNN in which the optimal label transport may determine the graph edge weights optionally. By reformulating the strict constraint of the label transport to a Bregman divergence-based regularizer, we obtain the proposed Quasi-Wasserstein loss associated with two efficient solvers learning the GNN together with optimal label transport. When predicting node labels, our model combines the output of the GNN with the residual component provided by the optimal label transport, leading to a new transductive prediction paradigm. Experiments show that the proposed QW loss applies to various GNNs and helps to improve their performance in node-level classification and regression tasks. The code of this work can be found at \url{https://github.com/SDS-Lab/QW_Loss}.

cs.LG↗