Wenwu Yu
Publications
From Uniform to Learned Graph Priors: Diffusion for Structure Discovery
Neural relational inference (NRI) methods discover interaction graphs from trajectories through variational reasoning on discrete potential edges. However, these methods typically rely on oversimplified, factorized graph priors. Such priors, typically nearing uniform distributions, treat edges as independent entities. This systemic misalignment does not match the real-world systems and yields diffuse and indecisive edge posteriors limiting the reliability of structural discovery. To address this, we propose \textit{Diff-prior}, a diffusion-parameterized adaptive prior used to calibrate latent graph distribution rather than generate graphs. Our core insight is to reframe prior integration as a learnable denoising-style calibration that organizes scattered, uncertain edge posteriors into a more reliable overall structure which can be trained by the diffusion model. Diff-prior learns an adaptive structure prior that performs structured calibration on the edge posteriors during inference, guiding it towards a distribution closer to the underlying structure. The diff-prior operates before structural sampling and acts as a denoising calibrator directly on the encoder edge distribution, which provides a generic training paradigm over structured variables. Experiments on standard benchmarks validated our framework, and the results indicate that Diff-prior improves the performance of structure inference and generates more decisive edge posteriors across multiple NRI-family architectures. The code is available on https://github.com/Hardy158118/Diffprior.
TFWaveFormer: Temporal-Frequency Collaborative Multi-level Wavelet Transformer for Dynamic Link Prediction
Dynamic link prediction plays a crucial role in diverse applications including social network analysis, communication forecasting, and financial modeling. While recent Transformer-based approaches have demonstrated promising results in temporal graph learning, their performance remains limited when capturing complex multi-scale temporal dynamics. In this paper, we propose TFWaveFormer, a novel Transformer architecture that integrates temporal-frequency analysis with multi-resolution wavelet decomposition to enhance dynamic link prediction. Our framework comprises three key components: (i) a temporal-frequency coordination mechanism that jointly models temporal and spectral representations, (ii) a learnable multi-resolution wavelet decomposition module that adaptively extracts multi-scale temporal patterns through parallel convolutions, replacing traditional iterative wavelet transforms, and (iii) a hybrid Transformer module that effectively fuses local wavelet features with global temporal dependencies. Extensive experiments on benchmark datasets demonstrate that TFWaveFormer achieves state-of-the-art performance, outperforming existing Transformer-based and hybrid models by significant margins across multiple metrics. The superior performance of TFWaveFormer validates the effectiveness of combining temporal-frequency analysis with wavelet decomposition in capturing complex temporal dynamics for dynamic link prediction tasks.
CausalCompass: Evaluating the Robustness of Time-Series Causal Discovery in Misspecified Scenarios
Causal discovery from time series is a fundamental task in machine learning. However, its widespread adoption is hindered by a reliance on untestable causal assumptions and by the lack of robustness-oriented evaluation in existing benchmarks. To address these challenges, we propose CausalCompass, a flexible and extensible benchmark suite designed to assess the robustness of time-series causal discovery (TSCD) methods under violations of modeling assumptions. To demonstrate the practical utility of CausalCompass, we conduct extensive benchmarking of representative TSCD algorithms across eight assumption-violation scenarios. Our experimental results indicate that no single method consistently attains optimal performance across all settings. Nevertheless, the methods exhibiting superior overall performance across diverse scenarios are almost invariably deep learning-based approaches. We further provide hyperparameter sensitivity analyses to deepen the understanding of these findings. We also find, somewhat surprisingly, that NTS-NOTEARS relies heavily on standardized preprocessing in practice, performing poorly in the vanilla setting but exhibiting strong performance after standardization. Finally, our work aims to provide a comprehensive and systematic evaluation of TSCD methods under assumption violations, thereby facilitating their broader adoption in real-world applications. The code and datasets are available at https://github.com/huiyang-yi/CausalCompass.
CoDCL: Counterfactual Data Augmentation Contrastive Learning for Continuous-Time Dynamic Network Link Prediction
The rapid growth and continuous structural evolution of dynamic networks make effective predictions increasingly challenging. To enable prediction models to adapt to complex temporal environments, they need to be robust to emerging structural changes. We propose a dynamic network learning framework CoDCL, which combines counterfactual data augmentation with contrastive learning to address this deficiency.Furthermore, we devise a comprehensive strategy to generate high-quality counterfactual data, combining a dynamic treatments design with efficient structural neighborhood exploration to quantify the temporal changes in interaction patterns.Crucially, the entire CoDCL is designed as a plug-and-play universal module that can be seamlessly integrated into various existing temporal graph models without requiring architectural modifications.Extensive experiments on multiple real-world datasets demonstrate that CoDCL significantly gains state-of-the-art baseline models in the field of dynamic networks, confirming the critical role of integrating counterfactual data augmentation into dynamic representation learning.
CCMamba: Selective State-Space Models for Higher-Order Graph Learning on Combinatorial Complexes
Topological deep learning has emerged for modeling higher-order relational structures beyond pairwise interactions that standard graph neural networks fail to capture. Although combinatorial complexes offer a unified topological framework, most existing topological deep learning methods rely on local message passing via attention mechanisms, which incur quadratic complexity and remain low-dimensional, limiting scalability and rank-aware information aggregation in higher-order complexes.We propose Combinatorial Complex Mamba (CCMamba), the first unified mamba-based neural framework for learning on combinatorial complexes. CCMamba reformulates message passing as a selective state-space modeling problem by organizing multi-rank incidence relations into structured sequences processed by rank-aware state-space models. This enables adaptive, directional, and long range information propagation in linear time without self attention. We further establish the theoretical analysis that the expressive power upper-bound of CCMamba message passing is the 1-Weisfeiler-Lehman test. Experiments on graph, hypergraph, and simplicial benchmarks demonstrate that CCMamba consistently outperforms existing methods while exhibiting improved scalability and robustness to depth.