Hongyu Zhang
Publications
WaveFormer: Frequency-Time Decoupled Vision Modeling with Wave Equation
Vision modeling has advanced rapidly with Transformers, whose attention mechanisms capture visual dependencies but lack a principled account of how semantic information propagates spatially. We revisit this problem from a wave-based perspective: feature maps are treated as spatial signals whose evolution over an internal propagation time (aligned with network depth) is governed by an underdamped wave equation. In this formulation, spatial frequency-from low-frequency global layout to high-frequency edges and textures-is modeled explicitly, and its interaction with propagation time is controlled rather than implicitly fixed. We derive a closed-form, frequency-time decoupled solution and implement it as the Wave Propagation Operator (WPO), a lightweight module that models global interactions in O(N log N) time-far lower than attention. Building on WPO, we propose a family of WaveFormer models as drop-in replacements for standard ViTs and CNNs, achieving competitive accuracy across image classification, object detection, and semantic segmentation, while delivering up to 1.6x higher throughput and 30% fewer FLOPs than attention-based alternatives. Furthermore, our results demonstrate that wave propagation introduces a complementary modeling bias to heat-based methods, effectively capturing both global coherence and high-frequency details essential for rich visual semantics. Codes are available at: https://github.com/ZishanShu/WaveFormer.
Pseudodata-guided Invariant Representation Learning Boosts the Out-of-Distribution Generalization in Enzymatic Kinetic Parameter Prediction
Accurate prediction of enzyme kinetic parameters is essential for understanding catalytic mechanisms and guiding enzyme engineering.However, existing deep learning-based enzyme-substrate interaction (ESI) predictors often exhibit performance degradation on sequence-divergent, out-of-distribution (OOD) cases, limiting robustness under biologically relevant perturbations.We propose O$^2$DENet, a lightweight, plug-and-play module that enhances OOD generalization via biologically and chemically informed perturbation augmentation and invariant representation learning.O$^2$DENet introduces enzyme-substrate perturbations and enforces consistency between original and augmented enzyme-substrate-pair representations to encourage invariance to distributional shifts.When integrated with representative ESI models, O$^2$DENet consistently improves predictive performance for both $k_{cat}$ and $K_m$ across stringent sequence-identity-based OOD benchmarks, achieving state-of-the-art results among the evaluated methods in terms of accuracy and robustness metrics.Overall, O$^2$DENet provides a general and effective strategy to enhance the stability and deployability of data-driven enzyme kinetics predictors for real-world enzyme engineering applications.