Wenkai Xiang

Kaihui Cheng, Zhiqiang Cai, Wenkai Xiang et al.

Generative emulators of protein dynamics produce plausible trajectories at a fraction of the cost of molecular dynamics, but they inherit their training distribution and tend to revisit known states rather than reach rare ones under long-horizon extrapolation. Inspired by classical enhanced sampling, we introduce an implicit, history-dependent bias in the generative space of a pretrained emulator. Specifically, a history-aware score estimator augments the frozen emulator with a distance-weighted bias that steers reverse-time sampling away from previously generated structures, regularized by an environment-support term. To preserve structural validity at long horizons, a score-based refinement step re-projects drifted samples onto the data manifold using the frozen emulator. Our experiments demonstrate that the method (i) raises diversity by $35\%$ on DynamicPDB-80; (ii) on $12$ zero-shot Fast-Folding proteins, the learned bias alone reaches the unbiased emulator's coverage up to ${\sim}15\times$ faster, and pairing it with refinement reaches the coverage up to ${\sim}37\times$ faster while covering ${\sim}3\times$ as many low-energy states. Code will be released soon.

Yaowei Jin, Junjie Wang, Wenkai Xiang et al.

Advances in deep learning for molecular generation show promise in accelerating drug discovery. Bayesian Flow Networks (BFNs) have recently shown impressive performance across diverse chemical tasks, with their success often ascribed to the paradigm of modeling in a low-variance parameter space. However, the Bayesian inference-based strategy imposes limitations on designing more flexible distribution transformation pathways, making it challenging to adapt to diverse data distributions and varied task requirements. Furthermore, the potential for simpler, more efficient parameter-space-based models is unexplored. To address this, we propose a novel Parameter Interpolation Flow model (named PIF) with detailed theoretical foundation, training, and inference procedures. We then develop MolPIF for structure-based drug design, demonstrating its superior performance across diverse metrics compared to baselines. This work validates the effectiveness of parameter-space-based generative modeling paradigm for molecules and offers new perspectives for model design.