Lyapunov Guidance: A Unified Framework for Stabilizing Generative Flows

Flow matching has emerged as an effective framework for learning complex data distributions, but adapting pretrained flow models to new tasks often requires computationally expensive retraining. Post-training guidance provides a more efficient alternative, but existing methods are largely heuristic and offer no explicit stability guarantees. We address this limitation by proposing LyaGuide, a unified Lyapunov-guided framework that formulates flow guidance as a Lyapunov control problem. Our main theoretical result establishes an equivalence between guided flow matching and Lyapunov control, thereby unifying common guidance strategies, such as classifier guidance, reward guidance, and energy-based guidance, within a single control-theoretic framework. To enforce the Lyapunov condition, we introduce a pseudo-projection operator with a closed-form expression that endows learned or heuristic guidance terms with explicit stability guarantees. LyaGuide supports two practical settings: a model-driven setting, where the target guidance distribution is specified through a known Lyapunov function, and a data-driven setting, where the guidance is adapted from task-specific downstream data. LyaGuide is compatible with existing guidance methods, introduces minimal additional computational overhead, and is straightforward to integrate in practice. Extensive experiments on synthetic benchmarks, image inverse problems, reinforcement learning planning, and energy-based modeling demonstrate consistent improvements in sample quality, guidance fidelity, and robustness, while maintaining computational efficiency.

PoseX: AI Defeats Physics Approaches on Protein-Ligand Cross Docking

Recently, significant progress has been made in protein-ligand docking, especially in modern deep learning methods, and some benchmarks were proposed, e.g., PoseBench, Plinder. However, these benchmarks suffer from less practical evaluation setups (e.g., blind docking, self docking), or heavy framework that involves training, raising challenges to assess docking methods efficiently. To fill this gap, we proposed PoseX, an open-source benchmark focusing on self-docking and cross-docking, to evaluate the algorithmic advances practically and comprehensively. Specifically, first, we curate a new evaluation dataset with 718 entries for self docking and 1,312 for cross docking; second, we incorporate 22 docking methods across three methodological categories, including (1) traditional physics-based methods (e.g., Schr\"odinger Glide), (2) AI docking methods (e.g., DiffDock), (3) AI co-folding methods (e.g., AlphaFold3); third, we design a relaxation method as post-processing to minimize conformation energy and refine binding pose; fourth, we released a leaderboard to rank submitted models in real time. We draw some key insights via extensive experiments: (1) AI-based approaches have already surpassed traditional physics-based approaches in overall docking accuracy (RMSD). The longstanding generalization issues that have plagued AI molecular docking have been significantly alleviated in the latest models. (2) The stereochemical deficiencies of AI-based approaches can be greatly alleviated with post-processing relaxation. Combining AI docking methods with the enhanced relaxation method achieves the best performance to date. (3) AI co-folding methods commonly face ligand chirality issues, which cannot be resolved by relaxation. The code, curated dataset and leaderboard are released at https://github.com/CataAI/PoseX.