Ben Fei
Publications
ED-DiT: Physics-Guided Diffusion Pretraining for Transferable Molecular Representations from Electron Density
Pretraining has shown strong potential for learning transferable representations, yet it remains underexplored for electron-density-based molecular learning. Electron density provides a continuous three-dimensional description of molecular electronic structure, capturing both local spatial patterns and global physical quantities. This raises a key question: can electron-density fields be used for self-supervised pretraining to learn a shared representation that transfers across diverse electronic-structure-related tasks? We propose ED-DiT, a physics-guided Diffusion Transformer for self-supervised pretraining on electron-density point clouds. ED-DiT learns reusable representations by reconstructing corrupted and partially masked log-density fields across diffusion noise levels. An electron-number consistency constraint is further introduced to preserve the total electronic mass. The pretrained encoder can be adapted to property prediction, open-/closed-shell classification, molecule-electron-density retrieval, and molecule-conditioned electron-density prediction. Experiments on six EDBench tasks show that ED-DiT consistently outperforms the same architecture trained from scratch, especially under limited supervision. For molecule-conditioned electron-density prediction, it reduces RMSE from 2.2474 to 1.3753 and surpasses the available baseline. With only 10% labels, it improves orbital energy prediction RMSE from 0.0293 to 0.0138. These results demonstrate the effectiveness of physics-guided electron-density pretraining for learning transferable molecular representations.
The Geometry of Flow-Matching Uncertainty: A Cost-free Uncertainty Proxy and Its Application in Flow-based VLA Failure Detection
Flow matching (FM) has become a popular action head paradigm for modern embodied models. However, as a conditional generative model, it does not explicitly expose its inherent uncertainty, producing faulty action chunks even when it misinterprets the scene or encounters out-of-distribution (OOD) inputs. Therefore, determining when an FM-generated action can be trusted is essential for safe deployment, yet existing uncertainty estimation methods on real-time control suffer from several issues: extra training budget, high computational overhead, and low generalization ability. In this work, we provide a geometric interpretation of FM uncertainty in the velocity field, showing that uncertainty manifests as deviation from an ideal affine-isotropic contraction field. Building on this observation, we introduce denoising acceleration ($\mathrm{accel}$), a highly-generalizable and cost-free uncertainty proxy that measures the bending of the denoising trajectory from a single forward pass, without additional model evaluations, training, or resampling. We theoretically and empirically demonstrate that $\mathrm{accel}$ is a faithful proxy for FM uncertainty and further test its utility in online failure detection. Results show that $\mathrm{accel}$ identifies failing rollouts well before termination, matching or even outperforming costly resampling- and training-based baselines across settings under realistic deployment budget. Code and demos available at: https://github.com/rrrrrrzy/fm-geometry.