Shuquan Ye
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.
From Static Spectra to Operando Infrared Dynamics: Physics Informed Flow Modeling and a Benchmark
The Solid Electrolyte Interphase (SEI) is critical to the performance of lithium-ion batteries, yet its analysis via Operando Infrared (IR) spectroscopy remains experimentally complex and expensive, which limits its accessibility for standard research facilities. To overcome this bottleneck, we formulate a novel task, Operando IR Prediction, which aims to forecast the time-resolved evolution of spectral ``fingerprints'' from a single static spectrum. To facilitate this, we introduce OpIRSpec-7K, the first large-scale operando dataset comprising 7,118 high-quality samples across 10 distinct battery systems, alongside OpIRBench, a comprehensive evaluation benchmark with carefully designed protocols. Addressing the limitations of standard spectrum, video, and sequence models in capturing voltage-driven chemical dynamics and complex composition, we propose Aligned Bi-stream Chemical Constraint (ABCC), an end-to-end physics-aware framework. It reformulates MeanFlow and introduces a novel Chemical Flow to explicitly model reaction trajectories, employs a two-stream disentanglement mechanism for solvent-SEI separation, and enforces physics and spectrum constraints such as mass conservation and peak shifts. ABCC significantly outperforms state-of-the-art static, sequential, and generative baselines. ABCC even generalizes to unseen systems and enables interpretable downstream recovery of SEI formation pathways, supporting AI-driven electrochemical discovery.