arXiv:2605.25577v1 Announce Type: cross Abstract: The generation of accurate 3D molecular conformations is a pivotal challenge in computational chemistry and drug discovery. Recently, diffusion and flow matching models have achieved remarkable success. However, there is a critical misalignment between their mathematical formulation and the physical reality of molecules. Existing approaches predominantly treat molecules as unstructured point clouds in Cartesian space, overlooking the intrinsic hierarchical mechanics where bond lengths and bond angles are relatively stiff, whereas torsion angles constitute the dominant flexible degrees of freedom. This lack of manifold awareness forces models to relearn fundamental geometric constraints from scratch, often leading to physically implausible intermediate structures. To address this, we propose GO-Flow that aligns generative modeling with molecular geometry via manifold decomposition. Instead of forcing motion through Euclidean space, GO-Flow decomposes the generation process into three physically motivated subspaces: translation space with linear optimal transport, rotation space with geodesic flows on $SO(3)$, and conformation space with entropic optimal transport. This decomposition injects geometric inductive biases and makes the generative paths better aligned with molecular degrees of freedom. When combined with equivariant neural architectures, it encourages rotation-consistent generation and improves geometric validity. Extensive experiments on GEOM-Drugs and GEOM-QM9 demonstrate that GO-Flow achieves state-of-the-art generation quality. Notably, by learning straighter probability paths on the correct manifolds naturally, our method enables high-fidelity sampling with as few as 50 steps, effectively bridging the gap between structural precision and computational efficiency.

arXiv:2605.25698v1 Announce Type: cross Abstract: High-quality data is scarce in large language model (LLM) training, yet how to schedule its use jointly with training dynamics lacks theoretical guidance. We extend functional scaling laws by incorporating a data-quality dimension, and solve the joint data-quality and batch-size scheduling problem in asymptotic closed form. The solution reveals two regimes and a dual role of high-quality data. In the noise-limited regime, high-quality data should be used as a signal amplifier: lowering the batch size converts cleaner data into more signal without amplifying noise. In the signal-limited regime, it should be used as a noise suppressor: late placement reduces terminal noise without sacrificing signal accumulation. Existing curriculum-style pipelines primarily exploit the second role by placing cleaner data late, but miss the first role because conventional decay schedules reduce update intensity exactly when high-quality data becomes available. Guided by this, we propose Drop-Stable-Rampup for LLM midtraining: upon the quality transition, drop the batch size, hold it stable to accumulate signal, then ramp up to suppress terminal noise. On a 15B Mixture-of-Experts model midtrained on 108B tokens, Drop-Stable-Rampup improves average accuracy over Warmup-Stable-Decay (WSD) by +1.70 and over Cosine-decay by +2.98, with particularly large gains on mathematical reasoning benchmarks such as GSM8K (+4.23) and MATH (+2.80).