Inference-Time Projection for Physically Valid Biomolecular Diffusion Models

תקציר מקורי באנגליתarXiv:2610.07037v1 Announce Type: cross Abstract: AlphaFold 3-style cofolding models predict biomolecular complexes with high structural accuracy, yet a large fraction of their outputs are physically invalid: chains overlap at interfaces, ligand bond lengths and angles are distorted, rings are non-planar, and stereocentres are inverted. Current approaches either steer the sampler with physics-informed potentials, which multiplies sampling cost and memory overhead making inference impossible on large complexes, or finetune the model, costing time and tying the fix to one architecture. We observe that, unlike structural accuracy, physical validity is fully verifiable at inference time from quantities the sampler already holds. We therefore treat physical validity as a constrained inference p