Fractional Denoising for 3D Molecular Pre-training

arXiv:2307.10683v3 Announce Type: replace-cross
Abstract: Coordinate denoising is a promising 3D molecular pre-training method, which has achieved remarkable performance in various downstream drug discovery tasks. Theoretically, the objective is equivalent to learning the force field, which is revealed helpful for downstream tasks. Nevertheless, there are two challenges for coordinate denoising to learn an effective force field, i.e. low coverage samples and isotropic force field. The underlying reason is that molecular distributions assumed by existing denoising methods fail to capture the …

abstract arxiv challenges cs.lg denoising discovery drug discovery learn performance physics.chem-ph pre-training q-bio.qm tasks training type