{"about":{"site":"https://codewithpapers.app","non_affiliation":"Code with Papers and Syntology are not affiliated with, endorsed by, or sponsored by Papers with Code, Meta, or the pwc-archive mirror.","licence":"CC BY-SA 4.0","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","attribution":"https://codewithpapers.app/attribution","modified":"archive material modified by Syntology; see the attribution page"},"url":"/paper/fractional-denoising-for-3d-molecular-pre","title":"Fractional Denoising for 3D Molecular Pre-training","arxiv_id":"2307.10683","date":"2023-07-20","proceeding":null,"authors":["Shikun Feng","Yuyan Ni","Yanyan Lan","Zhi-Ming Ma","Wei-Ying Ma"],"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 anisotropic characteristic of molecules. To tackle these challenges, we propose a novel hybrid noise strategy, including noises on both dihedral angel and coordinate. However, denoising such hybrid noise in a traditional way is no more equivalent to learning the force field. Through theoretical deductions, we find that the problem is caused by the dependency of the input conformation for covariance. To this end, we propose to decouple the two types of noise and design a novel fractional denoising method (Frad), which only denoises the latter coordinate part. In this way, Frad enjoys both the merits of sampling more low-energy structures and the force field equivalence. Extensive experiments show the effectiveness of Frad in molecular representation, with a new state-of-the-art on 9 out of 12 tasks of QM9 and on 7 out of 8 targets of MD17.","url_abs":"https://arxiv.org/abs/2307.10683v3","url_pdf":"https://arxiv.org/pdf/2307.10683v3.pdf","source":{"archive":"pwc-archive (Hugging Face), CC BY-SA 4.0","snapshot":"2025-07-28","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","row_kind":"abstracts"},"code_links":[{"paper_slug":"fractional-denoising-for-3d-molecular-pre","repo_url":"https://github.com/fengshikun/frad","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":0,"framework":"pytorch","reach":{"status":"ok","spdx":"MIT"}}],"tasks":[{"task_slug":"denoising","task_name":"Denoising"},{"task_slug":"drug-discovery","task_name":"Drug Discovery"},{"task_slug":"molecular-representation","task_name":"molecular representation"}],"methods":[{"method_slug":"fail","method_name":"fail"}],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"syntology_url":"https://syntology.ai/paper/2307.10683","atlas_url":"https://app.syntology.ai/?focus=2307.10683","mcp":{"get_harvested_code_for_paper":{"arxiv_id":"2307.10683"}},"developers":"https://syntology.ai/developers","read_at":"2026-09-25T09:33:49+00:00","read_at_is":"when the build read Syntology's graph, not when any sample ran","claim":"Per-sample execution status on synthesized fixtures; not a correctness claim about the paper. 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