{"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/motifretro-exploring-the-combinability","title":"MotifRetro: Exploring the Combinability-Consistency Trade-offs in retrosynthesis via Dynamic Motif Editing","arxiv_id":"2305.15153","date":"2023-05-20","proceeding":null,"authors":["Zhangyang Gao","Xingran Chen","Cheng Tan","Stan Z. Li"],"abstract":"Is there a unified framework for graph-based retrosynthesis prediction? Through analysis of full-, semi-, and non-template retrosynthesis methods, we discovered that they strive to strike an optimal balance between combinability and consistency: \\textit{Should atoms be combined as motifs to simplify the molecular editing process, or should motifs be broken down into atoms to reduce the vocabulary and improve predictive consistency?} Recent works have studied several specific cases, while none of them explores different combinability-consistency trade-offs. Therefore, we propose MotifRetro, a dynamic motif editing framework for retrosynthesis prediction that can explore the entire trade-off space and unify graph-based models. MotifRetro comprises two components: RetroBPE, which controls the combinability-consistency trade-off, and a motif editing model, where we introduce a novel LG-EGAT module to dynamiclly add motifs to the molecule. We conduct extensive experiments on USPTO-50K to explore how the trade-off affects the model performance and finally achieve state-of-the-art performance.","url_abs":"https://arxiv.org/abs/2305.15153v1","url_pdf":"https://arxiv.org/pdf/2305.15153v1.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":"motifretro-exploring-the-combinability","repo_url":"https://github.com/A4Bio/MotifRetro_open","is_official":1,"mentioned_in_paper":0,"mentioned_in_github":0,"framework":"pytorch","reach":{"status":"ok"}}],"tasks":[{"task_slug":"retrosynthesis","task_name":"Retrosynthesis"}],"methods":[{"method_slug":null,"method_name":"None"}],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"atlas_url":"https://app.syntology.ai/?focus=2305.15153","mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}