{"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/root-aligned-smiles-for-molecular","title":"Root-aligned SMILES: A Tight Representation for Chemical Reaction Prediction","arxiv_id":"2203.11444","date":"2022-03-22","proceeding":null,"authors":["Zipeng Zhong","Jie Song","Zunlei Feng","Tiantao Liu","Lingxiang Jia","Shaolun Yao","Min Wu","Tingjun Hou","Mingli Song"],"abstract":"Chemical reaction prediction, involving forward synthesis and retrosynthesis prediction, is a fundamental problem in organic synthesis. A popular computational paradigm formulates synthesis prediction as a sequence-to-sequence translation problem, where the typical SMILES is adopted for molecule representations. However, the general-purpose SMILES neglects the characteristics of chemical reactions, where the molecular graph topology is largely unaltered from reactants to products, resulting in the suboptimal performance of SMILES if straightforwardly applied. In this article, we propose the root-aligned SMILES (R-SMILES), which specifies a tightly aligned one-to-one mapping between the product and the reactant SMILES for more efficient synthesis prediction. Due to the strict one-to-one mapping and reduced edit distance, the computational model is largely relieved from learning the complex syntax and dedicated to learning the chemical knowledge for reactions. We compare the proposed R-SMILES with various state-of-the-art baselines and show that it significantly outperforms them all, demonstrating the superiority of the proposed method.","url_abs":"https://arxiv.org/abs/2203.11444v5","url_pdf":"https://arxiv.org/pdf/2203.11444v5.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":"root-aligned-smiles-for-molecular","repo_url":"https://github.com/otori-bird/retrosynthesis","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":1,"framework":"pytorch","reach":null}],"tasks":[{"task_slug":"chemical-reaction-prediction","task_name":"Chemical Reaction Prediction"},{"task_slug":"prediction","task_name":"Prediction"},{"task_slug":"retrosynthesis","task_name":"Retrosynthesis"},{"task_slug":"single-step-retrosynthesis","task_name":"Single-step retrosynthesis"}],"methods":[],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"syntology_url":"https://syntology.ai/paper/2203.11444","atlas_url":"https://app.syntology.ai/?focus=2203.11444","mcp":{"get_harvested_code_for_paper":{"arxiv_id":"2203.11444"}},"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. Samples come from repositories linked to the paper, official or community; repo_kind says which.","repos":[{"provenance":"external:paperswithcode_snapshot_2025-07-28","url":"https://github.com/otori-bird/retrosynthesis","reach":null}],"summary":{"ran_draft_wrong":1},"by_repo_kind":{"official":{"samples":1,"ran":1,"repositories":1}},"repo_kind_vocabulary":{"official":"The archive marks this repository official for the paper","named_in_paper":"The archive records that the paper mentions this repository; it is not marked official","listed":"In the archive's code links for this paper, not marked official and not recorded as mentioned in the paper","found_in_text":"Syntology found this repository in the paper's own text; whether it is the authors' implementation is not asserted","community":"Not in the archive's code links for this paper; a community repository Syntology harvested"},"n_pointer_only_for_licence":0,"samples":[{"code_sha256_prefix":"558cf4a6aec8bf94","entry":"smi_tokenizer","repo":"otori-bird/retrosynthesis","repo_kind":"official","path":"preprocessing/generate_PtoR_data.py","file_url":"https://github.com/otori-bird/retrosynthesis/blob/HEAD/preprocessing/generate_PtoR_data.py","link_basis":"first_harvest_node","language":"python","status":"ran_draft_wrong","verification_level":1,"contract_check":"OUTPUT_MISDECLARED","metamorphic_tier":"deterministic","behaviour_fingerprint":true,"licence":"MIT","inline_ok":true,"mcp_get_code":{"code_sha256":"558cf4a6aec8bf94"}}]},"arxiv_metadata":null,"syntology_extracted_results":null}