{"id":"https://openalex.org/W4409365581","doi":"https://doi.org/10.1609/aaai.v39i12.33373","title":"GDiffRetro: Retrosynthesis Prediction with Dual Graph Enhanced Molecular Representation and Diffusion Generation","display_name":"GDiffRetro: Retrosynthesis Prediction with Dual Graph Enhanced Molecular Representation and Diffusion Generation","publication_year":2025,"publication_date":"2025-04-11","ids":{"openalex":"https://openalex.org/W4409365581","doi":"https://doi.org/10.1609/aaai.v39i12.33373"},"language":"en","primary_location":{"id":"doi:10.1609/aaai.v39i12.33373","is_oa":true,"landing_page_url":"https://doi.org/10.1609/aaai.v39i12.33373","pdf_url":"https://ojs.aaai.org/index.php/AAAI/article/download/33373/35528","source":{"id":"https://openalex.org/S4210191458","display_name":"Proceedings of the AAAI Conference on Artificial Intelligence","issn_l":"2159-5399","issn":["2159-5399","2374-3468"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/P4310320058","host_organization_name":"Association for the Advancement of Artificial Intelligence","host_organization_lineage":["https://openalex.org/P4310320058"],"host_organization_lineage_names":["Association for the Advancement of Artificial Intelligence"],"type":"conference"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the AAAI Conference on Artificial Intelligence","raw_type":"journal-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"diamond","oa_url":"https://ojs.aaai.org/index.php/AAAI/article/download/33373/35528","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5090360604","display_name":"Shengyin Sun","orcid":"https://orcid.org/0000-0002-6687-6377"},"institutions":[{"id":"https://openalex.org/I168719708","display_name":"City University of Hong Kong","ror":"https://ror.org/03q8dnn23","country_code":"HK","type":"education","lineage":["https://openalex.org/I168719708"]}],"countries":["HK"],"is_corresponding":true,"raw_author_name":"Shengyin Sun","raw_affiliation_strings":["Department of Computer Science, City University of Hong Kong"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, City University of Hong Kong","institution_ids":["https://openalex.org/I168719708"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039394884","display_name":"Wenhao Yu","orcid":"https://orcid.org/0000-0003-1521-2674"},"institutions":[{"id":"https://openalex.org/I177725633","display_name":"Chinese University of Hong Kong","ror":"https://ror.org/00t33hh48","country_code":"CN","type":"education","lineage":["https://openalex.org/I177725633"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Wenhao Yu","raw_affiliation_strings":["Department of Computer Science and Engineering, The Chinese University of Hong Kong"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, The Chinese University of Hong Kong","institution_ids":["https://openalex.org/I177725633"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007581371","display_name":"Yuxiang Ren","orcid":"https://orcid.org/0000-0002-0760-796X"},"institutions":[{"id":"https://openalex.org/I4210160618","display_name":"Huawei Technologies (United Kingdom)","ror":"https://ror.org/056gzgs71","country_code":"GB","type":"company","lineage":["https://openalex.org/I2250955327","https://openalex.org/I4210160618"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Yuxiang Ren","raw_affiliation_strings":["Advance Computing and Storage Lab, Huawei Technologies"],"affiliations":[{"raw_affiliation_string":"Advance Computing and Storage Lab, Huawei Technologies","institution_ids":["https://openalex.org/I4210160618"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100544782","display_name":"Weitao Du","orcid":null},"institutions":[{"id":"https://openalex.org/I4210120485","display_name":"Academy of Mathematics and Systems Science","ror":"https://ror.org/02jkmyk67","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210120485"]},{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"funder","lineage":["https://openalex.org/I19820366"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Weitao Du","raw_affiliation_strings":["Academy of Mathematics and Systems Science, Chinese Academy of Sciences"],"affiliations":[{"raw_affiliation_string":"Academy of Mathematics and Systems Science, Chinese Academy of Sciences","institution_ids":["https://openalex.org/I4210120485","https://openalex.org/I19820366"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060372724","display_name":"Liwei Liu","orcid":"https://orcid.org/0000-0001-5884-7333"},"institutions":[{"id":"https://openalex.org/I4210160618","display_name":"Huawei Technologies (United Kingdom)","ror":"https://ror.org/056gzgs71","country_code":"GB","type":"company","lineage":["https://openalex.org/I2250955327","https://openalex.org/I4210160618"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Liwei Liu","raw_affiliation_strings":["Advance Computing and Storage Lab, Huawei Technologies"],"affiliations":[{"raw_affiliation_string":"Advance Computing and Storage Lab, Huawei Technologies","institution_ids":["https://openalex.org/I4210160618"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002546886","display_name":"Xuecang Zhang","orcid":"https://orcid.org/0009-0003-8638-2985"},"institutions":[{"id":"https://openalex.org/I4210160618","display_name":"Huawei Technologies (United Kingdom)","ror":"https://ror.org/056gzgs71","country_code":"GB","type":"company","lineage":["https://openalex.org/I2250955327","https://openalex.org/I4210160618"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Xuecang Zhang","raw_affiliation_strings":["Advance Computing and Storage Lab, Huawei Technologies"],"affiliations":[{"raw_affiliation_string":"Advance Computing and Storage Lab, Huawei Technologies","institution_ids":["https://openalex.org/I4210160618"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101687283","display_name":"Ying Hu","orcid":"https://orcid.org/0000-0002-4113-4369"},"institutions":[{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Ying Hu","raw_affiliation_strings":["Department of Electronic Engineering, Tsinghua University"],"affiliations":[{"raw_affiliation_string":"Department of Electronic Engineering, Tsinghua University","institution_ids":["https://openalex.org/I99065089"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100545258","display_name":"Chen Ma","orcid":null},"institutions":[{"id":"https://openalex.org/I168719708","display_name":"City University of Hong Kong","ror":"https://ror.org/03q8dnn23","country_code":"HK","type":"education","lineage":["https://openalex.org/I168719708"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Chen Ma","raw_affiliation_strings":["Department of Computer Science, City University of Hong Kong"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, City University of Hong Kong","institution_ids":["https://openalex.org/I168719708"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5090360604"],"corresponding_institution_ids":["https://openalex.org/I168719708"],"apc_list":null,"apc_paid":null,"fwci":10.3881,"has_fulltext":true,"cited_by_count":3,"citation_normalized_percentile":{"value":0.98268398,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":95,"max":98},"biblio":{"volume":"39","issue":"12","first_page":"12595","last_page":"12603"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11948","display_name":"Machine Learning in Materials Science","score":0.9966999888420105,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T11948","display_name":"Machine Learning in Materials Science","score":0.9966999888420105,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9699000120162964,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10836","display_name":"Metabolomics and Mass Spectrometry Studies","score":0.9578999876976013,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/retrosynthetic-analysis","display_name":"Retrosynthetic analysis","score":0.726073682308197},{"id":"https://openalex.org/keywords/dual","display_name":"Dual (grammatical number)","score":0.616858959197998},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.6031107902526855},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.5793232321739197},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5277919173240662},{"id":"https://openalex.org/keywords/diffusion","display_name":"Diffusion","score":0.4616512060165405},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3928396701812744},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3426651954650879},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.1876991093158722},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.09996464848518372},{"id":"https://openalex.org/keywords/linguistics","display_name":"Linguistics","score":0.09337511658668518},{"id":"https://openalex.org/keywords/stereochemistry","display_name":"Stereochemistry","score":0.09022372961044312},{"id":"https://openalex.org/keywords/political-science","display_name":"Political science","score":0.06525009870529175}],"concepts":[{"id":"https://openalex.org/C42437451","wikidata":"https://www.wikidata.org/wiki/Q902227","display_name":"Retrosynthetic analysis","level":3,"score":0.726073682308197},{"id":"https://openalex.org/C2780980858","wikidata":"https://www.wikidata.org/wiki/Q110022","display_name":"Dual (grammatical number)","level":2,"score":0.616858959197998},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.6031107902526855},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.5793232321739197},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5277919173240662},{"id":"https://openalex.org/C69357855","wikidata":"https://www.wikidata.org/wiki/Q163214","display_name":"Diffusion","level":2,"score":0.4616512060165405},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3928396701812744},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3426651954650879},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.1876991093158722},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.09996464848518372},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.09337511658668518},{"id":"https://openalex.org/C71240020","wikidata":"https://www.wikidata.org/wiki/Q186011","display_name":"Stereochemistry","level":1,"score":0.09022372961044312},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.06525009870529175},{"id":"https://openalex.org/C35753019","wikidata":"https://www.wikidata.org/wiki/Q644785","display_name":"Total synthesis","level":2,"score":0.0},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"score":0.0},{"id":"https://openalex.org/C97355855","wikidata":"https://www.wikidata.org/wiki/Q11473","display_name":"Thermodynamics","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1609/aaai.v39i12.33373","is_oa":true,"landing_page_url":"https://doi.org/10.1609/aaai.v39i12.33373","pdf_url":"https://ojs.aaai.org/index.php/AAAI/article/download/33373/35528","source":{"id":"https://openalex.org/S4210191458","display_name":"Proceedings of the AAAI Conference on Artificial Intelligence","issn_l":"2159-5399","issn":["2159-5399","2374-3468"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/P4310320058","host_organization_name":"Association for the Advancement of Artificial Intelligence","host_organization_lineage":["https://openalex.org/P4310320058"],"host_organization_lineage_names":["Association for the Advancement of Artificial Intelligence"],"type":"conference"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the AAAI Conference on Artificial Intelligence","raw_type":"journal-article"}],"best_oa_location":{"id":"doi:10.1609/aaai.v39i12.33373","is_oa":true,"landing_page_url":"https://doi.org/10.1609/aaai.v39i12.33373","pdf_url":"https://ojs.aaai.org/index.php/AAAI/article/download/33373/35528","source":{"id":"https://openalex.org/S4210191458","display_name":"Proceedings of the AAAI Conference on Artificial Intelligence","issn_l":"2159-5399","issn":["2159-5399","2374-3468"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/P4310320058","host_organization_name":"Association for the Advancement of Artificial Intelligence","host_organization_lineage":["https://openalex.org/P4310320058"],"host_organization_lineage_names":["Association for the Advancement of Artificial Intelligence"],"type":"conference"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the AAAI Conference on Artificial Intelligence","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2802911279","display_name":null,"funder_award_id":"Young","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G37568934","display_name":null,"funder_award_id":"Grant","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G391238517","display_name":null,"funder_award_id":", and","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5760752404","display_name":null,"funder_award_id":"Projects","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G7033253288","display_name":null,"funder_award_id":"Grants","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320309893","display_name":"City University of Hong Kong","ror":"https://ror.org/03q8dnn23"},{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320335581","display_name":"Young Scientists Fund","ror":null}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4409365581.pdf","grobid_xml":"https://content.openalex.org/works/W4409365581.grobid-xml"},"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W1443743067","https://openalex.org/W4385784498","https://openalex.org/W4385842036","https://openalex.org/W4288371066","https://openalex.org/W4285670373","https://openalex.org/W2910734083","https://openalex.org/W3101473090","https://openalex.org/W4385784463","https://openalex.org/W4390658374","https://openalex.org/W4285584547"],"abstract_inverted_index":{"Retrosynthesis":[0],"prediction":[1,15],"focuses":[2],"on":[3,126],"identifying":[4],"reactants":[5],"capable":[6],"of":[7],"synthesizing":[8],"a":[9,70,138,151],"target":[10],"product.":[11],"Typically,":[12],"the":[13,37,47,54,62,92,99,106,121,127,130,133,147],"retrosynthesis":[14],"involves":[16],"two":[17,34,38],"phases:":[18,39],"Reaction":[19],"Center":[20],"Identification":[21],"and":[22,84],"Reactant":[23],"Generation.":[24],"However,":[25],"we":[26,95],"argue":[27],"that":[28,158],"most":[29],"existing":[30],"methods":[31],"suffer":[32],"from":[33],"limitations":[35],"in":[36,50,69,76,129,142],"(i)":[40],"Existing":[41],"models":[42,163],"do":[43],"not":[44],"adequately":[45],"capture":[46],"``face''":[48],"information":[49],"molecular":[51,116],"graphs":[52],"for":[53,61,80],"reaction":[55,100],"center":[56,101],"identification.":[57],"(ii)":[58],"Current":[59],"approaches":[60],"reactant":[63,134],"generation":[64,68],"predominantly":[65],"use":[66],"sequence":[67],"2D":[71],"space,":[72],"which":[73,118],"lacks":[74],"versatility":[75],"generating":[77],"reasonable":[78],"distributions":[79],"completed":[81],"reactive":[82],"groups":[83],"overlooks":[85],"molecules'":[86],"inherent":[87],"3D":[88,143],"properties.":[89],"To":[90],"overcome":[91],"above":[93],"limitations,":[94],"propose":[96],"GDiffRetro.":[97],"For":[98,132],"identification,":[102],"GDiffRetro":[103,136,159],"uniquely":[104],"integrates":[105],"original":[107],"graph":[108,113],"with":[109],"its":[110],"corresponding":[111],"dual":[112],"to":[114,123,144],"represent":[115],"structures,":[117],"helps":[119],"guide":[120],"model":[122,141],"focus":[124],"more":[125],"faces":[128],"graph.":[131],"generation,":[135],"employs":[137],"conditional":[139],"diffusion":[140],"further":[145],"transform":[146],"obtained":[148],"synthon":[149],"into":[150],"complete":[152],"reactant.":[153],"Our":[154],"experimental":[155],"findings":[156],"reveal":[157],"outperforms":[160],"state-of-the-art":[161],"semi-template":[162],"across":[164],"various":[165],"evaluative":[166],"metrics.":[167]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":2}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}