{"id":"https://openalex.org/W3137551757","doi":"https://doi.org/10.1093/bioinformatics/btab195","title":"FraGAT: a fragment-oriented multi-scale graph attention model for molecular property prediction","display_name":"FraGAT: a fragment-oriented multi-scale graph attention model for molecular property prediction","publication_year":2021,"publication_date":"2021-03-24","ids":{"openalex":"https://openalex.org/W3137551757","doi":"https://doi.org/10.1093/bioinformatics/btab195","mag":"3137551757","pmid":"https://pubmed.ncbi.nlm.nih.gov/33769437"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btab195","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab195","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/37/18/2981/40471415/btab195.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/37/18/2981/40471415/btab195.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5103007849","display_name":"Ziqiao Zhang","orcid":"https://orcid.org/0000-0003-3747-7673"},"institutions":[{"id":"https://openalex.org/I24943067","display_name":"Fudan University","ror":"https://ror.org/013q1eq08","country_code":"CN","type":"education","lineage":["https://openalex.org/I24943067"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Ziqiao Zhang","raw_affiliation_strings":["Shanghai Key Lab of Intelligent Information Processing, and School of Computer Science, Fudan University , Shanghai 200433, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Shanghai Key Lab of Intelligent Information Processing, and School of Computer Science, Fudan University , Shanghai 200433, China","institution_ids":["https://openalex.org/I24943067"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086316879","display_name":"Jihong Guan","orcid":"https://orcid.org/0000-0003-2313-7635"},"institutions":[{"id":"https://openalex.org/I116953780","display_name":"Tongji University","ror":"https://ror.org/03rc6as71","country_code":"CN","type":"education","lineage":["https://openalex.org/I116953780"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jihong Guan","raw_affiliation_strings":["Department of Computer Science and Technology, Tongji University , Shanghai 201804, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Technology, Tongji University , Shanghai 201804, China","institution_ids":["https://openalex.org/I116953780"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5017862559","display_name":"Shuigeng Zhou","orcid":"https://orcid.org/0000-0002-1949-2768"},"institutions":[{"id":"https://openalex.org/I24943067","display_name":"Fudan University","ror":"https://ror.org/013q1eq08","country_code":"CN","type":"education","lineage":["https://openalex.org/I24943067"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Shuigeng Zhou","raw_affiliation_strings":["Shanghai Key Lab of Intelligent Information Processing, and School of Computer Science, Fudan University , Shanghai 200433, China"],"raw_orcid":"https://orcid.org/0000-0002-1949-2768","affiliations":[{"raw_affiliation_string":"Shanghai Key Lab of Intelligent Information Processing, and School of Computer Science, Fudan University , Shanghai 200433, China","institution_ids":["https://openalex.org/I24943067"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5017862559"],"corresponding_institution_ids":["https://openalex.org/I24943067"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":6.3397,"has_fulltext":true,"cited_by_count":78,"citation_normalized_percentile":{"value":0.97091893,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":93,"max":100},"biblio":{"volume":"37","issue":"18","first_page":"2981","last_page":"2987"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9413999915122986,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9413999915122986,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11273","display_name":"Advanced Graph Neural Networks","score":0.020999999716877937,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.008200000040233135,"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/interpretability","display_name":"Interpretability","score":0.8229789733886719},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7283241152763367},{"id":"https://openalex.org/keywords/molecular-graph","display_name":"Molecular graph","score":0.579625129699707},{"id":"https://openalex.org/keywords/property","display_name":"Property (philosophy)","score":0.5652071237564087},{"id":"https://openalex.org/keywords/fragment","display_name":"Fragment (logic)","score":0.514712393283844},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.509769856929779},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.4584803581237793},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3590925931930542},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.30598950386047363},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.2854852080345154}],"concepts":[{"id":"https://openalex.org/C2781067378","wikidata":"https://www.wikidata.org/wiki/Q17027399","display_name":"Interpretability","level":2,"score":0.8229789733886719},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7283241152763367},{"id":"https://openalex.org/C2780022179","wikidata":"https://www.wikidata.org/wiki/Q1986794","display_name":"Molecular graph","level":3,"score":0.579625129699707},{"id":"https://openalex.org/C189950617","wikidata":"https://www.wikidata.org/wiki/Q937228","display_name":"Property (philosophy)","level":2,"score":0.5652071237564087},{"id":"https://openalex.org/C2776235265","wikidata":"https://www.wikidata.org/wiki/Q18392052","display_name":"Fragment (logic)","level":2,"score":0.514712393283844},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.509769856929779},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.4584803581237793},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3590925931930542},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.30598950386047363},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.2854852080345154},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","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}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btab195","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab195","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/37/18/2981/40471415/btab195.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:33769437","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33769437","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:europepmc.org:7375456","is_oa":true,"landing_page_url":"http://europepmc.org/pmc/articles/PMC8479684","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:8479684","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8479684","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btab195","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab195","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/37/18/2981/40471415/btab195.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1487418658","display_name":"\u5355\u7ec6\u80deRNA\u6d4b\u5e8f\u6570\u636e\u805a\u7c7b\u65b9\u6cd5\u7814\u7a76","funder_award_id":"61972100","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G2504302143","display_name":"\u57fa\u4e8e\u8ba1\u7b97\u7684\u86cb\u767d\u8d28\u590d\u5408\u7269\u68c0\u6d4b\u65b0\u65b9\u6cd5\u7814\u7a76","funder_award_id":"61772367","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G4924742943","display_name":null,"funder_award_id":"2016YFC0901704","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320335777","display_name":"National Key Research and Development Program of China","ror":null}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3137551757.pdf","grobid_xml":"https://content.openalex.org/works/W3137551757.grobid-xml"},"referenced_works_count":18,"referenced_works":["https://openalex.org/W2019926612","https://openalex.org/W2087155419","https://openalex.org/W2121776789","https://openalex.org/W2264719596","https://openalex.org/W2290847742","https://openalex.org/W2413828568","https://openalex.org/W2464219193","https://openalex.org/W2475259576","https://openalex.org/W2594183968","https://openalex.org/W2735246657","https://openalex.org/W2784213390","https://openalex.org/W2885020292","https://openalex.org/W2968734407","https://openalex.org/W2992586577","https://openalex.org/W3027099090","https://openalex.org/W3042595256","https://openalex.org/W3085717162","https://openalex.org/W3100157108"],"related_works":["https://openalex.org/W2905433371","https://openalex.org/W2888392564","https://openalex.org/W4310278675","https://openalex.org/W4388422664","https://openalex.org/W4390569940","https://openalex.org/W4361193272","https://openalex.org/W2963326959","https://openalex.org/W4388685194","https://openalex.org/W2013842271","https://openalex.org/W2808877228"],"abstract_inverted_index":{"MOTIVATION:":[0],"Molecular":[1],"property":[2,60,72,106],"prediction":[3],"is":[4,109],"a":[5,77,98],"hot":[6],"topic":[7],"in":[8,132,184],"recent":[9],"years.":[10],"Existing":[11],"graph-based":[12],"models":[13],"ignore":[14],"the":[15,22,28,68,142,147,153,166,169],"hierarchical":[16],"structures":[17],"of":[18,24,31,70,79,168],"molecules.":[19],"According":[20],"to":[21,36,48,66,93,120,145,161],"knowledge":[23],"chemistry":[25],"and":[26,40,164,177],"pharmacy,":[27],"functional":[29,56,88,151],"groups":[30,57],"molecules":[32],"are":[33,91,118,182,192],"closely":[34],"related":[35],"its":[37],"physio-chemical":[38],"properties":[39],"binding":[41],"affinities.":[42],"So,":[43],"it":[44],"should":[45],"be":[46,85],"helpful":[47],"represent":[49,146],"molecular":[50,59,94,105],"graphs":[51,149],"by":[52],"fragments":[53,82,143],"that":[54,83,126,140],"contain":[55,87,150],"for":[58,104],"prediction.":[61],"RESULTS:":[62],"In":[63],"this":[64,180],"article,":[65],"boost":[67],"performance":[69,131],"molecule":[71,80,148],"prediction,":[73,107],"we":[74],"first":[75],"propose":[76],"definition":[78],"graph":[81,101],"may":[84],"or":[86],"groups,":[89,152],"which":[90,108],"relevant":[92],"properties,":[95],"then":[96],"develop":[97],"fragment-oriented":[99],"multi-scale":[100],"attention":[102],"network":[103],"called":[110],"FraGAT.":[111,122],"Experiments":[112],"on":[113],"several":[114],"widely":[115],"used":[116,144],"benchmarks":[117],"conducted":[119],"evaluate":[121],"Experimental":[123],"results":[124],"show":[125,139],"FraGAT":[127],"achieves":[128],"state-of-the-art":[129],"predictive":[130],"most":[133],"cases.":[134],"Furthermore,":[135],"our":[136,162],"case":[137],"studies":[138],"when":[141],"model":[154],"can":[155],"make":[156],"better":[157],"predictions.":[158],"This":[159],"conforms":[160],"expectation":[163],"demonstrates":[165],"interpretability":[167],"proposed":[170],"model.":[171],"AVAILABILITY":[172],"AND":[173],"IMPLEMENTATION:":[174],"The":[175],"code":[176],"data":[178,191],"underlying":[179],"work":[181],"available":[183,193],"GitHub,":[185],"at":[186,194],"https://github.com/ZiqiaoZhang/FraGAT.":[187],"SUPPLEMENTARY":[188],"INFORMATION:":[189],"Supplementary":[190],"Bioinformatics":[195],"online.":[196]},"counts_by_year":[{"year":2026,"cited_by_count":9},{"year":2025,"cited_by_count":21},{"year":2024,"cited_by_count":12},{"year":2023,"cited_by_count":20},{"year":2022,"cited_by_count":14},{"year":2021,"cited_by_count":2}],"updated_date":"2026-07-30T17:31:21.811387","created_date":"2025-10-10T00:00:00"}
