{"id":"https://openalex.org/W4210313485","doi":"https://doi.org/10.1093/bioinformatics/btac039","title":"Cross-dependent graph neural networks for molecular property prediction","display_name":"Cross-dependent graph neural networks for molecular property prediction","publication_year":2022,"publication_date":"2022-01-25","ids":{"openalex":"https://openalex.org/W4210313485","doi":"https://doi.org/10.1093/bioinformatics/btac039","pmid":"https://pubmed.ncbi.nlm.nih.gov/35094072"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btac039","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac039","pdf_url":null,"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":null,"license_id":null,"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":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5078917190","display_name":"Hehuan Ma","orcid":"https://orcid.org/0000-0002-5971-0053"},"institutions":[{"id":"https://openalex.org/I189196454","display_name":"The University of Texas at Arlington","ror":"https://ror.org/019kgqr73","country_code":"US","type":"education","lineage":["https://openalex.org/I189196454"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Hehuan Ma","raw_affiliation_strings":["Department of Computer Science, University of Texas at Arlington , Arlington 76019, USA"],"raw_orcid":"https://orcid.org/0000-0002-5971-0053","affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Texas at Arlington , Arlington 76019, USA","institution_ids":["https://openalex.org/I189196454"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045777220","display_name":"Yatao Bian","orcid":"https://orcid.org/0000-0002-2368-4084"},"institutions":[{"id":"https://openalex.org/I2250653659","display_name":"Tencent (China)","ror":"https://ror.org/00hhjss72","country_code":"CN","type":"company","lineage":["https://openalex.org/I2250653659"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yatao Bian","raw_affiliation_strings":["AI Lab, Tencent , Shenzhen 518057, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"AI Lab, Tencent , Shenzhen 518057, China","institution_ids":["https://openalex.org/I2250653659"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100767600","display_name":"Yu Rong","orcid":"https://orcid.org/0000-0001-7387-302X"},"institutions":[{"id":"https://openalex.org/I2250653659","display_name":"Tencent (China)","ror":"https://ror.org/00hhjss72","country_code":"CN","type":"company","lineage":["https://openalex.org/I2250653659"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yu Rong","raw_affiliation_strings":["AI Lab, Tencent , Shenzhen 518057, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"AI Lab, Tencent , Shenzhen 518057, China","institution_ids":["https://openalex.org/I2250653659"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032642601","display_name":"Wenbing Huang","orcid":"https://orcid.org/0000-0002-2566-4159"},"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":"Wenbing Huang","raw_affiliation_strings":["Institute for AI Industry Research, Tsinghua University , Beijing 100084, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for AI Industry Research, Tsinghua University , Beijing 100084, China","institution_ids":["https://openalex.org/I99065089"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005345630","display_name":"Tingyang Xu","orcid":"https://orcid.org/0000-0002-8487-9045"},"institutions":[{"id":"https://openalex.org/I2250653659","display_name":"Tencent (China)","ror":"https://ror.org/00hhjss72","country_code":"CN","type":"company","lineage":["https://openalex.org/I2250653659"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Tingyang Xu","raw_affiliation_strings":["AI Lab, Tencent , Shenzhen 518057, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"AI Lab, Tencent , Shenzhen 518057, China","institution_ids":["https://openalex.org/I2250653659"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007120124","display_name":"Weiyang Xie","orcid":null},"institutions":[{"id":"https://openalex.org/I2250653659","display_name":"Tencent (China)","ror":"https://ror.org/00hhjss72","country_code":"CN","type":"company","lineage":["https://openalex.org/I2250653659"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Weiyang Xie","raw_affiliation_strings":["AI Lab, Tencent , Shenzhen 518057, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"AI Lab, Tencent , Shenzhen 518057, China","institution_ids":["https://openalex.org/I2250653659"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5068720367","display_name":"Geyan Ye","orcid":null},"institutions":[{"id":"https://openalex.org/I2250653659","display_name":"Tencent (China)","ror":"https://ror.org/00hhjss72","country_code":"CN","type":"company","lineage":["https://openalex.org/I2250653659"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Geyan Ye","raw_affiliation_strings":["AI Lab, Tencent , Shenzhen 518057, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"AI Lab, Tencent , Shenzhen 518057, China","institution_ids":["https://openalex.org/I2250653659"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5068865316","display_name":"Junzhou Huang","orcid":"https://orcid.org/0000-0002-9548-1227"},"institutions":[{"id":"https://openalex.org/I189196454","display_name":"The University of Texas at Arlington","ror":"https://ror.org/019kgqr73","country_code":"US","type":"education","lineage":["https://openalex.org/I189196454"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Junzhou Huang","raw_affiliation_strings":["Department of Computer Science, University of Texas at Arlington , Arlington 76019, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Texas at Arlington , Arlington 76019, USA","institution_ids":["https://openalex.org/I189196454"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5068865316"],"corresponding_institution_ids":["https://openalex.org/I189196454"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":8.5182,"has_fulltext":false,"cited_by_count":79,"citation_normalized_percentile":{"value":0.9809324,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":100},"biblio":{"volume":"38","issue":"7","first_page":"2003","last_page":"2009"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11273","display_name":"Advanced Graph Neural Networks","score":0.6880999803543091,"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"}},"topics":[{"id":"https://openalex.org/T11273","display_name":"Advanced Graph Neural Networks","score":0.6880999803543091,"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/T11948","display_name":"Machine Learning in Materials Science","score":0.14259999990463257,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.11079999804496765,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/interpretability","display_name":"Interpretability","score":0.8296927213668823},{"id":"https://openalex.org/keywords/exploit","display_name":"Exploit","score":0.820372462272644},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8059223294258118},{"id":"https://openalex.org/keywords/expressive-power","display_name":"Expressive power","score":0.6496520042419434},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.550832211971283},{"id":"https://openalex.org/keywords/molecular-graph","display_name":"Molecular graph","score":0.5412871241569519},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.528901994228363},{"id":"https://openalex.org/keywords/node","display_name":"Node (physics)","score":0.5235024094581604},{"id":"https://openalex.org/keywords/property","display_name":"Property (philosophy)","score":0.48724380135536194},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.48244744539260864},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.47748303413391113},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.4749600887298584},{"id":"https://openalex.org/keywords/graph-isomorphism","display_name":"Graph isomorphism","score":0.4444868266582489},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.38289177417755127},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.10789299011230469},{"id":"https://openalex.org/keywords/line-graph","display_name":"Line graph","score":0.1073373556137085}],"concepts":[{"id":"https://openalex.org/C2781067378","wikidata":"https://www.wikidata.org/wiki/Q17027399","display_name":"Interpretability","level":2,"score":0.8296927213668823},{"id":"https://openalex.org/C165696696","wikidata":"https://www.wikidata.org/wiki/Q11287","display_name":"Exploit","level":2,"score":0.820372462272644},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8059223294258118},{"id":"https://openalex.org/C195818886","wikidata":"https://www.wikidata.org/wiki/Q5421724","display_name":"Expressive power","level":2,"score":0.6496520042419434},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.550832211971283},{"id":"https://openalex.org/C2780022179","wikidata":"https://www.wikidata.org/wiki/Q1986794","display_name":"Molecular graph","level":3,"score":0.5412871241569519},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.528901994228363},{"id":"https://openalex.org/C62611344","wikidata":"https://www.wikidata.org/wiki/Q1062658","display_name":"Node (physics)","level":2,"score":0.5235024094581604},{"id":"https://openalex.org/C189950617","wikidata":"https://www.wikidata.org/wiki/Q937228","display_name":"Property (philosophy)","level":2,"score":0.48724380135536194},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.48244744539260864},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.47748303413391113},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.4749600887298584},{"id":"https://openalex.org/C61665672","wikidata":"https://www.wikidata.org/wiki/Q303100","display_name":"Graph isomorphism","level":4,"score":0.4444868266582489},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.38289177417755127},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.10789299011230469},{"id":"https://openalex.org/C203776342","wikidata":"https://www.wikidata.org/wiki/Q1378376","display_name":"Line graph","level":3,"score":0.1073373556137085},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0},{"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},{"id":"https://openalex.org/C38652104","wikidata":"https://www.wikidata.org/wiki/Q3510521","display_name":"Computer security","level":1,"score":0.0},{"id":"https://openalex.org/C66938386","wikidata":"https://www.wikidata.org/wiki/Q633538","display_name":"Structural engineering","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btac039","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac039","pdf_url":null,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:35094072","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35094072","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}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G7363998610","display_name":"Digital Pathology Analysis for Lung Cancer Patient Care","funder_award_id":"RP190107","funder_id":"https://openalex.org/F4320308129","funder_display_name":"Cancer Prevention and Research Institute of Texas"},{"id":"https://openalex.org/G8434690768","display_name":"CAREER: Large Scale Learning for Complex Image-Omics Data Analytics","funder_award_id":"1553687","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320308129","display_name":"Cancer Prevention and Research Institute of Texas","ror":"https://ror.org/0003xa228"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":36,"referenced_works":["https://openalex.org/W1780364926","https://openalex.org/W2009867031","https://openalex.org/W2010700988","https://openalex.org/W2024046085","https://openalex.org/W2093882311","https://openalex.org/W2177317049","https://openalex.org/W2290847742","https://openalex.org/W2473190403","https://openalex.org/W2590019597","https://openalex.org/W2594183968","https://openalex.org/W2606780347","https://openalex.org/W2726670313","https://openalex.org/W2946750843","https://openalex.org/W2962711740","https://openalex.org/W2962876364","https://openalex.org/W2964113829","https://openalex.org/W2966357564","https://openalex.org/W2968734407","https://openalex.org/W2977595407","https://openalex.org/W2987522751","https://openalex.org/W2997128522","https://openalex.org/W3095883070","https://openalex.org/W3100157108","https://openalex.org/W3166604846","https://openalex.org/W4285584547","https://openalex.org/W4297733535","https://openalex.org/W4300537282","https://openalex.org/W6685350579","https://openalex.org/W6736685754","https://openalex.org/W6754929296","https://openalex.org/W6756816090","https://openalex.org/W6770257887","https://openalex.org/W6772677771","https://openalex.org/W6784614190","https://openalex.org/W6784819614","https://openalex.org/W6796306279"],"related_works":["https://openalex.org/W2905433371","https://openalex.org/W2888392564","https://openalex.org/W4310278675","https://openalex.org/W4388422664","https://openalex.org/W2960216239","https://openalex.org/W2785816923","https://openalex.org/W4288282901","https://openalex.org/W3042133669","https://openalex.org/W3097737864","https://openalex.org/W4210313485"],"abstract_inverted_index":{"MOTIVATION:":[0],"The":[1,135,197],"crux":[2],"of":[3,12,39,120,132,148,154,178,192],"molecular":[4,22,85],"property":[5],"prediction":[6],"is":[7,18,91,97,138],"to":[8,19,47,69,109,128],"generate":[9],"meaningful":[10],"representations":[11],"the":[13,21,36,63,94,100,117,146,149,168,179,189],"molecules.":[14],"One":[15],"promising":[16],"route":[17],"exploit":[20,48],"graph":[23,26],"structure":[24],"through":[25],"neural":[27],"networks":[28],"(GNNs).":[29],"Both":[30],"atoms":[31,78],"and":[32,52,79,93,199],"bonds":[33,80],"significantly":[34],"affect":[35],"chemical":[37],"properties":[38],"a":[40,71,124],"molecule,":[41],"so":[42],"an":[43],"expressive":[44,118],"model":[45,151],"ought":[46],"both":[49,77],"node":[50,180],"(atom)":[51],"edge":[53],"(bond)":[54],"information":[55,130],"simultaneously.":[56],"Inspired":[57],"by":[58],"this":[59,202],"observation,":[60],"we":[61,122],"explore":[62],"multi-view":[64],"modeling":[65],"with":[66,184],"GNN":[67],"(MVGNN)":[68],"form":[70],"novel":[72],"paralleled":[73],"framework,":[74],"which":[75,187],"considers":[76],"equally":[81],"important":[82],"when":[83],"learning":[84],"representations.":[86],"In":[87],"specific,":[88],"one":[89],"view":[90,96],"atom-central":[92],"other":[95],"bond-central,":[98],"then":[99],"two":[101],"views":[102],"are":[103,182,204,214],"circulated":[104],"via":[105],"specifically":[106],"designed":[107],"components":[108],"enable":[110],"more":[111],"accurate":[112],"predictions.":[113],"To":[114],"further":[115],"enhance":[116,129],"power":[119,191],"MVGNN,":[121],"propose":[123],"cross-dependent":[125],"message-passing":[126],"scheme":[127],"communication":[131],"different":[133],"views.":[134],"overall":[136],"framework":[137],"termed":[139],"as":[140],"CD-MVGNN.":[141,193],"RESULTS:":[142],"We":[143],"theoretically":[144],"justify":[145],"expressiveness":[147],"proposed":[150],"in":[152,206],"terms":[153],"distinguishing":[155],"non-isomorphism":[156],"graphs.":[157],"Extensive":[158],"experiments":[159],"demonstrate":[160],"that":[161],"CD-MVGNN":[162],"achieves":[163],"remarkably":[164],"superior":[165],"performance":[166],"over":[167],"state-of-the-art":[169],"models":[170],"on":[171],"various":[172],"challenging":[173],"benchmarks.":[174],"Meanwhile,":[175],"visualization":[176],"results":[177],"importance":[181],"consistent":[183],"prior":[185],"knowledge,":[186],"confirms":[188],"interpretability":[190],"AVAILABILITY":[194],"AND":[195],"IMPLEMENTATION:":[196],"code":[198],"data":[200,213],"underlying":[201],"work":[203],"available":[205,215],"GitHub":[207],"at":[208,216],"https://github.com/uta-smile/CD-MVGNN.":[209],"SUPPLEMENTARY":[210],"INFORMATION:":[211],"Supplementary":[212],"Bioinformatics":[217],"online.":[218]},"counts_by_year":[{"year":2026,"cited_by_count":5},{"year":2025,"cited_by_count":21},{"year":2024,"cited_by_count":26},{"year":2023,"cited_by_count":20},{"year":2022,"cited_by_count":6},{"year":2021,"cited_by_count":1}],"updated_date":"2026-08-08T01:25:22.217667","created_date":"2025-10-10T00:00:00"}