{"id":"https://openalex.org/W4401185818","doi":"https://doi.org/10.1089/cmb.2023.0452","title":"A Hybrid GNN Approach for Improved Molecular Property Prediction","display_name":"A Hybrid GNN Approach for Improved Molecular Property Prediction","publication_year":2024,"publication_date":"2024-07-31","ids":{"openalex":"https://openalex.org/W4401185818","doi":"https://doi.org/10.1089/cmb.2023.0452","pmid":"https://pubmed.ncbi.nlm.nih.gov/39082155"},"language":"en","primary_location":{"id":"doi:10.1089/cmb.2023.0452","is_oa":false,"landing_page_url":"https://doi.org/10.1089/cmb.2023.0452","pdf_url":null,"source":{"id":"https://openalex.org/S78571599","display_name":"Journal of Computational Biology","issn_l":"1066-5277","issn":["1066-5277","1557-8666"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320443","host_organization_name":"Mary Ann Liebert, Inc.","host_organization_lineage":["https://openalex.org/P4310320443"],"host_organization_lineage_names":["Mary Ann Liebert, Inc."],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","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/A5105966947","display_name":"Pedro Quesado","orcid":null},"institutions":[{"id":"https://openalex.org/I76903346","display_name":"University of Coimbra","ror":"https://ror.org/04z8k9a98","country_code":"PT","type":"education","lineage":["https://openalex.org/I76903346"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"Pedro Quesado","raw_affiliation_strings":["Department of Informatics Engineering, Centre for Informatics and Systems of the University of Coimbra, Univ Coimbra, Coimbra, Portugal"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Informatics Engineering, Centre for Informatics and Systems of the University of Coimbra, Univ Coimbra, Coimbra, Portugal","institution_ids":["https://openalex.org/I76903346"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047602372","display_name":"Luis H.M. Torres","orcid":"https://orcid.org/0000-0002-9243-680X"},"institutions":[{"id":"https://openalex.org/I76903346","display_name":"University of Coimbra","ror":"https://ror.org/04z8k9a98","country_code":"PT","type":"education","lineage":["https://openalex.org/I76903346"]}],"countries":["PT"],"is_corresponding":true,"raw_author_name":"Luis H.M. Torres","raw_affiliation_strings":["Department of Informatics Engineering, Centre for Informatics and Systems of the University of Coimbra, Univ Coimbra, Coimbra, Portugal"],"raw_orcid":"https://orcid.org/0000-0002-9243-680X","affiliations":[{"raw_affiliation_string":"Department of Informatics Engineering, Centre for Informatics and Systems of the University of Coimbra, Univ Coimbra, Coimbra, Portugal","institution_ids":["https://openalex.org/I76903346"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046882659","display_name":"Bernardete Ribeiro","orcid":"https://orcid.org/0000-0002-9770-7672"},"institutions":[{"id":"https://openalex.org/I76903346","display_name":"University of Coimbra","ror":"https://ror.org/04z8k9a98","country_code":"PT","type":"education","lineage":["https://openalex.org/I76903346"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"Bernardete Ribeiro","raw_affiliation_strings":["Department of Informatics Engineering, Centre for Informatics and Systems of the University of Coimbra, Univ Coimbra, Coimbra, Portugal"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Informatics Engineering, Centre for Informatics and Systems of the University of Coimbra, Univ Coimbra, Coimbra, Portugal","institution_ids":["https://openalex.org/I76903346"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5043572862","display_name":"Joel P. Arrais","orcid":"https://orcid.org/0000-0003-4937-2334"},"institutions":[{"id":"https://openalex.org/I76903346","display_name":"University of Coimbra","ror":"https://ror.org/04z8k9a98","country_code":"PT","type":"education","lineage":["https://openalex.org/I76903346"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"Joel P. Arrais","raw_affiliation_strings":["Department of Informatics Engineering, Centre for Informatics and Systems of the University of Coimbra, Univ Coimbra, Coimbra, Portugal"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Informatics Engineering, Centre for Informatics and Systems of the University of Coimbra, Univ Coimbra, Coimbra, Portugal","institution_ids":["https://openalex.org/I76903346"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5047602372"],"corresponding_institution_ids":["https://openalex.org/I76903346"],"apc_list":null,"apc_paid":null,"fwci":2.0175,"has_fulltext":false,"cited_by_count":7,"citation_normalized_percentile":{"value":0.87867586,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"31","issue":"11","first_page":"1146","last_page":"1157"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9998000264167786,"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":0.9998000264167786,"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/T11948","display_name":"Machine Learning in Materials Science","score":0.9995999932289124,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9894000291824341,"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/property","display_name":"Property (philosophy)","score":0.644180953502655},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4588286578655243},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.40292495489120483},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.36747997999191284},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.29135367274284363}],"concepts":[{"id":"https://openalex.org/C189950617","wikidata":"https://www.wikidata.org/wiki/Q937228","display_name":"Property (philosophy)","level":2,"score":0.644180953502655},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4588286578655243},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.40292495489120483},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.36747997999191284},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.29135367274284363},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","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}],"mesh":[{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"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":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1089/cmb.2023.0452","is_oa":false,"landing_page_url":"https://doi.org/10.1089/cmb.2023.0452","pdf_url":null,"source":{"id":"https://openalex.org/S78571599","display_name":"Journal of Computational Biology","issn_l":"1066-5277","issn":["1066-5277","1557-8666"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320443","host_organization_name":"Mary Ann Liebert, Inc.","host_organization_lineage":["https://openalex.org/P4310320443"],"host_organization_lineage_names":["Mary Ann Liebert, Inc."],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computational Biology","raw_type":"journal-article"},{"id":"pmid:39082155","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39082155","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":"Journal of computational biology : a journal of computational molecular cell biology","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":31,"referenced_works":["https://openalex.org/W26940188","https://openalex.org/W1972978214","https://openalex.org/W1975147762","https://openalex.org/W2024741523","https://openalex.org/W2064675550","https://openalex.org/W2131036894","https://openalex.org/W2152158712","https://openalex.org/W2154088065","https://openalex.org/W2161381512","https://openalex.org/W2161782568","https://openalex.org/W2166550586","https://openalex.org/W2594183968","https://openalex.org/W2606780347","https://openalex.org/W2735246657","https://openalex.org/W2895884529","https://openalex.org/W2937307539","https://openalex.org/W2962711740","https://openalex.org/W2964015378","https://openalex.org/W2964321699","https://openalex.org/W2966357564","https://openalex.org/W3003257820","https://openalex.org/W3096561213","https://openalex.org/W3110901318","https://openalex.org/W3116202926","https://openalex.org/W3130891725","https://openalex.org/W3134958209","https://openalex.org/W3152893301","https://openalex.org/W4294558607","https://openalex.org/W4319320230","https://openalex.org/W4385245566","https://openalex.org/W4394642372"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W4396696052","https://openalex.org/W2382290278","https://openalex.org/W4395014643"],"abstract_inverted_index":{"The":[0,180,224],"development":[1,44],"of":[2,55,108,128],"new":[3],"drugs":[4],"is":[5,24],"a":[6,25,52,68,106,159,185],"vital":[7],"effort":[8],"that":[9,162,190,214],"has":[10,134],"the":[11,126,220,231,236],"potential":[12,36],"to":[13,34,72,75,92,116,167,175,195,212,229],"improve":[14],"human":[15],"health,":[16],"well-being":[17],"and":[18,49,111,171,226],"life":[19],"expectancy.":[20],"Molecular":[21],"property":[22,201],"prediction":[23],"crucial":[26],"step":[27],"in":[28,79,143,152,184,235],"drug":[29,43,95],"discovery,":[30],"as":[31,67,105,150],"it":[32],"helps":[33],"identify":[35,76,93],"therapeutic":[37],"compounds.":[38],"However,":[39],"experimental":[40],"methods":[41,64,102,166],"for":[42,120,199],"can":[45],"often":[46],"be":[47],"time-consuming":[48],"resource-intensive,":[50],"with":[51,97],"low":[53],"probability":[54],"success.":[56],"To":[57],"address":[58],"such":[59],"limitations,":[60],"deep":[61],"learning":[62],"(DL)":[63],"have":[65],"emerged":[66],"viable":[69],"alternative":[70],"due":[71],"their":[73,169,173],"ability":[74],"high-discriminating":[77],"patterns":[78],"molecular":[80,99,121,178,200],"data.":[81],"In":[82,154],"particular,":[83],"graph":[84,122,197],"neural":[85],"networks":[86],"(GNNs)":[87],"operate":[88],"on":[89,208],"graph-structured":[90],"data":[91,225],"promising":[94],"candidates":[96],"desirable":[98],"properties.":[100,179],"These":[101],"represent":[103],"molecules":[104],"set":[107],"node":[109],"(atoms)":[110],"edge":[112],"(chemical":[113],"bonds)":[114],"features":[115],"aggregate":[117],"local":[118],"information":[119],"representation":[123],"learning.":[124],"Despite":[125],"availability":[127],"several":[129],"GNN":[130,188,193],"frameworks,":[131],"each":[132],"approach":[133,161,182,217],"its":[135],"own":[136],"shortcomings.":[137],"Although,":[138],"some":[139],"GNNs":[140],"may":[141,147],"excel":[142],"certain":[144],"tasks,":[145],"they":[146],"not":[148],"perform":[149],"well":[151],"others.":[153],"this":[155],"work,":[156],"we":[157,204],"propose":[158],"hybrid":[160,187,216],"incorporates":[163],"different":[164],"graph-based":[165,222],"combine":[168],"strengths":[170],"mitigate":[172],"limitations":[174],"accurately":[176],"predict":[177],"proposed":[181],"consists":[183],"multi-layered":[186],"architecture":[189],"integrates":[191],"multiple":[192,209],"frameworks":[194],"compute":[196],"embeddings":[198],"prediction.":[202],"Furthermore,":[203],"conduct":[205],"extensive":[206],"experiments":[207],"benchmark":[210],"datasets":[211],"demonstrate":[213],"our":[215],"significantly":[218],"outperforms":[219],"state-of-the-art":[221],"models.":[223],"code":[227],"scripts":[228],"reproduce":[230],"results":[232],"are":[233],"available":[234],"repository,":[237],"https://github.com/pedro-quesado/HybridGNN.":[238]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":1}],"updated_date":"2026-06-14T06:11:07.267592","created_date":"2025-10-10T00:00:00"}
