{"id":"https://openalex.org/W4412605378","doi":"https://doi.org/10.1109/access.2025.3591966","title":"Graphormer Boosted: Molecular Property Prediction With Enhanced Graph Spatial and Edge Encodings","display_name":"Graphormer Boosted: Molecular Property Prediction With Enhanced Graph Spatial and Edge Encodings","publication_year":2025,"publication_date":"2025-01-01","ids":{"openalex":"https://openalex.org/W4412605378","doi":"https://doi.org/10.1109/access.2025.3591966"},"language":"en","primary_location":{"id":"doi:10.1109/access.2025.3591966","is_oa":true,"landing_page_url":"https://doi.org/10.1109/access.2025.3591966","pdf_url":null,"source":{"id":"https://openalex.org/S2485537415","display_name":"IEEE Access","issn_l":"2169-3536","issn":["2169-3536"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Access","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1109/access.2025.3591966","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5015441370","display_name":"Sarah Fadlallah","orcid":"https://orcid.org/0000-0003-0758-5913"},"institutions":[{"id":"https://openalex.org/I55952717","display_name":"Universitat Rovira i Virgili","ror":"https://ror.org/00g5sqv46","country_code":"ES","type":"education","lineage":["https://openalex.org/I55952717"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Sarah A. Fadlallah","raw_affiliation_strings":["Department of Enginyeria Inform&#x00E0;tica i Matem&#x00E0;tiques, Computer Engineering and Mathematics, Universitat Rovira i Virgili, Tarragona, Spain","Universitat Rovira i Virgili, Tarragona, Catalonia, Spain"],"raw_orcid":"https://orcid.org/0000-0003-0758-5913","affiliations":[{"raw_affiliation_string":"Department of Enginyeria Inform&#x00E0;tica i Matem&#x00E0;tiques, Computer Engineering and Mathematics, Universitat Rovira i Virgili, Tarragona, Spain","institution_ids":["https://openalex.org/I55952717"]},{"raw_affiliation_string":"Universitat Rovira i Virgili, Tarragona, Catalonia, Spain","institution_ids":["https://openalex.org/I55952717"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090033395","display_name":"Francesc Serratosa","orcid":"https://orcid.org/0000-0001-6112-5913"},"institutions":[{"id":"https://openalex.org/I55952717","display_name":"Universitat Rovira i Virgili","ror":"https://ror.org/00g5sqv46","country_code":"ES","type":"education","lineage":["https://openalex.org/I55952717"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Francesc Serratosa","raw_affiliation_strings":["Department of Enginyeria Inform&#x00E0;tica i Matem&#x00E0;tiques, Computer Engineering and Mathematics, Universitat Rovira i Virgili, Tarragona, Spain","Universitat Rovira i Virgili, Tarragona, Catalonia, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Enginyeria Inform&#x00E0;tica i Matem&#x00E0;tiques, Computer Engineering and Mathematics, Universitat Rovira i Virgili, Tarragona, Spain","institution_ids":["https://openalex.org/I55952717"]},{"raw_affiliation_string":"Universitat Rovira i Virgili, Tarragona, Catalonia, Spain","institution_ids":["https://openalex.org/I55952717"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5046999910","display_name":"Carme Juli\u00e0","orcid":"https://orcid.org/0000-0003-3440-6175"},"institutions":[{"id":"https://openalex.org/I55952717","display_name":"Universitat Rovira i Virgili","ror":"https://ror.org/00g5sqv46","country_code":"ES","type":"education","lineage":["https://openalex.org/I55952717"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Carme Juli\u00e0","raw_affiliation_strings":["Department of Enginyeria Inform&#x00E0;tica i Matem&#x00E0;tiques, Computer Engineering and Mathematics, Universitat Rovira i Virgili, Tarragona, Spain","Universitat Rovira i Virgili, Tarragona, Catalonia, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Enginyeria Inform&#x00E0;tica i Matem&#x00E0;tiques, Computer Engineering and Mathematics, Universitat Rovira i Virgili, Tarragona, Spain","institution_ids":["https://openalex.org/I55952717"]},{"raw_affiliation_string":"Universitat Rovira i Virgili, Tarragona, Catalonia, Spain","institution_ids":["https://openalex.org/I55952717"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I55952717"],"apc_list":{"value":1850,"currency":"USD","value_usd":1850},"apc_paid":{"value":1850,"currency":"USD","value_usd":1850},"fwci":2.9598,"has_fulltext":false,"cited_by_count":4,"citation_normalized_percentile":{"value":0.92048833,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":95,"max":98},"biblio":{"volume":"13","issue":null,"first_page":"130492","last_page":"130504"},"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":0.996999979019165,"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/T12327","display_name":"Various Chemistry Research Topics","score":0.9789999723434448,"subfield":{"id":"https://openalex.org/subfields/1606","display_name":"Physical and Theoretical Chemistry"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6658420562744141},{"id":"https://openalex.org/keywords/property","display_name":"Property (philosophy)","score":0.6177621483802795},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.5021054744720459},{"id":"https://openalex.org/keywords/enhanced-data-rates-for-gsm-evolution","display_name":"Enhanced Data Rates for GSM Evolution","score":0.4564180374145508},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.4078720211982727},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.37244948744773865}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6658420562744141},{"id":"https://openalex.org/C189950617","wikidata":"https://www.wikidata.org/wiki/Q937228","display_name":"Property (philosophy)","level":2,"score":0.6177621483802795},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.5021054744720459},{"id":"https://openalex.org/C162307627","wikidata":"https://www.wikidata.org/wiki/Q204833","display_name":"Enhanced Data Rates for GSM Evolution","level":2,"score":0.4564180374145508},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.4078720211982727},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.37244948744773865},{"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":[],"locations_count":2,"locations":[{"id":"doi:10.1109/access.2025.3591966","is_oa":true,"landing_page_url":"https://doi.org/10.1109/access.2025.3591966","pdf_url":null,"source":{"id":"https://openalex.org/S2485537415","display_name":"IEEE Access","issn_l":"2169-3536","issn":["2169-3536"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Access","raw_type":"journal-article"},{"id":"pmh:oai:doaj.org/article:37952647cfbf43bda3c643a138b0e8dd","is_oa":true,"landing_page_url":"https://doaj.org/article/37952647cfbf43bda3c643a138b0e8dd","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"IEEE Access, Vol 13, Pp 130492-130504 (2025)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1109/access.2025.3591966","is_oa":true,"landing_page_url":"https://doi.org/10.1109/access.2025.3591966","pdf_url":null,"source":{"id":"https://openalex.org/S2485537415","display_name":"IEEE Access","issn_l":"2169-3536","issn":["2169-3536"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Access","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":46,"referenced_works":["https://openalex.org/W1975147762","https://openalex.org/W2007572995","https://openalex.org/W2008505552","https://openalex.org/W2076498053","https://openalex.org/W2116341502","https://openalex.org/W2940939841","https://openalex.org/W2990045899","https://openalex.org/W3080863822","https://openalex.org/W3113177135","https://openalex.org/W3152893301","https://openalex.org/W3155314443","https://openalex.org/W3169499336","https://openalex.org/W3188579603","https://openalex.org/W4200301490","https://openalex.org/W4206482253","https://openalex.org/W4210292100","https://openalex.org/W4220857054","https://openalex.org/W4220980941","https://openalex.org/W4281706128","https://openalex.org/W4312333792","https://openalex.org/W4372267124","https://openalex.org/W4376226279","https://openalex.org/W4385245566","https://openalex.org/W4385895548","https://openalex.org/W4387623751","https://openalex.org/W4389519899","https://openalex.org/W4391855109","https://openalex.org/W4391881499","https://openalex.org/W4396749103","https://openalex.org/W4396834978","https://openalex.org/W4400269519","https://openalex.org/W4400672326","https://openalex.org/W4401691948","https://openalex.org/W4402191334","https://openalex.org/W6695676441","https://openalex.org/W6726873649","https://openalex.org/W6734561206","https://openalex.org/W6745265922","https://openalex.org/W6763700448","https://openalex.org/W6783944145","https://openalex.org/W6796768152","https://openalex.org/W6796801894","https://openalex.org/W6802810016","https://openalex.org/W6850204008","https://openalex.org/W6851318867","https://openalex.org/W6870293747"],"related_works":["https://openalex.org/W2582753012","https://openalex.org/W4300101497","https://openalex.org/W2962977872","https://openalex.org/W2379797514","https://openalex.org/W2391763874","https://openalex.org/W2036456628","https://openalex.org/W2391530279","https://openalex.org/W3188962172","https://openalex.org/W2052899165","https://openalex.org/W2008562718"],"abstract_inverted_index":{"Transformer-based":[0],"architectures":[1,35],"have":[2],"gained":[3],"popularity":[4],"across":[5],"various":[6],"domains,":[7],"including":[8],"graph":[9,54,138,182,199,209],"representation":[10,210],"learning.":[11,211],"However,":[12],"selecting":[13],"an":[14,61],"optimal":[15],"transformer":[16],"configuration":[17],"remains":[18],"challenging,":[19],"as":[20],"attention-based":[21],"models":[22],"are":[23],"highly":[24],"sensitive":[25],"to":[26,63,90,122,131],"parameter":[27],"choices":[28],"and":[29,78,125,128,151,157],"input":[30],"value":[31,110],"ranges.":[32,111],"Even":[33],"state-of-the-art":[34],"can":[36,46],"underperform":[37],"without":[38],"proper":[39],"tuning,":[40],"while":[41],"simple":[42,203],"yet":[43,204],"thoughtful":[44],"modifications":[45],"unlock":[47],"significant":[48],"performance":[49,165],"gains":[50],"by":[51,72,108],"better":[52],"leveraging":[53],"structures.":[55],"In":[56],"this":[57],"work,":[58],"we":[59,82],"propose":[60],"enhancement":[62],"the":[64,69,95,137,146,149,153,168,172],"Graphormer":[65],"architecture":[66],"that":[67,188],"refines":[68],"attention":[70,96],"mechanism":[71],"unifying":[73],"spatial":[74,124],"encodings,":[75,77],"edge":[76,126],"similarity":[79],"matrices.":[80],"Specifically,":[81],"introduce":[83],"nonlinear":[84,191],"transformations,":[85],"such":[86],"assoftmax,":[87],"sigmoid,":[88],"ortanh,":[89],"normalize":[91],"these":[92],"encodings":[93,127,195],"within":[94,136],"calculation.":[97],"This":[98],"ensures":[99],"balanced":[100],"contributions":[101],"from":[102],"all":[103],"terms,":[104],"mitigating":[105],"drawbacks":[106],"caused":[107],"disparate":[109],"We":[112],"explore":[113],"two":[114],"main":[115],"approaches:":[116],"(1)":[117],"element-wise":[118],"application":[119],"of":[120,148,155,174],"nonlinearities":[121],"bound":[123],"(2)":[129],"row-wisesoftmaxnormalization":[130],"emphasize":[132],"their":[133],"relative":[134],"importance":[135],"structure.":[139],"The":[140],"latter":[141],"preserves":[142],"relational":[143],"information,":[144],"enhancing":[145],"expressiveness":[147],"model":[150,179],"improving":[152],"prioritization":[154],"node":[156],"edge.":[158],"Experiments":[159],"on":[160],"molecular":[161],"datasets":[162],"demonstrate":[163],"consistent":[164],"improvements":[166],"over":[167,193],"baseline":[169],"Graphormer,":[170],"highlighting":[171],"effectiveness":[173],"our":[175,178],"approach.":[176],"Additionally,":[177],"outperforms":[180],"traditional":[181],"learning":[183],"models.":[184],"Our":[185],"findings":[186],"suggest":[187],"carefully":[189],"designed":[190],"transformations":[192],"structural":[194],"significantly":[196],"boost":[197],"transformer-based":[198],"models,":[200],"offering":[201],"a":[202],"powerful":[205],"strategy":[206],"for":[207],"improved":[208]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":2}],"updated_date":"2026-08-02T14:50:37.381335","created_date":"2025-10-10T00:00:00"}
