{"id":"https://openalex.org/W4402643002","doi":"https://doi.org/10.1007/978-3-031-72381-0_7","title":"Atom-Level Quantum Pretraining Enhances the\u00a0Spectral Perception of\u00a0Molecular Graphs in\u00a0Graphormer","display_name":"Atom-Level Quantum Pretraining Enhances the\u00a0Spectral Perception of\u00a0Molecular Graphs in\u00a0Graphormer","publication_year":2024,"publication_date":"2024-09-19","ids":{"openalex":"https://openalex.org/W4402643002","doi":"https://doi.org/10.1007/978-3-031-72381-0_7"},"language":"en","primary_location":{"id":"doi:10.1007/978-3-031-72381-0_7","is_oa":true,"landing_page_url":"https://doi.org/10.1007/978-3-031-72381-0_7","pdf_url":"https://link.springer.com/content/pdf/10.1007/978-3-031-72381-0_7.pdf","source":{"id":"https://openalex.org/S106296714","display_name":"Lecture notes in computer science","issn_l":"0302-9743","issn":["0302-9743","1611-3349"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"book series"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Lecture Notes in Computer Science","raw_type":"book-chapter"},"type":"book-chapter","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://link.springer.com/content/pdf/10.1007/978-3-031-72381-0_7.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5086916366","display_name":"Alessio Fallani","orcid":"https://orcid.org/0009-0001-7857-5010"},"institutions":[{"id":"https://openalex.org/I137982388","display_name":"Janssen (Belgium)","ror":"https://ror.org/04yzcpd71","country_code":"BE","type":"company","lineage":["https://openalex.org/I1330063522","https://openalex.org/I137982388"]},{"id":"https://openalex.org/I186903577","display_name":"University of Luxembourg","ror":"https://ror.org/036x5ad56","country_code":"LU","type":"education","lineage":["https://openalex.org/I186903577"]}],"countries":["BE","LU"],"is_corresponding":true,"raw_author_name":"Alessio Fallani","raw_affiliation_strings":["Department of Physics and Materials Science, University of Luxembourg, 1511, Luxembourg City, Luxembourg","Drug Discovery Data Sciences, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Physics and Materials Science, University of Luxembourg, 1511, Luxembourg City, Luxembourg","institution_ids":["https://openalex.org/I186903577"]},{"raw_affiliation_string":"Drug Discovery Data Sciences, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium","institution_ids":["https://openalex.org/I137982388"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039286688","display_name":"Jose A. Arjona-Medina","orcid":"https://orcid.org/0000-0002-5033-4725"},"institutions":[{"id":"https://openalex.org/I137982388","display_name":"Janssen (Belgium)","ror":"https://ror.org/04yzcpd71","country_code":"BE","type":"company","lineage":["https://openalex.org/I1330063522","https://openalex.org/I137982388"]}],"countries":["BE"],"is_corresponding":false,"raw_author_name":"Jos\u00e9 Arjona-Medina","raw_affiliation_strings":["Drug Discovery Data Sciences, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Drug Discovery Data Sciences, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium","institution_ids":["https://openalex.org/I137982388"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076385603","display_name":"Konstantin Chernichenko","orcid":"https://orcid.org/0000-0002-6425-5075"},"institutions":[{"id":"https://openalex.org/I137982388","display_name":"Janssen (Belgium)","ror":"https://ror.org/04yzcpd71","country_code":"BE","type":"company","lineage":["https://openalex.org/I1330063522","https://openalex.org/I137982388"]}],"countries":["BE"],"is_corresponding":false,"raw_author_name":"Konstantin Chernichenko","raw_affiliation_strings":["Drug Discovery Data Sciences, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Drug Discovery Data Sciences, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium","institution_ids":["https://openalex.org/I137982388"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091636547","display_name":"Ramil Nugmanov","orcid":"https://orcid.org/0000-0002-8541-9681"},"institutions":[{"id":"https://openalex.org/I137982388","display_name":"Janssen (Belgium)","ror":"https://ror.org/04yzcpd71","country_code":"BE","type":"company","lineage":["https://openalex.org/I1330063522","https://openalex.org/I137982388"]}],"countries":["BE"],"is_corresponding":false,"raw_author_name":"Ramil Nugmanov","raw_affiliation_strings":["Drug Discovery Data Sciences, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Drug Discovery Data Sciences, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium","institution_ids":["https://openalex.org/I137982388"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081681147","display_name":"J\u00f6rg K. Wegner","orcid":"https://orcid.org/0000-0002-1852-9434"},"institutions":[{"id":"https://openalex.org/I1330063522","display_name":"Johnson & Johnson (United States)","ror":"https://ror.org/03qd7mz70","country_code":"US","type":"company","lineage":["https://openalex.org/I1330063522"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"J\u00f6rg Kurt Wegner","raw_affiliation_strings":["Johnson & Johnson Innovative Medicine, 301 Binney Street, Cambridge, MA, 02142, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Johnson & Johnson Innovative Medicine, 301 Binney Street, Cambridge, MA, 02142, USA","institution_ids":["https://openalex.org/I1330063522"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5026929463","display_name":"Alexandre Tkatchenko","orcid":"https://orcid.org/0000-0002-1012-4854"},"institutions":[{"id":"https://openalex.org/I186903577","display_name":"University of Luxembourg","ror":"https://ror.org/036x5ad56","country_code":"LU","type":"education","lineage":["https://openalex.org/I186903577"]}],"countries":["LU"],"is_corresponding":false,"raw_author_name":"Alexandre Tkatchenko","raw_affiliation_strings":["Department of Physics and Materials Science, University of Luxembourg, 1511, Luxembourg City, Luxembourg"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Physics and Materials Science, University of Luxembourg, 1511, Luxembourg City, Luxembourg","institution_ids":["https://openalex.org/I186903577"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5086916366"],"corresponding_institution_ids":["https://openalex.org/I137982388","https://openalex.org/I186903577"],"apc_list":{"value":5000,"currency":"EUR","value_usd":5392},"apc_paid":{"value":5000,"currency":"EUR","value_usd":5392},"fwci":2.1635,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":{"value":0.88047138,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":98},"biblio":{"volume":null,"issue":null,"first_page":"71","last_page":"81"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10083","display_name":"Graphene research and applications","score":0.9973000288009644,"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/T10083","display_name":"Graphene research and applications","score":0.9973000288009644,"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/T10913","display_name":"Molecular Junctions and Nanostructures","score":0.9973000288009644,"subfield":{"id":"https://openalex.org/subfields/2208","display_name":"Electrical and Electronic Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10682","display_name":"Quantum Computing Algorithms and Architecture","score":0.996999979019165,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6717227697372437},{"id":"https://openalex.org/keywords/atom","display_name":"Atom (system on chip)","score":0.6674165725708008},{"id":"https://openalex.org/keywords/quantum","display_name":"Quantum","score":0.599016547203064},{"id":"https://openalex.org/keywords/perception","display_name":"Perception","score":0.5942583084106445},{"id":"https://openalex.org/keywords/quantum-mechanics","display_name":"Quantum mechanics","score":0.2664257287979126},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.2304249405860901},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.1056462824344635},{"id":"https://openalex.org/keywords/psychology","display_name":"Psychology","score":0.1009635329246521},{"id":"https://openalex.org/keywords/neuroscience","display_name":"Neuroscience","score":0.08711349964141846}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6717227697372437},{"id":"https://openalex.org/C58312451","wikidata":"https://www.wikidata.org/wiki/Q4817200","display_name":"Atom (system on chip)","level":2,"score":0.6674165725708008},{"id":"https://openalex.org/C84114770","wikidata":"https://www.wikidata.org/wiki/Q46344","display_name":"Quantum","level":2,"score":0.599016547203064},{"id":"https://openalex.org/C26760741","wikidata":"https://www.wikidata.org/wiki/Q160402","display_name":"Perception","level":2,"score":0.5942583084106445},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.2664257287979126},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.2304249405860901},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.1056462824344635},{"id":"https://openalex.org/C15744967","wikidata":"https://www.wikidata.org/wiki/Q9418","display_name":"Psychology","level":0,"score":0.1009635329246521},{"id":"https://openalex.org/C169760540","wikidata":"https://www.wikidata.org/wiki/Q207011","display_name":"Neuroscience","level":1,"score":0.08711349964141846}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1007/978-3-031-72381-0_7","is_oa":true,"landing_page_url":"https://doi.org/10.1007/978-3-031-72381-0_7","pdf_url":"https://link.springer.com/content/pdf/10.1007/978-3-031-72381-0_7.pdf","source":{"id":"https://openalex.org/S106296714","display_name":"Lecture notes in computer science","issn_l":"0302-9743","issn":["0302-9743","1611-3349"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"book series"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Lecture Notes in Computer Science","raw_type":"book-chapter"}],"best_oa_location":{"id":"doi:10.1007/978-3-031-72381-0_7","is_oa":true,"landing_page_url":"https://doi.org/10.1007/978-3-031-72381-0_7","pdf_url":"https://link.springer.com/content/pdf/10.1007/978-3-031-72381-0_7.pdf","source":{"id":"https://openalex.org/S106296714","display_name":"Lecture notes in computer science","issn_l":"0302-9743","issn":["0302-9743","1611-3349"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"book series"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Lecture Notes in Computer Science","raw_type":"book-chapter"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G223242278","display_name":"Advanced machine learning for Innovative Drug Discovery","funder_award_id":"956832","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"}],"funders":[{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4402643002.pdf","grobid_xml":"https://content.openalex.org/works/W4402643002.grobid-xml"},"referenced_works_count":26,"referenced_works":["https://openalex.org/W2155184221","https://openalex.org/W2613900957","https://openalex.org/W2790808809","https://openalex.org/W2983997668","https://openalex.org/W3023204497","https://openalex.org/W3035422918","https://openalex.org/W3038008928","https://openalex.org/W3109892317","https://openalex.org/W3114339437","https://openalex.org/W3126732720","https://openalex.org/W3137459879","https://openalex.org/W3200120268","https://openalex.org/W3216996162","https://openalex.org/W4210852924","https://openalex.org/W4282053982","https://openalex.org/W4283836015","https://openalex.org/W4296551289","https://openalex.org/W4307717106","https://openalex.org/W4362503491","https://openalex.org/W4365455552","https://openalex.org/W4382657017","https://openalex.org/W4385767952","https://openalex.org/W4391568364","https://openalex.org/W4392344527","https://openalex.org/W4400396982","https://openalex.org/W6772452955"],"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":{"Abstract":[0],"This":[1],"study":[2],"explores":[3],"the":[4,20,28,43,46,64,87,112],"impact":[5],"of":[6,30,45,81],"pretraining":[7,37,55],"Graph":[8],"Transformers":[9],"using":[10,69],"atom-level":[11,101],"quantum-mechanical":[12],"features":[13],"for":[14,90],"molecular":[15,60,113],"property":[16],"modeling.":[17],"We":[18,49],"utilize":[19],"ADMET":[21],"Therapeutic":[22],"Data":[23],"Commons":[24],"datasets":[25],"to":[26,85],"evaluate":[27],"benefits":[29],"this":[31],"approach.":[32],"Our":[33,94],"results":[34],"show":[35],"that":[36,97],"on":[38,59,100,120],"quantum":[39,61,102],"atomic":[40],"properties":[41,62],"improves":[42],"performance":[44,92],"Graphormer":[47],"model.":[48],"conduct":[50],"comparisons":[51],"with":[52,117],"two":[53],"other":[54],"strategies:":[56],"one":[57],"based":[58],"(specifically":[63],"HOMO-LUMO":[65],"gap)":[66],"and":[67],"another":[68],"a":[70,78],"self-supervised":[71],"atom":[72],"masking":[73],"technique.":[74],"Additionally,":[75],"we":[76],"employ":[77],"spectral":[79],"analysis":[80],"Attention":[82],"Rollout":[83],"matrices":[84],"understand":[86],"underlying":[88],"reasons":[89],"these":[91],"enhancements.":[93],"findings":[95],"suggest":[96],"models":[98],"pretrained":[99],"mechanics":[103],"are":[104],"better":[105],"at":[106],"capturing":[107],"low-frequency":[108],"Laplacian":[109],"eigenmodes":[110],"from":[111],"graphs,":[114],"which":[115],"correlates":[116],"improved":[118],"outcomes":[119],"most":[121],"evaluated":[122],"downstream":[123],"tasks,":[124],"as":[125],"measured":[126],"by":[127],"our":[128],"custom":[129],"metric.":[130]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1}],"updated_date":"2026-06-22T08:00:12.763002","created_date":"2025-10-10T00:00:00"}
