{"id":"https://openalex.org/W4411742211","doi":"https://doi.org/10.1002/qub2.70008","title":"Graph transformer with disease subgraph positional encoding for improved comorbidity prediction","display_name":"Graph transformer with disease subgraph positional encoding for improved comorbidity prediction","publication_year":2025,"publication_date":"2025-06-26","ids":{"openalex":"https://openalex.org/W4411742211","doi":"https://doi.org/10.1002/qub2.70008","pmid":"https://pubmed.ncbi.nlm.nih.gov/41674718"},"language":"en","primary_location":{"id":"doi:10.1002/qub2.70008","is_oa":true,"landing_page_url":"https://doi.org/10.1002/qub2.70008","pdf_url":"https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/qub2.70008","source":{"id":"https://openalex.org/S4210172333","display_name":"Quantitative Biology","issn_l":"2095-4689","issn":["2095-4689","2095-4697"],"is_oa":true,"is_in_doaj":true,"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":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Quantitative Biology","raw_type":"journal-article"},"type":"article","indexed_in":["arxiv","crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/qub2.70008","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5029474278","display_name":"Xihan Qin","orcid":"https://orcid.org/0000-0003-1096-5941"},"institutions":[{"id":"https://openalex.org/I86501945","display_name":"University of Delaware","ror":"https://ror.org/01sbq1a82","country_code":"US","type":"education","lineage":["https://openalex.org/I86501945"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Xihan Qin","raw_affiliation_strings":["Department of Computer and Information Sciences University of Delaware  Newark Delaware USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer and Information Sciences University of Delaware  Newark Delaware USA","institution_ids":["https://openalex.org/I86501945"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5101595032","display_name":"Li Liao","orcid":"https://orcid.org/0000-0002-1197-1879"},"institutions":[{"id":"https://openalex.org/I86501945","display_name":"University of Delaware","ror":"https://ror.org/01sbq1a82","country_code":"US","type":"education","lineage":["https://openalex.org/I86501945"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Li Liao","raw_affiliation_strings":["Department of Computer and Information Sciences University of Delaware  Newark Delaware USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer and Information Sciences University of Delaware  Newark Delaware USA","institution_ids":["https://openalex.org/I86501945"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5029474278","https://openalex.org/A5101595032"],"corresponding_institution_ids":["https://openalex.org/I86501945"],"apc_list":{"value":1990,"currency":"USD","value_usd":1990},"apc_paid":{"value":1990,"currency":"USD","value_usd":1990},"fwci":0.4128,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.59264554,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":97},"biblio":{"volume":"13","issue":"4","first_page":"e70008","last_page":"e70008"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.991100013256073,"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"}},"topics":[{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.991100013256073,"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"}},{"id":"https://openalex.org/T11396","display_name":"Artificial Intelligence in Healthcare","score":0.9848999977111816,"subfield":{"id":"https://openalex.org/subfields/3605","display_name":"Health Information Management"},"field":{"id":"https://openalex.org/fields/36","display_name":"Health Professions"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.9445000290870667,"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/comorbidity","display_name":"Comorbidity","score":0.5230560898780823},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4999845027923584},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.4796919524669647},{"id":"https://openalex.org/keywords/transformer","display_name":"Transformer","score":0.45771756768226624},{"id":"https://openalex.org/keywords/induced-subgraph-isomorphism-problem","display_name":"Induced subgraph isomorphism problem","score":0.4532400965690613},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.20557233691215515},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.20306149125099182},{"id":"https://openalex.org/keywords/line-graph","display_name":"Line graph","score":0.1474350094795227},{"id":"https://openalex.org/keywords/voltage-graph","display_name":"Voltage graph","score":0.11159497499465942},{"id":"https://openalex.org/keywords/internal-medicine","display_name":"Internal medicine","score":0.08550107479095459},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.07941657304763794},{"id":"https://openalex.org/keywords/electrical-engineering","display_name":"Electrical engineering","score":0.05877774953842163}],"concepts":[{"id":"https://openalex.org/C2779159551","wikidata":"https://www.wikidata.org/wiki/Q1414874","display_name":"Comorbidity","level":2,"score":0.5230560898780823},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4999845027923584},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.4796919524669647},{"id":"https://openalex.org/C66322947","wikidata":"https://www.wikidata.org/wiki/Q11658","display_name":"Transformer","level":3,"score":0.45771756768226624},{"id":"https://openalex.org/C191241153","wikidata":"https://www.wikidata.org/wiki/Q6027240","display_name":"Induced subgraph isomorphism problem","level":5,"score":0.4532400965690613},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.20557233691215515},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.20306149125099182},{"id":"https://openalex.org/C203776342","wikidata":"https://www.wikidata.org/wiki/Q1378376","display_name":"Line graph","level":3,"score":0.1474350094795227},{"id":"https://openalex.org/C22149727","wikidata":"https://www.wikidata.org/wiki/Q7940747","display_name":"Voltage graph","level":4,"score":0.11159497499465942},{"id":"https://openalex.org/C126322002","wikidata":"https://www.wikidata.org/wiki/Q11180","display_name":"Internal medicine","level":1,"score":0.08550107479095459},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.07941657304763794},{"id":"https://openalex.org/C119599485","wikidata":"https://www.wikidata.org/wiki/Q43035","display_name":"Electrical engineering","level":1,"score":0.05877774953842163},{"id":"https://openalex.org/C165801399","wikidata":"https://www.wikidata.org/wiki/Q25428","display_name":"Voltage","level":2,"score":0.0}],"mesh":[],"locations_count":6,"locations":[{"id":"doi:10.1002/qub2.70008","is_oa":true,"landing_page_url":"https://doi.org/10.1002/qub2.70008","pdf_url":"https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/qub2.70008","source":{"id":"https://openalex.org/S4210172333","display_name":"Quantitative Biology","issn_l":"2095-4689","issn":["2095-4689","2095-4697"],"is_oa":true,"is_in_doaj":true,"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":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Quantitative Biology","raw_type":"journal-article"},{"id":"pmid:41674718","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41674718","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":"Quantitative biology (Beijing, China)","raw_type":null},{"id":"pmh:oai:arXiv.org:2503.03046","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2503.03046","pdf_url":"https://arxiv.org/pdf/2503.03046","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null},{"id":"pmh:oai:doaj.org/article:b7ce4e0b00d84f26b3f8d17bfe4d5cf3","is_oa":true,"landing_page_url":"https://doaj.org/article/b7ce4e0b00d84f26b3f8d17bfe4d5cf3","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":"Quantitative Biology, Vol 13, Iss 4, Pp n/a-n/a (2025)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:11693207","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12806012","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:12806012","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12806012/","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Quant Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1002/qub2.70008","is_oa":true,"landing_page_url":"https://doi.org/10.1002/qub2.70008","pdf_url":"https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/qub2.70008","source":{"id":"https://openalex.org/S4210172333","display_name":"Quantitative Biology","issn_l":"2095-4689","issn":["2095-4689","2095-4697"],"is_oa":true,"is_in_doaj":true,"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":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Quantitative Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320312559","display_name":"Sigma Xia","ror":"https://ror.org/04nmj5x57"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4411742211.pdf","grobid_xml":"https://content.openalex.org/works/W4411742211.grobid-xml"},"referenced_works_count":39,"referenced_works":["https://openalex.org/W134646214","https://openalex.org/W1543134559","https://openalex.org/W1966716734","https://openalex.org/W2001141328","https://openalex.org/W2004634778","https://openalex.org/W2056782561","https://openalex.org/W2109553965","https://openalex.org/W2141627824","https://openalex.org/W2152575748","https://openalex.org/W2162120660","https://openalex.org/W2750779823","https://openalex.org/W2801359717","https://openalex.org/W2822910560","https://openalex.org/W2962756421","https://openalex.org/W2994685918","https://openalex.org/W2997029448","https://openalex.org/W3013125498","https://openalex.org/W3028589594","https://openalex.org/W3038063455","https://openalex.org/W3043794926","https://openalex.org/W3113177135","https://openalex.org/W3119977957","https://openalex.org/W3126232929","https://openalex.org/W4206300474","https://openalex.org/W4213041764","https://openalex.org/W4224911270","https://openalex.org/W4241366218","https://openalex.org/W4293101460","https://openalex.org/W4297733535","https://openalex.org/W4310461505","https://openalex.org/W4312195044","https://openalex.org/W4324026004","https://openalex.org/W4367598041","https://openalex.org/W4380763457","https://openalex.org/W4385245566","https://openalex.org/W4390673439","https://openalex.org/W4392589742","https://openalex.org/W6739901393","https://openalex.org/W6745537798"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W231720905","https://openalex.org/W1978188354","https://openalex.org/W3141224953","https://openalex.org/W1482551403","https://openalex.org/W2155091457","https://openalex.org/W4240532399","https://openalex.org/W2765738011"],"abstract_inverted_index":{"Comorbidity,":[0],"the":[1,33,96,123,137],"co-occurrence":[2],"of":[3,98],"multiple":[4],"medical":[5],"conditions":[6],"in":[7,24,38,89],"a":[8],"single":[9],"patient,":[10],"profoundly":[11],"impacts":[12],"disease":[13,51,75],"management":[14],"and":[15,36,64,74,101,115,139,154],"outcomes.":[16,29],"Understanding":[17],"these":[18],"complex":[19,151],"interconnections":[20],"is":[21,159],"crucial,":[22],"especially":[23],"contexts":[25],"where":[26],"comorbidities":[27],"exacerbate":[28],"Leveraging":[30],"insights":[31],"from":[32],"human":[34],"interactome":[35],"advancements":[37],"graph-based":[39,152],"methodologies,":[40],"this":[41],"study":[42],"introduces":[43],"transformer":[44],"with":[45],"subgraph":[46,65],"positional":[47,66,85],"encoding":[48,67],"(TSPE)":[49],"for":[50,104,147],"comorbidity":[52],"prediction.":[53],"Inspired":[54],"by":[55],"biologically":[56],"supervised":[57],"embedding,":[58],"TSPE":[59,117],"employs":[60],"transformer's":[61],"attention":[62],"mechanisms":[63],"(SPE)":[68],"to":[69,128,149],"capture":[70],"interactions":[71],"between":[72],"nodes":[73],"associations.":[76],"Our":[77],"proposed":[78],"SPE":[79],"proves":[80],"more":[81],"effective":[82],"than":[83],"Laplacian":[84],"encoding,":[86],"as":[87],"used":[88],"Dwivedi":[90],"et":[91],"al.'s":[92],"graph":[93],"transformer,":[94],"underscoring":[95],"importance":[97],"integrating":[99],"clustering":[100],"disease-specific":[102],"information":[103],"improved":[105],"predictive":[106],"accuracy.":[107,142],"Evaluated":[108],"on":[109],"real":[110],"clinical":[111],"benchmark":[112],"datasets":[113],"(RR0":[114],"RR1),":[116],"demonstrates":[118],"substantial":[119],"performance":[120],"enhancements":[121],"over":[122],"state-of-the-art":[124],"method,":[125],"achieving":[126],"up":[127],"28.24%":[129],"higher":[130,141],"ROC":[131],"AUC":[132],"(receiver":[133],"operating":[134],"characteristic-area":[135],"under":[136],"curve)":[138],"4.93%":[140],"This":[143],"method":[144],"shows":[145],"promise":[146],"adaptation":[148],"other":[150],"tasks":[153],"applications.":[155],"The":[156],"source":[157],"code":[158],"available":[160],"at":[161],"GitHub":[162],"website":[163],"(xihan-qin/TSPE-GraphTransformer).":[164]},"counts_by_year":[{"year":2026,"cited_by_count":1}],"updated_date":"2026-07-29T09:40:50.615796","created_date":"2025-06-28T00:00:00"}
