{"id":"https://openalex.org/W7138209035","doi":"https://doi.org/10.1609/aaai.v40i1.36980","title":"Topology-Enhanced and Label Correlation-Aware Model for Protein-Protein Interaction Prediction","display_name":"Topology-Enhanced and Label Correlation-Aware Model for Protein-Protein Interaction Prediction","publication_year":2026,"publication_date":"2026-03-14","ids":{"openalex":"https://openalex.org/W7138209035","doi":"https://doi.org/10.1609/aaai.v40i1.36980"},"language":"en","primary_location":{"id":"doi:10.1609/aaai.v40i1.36980","is_oa":true,"landing_page_url":"https://doi.org/10.1609/aaai.v40i1.36980","pdf_url":null,"source":{"id":"https://openalex.org/S4210191458","display_name":"Proceedings of the AAAI Conference on Artificial Intelligence","issn_l":"2159-5399","issn":["2159-5399","2374-3468"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/P4310320058","host_organization_name":"Association for the Advancement of Artificial Intelligence","host_organization_lineage":["https://openalex.org/P4310320058"],"host_organization_lineage_names":["Association for the Advancement of Artificial Intelligence"],"type":"conference"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the AAAI Conference on Artificial Intelligence","raw_type":"journal-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"diamond","oa_url":"https://doi.org/10.1609/aaai.v40i1.36980","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5129738904","display_name":"Bin Deng","orcid":null},"institutions":[{"id":"https://openalex.org/I68986083","display_name":"Northwest Normal University","ror":"https://ror.org/00gx3j908","country_code":"CN","type":"education","lineage":["https://openalex.org/I68986083"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Bin Deng","raw_affiliation_strings":["Northwest Normal University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Northwest Normal University","institution_ids":["https://openalex.org/I68986083"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5129711219","display_name":"Huifang Ma","orcid":null},"institutions":[{"id":"https://openalex.org/I68986083","display_name":"Northwest Normal University","ror":"https://ror.org/00gx3j908","country_code":"CN","type":"education","lineage":["https://openalex.org/I68986083"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Huifang Ma","raw_affiliation_strings":["Northwest Normal University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Northwest Normal University","institution_ids":["https://openalex.org/I68986083"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102521405","display_name":"Ruijia Zhang","orcid":null},"institutions":[{"id":"https://openalex.org/I68986083","display_name":"Northwest Normal University","ror":"https://ror.org/00gx3j908","country_code":"CN","type":"education","lineage":["https://openalex.org/I68986083"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Ruijia Zhang","raw_affiliation_strings":["Northwest Normal University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Northwest Normal University","institution_ids":["https://openalex.org/I68986083"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024179471","display_name":"Meihuizi Jia","orcid":"https://orcid.org/0009-0003-5624-9980"},"institutions":[{"id":"https://openalex.org/I68986083","display_name":"Northwest Normal University","ror":"https://ror.org/00gx3j908","country_code":"CN","type":"education","lineage":["https://openalex.org/I68986083"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Meihuizi Jia","raw_affiliation_strings":["Northwest Normal University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Northwest Normal University","institution_ids":["https://openalex.org/I68986083"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5129729321","display_name":"Rui Bing","orcid":null},"institutions":[{"id":"https://openalex.org/I68986083","display_name":"Northwest Normal University","ror":"https://ror.org/00gx3j908","country_code":"CN","type":"education","lineage":["https://openalex.org/I68986083"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Rui Bing","raw_affiliation_strings":["Northwest Normal University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Northwest Normal University","institution_ids":["https://openalex.org/I68986083"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I68986083"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.33043478,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"40","issue":"1","first_page":"202","last_page":"210"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.8729000091552734,"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":0.8729000091552734,"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/T11273","display_name":"Advanced Graph Neural Networks","score":0.044199999421834946,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.03840000182390213,"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/smoothing","display_name":"Smoothing","score":0.5059000253677368},{"id":"https://openalex.org/keywords/limiting","display_name":"Limiting","score":0.4819999933242798},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.45809999108314514},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.445499986410141},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.4343999922275543},{"id":"https://openalex.org/keywords/interaction-network","display_name":"Interaction network","score":0.38280001282691956},{"id":"https://openalex.org/keywords/interaction-information","display_name":"Interaction information","score":0.3677999973297119},{"id":"https://openalex.org/keywords/data-modeling","display_name":"Data modeling","score":0.3402999937534332}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.697700023651123},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.5827999711036682},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5752999782562256},{"id":"https://openalex.org/C3770464","wikidata":"https://www.wikidata.org/wiki/Q775963","display_name":"Smoothing","level":2,"score":0.5059000253677368},{"id":"https://openalex.org/C188198153","wikidata":"https://www.wikidata.org/wiki/Q1613840","display_name":"Limiting","level":2,"score":0.4819999933242798},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.45809999108314514},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.445499986410141},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.4343999922275543},{"id":"https://openalex.org/C55105296","wikidata":"https://www.wikidata.org/wiki/Q841382","display_name":"Interaction network","level":3,"score":0.38280001282691956},{"id":"https://openalex.org/C38764148","wikidata":"https://www.wikidata.org/wiki/Q17098245","display_name":"Interaction information","level":2,"score":0.3677999973297119},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.36559998989105225},{"id":"https://openalex.org/C67186912","wikidata":"https://www.wikidata.org/wiki/Q367664","display_name":"Data modeling","level":2,"score":0.3402999937534332},{"id":"https://openalex.org/C2781067378","wikidata":"https://www.wikidata.org/wiki/Q17027399","display_name":"Interpretability","level":2,"score":0.3393000066280365},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.33090001344680786},{"id":"https://openalex.org/C2776482837","wikidata":"https://www.wikidata.org/wiki/Q3553958","display_name":"Multi-label classification","level":2,"score":0.3188999891281128},{"id":"https://openalex.org/C59404180","wikidata":"https://www.wikidata.org/wiki/Q17013334","display_name":"Feature learning","level":2,"score":0.30230000615119934},{"id":"https://openalex.org/C2776145971","wikidata":"https://www.wikidata.org/wiki/Q30673951","display_name":"Labeled data","level":2,"score":0.2944999933242798},{"id":"https://openalex.org/C11804247","wikidata":"https://www.wikidata.org/wiki/Q896177","display_name":"Protein\u2013protein interaction","level":2,"score":0.28380000591278076},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.2784999907016754},{"id":"https://openalex.org/C51632099","wikidata":"https://www.wikidata.org/wiki/Q3985153","display_name":"Training set","level":2,"score":0.2687999904155731},{"id":"https://openalex.org/C104122410","wikidata":"https://www.wikidata.org/wiki/Q1416406","display_name":"Network model","level":2,"score":0.2572000026702881},{"id":"https://openalex.org/C155846161","wikidata":"https://www.wikidata.org/wiki/Q1143367","display_name":"Graphical model","level":2,"score":0.251800000667572}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1609/aaai.v40i1.36980","is_oa":true,"landing_page_url":"https://doi.org/10.1609/aaai.v40i1.36980","pdf_url":null,"source":{"id":"https://openalex.org/S4210191458","display_name":"Proceedings of the AAAI Conference on Artificial Intelligence","issn_l":"2159-5399","issn":["2159-5399","2374-3468"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/P4310320058","host_organization_name":"Association for the Advancement of Artificial Intelligence","host_organization_lineage":["https://openalex.org/P4310320058"],"host_organization_lineage_names":["Association for the Advancement of Artificial Intelligence"],"type":"conference"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the AAAI Conference on Artificial Intelligence","raw_type":"journal-article"},{"id":"pmh:oai:ojs.aaai.org:article/36980","is_oa":false,"landing_page_url":"https://ojs.aaai.org/index.php/AAAI/article/view/36980","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"2159-5399","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1609/aaai.v40i1.36980","is_oa":true,"landing_page_url":"https://doi.org/10.1609/aaai.v40i1.36980","pdf_url":null,"source":{"id":"https://openalex.org/S4210191458","display_name":"Proceedings of the AAAI Conference on Artificial Intelligence","issn_l":"2159-5399","issn":["2159-5399","2374-3468"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/P4310320058","host_organization_name":"Association for the Advancement of Artificial Intelligence","host_organization_lineage":["https://openalex.org/P4310320058"],"host_organization_lineage_names":["Association for the Advancement of Artificial Intelligence"],"type":"conference"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the AAAI Conference on Artificial Intelligence","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":[],"abstract_inverted_index":{"Protein-Protein":[0],"Interactions":[1],"(PPIs)":[2],"prediction":[3,79],"is":[4],"crucial":[5],"for":[6,54,94],"understanding":[7],"cellular":[8],"functions":[9],"and":[10,90,114,140],"disease":[11],"mechanisms.":[12],"Existing":[13],"deep":[14],"learning\u2013based":[15],"methods":[16],"primarily":[17],"rely":[18],"on":[19,137],"direct":[20],"interaction":[21,69],"within":[22],"the":[23,35,43,65,107,111,115,130,154],"PPI":[24,78,112],"network":[25,113],"to":[26,62],"update":[27],"protein":[28],"representations.":[29],"However,":[30],"(1)":[31],"such":[32],"networks":[33],"overlook":[34],"potential":[36],"associations":[37],"between":[38],"functionally":[39],"similar":[40,55,102],"proteins,":[41],"limiting":[42],"smoothing":[44],"capability":[45],"of":[46,110,118,132,156],"Graph":[47],"Neural":[48],"Networks":[49],"(GNNs)":[50],"in":[51,77],"learning":[52,131],"representations":[53],"nodes.":[56],"(2)":[57],"Additionally,":[58],"most":[59],"approaches":[60],"fail":[61],"adequately":[63],"model":[64,93,158],"latent":[66],"dependencies":[67],"among":[68],"types":[70],"(edge":[71],"labels),":[72],"which":[73],"hinders":[74],"their":[75],"performance":[76],"tasks.":[80],"To":[81],"address":[82],"these":[83],"limitations,":[84],"we":[85],"propose":[86],"TELC-PPI,":[87],"a":[88],"topology-enhanced":[89],"label":[91,116,126,133],"correlation-aware":[92],"protein-protein":[95],"interactions":[96],"prediction.":[97],"Specifically,":[98],"TELC-PPI":[99,148],"first":[100],"identifies":[101],"proteins":[103],"by":[104],"leveraging":[105],"both":[106],"topological":[108],"information":[109],"distributions":[117],"nodes,":[119],"constructing":[120],"similarity":[121],"edges.":[122],"Then,":[123],"it":[124],"incorporates":[125],"co-occurrence":[127],"statistics":[128],"into":[129],"embeddings.":[134],"Experimental":[135],"results":[136],"multiple":[138],"datasets":[139],"under":[141],"various":[142],"data":[143],"split":[144],"settings":[145],"demonstrate":[146],"that":[147],"significantly":[149],"outperforms":[150],"existing":[151],"methods,":[152],"validating":[153],"effectiveness":[155],"our":[157],"design.":[159]},"counts_by_year":[],"updated_date":"2026-07-02T09:51:11.867554","created_date":"2026-03-18T00:00:00"}