{"id":"https://openalex.org/W4385768160","doi":"https://doi.org/10.24963/ijcai.2023/554","title":"SemiGNN-PPI: Self-Ensembling Multi-Graph Neural Network for Efficient and Generalizable Protein\u2013Protein Interaction Prediction","display_name":"SemiGNN-PPI: Self-Ensembling Multi-Graph Neural Network for Efficient and Generalizable Protein\u2013Protein Interaction Prediction","publication_year":2023,"publication_date":"2023-08-01","ids":{"openalex":"https://openalex.org/W4385768160","doi":"https://doi.org/10.24963/ijcai.2023/554"},"language":"en","primary_location":{"id":"doi:10.24963/ijcai.2023/554","is_oa":true,"landing_page_url":"https://doi.org/10.24963/ijcai.2023/554","pdf_url":"https://www.ijcai.org/proceedings/2023/0554.pdf","source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the Thirty-Second International Joint Conference on Artificial Intelligence","raw_type":"proceedings-article"},"type":"conference-paper","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://www.ijcai.org/proceedings/2023/0554.pdf","any_repository_has_fulltext":null},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5050743199","display_name":"Ziyuan Zhao","orcid":"https://orcid.org/0000-0002-4403-825X"},"institutions":[{"id":"https://openalex.org/I115228651","display_name":"Agency for Science, Technology and Research","ror":"https://ror.org/036wvzt09","country_code":"SG","type":"government","lineage":["https://openalex.org/I115228651"]},{"id":"https://openalex.org/I172675005","display_name":"Nanyang Technological University","ror":"https://ror.org/02e7b5302","country_code":"SG","type":"education","lineage":["https://openalex.org/I172675005"]},{"id":"https://openalex.org/I3005327000","display_name":"Institute for Infocomm Research","ror":"https://ror.org/053rfa017","country_code":"SG","type":"facility","lineage":["https://openalex.org/I115228651","https://openalex.org/I3005327000","https://openalex.org/I91275662"]}],"countries":["SG"],"is_corresponding":false,"raw_author_name":"Ziyuan Zhao","raw_affiliation_strings":["Institute for Infocomm Research (I2R), A*STAR, Singapore","School of Computer Science and Engineering (SCSE), Nanyang Technological University, Singapore","Institute for Infocomm Research (I2R), A*STAR, Singapore; School of Computer Science and Engineering (SCSE), Nanyang Technological University, Singapore"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Infocomm Research (I2R), A*STAR, Singapore","institution_ids":["https://openalex.org/I3005327000","https://openalex.org/I115228651"]},{"raw_affiliation_string":"School of Computer Science and Engineering (SCSE), Nanyang Technological University, Singapore","institution_ids":["https://openalex.org/I172675005"]},{"raw_affiliation_string":"Institute for Infocomm Research (I2R), A*STAR, Singapore; School of Computer Science and Engineering (SCSE), Nanyang Technological University, Singapore","institution_ids":["https://openalex.org/I3005327000","https://openalex.org/I172675005","https://openalex.org/I115228651"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5018528574","display_name":"Peisheng Qian","orcid":null},"institutions":[{"id":"https://openalex.org/I115228651","display_name":"Agency for Science, Technology and Research","ror":"https://ror.org/036wvzt09","country_code":"SG","type":"government","lineage":["https://openalex.org/I115228651"]},{"id":"https://openalex.org/I3005327000","display_name":"Institute for Infocomm Research","ror":"https://ror.org/053rfa017","country_code":"SG","type":"facility","lineage":["https://openalex.org/I115228651","https://openalex.org/I3005327000","https://openalex.org/I91275662"]}],"countries":["SG"],"is_corresponding":false,"raw_author_name":"Peisheng Qian","raw_affiliation_strings":["Institute for Infocomm Research (I2R), A*STAR, Singapore"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Infocomm Research (I2R), A*STAR, Singapore","institution_ids":["https://openalex.org/I3005327000","https://openalex.org/I115228651"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5104272403","display_name":"Xulei Yang","orcid":null},"institutions":[{"id":"https://openalex.org/I115228651","display_name":"Agency for Science, Technology and Research","ror":"https://ror.org/036wvzt09","country_code":"SG","type":"government","lineage":["https://openalex.org/I115228651"]},{"id":"https://openalex.org/I3005327000","display_name":"Institute for Infocomm Research","ror":"https://ror.org/053rfa017","country_code":"SG","type":"facility","lineage":["https://openalex.org/I115228651","https://openalex.org/I3005327000","https://openalex.org/I91275662"]}],"countries":["SG"],"is_corresponding":false,"raw_author_name":"Xulei Yang","raw_affiliation_strings":["Institute for Infocomm Research (I2R), A*STAR, Singapore"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Infocomm Research (I2R), A*STAR, Singapore","institution_ids":["https://openalex.org/I3005327000","https://openalex.org/I115228651"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5010092389","display_name":"Zeng Zeng","orcid":"https://orcid.org/0000-0002-2405-0323"},"institutions":[{"id":"https://openalex.org/I113940042","display_name":"Shanghai University","ror":"https://ror.org/006teas31","country_code":"CN","type":"education","lineage":["https://openalex.org/I113940042"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zeng Zeng","raw_affiliation_strings":["School of Microelectronics, Shanghai University, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Microelectronics, Shanghai University, China","institution_ids":["https://openalex.org/I113940042"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031778999","display_name":"Cuntai Guan","orcid":"https://orcid.org/0000-0002-0872-3276"},"institutions":[{"id":"https://openalex.org/I172675005","display_name":"Nanyang Technological University","ror":"https://ror.org/02e7b5302","country_code":"SG","type":"education","lineage":["https://openalex.org/I172675005"]}],"countries":["SG"],"is_corresponding":false,"raw_author_name":"Cuntai Guan","raw_affiliation_strings":["School of Computer Science and Engineering (SCSE), Nanyang Technological University, Singapore"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering (SCSE), Nanyang Technological University, Singapore","institution_ids":["https://openalex.org/I172675005"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081808759","display_name":"Wai Leong Tam","orcid":"https://orcid.org/0000-0003-2365-5264"},"institutions":[{"id":"https://openalex.org/I115228651","display_name":"Agency for Science, Technology and Research","ror":"https://ror.org/036wvzt09","country_code":"SG","type":"government","lineage":["https://openalex.org/I115228651"]},{"id":"https://openalex.org/I66068411","display_name":"Genome Institute of Singapore","ror":"https://ror.org/05k8wg936","country_code":"SG","type":"facility","lineage":["https://openalex.org/I115228651","https://openalex.org/I2801752549","https://openalex.org/I66068411"]}],"countries":["SG"],"is_corresponding":false,"raw_author_name":"Wai Leong Tam","raw_affiliation_strings":["Genome Institute of Singapore (GIS), A*STAR, Singapore"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Genome Institute of Singapore (GIS), A*STAR, Singapore","institution_ids":["https://openalex.org/I66068411","https://openalex.org/I115228651"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100418684","display_name":"Xiaoli Li","orcid":"https://orcid.org/0000-0002-0762-6562"},"institutions":[{"id":"https://openalex.org/I115228651","display_name":"Agency for Science, Technology and Research","ror":"https://ror.org/036wvzt09","country_code":"SG","type":"government","lineage":["https://openalex.org/I115228651"]},{"id":"https://openalex.org/I172675005","display_name":"Nanyang Technological University","ror":"https://ror.org/02e7b5302","country_code":"SG","type":"education","lineage":["https://openalex.org/I172675005"]},{"id":"https://openalex.org/I3005327000","display_name":"Institute for Infocomm Research","ror":"https://ror.org/053rfa017","country_code":"SG","type":"facility","lineage":["https://openalex.org/I115228651","https://openalex.org/I3005327000","https://openalex.org/I91275662"]}],"countries":["SG"],"is_corresponding":false,"raw_author_name":"Xiaoli Li","raw_affiliation_strings":["Institute for Infocomm Research (I2R), A*STAR, Singapore","School of Computer Science and Engineering (SCSE), Nanyang Technological University, Singapore","Institute for Infocomm Research (I2R), A*STAR, Singapore; School of Computer Science and Engineering (SCSE), Nanyang Technological University, Singapore"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Infocomm Research (I2R), A*STAR, Singapore","institution_ids":["https://openalex.org/I3005327000","https://openalex.org/I115228651"]},{"raw_affiliation_string":"School of Computer Science and Engineering (SCSE), Nanyang Technological University, Singapore","institution_ids":["https://openalex.org/I172675005"]},{"raw_affiliation_string":"Institute for Infocomm Research (I2R), A*STAR, Singapore; School of Computer Science and Engineering (SCSE), Nanyang Technological University, Singapore","institution_ids":["https://openalex.org/I3005327000","https://openalex.org/I172675005","https://openalex.org/I115228651"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":33,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"4984","last_page":"4992"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9994000196456909,"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":0.9994000196456909,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9983999729156494,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9879999756813049,"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/computer-science","display_name":"Computer science","score":0.7557693719863892},{"id":"https://openalex.org/keywords/leverage","display_name":"Leverage (statistics)","score":0.6765157580375671},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.6110798716545105},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.5839183330535889},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5644354224205017},{"id":"https://openalex.org/keywords/embedding","display_name":"Embedding","score":0.5006754398345947},{"id":"https://openalex.org/keywords/graph-embedding","display_name":"Graph embedding","score":0.4575561285018921},{"id":"https://openalex.org/keywords/labeled-data","display_name":"Labeled data","score":0.4475817382335663},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.41369736194610596},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3403671979904175},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.2592485547065735}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7557693719863892},{"id":"https://openalex.org/C153083717","wikidata":"https://www.wikidata.org/wiki/Q6535263","display_name":"Leverage (statistics)","level":2,"score":0.6765157580375671},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.6110798716545105},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.5839183330535889},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5644354224205017},{"id":"https://openalex.org/C41608201","wikidata":"https://www.wikidata.org/wiki/Q980509","display_name":"Embedding","level":2,"score":0.5006754398345947},{"id":"https://openalex.org/C75564084","wikidata":"https://www.wikidata.org/wiki/Q5597085","display_name":"Graph embedding","level":3,"score":0.4575561285018921},{"id":"https://openalex.org/C2776145971","wikidata":"https://www.wikidata.org/wiki/Q30673951","display_name":"Labeled data","level":2,"score":0.4475817382335663},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.41369736194610596},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3403671979904175},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.2592485547065735}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.24963/ijcai.2023/554","is_oa":true,"landing_page_url":"https://doi.org/10.24963/ijcai.2023/554","pdf_url":"https://www.ijcai.org/proceedings/2023/0554.pdf","source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the Thirty-Second International Joint Conference on Artificial Intelligence","raw_type":"proceedings-article"}],"best_oa_location":{"id":"doi:10.24963/ijcai.2023/554","is_oa":true,"landing_page_url":"https://doi.org/10.24963/ijcai.2023/554","pdf_url":"https://www.ijcai.org/proceedings/2023/0554.pdf","source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the Thirty-Second International Joint Conference on Artificial Intelligence","raw_type":"proceedings-article"},"sustainable_development_goals":[{"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3","score":0.6200000047683716}],"awards":[{"id":"https://openalex.org/G7037342858","display_name":null,"funder_award_id":"NRF-CRP22-2019-0003","funder_id":"https://openalex.org/F4320320709","funder_display_name":"National Research Foundation Singapore"}],"funders":[{"id":"https://openalex.org/F4320320671","display_name":"National Research Foundation","ror":"https://ror.org/05s0g1g46"},{"id":"https://openalex.org/F4320320709","display_name":"National Research Foundation Singapore","ror":"https://ror.org/03cpyc314"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4385768160.pdf"},"referenced_works_count":64,"referenced_works":["https://openalex.org/W20514746","https://openalex.org/W2029476889","https://openalex.org/W2037036397","https://openalex.org/W2043568498","https://openalex.org/W2047998870","https://openalex.org/W2075337064","https://openalex.org/W2100070946","https://openalex.org/W2120973253","https://openalex.org/W2145427519","https://openalex.org/W2152705149","https://openalex.org/W2163296115","https://openalex.org/W2340382781","https://openalex.org/W2342374505","https://openalex.org/W2405065882","https://openalex.org/W2519887557","https://openalex.org/W2592691248","https://openalex.org/W2616246685","https://openalex.org/W2618265628","https://openalex.org/W2885583144","https://openalex.org/W2890911678","https://openalex.org/W2900569176","https://openalex.org/W2932399282","https://openalex.org/W2944400536","https://openalex.org/W2951970475","https://openalex.org/W2953070460","https://openalex.org/W2957436444","https://openalex.org/W2962711740","https://openalex.org/W2963745697","https://openalex.org/W2964015378","https://openalex.org/W2970449868","https://openalex.org/W2971013993","https://openalex.org/W2971476302","https://openalex.org/W2987385519","https://openalex.org/W2990202188","https://openalex.org/W2993761465","https://openalex.org/W2998420437","https://openalex.org/W3045012301","https://openalex.org/W3095602948","https://openalex.org/W3099289621","https://openalex.org/W3101215053","https://openalex.org/W3109774165","https://openalex.org/W3162102484","https://openalex.org/W3167014763","https://openalex.org/W3189432583","https://openalex.org/W3196463692","https://openalex.org/W3200982107","https://openalex.org/W3205749498","https://openalex.org/W4280557428","https://openalex.org/W4281795839","https://openalex.org/W4285198992","https://openalex.org/W4296293027","https://openalex.org/W4306168172","https://openalex.org/W4308237662","https://openalex.org/W4310266072","https://openalex.org/W6644479924","https://openalex.org/W6755811877","https://openalex.org/W6759363029","https://openalex.org/W6764051988","https://openalex.org/W6785623580","https://openalex.org/W6791858558","https://openalex.org/W6803771590","https://openalex.org/W6863994431","https://openalex.org/W6864014924","https://openalex.org/W6864487941"],"related_works":["https://openalex.org/W2129767422","https://openalex.org/W3210196349","https://openalex.org/W4214728004","https://openalex.org/W2950181282","https://openalex.org/W3036264823","https://openalex.org/W3206528106","https://openalex.org/W2912814903","https://openalex.org/W2798287483","https://openalex.org/W2123605750","https://openalex.org/W2088740331"],"abstract_inverted_index":{"Protein-protein":[0],"interactions":[1],"(PPIs)":[2],"are":[3],"crucial":[4],"in":[5,94,131,172],"various":[6,36],"biological":[7],"processes":[8],"and":[9,18,41,64,82,92,128,181],"their":[10],"study":[11],"has":[12],"significant":[13,27],"implications":[14],"for":[15,113],"drug":[16],"development":[17],"disease":[19],"diagnosis.":[20],"Existing":[21],"deep":[22],"learning":[23,97],"methods":[24],"suffer":[25],"from":[26,86,143],"performance":[28],"degradation":[29],"under":[30],"complex":[31],"real-world":[32],"scenarios":[33,174],"due":[34],"to":[35,106,124,140],"factors,":[37],"e.g.,":[38],"label":[39,78],"scarcity":[40],"domain":[42],"shift.":[43],"In":[44,66],"this":[45],"paper,":[46],"we":[47,68],"propose":[48],"a":[49],"self-ensembling":[50],"multi-graph":[51],"neural":[52],"network":[53],"(SemiGNN-PPI)":[54],"that":[55,164],"can":[56],"effectively":[57,107],"predict":[58],"PPIs":[59],"while":[60],"being":[61],"both":[62,90],"efficient":[63],"generalizable.":[65],"SemiGNN-PPI,":[67],"not":[69],"only":[70],"model":[71,139,146],"the":[72,77,87,95,126,132,137,144],"protein":[73],"correlations":[74],"but":[75],"explore":[76],"dependencies":[79],"by":[80,147],"constructing":[81],"processing":[83],"multiple":[84,120],"graphs":[85,130],"perspectives":[88],"of":[89,156],"features":[91],"labels":[93],"graph":[96,115,121],"process.":[98],"We":[99,117],"further":[100],"marry":[101],"GNN":[102],"with":[103,159,178],"Mean":[104],"Teacher":[105],"leverage":[108],"unlabeled":[109],"graph-structured":[110],"PPI":[111,154,168],"data":[112],"self-ensemble":[114],"learning.":[116],"also":[118],"design":[119],"consistency":[122],"constraints":[123],"align":[125],"student":[127,138],"teacher":[129,145],"feature":[133],"embedding":[134],"space,":[135],"enabling":[136],"better":[141],"learn":[142],"incorporating":[148],"more":[149],"relationships.":[150],"Extensive":[151],"experiments":[152],"on":[153,183],"datasets":[155],"different":[157,160],"scales":[158],"evaluation":[161],"settings":[162],"demonstrate":[163],"SemiGNN-PPI":[165],"outperforms":[166],"state-of-the-art":[167],"prediction":[169],"methods,":[170],"particularly":[171],"challenging":[173],"such":[175],"as":[176],"training":[177],"limited":[179],"annotations":[180],"testing":[182],"unseen":[184],"data.":[185]},"counts_by_year":[{"year":2026,"cited_by_count":8},{"year":2025,"cited_by_count":13},{"year":2024,"cited_by_count":11},{"year":2023,"cited_by_count":1}],"updated_date":"2026-07-14T23:27:15.235271","created_date":"2025-10-10T00:00:00"}
