{"id":"https://openalex.org/W4411042546","doi":"https://doi.org/10.1093/bib/bbaf248","title":"Gated-GPS: enhancing protein\u2013protein interaction site prediction with scalable learning and imbalance-aware optimization","display_name":"Gated-GPS: enhancing protein\u2013protein interaction site prediction with scalable learning and imbalance-aware optimization","publication_year":2025,"publication_date":"2025-05-01","ids":{"openalex":"https://openalex.org/W4411042546","doi":"https://doi.org/10.1093/bib/bbaf248","pmid":"https://pubmed.ncbi.nlm.nih.gov/40462513"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbaf248","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf248","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1093/bib/bbaf248","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5080034477","display_name":"Xin Gao","orcid":"https://orcid.org/0000-0001-8736-1172"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xin Gao","raw_affiliation_strings":["Department of Computer Science and Engineering, University of California San Diego , 9500 Gilman Drive, La Jolla, California 92093 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, University of California San Diego , 9500 Gilman Drive, La Jolla, California 92093 ,","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036649546","display_name":"Hanqun Cao","orcid":"https://orcid.org/0000-0002-8104-1845"},"institutions":[{"id":"https://openalex.org/I177725633","display_name":"Chinese University of Hong Kong","ror":"https://ror.org/00t33hh48","country_code":"HK","type":"education","lineage":["https://openalex.org/I177725633"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Hanqun Cao","raw_affiliation_strings":["Department of Computer Science and Engineering, The Chinese University of Hong Kong, Ma Liu Shui , Shatin, Hong Kong SAR, Hong Kong SAR 000000 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, The Chinese University of Hong Kong, Ma Liu Shui , Shatin, Hong Kong SAR, Hong Kong SAR 000000 ,","institution_ids":["https://openalex.org/I177725633"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100782329","display_name":"Jinpeng Li","orcid":"https://orcid.org/0009-0007-2572-117X"},"institutions":[{"id":"https://openalex.org/I177725633","display_name":"Chinese University of Hong Kong","ror":"https://ror.org/00t33hh48","country_code":"HK","type":"education","lineage":["https://openalex.org/I177725633"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Jinpeng Li","raw_affiliation_strings":["Department of Computer Science and Engineering, The Chinese University of Hong Kong, Ma Liu Shui , Shatin, Hong Kong SAR, Hong Kong SAR 000000 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, The Chinese University of Hong Kong, Ma Liu Shui , Shatin, Hong Kong SAR, Hong Kong SAR 000000 ,","institution_ids":["https://openalex.org/I177725633"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083333630","display_name":"Jiezhong Qiu","orcid":"https://orcid.org/0000-0001-9514-0708"},"institutions":[{"id":"https://openalex.org/I4210123185","display_name":"Zhejiang Lab","ror":"https://ror.org/02m2h7991","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210123185"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jiezhong Qiu","raw_affiliation_strings":["Zhejiang Lab, Kechu ang Avenue , Hangzhou Zhejiang 311121 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Zhejiang Lab, Kechu ang Avenue , Hangzhou Zhejiang 311121 ,","institution_ids":["https://openalex.org/I4210123185"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101415870","display_name":"Guangyong Chen","orcid":"https://orcid.org/0000-0002-5892-8608"},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210123185","display_name":"Zhejiang Lab","ror":"https://ror.org/02m2h7991","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210123185"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Guangyong Chen","raw_affiliation_strings":["Hangzhou Institute of Medicine, Chinese Academy of Sciences , 150 Dongfang Street Xiasha, Hangzhou, Zhejiang, 310000 ,","Zhejiang Lab, Kechu ang Avenue , Hangzhou Zhejiang 311121 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Hangzhou Institute of Medicine, Chinese Academy of Sciences , 150 Dongfang Street Xiasha, Hangzhou, Zhejiang, 310000 ,","institution_ids":["https://openalex.org/I19820366"]},{"raw_affiliation_string":"Zhejiang Lab, Kechu ang Avenue , Hangzhou Zhejiang 311121 ,","institution_ids":["https://openalex.org/I4210123185"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5032708386","display_name":"Pheng\u2010Ann Heng","orcid":"https://orcid.org/0000-0003-3055-5034"},"institutions":[{"id":"https://openalex.org/I177725633","display_name":"Chinese University of Hong Kong","ror":"https://ror.org/00t33hh48","country_code":"HK","type":"education","lineage":["https://openalex.org/I177725633"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Pheng-Ann Heng","raw_affiliation_strings":["Department of Computer Science and Engineering, The Chinese University of Hong Kong, Ma Liu Shui , Shatin, Hong Kong SAR, Hong Kong SAR 000000 ,","Institute of Medical Intelligence and XR, The Chinese University of Hong Kong, Ma Liu Shui , Shatin, Hong Kong SAR, Hong Kong SAR 000000 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, The Chinese University of Hong Kong, Ma Liu Shui , Shatin, Hong Kong SAR, Hong Kong SAR 000000 ,","institution_ids":["https://openalex.org/I177725633"]},{"raw_affiliation_string":"Institute of Medical Intelligence and XR, The Chinese University of Hong Kong, Ma Liu Shui , Shatin, Hong Kong SAR, Hong Kong SAR 000000 ,","institution_ids":["https://openalex.org/I177725633"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":4,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":0.8854,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.76820051,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":97},"biblio":{"volume":"26","issue":"3","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9976000189781189,"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":0.9976000189781189,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.994700014591217,"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/T13326","display_name":"Biochemical and Structural Characterization","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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.714818000793457},{"id":"https://openalex.org/keywords/leverage","display_name":"Leverage (statistics)","score":0.604577898979187},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.5477690696716309},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5381470918655396},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.5250713229179382},{"id":"https://openalex.org/keywords/protein\u2013protein-interaction","display_name":"Protein\u2013protein interaction","score":0.4370258152484894},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.1532181203365326}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.714818000793457},{"id":"https://openalex.org/C153083717","wikidata":"https://www.wikidata.org/wiki/Q6535263","display_name":"Leverage (statistics)","level":2,"score":0.604577898979187},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.5477690696716309},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5381470918655396},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.5250713229179382},{"id":"https://openalex.org/C11804247","wikidata":"https://www.wikidata.org/wiki/Q896177","display_name":"Protein\u2013protein interaction","level":2,"score":0.4370258152484894},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.1532181203365326},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbaf248","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf248","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40462513","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40462513","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":"Briefings in bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:12133684","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12133684","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbaf248","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf248","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2025695351","display_name":null,"funder_award_id":"62306290","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G4096701808","display_name":null,"funder_award_id":"32341017","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G455209869","display_name":null,"funder_award_id":"62376254","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G6691289981","display_name":null,"funder_award_id":"32341018","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":62,"referenced_works":["https://openalex.org/W2001457899","https://openalex.org/W2056169996","https://openalex.org/W2076048958","https://openalex.org/W2105594594","https://openalex.org/W2108134720","https://openalex.org/W2114162221","https://openalex.org/W2128900650","https://openalex.org/W2130479394","https://openalex.org/W2141627824","https://openalex.org/W2143210482","https://openalex.org/W2153187042","https://openalex.org/W2155194485","https://openalex.org/W2280888683","https://openalex.org/W2557595285","https://openalex.org/W2754800853","https://openalex.org/W2899663614","https://openalex.org/W2944679105","https://openalex.org/W2955690154","https://openalex.org/W2971405760","https://openalex.org/W2984274952","https://openalex.org/W2990458240","https://openalex.org/W2990714382","https://openalex.org/W2992752586","https://openalex.org/W3009202743","https://openalex.org/W3013976849","https://openalex.org/W3080498684","https://openalex.org/W3129073614","https://openalex.org/W3146944767","https://openalex.org/W3177272212","https://openalex.org/W3177500196","https://openalex.org/W3190341154","https://openalex.org/W3197696221","https://openalex.org/W4297138475","https://openalex.org/W4308559752","https://openalex.org/W4320495200","https://openalex.org/W4323348775","https://openalex.org/W4362522229","https://openalex.org/W4385245566","https://openalex.org/W4388663283","https://openalex.org/W4389330752","https://openalex.org/W4389836928","https://openalex.org/W4390035122","https://openalex.org/W4390740875","https://openalex.org/W4390955747","https://openalex.org/W4390991996","https://openalex.org/W4392518459","https://openalex.org/W4392642247","https://openalex.org/W4396945180","https://openalex.org/W4402632138","https://openalex.org/W4403099537","https://openalex.org/W4404344158","https://openalex.org/W4406385633","https://openalex.org/W6726873649","https://openalex.org/W6739901393","https://openalex.org/W6740220579","https://openalex.org/W6745537798","https://openalex.org/W6755977528","https://openalex.org/W6762363781","https://openalex.org/W6772452955","https://openalex.org/W6780226713","https://openalex.org/W6797562226","https://openalex.org/W6866741285"],"related_works":["https://openalex.org/W2961085424","https://openalex.org/W4306674287","https://openalex.org/W4387369504","https://openalex.org/W4394896187","https://openalex.org/W3170094116","https://openalex.org/W4386462264","https://openalex.org/W3107602296","https://openalex.org/W4364306694","https://openalex.org/W4312192474","https://openalex.org/W4283697347"],"abstract_inverted_index":{"In":[0,149],"protein-protein":[1,59],"interaction":[2,162],"site":[3],"(PPIS)":[4],"prediction,":[5],"existing":[6],"machine":[7],"learning":[8],"models":[9,117],"struggle":[10],"with":[11,73,90],"small":[12,32],"datasets,":[13],"limiting":[14],"their":[15],"predictive":[16],"accuracy":[17],"for":[18,167],"unseen":[19],"proteins.":[20],"Additionally,":[21,85],"class":[22,102],"imbalance":[23,103],"in":[24],"protein":[25,176],"complexes,":[26],"where":[27],"binding":[28,107],"residues":[29],"constitute":[30],"a":[31,46,69,74,150],"fraction":[33],"of":[34,153,174],"all":[35],"residues,":[36],"hinders":[37],"model":[38,72,159],"performance.":[39],"To":[40],"address":[41],"these":[42],"challenges,":[43],"we":[44,86],"constructed":[45],"training":[47],"dataset":[48],"9$\\times":[49],"$":[50],"larger":[51],"than":[52],"previous":[53,147],"benchmarks":[54],"by":[55,104,140],"filtering":[56],"the":[57,124,146,172],"latest":[58],"complex":[60,175],"data,":[61],"improving":[62],"diversity":[63],"and":[64,98,138,142,170],"generalization.":[65],"We":[66],"propose":[67],"Gated-GPS,":[68],"Graph":[70],"Transformer":[71],"novel":[75],"gating":[76],"mechanism":[77],"designed":[78,127],"to":[79,93,96,128],"effectively":[80],"leverage":[81],"this":[82],"expanded":[83],"dataset.":[84],"integrate":[87],"cross-entropy":[88],"loss":[89],"Tversky":[91],"Loss":[92],"adjust":[94],"sensitivity":[95],"positive":[97],"negative":[99],"samples,":[100],"mitigating":[101],"emphasizing":[105],"underrepresented":[106],"residues.":[108],"Experimental":[109],"results":[110],"show":[111],"that":[112],"Gated-GPS":[113],"outperforms":[114],"state-of-the-art":[115],"(SOTA)":[116],"across":[118],"four":[119],"test":[120],"sets.":[121],"Notably,":[122],"on":[123,131],"UBTest":[125],"dataset,":[126],"evaluate":[129],"generalization":[130],"unbounded":[132],"proteins,":[133],"our":[134,158],"method":[135],"improves":[136],"MCC":[137],"AUPRC":[139],"18.5%":[141],"21.4%,":[143],"respectively,":[144],"over":[145],"SOTA.":[148],"case":[151],"study":[152],"snake":[154],"venom":[155],"toxin-protein":[156],"interactions,":[157],"accurately":[160],"identified":[161],"sites,":[163],"demonstrating":[164],"its":[165],"potential":[166],"therapeutic":[168],"design":[169],"advancing":[171],"understanding":[173],"interactions.":[177]},"counts_by_year":[{"year":2026,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
