{"id":"https://openalex.org/W4414751411","doi":"https://doi.org/10.1093/bib/bbaf517","title":"Dual-protein embedding-based graph model with dynamic attention for interaction prediction","display_name":"Dual-protein embedding-based graph model with dynamic attention for interaction prediction","publication_year":2025,"publication_date":"2025-08-31","ids":{"openalex":"https://openalex.org/W4414751411","doi":"https://doi.org/10.1093/bib/bbaf517","pmid":"https://pubmed.ncbi.nlm.nih.gov/41031876"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbaf517","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf517","pdf_url":"https://academic.oup.com/bib/article-pdf/26/5/bbaf517/64460706/bbaf517.pdf","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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","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://academic.oup.com/bib/article-pdf/26/5/bbaf517/64460706/bbaf517.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5056260594","display_name":"Shunpeng Pang","orcid":null},"institutions":[{"id":"https://openalex.org/I66883779","display_name":"Weifang University","ror":"https://ror.org/01frp7483","country_code":"CN","type":"education","lineage":["https://openalex.org/I66883779"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Shunpeng Pang","raw_affiliation_strings":["School of Computer Engineering , WeiFang University, 5147 East Dongfeng Road, Kuiwen District, Weifang, Shandong 261061,","School of Computer Engineering, WeiFang University, 5147 East Dongfeng Road, Kuiwen District, Weifang, Shandong 261061, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Engineering , WeiFang University, 5147 East Dongfeng Road, Kuiwen District, Weifang, Shandong 261061,","institution_ids":["https://openalex.org/I66883779"]},{"raw_affiliation_string":"School of Computer Engineering, WeiFang University, 5147 East Dongfeng Road, Kuiwen District, Weifang, Shandong 261061, China","institution_ids":["https://openalex.org/I66883779"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076937227","display_name":"Mingjian Jiang","orcid":"https://orcid.org/0000-0002-0716-5292"},"institutions":[{"id":"https://openalex.org/I108688024","display_name":"Qingdao University","ror":"https://ror.org/021cj6z65","country_code":"CN","type":"education","lineage":["https://openalex.org/I108688024"]},{"id":"https://openalex.org/I143413998","display_name":"Qingdao University of Science and Technology","ror":"https://ror.org/041j8js14","country_code":"CN","type":"education","lineage":["https://openalex.org/I143413998"]},{"id":"https://openalex.org/I80143920","display_name":"Shandong University of Science and Technology","ror":"https://ror.org/04gtjhw98","country_code":"CN","type":"education","lineage":["https://openalex.org/I80143920"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Mingjian Jiang","raw_affiliation_strings":["School of Information and Control Engineering, Qingdao University of Technology , 777 East Jialingjiang Road, Huangdao District, Qingdao, Shandong 266525 ,","School of Information and Control Engineering, Qingdao University of Technology, 777 East Jialingjiang Road, Huangdao District, Qingdao, Shandong 266525, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Information and Control Engineering, Qingdao University of Technology , 777 East Jialingjiang Road, Huangdao District, Qingdao, Shandong 266525 ,","institution_ids":["https://openalex.org/I143413998","https://openalex.org/I108688024"]},{"raw_affiliation_string":"School of Information and Control Engineering, Qingdao University of Technology, 777 East Jialingjiang Road, Huangdao District, Qingdao, Shandong 266525, China","institution_ids":["https://openalex.org/I143413998","https://openalex.org/I80143920"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101822148","display_name":"Shugang Zhang","orcid":"https://orcid.org/0000-0002-9774-9709"},"institutions":[{"id":"https://openalex.org/I59028903","display_name":"Ocean University of China","ror":"https://ror.org/04rdtx186","country_code":"CN","type":"education","lineage":["https://openalex.org/I59028903"]},{"id":"https://openalex.org/I80143920","display_name":"Shandong University of Science and Technology","ror":"https://ror.org/04gtjhw98","country_code":"CN","type":"education","lineage":["https://openalex.org/I80143920"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Shugang Zhang","raw_affiliation_strings":["College of Computer Science and Technology, Ocean University of China , 1299 Sansha Road, Huangdao District, Qingdao, Shandong 266100 ,","College of Computer Science and Technology, Ocean University of China, 1299 Sansha Road, Huangdao District, Qingdao, Shandong 266100, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Computer Science and Technology, Ocean University of China , 1299 Sansha Road, Huangdao District, Qingdao, Shandong 266100 ,","institution_ids":["https://openalex.org/I59028903","https://openalex.org/I80143920"]},{"raw_affiliation_string":"College of Computer Science and Technology, Ocean University of China, 1299 Sansha Road, Huangdao District, Qingdao, Shandong 266100, China","institution_ids":["https://openalex.org/I59028903","https://openalex.org/I80143920"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100375587","display_name":"Shuang Wang","orcid":"https://orcid.org/0000-0002-6779-9537"},"institutions":[{"id":"https://openalex.org/I4210162190","display_name":"China University of Petroleum, East China","ror":"https://ror.org/05gbn2817","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210162190"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Shuang Wang","raw_affiliation_strings":["College of Computer Science and Technology, China University of Petroleum , 66 West Changjiang Road, Huangdao District, Qingdao, Shandong 266580 ,","College of Computer Science and Technology, China University of Petroleum, 66 West Changjiang Road, Huangdao District, Qingdao, Shandong 266580, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Computer Science and Technology, China University of Petroleum , 66 West Changjiang Road, Huangdao District, Qingdao, Shandong 266580 ,","institution_ids":["https://openalex.org/I4210162190"]},{"raw_affiliation_string":"College of Computer Science and Technology, China University of Petroleum, 66 West Changjiang Road, Huangdao District, Qingdao, Shandong 266580, China","institution_ids":["https://openalex.org/I4210162190"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100332597","display_name":"Zhen Li","orcid":"https://orcid.org/0000-0002-4033-8650"},"institutions":[{"id":"https://openalex.org/I108688024","display_name":"Qingdao University","ror":"https://ror.org/021cj6z65","country_code":"CN","type":"education","lineage":["https://openalex.org/I108688024"]},{"id":"https://openalex.org/I143413998","display_name":"Qingdao University of Science and Technology","ror":"https://ror.org/041j8js14","country_code":"CN","type":"education","lineage":["https://openalex.org/I143413998"]},{"id":"https://openalex.org/I80143920","display_name":"Shandong University of Science and Technology","ror":"https://ror.org/04gtjhw98","country_code":"CN","type":"education","lineage":["https://openalex.org/I80143920"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhen Li","raw_affiliation_strings":["College of Computer Science and Technology, Qingdao University , 308 Ningxia Road, Laoshan District, Qingdao, Shandong 266071 ,","College of Computer Science and Technology, Qingdao University, 308 Ningxia Road, Laoshan District, Qingdao, Shandong 266071, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Computer Science and Technology, Qingdao University , 308 Ningxia Road, Laoshan District, Qingdao, Shandong 266071 ,","institution_ids":["https://openalex.org/I108688024"]},{"raw_affiliation_string":"College of Computer Science and Technology, Qingdao University, 308 Ningxia Road, Laoshan District, Qingdao, Shandong 266071, China","institution_ids":["https://openalex.org/I108688024","https://openalex.org/I80143920","https://openalex.org/I143413998"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012471887","display_name":"Jing Zhi Sun","orcid":"https://orcid.org/0000-0001-5478-5841"},"institutions":[{"id":"https://openalex.org/I66883779","display_name":"Weifang University","ror":"https://ror.org/01frp7483","country_code":"CN","type":"education","lineage":["https://openalex.org/I66883779"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jing Sun","raw_affiliation_strings":["School of Computer Engineering, WeiFang University , 5147 East Dongfeng Road, Kuiwen District, Weifang, Shandong 261061 ,","School of Computer Engineering, WeiFang University, 5147 East Dongfeng Road, Kuiwen District, Weifang, Shandong 261061, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Engineering, WeiFang University , 5147 East Dongfeng Road, Kuiwen District, Weifang, Shandong 261061 ,","institution_ids":["https://openalex.org/I66883779"]},{"raw_affiliation_string":"School of Computer Engineering, WeiFang University, 5147 East Dongfeng Road, Kuiwen District, Weifang, Shandong 261061, China","institution_ids":["https://openalex.org/I66883779"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100746477","display_name":"Yuanyuan Zhang","orcid":"https://orcid.org/0000-0003-3935-3201"},"institutions":[{"id":"https://openalex.org/I108688024","display_name":"Qingdao University","ror":"https://ror.org/021cj6z65","country_code":"CN","type":"education","lineage":["https://openalex.org/I108688024"]},{"id":"https://openalex.org/I143413998","display_name":"Qingdao University of Science and Technology","ror":"https://ror.org/041j8js14","country_code":"CN","type":"education","lineage":["https://openalex.org/I143413998"]},{"id":"https://openalex.org/I80143920","display_name":"Shandong University of Science and Technology","ror":"https://ror.org/04gtjhw98","country_code":"CN","type":"education","lineage":["https://openalex.org/I80143920"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yuanyuan Zhang","raw_affiliation_strings":["School of Information and Control Engineering, Qingdao University of Technology , 777 East Jialingjiang Road, Huangdao District, Qingdao, Shandong 266525 ,","School of Information and Control Engineering, Qingdao University of Technology, 777 East Jialingjiang Road, Huangdao District, Qingdao, Shandong 266525, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Information and Control Engineering, Qingdao University of Technology , 777 East Jialingjiang Road, Huangdao District, Qingdao, Shandong 266525 ,","institution_ids":["https://openalex.org/I143413998","https://openalex.org/I108688024"]},{"raw_affiliation_string":"School of Information and Control Engineering, Qingdao University of Technology, 777 East Jialingjiang Road, Huangdao District, Qingdao, Shandong 266525, China","institution_ids":["https://openalex.org/I143413998","https://openalex.org/I80143920"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5023132579","display_name":"Li Guo","orcid":"https://orcid.org/0000-0002-7445-5257"},"institutions":[{"id":"https://openalex.org/I66883779","display_name":"Weifang University","ror":"https://ror.org/01frp7483","country_code":"CN","type":"education","lineage":["https://openalex.org/I66883779"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Li Guo","raw_affiliation_strings":["Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang Key Laboratory of Grapevine Improvement and Utilization , 699 Binhu Road, Xiashan District, Weifang, Shandong 261325 ,","Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang Key Laboratory of Grapevine Improvement and Utilization, 699 Binhu Road, Xiashan District, Weifang, Shandong 261325, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang Key Laboratory of Grapevine Improvement and Utilization , 699 Binhu Road, Xiashan District, Weifang, Shandong 261325 ,","institution_ids":["https://openalex.org/I66883779"]},{"raw_affiliation_string":"Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang Key Laboratory of Grapevine Improvement and Utilization, 699 Binhu Road, Xiashan District, Weifang, Shandong 261325, China","institution_ids":["https://openalex.org/I66883779"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":8,"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":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.20816403,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"26","issue":"5","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9945999979972839,"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":0.9945999979972839,"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9861999750137329,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9753000140190125,"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/scalability","display_name":"Scalability","score":0.6592000126838684},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.5699999928474426},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.4099999964237213},{"id":"https://openalex.org/keywords/domain","display_name":"Domain (mathematical analysis)","score":0.38589999079704285},{"id":"https://openalex.org/keywords/computational-model","display_name":"Computational model","score":0.3416999876499176},{"id":"https://openalex.org/keywords/semantics","display_name":"Semantics (computer science)","score":0.32260000705718994},{"id":"https://openalex.org/keywords/computational-complexity-theory","display_name":"Computational complexity theory","score":0.3224000036716461}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7882999777793884},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.6592000126838684},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.5699999928474426},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.46549999713897705},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4189999997615814},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.4099999964237213},{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.38589999079704285},{"id":"https://openalex.org/C66024118","wikidata":"https://www.wikidata.org/wiki/Q1122506","display_name":"Computational model","level":2,"score":0.3416999876499176},{"id":"https://openalex.org/C184337299","wikidata":"https://www.wikidata.org/wiki/Q1437428","display_name":"Semantics (computer science)","level":2,"score":0.32260000705718994},{"id":"https://openalex.org/C179799912","wikidata":"https://www.wikidata.org/wiki/Q205084","display_name":"Computational complexity theory","level":2,"score":0.3224000036716461},{"id":"https://openalex.org/C74197172","wikidata":"https://www.wikidata.org/wiki/Q1195339","display_name":"Directed acyclic graph","level":2,"score":0.3059000074863434},{"id":"https://openalex.org/C28225019","wikidata":"https://www.wikidata.org/wiki/Q4915005","display_name":"Biological network","level":2,"score":0.3034999966621399},{"id":"https://openalex.org/C201797286","wikidata":"https://www.wikidata.org/wiki/Q4914986","display_name":"Biological data","level":2,"score":0.29100000858306885},{"id":"https://openalex.org/C2779304628","wikidata":"https://www.wikidata.org/wiki/Q3503480","display_name":"Face (sociological concept)","level":2,"score":0.2896000146865845},{"id":"https://openalex.org/C117745874","wikidata":"https://www.wikidata.org/wiki/Q901612","display_name":"Sequence motif","level":3,"score":0.2793999910354614},{"id":"https://openalex.org/C89611455","wikidata":"https://www.wikidata.org/wiki/Q6804646","display_name":"Mechanism (biology)","level":2,"score":0.26989999413490295},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.2615000009536743},{"id":"https://openalex.org/C11804247","wikidata":"https://www.wikidata.org/wiki/Q896177","display_name":"Protein\u2013protein interaction","level":2,"score":0.2547000050544739},{"id":"https://openalex.org/C106937863","wikidata":"https://www.wikidata.org/wiki/Q7236518","display_name":"Power graph analysis","level":3,"score":0.2524999976158142}],"mesh":[{"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":"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":"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":4,"locations":[{"id":"doi:10.1093/bib/bbaf517","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf517","pdf_url":"https://academic.oup.com/bib/article-pdf/26/5/bbaf517/64460706/bbaf517.pdf","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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:41031876","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41031876","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:europepmc.org:11294529","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12486248","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:12486248","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12486248/","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/bbaf517","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf517","pdf_url":"https://academic.oup.com/bib/article-pdf/26/5/bbaf517/64460706/bbaf517.pdf","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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","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/G1687351987","display_name":null,"funder_award_id":"ZR2022QF111","funder_id":"https://openalex.org/F4320324174","funder_display_name":"Natural Science Foundation of Shandong Province"},{"id":"https://openalex.org/G2122243128","display_name":null,"funder_award_id":"No. WFU2023BS47","funder_id":"https://openalex.org/F4320324174","funder_display_name":"Natural Science Foundation of Shandong Province"}],"funders":[{"id":"https://openalex.org/F4320324174","display_name":"Natural Science Foundation of Shandong Province","ror":null}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4414751411.pdf","grobid_xml":"https://content.openalex.org/works/W4414751411.grobid-xml"},"referenced_works_count":32,"referenced_works":["https://openalex.org/W1985919127","https://openalex.org/W2130687290","https://openalex.org/W2132582966","https://openalex.org/W2152705149","https://openalex.org/W2156125289","https://openalex.org/W2340589369","https://openalex.org/W2890911678","https://openalex.org/W2913256647","https://openalex.org/W2917858269","https://openalex.org/W2950742983","https://openalex.org/W2952253955","https://openalex.org/W2957436444","https://openalex.org/W3048218277","https://openalex.org/W3111467036","https://openalex.org/W3134084134","https://openalex.org/W3138006998","https://openalex.org/W3174714560","https://openalex.org/W3177828909","https://openalex.org/W3184519053","https://openalex.org/W3184607641","https://openalex.org/W3195026381","https://openalex.org/W3209369100","https://openalex.org/W3210147532","https://openalex.org/W4220824576","https://openalex.org/W4295107433","https://openalex.org/W4310388280","https://openalex.org/W4312198087","https://openalex.org/W4353066697","https://openalex.org/W4386148351","https://openalex.org/W4389742650","https://openalex.org/W4399142722","https://openalex.org/W4400416808"],"related_works":[],"abstract_inverted_index":{"Protein-protein":[0],"interactions":[1],"(PPIs)":[2],"are":[3],"fundamental":[4],"to":[5,49,68,95,138],"biological":[6],"processes,":[7],"yet":[8],"experimental":[9],"determination":[10],"of":[11,120],"PPIs":[12],"remains":[13],"costly":[14],"and":[15,35,42,103,164,171,193],"labor-intensive.":[16],"While":[17],"computational":[18,45],"methods":[19],"have":[20],"emerged":[21],"as":[22,123],"promising":[23],"alternatives,":[24],"sequence-based":[25],"approaches":[26],"face":[27],"critical":[28,36,150],"challenges:":[29],"(1)":[30],"effectively":[31],"capturing":[32],"long-range":[33],"dependencies":[34],"biochemical":[37],"patterns":[38],"in":[39],"variable-length":[40],"sequences,":[41],"(2)":[43],"balancing":[44],"efficiency":[46],"with":[47,181],"sensitivity":[48],"subtle":[50],"residue-level":[51,99],"interactions.":[52],"Here,":[53],"we":[54,92,111],"present":[55],"Dual":[56],"Protein":[57],"Embedding-based":[58],"Graph":[59],"Model":[60],"(DPEG),":[61],"which":[62],"leverages":[63],"dynamic":[64,145],"graph":[65,124],"attention":[66,134,146],"networks":[67,125],"enable":[69],"robust":[70],"sequence-driven":[71],"PPI":[72,159,188],"prediction.":[73],"Unlike":[74],"structure-dependent":[75],"methods,":[76],"DPEG":[77,167,185],"operates":[78],"solely":[79],"on":[80,156],"sequence":[81,109,179],"data,":[82],"bypassing":[83],"the":[84,127,153],"need":[85],"for":[86,197],"structural":[87],"or":[88],"domain":[89],"annotations.":[90],"Specifically,":[91],"employ":[93],"ESM-2":[94],"transform":[96],"sequences":[97,119],"into":[98],"graphs,":[100],"preserving":[101],"evolutionary":[102],"physicochemical":[104],"context.":[105],"To":[106],"address":[107],"variable":[108],"lengths,":[110],"design":[112],"a":[113,132,144,191],"module":[114],"that":[115],"can":[116],"represent":[117],"protein":[118],"arbitrary":[121],"lengths":[122],"at":[126],"amino":[128],"acid":[129],"level.":[130],"Further,":[131],"gated":[133],"mechanism":[135,147],"is":[136],"introduced":[137],"adaptively":[139],"refining":[140],"residue":[141],"representations.":[142],"Finally,":[143],"prioritizes":[148],"functionally":[149],"motifs":[151],"within":[152],"graph.":[154],"Evaluated":[155],"four":[157],"diverse":[158],"datasets":[160],"spanning":[161],"different":[162],"species":[163],"interaction":[165,183],"types,":[166],"achieves":[168],"state-of-the-art":[169],"performance":[170],"demonstrates":[172],"strong":[173],"cross-dataset":[174],"generalizability.":[175],"By":[176],"integrating":[177],"deep":[178],"semantics":[180],"graph-based":[182],"modeling,":[184],"advances":[186],"sequence-only":[187],"prediction,":[189],"offering":[190],"scalable":[192],"biologically":[194],"plausible":[195],"framework":[196],"proteome-wide":[198],"studies.":[199]},"counts_by_year":[],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}
