{"id":"https://openalex.org/W7118288147","doi":"https://doi.org/10.3389/fbinf.2025.1710937","title":"Advances in protein-protein interaction prediction: a deep learning perspective","display_name":"Advances in protein-protein interaction prediction: a deep learning perspective","publication_year":2026,"publication_date":"2026-01-07","ids":{"openalex":"https://openalex.org/W7118288147","doi":"https://doi.org/10.3389/fbinf.2025.1710937","pmid":"https://pubmed.ncbi.nlm.nih.gov/41574108"},"language":"en","primary_location":{"id":"doi:10.3389/fbinf.2025.1710937","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2025.1710937","pdf_url":null,"source":{"id":"https://openalex.org/S4210219554","display_name":"Frontiers in Bioinformatics","issn_l":"2673-7647","issn":["2673-7647"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers 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/10.3389/fbinf.2025.1710937","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5116806279","display_name":"Noor Jamal Alkhateeb","orcid":null},"institutions":[{"id":"https://openalex.org/I201726411","display_name":"United Arab Emirates University","ror":"https://ror.org/01km6p862","country_code":"AE","type":"education","lineage":["https://openalex.org/I201726411"]}],"countries":["AE"],"is_corresponding":true,"raw_author_name":"Noor Alkhateeb","raw_affiliation_strings":["College of IT, UAE University, Al-Ain, United Arab Emirates"],"affiliations":[{"raw_affiliation_string":"College of IT, UAE University, Al-Ain, United Arab Emirates","institution_ids":["https://openalex.org/I201726411"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5081389915","display_name":"Mamoun Awad","orcid":"https://orcid.org/0000-0001-7424-4129"},"institutions":[{"id":"https://openalex.org/I201726411","display_name":"United Arab Emirates University","ror":"https://ror.org/01km6p862","country_code":"AE","type":"education","lineage":["https://openalex.org/I201726411"]}],"countries":["AE"],"is_corresponding":false,"raw_author_name":"Mamoun Awad","raw_affiliation_strings":["College of IT, UAE University, Al-Ain, United Arab Emirates"],"affiliations":[{"raw_affiliation_string":"College of IT, UAE University, Al-Ain, United Arab Emirates","institution_ids":["https://openalex.org/I201726411"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5116806279"],"corresponding_institution_ids":["https://openalex.org/I201726411"],"apc_list":{"value":1900,"currency":"USD","value_usd":1900},"apc_paid":{"value":1900,"currency":"USD","value_usd":1900},"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.02707597,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"5","issue":null,"first_page":"1710937","last_page":"1710937"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.8560000061988831,"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":0.8560000061988831,"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":0.0763000026345253,"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":0.019200000911951065,"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/deep-learning","display_name":"Deep learning","score":0.7911999821662903},{"id":"https://openalex.org/keywords/convolutional-neural-network","display_name":"Convolutional neural network","score":0.5690000057220459},{"id":"https://openalex.org/keywords/perspective","display_name":"Perspective (graphical)","score":0.4830999970436096},{"id":"https://openalex.org/keywords/feature","display_name":"Feature (linguistics)","score":0.40880000591278076},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.39419999718666077},{"id":"https://openalex.org/keywords/deep-neural-networks","display_name":"Deep neural networks","score":0.35190001130104065}],"concepts":[{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.7911999821662903},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.7520999908447266},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7466999888420105},{"id":"https://openalex.org/C81363708","wikidata":"https://www.wikidata.org/wiki/Q17084460","display_name":"Convolutional neural network","level":2,"score":0.5690000057220459},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.5511999726295471},{"id":"https://openalex.org/C12713177","wikidata":"https://www.wikidata.org/wiki/Q1900281","display_name":"Perspective (graphical)","level":2,"score":0.4830999970436096},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.40880000591278076},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.39419999718666077},{"id":"https://openalex.org/C2984842247","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep neural networks","level":3,"score":0.35190001130104065},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.3321000039577484},{"id":"https://openalex.org/C52622490","wikidata":"https://www.wikidata.org/wiki/Q1026626","display_name":"Feature extraction","level":2,"score":0.32679998874664307},{"id":"https://openalex.org/C66024118","wikidata":"https://www.wikidata.org/wiki/Q1122506","display_name":"Computational model","level":2,"score":0.30709999799728394},{"id":"https://openalex.org/C59404180","wikidata":"https://www.wikidata.org/wiki/Q17013334","display_name":"Feature learning","level":2,"score":0.3068999946117401},{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.304500013589859},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.29490000009536743},{"id":"https://openalex.org/C2778464652","wikidata":"https://www.wikidata.org/wiki/Q309849","display_name":"Open research","level":2,"score":0.27149999141693115}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.3389/fbinf.2025.1710937","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2025.1710937","pdf_url":null,"source":{"id":"https://openalex.org/S4210219554","display_name":"Frontiers in Bioinformatics","issn_l":"2673-7647","issn":["2673-7647"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:41574108","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41574108","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":"Frontiers in bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:12819794","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12819794/","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Front Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.3389/fbinf.2025.1710937","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2025.1710937","pdf_url":null,"source":{"id":"https://openalex.org/S4210219554","display_name":"Frontiers in Bioinformatics","issn_l":"2673-7647","issn":["2673-7647"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320323593","display_name":"United Arab Emirates University","ror":"https://ror.org/01km6p862"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":110,"referenced_works":["https://openalex.org/W76924599","https://openalex.org/W1030883578","https://openalex.org/W1484777458","https://openalex.org/W1501531009","https://openalex.org/W1543773936","https://openalex.org/W1614298861","https://openalex.org/W1759240213","https://openalex.org/W1886978693","https://openalex.org/W1951403192","https://openalex.org/W1964084224","https://openalex.org/W1964880253","https://openalex.org/W1969051510","https://openalex.org/W1975304761","https://openalex.org/W1985919127","https://openalex.org/W1991141438","https://openalex.org/W2018661561","https://openalex.org/W2026593599","https://openalex.org/W2033893117","https://openalex.org/W2043764521","https://openalex.org/W2044523575","https://openalex.org/W2048917743","https://openalex.org/W2051210555","https://openalex.org/W2055043387","https://openalex.org/W2065232574","https://openalex.org/W2073229442","https://openalex.org/W2094148990","https://openalex.org/W2110498021","https://openalex.org/W2130670576","https://openalex.org/W2136206140","https://openalex.org/W2140883620","https://openalex.org/W2142757818","https://openalex.org/W2143426320","https://openalex.org/W2147209844","https://openalex.org/W2150452800","https://openalex.org/W2155194485","https://openalex.org/W2157735020","https://openalex.org/W2157807259","https://openalex.org/W2160257187","https://openalex.org/W2162392441","https://openalex.org/W2163352757","https://openalex.org/W2168164063","https://openalex.org/W2168637722","https://openalex.org/W2236856444","https://openalex.org/W2257979135","https://openalex.org/W2270702445","https://openalex.org/W2280888683","https://openalex.org/W2283929195","https://openalex.org/W2290562923","https://openalex.org/W2314868955","https://openalex.org/W2363637013","https://openalex.org/W2428593791","https://openalex.org/W2557595285","https://openalex.org/W2570083522","https://openalex.org/W2579420628","https://openalex.org/W2616246685","https://openalex.org/W2618265628","https://openalex.org/W2618529956","https://openalex.org/W2749147866","https://openalex.org/W2757108520","https://openalex.org/W2783162988","https://openalex.org/W2789316776","https://openalex.org/W2793168264","https://openalex.org/W2804331675","https://openalex.org/W2885583144","https://openalex.org/W2890911678","https://openalex.org/W2897596315","https://openalex.org/W2898320067","https://openalex.org/W2898402099","https://openalex.org/W2900569176","https://openalex.org/W2902392247","https://openalex.org/W2906946803","https://openalex.org/W2907063321","https://openalex.org/W2908914784","https://openalex.org/W2911930496","https://openalex.org/W2919115771","https://openalex.org/W2944679105","https://openalex.org/W2955690154","https://openalex.org/W2957180077","https://openalex.org/W2957436444","https://openalex.org/W2971405760","https://openalex.org/W2998799485","https://openalex.org/W3015964336","https://openalex.org/W3028296077","https://openalex.org/W3043299403","https://openalex.org/W3045012301","https://openalex.org/W3080498684","https://openalex.org/W3093053585","https://openalex.org/W3162082122","https://openalex.org/W3165600191","https://openalex.org/W3185245858","https://openalex.org/W3197696221","https://openalex.org/W4206247924","https://openalex.org/W4283586679","https://openalex.org/W4286500588","https://openalex.org/W4294170691","https://openalex.org/W4295107433","https://openalex.org/W4308516830","https://openalex.org/W4309242540","https://openalex.org/W4309438076","https://openalex.org/W4316465078","https://openalex.org/W4361217235","https://openalex.org/W4366464115","https://openalex.org/W4382894252","https://openalex.org/W4399155608","https://openalex.org/W4401095369","https://openalex.org/W4401167220","https://openalex.org/W4402670712","https://openalex.org/W4408861944","https://openalex.org/W4412813535","https://openalex.org/W4413679621"],"related_works":[],"abstract_inverted_index":{"Protein-protein":[0],"interactions":[1],"(PPIs)":[2],"are":[3,14,23,120],"vital":[4],"for":[5,62,126,148],"regulating":[6],"various":[7],"cellular":[8],"functions":[9],"and":[10,25,50,82,93,99,105,116,134,143],"understanding":[11],"how":[12],"diseases":[13],"developed.":[15],"The":[16,85],"traditional":[17],"ways":[18],"to":[19,138],"identify":[20],"the":[21,30,110],"PPIs":[22],"costly":[24],"time-consuming.":[26],"In":[27,108],"recent":[28],"years,":[29],"disruptive":[31],"advances":[32],"in":[33,101,123],"deep":[34,74],"learning":[35,91],"(DL)":[36],"have":[37],"transformed":[38],"computational":[39],"PPI":[40,63,150],"prediction":[41],"by":[42],"enabling":[43],"automatic":[44],"feature":[45,89],"extraction":[46],"from":[47],"protein":[48],"sequences":[49],"structures.":[51],"This":[52],"survey":[53],"presents":[54],"a":[55],"comprehensive":[56],"analysis":[57],"of":[58],"DL-based":[59],"models":[60],"developed":[61],"prediction,":[64],"including":[65],"convolutional":[66,79],"neural":[67,71,75],"networks":[68,72,76,80],"(CNNs),":[69],"recurrent":[70],"(RNNs),":[73],"(DNNs),":[77],"graph":[78],"(GCNs),":[81],"ensemble":[83],"architectures.":[84],"review":[86],"compares":[87],"their":[88,97],"representations,":[90],"strategies,":[92],"evaluation":[94],"benchmarks,":[95],"emphasizing":[96],"strengths":[98],"limitations":[100],"capturing":[102],"complex":[103],"dependencies":[104],"structural":[106],"relationships.":[107],"addition,":[109],"paper":[111],"elaborates":[112],"on":[113],"different":[114,124],"benchmarks":[115],"biological":[117,146],"databases":[118],"that":[119],"commonly":[121],"used":[122],"experiments":[125],"performance":[127],"comparison.":[128],"Finally,":[129],"we":[130],"outline":[131],"open":[132],"challenges":[133],"future":[135],"research":[136],"directions":[137],"enhance":[139],"model":[140],"generalization,":[141],"interpretability,":[142],"integration":[144],"with":[145],"knowledge":[147],"reliable":[149],"prediction.":[151]},"counts_by_year":[],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2026-01-08T00:00:00"}
