{"id":"https://openalex.org/W4411336530","doi":"https://doi.org/10.1186/s13040-025-00457-6","title":"Recent advances in deep learning for protein-protein interaction: a review","display_name":"Recent advances in deep learning for protein-protein interaction: a review","publication_year":2025,"publication_date":"2025-06-16","ids":{"openalex":"https://openalex.org/W4411336530","doi":"https://doi.org/10.1186/s13040-025-00457-6","pmid":"https://pubmed.ncbi.nlm.nih.gov/40524189"},"language":"en","primary_location":{"id":"doi:10.1186/s13040-025-00457-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13040-025-00457-6","pdf_url":"https://biodatamining.biomedcentral.com/counter/pdf/10.1186/s13040-025-00457-6","source":{"id":"https://openalex.org/S84409260","display_name":"BioData Mining","issn_l":"1756-0381","issn":["1756-0381"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BioData Mining","raw_type":"journal-article"},"type":"review","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://biodatamining.biomedcentral.com/counter/pdf/10.1186/s13040-025-00457-6","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":null,"display_name":"Jiafu Cui","orcid":null},"institutions":[{"id":"https://openalex.org/I2722730","display_name":"Inner Mongolia University","ror":"https://ror.org/0106qb496","country_code":"CN","type":"education","lineage":["https://openalex.org/I2722730"]},{"id":"https://openalex.org/I4210159228","display_name":"Inner Mongolia International Mongolian Hospital","ror":"https://ror.org/04xwcs454","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210159228"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Jiafu Cui","raw_affiliation_strings":["Inner Mongolia International Mongolian Hospital, Hohhot, 010065, China","State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Institutes of Biomedical Sciences, College of Life Sciences, Inner Mongolia University, Hohhot, 010021, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Inner Mongolia International Mongolian Hospital, Hohhot, 010065, China","institution_ids":["https://openalex.org/I4210159228"]},{"raw_affiliation_string":"State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Institutes of Biomedical Sciences, College of Life Sciences, Inner Mongolia University, Hohhot, 010021, China","institution_ids":["https://openalex.org/I2722730"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073518856","display_name":"Siqi Yang","orcid":"https://orcid.org/0000-0002-2785-6509"},"institutions":[{"id":"https://openalex.org/I2722730","display_name":"Inner Mongolia University","ror":"https://ror.org/0106qb496","country_code":"CN","type":"education","lineage":["https://openalex.org/I2722730"]},{"id":"https://openalex.org/I4210159228","display_name":"Inner Mongolia International Mongolian Hospital","ror":"https://ror.org/04xwcs454","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210159228"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Siqi Yang","raw_affiliation_strings":["Inner Mongolia International Mongolian Hospital, Hohhot, 010065, China","State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Institutes of Biomedical Sciences, College of Life Sciences, Inner Mongolia University, Hohhot, 010021, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Inner Mongolia International Mongolian Hospital, Hohhot, 010065, China","institution_ids":["https://openalex.org/I4210159228"]},{"raw_affiliation_string":"State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Institutes of Biomedical Sciences, College of Life Sciences, Inner Mongolia University, Hohhot, 010021, China","institution_ids":["https://openalex.org/I2722730"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053445346","display_name":"Litai Yi","orcid":null},"institutions":[{"id":"https://openalex.org/I2722730","display_name":"Inner Mongolia University","ror":"https://ror.org/0106qb496","country_code":"CN","type":"education","lineage":["https://openalex.org/I2722730"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Litai Yi","raw_affiliation_strings":["State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Institutes of Biomedical Sciences, College of Life Sciences, Inner Mongolia University, Hohhot, 010021, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Institutes of Biomedical Sciences, College of Life Sciences, Inner Mongolia University, Hohhot, 010021, China","institution_ids":["https://openalex.org/I2722730"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071202132","display_name":"Qilemuge Xi","orcid":null},"institutions":[{"id":"https://openalex.org/I2722730","display_name":"Inner Mongolia University","ror":"https://ror.org/0106qb496","country_code":"CN","type":"education","lineage":["https://openalex.org/I2722730"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Qilemuge Xi","raw_affiliation_strings":["State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Institutes of Biomedical Sciences, College of Life Sciences, Inner Mongolia University, Hohhot, 010021, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Institutes of Biomedical Sciences, College of Life Sciences, Inner Mongolia University, Hohhot, 010021, China","institution_ids":["https://openalex.org/I2722730"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071956873","display_name":"Dezhi Yang","orcid":"https://orcid.org/0000-0003-4653-9856"},"institutions":[{"id":"https://openalex.org/I2722730","display_name":"Inner Mongolia University","ror":"https://ror.org/0106qb496","country_code":"CN","type":"education","lineage":["https://openalex.org/I2722730"]},{"id":"https://openalex.org/I4210159228","display_name":"Inner Mongolia International Mongolian Hospital","ror":"https://ror.org/04xwcs454","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210159228"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Dezhi Yang","raw_affiliation_strings":["Inner Mongolia International Mongolian Hospital, Hohhot, 010065, China. imudezhi@hotmail.com","State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Institutes of Biomedical Sciences, College of Life Sciences, Inner Mongolia University, Hohhot, 010021, China. imudezhi@hotmail.com"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Inner Mongolia International Mongolian Hospital, Hohhot, 010065, China. imudezhi@hotmail.com","institution_ids":["https://openalex.org/I4210159228"]},{"raw_affiliation_string":"State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Institutes of Biomedical Sciences, College of Life Sciences, Inner Mongolia University, Hohhot, 010021, China. imudezhi@hotmail.com","institution_ids":["https://openalex.org/I2722730"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5001300435","display_name":"Yongchun Zuo","orcid":"https://orcid.org/0000-0002-6065-7835"},"institutions":[{"id":"https://openalex.org/I2722730","display_name":"Inner Mongolia University","ror":"https://ror.org/0106qb496","country_code":"CN","type":"education","lineage":["https://openalex.org/I2722730"]},{"id":"https://openalex.org/I4210159228","display_name":"Inner Mongolia International Mongolian Hospital","ror":"https://ror.org/04xwcs454","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210159228"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yongchun Zuo","raw_affiliation_strings":["Inner Mongolia International Mongolian Hospital, Hohhot, 010065, China. yczuo@imu.edu.cn","State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Institutes of Biomedical Sciences, College of Life Sciences, Inner Mongolia University, Hohhot, 010021, China. yczuo@imu.edu.cn"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Inner Mongolia International Mongolian Hospital, Hohhot, 010065, China. yczuo@imu.edu.cn","institution_ids":["https://openalex.org/I4210159228"]},{"raw_affiliation_string":"State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Institutes of Biomedical Sciences, College of Life Sciences, Inner Mongolia University, Hohhot, 010021, China. yczuo@imu.edu.cn","institution_ids":["https://openalex.org/I2722730"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I2722730","https://openalex.org/I4210159228"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":12.9381,"has_fulltext":true,"cited_by_count":20,"citation_normalized_percentile":{"value":0.99108701,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":100},"biblio":{"volume":"18","issue":"1","first_page":"43","last_page":"43"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9957000017166138,"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":0.9957000017166138,"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":0.9865000247955322,"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":0.9854000210762024,"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":0.6472318172454834},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.4749099016189575},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.45369675755500793},{"id":"https://openalex.org/keywords/protein\u2013protein-interaction","display_name":"Protein\u2013protein interaction","score":0.4122447371482849},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.39363014698028564},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.1391439437866211}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6472318172454834},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.4749099016189575},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.45369675755500793},{"id":"https://openalex.org/C11804247","wikidata":"https://www.wikidata.org/wiki/Q896177","display_name":"Protein\u2013protein interaction","level":2,"score":0.4122447371482849},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.39363014698028564},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.1391439437866211},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1186/s13040-025-00457-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13040-025-00457-6","pdf_url":"https://biodatamining.biomedcentral.com/counter/pdf/10.1186/s13040-025-00457-6","source":{"id":"https://openalex.org/S84409260","display_name":"BioData Mining","issn_l":"1756-0381","issn":["1756-0381"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BioData Mining","raw_type":"journal-article"},{"id":"pmid:40524189","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40524189","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":"BioData mining","raw_type":null},{"id":"pmh:oai:doaj.org/article:4c8e7243aa1c4cd28bdba976626a9a1b","is_oa":true,"landing_page_url":"https://doaj.org/article/4c8e7243aa1c4cd28bdba976626a9a1b","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BioData Mining, Vol 18, Iss 1, Pp 1-23 (2025)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:12168265","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12168265","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":"BioData Min","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s13040-025-00457-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13040-025-00457-6","pdf_url":"https://biodatamining.biomedcentral.com/counter/pdf/10.1186/s13040-025-00457-6","source":{"id":"https://openalex.org/S84409260","display_name":"BioData Mining","issn_l":"1756-0381","issn":["1756-0381"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BioData Mining","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1279121783","display_name":null,"funder_award_id":"62171241","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G2789726379","display_name":null,"funder_award_id":"62403390","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":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4411336530.pdf","grobid_xml":"https://content.openalex.org/works/W4411336530.grobid-xml"},"referenced_works_count":116,"referenced_works":["https://openalex.org/W330916586","https://openalex.org/W755588900","https://openalex.org/W1970008650","https://openalex.org/W1975390541","https://openalex.org/W2082224475","https://openalex.org/W2102475066","https://openalex.org/W2105106534","https://openalex.org/W2118732215","https://openalex.org/W2123060905","https://openalex.org/W2150452800","https://openalex.org/W2163487866","https://openalex.org/W2254563062","https://openalex.org/W2478699542","https://openalex.org/W2486601106","https://openalex.org/W2795471740","https://openalex.org/W2885195348","https://openalex.org/W2972498556","https://openalex.org/W2992433902","https://openalex.org/W3003053789","https://openalex.org/W3070389369","https://openalex.org/W3120634523","https://openalex.org/W3124662554","https://openalex.org/W3153131045","https://openalex.org/W3156270925","https://openalex.org/W3171660645","https://openalex.org/W3172759965","https://openalex.org/W3174714560","https://openalex.org/W3185942550","https://openalex.org/W3186179742","https://openalex.org/W3216616254","https://openalex.org/W3217151645","https://openalex.org/W3217568487","https://openalex.org/W4200404717","https://openalex.org/W4205106657","https://openalex.org/W4205773061","https://openalex.org/W4206718607","https://openalex.org/W4212886242","https://openalex.org/W4212928786","https://openalex.org/W4213041764","https://openalex.org/W4214866973","https://openalex.org/W4220824576","https://openalex.org/W4220897703","https://openalex.org/W4229014893","https://openalex.org/W4233069070","https://openalex.org/W4283278367","https://openalex.org/W4283397333","https://openalex.org/W4283586679","https://openalex.org/W4283716699","https://openalex.org/W4285606307","https://openalex.org/W4290877452","https://openalex.org/W4296564676","https://openalex.org/W4307002224","https://openalex.org/W4309362167","https://openalex.org/W4309438076","https://openalex.org/W4311114767","https://openalex.org/W4317496130","https://openalex.org/W4317867801","https://openalex.org/W4319601650","https://openalex.org/W4319986496","https://openalex.org/W4323545743","https://openalex.org/W4367043522","https://openalex.org/W4376131137","https://openalex.org/W4376649056","https://openalex.org/W4377710512","https://openalex.org/W4381952528","https://openalex.org/W4382407548","https://openalex.org/W4382982095","https://openalex.org/W4384401175","https://openalex.org/W4384818885","https://openalex.org/W4385514835","https://openalex.org/W4386316491","https://openalex.org/W4386634093","https://openalex.org/W4388590853","https://openalex.org/W4388663283","https://openalex.org/W4389166162","https://openalex.org/W4389355715","https://openalex.org/W4390836820","https://openalex.org/W4390906246","https://openalex.org/W4390946589","https://openalex.org/W4391175076","https://openalex.org/W4391792219","https://openalex.org/W4392361079","https://openalex.org/W4392563246","https://openalex.org/W4392817525","https://openalex.org/W4392889312","https://openalex.org/W4395663162","https://openalex.org/W4396858080","https://openalex.org/W4398547136","https://openalex.org/W4399155608","https://openalex.org/W4399303086","https://openalex.org/W4399411203","https://openalex.org/W4400416450","https://openalex.org/W4400449186","https://openalex.org/W4400584406","https://openalex.org/W4400624111","https://openalex.org/W4400766125","https://openalex.org/W4400984795","https://openalex.org/W4401435582","https://openalex.org/W4401728779","https://openalex.org/W4401794303","https://openalex.org/W4402458171","https://openalex.org/W4402847507","https://openalex.org/W4402903640","https://openalex.org/W4403557729","https://openalex.org/W4403762549","https://openalex.org/W4403795029","https://openalex.org/W4404171049","https://openalex.org/W4404184058","https://openalex.org/W4404207188","https://openalex.org/W4404755712","https://openalex.org/W4404850613","https://openalex.org/W4406682344","https://openalex.org/W4408417595","https://openalex.org/W6730084236","https://openalex.org/W6739901393","https://openalex.org/W6875005780"],"related_works":["https://openalex.org/W2731899572","https://openalex.org/W3215138031","https://openalex.org/W3009238340","https://openalex.org/W4360585206","https://openalex.org/W4321369474","https://openalex.org/W4285208911","https://openalex.org/W3082895349","https://openalex.org/W4213079790","https://openalex.org/W2248239756","https://openalex.org/W3086377361"],"abstract_inverted_index":{"Deep":[0],"learning,":[1],"a":[2,45,60,177],"cornerstone":[3],"of":[4,20,26,50,63,95,151,172,185],"artificial":[5],"intelligence,":[6],"is":[7,34,40],"driving":[8],"rapid":[9],"advancements":[10],"in":[11,29,73,166,169,182],"computational":[12,186],"biology.":[13],"Protein-protein":[14],"interactions":[15,135],"(PPIs)":[16],"are":[17],"fundamental":[18],"regulators":[19],"biological":[21],"functions.":[22],"With":[23],"the":[24,32,149,152,160,170,183],"inclusion":[25],"deep":[27,70,167,189],"learning":[28,71,101,168],"PPI":[30,74],"research,":[31],"field":[33,171],"undergoing":[35],"transformative":[36],"changes.":[37],"Therefore,":[38],"there":[39],"an":[41],"urgent":[42],"need":[43],"for":[44,108,116,180],"comprehensive":[46],"review":[47,67,157],"and":[48,57,87,97,104,106,122,139,145,163,188],"assessment":[49],"recent":[51],"developments":[52],"to":[53,78],"improve":[54],"analytical":[55],"methods":[56],"open":[58],"up":[59],"wider":[61],"range":[62],"biomedical":[64],"applications.":[65],"This":[66],"meticulously":[68],"assesses":[69],"progress":[72],"prediction":[75],"from":[76],"2021":[77],"2025.":[79],"We":[80],"evaluate":[81],"core":[82],"architectures":[83],"(GNNs,":[84],"CNNs,":[85],"RNNs)":[86],"pioneering":[88],"approaches-attention-driven":[89],"Transformers,":[90],"multi-task":[91],"frameworks,":[92],"multimodal":[93],"integration":[94],"sequence":[96],"structural":[98],"data,":[99],"transfer":[100],"via":[102],"BERT":[103],"ESM,":[105],"autoencoders":[107],"interaction":[109,174],"characterization.":[110],"Moreover,":[111],"we":[112],"examined":[113],"enhanced":[114],"algorithms":[115],"dealing":[117],"with":[118,136],"data":[119],"imbalances,":[120],"variations,":[121],"high-dimensional":[123],"feature":[124],"sparsity,":[125],"as":[126,128],"well":[127],"industry":[129],"challenges":[130,165],"(including":[131],"shifting":[132],"protein":[133,143,173],"interactions,":[134],"non-model":[137],"organisms,":[138],"rare":[140],"or":[141],"unannotated":[142],"interactions),":[144],"offered":[146],"perspectives":[147],"on":[148],"future":[150],"field.":[153],"In":[154],"summary,":[155],"this":[156],"systematically":[158],"summarizes":[159],"latest":[161],"advances":[162],"existing":[164],"analysis,":[175],"providing":[176],"valuable":[178],"reference":[179],"researchers":[181],"fields":[184],"biology":[187],"learning.":[190]},"counts_by_year":[{"year":2026,"cited_by_count":14},{"year":2025,"cited_by_count":6}],"updated_date":"2026-05-16T08:24:45.110214","created_date":"2025-10-10T00:00:00"}