{"id":"https://openalex.org/W4413775728","doi":"https://doi.org/10.1093/bib/bbaf434","title":"ESM2_AMP: an interpretable framework for protein\u2013protein interactions prediction and biological mechanism discovery","display_name":"ESM2_AMP: an interpretable framework for protein\u2013protein interactions prediction and biological mechanism discovery","publication_year":2025,"publication_date":"2025-07-01","ids":{"openalex":"https://openalex.org/W4413775728","doi":"https://doi.org/10.1093/bib/bbaf434","pmid":"https://pubmed.ncbi.nlm.nih.gov/40874821"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbaf434","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf434","pdf_url":"https://academic.oup.com/bib/article-pdf/26/4/bbaf434/64148085/bbaf434.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","license_id":"https://openalex.org/licenses/cc-by","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/26/4/bbaf434/64148085/bbaf434.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5101494206","display_name":"Yawen Sun","orcid":"https://orcid.org/0009-0001-8955-6333"},"institutions":[{"id":"https://openalex.org/I126924076","display_name":"Chongqing Normal University","ror":"https://ror.org/01dcw5w74","country_code":"CN","type":"education","lineage":["https://openalex.org/I126924076"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yawen Sun","raw_affiliation_strings":["College of Life Science, Chongqing Normal University , No. 37 University Town Road, high-tech District, Chongqing 401331 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Life Science, Chongqing Normal University , No. 37 University Town Road, high-tech District, Chongqing 401331 ,","institution_ids":["https://openalex.org/I126924076"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5092030203","display_name":"Rui Wang","orcid":"https://orcid.org/0009-0004-4099-2267"},"institutions":[{"id":"https://openalex.org/I126924076","display_name":"Chongqing Normal University","ror":"https://ror.org/01dcw5w74","country_code":"CN","type":"education","lineage":["https://openalex.org/I126924076"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Rui Wang","raw_affiliation_strings":["College of Life Science, Chongqing Normal University , No. 37 University Town Road, high-tech District, Chongqing 401331 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Life Science, Chongqing Normal University , No. 37 University Town Road, high-tech District, Chongqing 401331 ,","institution_ids":["https://openalex.org/I126924076"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101920182","display_name":"Zeyu Luo","orcid":"https://orcid.org/0000-0001-6650-9975"},"institutions":[{"id":"https://openalex.org/I126924076","display_name":"Chongqing Normal University","ror":"https://ror.org/01dcw5w74","country_code":"CN","type":"education","lineage":["https://openalex.org/I126924076"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zeyu Luo","raw_affiliation_strings":["College of Life Science, Chongqing Normal University , No. 37 University Town Road, high-tech District, Chongqing 401331 ,"],"raw_orcid":"https://orcid.org/0000-0001-6650-9975","affiliations":[{"raw_affiliation_string":"College of Life Science, Chongqing Normal University , No. 37 University Town Road, high-tech District, Chongqing 401331 ,","institution_ids":["https://openalex.org/I126924076"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Lejia Tan","orcid":null},"institutions":[{"id":"https://openalex.org/I126924076","display_name":"Chongqing Normal University","ror":"https://ror.org/01dcw5w74","country_code":"CN","type":"education","lineage":["https://openalex.org/I126924076"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Lejia Tan","raw_affiliation_strings":["College of Life Science, Chongqing Normal University , No. 37 University Town Road, high-tech District, Chongqing 401331 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Life Science, Chongqing Normal University , No. 37 University Town Road, high-tech District, Chongqing 401331 ,","institution_ids":["https://openalex.org/I126924076"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100725207","display_name":"Junhao Liu","orcid":"https://orcid.org/0009-0004-8535-4349"},"institutions":[{"id":"https://openalex.org/I126924076","display_name":"Chongqing Normal University","ror":"https://ror.org/01dcw5w74","country_code":"CN","type":"education","lineage":["https://openalex.org/I126924076"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Junhao Liu","raw_affiliation_strings":["College of Life Science, Chongqing Normal University , No. 37 University Town Road, high-tech District, Chongqing 401331 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Life Science, Chongqing Normal University , No. 37 University Town Road, high-tech District, Chongqing 401331 ,","institution_ids":["https://openalex.org/I126924076"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008420397","display_name":"Ruimeng Li","orcid":"https://orcid.org/0000-0001-8138-5384"},"institutions":[{"id":"https://openalex.org/I126924076","display_name":"Chongqing Normal University","ror":"https://ror.org/01dcw5w74","country_code":"CN","type":"education","lineage":["https://openalex.org/I126924076"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Ruimeng Li","raw_affiliation_strings":["College of Life Science, Chongqing Normal University , No. 37 University Town Road, high-tech District, Chongqing 401331 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Life Science, Chongqing Normal University , No. 37 University Town Road, high-tech District, Chongqing 401331 ,","institution_ids":["https://openalex.org/I126924076"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041491902","display_name":"Dong\u2010Qing Wei","orcid":"https://orcid.org/0000-0003-4200-7502"},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Dongqing Wei","raw_affiliation_strings":["State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University , 800 Dongchuan RD. Minhang District, Shanghai 200030 ,"],"raw_orcid":"https://orcid.org/0000-0003-4200-7502","affiliations":[{"raw_affiliation_string":"State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University , 800 Dongchuan RD. Minhang District, Shanghai 200030 ,","institution_ids":["https://openalex.org/I183067930"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100641285","display_name":"Yu\u2010Juan Zhang","orcid":"https://orcid.org/0000-0001-6361-0840"},"institutions":[{"id":"https://openalex.org/I126924076","display_name":"Chongqing Normal University","ror":"https://ror.org/01dcw5w74","country_code":"CN","type":"education","lineage":["https://openalex.org/I126924076"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yu-Juan Zhang","raw_affiliation_strings":["College of Life Science, Chongqing Normal University , No. 37 University Town Road, high-tech District, Chongqing 401331 ,"],"raw_orcid":"https://orcid.org/0000-0001-6361-0840","affiliations":[{"raw_affiliation_string":"College of Life Science, Chongqing Normal University , No. 37 University Town Road, high-tech District, Chongqing 401331 ,","institution_ids":["https://openalex.org/I126924076"]}]}],"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":3.4558,"has_fulltext":true,"cited_by_count":6,"citation_normalized_percentile":{"value":0.92947788,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":95,"max":99},"biblio":{"volume":"26","issue":"4","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":0.9980999827384949,"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":0.9980999827384949,"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":0.9930999875068665,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9833999872207642,"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/mechanism","display_name":"Mechanism (biology)","score":0.7556264400482178},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6016355752944946},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.48216456174850464},{"id":"https://openalex.org/keywords/protein\u2013protein-interaction","display_name":"Protein\u2013protein interaction","score":0.42441922426223755},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3979964554309845},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.20160865783691406},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.06925368309020996},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.049199074506759644}],"concepts":[{"id":"https://openalex.org/C89611455","wikidata":"https://www.wikidata.org/wiki/Q6804646","display_name":"Mechanism (biology)","level":2,"score":0.7556264400482178},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6016355752944946},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.48216456174850464},{"id":"https://openalex.org/C11804247","wikidata":"https://www.wikidata.org/wiki/Q896177","display_name":"Protein\u2013protein interaction","level":2,"score":0.42441922426223755},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3979964554309845},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.20160865783691406},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.06925368309020996},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.049199074506759644},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep 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":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","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":"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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"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":"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/bbaf434","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf434","pdf_url":"https://academic.oup.com/bib/article-pdf/26/4/bbaf434/64148085/bbaf434.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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40874821","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40874821","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:12392411","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12392411","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":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbaf434","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf434","pdf_url":"https://academic.oup.com/bib/article-pdf/26/4/bbaf434/64148085/bbaf434.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","license_id":"https://openalex.org/licenses/cc-by","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/G2796437284","display_name":null,"funder_award_id":"CSTB2022NSCQ","funder_id":"https://openalex.org/F4320323172","funder_display_name":"Natural Science Foundation of Chongqing"},{"id":"https://openalex.org/G8160223316","display_name":null,"funder_award_id":"31871274","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"},{"id":"https://openalex.org/F4320323172","display_name":"Natural Science Foundation of Chongqing","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320327639","display_name":"Centre Scientifique et Technique du B\u00e2timent","ror":"https://ror.org/02fsd1928"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4413775728.pdf","grobid_xml":"https://content.openalex.org/works/W4413775728.grobid-xml"},"referenced_works_count":59,"referenced_works":["https://openalex.org/W1502414852","https://openalex.org/W1924770834","https://openalex.org/W1977186059","https://openalex.org/W1982267716","https://openalex.org/W2044523575","https://openalex.org/W2060167685","https://openalex.org/W2129328366","https://openalex.org/W2131562240","https://openalex.org/W2144327682","https://openalex.org/W2152705149","https://openalex.org/W2890911678","https://openalex.org/W2896457183","https://openalex.org/W2898221567","https://openalex.org/W2908510526","https://openalex.org/W2912250830","https://openalex.org/W2912351236","https://openalex.org/W2949608135","https://openalex.org/W2952253955","https://openalex.org/W2957436444","https://openalex.org/W2962897394","https://openalex.org/W2999615587","https://openalex.org/W3035800748","https://openalex.org/W3134169372","https://openalex.org/W3177500196","https://openalex.org/W3199468887","https://openalex.org/W4200461926","https://openalex.org/W4206472390","https://openalex.org/W4206994187","https://openalex.org/W4212946592","https://openalex.org/W4226343290","https://openalex.org/W4243150065","https://openalex.org/W4283776301","https://openalex.org/W4309506674","https://openalex.org/W4315641887","https://openalex.org/W4321214126","https://openalex.org/W4321851522","https://openalex.org/W4323348775","https://openalex.org/W4327550249","https://openalex.org/W4376613177","https://openalex.org/W4382931089","https://openalex.org/W4385245566","https://openalex.org/W4387355882","https://openalex.org/W4388094481","https://openalex.org/W4388422655","https://openalex.org/W4388627827","https://openalex.org/W4389956103","https://openalex.org/W4391280974","https://openalex.org/W4392050246","https://openalex.org/W4392500220","https://openalex.org/W4392633839","https://openalex.org/W4394662631","https://openalex.org/W4399307561","https://openalex.org/W4400984795","https://openalex.org/W4401455176","https://openalex.org/W4404141244","https://openalex.org/W4404374284","https://openalex.org/W4404531735","https://openalex.org/W4405534159","https://openalex.org/W4406167408"],"related_works":["https://openalex.org/W2899084033","https://openalex.org/W2099982459","https://openalex.org/W2109298101","https://openalex.org/W2007507741","https://openalex.org/W2159860826","https://openalex.org/W3192210502","https://openalex.org/W1981737222","https://openalex.org/W1569394480","https://openalex.org/W4390876228","https://openalex.org/W1998222399"],"abstract_inverted_index":{"The":[0,93],"prediction":[1,181],"of":[2,25,80,117,159,166,193,213],"binary":[3,62],"protein-protein":[4,197],"interactions":[5],"(PPIs)":[6],"is":[7,20],"essential":[8],"for":[9,44,58,179,203],"protein":[10,41],"engineering,":[11],"but":[12,183],"a":[13],"major":[14],"challenge":[15],"in":[16,61,89,169,196,210],"deep":[17],"learning-based":[18],"methods":[19,178],"the":[21,26,34,39,55,66,78,90,98,139,151,163,176,189,211],"unknown":[22],"decision-making":[23,91],"process":[24],"model.":[27],"To":[28],"address":[29],"this":[30],"challenge,":[31],"we":[32,149],"propose":[33],"ESM2_AMP":[35],"framework,":[36],"which":[37],"utilizes":[38],"ESM2":[40],"language":[42],"model":[43,57,99],"extracting":[45],"segment":[46,81,102,157],"features":[47,82,88,103,158],"from":[48],"actual":[49],"amino":[50,118],"acid":[51,119],"sequences":[52,195],"and":[53,71,83,113,134,146,161,206],"integrates":[54],"Transformer":[56],"feature":[59],"fusion":[60],"PPIs":[63,160],"prediction.":[64],"Further,":[65],"two":[67],"distinct":[68],"models,":[69],"ESM2_AMPS":[70],"ESM2_AMP_CSE":[72],"are":[73],"developed":[74],"to":[75,126,154],"systematically":[76],"explore":[77],"contributions":[79],"combine":[84],"with":[85,109],"special":[86],"tokens":[87],"process.":[92],"experimental":[94,207],"results":[95],"reveal":[96],"that":[97,124],"relying":[100],"on":[101],"demonstrates":[104],"strong":[105],"correlations":[106],"between":[107,142],"segments":[108,128],"high":[110],"attention":[111,125],"weights":[112],"known":[114],"functional":[115,133,147,167,194],"regions":[116],"sequences.":[120],"This":[121,171],"insight":[122],"suggests":[123],"these":[127],"helps":[129],"capture":[130,155],"biologically":[131],"relevant":[132],"interaction-related":[135],"information.":[136],"By":[137],"analyzing":[138],"coverage":[140],"relationship":[141],"high-attention":[143],"sequence":[144],"fragments":[145],"regions,":[148],"validated":[150],"model's":[152],"ability":[153],"key":[156],"revealed":[162],"critical":[164],"role":[165,192],"domains":[168],"PPIs.":[170],"finding":[172],"not":[173],"only":[174],"enhances":[175],"interpretability":[177],"sequence-based":[180],"models":[182],"also":[184],"provides":[185],"biological":[186],"evidence":[187],"supporting":[188],"important":[190],"regulatory":[191],"interactions.":[198],"It":[199],"offers":[200],"cross-disciplinary":[201],"insights":[202],"algorithm":[204],"optimization":[205],"validation":[208],"research":[209],"field":[212],"computational":[214],"biology.":[215]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":2}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}
