{"id":"https://openalex.org/W4412454121","doi":"https://doi.org/10.1093/bioinformatics/btaf192","title":"Deep learning models for unbiased sequence-based PPI prediction plateau at an accuracy of 0.65","display_name":"Deep learning models for unbiased sequence-based PPI prediction plateau at an accuracy of 0.65","publication_year":2025,"publication_date":"2025-07-01","ids":{"openalex":"https://openalex.org/W4412454121","doi":"https://doi.org/10.1093/bioinformatics/btaf192","pmid":"https://pubmed.ncbi.nlm.nih.gov/40662806"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaf192","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf192","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/41/Supplement_1/i590/63745496/btaf192.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"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/bioinformatics/article-pdf/41/Supplement_1/i590/63745496/btaf192.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5116033015","display_name":"Timo Reim","orcid":null},"institutions":[{"id":"https://openalex.org/I181369854","display_name":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","ror":"https://ror.org/00f7hpc57","country_code":"DE","type":"education","lineage":["https://openalex.org/I181369854"]},{"id":"https://openalex.org/I62916508","display_name":"Technical University of Munich","ror":"https://ror.org/02kkvpp62","country_code":"DE","type":"education","lineage":["https://openalex.org/I62916508"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Timo Reim","raw_affiliation_strings":["Data Science in Systems Biology, TUM School of Life Sciences, Technical University of Munich , Freising, 85354,","Department Artificial Intelligence in Biomedical Engineering, Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg , Erlangen, 91052,"],"raw_orcid":"https://orcid.org/0009-0002-7307-1347","affiliations":[{"raw_affiliation_string":"Data Science in Systems Biology, TUM School of Life Sciences, Technical University of Munich , Freising, 85354,","institution_ids":["https://openalex.org/I62916508"]},{"raw_affiliation_string":"Department Artificial Intelligence in Biomedical Engineering, Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg , Erlangen, 91052,","institution_ids":["https://openalex.org/I181369854"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075534812","display_name":"Anne Hartebrodt","orcid":"https://orcid.org/0000-0002-9172-3137"},"institutions":[{"id":"https://openalex.org/I181369854","display_name":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","ror":"https://ror.org/00f7hpc57","country_code":"DE","type":"education","lineage":["https://openalex.org/I181369854"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Anne Hartebrodt","raw_affiliation_strings":["Department Artificial Intelligence in Biomedical Engineering, Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg , Erlangen, 91052,"],"raw_orcid":"https://orcid.org/0000-0002-9172-3137","affiliations":[{"raw_affiliation_string":"Department Artificial Intelligence in Biomedical Engineering, Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg , Erlangen, 91052,","institution_ids":["https://openalex.org/I181369854"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5087738237","display_name":"David B. Blumenthal","orcid":"https://orcid.org/0000-0001-8651-750X"},"institutions":[{"id":"https://openalex.org/I181369854","display_name":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","ror":"https://ror.org/00f7hpc57","country_code":"DE","type":"education","lineage":["https://openalex.org/I181369854"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"David B Blumenthal","raw_affiliation_strings":["Department Artificial Intelligence in Biomedical Engineering, Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg , Erlangen, 91052,"],"raw_orcid":"https://orcid.org/0000-0001-8651-750X","affiliations":[{"raw_affiliation_string":"Department Artificial Intelligence in Biomedical Engineering, Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg , Erlangen, 91052,","institution_ids":["https://openalex.org/I181369854"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032713341","display_name":"Judith Bernett","orcid":"https://orcid.org/0000-0001-5812-8013"},"institutions":[{"id":"https://openalex.org/I62916508","display_name":"Technical University of Munich","ror":"https://ror.org/02kkvpp62","country_code":"DE","type":"education","lineage":["https://openalex.org/I62916508"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Judith Bernett","raw_affiliation_strings":["Data Science in Systems Biology, TUM School of Life Sciences, Technical University of Munich , Freising, 85354,"],"raw_orcid":"https://orcid.org/0000-0001-5812-8013","affiliations":[{"raw_affiliation_string":"Data Science in Systems Biology, TUM School of Life Sciences, Technical University of Munich , Freising, 85354,","institution_ids":["https://openalex.org/I62916508"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5035928806","display_name":"Markus List","orcid":null},"institutions":[{"id":"https://openalex.org/I62916508","display_name":"Technical University of Munich","ror":"https://ror.org/02kkvpp62","country_code":"DE","type":"education","lineage":["https://openalex.org/I62916508"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Markus List","raw_affiliation_strings":["Data Science in Systems Biology, TUM School of Life Sciences, Technical University of Munich , Freising, 85354,","Munich Data Science Institute (MDSI), Technical University of Munich , Garching bei M\u00fcnchen, 85748,"],"raw_orcid":"https://orcid.org/0000-0002-0941-4168","affiliations":[{"raw_affiliation_string":"Data Science in Systems Biology, TUM School of Life Sciences, Technical University of Munich , Freising, 85354,","institution_ids":["https://openalex.org/I62916508"]},{"raw_affiliation_string":"Munich Data Science Institute (MDSI), Technical University of Munich , Garching bei M\u00fcnchen, 85748,","institution_ids":["https://openalex.org/I62916508"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5116033015"],"corresponding_institution_ids":["https://openalex.org/I181369854","https://openalex.org/I62916508"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":3.5287,"has_fulltext":true,"cited_by_count":6,"citation_normalized_percentile":{"value":0.9297339,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":99},"biblio":{"volume":"41","issue":"Supplement_1","first_page":"i590","last_page":"i598"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.6007999777793884,"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":0.6007999777793884,"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":0.2793000042438507,"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":0.011599999852478504,"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/python","display_name":"Python (programming language)","score":0.8779366612434387},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.808812141418457},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.6063662171363831},{"id":"https://openalex.org/keywords/code","display_name":"Code (set theory)","score":0.49018603563308716},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.47975218296051025},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.45686811208724976},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4017845392227173},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3850550651550293},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.18426725268363953},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.10336419939994812}],"concepts":[{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.8779366612434387},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.808812141418457},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.6063662171363831},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.49018603563308716},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.47975218296051025},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.45686811208724976},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4017845392227173},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3850550651550293},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.18426725268363953},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.10336419939994812},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","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":"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":"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":"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":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btaf192","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf192","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/41/Supplement_1/i590/63745496/btaf192.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40662806","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40662806","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:12261406","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12261406","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":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btaf192","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf192","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/41/Supplement_1/i590/63745496/btaf192.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1787481955","display_name":null,"funder_award_id":"031L0309A","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"},{"id":"https://openalex.org/G191025471","display_name":null,"funder_award_id":"422216132","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G2719516887","display_name":null,"funder_award_id":"00.003.2024","funder_id":"https://openalex.org/F4320324316","funder_display_name":"Klaus Tschira Stiftung"},{"id":"https://openalex.org/G3185613439","display_name":null,"funder_award_id":"031L0305A","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"}],"funders":[{"id":"https://openalex.org/F4320320879","display_name":"Deutsche Forschungsgemeinschaft","ror":"https://ror.org/018mejw64"},{"id":"https://openalex.org/F4320321114","display_name":"Bundesministerium f\u00fcr Bildung und Forschung","ror":"https://ror.org/04pz7b180"},{"id":"https://openalex.org/F4320324316","display_name":"Klaus Tschira Stiftung","ror":"https://ror.org/052jep661"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4412454121.pdf","grobid_xml":"https://content.openalex.org/works/W4412454121.grobid-xml"},"referenced_works_count":19,"referenced_works":["https://openalex.org/W1982732642","https://openalex.org/W1990315216","https://openalex.org/W2130479394","https://openalex.org/W2252854990","https://openalex.org/W2534390616","https://openalex.org/W2908914784","https://openalex.org/W2909727437","https://openalex.org/W3177828909","https://openalex.org/W3199468887","https://openalex.org/W4392500220","https://openalex.org/W4397043191","https://openalex.org/W4399849668","https://openalex.org/W4400984795","https://openalex.org/W4401662181","https://openalex.org/W4401889166","https://openalex.org/W4403170495","https://openalex.org/W4406440058","https://openalex.org/W4406604520","https://openalex.org/W6902324070"],"related_works":["https://openalex.org/W2341492732","https://openalex.org/W3187193180","https://openalex.org/W106542691","https://openalex.org/W1699080303","https://openalex.org/W4297799326","https://openalex.org/W3116064965","https://openalex.org/W4287027380","https://openalex.org/W2789551765","https://openalex.org/W2348534359","https://openalex.org/W3081644756"],"abstract_inverted_index":{"MOTIVATION:":[0],"As":[1],"most":[2],"proteins":[3,7],"interact":[4],"with":[5,84],"other":[6,131,180],"to":[8,14],"perform":[9],"their":[10],"respective":[11],"functions,":[12],"methods":[13,48],"computationally":[15],"predict":[16],"these":[17],"interactions":[18],"have":[19,32,56],"been":[20,57],"developed.":[21],"However,":[22],"flawed":[23],"evaluation":[24],"schemes":[25],"and":[26,88,152,164],"data":[27,55,192],"leakage":[28],"in":[29,186],"test":[30],"sets":[31],"obscured":[33],"the":[34,64,80,94,113,155,176,187],"fact":[35],"that":[36,63,112,130],"sequence-based":[37,115],"protein-protein":[38],"interaction":[39],"(PPI)":[40],"prediction":[41],"is":[42,157],"still":[43],"an":[44,105,124],"open":[45],"problem.":[46],"Recently,":[47],"achieving":[49],"better-than-random":[50],"performance":[51,72,81],"on":[52],"leakage-reduced":[53],"PPI":[54,143],"proposed.":[58],"RESULTS:":[59],"Here,":[60],"we":[61,110],"show":[62,111],"use":[65],"of":[66,75,82,96,107,154,178],"ESM-2":[67],"protein":[68],"embeddings":[69],"explains":[70],"this":[71,171],"gain":[73],"irrespective":[74],"model":[76],"architecture.":[77],"We":[78],"compared":[79],"models":[83,102,116,151,156],"varying":[85],"complexity,":[86],"per-protein,":[87],"per-token":[89],"embeddings,":[90],"as":[91,93,123,135],"well":[92],"influence":[95],"self-":[97],"or":[98],"cross-attention,":[99],"where":[100],"all":[101,179],"plateaued":[103],"at":[104,159,195],"accuracy":[106],"0.65.":[108],"Moreover,":[109],"tested":[114],"cannot":[117],"implicitly":[118],"learn":[119],"a":[120],"contact":[121],"map":[122],"intermediate":[125],"layer.":[126],"These":[127],"results":[128],"imply":[129],"input":[132],"types,":[133],"such":[134],"structure,":[136],"might":[137],"be":[138,184],"necessary":[139],"for":[140,150,170],"producing":[141],"reliable":[142],"predictions.":[144],"AVAILABILITY":[145],"AND":[146],"IMPLEMENTATION:":[147],"All":[148],"code":[149],"execution":[153],"available":[158,194],"https://github.com/daisybio/PPI_prediction_study.":[160],"Python":[161],"version":[162,166],"3.8.18":[163],"PyTorch":[165],"2.1.1":[167],"were":[168],"used":[169,182,191],"study.":[172],"The":[173,190],"environment":[174],"containing":[175],"versions":[177],"packages":[181],"can":[183],"found":[185],"GitHub":[188],"repository.":[189],"are":[193],"https://doi.org/10.6084/m9.figshare.21591618.v3.":[196]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":3}],"updated_date":"2026-06-06T09:05:17.133730","created_date":"2025-10-10T00:00:00"}
