{"id":"https://openalex.org/W4409229134","doi":"https://doi.org/10.1093/bioinformatics/btaf148","title":"Topology-driven negative sampling enhances generalizability in protein\u2013protein interaction prediction","display_name":"Topology-driven negative sampling enhances generalizability in protein\u2013protein interaction prediction","publication_year":2025,"publication_date":"2025-04-07","ids":{"openalex":"https://openalex.org/W4409229134","doi":"https://doi.org/10.1093/bioinformatics/btaf148","pmid":"https://pubmed.ncbi.nlm.nih.gov/40193392"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaf148","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf148","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf148/62884278/btaf148.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/advance-article-pdf/doi/10.1093/bioinformatics/btaf148/62884278/btaf148.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5109577234","display_name":"Aparajita Chatterjee","orcid":"https://orcid.org/0000-0002-8662-4863"},"institutions":[{"id":"https://openalex.org/I12912129","display_name":"Northeastern University","ror":"https://ror.org/04t5xt781","country_code":"US","type":"education","lineage":["https://openalex.org/I12912129"]},{"id":"https://openalex.org/I145236414","display_name":"Alliance Bioversity International - CIAT","ror":"https://ror.org/04xsxqp89","country_code":"IT","type":"nonprofit","lineage":["https://openalex.org/I1286583668","https://openalex.org/I145236414"]},{"id":"https://openalex.org/I4210116875","display_name":"AstraZeneca (Brazil)","ror":"https://ror.org/026m9xy48","country_code":"BR","type":"company","lineage":["https://openalex.org/I105036370","https://openalex.org/I4210116875"]},{"id":"https://openalex.org/I4210150756","display_name":"AstraZeneca (United States)","ror":"https://ror.org/043cec594","country_code":"US","type":"company","lineage":["https://openalex.org/I105036370","https://openalex.org/I4210150756"]},{"id":"https://openalex.org/I49313256","display_name":"Alexion Pharma (Switzerland)","ror":"https://ror.org/05hkjyh45","country_code":"CH","type":"company","lineage":["https://openalex.org/I49313256"]}],"countries":["BR","CH","IT","US"],"is_corresponding":false,"raw_author_name":"Ayan Chatterjee","raw_affiliation_strings":["BioClarity AI , Boston, MA 02130,","Bioinformatics and Data Science, Alexion AstraZeneca Rare Disease , Boston, MA 02210,","Network Science Institute, Northeastern University , Boston, MA 02115,","Alexion AstraZeneca Rare Disease Bioinformatics and Data Science, , Boston, MA","BioClarity AI , Boston, MA","Northeastern University Network Science Institute, , Boston, MA"],"raw_orcid":"https://orcid.org/0000-0002-8662-4863","affiliations":[{"raw_affiliation_string":"BioClarity AI , Boston, MA 02130,","institution_ids":["https://openalex.org/I145236414"]},{"raw_affiliation_string":"Bioinformatics and Data Science, Alexion AstraZeneca Rare Disease , Boston, MA 02210,","institution_ids":["https://openalex.org/I49313256","https://openalex.org/I4210116875"]},{"raw_affiliation_string":"Network Science Institute, Northeastern University , Boston, MA 02115,","institution_ids":["https://openalex.org/I12912129"]},{"raw_affiliation_string":"Alexion AstraZeneca Rare Disease Bioinformatics and Data Science, , Boston, MA","institution_ids":["https://openalex.org/I4210150756"]},{"raw_affiliation_string":"BioClarity AI , Boston, MA","institution_ids":[]},{"raw_affiliation_string":"Northeastern University Network Science Institute, , Boston, MA","institution_ids":["https://openalex.org/I12912129"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076067124","display_name":"Babak Ravandi","orcid":"https://orcid.org/0000-0003-0203-5605"},"institutions":[{"id":"https://openalex.org/I12912129","display_name":"Northeastern University","ror":"https://ror.org/04t5xt781","country_code":"US","type":"education","lineage":["https://openalex.org/I12912129"]},{"id":"https://openalex.org/I4210116875","display_name":"AstraZeneca (Brazil)","ror":"https://ror.org/026m9xy48","country_code":"BR","type":"company","lineage":["https://openalex.org/I105036370","https://openalex.org/I4210116875"]},{"id":"https://openalex.org/I4210150756","display_name":"AstraZeneca (United States)","ror":"https://ror.org/043cec594","country_code":"US","type":"company","lineage":["https://openalex.org/I105036370","https://openalex.org/I4210150756"]},{"id":"https://openalex.org/I49313256","display_name":"Alexion Pharma (Switzerland)","ror":"https://ror.org/05hkjyh45","country_code":"CH","type":"company","lineage":["https://openalex.org/I49313256"]}],"countries":["BR","CH","US"],"is_corresponding":false,"raw_author_name":"Babak Ravandi","raw_affiliation_strings":["Bioinformatics and Data Science, Alexion AstraZeneca Rare Disease , Boston, MA 02210,","Department of Physics, Northeastern University , Boston, MA 02115,","Network Science Institute, Northeastern University , Boston, MA 02115,","Alexion AstraZeneca Rare Disease Bioinformatics and Data Science, , Boston, MA","Northeastern University Department of Physics, , Boston, MA","Northeastern University Network Science Institute, , Boston, MA"],"raw_orcid":"https://orcid.org/0000-0003-0203-5605","affiliations":[{"raw_affiliation_string":"Bioinformatics and Data Science, Alexion AstraZeneca Rare Disease , Boston, MA 02210,","institution_ids":["https://openalex.org/I49313256","https://openalex.org/I4210116875"]},{"raw_affiliation_string":"Department of Physics, Northeastern University , Boston, MA 02115,","institution_ids":["https://openalex.org/I12912129"]},{"raw_affiliation_string":"Network Science Institute, Northeastern University , Boston, MA 02115,","institution_ids":["https://openalex.org/I12912129"]},{"raw_affiliation_string":"Alexion AstraZeneca Rare Disease Bioinformatics and Data Science, , Boston, MA","institution_ids":["https://openalex.org/I4210150756"]},{"raw_affiliation_string":"Northeastern University Department of Physics, , Boston, MA","institution_ids":["https://openalex.org/I12912129"]},{"raw_affiliation_string":"Northeastern University Network Science Institute, , Boston, MA","institution_ids":["https://openalex.org/I12912129"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054738550","display_name":"Parham Haddadi","orcid":"https://orcid.org/0000-0002-1876-4055"},"institutions":[{"id":"https://openalex.org/I4210116875","display_name":"AstraZeneca (Brazil)","ror":"https://ror.org/026m9xy48","country_code":"BR","type":"company","lineage":["https://openalex.org/I105036370","https://openalex.org/I4210116875"]},{"id":"https://openalex.org/I4210150756","display_name":"AstraZeneca (United States)","ror":"https://ror.org/043cec594","country_code":"US","type":"company","lineage":["https://openalex.org/I105036370","https://openalex.org/I4210150756"]},{"id":"https://openalex.org/I49313256","display_name":"Alexion Pharma (Switzerland)","ror":"https://ror.org/05hkjyh45","country_code":"CH","type":"company","lineage":["https://openalex.org/I49313256"]}],"countries":["BR","CH","US"],"is_corresponding":false,"raw_author_name":"Parham Haddadi","raw_affiliation_strings":["Bioinformatics and Data Science, Alexion AstraZeneca Rare Disease , Boston, MA 02210,","Alexion AstraZeneca Rare Disease Bioinformatics and Data Science, , Boston, MA"],"raw_orcid":"https://orcid.org/0000-0002-1876-4055","affiliations":[{"raw_affiliation_string":"Bioinformatics and Data Science, Alexion AstraZeneca Rare Disease , Boston, MA 02210,","institution_ids":["https://openalex.org/I49313256","https://openalex.org/I4210116875"]},{"raw_affiliation_string":"Alexion AstraZeneca Rare Disease Bioinformatics and Data Science, , Boston, MA","institution_ids":["https://openalex.org/I4210150756"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076130891","display_name":"Naomi H. Philip","orcid":"https://orcid.org/0000-0002-1475-8635"},"institutions":[{"id":"https://openalex.org/I4210116875","display_name":"AstraZeneca (Brazil)","ror":"https://ror.org/026m9xy48","country_code":"BR","type":"company","lineage":["https://openalex.org/I105036370","https://openalex.org/I4210116875"]},{"id":"https://openalex.org/I4210150756","display_name":"AstraZeneca (United States)","ror":"https://ror.org/043cec594","country_code":"US","type":"company","lineage":["https://openalex.org/I105036370","https://openalex.org/I4210150756"]},{"id":"https://openalex.org/I49313256","display_name":"Alexion Pharma (Switzerland)","ror":"https://ror.org/05hkjyh45","country_code":"CH","type":"company","lineage":["https://openalex.org/I49313256"]}],"countries":["BR","CH","US"],"is_corresponding":false,"raw_author_name":"Naomi H Philip","raw_affiliation_strings":["Bioinformatics and Data Science, Alexion AstraZeneca Rare Disease , Boston, MA 02210,","Alexion AstraZeneca Rare Disease Bioinformatics and Data Science, , Boston, MA"],"raw_orcid":"https://orcid.org/0000-0002-1475-8635","affiliations":[{"raw_affiliation_string":"Bioinformatics and Data Science, Alexion AstraZeneca Rare Disease , Boston, MA 02210,","institution_ids":["https://openalex.org/I49313256","https://openalex.org/I4210116875"]},{"raw_affiliation_string":"Alexion AstraZeneca Rare Disease Bioinformatics and Data Science, , Boston, MA","institution_ids":["https://openalex.org/I4210150756"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5095925777","display_name":"Mario Abdelmessih","orcid":"https://orcid.org/0000-0003-2887-5741"},"institutions":[{"id":"https://openalex.org/I4210116875","display_name":"AstraZeneca (Brazil)","ror":"https://ror.org/026m9xy48","country_code":"BR","type":"company","lineage":["https://openalex.org/I105036370","https://openalex.org/I4210116875"]},{"id":"https://openalex.org/I4210150756","display_name":"AstraZeneca (United States)","ror":"https://ror.org/043cec594","country_code":"US","type":"company","lineage":["https://openalex.org/I105036370","https://openalex.org/I4210150756"]},{"id":"https://openalex.org/I49313256","display_name":"Alexion Pharma (Switzerland)","ror":"https://ror.org/05hkjyh45","country_code":"CH","type":"company","lineage":["https://openalex.org/I49313256"]}],"countries":["BR","CH","US"],"is_corresponding":false,"raw_author_name":"Mario Abdelmessih","raw_affiliation_strings":["Bioinformatics and Data Science, Alexion AstraZeneca Rare Disease , Boston, MA 02210,","Alexion AstraZeneca Rare Disease Bioinformatics and Data Science, , Boston, MA"],"raw_orcid":"https://orcid.org/0000-0003-2887-5741","affiliations":[{"raw_affiliation_string":"Bioinformatics and Data Science, Alexion AstraZeneca Rare Disease , Boston, MA 02210,","institution_ids":["https://openalex.org/I49313256","https://openalex.org/I4210116875"]},{"raw_affiliation_string":"Alexion AstraZeneca Rare Disease Bioinformatics and Data Science, , Boston, MA","institution_ids":["https://openalex.org/I4210150756"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5027244211","display_name":"William R. Mowrey","orcid":"https://orcid.org/0000-0001-9531-9409"},"institutions":[{"id":"https://openalex.org/I4210116875","display_name":"AstraZeneca (Brazil)","ror":"https://ror.org/026m9xy48","country_code":"BR","type":"company","lineage":["https://openalex.org/I105036370","https://openalex.org/I4210116875"]},{"id":"https://openalex.org/I4210150756","display_name":"AstraZeneca (United States)","ror":"https://ror.org/043cec594","country_code":"US","type":"company","lineage":["https://openalex.org/I105036370","https://openalex.org/I4210150756"]},{"id":"https://openalex.org/I49313256","display_name":"Alexion Pharma (Switzerland)","ror":"https://ror.org/05hkjyh45","country_code":"CH","type":"company","lineage":["https://openalex.org/I49313256"]}],"countries":["BR","CH","US"],"is_corresponding":false,"raw_author_name":"William R Mowrey","raw_affiliation_strings":["Bioinformatics and Data Science, Alexion AstraZeneca Rare Disease , Boston, MA 02210,","Alexion AstraZeneca Rare Disease Bioinformatics and Data Science, , Boston, MA"],"raw_orcid":"https://orcid.org/0000-0001-9531-9409","affiliations":[{"raw_affiliation_string":"Bioinformatics and Data Science, Alexion AstraZeneca Rare Disease , Boston, MA 02210,","institution_ids":["https://openalex.org/I49313256","https://openalex.org/I4210116875"]},{"raw_affiliation_string":"Alexion AstraZeneca Rare Disease Bioinformatics and Data Science, , Boston, MA","institution_ids":["https://openalex.org/I4210150756"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5013701219","display_name":"Piero Ricchiuto","orcid":"https://orcid.org/0000-0002-8525-6624"},"institutions":[{"id":"https://openalex.org/I4210116875","display_name":"AstraZeneca (Brazil)","ror":"https://ror.org/026m9xy48","country_code":"BR","type":"company","lineage":["https://openalex.org/I105036370","https://openalex.org/I4210116875"]},{"id":"https://openalex.org/I4210150756","display_name":"AstraZeneca (United States)","ror":"https://ror.org/043cec594","country_code":"US","type":"company","lineage":["https://openalex.org/I105036370","https://openalex.org/I4210150756"]},{"id":"https://openalex.org/I49313256","display_name":"Alexion Pharma (Switzerland)","ror":"https://ror.org/05hkjyh45","country_code":"CH","type":"company","lineage":["https://openalex.org/I49313256"]}],"countries":["BR","CH","US"],"is_corresponding":false,"raw_author_name":"Piero Ricchiuto","raw_affiliation_strings":["Bioinformatics and Data Science, Alexion AstraZeneca Rare Disease , Boston, MA 02210,","Alexion AstraZeneca Rare Disease Bioinformatics and Data Science, , Boston, MA"],"raw_orcid":"https://orcid.org/0000-0002-8525-6624","affiliations":[{"raw_affiliation_string":"Bioinformatics and Data Science, Alexion AstraZeneca Rare Disease , Boston, MA 02210,","institution_ids":["https://openalex.org/I49313256","https://openalex.org/I4210116875"]},{"raw_affiliation_string":"Alexion AstraZeneca Rare Disease Bioinformatics and Data Science, , Boston, MA","institution_ids":["https://openalex.org/I4210150756"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016559205","display_name":"Yupu Liang","orcid":"https://orcid.org/0000-0003-4074-463X"},"institutions":[{"id":"https://openalex.org/I4210116875","display_name":"AstraZeneca (Brazil)","ror":"https://ror.org/026m9xy48","country_code":"BR","type":"company","lineage":["https://openalex.org/I105036370","https://openalex.org/I4210116875"]},{"id":"https://openalex.org/I4210150756","display_name":"AstraZeneca (United States)","ror":"https://ror.org/043cec594","country_code":"US","type":"company","lineage":["https://openalex.org/I105036370","https://openalex.org/I4210150756"]},{"id":"https://openalex.org/I49313256","display_name":"Alexion Pharma (Switzerland)","ror":"https://ror.org/05hkjyh45","country_code":"CH","type":"company","lineage":["https://openalex.org/I49313256"]}],"countries":["BR","CH","US"],"is_corresponding":false,"raw_author_name":"Yupu Liang","raw_affiliation_strings":["Bioinformatics and Data Science, Alexion AstraZeneca Rare Disease , Boston, MA 02210,","Alexion AstraZeneca Rare Disease Bioinformatics and Data Science, , Boston, MA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioinformatics and Data Science, Alexion AstraZeneca Rare Disease , Boston, MA 02210,","institution_ids":["https://openalex.org/I49313256","https://openalex.org/I4210116875"]},{"raw_affiliation_string":"Alexion AstraZeneca Rare Disease Bioinformatics and Data Science, , Boston, MA","institution_ids":["https://openalex.org/I4210150756"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5115597224","display_name":"Wei Ding","orcid":"https://orcid.org/0009-0008-2629-2167"},"institutions":[{"id":"https://openalex.org/I4210116875","display_name":"AstraZeneca (Brazil)","ror":"https://ror.org/026m9xy48","country_code":"BR","type":"company","lineage":["https://openalex.org/I105036370","https://openalex.org/I4210116875"]},{"id":"https://openalex.org/I4210150756","display_name":"AstraZeneca (United States)","ror":"https://ror.org/043cec594","country_code":"US","type":"company","lineage":["https://openalex.org/I105036370","https://openalex.org/I4210150756"]},{"id":"https://openalex.org/I49313256","display_name":"Alexion Pharma (Switzerland)","ror":"https://ror.org/05hkjyh45","country_code":"CH","type":"company","lineage":["https://openalex.org/I49313256"]}],"countries":["BR","CH","US"],"is_corresponding":false,"raw_author_name":"Wei Ding","raw_affiliation_strings":["Bioinformatics and Data Science, Alexion AstraZeneca Rare Disease , Boston, MA 02210,","Alexion AstraZeneca Rare Disease Bioinformatics and Data Science, , Boston, MA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioinformatics and Data Science, Alexion AstraZeneca Rare Disease , Boston, MA 02210,","institution_ids":["https://openalex.org/I49313256","https://openalex.org/I4210116875"]},{"raw_affiliation_string":"Alexion AstraZeneca Rare Disease Bioinformatics and Data Science, , Boston, MA","institution_ids":["https://openalex.org/I4210150756"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000568082","display_name":"Juan Carlos Mobarec","orcid":"https://orcid.org/0000-0001-9482-4294"},"institutions":[{"id":"https://openalex.org/I105036370","display_name":"AstraZeneca (United Kingdom)","ror":"https://ror.org/04r9x1a08","country_code":"GB","type":"company","lineage":["https://openalex.org/I105036370"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Juan Carlos Mobarec","raw_affiliation_strings":["Protein Structure and Biophysics, Discovery Sciences, R&D, AstraZeneca, Cambridge, UK","R&D, AstraZeneca Mechanistic and Structural Biology, Discovery Sciences, , Cambridge,"],"raw_orcid":"https://orcid.org/0000-0001-9482-4294","affiliations":[{"raw_affiliation_string":"Protein Structure and Biophysics, Discovery Sciences, R&D, AstraZeneca, Cambridge, UK","institution_ids":["https://openalex.org/I105036370"]},{"raw_affiliation_string":"R&D, AstraZeneca Mechanistic and Structural Biology, Discovery Sciences, , Cambridge,","institution_ids":["https://openalex.org/I105036370"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5080731595","display_name":"Tina Eliassi\u2010Rad","orcid":"https://orcid.org/0000-0002-1892-1188"},"institutions":[{"id":"https://openalex.org/I12912129","display_name":"Northeastern University","ror":"https://ror.org/04t5xt781","country_code":"US","type":"education","lineage":["https://openalex.org/I12912129"]},{"id":"https://openalex.org/I1308548392","display_name":"Santa Fe Institute","ror":"https://ror.org/01arysc35","country_code":"US","type":"funder","lineage":["https://openalex.org/I1308548392"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Tina Eliassi-Rad","raw_affiliation_strings":["Khoury College of Computer Sciences, Northeastern University , Boston, MA CB2 0AA,","Network Science Institute, Northeastern University , Boston, MA 02115,","Santa Fe Institute , Santa Fe, NM 87501,","Northeastern University Network Science Institute, , Boston, MA","Northeastern University The Institute for Experiential AI, , Boston, MA","Northeastern University Khoury College of Computer Sciences, , Boston, MA","Santa Fe Institute , NM"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Khoury College of Computer Sciences, Northeastern University , Boston, MA CB2 0AA,","institution_ids":["https://openalex.org/I12912129"]},{"raw_affiliation_string":"Network Science Institute, Northeastern University , Boston, MA 02115,","institution_ids":["https://openalex.org/I12912129"]},{"raw_affiliation_string":"Santa Fe Institute , Santa Fe, NM 87501,","institution_ids":["https://openalex.org/I1308548392"]},{"raw_affiliation_string":"Northeastern University Network Science Institute, , Boston, MA","institution_ids":["https://openalex.org/I12912129"]},{"raw_affiliation_string":"Northeastern University The Institute for Experiential AI, , Boston, MA","institution_ids":["https://openalex.org/I12912129"]},{"raw_affiliation_string":"Northeastern University Khoury College of Computer Sciences, , Boston, MA","institution_ids":["https://openalex.org/I12912129"]},{"raw_affiliation_string":"Santa Fe Institute , NM","institution_ids":["https://openalex.org/I1308548392"]}]}],"institutions":[],"countries_distinct_count":5,"institutions_distinct_count":7,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.9736,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":{"value":0.73136876,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":95,"max":96},"biblio":{"volume":"41","issue":"5","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.8447999954223633,"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":0.8447999954223633,"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/T11273","display_name":"Advanced Graph Neural Networks","score":0.050599999725818634,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.04600000008940697,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.755452036857605},{"id":"https://openalex.org/keywords/generalizability-theory","display_name":"Generalizability theory","score":0.7477031946182251},{"id":"https://openalex.org/keywords/interpretability","display_name":"Interpretability","score":0.6299342513084412},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.6235722899436951},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.48298776149749756},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.4259505569934845},{"id":"https://openalex.org/keywords/sampling","display_name":"Sampling (signal processing)","score":0.41170021891593933},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3948689103126526},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.32202857732772827},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.2131211757659912},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.17494356632232666}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.755452036857605},{"id":"https://openalex.org/C27158222","wikidata":"https://www.wikidata.org/wiki/Q5532422","display_name":"Generalizability theory","level":2,"score":0.7477031946182251},{"id":"https://openalex.org/C2781067378","wikidata":"https://www.wikidata.org/wiki/Q17027399","display_name":"Interpretability","level":2,"score":0.6299342513084412},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.6235722899436951},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.48298776149749756},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.4259505569934845},{"id":"https://openalex.org/C140779682","wikidata":"https://www.wikidata.org/wiki/Q210868","display_name":"Sampling (signal processing)","level":3,"score":0.41170021891593933},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3948689103126526},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.32202857732772827},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.2131211757659912},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.17494356632232666},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0},{"id":"https://openalex.org/C106131492","wikidata":"https://www.wikidata.org/wiki/Q3072260","display_name":"Filter (signal processing)","level":2,"score":0.0},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0},{"id":"https://openalex.org/C31972630","wikidata":"https://www.wikidata.org/wiki/Q844240","display_name":"Computer vision","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","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":"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":"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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"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},{"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/btaf148","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf148","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf148/62884278/btaf148.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:40193392","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40193392","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:12080959","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12080959","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":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btaf148","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf148","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf148/62884278/btaf148.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":[],"funders":[{"id":"https://openalex.org/F4320307770","display_name":"AstraZeneca","ror":"https://ror.org/04r9x1a08"},{"id":"https://openalex.org/F4320309052","display_name":"Alexion Pharmaceuticals","ror":"https://ror.org/031ywxc85"},{"id":"https://openalex.org/F4320309475","display_name":"Northwestern University","ror":"https://ror.org/000e0be47"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4409229134.pdf","grobid_xml":"https://content.openalex.org/works/W4409229134.grobid-xml"},"referenced_works_count":107,"referenced_works":["https://openalex.org/W1501531009","https://openalex.org/W1576278180","https://openalex.org/W1600604896","https://openalex.org/W1611787727","https://openalex.org/W1975304761","https://openalex.org/W1980831278","https://openalex.org/W1982597966","https://openalex.org/W1988097700","https://openalex.org/W1988769775","https://openalex.org/W1990200948","https://openalex.org/W1990315216","https://openalex.org/W1991953772","https://openalex.org/W1994803330","https://openalex.org/W2007272533","https://openalex.org/W2015214828","https://openalex.org/W2018661561","https://openalex.org/W2021025020","https://openalex.org/W2021579368","https://openalex.org/W2027377866","https://openalex.org/W2038147884","https://openalex.org/W2050023895","https://openalex.org/W2058591057","https://openalex.org/W2064675550","https://openalex.org/W2069463493","https://openalex.org/W2074990030","https://openalex.org/W2076158096","https://openalex.org/W2078997561","https://openalex.org/W2083918648","https://openalex.org/W2091019377","https://openalex.org/W2091411809","https://openalex.org/W2099862356","https://openalex.org/W2101181377","https://openalex.org/W2102281458","https://openalex.org/W2107580398","https://openalex.org/W2108134720","https://openalex.org/W2110553827","https://openalex.org/W2114850508","https://openalex.org/W2123922822","https://openalex.org/W2127637605","https://openalex.org/W2131562240","https://openalex.org/W2136957665","https://openalex.org/W2140883620","https://openalex.org/W2143720865","https://openalex.org/W2146841526","https://openalex.org/W2148958646","https://openalex.org/W2149310258","https://openalex.org/W2150452800","https://openalex.org/W2155004936","https://openalex.org/W2155699197","https://openalex.org/W2156737316","https://openalex.org/W2163485494","https://openalex.org/W2165345221","https://openalex.org/W2166020074","https://openalex.org/W2171273050","https://openalex.org/W2198225506","https://openalex.org/W2215000673","https://openalex.org/W2350845555","https://openalex.org/W2417010772","https://openalex.org/W2506377511","https://openalex.org/W2534390616","https://openalex.org/W2613629789","https://openalex.org/W2804501929","https://openalex.org/W2887551661","https://openalex.org/W2902060950","https://openalex.org/W2913996609","https://openalex.org/W2922828897","https://openalex.org/W2948947101","https://openalex.org/W2949564348","https://openalex.org/W2950742983","https://openalex.org/W3015074824","https://openalex.org/W3015964336","https://openalex.org/W3016970897","https://openalex.org/W3047366767","https://openalex.org/W3080456792","https://openalex.org/W3080781457","https://openalex.org/W3087769169","https://openalex.org/W3095543875","https://openalex.org/W3111380104","https://openalex.org/W3112376646","https://openalex.org/W3156083564","https://openalex.org/W3177828909","https://openalex.org/W3202105508","https://openalex.org/W3209369100","https://openalex.org/W4200461926","https://openalex.org/W4200602489","https://openalex.org/W4205588764","https://openalex.org/W4205848394","https://openalex.org/W4206337041","https://openalex.org/W4210564571","https://openalex.org/W4212886450","https://openalex.org/W4223956519","https://openalex.org/W4243979784","https://openalex.org/W4280617006","https://openalex.org/W4283716699","https://openalex.org/W4283776301","https://openalex.org/W4287982101","https://openalex.org/W4293192557","https://openalex.org/W4313597598","https://openalex.org/W4321596020","https://openalex.org/W4353060041","https://openalex.org/W4362720950","https://openalex.org/W4381799116","https://openalex.org/W4387931208","https://openalex.org/W4396757487","https://openalex.org/W4399982595","https://openalex.org/W4403253406","https://openalex.org/W6635873800"],"related_works":["https://openalex.org/W2905433371","https://openalex.org/W2888392564","https://openalex.org/W4310278675","https://openalex.org/W4388422664","https://openalex.org/W4390569940","https://openalex.org/W4361193272","https://openalex.org/W2963326959","https://openalex.org/W2118717649","https://openalex.org/W4388685194","https://openalex.org/W4378220270"],"abstract_inverted_index":{"MOTIVATION:":[0],"Unraveling":[1],"the":[2,68,117,139,146,158],"human":[3],"interactome":[4],"to":[5,29,42],"uncover":[6],"disease-specific":[7],"patterns":[8],"and":[9,39,125,144,154,180],"discover":[10],"drug":[11],"targets":[12],"hinges":[13],"on":[14,134],"accurate":[15],"protein-protein":[16,58],"interaction":[17],"(PPI)":[18],"predictions.":[19],"However,":[20],"challenges":[21],"persist":[22],"in":[23,95,115,128,166],"machine":[24,168],"learning":[25,98,169],"(ML)":[26],"models":[27],"due":[28],"a":[30,51,86,161],"scarcity":[31],"of":[32,57,72,79,105,109,141,148],"quality":[33],"hard":[34],"negative":[35,163],"samples,":[36,103],"shortcut":[37],"learning,":[38],"limited":[40],"generalizability":[41,124],"novel":[43,52],"proteins.":[44],"RESULTS:":[45],"In":[46],"this":[47],"study,":[48],"we":[49,75,120],"introduce":[50,76],"approach":[53],"for":[54,83,160],"strategic":[55],"sampling":[56,164],"noninteractions":[59],"(PPNIs)":[60],"by":[61,170],"leveraging":[62],"higher-order":[63],"network":[64,174],"characteristics":[65],"that":[66],"capture":[67],"inherent":[69],"complementarity-driven":[70],"mechanisms":[71],"PPIs.":[73],"Next,":[74],"Unsupervised":[77],"Pre-training":[78],"Node":[80],"Attributes":[81],"tuned":[82],"PPI":[84,122],"(UPNA-PPI),":[85],"high":[87],"throughput":[88],"sequence-to-function":[89],"ML":[90,149],"pipeline,":[91],"integrating":[92,171],"unsupervised":[93],"pre-training":[94],"protein":[96,152],"representation":[97],"with":[99],"Topological":[100],"PPNI":[101],"(TPPNI)":[102],"capable":[104],"efficiently":[106],"screening":[107,142],"billions":[108],"interactions.":[110],"By":[111],"using":[112],"our":[113],"TPPNI":[114],"training":[116],"UPNA-PPI":[118,156,181],"model,":[119],"improve":[121],"prediction":[123],"interpretability,":[126],"particularly":[127],"identifying":[129],"potential":[130],"binding":[131],"sites":[132],"locations":[133],"amino":[135],"acid":[136],"sequences,":[137],"strengthening":[138],"prioritization":[140],"assays":[143],"facilitating":[145],"transferability":[147],"predictions":[150,182],"across":[151],"families":[153],"homodimers.":[155],"establishes":[157],"foundation":[159],"fundamental":[162],"methodology":[165],"graph":[167],"insights":[172],"from":[173],"topology.":[175],"AVAILABILITY":[176],"AND":[177],"IMPLEMENTATION:":[178],"Code":[179],"are":[183],"freely":[184],"available":[185],"at":[186],"https://github.com/alxndgb/UPNA-PPI.":[187]},"counts_by_year":[{"year":2025,"cited_by_count":2}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
