{"id":"https://openalex.org/W2065516946","doi":"https://doi.org/10.1186/1471-2105-15-103","title":"Improved multi-level protein\u2013protein interaction prediction with semantic-based regularization","display_name":"Improved multi-level protein\u2013protein interaction prediction with semantic-based regularization","publication_year":2014,"publication_date":"2014-04-12","ids":{"openalex":"https://openalex.org/W2065516946","doi":"https://doi.org/10.1186/1471-2105-15-103","mag":"2065516946","pmid":"https://pubmed.ncbi.nlm.nih.gov/24725682"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-15-103","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-15-103","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-15-103","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-15-103","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5044117954","display_name":"Claudio Sacc\u00e0","orcid":null},"institutions":[{"id":"https://openalex.org/I102064193","display_name":"University of Siena","ror":"https://ror.org/01tevnk56","country_code":"IT","type":"education","lineage":["https://openalex.org/I102064193"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Claudio Sacc\u00e0","raw_affiliation_strings":["Dipartimento di Ingegneria dell\u2019Informazione e Scienze Matematiche, University of Siena, Siena, Italy","Dipartimento di Ingegneria dell'Informazione e Scienze Matematiche, University of Siena, Siena, Italy -"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dipartimento di Ingegneria dell\u2019Informazione e Scienze Matematiche, University of Siena, Siena, Italy","institution_ids":["https://openalex.org/I102064193"]},{"raw_affiliation_string":"Dipartimento di Ingegneria dell'Informazione e Scienze Matematiche, University of Siena, Siena, Italy -","institution_ids":["https://openalex.org/I102064193"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5001174680","display_name":"Stefano Teso","orcid":"https://orcid.org/0000-0002-2340-9461"},"institutions":[{"id":"https://openalex.org/I193223587","display_name":"University of Trento","ror":"https://ror.org/05trd4x28","country_code":"IT","type":"education","lineage":["https://openalex.org/I193223587"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Stefano Teso","raw_affiliation_strings":["Dipartimento di Ingegneria e Scienza dell\u2019Informazione, University of Trento, Trento, Italy","[Dipartimento di Ingegneria e Scienza dell\u2019Informazione, University of Trento, Trento, Italy]"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dipartimento di Ingegneria e Scienza dell\u2019Informazione, University of Trento, Trento, Italy","institution_ids":["https://openalex.org/I193223587"]},{"raw_affiliation_string":"[Dipartimento di Ingegneria e Scienza dell\u2019Informazione, University of Trento, Trento, Italy]","institution_ids":["https://openalex.org/I193223587"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5109267259","display_name":"Michelangelo Diligenti","orcid":null},"institutions":[{"id":"https://openalex.org/I102064193","display_name":"University of Siena","ror":"https://ror.org/01tevnk56","country_code":"IT","type":"education","lineage":["https://openalex.org/I102064193"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Michelangelo Diligenti","raw_affiliation_strings":["Dipartimento di Ingegneria dell\u2019Informazione e Scienze Matematiche, University of Siena, Siena, Italy","Dipartimento di Ingegneria dell'Informazione e Scienze Matematiche, University of Siena, Siena, Italy -"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dipartimento di Ingegneria dell\u2019Informazione e Scienze Matematiche, University of Siena, Siena, Italy","institution_ids":["https://openalex.org/I102064193"]},{"raw_affiliation_string":"Dipartimento di Ingegneria dell'Informazione e Scienze Matematiche, University of Siena, Siena, Italy -","institution_ids":["https://openalex.org/I102064193"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5066187890","display_name":"Andrea Passerini","orcid":"https://orcid.org/0000-0002-2765-5395"},"institutions":[{"id":"https://openalex.org/I193223587","display_name":"University of Trento","ror":"https://ror.org/05trd4x28","country_code":"IT","type":"education","lineage":["https://openalex.org/I193223587"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"Andrea Passerini","raw_affiliation_strings":["Dipartimento di Ingegneria e Scienza dell'Informazione, University of Trento, Trento, Italy. passerini@disi.unitn.it","[Dipartimento di Ingegneria e Scienza dell\u2019Informazione, University of Trento, Trento, Italy]"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dipartimento di Ingegneria e Scienza dell'Informazione, University of Trento, Trento, Italy. passerini@disi.unitn.it","institution_ids":["https://openalex.org/I193223587"]},{"raw_affiliation_string":"[Dipartimento di Ingegneria e Scienza dell\u2019Informazione, University of Trento, Trento, Italy]","institution_ids":["https://openalex.org/I193223587"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5066187890"],"corresponding_institution_ids":["https://openalex.org/I193223587"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":1.2996,"has_fulltext":true,"cited_by_count":22,"citation_normalized_percentile":{"value":0.79207249,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"15","issue":"1","first_page":"103","last_page":"103"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.3928999900817871,"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":0.3928999900817871,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.21580000221729279,"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"}},{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.1898999959230423,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7479611039161682},{"id":"https://openalex.org/keywords/leverage","display_name":"Leverage (statistics)","score":0.6908257603645325},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.5876775979995728},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5383433103561401},{"id":"https://openalex.org/keywords/regularization","display_name":"Regularization (linguistics)","score":0.5049534440040588},{"id":"https://openalex.org/keywords/hierarchy","display_name":"Hierarchy","score":0.45661136507987976},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.45309287309646606},{"id":"https://openalex.org/keywords/protein\u2013protein-interaction","display_name":"Protein\u2013protein interaction","score":0.4468473196029663},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.34698718786239624},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3260708749294281},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.12313878536224365}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7479611039161682},{"id":"https://openalex.org/C153083717","wikidata":"https://www.wikidata.org/wiki/Q6535263","display_name":"Leverage (statistics)","level":2,"score":0.6908257603645325},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.5876775979995728},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5383433103561401},{"id":"https://openalex.org/C2776135515","wikidata":"https://www.wikidata.org/wiki/Q17143721","display_name":"Regularization (linguistics)","level":2,"score":0.5049534440040588},{"id":"https://openalex.org/C31170391","wikidata":"https://www.wikidata.org/wiki/Q188619","display_name":"Hierarchy","level":2,"score":0.45661136507987976},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.45309287309646606},{"id":"https://openalex.org/C11804247","wikidata":"https://www.wikidata.org/wiki/Q896177","display_name":"Protein\u2013protein interaction","level":2,"score":0.4468473196029663},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.34698718786239624},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3260708749294281},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.12313878536224365},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.0},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0},{"id":"https://openalex.org/C34447519","wikidata":"https://www.wikidata.org/wiki/Q179522","display_name":"Market economy","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","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":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012660","descriptor_name":"Semantics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012660","descriptor_name":"Semantics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012660","descriptor_name":"Semantics","qualifier_ui":null,"qualifier_name":null,"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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054730","descriptor_name":"Protein Interaction Domains and Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D054730","descriptor_name":"Protein Interaction Domains and Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D054730","descriptor_name":"Protein Interaction Domains and Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1186/1471-2105-15-103","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-15-103","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-15-103","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:24725682","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24725682","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:europepmc.org:3001260","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4004462","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":null,"raw_type":"Text"},{"id":"pmh:oai:iris.unitn.it:11572/101242","is_oa":true,"landing_page_url":"http://hdl.handle.net/11572/101242","pdf_url":null,"source":{"id":"https://openalex.org/S4306401913","display_name":"Institutional Research Information System (Universit\u00e0 degli Studi di Trento)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I193223587","host_organization_name":"University of Trento","host_organization_lineage":["https://openalex.org/I193223587"],"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":null,"raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:usiena-air.unisi.it:11365/46689","is_oa":false,"landing_page_url":"http://hdl.handle.net/11365/46689","pdf_url":null,"source":{"id":"https://openalex.org/S4377196319","display_name":"Use Siena air (University of Siena)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I102064193","host_organization_name":"University of Siena","host_organization_lineage":["https://openalex.org/I102064193"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-15-103","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-15-103","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-15-103","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2065516946.pdf","grobid_xml":"https://content.openalex.org/works/W2065516946.grobid-xml"},"referenced_works_count":50,"referenced_works":["https://openalex.org/W1479807131","https://openalex.org/W1585529040","https://openalex.org/W1590164092","https://openalex.org/W1898259180","https://openalex.org/W1964357740","https://openalex.org/W1977186059","https://openalex.org/W1985669994","https://openalex.org/W2001457899","https://openalex.org/W2029574260","https://openalex.org/W2033591223","https://openalex.org/W2048679005","https://openalex.org/W2048919592","https://openalex.org/W2049871748","https://openalex.org/W2055114099","https://openalex.org/W2062414926","https://openalex.org/W2064383522","https://openalex.org/W2066201825","https://openalex.org/W2087574732","https://openalex.org/W2099862356","https://openalex.org/W2104239076","https://openalex.org/W2107340752","https://openalex.org/W2110095004","https://openalex.org/W2117486996","https://openalex.org/W2119821739","https://openalex.org/W2120973253","https://openalex.org/W2123375001","https://openalex.org/W2127637605","https://openalex.org/W2128733887","https://openalex.org/W2130494178","https://openalex.org/W2136504847","https://openalex.org/W2140239055","https://openalex.org/W2141624700","https://openalex.org/W2152521138","https://openalex.org/W2153954618","https://openalex.org/W2155004936","https://openalex.org/W2156125289","https://openalex.org/W2156269526","https://openalex.org/W2158714788","https://openalex.org/W2159247826","https://openalex.org/W2159830506","https://openalex.org/W2161441225","https://openalex.org/W2162682281","https://openalex.org/W2164837103","https://openalex.org/W2168029744","https://openalex.org/W2287132924","https://openalex.org/W2375970338","https://openalex.org/W2487770199","https://openalex.org/W3101749733","https://openalex.org/W3119651796","https://openalex.org/W4234672050"],"related_works":["https://openalex.org/W2365264209","https://openalex.org/W2509431957","https://openalex.org/W2026999166","https://openalex.org/W1599954583","https://openalex.org/W1992685502","https://openalex.org/W4211007821","https://openalex.org/W2802395037","https://openalex.org/W4389565704","https://openalex.org/W1996802783","https://openalex.org/W3207031006"],"abstract_inverted_index":{"BACKGROUND:":[0],"Protein-protein":[1],"interactions":[2,276],"can":[3,262],"be":[4,112],"seen":[5],"as":[6,137],"a":[7,41,73,138,153,176,198,222],"hierarchical":[8,86,257],"process":[9,55],"occurring":[10],"at":[11,96],"three":[12],"related":[13],"levels:":[14],"proteins":[15],"bind":[16],"by":[17,118],"means":[18],"of":[19,29,52,72,88,121,163,200,218,259],"specific":[20],"domains,":[21],"which":[22,34,70],"in":[23,40,129,249],"turn":[24],"form":[25],"interfaces":[26],"through":[27],"patches":[28],"residues.":[30],"Detailed":[31],"knowledge":[32],"about":[33],"domains":[35,148],"and":[36,56,149,151,178,226],"residues":[37],"are":[38,109,278],"involved":[39],"given":[42],"interaction":[43,64],"has":[44],"extensive":[45],"applications":[46],"to":[47,83,111,190,264,274,282],"biology,":[48],"including":[49],"better":[50,265],"understanding":[51],"the":[53,85,89,97,130,135,160,192,209,215,231,247,256,260,283],"binding":[54,161],"more":[57],"efficient":[58],"drug/enzyme":[59],"design.":[60],"Alas,":[61],"most":[62],"current":[63],"prediction":[65,236],"methods":[66],"do":[67,104],"not":[68,105],"identify":[69],"parts":[71],"protein":[74],"actually":[75],"instantiate":[76],"an":[77],"interaction.":[78],"Furthermore,":[79],"they":[80,101,103],"also":[81,272],"fail":[82],"leverage":[84],"nature":[87,258],"problem,":[90],"ignoring":[91],"otherwise":[92],"useful":[93],"information":[94],"available":[95],"lower":[98],"levels;":[99],"when":[100],"do,":[102],"generate":[106],"predictions":[107,207],"that":[108,157,184,204,242,254,277],"guaranteed":[110,273],"consistent":[113,206,279],"between":[114,208],"levels.":[115,211],"RESULTS:":[116],"Inspired":[117],"earlier":[119],"ideas":[120],"Yip":[122],"et":[123],"al.":[124],"(BMC":[125],"Bioinformatics":[126],"10:241,":[127],"2009),":[128],"present":[131,239],"paper":[132],"we":[133],"view":[134],"problem":[136,261],"multi-level":[139,235],"learning":[140,155,182,193],"task,":[141],"with":[142,280],"one":[143],"task":[144],"per":[145],"level":[146],"(proteins,":[147],"residues),":[150],"propose":[152],"machine":[154,181],"method":[156,168,220,244,270],"collectively":[158],"infers":[159],"state":[162],"all":[164],"object":[165],"pairs.":[166],"Our":[167],"is":[169,271],"based":[170],"on":[171],"Semantic":[172],"Based":[173],"Regularization":[174],"(SBR),":[175],"flexible":[177],"theoretically":[179],"sound":[180],"framework":[183],"uses":[185],"First":[186],"Order":[187],"Logic":[188],"constraints":[189],"tie":[191],"tasks":[194],"together.":[195],"We":[196,213,238],"introduce":[197],"set":[199],"biologically":[201],"motivated":[202],"rules":[203],"enforce":[205],"hierarchy":[210],"CONCLUSIONS:":[212],"study":[214],"empirical":[216],"performance":[217,229],"our":[219,243,269],"using":[221],"standard":[223],"validation":[224],"procedure,":[225],"compare":[227],"its":[228],"against":[230],"only":[232],"other":[233],"existing":[234],"technique.":[237],"results":[240],"showing":[241],"substantially":[245],"outperforms":[246],"competitor":[248],"several":[250],"experimental":[251],"settings,":[252],"indicating":[253],"exploiting":[255],"lead":[263],"predictions.":[266],"In":[267],"addition,":[268],"produce":[275],"respect":[281],"protein-domain-residue":[284],"hierarchy.":[285]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":5},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":1}],"updated_date":"2026-07-23T08:03:31.855105","created_date":"2025-10-10T00:00:00"}
