{"id":"https://openalex.org/W2069313265","doi":"https://doi.org/10.1186/s12859-014-0430-y","title":"Predicting protein functions using incomplete hierarchical labels","display_name":"Predicting protein functions using incomplete hierarchical labels","publication_year":2015,"publication_date":"2015-01-15","ids":{"openalex":"https://openalex.org/W2069313265","doi":"https://doi.org/10.1186/s12859-014-0430-y","mag":"2069313265","pmid":"https://pubmed.ncbi.nlm.nih.gov/25591917"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-014-0430-y","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-014-0430-y","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-014-0430-y","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/s12859-014-0430-y","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5027082940","display_name":"Guoxian Yu","orcid":"https://orcid.org/0000-0002-1667-6705"},"institutions":[{"id":"https://openalex.org/I141568987","display_name":"Hong Kong Baptist University","ror":"https://ror.org/0145fw131","country_code":"HK","type":"education","lineage":["https://openalex.org/I141568987"]},{"id":"https://openalex.org/I142108993","display_name":"Southwest University","ror":"https://ror.org/01kj4z117","country_code":"CN","type":"education","lineage":["https://openalex.org/I142108993"]}],"countries":["CN","HK"],"is_corresponding":true,"raw_author_name":"Guoxian Yu","raw_affiliation_strings":["College of Computer and Information Sciences, Southwest University, Chongqing, China. guoxian85@gmail.com","Department of Computer Science, Hong Kong Baptist University, Kowloon Tong, Hong Kong, China. guoxian85@gmail.com","College of Computer and Information Sciences, Southwest University, Chongqing, China","Department of Computer Science, Hong Kong Baptist University, Kowloon Tong, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Computer and Information Sciences, Southwest University, Chongqing, China. guoxian85@gmail.com","institution_ids":["https://openalex.org/I142108993"]},{"raw_affiliation_string":"Department of Computer Science, Hong Kong Baptist University, Kowloon Tong, Hong Kong, China. guoxian85@gmail.com","institution_ids":["https://openalex.org/I141568987"]},{"raw_affiliation_string":"College of Computer and Information Sciences, Southwest University, Chongqing, China","institution_ids":["https://openalex.org/I142108993"]},{"raw_affiliation_string":"Department of Computer Science, Hong Kong Baptist University, Kowloon Tong, China","institution_ids":["https://openalex.org/I141568987"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101965303","display_name":"Hailong Zhu","orcid":"https://orcid.org/0000-0003-0633-5525"},"institutions":[{"id":"https://openalex.org/I141568987","display_name":"Hong Kong Baptist University","ror":"https://ror.org/0145fw131","country_code":"HK","type":"education","lineage":["https://openalex.org/I141568987"]}],"countries":["HK"],"is_corresponding":true,"raw_author_name":"Hailong Zhu","raw_affiliation_strings":["Department of Computer Science, Hong Kong Baptist University, Kowloon Tong, Hong Kong, China. hlzhu@comp.hkbu.edu.hk","Department of Computer Science, Hong Kong Baptist University, Kowloon Tong, China#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Hong Kong Baptist University, Kowloon Tong, Hong Kong, China. hlzhu@comp.hkbu.edu.hk","institution_ids":["https://openalex.org/I141568987"]},{"raw_affiliation_string":"Department of Computer Science, Hong Kong Baptist University, Kowloon Tong, China#TAB#","institution_ids":["https://openalex.org/I141568987"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5090148962","display_name":"Carlotta Domeniconi","orcid":"https://orcid.org/0000-0003-2140-9596"},"institutions":[{"id":"https://openalex.org/I162714631","display_name":"George Mason University","ror":"https://ror.org/02jqj7156","country_code":"US","type":"education","lineage":["https://openalex.org/I162714631"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Carlotta Domeniconi","raw_affiliation_strings":["Department of Computer Science, George Mason University, Fairfax, VA, USA. carlotta@cs.gmu.edu","Dept. of Computer Science, George Mason Univ., Fairfax, USA#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, George Mason University, Fairfax, VA, USA. carlotta@cs.gmu.edu","institution_ids":["https://openalex.org/I162714631"]},{"raw_affiliation_string":"Dept. of Computer Science, George Mason Univ., Fairfax, USA#TAB#","institution_ids":["https://openalex.org/I162714631"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5027082940","https://openalex.org/A5101965303"],"corresponding_institution_ids":["https://openalex.org/I141568987","https://openalex.org/I142108993"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":11.0223,"has_fulltext":true,"cited_by_count":363,"citation_normalized_percentile":{"value":0.98999393,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"16","issue":"1","first_page":"1","last_page":"1"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9564999938011169,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9564999938011169,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.02419999986886978,"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.0024999999441206455,"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/protein-function-prediction","display_name":"Protein function prediction","score":0.8554269671440125},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6591969728469849},{"id":"https://openalex.org/keywords/missing-data","display_name":"Missing data","score":0.5194791555404663},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.517866849899292},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.5025112628936768},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.49003517627716064},{"id":"https://openalex.org/keywords/hierarchy","display_name":"Hierarchy","score":0.48535647988319397},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.4675266742706299},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.42568591237068176},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4052407145500183},{"id":"https://openalex.org/keywords/protein-function","display_name":"Protein function","score":0.31312495470046997},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1329226791858673},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.09239095449447632}],"concepts":[{"id":"https://openalex.org/C207060522","wikidata":"https://www.wikidata.org/wiki/Q7251473","display_name":"Protein function prediction","level":4,"score":0.8554269671440125},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6591969728469849},{"id":"https://openalex.org/C9357733","wikidata":"https://www.wikidata.org/wiki/Q6878417","display_name":"Missing data","level":2,"score":0.5194791555404663},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.517866849899292},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.5025112628936768},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.49003517627716064},{"id":"https://openalex.org/C31170391","wikidata":"https://www.wikidata.org/wiki/Q188619","display_name":"Hierarchy","level":2,"score":0.48535647988319397},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.4675266742706299},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.42568591237068176},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4052407145500183},{"id":"https://openalex.org/C2986374874","wikidata":"https://www.wikidata.org/wiki/Q8054","display_name":"Protein function","level":3,"score":0.31312495470046997},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1329226791858673},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.09239095449447632},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"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":"D000465","descriptor_name":"Algorithms","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":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":true},{"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":"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":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1186/s12859-014-0430-y","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-014-0430-y","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-014-0430-y","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:25591917","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25591917","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:3349854","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4384381","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"}],"best_oa_location":{"id":"doi:10.1186/s12859-014-0430-y","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-014-0430-y","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-014-0430-y","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":[{"id":"https://openalex.org/G1514361433","display_name":null,"funder_award_id":"61402378","funder_id":"https://openalex.org/F4320335787","funder_display_name":"Fundamental Research Funds for the Central Universities"},{"id":"https://openalex.org/G2296587852","display_name":null,"funder_award_id":"212111","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3586237594","display_name":"\u57fa\u4e8e\u6982\u7387\u56fe\u4e0e\u81ea\u9002\u5e94\u805a\u7c7b\u7684\u6df7\u5408\u7279\u5f81\u79cd\u7fa4\u7ed3\u6784\u63a8\u65ad\u65b9\u6cd5\u7814\u7a76","funder_award_id":"61101234","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3781955951","display_name":null,"funder_award_id":"cstc2014jcyjA40031","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G4372538537","display_name":null,"funder_award_id":"61402378","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G443251992","display_name":null,"funder_award_id":"XDJK2014C044","funder_id":"https://openalex.org/F4320335787","funder_display_name":"Fundamental Research Funds for the Central Universities"},{"id":"https://openalex.org/G8554807024","display_name":null,"funder_award_id":"cstc2014jcyjA40031","funder_id":"https://openalex.org/F4320335787","funder_display_name":"Fundamental Research Funds for the Central Universities"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320321550","display_name":"Chongqing Science and Technology Commission","ror":"https://ror.org/05w9erc61"},{"id":"https://openalex.org/F4320323711","display_name":"Southwest University","ror":"https://ror.org/01kj4z117"},{"id":"https://openalex.org/F4320335787","display_name":"Fundamental Research Funds for the Central Universities","ror":null}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2069313265.pdf","grobid_xml":"https://content.openalex.org/works/W2069313265.grobid-xml"},"referenced_works_count":49,"referenced_works":["https://openalex.org/W135042460","https://openalex.org/W195996384","https://openalex.org/W1486817521","https://openalex.org/W1647729745","https://openalex.org/W1965917470","https://openalex.org/W1974235890","https://openalex.org/W1975842369","https://openalex.org/W1976463269","https://openalex.org/W2001004762","https://openalex.org/W2012336263","https://openalex.org/W2019899889","https://openalex.org/W2037248153","https://openalex.org/W2046163764","https://openalex.org/W2061453990","https://openalex.org/W2068072987","https://openalex.org/W2069313265","https://openalex.org/W2075545346","https://openalex.org/W2076743129","https://openalex.org/W2082380079","https://openalex.org/W2084168100","https://openalex.org/W2094124219","https://openalex.org/W2098427571","https://openalex.org/W2101291993","https://openalex.org/W2102814386","https://openalex.org/W2103017472","https://openalex.org/W2107710781","https://openalex.org/W2107952955","https://openalex.org/W2108892946","https://openalex.org/W2114315281","https://openalex.org/W2117486996","https://openalex.org/W2124842489","https://openalex.org/W2131114385","https://openalex.org/W2133442079","https://openalex.org/W2137917513","https://openalex.org/W2140335411","https://openalex.org/W2148722247","https://openalex.org/W2155440340","https://openalex.org/W2155977075","https://openalex.org/W2158216734","https://openalex.org/W2164996392","https://openalex.org/W2166468869","https://openalex.org/W2166985665","https://openalex.org/W2169896388","https://openalex.org/W2171403830","https://openalex.org/W2178814878","https://openalex.org/W2390394804","https://openalex.org/W4210561386","https://openalex.org/W6605540968","https://openalex.org/W6681153989"],"related_works":["https://openalex.org/W2094822546","https://openalex.org/W4388708026","https://openalex.org/W1969080446","https://openalex.org/W3108941781","https://openalex.org/W1578069856","https://openalex.org/W2084200259","https://openalex.org/W2134206588","https://openalex.org/W2065993463","https://openalex.org/W2401071219","https://openalex.org/W2554237979"],"abstract_inverted_index":{"BACKGROUND:":[0],"Protein":[1],"function":[2,28,44,119,152,195,249,263],"prediction":[3,264],"is":[4,15,31,74,114,198,240,273],"to":[5,11,129,160,188,200,242],"assign":[6],"biological":[7],"or":[8],"biochemical":[9],"functions":[10,132,214],"proteins,":[12],"and":[13,51,92,111,146,154,177,184,210,229],"it":[14,239],"a":[16,34,49,90,109,156,172,186,258],"challenging":[17,110],"computational":[18],"problem":[19],"characterized":[20],"by":[21],"several":[22],"factors:":[23],"(1)":[24],"the":[25,43,53,63,66,144,147,162,168,178,182,190,207,213,244],"number":[26],"of":[27,65,84,89,105,181,215,271],"labels":[29,45,54,64,88,170,180,209],"(annotations)":[30],"large;":[32],"(2)":[33],"protein":[35,118,131,173,248,262],"may":[36,81,94],"be":[37,82],"associated":[38],"with":[39,225],"multiple":[40],"labels;":[41],"(3)":[42],"are":[46,55,69,100],"structured":[47],"in":[48,77,117,138,205,211],"hierarchy;":[50],"(4)":[52],"incomplete.":[56],"Current":[57],"predictive":[58],"models":[59],"often":[60],"assume":[61],"that":[62,238],"labeled":[67],"proteins":[68,193,218],"complete,":[70],"i.e.":[71],"no":[72],"label":[73],"missing.":[75],"But":[76],"real":[78],"scenarios,":[79],"we":[80,93,125],"aware":[83],"only":[85],"some":[86],"hierarchical":[87,107,135,145],"protein,":[91,183],"not":[95],"know":[96],"whether":[97],"additional":[98],"ones":[99],"actually":[101],"present.":[102],"The":[103,234,251,268],"scenario":[104],"incomplete":[106,245,266],"labels,":[108,153],"practical":[112],"problem,":[113],"seldom":[115],"studied":[116],"prediction.":[120,196,250],"RESULTS:":[121],"In":[122],"this":[123],"paper,":[124],"propose":[126],"an":[127],"algorithm":[128],"Predict":[130],"using":[133,265],"Incomplete":[134],"LabeLs":[136],"(PILL":[137],"short).":[139],"PILL":[140,166,197,272],"takes":[141],"into":[142],"account":[143],"flat":[148],"taxonomy":[149],"similarity":[150],"between":[151,164,192],"defines":[155],"Combined":[157],"Similarity":[158],"(ComSim)":[159],"measure":[161],"correlation":[163],"labels.":[165,232,267],"estimates":[167],"missing":[169,208],"for":[171,194,247,261],"based":[174],"on":[175,219],"ComSim":[176],"known":[179],"uses":[185],"regularization":[187],"exploit":[189],"interactions":[191],"shown":[199],"outperform":[201],"other":[202],"related":[203],"techniques":[204],"replenishing":[206],"predicting":[212],"completely":[216],"unlabeled":[217],"publicly":[220],"available":[221,274],"PPI":[222],"datasets":[223],"annotated":[224],"MIPS":[226],"Functional":[227],"Catalogue":[228],"Gene":[230],"Ontology":[231],"CONCLUSION:":[233],"empirical":[235],"study":[236],"shows":[237],"important":[241],"consider":[243],"annotation":[246],"proposed":[252],"method":[253],"(PILL)":[254],"can":[255],"serve":[256],"as":[257],"valuable":[259],"tool":[260],"Matlab":[269],"code":[270],"upon":[275],"request.":[276]},"counts_by_year":[{"year":2026,"cited_by_count":12},{"year":2025,"cited_by_count":33},{"year":2024,"cited_by_count":44},{"year":2023,"cited_by_count":44},{"year":2022,"cited_by_count":37},{"year":2021,"cited_by_count":54},{"year":2020,"cited_by_count":35},{"year":2019,"cited_by_count":24},{"year":2018,"cited_by_count":22},{"year":2017,"cited_by_count":21},{"year":2016,"cited_by_count":30},{"year":2015,"cited_by_count":7}],"updated_date":"2026-07-27T08:26:11.824852","created_date":"2025-10-10T00:00:00"}
