{"id":"https://openalex.org/W2205203491","doi":"https://doi.org/10.1186/s12859-015-0841-4","title":"Multi-label multi-instance transfer learning for simultaneous reconstruction and cross-talk modeling of multiple human signaling pathways","display_name":"Multi-label multi-instance transfer learning for simultaneous reconstruction and cross-talk modeling of multiple human signaling pathways","publication_year":2015,"publication_date":"2015-12-01","ids":{"openalex":"https://openalex.org/W2205203491","doi":"https://doi.org/10.1186/s12859-015-0841-4","mag":"2205203491","pmid":"https://pubmed.ncbi.nlm.nih.gov/26718335"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-015-0841-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-015-0841-4","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-015-0841-4","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/track/pdf/10.1186/s12859-015-0841-4","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5063476392","display_name":"Suyu Mei","orcid":"https://orcid.org/0000-0002-9701-266X"},"institutions":[{"id":"https://openalex.org/I32399674","display_name":"Shenyang Normal University","ror":"https://ror.org/05cdfgm80","country_code":"CN","type":"education","lineage":["https://openalex.org/I32399674"]},{"id":"https://openalex.org/I58200834","display_name":"Southern Medical University","ror":"https://ror.org/01vjw4z39","country_code":"CN","type":"education","lineage":["https://openalex.org/I58200834"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Suyu Mei","raw_affiliation_strings":["Bioinformatics Section, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China. meisygle@gmail.com","Software College, Shenyang Normal University, Shenyang, China. meisygle@gmail.com","Bioinformatics Section, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China","Software College, Shenyang Normal University, Shenyang, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioinformatics Section, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China. meisygle@gmail.com","institution_ids":["https://openalex.org/I58200834"]},{"raw_affiliation_string":"Software College, Shenyang Normal University, Shenyang, China. meisygle@gmail.com","institution_ids":["https://openalex.org/I32399674"]},{"raw_affiliation_string":"Bioinformatics Section, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China","institution_ids":["https://openalex.org/I58200834"]},{"raw_affiliation_string":"Software College, Shenyang Normal University, Shenyang, China","institution_ids":["https://openalex.org/I32399674"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5082676682","display_name":"Hao Zhu","orcid":"https://orcid.org/0000-0001-7384-3840"},"institutions":[{"id":"https://openalex.org/I58200834","display_name":"Southern Medical University","ror":"https://ror.org/01vjw4z39","country_code":"CN","type":"education","lineage":["https://openalex.org/I58200834"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Hao Zhu","raw_affiliation_strings":["Bioinformatics Section, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China. zhuhao@smu.edu.cn","Bioinformatics Section, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioinformatics Section, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China. zhuhao@smu.edu.cn","institution_ids":["https://openalex.org/I58200834"]},{"raw_affiliation_string":"Bioinformatics Section, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China","institution_ids":["https://openalex.org/I58200834"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5063476392"],"corresponding_institution_ids":["https://openalex.org/I32399674","https://openalex.org/I58200834"],"apc_list":{"value":2990,"currency":"USD","value_usd":2990},"apc_paid":{"value":2990,"currency":"USD","value_usd":2990},"fwci":0.5504,"has_fulltext":true,"cited_by_count":19,"citation_normalized_percentile":{"value":0.67124099,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":97},"biblio":{"volume":"16","issue":"1","first_page":"417","last_page":"417"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.4830000102519989,"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":0.4830000102519989,"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":0.1704999953508377,"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":0.12110000103712082,"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/signal-transduction","display_name":"Signal transduction","score":0.6796969175338745},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5532886981964111},{"id":"https://openalex.org/keywords/cell-signaling","display_name":"Cell signaling","score":0.4898762106895447},{"id":"https://openalex.org/keywords/biological-pathway","display_name":"Biological pathway","score":0.45835936069488525},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4447599947452545},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4298486113548279},{"id":"https://openalex.org/keywords/systems-biology","display_name":"Systems biology","score":0.41029471158981323},{"id":"https://openalex.org/keywords/cell-biology","display_name":"Cell biology","score":0.25022098422050476},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.14111730456352234},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.12092664837837219}],"concepts":[{"id":"https://openalex.org/C62478195","wikidata":"https://www.wikidata.org/wiki/Q828130","display_name":"Signal transduction","level":2,"score":0.6796969175338745},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5532886981964111},{"id":"https://openalex.org/C150555746","wikidata":"https://www.wikidata.org/wiki/Q210973","display_name":"Cell signaling","level":3,"score":0.4898762106895447},{"id":"https://openalex.org/C9927688","wikidata":"https://www.wikidata.org/wiki/Q4915012","display_name":"Biological pathway","level":4,"score":0.45835936069488525},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4447599947452545},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4298486113548279},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.41029471158981323},{"id":"https://openalex.org/C95444343","wikidata":"https://www.wikidata.org/wiki/Q7141","display_name":"Cell biology","level":1,"score":0.25022098422050476},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.14111730456352234},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.12092664837837219},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0}],"mesh":[{"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":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D013194","descriptor_name":"Staining and Labeling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013194","descriptor_name":"Staining and Labeling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013194","descriptor_name":"Staining and Labeling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D021381","descriptor_name":"Protein Transport","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D021381","descriptor_name":"Protein Transport","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D021381","descriptor_name":"Protein Transport","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","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":"D063990","descriptor_name":"Gene Ontology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D063990","descriptor_name":"Gene Ontology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D063990","descriptor_name":"Gene Ontology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1186/s12859-015-0841-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-015-0841-4","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-015-0841-4","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:26718335","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26718335","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":"Journal Article"},{"id":"pmh:oai:europepmc.org:3674421","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4697333","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/s12859-015-0841-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-015-0841-4","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-015-0841-4","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":[{"id":"https://metadata.un.org/sdg/12","display_name":"Responsible consumption and production","score":0.41999998688697815}],"awards":[],"funders":[{"id":"https://openalex.org/F4320321543","display_name":"China Postdoctoral Science Foundation","ror":"https://ror.org/0426zh255"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2205203491.pdf","grobid_xml":"https://content.openalex.org/works/W2205203491.grobid-xml"},"referenced_works_count":47,"referenced_works":["https://openalex.org/W1968245645","https://openalex.org/W1981421887","https://openalex.org/W1987677444","https://openalex.org/W1998222399","https://openalex.org/W2000512547","https://openalex.org/W2002582122","https://openalex.org/W2004454306","https://openalex.org/W2009556149","https://openalex.org/W2012672486","https://openalex.org/W2023159617","https://openalex.org/W2026368033","https://openalex.org/W2028273907","https://openalex.org/W2029476889","https://openalex.org/W2030567185","https://openalex.org/W2039409491","https://openalex.org/W2049466649","https://openalex.org/W2053881125","https://openalex.org/W2061826097","https://openalex.org/W2062782541","https://openalex.org/W2076883893","https://openalex.org/W2092407630","https://openalex.org/W2095885101","https://openalex.org/W2096939566","https://openalex.org/W2120826041","https://openalex.org/W2122863289","https://openalex.org/W2123247102","https://openalex.org/W2125917665","https://openalex.org/W2125984976","https://openalex.org/W2128326300","https://openalex.org/W2132805085","https://openalex.org/W2136377055","https://openalex.org/W2137687319","https://openalex.org/W2137804845","https://openalex.org/W2141152663","https://openalex.org/W2147714160","https://openalex.org/W2148853951","https://openalex.org/W2153635508","https://openalex.org/W2156269526","https://openalex.org/W2158714788","https://openalex.org/W2159482845","https://openalex.org/W2165698076","https://openalex.org/W2167050411","https://openalex.org/W2169240889","https://openalex.org/W2171599819","https://openalex.org/W2174632898","https://openalex.org/W2418847844","https://openalex.org/W4294216483"],"related_works":["https://openalex.org/W2151866902","https://openalex.org/W2068787210","https://openalex.org/W4245853730","https://openalex.org/W4390006811","https://openalex.org/W3203208080","https://openalex.org/W2157193718","https://openalex.org/W1971040006","https://openalex.org/W3092591054","https://openalex.org/W1504782610","https://openalex.org/W2008572054"],"abstract_inverted_index":{"BACKGROUND:":[0],"Signaling":[1],"pathways":[2,44,62,99,142,235,246],"play":[3],"important":[4],"roles":[5],"in":[6,211],"the":[7,20,42,51,68,75,108,144,152,157,160,178,198,216,248],"life":[8],"processes":[9],"of":[10,70,159,251],"cell":[11,13],"growth,":[12],"apoptosis":[14],"and":[15,74,100,116,166,180,234,247],"organism":[16],"development.":[17],"At":[18],"present":[19],"signal":[21],"transduction":[22],"networks":[23],"are":[24,138,238],"far":[25],"from":[26],"complete.":[27],"As":[28,229],"an":[29],"effective":[30,210],"complement":[31],"to":[32,39,93,141,150,173,193,214,223,240],"experimental":[33],"methods,":[34],"computational":[35,53],"modeling":[36,77],"is":[37,170,191],"suited":[38],"rapidly":[40],"reconstruct":[41,95,151,242],"signaling":[43,61,72,79,98,122,136,154,164,168,184,201,220,227,232,245],"at":[45],"low":[46],"cost.":[47],"To":[48],"our":[49],"knowledge,":[50],"existing":[52],"methods":[54],"seldom":[55],"simultaneously":[56,94,241],"exploit":[57],"more":[58,224],"than":[59,225],"three":[60],"into":[63,177],"one":[64,226],"predictive":[65],"model":[66,101,215],"for":[67,254],"discovery":[69],"novel":[71,231],"components":[73,123,137,165,233],"cross-talk":[76],"between":[78,183],"pathways.":[80,155,185,202],"RESULTS:":[81],"In":[82],"this":[83,212],"work,":[84],"we":[85],"propose":[86],"a":[87,219],"multi-label":[88,113],"multi-instance":[89],"transfer":[90],"learning":[91,114,205],"method":[92,110],"27":[96],"human":[97,153,200,244],"their":[102,252],"cross-talks.":[103],"Computational":[104],"results":[105],"show":[106],"that":[107,218],"proposed":[109],"demonstrates":[111],"satisfactory":[112],"performance":[115],"rational":[117],"proteome-wide":[118],"predictions.":[119],"Some":[120],"predicted":[121,135,239],"or":[124],"pathway":[125],"targeted":[126,236],"proteins":[127,237],"have":[128],"been":[129,208],"validated":[130],"by":[131],"recent":[132],"literature.":[133],"The":[134],"further":[139,255],"linked":[140],"using":[143],"experimentally":[145],"derived":[146],"PPIs":[147,169],"(protein-protein":[148],"interactions)":[149],"Thus":[156],"map":[158,250],"cross-talks":[161,253],"via":[162],"common":[163,167],"conveniently":[171],"inferred":[172],"provide":[174],"valuable":[175],"insights":[176],"regulatory":[179],"cooperative":[181],"relationships":[182],"Lastly,":[186],"gene":[187],"ontology":[188],"enrichment":[189],"analysis":[190],"conducted":[192],"gain":[194],"statistical":[195],"knowledge":[196],"about":[197],"reconstructed":[199],"CONCLUSIONS:":[203],"Multi-label":[204],"framework":[206],"has":[207],"demonstrated":[209],"work":[213],"phenomena":[217],"protein":[221],"belongs":[222],"pathway.":[228],"results,":[230],"multiple":[243],"static":[249],"biomedical":[256],"research.":[257]},"counts_by_year":[{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":2}],"updated_date":"2026-08-21T09:56:20.448147","created_date":"2025-10-10T00:00:00"}
