{"id":"https://openalex.org/W4386420840","doi":"https://doi.org/10.1007/s40747-023-01221-1","title":"A multi-task positive-unlabeled learning framework to predict secreted proteins in human body fluids","display_name":"A multi-task positive-unlabeled learning framework to predict secreted proteins in human body fluids","publication_year":2023,"publication_date":"2023-09-04","ids":{"openalex":"https://openalex.org/W4386420840","doi":"https://doi.org/10.1007/s40747-023-01221-1"},"language":"en","primary_location":{"id":"doi:10.1007/s40747-023-01221-1","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s40747-023-01221-1","pdf_url":"https://link.springer.com/content/pdf/10.1007/s40747-023-01221-1.pdf","source":{"id":"https://openalex.org/S3035462843","display_name":"Complex & Intelligent Systems","issn_l":"2198-6053","issn":["2198-6053","2199-4536"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","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":"Complex &amp; Intelligent Systems","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://link.springer.com/content/pdf/10.1007/s40747-023-01221-1.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5081523181","display_name":"Kai He","orcid":"https://orcid.org/0000-0003-3631-2172"},"institutions":[{"id":"https://openalex.org/I194450716","display_name":"Jilin University","ror":"https://ror.org/00js3aw79","country_code":"CN","type":"education","lineage":["https://openalex.org/I194450716"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Kai He","raw_affiliation_strings":["Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun, 130012, China"],"raw_orcid":"https://orcid.org/0000-0003-3631-2172","affiliations":[{"raw_affiliation_string":"Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun, 130012, China","institution_ids":["https://openalex.org/I194450716"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100322699","display_name":"Yan Wang","orcid":"https://orcid.org/0000-0002-4751-0708"},"institutions":[{"id":"https://openalex.org/I194450716","display_name":"Jilin University","ror":"https://ror.org/00js3aw79","country_code":"CN","type":"education","lineage":["https://openalex.org/I194450716"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yan Wang","raw_affiliation_strings":["Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun, 130012, China","School of Artificial Intelligence, Jilin University, Changchun, 130012, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun, 130012, China","institution_ids":["https://openalex.org/I194450716"]},{"raw_affiliation_string":"School of Artificial Intelligence, Jilin University, Changchun, 130012, China","institution_ids":["https://openalex.org/I194450716"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101498841","display_name":"Xuping Xie","orcid":"https://orcid.org/0000-0002-3143-8262"},"institutions":[{"id":"https://openalex.org/I194450716","display_name":"Jilin University","ror":"https://ror.org/00js3aw79","country_code":"CN","type":"education","lineage":["https://openalex.org/I194450716"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xuping Xie","raw_affiliation_strings":["Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun, 130012, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun, 130012, China","institution_ids":["https://openalex.org/I194450716"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5023665938","display_name":"Dan Shao","orcid":"https://orcid.org/0000-0003-1050-2808"},"institutions":[{"id":"https://openalex.org/I106645853","display_name":"Changchun University of Science and Technology","ror":"https://ror.org/007mntk44","country_code":"CN","type":"education","lineage":["https://openalex.org/I106645853"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Dan Shao","raw_affiliation_strings":["College of Computer Science and Technology, Changchun University, Changchun, 130022, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Computer Science and Technology, Changchun University, Changchun, 130022, China","institution_ids":["https://openalex.org/I106645853"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5081523181"],"corresponding_institution_ids":["https://openalex.org/I194450716"],"apc_list":{"value":1320,"currency":"GBP","value_usd":1619},"apc_paid":{"value":1320,"currency":"GBP","value_usd":1619},"fwci":0.5998,"has_fulltext":true,"cited_by_count":4,"citation_normalized_percentile":{"value":0.70168917,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":96},"biblio":{"volume":"10","issue":"1","first_page":"1319","last_page":"1331"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9970999956130981,"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":0.9970999956130981,"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/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.9962000250816345,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12535","display_name":"Machine Learning and Data Classification","score":0.9355000257492065,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/overfitting","display_name":"Overfitting","score":0.8470181226730347},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6167066097259521},{"id":"https://openalex.org/keywords/convolutional-neural-network","display_name":"Convolutional neural network","score":0.5648592710494995},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5647413730621338},{"id":"https://openalex.org/keywords/body-fluid","display_name":"Body fluid","score":0.5432388186454773},{"id":"https://openalex.org/keywords/computational-intelligence","display_name":"Computational intelligence","score":0.5300557017326355},{"id":"https://openalex.org/keywords/biomarker-discovery","display_name":"Biomarker discovery","score":0.4869476556777954},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.4621245861053467},{"id":"https://openalex.org/keywords/task","display_name":"Task (project management)","score":0.46154266595840454},{"id":"https://openalex.org/keywords/binary-classification","display_name":"Binary classification","score":0.45398157835006714},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.44079411029815674},{"id":"https://openalex.org/keywords/biological-fluids","display_name":"Biological fluids","score":0.4284569025039673},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.4268072843551636},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.362712562084198},{"id":"https://openalex.org/keywords/proteomics","display_name":"Proteomics","score":0.36128270626068115},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.3392307758331299},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.23299184441566467},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.14860063791275024},{"id":"https://openalex.org/keywords/chromatography","display_name":"Chromatography","score":0.14202910661697388},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.10403695702552795},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.10203590989112854},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.09092089533805847},{"id":"https://openalex.org/keywords/support-vector-machine","display_name":"Support vector machine","score":0.07255491614341736}],"concepts":[{"id":"https://openalex.org/C22019652","wikidata":"https://www.wikidata.org/wiki/Q331309","display_name":"Overfitting","level":3,"score":0.8470181226730347},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6167066097259521},{"id":"https://openalex.org/C81363708","wikidata":"https://www.wikidata.org/wiki/Q17084460","display_name":"Convolutional neural network","level":2,"score":0.5648592710494995},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5647413730621338},{"id":"https://openalex.org/C2776735168","wikidata":"https://www.wikidata.org/wiki/Q1058795","display_name":"Body fluid","level":2,"score":0.5432388186454773},{"id":"https://openalex.org/C139502532","wikidata":"https://www.wikidata.org/wiki/Q1122090","display_name":"Computational intelligence","level":2,"score":0.5300557017326355},{"id":"https://openalex.org/C124535831","wikidata":"https://www.wikidata.org/wiki/Q4915074","display_name":"Biomarker discovery","level":4,"score":0.4869476556777954},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.4621245861053467},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.46154266595840454},{"id":"https://openalex.org/C66905080","wikidata":"https://www.wikidata.org/wiki/Q17005494","display_name":"Binary classification","level":3,"score":0.45398157835006714},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.44079411029815674},{"id":"https://openalex.org/C3020728648","wikidata":"https://www.wikidata.org/wiki/Q1058795","display_name":"Biological fluids","level":2,"score":0.4284569025039673},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.4268072843551636},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.362712562084198},{"id":"https://openalex.org/C46111723","wikidata":"https://www.wikidata.org/wiki/Q471857","display_name":"Proteomics","level":3,"score":0.36128270626068115},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.3392307758331299},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.23299184441566467},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.14860063791275024},{"id":"https://openalex.org/C43617362","wikidata":"https://www.wikidata.org/wiki/Q170050","display_name":"Chromatography","level":1,"score":0.14202910661697388},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.10403695702552795},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.10203590989112854},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.09092089533805847},{"id":"https://openalex.org/C12267149","wikidata":"https://www.wikidata.org/wiki/Q282453","display_name":"Support vector machine","level":2,"score":0.07255491614341736},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.0},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0},{"id":"https://openalex.org/C142724271","wikidata":"https://www.wikidata.org/wiki/Q7208","display_name":"Pathology","level":1,"score":0.0},{"id":"https://openalex.org/C201995342","wikidata":"https://www.wikidata.org/wiki/Q682496","display_name":"Systems engineering","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1007/s40747-023-01221-1","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s40747-023-01221-1","pdf_url":"https://link.springer.com/content/pdf/10.1007/s40747-023-01221-1.pdf","source":{"id":"https://openalex.org/S3035462843","display_name":"Complex & Intelligent Systems","issn_l":"2198-6053","issn":["2198-6053","2199-4536"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","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":"Complex &amp; Intelligent Systems","raw_type":"journal-article"},{"id":"pmh:oai:doaj.org/article:529229abd5934322b6acf16fd7fdb30b","is_oa":true,"landing_page_url":"https://doaj.org/article/529229abd5934322b6acf16fd7fdb30b","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Complex & Intelligent Systems, Vol 10, Iss 1, Pp 1319-1331 (2023)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1007/s40747-023-01221-1","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s40747-023-01221-1","pdf_url":"https://link.springer.com/content/pdf/10.1007/s40747-023-01221-1.pdf","source":{"id":"https://openalex.org/S3035462843","display_name":"Complex & Intelligent Systems","issn_l":"2198-6053","issn":["2198-6053","2199-4536"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","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":"Complex &amp; Intelligent Systems","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2241915452","display_name":null,"funder_award_id":"62072212","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320322174","display_name":"People's Government of Jilin Province","ror":"https://ror.org/02fzqav45"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4386420840.pdf"},"referenced_works_count":46,"referenced_works":["https://openalex.org/W1525961903","https://openalex.org/W1969289070","https://openalex.org/W1974910252","https://openalex.org/W1975290591","https://openalex.org/W1981295186","https://openalex.org/W1994525010","https://openalex.org/W2029163288","https://openalex.org/W2040034810","https://openalex.org/W2050871273","https://openalex.org/W2089417302","https://openalex.org/W2095483652","https://openalex.org/W2097606916","https://openalex.org/W2118217143","https://openalex.org/W2120615054","https://openalex.org/W2152800101","https://openalex.org/W2158714788","https://openalex.org/W2160061958","https://openalex.org/W2518479197","https://openalex.org/W2550451727","https://openalex.org/W2742033716","https://openalex.org/W2898402099","https://openalex.org/W2899867782","https://openalex.org/W2919115771","https://openalex.org/W2983598759","https://openalex.org/W2996351488","https://openalex.org/W3004850558","https://openalex.org/W3005063595","https://openalex.org/W3025373576","https://openalex.org/W3036446235","https://openalex.org/W3136918052","https://openalex.org/W3141679280","https://openalex.org/W3141797743","https://openalex.org/W3153477281","https://openalex.org/W3177283014","https://openalex.org/W3195165594","https://openalex.org/W3195881367","https://openalex.org/W3205873152","https://openalex.org/W3214814050","https://openalex.org/W4213373251","https://openalex.org/W4225136054","https://openalex.org/W4283329238","https://openalex.org/W4285727809","https://openalex.org/W4287093265","https://openalex.org/W4294273350","https://openalex.org/W4309223931","https://openalex.org/W4366774177"],"related_works":["https://openalex.org/W4392713411","https://openalex.org/W2111663113","https://openalex.org/W181715402","https://openalex.org/W2765341339","https://openalex.org/W3111441298","https://openalex.org/W2301845948","https://openalex.org/W2982792801","https://openalex.org/W4283080446","https://openalex.org/W1989822344","https://openalex.org/W2765559212"],"abstract_inverted_index":{"Abstract":[0],"Body":[1],"fluid":[2,103],"biomarkers":[3],"are":[4,58],"very":[5],"important,":[6],"because":[7],"they":[8],"can":[9],"be":[10],"detected":[11],"in":[12,24,90,99,139,211],"a":[13,61,81,91,100,148],"non-invasive":[14],"or":[15],"minimally":[16],"invasive":[17],"way.":[18],"The":[19,95,144,162,196],"discovery":[20,98],"of":[21,56,158,171,179,186,190,194],"secreted":[22,48,88,96,137,212],"proteins":[23,49,89,138],"human":[25,37],"body":[26,93,102,141,160,173,181],"fluids":[27,142,182],"is":[28,66,104,121],"an":[29,116,184],"essential":[30],"step":[31],"toward":[32],"proteomic":[33],"biomarker":[34],"identification":[35],"for":[36],"diseases.":[38],"Recently,":[39],"many":[40],"computational":[41],"methods":[42,210],"have":[43],"been":[44],"proposed":[45],"to":[46,86,123,135,152],"predict":[47,87,136],"and":[50,69,110,167,175,192],"achieved":[51,183],"some":[52],"success.":[53],"However,":[54],"most":[55],"them":[57],"based":[59],"on":[60,169],"manual":[62],"negative":[63],"dataset,":[64],"which":[65],"usually":[67],"biased":[68],"therefore":[70],"limits":[71],"the":[72,125,155,176,201],"prediction":[73,156],"performances.":[74],"In":[75],"this":[76,133],"paper,":[77],"we":[78,130],"first":[79],"propose":[80],"novel":[82],"positive-unlabeled":[83],"learning":[84],"framework":[85,134,146,164,203],"single":[92,101],"fluid.":[94],"protein":[97,213],"transformed":[105],"into":[106],"multiple":[107,140],"binary":[108],"classifications":[109],"solved":[111],"via":[112],"multi-task":[113],"learning.":[114],"Also,":[115],"effective":[117],"convolutional":[118],"neural":[119],"network":[120,151],"employed":[122],"reduce":[124],"overfitting":[126],"problem.":[127],"After":[128],"that,":[129],"then":[131],"improve":[132,154],"simultaneously.":[143],"improved":[145,163,202],"adopts":[147],"globally":[149],"shared":[150],"further":[153],"performances":[157],"all":[159],"fluids.":[161],"was":[165],"trained":[166],"evaluated":[168],"datasets":[170],"17":[172,180],"fluids,":[174],"average":[177],"benchmarks":[178],"accuracy":[185],"89.48%,":[187],"F1":[188],"score":[189],"56.17%,":[191],"PRAUC":[193],"58.93%.":[195],"comparative":[197],"results":[198],"demonstrate":[199],"that":[200],"performs":[204],"much":[205],"better":[206],"than":[207],"other":[208],"state-of-the-art":[209],"discovery.":[214]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":2}],"updated_date":"2025-12-25T23:11:45.687758","created_date":"2025-10-10T00:00:00"}
