{"id":"https://openalex.org/W2743273864","doi":"https://doi.org/10.1145/3097983.3097984","title":"Functional Annotation of Human Protein Coding Isoforms via Non-convex Multi-Instance Learning","display_name":"Functional Annotation of Human Protein Coding Isoforms via Non-convex Multi-Instance Learning","publication_year":2017,"publication_date":"2017-08-04","ids":{"openalex":"https://openalex.org/W2743273864","doi":"https://doi.org/10.1145/3097983.3097984","mag":"2743273864"},"language":"en","primary_location":{"id":"doi:10.1145/3097983.3097984","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3097983.3097984","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 23rd ACM SIGKDD International Conference on Knowledge Discovery and Data Mining","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5074096377","display_name":"Tingjin Luo","orcid":"https://orcid.org/0000-0002-8171-3971"},"institutions":[{"id":"https://openalex.org/I170215575","display_name":"National University of Defense Technology","ror":"https://ror.org/05d2yfz11","country_code":"CN","type":"education","lineage":["https://openalex.org/I170215575"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Tingjin Luo","raw_affiliation_strings":["National University of Defense Technology, Changsha, China"],"affiliations":[{"raw_affiliation_string":"National University of Defense Technology, Changsha, China","institution_ids":["https://openalex.org/I170215575"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100693727","display_name":"Weizhong Zhang","orcid":"https://orcid.org/0000-0001-7311-0698"},"institutions":[{"id":"https://openalex.org/I76130692","display_name":"Zhejiang University","ror":"https://ror.org/00a2xv884","country_code":"CN","type":"education","lineage":["https://openalex.org/I76130692"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Weizhong Zhang","raw_affiliation_strings":["Zhejiang University, Hangzhou, China"],"affiliations":[{"raw_affiliation_string":"Zhejiang University, Hangzhou, China","institution_ids":["https://openalex.org/I76130692"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103213699","display_name":"Shuang Qiu","orcid":"https://orcid.org/0000-0002-9651-1061"},"institutions":[{"id":"https://openalex.org/I27837315","display_name":"University of Michigan\u2013Ann Arbor","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Shuang Qiu","raw_affiliation_strings":["University of Michigan, Ann Arbor, MI, USA"],"affiliations":[{"raw_affiliation_string":"University of Michigan, Ann Arbor, MI, USA","institution_ids":["https://openalex.org/I27837315"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100397465","display_name":"Yang Yang","orcid":"https://orcid.org/0000-0001-9172-1695"},"institutions":[{"id":"https://openalex.org/I82880672","display_name":"Beihang University","ror":"https://ror.org/00wk2mp56","country_code":"CN","type":"education","lineage":["https://openalex.org/I82880672"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yang Yang","raw_affiliation_strings":["Beihang University, Beijing, China"],"affiliations":[{"raw_affiliation_string":"Beihang University, Beijing, China","institution_ids":["https://openalex.org/I82880672"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064728173","display_name":"Dongyun Yi","orcid":null},"institutions":[{"id":"https://openalex.org/I170215575","display_name":"National University of Defense Technology","ror":"https://ror.org/05d2yfz11","country_code":"CN","type":"education","lineage":["https://openalex.org/I170215575"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Dongyun Yi","raw_affiliation_strings":["National University of Defense Technology, Changsha, China"],"affiliations":[{"raw_affiliation_string":"National University of Defense Technology, Changsha, China","institution_ids":["https://openalex.org/I170215575"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102889910","display_name":"Guangtao Wang","orcid":"https://orcid.org/0000-0003-2766-0917"},"institutions":[{"id":"https://openalex.org/I27837315","display_name":"University of Michigan\u2013Ann Arbor","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Guangtao Wang","raw_affiliation_strings":["University of Michigan, Ann Arbor, MI, USA"],"affiliations":[{"raw_affiliation_string":"University of Michigan, Ann Arbor, MI, USA","institution_ids":["https://openalex.org/I27837315"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5010419481","display_name":"Jieping Ye","orcid":"https://orcid.org/0000-0001-8662-5818"},"institutions":[{"id":"https://openalex.org/I27837315","display_name":"University of Michigan\u2013Ann Arbor","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jieping Ye","raw_affiliation_strings":["University of Michigan, Ann Arbor, MI, USA"],"affiliations":[{"raw_affiliation_string":"University of Michigan, Ann Arbor, MI, USA","institution_ids":["https://openalex.org/I27837315"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100440013","display_name":"Jie Wang","orcid":"https://orcid.org/0000-0001-7870-0646"},"institutions":[{"id":"https://openalex.org/I27837315","display_name":"University of Michigan\u2013Ann Arbor","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jie Wang","raw_affiliation_strings":["University of Michigan, Ann Arbor, MI, USA"],"affiliations":[{"raw_affiliation_string":"University of Michigan, Ann Arbor, MI, USA","institution_ids":["https://openalex.org/I27837315"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5074096377"],"corresponding_institution_ids":["https://openalex.org/I170215575"],"apc_list":null,"apc_paid":null,"fwci":0.8507,"has_fulltext":false,"cited_by_count":19,"citation_normalized_percentile":{"value":0.72201807,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":null,"issue":null,"first_page":"345","last_page":"354"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.9988999962806702,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9988999962806702,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9952999949455261,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9951000213623047,"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/annotation","display_name":"Annotation","score":0.6207810044288635},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6135671734809875},{"id":"https://openalex.org/keywords/coordinate-descent","display_name":"Coordinate descent","score":0.5534857511520386},{"id":"https://openalex.org/keywords/neural-coding","display_name":"Neural coding","score":0.4978492259979248},{"id":"https://openalex.org/keywords/discriminative-model","display_name":"Discriminative model","score":0.46190696954727173},{"id":"https://openalex.org/keywords/human-genome","display_name":"Human genome","score":0.45721009373664856},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.45121338963508606},{"id":"https://openalex.org/keywords/genome-project","display_name":"Genome project","score":0.43548089265823364},{"id":"https://openalex.org/keywords/feature-vector","display_name":"Feature vector","score":0.4177578389644623},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.38923001289367676},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.3512113094329834},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.3398999571800232},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.33090919256210327},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.33078527450561523},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.27143988013267517},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.13045796751976013}],"concepts":[{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.6207810044288635},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6135671734809875},{"id":"https://openalex.org/C157553263","wikidata":"https://www.wikidata.org/wiki/Q5168004","display_name":"Coordinate descent","level":2,"score":0.5534857511520386},{"id":"https://openalex.org/C77637269","wikidata":"https://www.wikidata.org/wiki/Q7002051","display_name":"Neural coding","level":2,"score":0.4978492259979248},{"id":"https://openalex.org/C97931131","wikidata":"https://www.wikidata.org/wiki/Q5282087","display_name":"Discriminative model","level":2,"score":0.46190696954727173},{"id":"https://openalex.org/C197077220","wikidata":"https://www.wikidata.org/wiki/Q720988","display_name":"Human genome","level":4,"score":0.45721009373664856},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.45121338963508606},{"id":"https://openalex.org/C89566754","wikidata":"https://www.wikidata.org/wiki/Q2273828","display_name":"Genome project","level":4,"score":0.43548089265823364},{"id":"https://openalex.org/C83665646","wikidata":"https://www.wikidata.org/wiki/Q42139305","display_name":"Feature vector","level":2,"score":0.4177578389644623},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.38923001289367676},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.3512113094329834},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3398999571800232},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.33090919256210327},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.33078527450561523},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.27143988013267517},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.13045796751976013}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1145/3097983.3097984","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3097983.3097984","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 23rd ACM SIGKDD International Conference on Knowledge Discovery and Data Mining","raw_type":"proceedings-article"},{"id":"pmh:oai:repository.hkust.edu.hk:1783.1-103711","is_oa":false,"landing_page_url":"http://repository.hkust.edu.hk/ir/Record/1783.1-103711","pdf_url":null,"source":{"id":"https://openalex.org/S4306401796","display_name":"Rare & Special e-Zone (The Hong Kong University of Science and Technology)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I200769079","host_organization_name":"Hong Kong University of Science and Technology","host_organization_lineage":["https://openalex.org/I200769079"],"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":"Conference paper"},{"id":"pmh:oai:repository.ust.hk:1783.1-103711","is_oa":false,"landing_page_url":"http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=LinksAMR&SrcApp=PARTNER_APP&DestLinkType=FullRecord&DestApp=WOS&KeyUT=000455787300049","pdf_url":null,"source":{"id":"https://openalex.org/S4306401796","display_name":"Rare & Special e-Zone (The Hong Kong University of Science and Technology)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I200769079","host_organization_name":"Hong Kong University of Science and Technology","host_organization_lineage":["https://openalex.org/I200769079"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Conference paper"}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/10","score":0.7200000286102295,"display_name":"Reduced inequalities"}],"awards":[{"id":"https://openalex.org/G2594830702","display_name":null,"funder_award_id":"III-1539722","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G4246749407","display_name":null,"funder_award_id":"III-1539991","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G7684759429","display_name":null,"funder_award_id":"IIS- 0953662","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":42,"referenced_works":["https://openalex.org/W1540007258","https://openalex.org/W1581034630","https://openalex.org/W1784654175","https://openalex.org/W1973948212","https://openalex.org/W1978259121","https://openalex.org/W1984068087","https://openalex.org/W1990381576","https://openalex.org/W1998767819","https://openalex.org/W2008056655","https://openalex.org/W2010792435","https://openalex.org/W2025855398","https://openalex.org/W2026141529","https://openalex.org/W2027898937","https://openalex.org/W2041399050","https://openalex.org/W2048827870","https://openalex.org/W2053784471","https://openalex.org/W2088338354","https://openalex.org/W2095647330","https://openalex.org/W2096465161","https://openalex.org/W2097065948","https://openalex.org/W2098166271","https://openalex.org/W2100305481","https://openalex.org/W2100556411","https://openalex.org/W2103017472","https://openalex.org/W2108745803","https://openalex.org/W2110119381","https://openalex.org/W2115672776","https://openalex.org/W2122825543","https://openalex.org/W2123060905","https://openalex.org/W2128541811","https://openalex.org/W2128678390","https://openalex.org/W2132851637","https://openalex.org/W2136549268","https://openalex.org/W2141831115","https://openalex.org/W2154318594","https://openalex.org/W2158698691","https://openalex.org/W2343974644","https://openalex.org/W2345998082","https://openalex.org/W2913668833","https://openalex.org/W2963648037","https://openalex.org/W4299689471","https://openalex.org/W6677467840"],"related_works":["https://openalex.org/W2102805523","https://openalex.org/W1461621550","https://openalex.org/W2311479510","https://openalex.org/W62482549","https://openalex.org/W2773500201","https://openalex.org/W2884291362","https://openalex.org/W1961939221","https://openalex.org/W4240599934","https://openalex.org/W2086630149","https://openalex.org/W2063853667"],"abstract_inverted_index":{"Functional":[0],"annotation":[1,80,221],"of":[2,13,24,32,46,55,62,65,72,98,112,219,223],"human":[3,25,204,224],"genes":[4,26,120,134],"is":[5,164],"fundamentally":[6],"important":[7],"for":[8],"understanding":[9,61],"the":[10,22,29,63,70,96,110,119,125,133,136,153,183,209,214],"molecular":[11],"basis":[12],"various":[14,168],"genetic":[15],"diseases.":[16],"A":[17],"major":[18],"challenge":[19],"in":[20,28,217],"determining":[21],"functions":[23,41,54,64,97,173],"lies":[27],"functional":[30,79,220],"diversity":[31],"proteins,":[33],"that":[34,121,151,208],"is,":[35,105],"a":[36,91,106,149,158],"gene":[37],"can":[38,57],"perform":[39],"different":[40],"as":[42,129,138,175],"it":[43],"may":[44],"consist":[45],"multiple":[47],"protein":[48],"coding":[49],"isoforms":[50],"(PCIs).":[51],"Therefore,":[52],"differentiating":[53],"PCIs":[56,99,225],"significantly":[58,212],"deepen":[59],"our":[60],"genes.":[66],"However,":[67],"due":[68],"to":[69,94,124,157,166],"lack":[71],"isoform-level":[73],"gold-standards":[74],"(ground-truth":[75],"annotation),":[76],"many":[77],"existing":[78],"approaches":[81,211],"are":[82,122],"developed":[83],"at":[84],"gene-level.":[85],"In":[86],"this":[87],"paper,":[88],"we":[89,117,147,192],"propose":[90],"novel":[92],"approach":[93],"differentiate":[95],"by":[100,142],"integrating":[101],"sparse":[102,143],"simplex":[103],"projection---that":[104],"nonconvex":[107],"sparsity-inducing":[108],"regularizer---with":[109],"framework":[111,163],"multi-instance":[113],"learning":[114],"(MIL).":[115],"Specifically,":[116],"label":[118],"annotated":[123],"function":[126,137],"under":[127],"consideration":[128],"positive":[130],"bags":[131],"and":[132,170,178,188,226],"without":[135],"negative":[139],"bags.":[140],"Then,":[141],"projections":[144],"onto":[145],"simplex,":[146],"learn":[148],"mapping":[150],"embeds":[152],"original":[154],"bag":[155],"space":[156],"discriminative":[159],"feature":[160],"space.":[161],"Our":[162],"flexible":[165],"incorporate":[167],"smooth":[169],"non-smooth":[171,189],"loss":[172,177],"such":[174],"logistic":[176],"hinge":[179],"loss.":[180],"To":[181],"solve":[182],"resulting":[184],"highly":[185],"nontrivial":[186],"non-convex":[187],"optimization":[190],"problem,":[191],"further":[193],"develop":[194],"an":[195],"efficient":[196],"block":[197],"coordinate":[198],"descent":[199],"algorithm.":[200],"Extensive":[201],"experiments":[202],"on":[203],"genome":[205],"data":[206],"demonstrate":[207],"proposed":[210],"outperform":[213],"state-of-the-art":[215],"methods":[216],"terms":[218],"accuracy":[222],"efficiency.":[227]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":4},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":5},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":4}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
