{"id":"https://openalex.org/W4292722771","doi":"https://doi.org/10.1093/bioinformatics/btac576","title":"Isoform function prediction by Gene Ontology embedding","display_name":"Isoform function prediction by Gene Ontology embedding","publication_year":2022,"publication_date":"2022-08-23","ids":{"openalex":"https://openalex.org/W4292722771","doi":"https://doi.org/10.1093/bioinformatics/btac576","pmid":"https://pubmed.ncbi.nlm.nih.gov/35997558"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btac576","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac576","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"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/A5038664632","display_name":"Sichao Qiu","orcid":null},"institutions":[{"id":"https://openalex.org/I154099455","display_name":"Shandong University","ror":"https://ror.org/0207yh398","country_code":"CN","type":"education","lineage":["https://openalex.org/I154099455"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Sichao Qiu","raw_affiliation_strings":["Joint SDU-NTU Centre for Artificial Intelligence Research, Shandong University , Jinan, Shandong 250101, China","School of Software, Shandong University , Jinan, Shandong 250101, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Joint SDU-NTU Centre for Artificial Intelligence Research, Shandong University , Jinan, Shandong 250101, China","institution_ids":["https://openalex.org/I154099455"]},{"raw_affiliation_string":"School of Software, Shandong University , Jinan, Shandong 250101, China","institution_ids":["https://openalex.org/I154099455"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5027082940","display_name":"Guoxian Yu","orcid":"https://orcid.org/0000-0002-1667-6705"},"institutions":[{"id":"https://openalex.org/I154099455","display_name":"Shandong University","ror":"https://ror.org/0207yh398","country_code":"CN","type":"education","lineage":["https://openalex.org/I154099455"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Guoxian Yu","raw_affiliation_strings":["Joint SDU-NTU Centre for Artificial Intelligence Research, Shandong University , Jinan, Shandong 250101, China","School of Software, Shandong University , Jinan, Shandong 250101, China"],"raw_orcid":"https://orcid.org/0000-0002-1667-6705","affiliations":[{"raw_affiliation_string":"Joint SDU-NTU Centre for Artificial Intelligence Research, Shandong University , Jinan, Shandong 250101, China","institution_ids":["https://openalex.org/I154099455"]},{"raw_affiliation_string":"School of Software, Shandong University , Jinan, Shandong 250101, China","institution_ids":["https://openalex.org/I154099455"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5050004899","display_name":"Xudong L\u00fc","orcid":"https://orcid.org/0000-0001-7658-5250"},"institutions":[{"id":"https://openalex.org/I154099455","display_name":"Shandong University","ror":"https://ror.org/0207yh398","country_code":"CN","type":"education","lineage":["https://openalex.org/I154099455"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xudong Lu","raw_affiliation_strings":["Joint SDU-NTU Centre for Artificial Intelligence Research, Shandong University , Jinan, Shandong 250101, China","School of Software, Shandong University , Jinan, Shandong 250101, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Joint SDU-NTU Centre for Artificial Intelligence Research, Shandong University , Jinan, Shandong 250101, China","institution_ids":["https://openalex.org/I154099455"]},{"raw_affiliation_string":"School of Software, Shandong University , Jinan, Shandong 250101, China","institution_ids":["https://openalex.org/I154099455"]}]},{"author_position":"middle","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 , VA 22030, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, George Mason University , VA 22030, USA","institution_ids":["https://openalex.org/I162714631"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5079800756","display_name":"Maozu Guo","orcid":"https://orcid.org/0000-0001-6228-6276"},"institutions":[{"id":"https://openalex.org/I62853816","display_name":"Beijing University of Civil Engineering and Architecture","ror":"https://ror.org/02yj0p855","country_code":"CN","type":"education","lineage":["https://openalex.org/I62853816"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Maozu Guo","raw_affiliation_strings":["College of Electrical and Information Engineering, Beijing University of Civil Engineering and Architecture , Beijing 100044, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Electrical and Information Engineering, Beijing University of Civil Engineering and Architecture , Beijing 100044, China","institution_ids":["https://openalex.org/I62853816"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5027082940"],"corresponding_institution_ids":["https://openalex.org/I154099455"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.1752,"has_fulltext":false,"cited_by_count":17,"citation_normalized_percentile":{"value":0.77364571,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":97,"max":99},"biblio":{"volume":"38","issue":"19","first_page":"4581","last_page":"4588"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9056000113487244,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9056000113487244,"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/T10885","display_name":"Gene expression and cancer classification","score":0.04320000112056732,"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":0.012299999594688416,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6918269991874695},{"id":"https://openalex.org/keywords/embedding","display_name":"Embedding","score":0.5707972645759583},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.556910514831543},{"id":"https://openalex.org/keywords/focus","display_name":"Focus (optics)","score":0.5414538383483887},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.5280436277389526},{"id":"https://openalex.org/keywords/interpretability","display_name":"Interpretability","score":0.5049708485603333},{"id":"https://openalex.org/keywords/gene-isoform","display_name":"Gene isoform","score":0.4940376877784729},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4708309471607208},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.4603677988052368},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4457738697528839},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.37295249104499817},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.34726017713546753},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.32375121116638184},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.2561541795730591},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.22297745943069458},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.12470319867134094}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6918269991874695},{"id":"https://openalex.org/C41608201","wikidata":"https://www.wikidata.org/wiki/Q980509","display_name":"Embedding","level":2,"score":0.5707972645759583},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.556910514831543},{"id":"https://openalex.org/C192209626","wikidata":"https://www.wikidata.org/wiki/Q190909","display_name":"Focus (optics)","level":2,"score":0.5414538383483887},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.5280436277389526},{"id":"https://openalex.org/C2781067378","wikidata":"https://www.wikidata.org/wiki/Q17027399","display_name":"Interpretability","level":2,"score":0.5049708485603333},{"id":"https://openalex.org/C53345823","wikidata":"https://www.wikidata.org/wiki/Q5531554","display_name":"Gene isoform","level":3,"score":0.4940376877784729},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4708309471607208},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.4603677988052368},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4457738697528839},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.37295249104499817},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.34726017713546753},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.32375121116638184},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2561541795730591},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.22297745943069458},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.12470319867134094},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C120665830","wikidata":"https://www.wikidata.org/wiki/Q14620","display_name":"Optics","level":1,"score":0.0},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"score":0.0},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D012660","descriptor_name":"Semantics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012660","descriptor_name":"Semantics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012660","descriptor_name":"Semantics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020033","descriptor_name":"Protein Isoforms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020033","descriptor_name":"Protein Isoforms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020033","descriptor_name":"Protein Isoforms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","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":2,"locations":[{"id":"doi:10.1093/bioinformatics/btac576","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac576","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:35997558","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35997558","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":"Bioinformatics (Oxford, England)","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G5564147583","display_name":"\u9762\u5411\u53ef\u53d8\u526a\u63a5\u5f02\u6784\u4f53\u529f\u80fd\u9884\u6d4b\u7684\u6570\u636e\u6574\u5408\u65b9\u6cd5\u7814\u7a76","funder_award_id":"61872300","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G6836859050","display_name":null,"funder_award_id":"62031003","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"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":33,"referenced_works":["https://openalex.org/W1784654175","https://openalex.org/W1963793607","https://openalex.org/W1980948656","https://openalex.org/W1982267716","https://openalex.org/W2027898937","https://openalex.org/W2041399050","https://openalex.org/W2055043387","https://openalex.org/W2103017472","https://openalex.org/W2108892946","https://openalex.org/W2125422443","https://openalex.org/W2133790733","https://openalex.org/W2171184528","https://openalex.org/W2560886373","https://openalex.org/W2615066396","https://openalex.org/W2790214985","https://openalex.org/W2792504918","https://openalex.org/W2887057068","https://openalex.org/W2891585877","https://openalex.org/W2900629010","https://openalex.org/W2904341255","https://openalex.org/W2954055267","https://openalex.org/W2956050535","https://openalex.org/W2962975498","https://openalex.org/W2976699283","https://openalex.org/W2988426147","https://openalex.org/W2989608901","https://openalex.org/W3001796202","https://openalex.org/W3021092377","https://openalex.org/W3089154911","https://openalex.org/W3112376646","https://openalex.org/W3120115416","https://openalex.org/W3173497303","https://openalex.org/W3184957809"],"related_works":["https://openalex.org/W2905433371","https://openalex.org/W2888392564","https://openalex.org/W4310278675","https://openalex.org/W4388422664","https://openalex.org/W4390569940","https://openalex.org/W4361193272","https://openalex.org/W2963326959","https://openalex.org/W4388685194","https://openalex.org/W4312407344","https://openalex.org/W2894289927"],"abstract_inverted_index":{"MOTIVATION:":[0],"High-resolution":[1],"annotation":[2,76],"of":[3,37,45,77,92,102,115,143,150,186,205,224],"gene":[4,23,79],"functions":[5,36,114,191],"is":[6,80,226],"a":[7,21,50,74,134],"central":[8],"task":[9],"in":[10],"functional":[11,32],"genomics.":[12],"Multiple":[13],"proteoforms":[14],"translated":[15],"from":[16,20],"alternatively":[17],"spliced":[18],"isoforms":[19,39,116,187],"single":[22],"are":[24,234],"actual":[25],"function":[26],"performers":[27],"and":[28,90,133,146,160,183,188,211,218],"greatly":[29,168],"increase":[30],"the":[31,42,78,87,170,203,208,216],"diversity.":[33],"The":[34,222],"specific":[35],"different":[38],"can":[40,98,214],"decipher":[41],"molecular":[43],"basis":[44],"various":[46],"complex":[47],"diseases":[48],"at":[49,228,236],"finer":[51],"granularity.":[52],"Multi-instance":[53],"learning":[54],"(MIL)-based":[55],"solutions":[56],"have":[57],"been":[58],"developed":[59],"to":[60,67,111,128,139,180,194],"distribute":[61],"gene(bag)-level":[62],"Gene":[63],"Ontology":[64],"(GO)":[65],"annotations":[66,149],"isoforms(instances),":[68],"but":[69,166],"they":[70],"simply":[71],"presume":[72],"that":[73],"particular":[75],"responsible":[81],"by":[82,117,192],"only":[83,99,158],"one":[84],"isoform,":[85],"neglect":[86],"hierarchical":[88,126],"structures":[89],"semantics":[91],"massive":[93,113,130],"GO":[94,118,131,135,144,148,164,209],"terms":[95,145,165],"(labels),":[96],"or":[97],"handle":[100],"dozens":[101],"terms.":[103],"RESULTS:":[104],"We":[105],"propose":[106],"an":[107,124,176],"efficacy":[108,204],"approach":[109],"IsofunGO":[110,121,225],"differentiate":[112],"embedding.":[119],"Particularly,":[120],"first":[122],"introduces":[123],"attributed":[125],"network":[127,136,179],"model":[129],"terms,":[132],"embedding":[137,210],"strategy":[138,156],"learn":[140],"compact":[141],"representations":[142],"project":[147],"genes":[151],"into":[152],"compressed":[153,195],"ones,":[154],"this":[155],"not":[157],"explores":[159],"preserves":[161],"hierarchy":[162],"between":[163],"also":[167],"reduces":[169],"prediction":[171],"load.":[172],"Next,":[173],"it":[174],"develops":[175],"attention-based":[177],"MIL":[178],"fuse":[181],"genomics":[182],"transcriptomics":[184],"data":[185,233],"predict":[189],"isoform":[190],"referring":[193],"annotations.":[196],"Extensive":[197],"experiments":[198],"on":[199],"benchmark":[200],"datasets":[201],"demonstrate":[202],"IsofunGO.":[206],"Both":[207],"attention":[212],"mechanism":[213],"boost":[215],"performance":[217],"interpretability.":[219],"AVAILABILITYAND":[220],"IMPLEMENTATION:":[221],"code":[223],"available":[227,235],"http://www.sdu-idea.cn/codes.php?name=IsofunGO.":[229],"SUPPLEMENTARY":[230],"INFORMATION:":[231],"Supplementary":[232],"Bioinformatics":[237],"online.":[238]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":5}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}