{"id":"https://openalex.org/W7166588197","doi":"https://doi.org/10.1093/bioinformatics/btag468","title":"OmicsTransformer: self-supervised masked consistency and uncertainty-aware fusion for robust multi-omics prediction","display_name":"OmicsTransformer: self-supervised masked consistency and uncertainty-aware fusion for robust multi-omics prediction","publication_year":2026,"publication_date":"2026-06-29","ids":{"openalex":"https://openalex.org/W7166588197","doi":"https://doi.org/10.1093/bioinformatics/btag468","pmid":"https://pubmed.ncbi.nlm.nih.gov/42371766"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btag468","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btag468","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","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":true,"oa_status":"gold","oa_url":"https://doi.org/10.1093/bioinformatics/btag468","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5025906570","display_name":"J. H. Feng","orcid":"https://orcid.org/0009-0000-3968-8760"},"institutions":[{"id":"https://openalex.org/I180726961","display_name":"Shenzhen University","ror":"https://ror.org/01vy4gh70","country_code":"CN","type":"education","lineage":["https://openalex.org/I180726961"]},{"id":"https://openalex.org/I4210152380","display_name":"Shenzhen Technology University","ror":"https://ror.org/04qzpec27","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210152380"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Junxuan Feng","raw_affiliation_strings":["College of Computer Science and Software Engineering, Shenzhen University , Shenzhen, 518060,","National Engineering Laboratory for Big Data System Computing Technology, Shenzhen University , Shenzhen, 518060,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Computer Science and Software Engineering, Shenzhen University , Shenzhen, 518060,","institution_ids":["https://openalex.org/I180726961"]},{"raw_affiliation_string":"National Engineering Laboratory for Big Data System Computing Technology, Shenzhen University , Shenzhen, 518060,","institution_ids":["https://openalex.org/I4210152380"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101482333","display_name":"Boxuan Shan","orcid":"https://orcid.org/0009-0006-0329-9978"},"institutions":[{"id":"https://openalex.org/I180726961","display_name":"Shenzhen University","ror":"https://ror.org/01vy4gh70","country_code":"CN","type":"education","lineage":["https://openalex.org/I180726961"]},{"id":"https://openalex.org/I4210152380","display_name":"Shenzhen Technology University","ror":"https://ror.org/04qzpec27","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210152380"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Bingshen Shan","raw_affiliation_strings":["College of Computer Science and Software Engineering, Shenzhen University , Shenzhen, 518060,","National Engineering Laboratory for Big Data System Computing Technology, Shenzhen University , Shenzhen, 518060,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Computer Science and Software Engineering, Shenzhen University , Shenzhen, 518060,","institution_ids":["https://openalex.org/I180726961"]},{"raw_affiliation_string":"National Engineering Laboratory for Big Data System Computing Technology, Shenzhen University , Shenzhen, 518060,","institution_ids":["https://openalex.org/I4210152380"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5139625721","display_name":"Jie Deng","orcid":null},"institutions":[{"id":"https://openalex.org/I180726961","display_name":"Shenzhen University","ror":"https://ror.org/01vy4gh70","country_code":"CN","type":"education","lineage":["https://openalex.org/I180726961"]},{"id":"https://openalex.org/I4210152380","display_name":"Shenzhen Technology University","ror":"https://ror.org/04qzpec27","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210152380"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jie Deng","raw_affiliation_strings":["College of Computer Science and Software Engineering, Shenzhen University , Shenzhen, 518060,","National Engineering Laboratory for Big Data System Computing Technology, Shenzhen University , Shenzhen, 518060,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Computer Science and Software Engineering, Shenzhen University , Shenzhen, 518060,","institution_ids":["https://openalex.org/I180726961"]},{"raw_affiliation_string":"National Engineering Laboratory for Big Data System Computing Technology, Shenzhen University , Shenzhen, 518060,","institution_ids":["https://openalex.org/I4210152380"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5139590082","display_name":"Zixin Jiang","orcid":null},"institutions":[{"id":"https://openalex.org/I180726961","display_name":"Shenzhen University","ror":"https://ror.org/01vy4gh70","country_code":"CN","type":"education","lineage":["https://openalex.org/I180726961"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zixin Jiang","raw_affiliation_strings":["College of Mechatronics and Control Engineering, Shenzhen University , Shenzhen, 518060,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Mechatronics and Control Engineering, Shenzhen University , Shenzhen, 518060,","institution_ids":["https://openalex.org/I180726961"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5069329996","display_name":"Siqin Peng","orcid":null},"institutions":[{"id":"https://openalex.org/I37461747","display_name":"Wuhan University","ror":"https://ror.org/033vjfk17","country_code":"CN","type":"education","lineage":["https://openalex.org/I37461747"]},{"id":"https://openalex.org/I4210158570","display_name":"Zhejiang University-University of Edinburgh Institute","ror":"https://ror.org/04jth1r26","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210158570","https://openalex.org/I76130692","https://openalex.org/I98677209"]},{"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":"Siqin Peng","raw_affiliation_strings":["School of Computer Science, Wuhan University , Wuhan, 430072,","Zhejiang University\u2013University of Edinburgh Institute, Zhejiang University , Hangzhou, 314400,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science, Wuhan University , Wuhan, 430072,","institution_ids":["https://openalex.org/I37461747"]},{"raw_affiliation_string":"Zhejiang University\u2013University of Edinburgh Institute, Zhejiang University , Hangzhou, 314400,","institution_ids":["https://openalex.org/I4210158570","https://openalex.org/I76130692"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5139618325","display_name":"Sijun Peng","orcid":null},"institutions":[{"id":"https://openalex.org/I37461747","display_name":"Wuhan University","ror":"https://ror.org/033vjfk17","country_code":"CN","type":"education","lineage":["https://openalex.org/I37461747"]},{"id":"https://openalex.org/I4210158570","display_name":"Zhejiang University-University of Edinburgh Institute","ror":"https://ror.org/04jth1r26","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210158570","https://openalex.org/I76130692","https://openalex.org/I98677209"]},{"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":"Sijun Peng","raw_affiliation_strings":["School of Computer Science, Wuhan University , Wuhan, 430072,","Zhejiang University\u2013University of Edinburgh Institute, Zhejiang University , Hangzhou, 314400,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science, Wuhan University , Wuhan, 430072,","institution_ids":["https://openalex.org/I37461747"]},{"raw_affiliation_string":"Zhejiang University\u2013University of Edinburgh Institute, Zhejiang University , Hangzhou, 314400,","institution_ids":["https://openalex.org/I4210158570","https://openalex.org/I76130692"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083088618","display_name":"Jian Yang","orcid":"https://orcid.org/0000-0002-8826-5198"},"institutions":[{"id":"https://openalex.org/I4210112448","display_name":"Beijing Anding Hospital","ror":"https://ror.org/021ky1s64","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210112448"]},{"id":"https://openalex.org/I4210165198","display_name":"Beijing Advanced Sciences and Innovation Center","ror":"https://ror.org/05qm21180","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210165198"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jian Yang","raw_affiliation_strings":["Advanced Innovation Center for Human Brain Protection, Capital Medical University , Beijing, 100088,","Beijing Key Laboratory of Mental Disorders, National Clinical Research Center for Mental Disorders and National Center for Mental Disorders, Beijing Anding Hospital, Capital Medical University , Beijing, 100088,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Advanced Innovation Center for Human Brain Protection, Capital Medical University , Beijing, 100088,","institution_ids":["https://openalex.org/I4210165198"]},{"raw_affiliation_string":"Beijing Key Laboratory of Mental Disorders, National Clinical Research Center for Mental Disorders and National Center for Mental Disorders, Beijing Anding Hospital, Capital Medical University , Beijing, 100088,","institution_ids":["https://openalex.org/I4210112448"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100367487","display_name":"Gang Wang","orcid":"https://orcid.org/0009-0009-2453-1854"},"institutions":[{"id":"https://openalex.org/I4210112448","display_name":"Beijing Anding Hospital","ror":"https://ror.org/021ky1s64","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210112448"]},{"id":"https://openalex.org/I4210165198","display_name":"Beijing Advanced Sciences and Innovation Center","ror":"https://ror.org/05qm21180","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210165198"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Gang Wang","raw_affiliation_strings":["Advanced Innovation Center for Human Brain Protection, Capital Medical University , Beijing, 100088,","Beijing Key Laboratory of Mental Disorders, National Clinical Research Center for Mental Disorders and National Center for Mental Disorders, Beijing Anding Hospital, Capital Medical University , Beijing, 100088,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Advanced Innovation Center for Human Brain Protection, Capital Medical University , Beijing, 100088,","institution_ids":["https://openalex.org/I4210165198"]},{"raw_affiliation_string":"Beijing Key Laboratory of Mental Disorders, National Clinical Research Center for Mental Disorders and National Center for Mental Disorders, Beijing Anding Hospital, Capital Medical University , Beijing, 100088,","institution_ids":["https://openalex.org/I4210112448"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082505204","display_name":"Xiaogang Peng","orcid":"https://orcid.org/0000-0002-8173-5118"},"institutions":[{"id":"https://openalex.org/I4210152380","display_name":"Shenzhen Technology University","ror":"https://ror.org/04qzpec27","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210152380"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Xiaogang Peng","raw_affiliation_strings":["National Engineering Laboratory for Big Data System Computing Technology, Shenzhen University , Shenzhen, 518060,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Engineering Laboratory for Big Data System Computing Technology, Shenzhen University , Shenzhen, 518060,","institution_ids":["https://openalex.org/I4210152380"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5045413149","display_name":"Xiaozheng Li","orcid":"https://orcid.org/0000-0002-0802-6454"},"institutions":[{"id":"https://openalex.org/I180726961","display_name":"Shenzhen University","ror":"https://ror.org/01vy4gh70","country_code":"CN","type":"education","lineage":["https://openalex.org/I180726961"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Xiaozheng Li","raw_affiliation_strings":["College of Life Sciences and Oceanography, Shenzhen University , Shenzhen, 518060,"],"raw_orcid":"https://orcid.org/0000-0002-0802-6454","affiliations":[{"raw_affiliation_string":"College of Life Sciences and Oceanography, Shenzhen University , Shenzhen, 518060,","institution_ids":["https://openalex.org/I180726961"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5045413149","https://openalex.org/A5082505204"],"corresponding_institution_ids":["https://openalex.org/I180726961","https://openalex.org/I4210152380"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.72726782,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"42","issue":"7","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.6647999882698059,"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":0.6647999882698059,"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/T11297","display_name":"Ferroptosis and cancer prognosis","score":0.060600001364946365,"subfield":{"id":"https://openalex.org/subfields/2740","display_name":"Pulmonary and Respiratory Medicine"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T10261","display_name":"Genetic Associations and Epidemiology","score":0.04360000044107437,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/consistency","display_name":"Consistency (knowledge bases)","score":0.5180000066757202},{"id":"https://openalex.org/keywords/missing-data","display_name":"Missing data","score":0.4733999967575073},{"id":"https://openalex.org/keywords/subtyping","display_name":"Subtyping","score":0.42719998955726624},{"id":"https://openalex.org/keywords/sensor-fusion","display_name":"Sensor fusion","score":0.3935000002384186},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.39169999957084656},{"id":"https://openalex.org/keywords/code","display_name":"Code (set theory)","score":0.3903999924659729},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.39010000228881836},{"id":"https://openalex.org/keywords/heuristic","display_name":"Heuristic","score":0.38119998574256897},{"id":"https://openalex.org/keywords/data-integration","display_name":"Data integration","score":0.3716000020503998}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6861000061035156},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.5437999963760376},{"id":"https://openalex.org/C2776436953","wikidata":"https://www.wikidata.org/wiki/Q5163215","display_name":"Consistency (knowledge bases)","level":2,"score":0.5180000066757202},{"id":"https://openalex.org/C9357733","wikidata":"https://www.wikidata.org/wiki/Q6878417","display_name":"Missing data","level":2,"score":0.4733999967575073},{"id":"https://openalex.org/C83852419","wikidata":"https://www.wikidata.org/wiki/Q2713292","display_name":"Subtyping","level":2,"score":0.42719998955726624},{"id":"https://openalex.org/C33954974","wikidata":"https://www.wikidata.org/wiki/Q486494","display_name":"Sensor fusion","level":2,"score":0.3935000002384186},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.39169999957084656},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.3903999924659729},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.39010000228881836},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3855000138282776},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3831000030040741},{"id":"https://openalex.org/C173801870","wikidata":"https://www.wikidata.org/wiki/Q201413","display_name":"Heuristic","level":2,"score":0.38119998574256897},{"id":"https://openalex.org/C72634772","wikidata":"https://www.wikidata.org/wiki/Q386824","display_name":"Data integration","level":2,"score":0.3716000020503998},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.36739999055862427},{"id":"https://openalex.org/C153668964","wikidata":"https://www.wikidata.org/wiki/Q27636","display_name":"Majority rule","level":2,"score":0.3538999855518341},{"id":"https://openalex.org/C156340839","wikidata":"https://www.wikidata.org/wiki/Q2704791","display_name":"Enumeration","level":2,"score":0.34619998931884766},{"id":"https://openalex.org/C2984074130","wikidata":"https://www.wikidata.org/wiki/Q73539779","display_name":"R package","level":2,"score":0.3296999931335449},{"id":"https://openalex.org/C58471807","wikidata":"https://www.wikidata.org/wiki/Q327120","display_name":"Receiver operating characteristic","level":2,"score":0.3158999979496002},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.31520000100135803},{"id":"https://openalex.org/C2780226545","wikidata":"https://www.wikidata.org/wiki/Q6888030","display_name":"Modality (human\u2013computer interaction)","level":2,"score":0.305400013923645},{"id":"https://openalex.org/C112972136","wikidata":"https://www.wikidata.org/wiki/Q7595718","display_name":"Stability (learning theory)","level":2,"score":0.29809999465942383},{"id":"https://openalex.org/C12725497","wikidata":"https://www.wikidata.org/wiki/Q810247","display_name":"Baseline (sea)","level":2,"score":0.28610000014305115},{"id":"https://openalex.org/C148483581","wikidata":"https://www.wikidata.org/wiki/Q446488","display_name":"Feature selection","level":2,"score":0.27379998564720154},{"id":"https://openalex.org/C93959086","wikidata":"https://www.wikidata.org/wiki/Q6888345","display_name":"Model selection","level":2,"score":0.2694999873638153},{"id":"https://openalex.org/C152124472","wikidata":"https://www.wikidata.org/wiki/Q1204361","display_name":"Redundancy (engineering)","level":2,"score":0.26190000772476196},{"id":"https://openalex.org/C83546350","wikidata":"https://www.wikidata.org/wiki/Q1139051","display_name":"Regression","level":2,"score":0.25519999861717224}],"mesh":[{"descriptor_ui":"D000095028","descriptor_name":"Multiomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000095028","descriptor_name":"Multiomics","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":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000175","qualifier_name":"diagnosis","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000175","qualifier_name":"diagnosis","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D035501","descriptor_name":"Uncertainty","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D035501","descriptor_name":"Uncertainty","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btag468","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btag468","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:42371766","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/42371766","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":"Journal Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:13384059","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC13384059/","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btag468","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btag468","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G7576449622","display_name":null,"funder_award_id":"82171526","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":46,"referenced_works":["https://openalex.org/W1539056764","https://openalex.org/W2023560061","https://openalex.org/W2042859558","https://openalex.org/W2063730216","https://openalex.org/W2080053685","https://openalex.org/W2080309550","https://openalex.org/W2086220666","https://openalex.org/W2100980426","https://openalex.org/W2118151706","https://openalex.org/W2119519240","https://openalex.org/W2130055251","https://openalex.org/W2131257577","https://openalex.org/W2139666812","https://openalex.org/W2141410747","https://openalex.org/W2149360212","https://openalex.org/W2158485828","https://openalex.org/W2163922914","https://openalex.org/W2197459998","https://openalex.org/W2562162676","https://openalex.org/W2768096340","https://openalex.org/W2789924919","https://openalex.org/W2895654791","https://openalex.org/W2896409065","https://openalex.org/W2936853956","https://openalex.org/W2950886245","https://openalex.org/W2971276572","https://openalex.org/W3017181475","https://openalex.org/W3147894994","https://openalex.org/W3148071990","https://openalex.org/W3170986249","https://openalex.org/W3184996951","https://openalex.org/W3205421900","https://openalex.org/W4206536750","https://openalex.org/W4213001400","https://openalex.org/W4294216483","https://openalex.org/W4302286441","https://openalex.org/W4309976975","https://openalex.org/W4327735947","https://openalex.org/W4361984358","https://openalex.org/W4377233107","https://openalex.org/W4385491154","https://openalex.org/W4391294262","https://openalex.org/W4395954533","https://openalex.org/W4402443775","https://openalex.org/W4407151613","https://openalex.org/W4407316259"],"related_works":[],"abstract_inverted_index":{"MOTIVATION:":[0],"Multi-omics":[1],"integration":[2],"can":[3,33],"improve":[4],"cancer":[5],"diagnosis":[6],"and":[7,22,82,91,104,136,155,164,171],"prognosis,":[8],"but":[9],"current":[10],"models":[11,74],"are":[12,166],"limited":[13],"by":[14,85,126],"extreme":[15],"dimensionality,":[16],"redundant":[17],"raw-feature":[18],"similarities,":[19],"missing":[20],"assays,":[21],"incomplete":[23],"pathway":[24],"priors.":[25],"We":[26,50],"ask":[27],"whether":[28],"biologically":[29],"meaningful":[30],"patient":[31],"manifolds":[32],"be":[34],"learned":[35],"directly":[36],"from":[37],"high-dimensional":[38],"multi-omics":[39],"data":[40],"without":[41],"heuristic":[42],"graph":[43],"construction":[44],"or":[45],"fixed":[46],"knowledge-base":[47],"constraints.":[48],"RESULTS:":[49],"present":[51],"OmicsTransformer,":[52],"an":[53,69],"end-to-end":[54],"framework":[55],"that":[56],"projects":[57],"each":[58],"omics":[59],"modality":[60],"into":[61],"latent":[62],"patches,":[63],"enforces":[64],"masked":[65],"semantic":[66],"consistency":[67],"through":[68],"Exponential":[70],"Cosine":[71],"Consistency":[72],"Loss,":[73],"global":[75],"patch":[76],"dependencies":[77],"with":[78,146],"a":[79],"Transformer":[80],"encoder,":[81],"fuses":[83],"modalities":[84],"sample-specific":[86],"uncertainty.":[87],"Across":[88],"eight":[89],"diagnostic":[90],"prognostic":[92],"cohorts,":[93],"OmicsTransformer":[94,173],"achieved":[95],"strong":[96],"performance,":[97],"including":[98],"89.4%":[99],"accuracy":[100,132],"for":[101,114],"TCGA-BRCA":[102],"subtyping":[103],"90.6%":[105],"area":[106],"under":[107],"the":[108,122],"receiver":[109],"operating":[110],"characteristic":[111],"curve":[112],"(AUC)":[113],"TCGA-LGG":[115],"grading.":[116],"It":[117],"improved":[118],"recurrence":[119],"prediction":[120],"over":[121],"pathway-restricted":[123],"DeepKEGG":[124],"baseline":[125],"approximately":[127],"21.5":[128],"percentage":[129,138],"points":[130,139],"in":[131,140,176],"(ACC)":[133],"on":[134,142],"TCGA-LIHC":[135],"11.1":[137],"ACC":[141],"TCGA-BLCA.":[143],"Variance-weighted":[144],"attribution":[145],"ensemble":[147],"stability":[148],"selection":[149],"recovered":[150],"reproducible":[151],"cross-modal":[152],"biomarker":[153],"cores":[154],"non-canonical":[156],"progression":[157],"drivers.":[158],"AVAILABILITY":[159],"AND":[160],"IMPLEMENTATION:":[161],"Source":[162],"code":[163],"datasets":[165],"freely":[167],"available":[168],"at":[169],"https://github.com/FFJXX/OmicTransformer":[170],"https://doi.org/10.6084/m9.figshare.31523905.":[172],"is":[174],"implemented":[175],"PyTorch.":[177]},"counts_by_year":[],"updated_date":"2026-07-27T08:26:11.824852","created_date":"2026-06-30T00:00:00"}
