{"id":"https://openalex.org/W7126180495","doi":"https://doi.org/10.1038/s43588-025-00945-z","title":"Improving atlas-scale single-cell annotation models with hierarchical cross-entropy loss","display_name":"Improving atlas-scale single-cell annotation models with hierarchical cross-entropy loss","publication_year":2026,"publication_date":"2026-01-30","ids":{"openalex":"https://openalex.org/W7126180495","doi":"https://doi.org/10.1038/s43588-025-00945-z","pmid":"https://pubmed.ncbi.nlm.nih.gov/41617882"},"language":"en","primary_location":{"id":"doi:10.1038/s43588-025-00945-z","is_oa":true,"landing_page_url":"https://doi.org/10.1038/s43588-025-00945-z","pdf_url":"https://www.nature.com/articles/s43588-025-00945-z.pdf","source":{"id":"https://openalex.org/S4210228084","display_name":"Nature Computational Science","issn_l":"2662-8457","issn":["2662-8457"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319908","host_organization_name":"Nature Portfolio","host_organization_lineage":["https://openalex.org/P4310319908","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Nature Portfolio","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":"Nature Computational Science","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://www.nature.com/articles/s43588-025-00945-z.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5090549356","display_name":"Sebastiano Cultrera di Montesano","orcid":"https://orcid.org/0000-0001-6249-0832"},"institutions":[{"id":"https://openalex.org/I107606265","display_name":"Broad Institute","ror":"https://ror.org/05a0ya142","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I107606265"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Sebastiano Cultrera di Montesano","raw_affiliation_strings":["Broad Institute of MIT and Harvard, Cambridge, MA, USA. scultrer@broadinstitute.org"],"raw_orcid":"https://orcid.org/0000-0001-6249-0832","affiliations":[{"raw_affiliation_string":"Broad Institute of MIT and Harvard, Cambridge, MA, USA. scultrer@broadinstitute.org","institution_ids":["https://openalex.org/I107606265"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5124411666","display_name":"Davide D\u2019Ascenzo","orcid":null},"institutions":[{"id":"https://openalex.org/I177477856","display_name":"Politecnico di Torino","ror":"https://ror.org/00bgk9508","country_code":"IT","type":"education","lineage":["https://openalex.org/I177477856"]},{"id":"https://openalex.org/I189158943","display_name":"University of Milan","ror":"https://ror.org/00wjc7c48","country_code":"IT","type":"education","lineage":["https://openalex.org/I189158943"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Davide D\u2019Ascenzo","raw_affiliation_strings":["Politecnico di Torino, Turin, Italy","Universit\u00e0 degli Studi di Milano, Milan, Italy"],"raw_orcid":"https://orcid.org/0000-0002-0607-8488","affiliations":[{"raw_affiliation_string":"Politecnico di Torino, Turin, Italy","institution_ids":["https://openalex.org/I177477856"]},{"raw_affiliation_string":"Universit\u00e0 degli Studi di Milano, Milan, Italy","institution_ids":["https://openalex.org/I189158943"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5027546748","display_name":"Srivatsan Raghavan","orcid":"https://orcid.org/0000-0002-5374-9918"},"institutions":[{"id":"https://openalex.org/I107606265","display_name":"Broad Institute","ror":"https://ror.org/05a0ya142","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I107606265"]},{"id":"https://openalex.org/I1283280774","display_name":"Brigham and Women's Hospital","ror":"https://ror.org/04b6nzv94","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1283280774","https://openalex.org/I48633490"]},{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]},{"id":"https://openalex.org/I4210117453","display_name":"Dana-Farber Cancer Institute","ror":"https://ror.org/02jzgtq86","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210117453"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Srivatsan Raghavan","raw_affiliation_strings":["Broad Institute of MIT and Harvard, Cambridge, MA, USA","Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA","Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA","Harvard Medical School, Boston, MA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Broad Institute of MIT and Harvard, Cambridge, MA, USA","institution_ids":["https://openalex.org/I107606265"]},{"raw_affiliation_string":"Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA","institution_ids":["https://openalex.org/I4210117453"]},{"raw_affiliation_string":"Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA","institution_ids":["https://openalex.org/I1283280774"]},{"raw_affiliation_string":"Harvard Medical School, Boston, MA, USA","institution_ids":["https://openalex.org/I136199984"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071306257","display_name":"Ava P. Amini","orcid":"https://orcid.org/0000-0002-8601-6040"},"institutions":[{"id":"https://openalex.org/I1290206253","display_name":"Microsoft (United States)","ror":"https://ror.org/00d0nc645","country_code":"US","type":"company","lineage":["https://openalex.org/I1290206253"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ava P. Amini","raw_affiliation_strings":["Microsoft Research, Cambridge, MA, USA"],"raw_orcid":"https://orcid.org/0000-0002-8601-6040","affiliations":[{"raw_affiliation_string":"Microsoft Research, Cambridge, MA, USA","institution_ids":["https://openalex.org/I1290206253"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066983733","display_name":"Peter Winter","orcid":"https://orcid.org/0000-0002-6557-3219"},"institutions":[{"id":"https://openalex.org/I107606265","display_name":"Broad Institute","ror":"https://ror.org/05a0ya142","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I107606265"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Peter S. Winter","raw_affiliation_strings":["Broad Institute of MIT and Harvard, Cambridge, MA, USA. pwinter@broadinstitute.org"],"raw_orcid":"https://orcid.org/0000-0002-6557-3219","affiliations":[{"raw_affiliation_string":"Broad Institute of MIT and Harvard, Cambridge, MA, USA. pwinter@broadinstitute.org","institution_ids":["https://openalex.org/I107606265"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5123097120","display_name":"Lorin Crawford","orcid":null},"institutions":[{"id":"https://openalex.org/I4210164937","display_name":"Microsoft Research (United Kingdom)","ror":"https://ror.org/05k87vq12","country_code":"GB","type":"company","lineage":["https://openalex.org/I1290206253","https://openalex.org/I4210164937"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Lorin Crawford","raw_affiliation_strings":["Microsoft Research, Cambridge, MA, USA. lcrawford@microsoft.com"],"raw_orcid":"https://orcid.org/0000-0003-0178-8242","affiliations":[{"raw_affiliation_string":"Microsoft Research, Cambridge, MA, USA. lcrawford@microsoft.com","institution_ids":["https://openalex.org/I4210164937"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5090549356"],"corresponding_institution_ids":["https://openalex.org/I107606265"],"apc_list":{"value":9750,"currency":"EUR","value_usd":11690},"apc_paid":{"value":9750,"currency":"EUR","value_usd":11690},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.1171356,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"6","issue":"3","first_page":"243","last_page":"249"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9979000091552734,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9979000091552734,"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/T12859","display_name":"Cell Image Analysis Techniques","score":0.0008999999845400453,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.00019999999494757503,"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/focus","display_name":"Focus (optics)","score":0.5306000113487244},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.5277000069618225},{"id":"https://openalex.org/keywords/computational-model","display_name":"Computational model","score":0.42969998717308044},{"id":"https://openalex.org/keywords/simple","display_name":"Simple (philosophy)","score":0.390500009059906},{"id":"https://openalex.org/keywords/hierarchical-database-model","display_name":"Hierarchical database model","score":0.3573000133037567},{"id":"https://openalex.org/keywords/training-set","display_name":"Training set","score":0.34470000863075256},{"id":"https://openalex.org/keywords/variety","display_name":"Variety (cybernetics)","score":0.3409999907016754}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.741100013256073},{"id":"https://openalex.org/C192209626","wikidata":"https://www.wikidata.org/wiki/Q190909","display_name":"Focus (optics)","level":2,"score":0.5306000113487244},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.5277000069618225},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4961000084877014},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.45100000500679016},{"id":"https://openalex.org/C66024118","wikidata":"https://www.wikidata.org/wiki/Q1122506","display_name":"Computational model","level":2,"score":0.42969998717308044},{"id":"https://openalex.org/C2780586882","wikidata":"https://www.wikidata.org/wiki/Q7520643","display_name":"Simple (philosophy)","level":2,"score":0.390500009059906},{"id":"https://openalex.org/C144986985","wikidata":"https://www.wikidata.org/wiki/Q871236","display_name":"Hierarchical database model","level":2,"score":0.3573000133037567},{"id":"https://openalex.org/C51632099","wikidata":"https://www.wikidata.org/wiki/Q3985153","display_name":"Training set","level":2,"score":0.34470000863075256},{"id":"https://openalex.org/C136197465","wikidata":"https://www.wikidata.org/wiki/Q1729295","display_name":"Variety (cybernetics)","level":2,"score":0.3409999907016754},{"id":"https://openalex.org/C67186912","wikidata":"https://www.wikidata.org/wiki/Q367664","display_name":"Data modeling","level":2,"score":0.29899999499320984},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.29420000314712524},{"id":"https://openalex.org/C160920958","wikidata":"https://www.wikidata.org/wiki/Q7662746","display_name":"Synthetic data","level":2,"score":0.29339998960494995},{"id":"https://openalex.org/C201797286","wikidata":"https://www.wikidata.org/wiki/Q4914986","display_name":"Biological data","level":2,"score":0.28790000081062317},{"id":"https://openalex.org/C115051666","wikidata":"https://www.wikidata.org/wiki/Q6522493","display_name":"Ranging","level":2,"score":0.2709999978542328},{"id":"https://openalex.org/C163175372","wikidata":"https://www.wikidata.org/wiki/Q3339222","display_name":"Linear model","level":2,"score":0.26809999346733093},{"id":"https://openalex.org/C124527596","wikidata":"https://www.wikidata.org/wiki/Q17029359","display_name":"Hierarchical control system","level":3,"score":0.2538999915122986}],"mesh":[{"descriptor_ui":"D000092386","descriptor_name":"Single-Cell Gene Expression Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000092386","descriptor_name":"Single-Cell Gene Expression Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000092386","descriptor_name":"Single-Cell Gene Expression Analysis","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":"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":"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":"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":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"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":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019277","descriptor_name":"Entropy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019277","descriptor_name":"Entropy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019277","descriptor_name":"Entropy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019277","descriptor_name":"Entropy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019277","descriptor_name":"Entropy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019277","descriptor_name":"Entropy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019277","descriptor_name":"Entropy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"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":"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":"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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1038/s43588-025-00945-z","is_oa":true,"landing_page_url":"https://doi.org/10.1038/s43588-025-00945-z","pdf_url":"https://www.nature.com/articles/s43588-025-00945-z.pdf","source":{"id":"https://openalex.org/S4210228084","display_name":"Nature Computational Science","issn_l":"2662-8457","issn":["2662-8457"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319908","host_organization_name":"Nature Portfolio","host_organization_lineage":["https://openalex.org/P4310319908","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Nature Portfolio","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":"Nature Computational Science","raw_type":"journal-article"},{"id":"pmid:41617882","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41617882","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":"Nature computational science","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:13021517","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC13021517/","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":"Nat Comput Sci","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1038/s43588-025-00945-z","is_oa":true,"landing_page_url":"https://doi.org/10.1038/s43588-025-00945-z","pdf_url":"https://www.nature.com/articles/s43588-025-00945-z.pdf","source":{"id":"https://openalex.org/S4210228084","display_name":"Nature Computational Science","issn_l":"2662-8457","issn":["2662-8457"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319908","host_organization_name":"Nature Portfolio","host_organization_lineage":["https://openalex.org/P4310319908","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Nature Portfolio","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":"Nature Computational Science","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2615780559","display_name":null,"funder_award_id":"K08 CA260442","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"}],"funders":[{"id":"https://openalex.org/F4320314070","display_name":"Broad Institute","ror":"https://ror.org/05a0ya142"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W7126180495.pdf","grobid_xml":"https://content.openalex.org/works/W7126180495.grobid-xml"},"referenced_works_count":21,"referenced_works":["https://openalex.org/W2612519453","https://openalex.org/W2763051133","https://openalex.org/W2901677030","https://openalex.org/W2971653850","https://openalex.org/W3113049731","https://openalex.org/W3124814274","https://openalex.org/W3132492725","https://openalex.org/W3173802674","https://openalex.org/W3174086521","https://openalex.org/W3200266566","https://openalex.org/W4280596398","https://openalex.org/W4297243391","https://openalex.org/W4316096017","https://openalex.org/W4377029825","https://openalex.org/W4378838672","https://openalex.org/W4392168151","https://openalex.org/W4401314781","https://openalex.org/W4404566628","https://openalex.org/W4404566935","https://openalex.org/W4409566559","https://openalex.org/W4409776992"],"related_works":[],"abstract_inverted_index":{"Accurately":[0],"annotating":[1],"cell":[2,16,89],"types":[3,17],"is":[4,96],"essential":[5],"for":[6],"extracting":[7],"biological":[8,49],"insight":[9],"from":[10,55],"single-cell":[11],"RNA":[12],"sequencing":[13],"data.":[14],"Although":[15],"are":[18],"naturally":[19],"organized":[20],"into":[21,33],"hierarchical":[22,41],"ontologies,":[23],"most":[24],"computational":[25,70],"models":[26,57],"do":[27],"not":[28],"explicitly":[29],"incorporate":[30],"this":[31,60,95],"structure":[32],"their":[34],"training":[35],"objectives.":[36],"Here,":[37],"we":[38,73],"introduce":[39],"a":[40],"cross-entropy":[42],"loss":[43],"that":[44,83,94],"aligns":[45],"model":[46,107],"objectives":[47],"with":[48],"structure.":[50],"Applied":[51],"to":[52,58,77,98],"architectures":[53],"ranging":[54],"linear":[56],"transformers,":[59],"simple":[61],"modification":[62],"improves":[63,84],"out-of-distribution":[64],"performance":[65],"by":[66],"12-15%":[67],"without":[68],"added":[69],"cost.":[71],"Critically,":[72],"underscore":[74],"the":[75,85],"need":[76],"focus":[78],"on":[79],"new":[80],"data":[81],"generation":[82],"connectivity":[86],"among":[87],"annotated":[88],"types.":[90],"Our":[91],"work":[92],"suggests":[93],"likely":[97],"yield":[99],"more":[100],"generalizable":[101],"algorithms":[102],"than":[103],"would":[104],"solely":[105],"increasing":[106],"complexity.":[108]},"counts_by_year":[],"updated_date":"2026-06-12T08:23:45.883708","created_date":"2026-02-01T00:00:00"}