{"id":"https://openalex.org/W4405828955","doi":"https://doi.org/10.1038/s42256-024-00934-3","title":"Delineating the effective use of self-supervised learning in single-cell genomics","display_name":"Delineating the effective use of self-supervised learning in single-cell genomics","publication_year":2024,"publication_date":"2024-12-27","ids":{"openalex":"https://openalex.org/W4405828955","doi":"https://doi.org/10.1038/s42256-024-00934-3"},"language":"en","primary_location":{"id":"doi:10.1038/s42256-024-00934-3","is_oa":true,"landing_page_url":"https://doi.org/10.1038/s42256-024-00934-3","pdf_url":"https://www.nature.com/articles/s42256-024-00934-3.pdf","source":{"id":"https://openalex.org/S2912241403","display_name":"Nature Machine Intelligence","issn_l":"2522-5839","issn":["2522-5839"],"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 Machine Intelligence","raw_type":"journal-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://www.nature.com/articles/s42256-024-00934-3.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5002993826","display_name":"Till Richter","orcid":"https://orcid.org/0000-0001-6008-8209"},"institutions":[{"id":"https://openalex.org/I3018134672","display_name":"Helmholtz Zentrum M\u00fcnchen","ror":"https://ror.org/00cfam450","country_code":"DE","type":"facility","lineage":["https://openalex.org/I1305996414","https://openalex.org/I3018134672"]},{"id":"https://openalex.org/I62916508","display_name":"Technical University of Munich","ror":"https://ror.org/02kkvpp62","country_code":"DE","type":"education","lineage":["https://openalex.org/I62916508"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Till Richter","raw_affiliation_strings":["Department of Computational Health, Institute of Computational Biology, Helmholtz Munich, Munich, Germany","TUM School of Computation, Information and Technology, Technical University of Munich, Munich, Germany"],"affiliations":[{"raw_affiliation_string":"Department of Computational Health, Institute of Computational Biology, Helmholtz Munich, Munich, Germany","institution_ids":["https://openalex.org/I3018134672"]},{"raw_affiliation_string":"TUM School of Computation, Information and Technology, Technical University of Munich, Munich, Germany","institution_ids":["https://openalex.org/I62916508"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101508393","display_name":"Mojtaba Bahrami","orcid":"https://orcid.org/0009-0003-0151-5196"},"institutions":[{"id":"https://openalex.org/I3018134672","display_name":"Helmholtz Zentrum M\u00fcnchen","ror":"https://ror.org/00cfam450","country_code":"DE","type":"facility","lineage":["https://openalex.org/I1305996414","https://openalex.org/I3018134672"]},{"id":"https://openalex.org/I62916508","display_name":"Technical University of Munich","ror":"https://ror.org/02kkvpp62","country_code":"DE","type":"education","lineage":["https://openalex.org/I62916508"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Mojtaba Bahrami","raw_affiliation_strings":["Department of Computational Health, Institute of Computational Biology, Helmholtz Munich, Munich, Germany","TUM School of Life Sciences Weihenstephan, Technical University of Munich, Munich, Germany"],"affiliations":[{"raw_affiliation_string":"Department of Computational Health, Institute of Computational Biology, Helmholtz Munich, Munich, Germany","institution_ids":["https://openalex.org/I3018134672"]},{"raw_affiliation_string":"TUM School of Life Sciences Weihenstephan, Technical University of Munich, Munich, Germany","institution_ids":["https://openalex.org/I62916508"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002172912","display_name":"Yufan Xia","orcid":"https://orcid.org/0000-0001-9680-6903"},"institutions":[{"id":"https://openalex.org/I62916508","display_name":"Technical University of Munich","ror":"https://ror.org/02kkvpp62","country_code":"DE","type":"education","lineage":["https://openalex.org/I62916508"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Yufan Xia","raw_affiliation_strings":["TUM School of Computation, Information and Technology, Technical University of Munich, Munich, Germany"],"affiliations":[{"raw_affiliation_string":"TUM School of Computation, Information and Technology, Technical University of Munich, Munich, Germany","institution_ids":["https://openalex.org/I62916508"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000053965","display_name":"David S. Fischer","orcid":"https://orcid.org/0000-0002-1293-7656"},"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/I3018134672","display_name":"Helmholtz Zentrum M\u00fcnchen","ror":"https://ror.org/00cfam450","country_code":"DE","type":"facility","lineage":["https://openalex.org/I1305996414","https://openalex.org/I3018134672"]}],"countries":["DE","US"],"is_corresponding":false,"raw_author_name":"David S. Fischer","raw_affiliation_strings":["Department of Computational Health, Institute of Computational Biology, Helmholtz Munich, Munich, Germany","Eric and Wendy Schmidt Center at the Broad Institute, Cambridge, MA, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computational Health, Institute of Computational Biology, Helmholtz Munich, Munich, Germany","institution_ids":["https://openalex.org/I3018134672"]},{"raw_affiliation_string":"Eric and Wendy Schmidt Center at the Broad Institute, Cambridge, MA, USA","institution_ids":["https://openalex.org/I107606265"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5083128670","display_name":"Fabian J. Theis","orcid":"https://orcid.org/0000-0002-2419-1943"},"institutions":[{"id":"https://openalex.org/I3018134672","display_name":"Helmholtz Zentrum M\u00fcnchen","ror":"https://ror.org/00cfam450","country_code":"DE","type":"facility","lineage":["https://openalex.org/I1305996414","https://openalex.org/I3018134672"]},{"id":"https://openalex.org/I62916508","display_name":"Technical University of Munich","ror":"https://ror.org/02kkvpp62","country_code":"DE","type":"education","lineage":["https://openalex.org/I62916508"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Fabian J. Theis","raw_affiliation_strings":["Department of Computational Health, Institute of Computational Biology, Helmholtz Munich, Munich, Germany","TUM School of Computation, Information and Technology, Technical University of Munich, Munich, Germany","TUM School of Life Sciences Weihenstephan, Technical University of Munich, Munich, Germany"],"affiliations":[{"raw_affiliation_string":"Department of Computational Health, Institute of Computational Biology, Helmholtz Munich, Munich, Germany","institution_ids":["https://openalex.org/I3018134672"]},{"raw_affiliation_string":"TUM School of Computation, Information and Technology, Technical University of Munich, Munich, Germany","institution_ids":["https://openalex.org/I62916508"]},{"raw_affiliation_string":"TUM School of Life Sciences Weihenstephan, Technical University of Munich, Munich, Germany","institution_ids":["https://openalex.org/I62916508"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5002993826"],"corresponding_institution_ids":["https://openalex.org/I3018134672","https://openalex.org/I62916508"],"apc_list":{"value":9750,"currency":"EUR","value_usd":11690},"apc_paid":{"value":9750,"currency":"EUR","value_usd":11690},"fwci":4.1215,"has_fulltext":true,"cited_by_count":18,"citation_normalized_percentile":{"value":0.94975319,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"7","issue":"1","first_page":"68","last_page":"78"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":1.0,"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":1.0,"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":0.984499990940094,"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/T10981","display_name":"Cytomegalovirus and herpesvirus research","score":0.9731000065803528,"subfield":{"id":"https://openalex.org/subfields/2713","display_name":"Epidemiology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8121886253356934},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.6268590688705444},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.6216864585876465},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.5520645380020142},{"id":"https://openalex.org/keywords/transfer-of-learning","display_name":"Transfer of learning","score":0.49148857593536377},{"id":"https://openalex.org/keywords/feature-learning","display_name":"Feature learning","score":0.4666701853275299},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.45034050941467285},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.44749048352241516},{"id":"https://openalex.org/keywords/modality","display_name":"Modality (human\u2013computer interaction)","score":0.43542978167533875},{"id":"https://openalex.org/keywords/masking","display_name":"Masking (illustration)","score":0.4226928949356079}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8121886253356934},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.6268590688705444},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.6216864585876465},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.5520645380020142},{"id":"https://openalex.org/C150899416","wikidata":"https://www.wikidata.org/wiki/Q1820378","display_name":"Transfer of learning","level":2,"score":0.49148857593536377},{"id":"https://openalex.org/C59404180","wikidata":"https://www.wikidata.org/wiki/Q17013334","display_name":"Feature learning","level":2,"score":0.4666701853275299},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.45034050941467285},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.44749048352241516},{"id":"https://openalex.org/C2780226545","wikidata":"https://www.wikidata.org/wiki/Q6888030","display_name":"Modality (human\u2013computer interaction)","level":2,"score":0.43542978167533875},{"id":"https://openalex.org/C2777402240","wikidata":"https://www.wikidata.org/wiki/Q6783436","display_name":"Masking (illustration)","level":2,"score":0.4226928949356079},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","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/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0},{"id":"https://openalex.org/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"score":0.0},{"id":"https://openalex.org/C153349607","wikidata":"https://www.wikidata.org/wiki/Q36649","display_name":"Visual arts","level":1,"score":0.0},{"id":"https://openalex.org/C142362112","wikidata":"https://www.wikidata.org/wiki/Q735","display_name":"Art","level":0,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1038/s42256-024-00934-3","is_oa":true,"landing_page_url":"https://doi.org/10.1038/s42256-024-00934-3","pdf_url":"https://www.nature.com/articles/s42256-024-00934-3.pdf","source":{"id":"https://openalex.org/S2912241403","display_name":"Nature Machine Intelligence","issn_l":"2522-5839","issn":["2522-5839"],"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 Machine Intelligence","raw_type":"journal-article"},{"id":"pmh:oai:push-zb.helmholtz-munich.de:72924","is_oa":true,"landing_page_url":"https://push-zb.helmholtz-munich.de/frontdoor.php?source_opus=72924","pdf_url":null,"source":{"id":"https://openalex.org/S7407055352","display_name":"PuSH - Publication Server of Helmholtz Zentrum M\u00fcnchen","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"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. Mach. Intell., DOI: 10.1038/s42256-024-00934-3 (2024)","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1038/s42256-024-00934-3","is_oa":true,"landing_page_url":"https://doi.org/10.1038/s42256-024-00934-3","pdf_url":"https://www.nature.com/articles/s42256-024-00934-3.pdf","source":{"id":"https://openalex.org/S2912241403","display_name":"Nature Machine Intelligence","issn_l":"2522-5839","issn":["2522-5839"],"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 Machine Intelligence","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.7400000095367432,"id":"https://metadata.un.org/sdg/4","display_name":"Quality Education"}],"awards":[{"id":"https://openalex.org/G4447653093","display_name":null,"funder_award_id":"Network","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G841662260","display_name":null,"funder_award_id":"101054957","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"}],"funders":[{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320336029","display_name":"Helmholtz Zentrum M\u00fcnchen","ror":"https://ror.org/00cfam450"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4405828955.pdf","grobid_xml":"https://content.openalex.org/works/W4405828955.grobid-xml"},"referenced_works_count":64,"referenced_works":["https://openalex.org/W2010457001","https://openalex.org/W2085442947","https://openalex.org/W2130410032","https://openalex.org/W2214074259","https://openalex.org/W2612519453","https://openalex.org/W2735067671","https://openalex.org/W2739492614","https://openalex.org/W2800392236","https://openalex.org/W2896457183","https://openalex.org/W2901677030","https://openalex.org/W3035060554","https://openalex.org/W3042462196","https://openalex.org/W3101697142","https://openalex.org/W3102560760","https://openalex.org/W3108737349","https://openalex.org/W3129866267","https://openalex.org/W3159762970","https://openalex.org/W3163972593","https://openalex.org/W3168661051","https://openalex.org/W3196650609","https://openalex.org/W3203263776","https://openalex.org/W3204844273","https://openalex.org/W3207404093","https://openalex.org/W4200289086","https://openalex.org/W4205916264","https://openalex.org/W4206176282","https://openalex.org/W4210607772","https://openalex.org/W4225598893","https://openalex.org/W4280598116","https://openalex.org/W4281476654","https://openalex.org/W4293237882","https://openalex.org/W4295717668","https://openalex.org/W4297243391","https://openalex.org/W4311000453","https://openalex.org/W4313156423","https://openalex.org/W4316096017","https://openalex.org/W4319866019","https://openalex.org/W4321611764","https://openalex.org/W4321748573","https://openalex.org/W4322832102","https://openalex.org/W4362521490","https://openalex.org/W4375955255","https://openalex.org/W4378838672","https://openalex.org/W4379879135","https://openalex.org/W4384821687","https://openalex.org/W4385928896","https://openalex.org/W4386114273","https://openalex.org/W4387452509","https://openalex.org/W4387568450","https://openalex.org/W4387569894","https://openalex.org/W4387595265","https://openalex.org/W4387595270","https://openalex.org/W4387866792","https://openalex.org/W4388183180","https://openalex.org/W4388218765","https://openalex.org/W4388717695","https://openalex.org/W4388979266","https://openalex.org/W4391512208","https://openalex.org/W4392168151","https://openalex.org/W4392607741","https://openalex.org/W4394930851","https://openalex.org/W4401314781","https://openalex.org/W6800751262","https://openalex.org/W6968264855"],"related_works":["https://openalex.org/W2378211422","https://openalex.org/W4321353415","https://openalex.org/W2745001401","https://openalex.org/W2130974462","https://openalex.org/W2028665553","https://openalex.org/W2086519370","https://openalex.org/W4246352526","https://openalex.org/W4295520087","https://openalex.org/W2440023763","https://openalex.org/W2962474440"],"abstract_inverted_index":{"Abstract":[0],"Self-supervised":[1],"learning":[2,30,52,99,136,198],"(SSL)":[3],"has":[4],"emerged":[5],"as":[6],"a":[7,55,72],"powerful":[8],"method":[9],"for":[10,69],"extracting":[11],"meaningful":[12],"representations":[13],"from":[14,154],"vast,":[15],"unlabelled":[16],"datasets,":[17],"transforming":[18],"computer":[19,155],"vision":[20,156],"and":[21,84,97,121,170,176,191],"natural":[22],"language":[23],"processing.":[24],"In":[25,179],"single-cell":[26],"genomics":[27],"(SCG),":[28],"representation":[29,197],"offers":[31],"insights":[32],"into":[33],"the":[34,60,66,128,162],"complex":[35],"biological":[36],"data,":[37],"especially":[38],"with":[39,93],"emerging":[40],"foundation":[41],"models.":[42],"However,":[43],"identifying":[44],"scenarios":[45,137],"in":[46,88,134,151,167,173,185],"SCG":[47,70,186],"where":[48],"SSL":[49,67,86,166,183],"outperforms":[50],"traditional":[51],"methods":[53,87,150,184],"remains":[54],"nuanced":[56,129],"challenge.":[57],"Furthermore,":[58],"selecting":[59],"most":[61],"effective":[62],"pretext":[63],"tasks":[64],"within":[65],"framework":[68],"is":[71],"critical":[73],"yet":[74],"unresolved":[75],"question.":[76],"Here":[77],"we":[78,181],"address":[79],"this":[80],"gap":[81],"by":[82],"adapting":[83],"benchmarking":[85],"SCG,":[89,152],"including":[90,114],"masked":[91],"autoencoders":[92,146],"multiple":[94,111],"masking":[95],"strategies":[96],"contrastive":[98,149],"methods.":[100],"Models":[101],"trained":[102],"on":[103,187],"over":[104,148],"20":[105],"million":[106],"cells":[107],"were":[108],"examined":[109],"across":[110,195],"downstream":[112],"tasks,":[113],"cell-type":[115],"prediction,":[116],"gene-expression":[117],"reconstruction,":[118],"cross-modality":[119,174],"prediction":[120,175],"data":[122,140,177],"integration.":[123,178],"Our":[124],"empirical":[125],"analyses":[126],"underscore":[127],"role":[130],"of":[131,165],"SSL,":[132],"namely,":[133],"transfer":[135],"leveraging":[138],"auxiliary":[139],"or":[141],"analysing":[142],"unseen":[143],"datasets.":[144],"Masked":[145],"excel":[147],"diverging":[153],"trends.":[157],"Moreover,":[158],"our":[159],"findings":[160],"reveal":[161],"notable":[163],"capabilities":[164],"zero-shot":[168],"settings":[169],"its":[171],"potential":[172],"summary,":[180],"study":[182],"fully":[188],"connected":[189],"networks":[190],"benchmark":[192],"their":[193],"utility":[194],"key":[196],"scenarios.":[199]},"counts_by_year":[{"year":2026,"cited_by_count":6},{"year":2025,"cited_by_count":11},{"year":2024,"cited_by_count":1}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
