{"id":"https://openalex.org/W4402754164","doi":"https://doi.org/10.1109/cvpr52733.2024.01117","title":"Masked Autoencoders for Microscopy are Scalable Learners of Cellular Biology","display_name":"Masked Autoencoders for Microscopy are Scalable Learners of Cellular Biology","publication_year":2024,"publication_date":"2024-06-16","ids":{"openalex":"https://openalex.org/W4402754164","doi":"https://doi.org/10.1109/cvpr52733.2024.01117"},"language":"en","primary_location":{"id":"doi:10.1109/cvpr52733.2024.01117","is_oa":false,"landing_page_url":"https://doi.org/10.1109/cvpr52733.2024.01117","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2024 IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR)","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5002800876","display_name":"Oren Kraus","orcid":"https://orcid.org/0000-0002-6328-9492"},"institutions":[{"id":"https://openalex.org/I4210159509","display_name":"Recursion (United States)","ror":"https://ror.org/05czpzc54","country_code":"US","type":"company","lineage":["https://openalex.org/I4210159509"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Oren Kraus","raw_affiliation_strings":["Recursion"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Recursion","institution_ids":["https://openalex.org/I4210159509"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012825977","display_name":"Kian Kenyon-Dean","orcid":null},"institutions":[{"id":"https://openalex.org/I4210159509","display_name":"Recursion (United States)","ror":"https://ror.org/05czpzc54","country_code":"US","type":"company","lineage":["https://openalex.org/I4210159509"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kian Kenyon-Dean","raw_affiliation_strings":["Recursion"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Recursion","institution_ids":["https://openalex.org/I4210159509"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002281168","display_name":"Saber Saberian","orcid":null},"institutions":[{"id":"https://openalex.org/I4210159509","display_name":"Recursion (United States)","ror":"https://ror.org/05czpzc54","country_code":"US","type":"company","lineage":["https://openalex.org/I4210159509"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Saber Saberian","raw_affiliation_strings":["Recursion"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Recursion","institution_ids":["https://openalex.org/I4210159509"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076087851","display_name":"Maryam Fallah","orcid":null},"institutions":[{"id":"https://openalex.org/I4210159509","display_name":"Recursion (United States)","ror":"https://ror.org/05czpzc54","country_code":"US","type":"company","lineage":["https://openalex.org/I4210159509"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Maryam Fallah","raw_affiliation_strings":["Recursion"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Recursion","institution_ids":["https://openalex.org/I4210159509"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056664985","display_name":"Peter McLean","orcid":"https://orcid.org/0000-0001-7938-5713"},"institutions":[{"id":"https://openalex.org/I4210159509","display_name":"Recursion (United States)","ror":"https://ror.org/05czpzc54","country_code":"US","type":"company","lineage":["https://openalex.org/I4210159509"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Peter McLean","raw_affiliation_strings":["Recursion"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Recursion","institution_ids":["https://openalex.org/I4210159509"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103394284","display_name":"J. W. Leung","orcid":null},"institutions":[{"id":"https://openalex.org/I4210159509","display_name":"Recursion (United States)","ror":"https://ror.org/05czpzc54","country_code":"US","type":"company","lineage":["https://openalex.org/I4210159509"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jess Leung","raw_affiliation_strings":["Recursion"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Recursion","institution_ids":["https://openalex.org/I4210159509"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032180163","display_name":"Vasudev Sharma","orcid":null},"institutions":[{"id":"https://openalex.org/I4210159509","display_name":"Recursion (United States)","ror":"https://ror.org/05czpzc54","country_code":"US","type":"company","lineage":["https://openalex.org/I4210159509"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Vasudev Sharma","raw_affiliation_strings":["Recursion"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Recursion","institution_ids":["https://openalex.org/I4210159509"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101185246","display_name":"Ayla Khan","orcid":null},"institutions":[{"id":"https://openalex.org/I4210159509","display_name":"Recursion (United States)","ror":"https://ror.org/05czpzc54","country_code":"US","type":"company","lineage":["https://openalex.org/I4210159509"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ayla Khan","raw_affiliation_strings":["Recursion"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Recursion","institution_ids":["https://openalex.org/I4210159509"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5104282897","display_name":"Jia Balakrishnan","orcid":null},"institutions":[{"id":"https://openalex.org/I4210159509","display_name":"Recursion (United States)","ror":"https://ror.org/05czpzc54","country_code":"US","type":"company","lineage":["https://openalex.org/I4210159509"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jia Balakrishnan","raw_affiliation_strings":["Recursion"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Recursion","institution_ids":["https://openalex.org/I4210159509"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040714786","display_name":"Safiye \u00c7elik","orcid":"https://orcid.org/0000-0001-6078-7229"},"institutions":[{"id":"https://openalex.org/I4210159509","display_name":"Recursion (United States)","ror":"https://ror.org/05czpzc54","country_code":"US","type":"company","lineage":["https://openalex.org/I4210159509"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Safiye Celik","raw_affiliation_strings":["Recursion"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Recursion","institution_ids":["https://openalex.org/I4210159509"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064214996","display_name":"Dominique Beaini","orcid":"https://orcid.org/0000-0002-4613-9388"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Dominique Beaini","raw_affiliation_strings":["Valence Labs"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Valence Labs","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5057763067","display_name":"Maciej Sypetkowski","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Maciej Sypetkowski","raw_affiliation_strings":["Valence Labs"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Valence Labs","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062372240","display_name":"Chi Vicky Cheng","orcid":"https://orcid.org/0009-0001-2763-8317"},"institutions":[{"id":"https://openalex.org/I4210159509","display_name":"Recursion (United States)","ror":"https://ror.org/05czpzc54","country_code":"US","type":"company","lineage":["https://openalex.org/I4210159509"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Chi Vicky Cheng","raw_affiliation_strings":["Recursion"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Recursion","institution_ids":["https://openalex.org/I4210159509"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086736449","display_name":"Kristen Morse","orcid":null},"institutions":[{"id":"https://openalex.org/I4210159509","display_name":"Recursion (United States)","ror":"https://ror.org/05czpzc54","country_code":"US","type":"company","lineage":["https://openalex.org/I4210159509"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kristen Morse","raw_affiliation_strings":["Recursion"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Recursion","institution_ids":["https://openalex.org/I4210159509"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5092978167","display_name":"Maureen Makes","orcid":null},"institutions":[{"id":"https://openalex.org/I4210159509","display_name":"Recursion (United States)","ror":"https://ror.org/05czpzc54","country_code":"US","type":"company","lineage":["https://openalex.org/I4210159509"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Maureen Makes","raw_affiliation_strings":["Recursion"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Recursion","institution_ids":["https://openalex.org/I4210159509"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024350243","display_name":"Ben Mabey","orcid":null},"institutions":[{"id":"https://openalex.org/I4210159509","display_name":"Recursion (United States)","ror":"https://ror.org/05czpzc54","country_code":"US","type":"company","lineage":["https://openalex.org/I4210159509"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ben Mabey","raw_affiliation_strings":["Recursion"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Recursion","institution_ids":["https://openalex.org/I4210159509"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5057304211","display_name":"Berton Earnshaw","orcid":"https://orcid.org/0000-0002-9728-2408"},"institutions":[{"id":"https://openalex.org/I4210159509","display_name":"Recursion (United States)","ror":"https://ror.org/05czpzc54","country_code":"US","type":"company","lineage":["https://openalex.org/I4210159509"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Berton Earnshaw","raw_affiliation_strings":["Recursion"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Recursion","institution_ids":["https://openalex.org/I4210159509"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":17,"corresponding_author_ids":["https://openalex.org/A5002800876"],"corresponding_institution_ids":["https://openalex.org/I4210159509"],"apc_list":null,"apc_paid":null,"fwci":19.4082,"has_fulltext":false,"cited_by_count":33,"citation_normalized_percentile":{"value":0.99347437,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":97,"max":100},"biblio":{"volume":null,"issue":null,"first_page":"11757","last_page":"11768"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12859","display_name":"Cell Image Analysis Techniques","score":0.9998999834060669,"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"}},"topics":[{"id":"https://openalex.org/T12859","display_name":"Cell Image Analysis Techniques","score":0.9998999834060669,"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/T13114","display_name":"Image Processing Techniques and Applications","score":0.992900013923645,"subfield":{"id":"https://openalex.org/subfields/2214","display_name":"Media Technology"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9897000193595886,"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/microscopy","display_name":"Microscopy","score":0.5979658365249634},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5617804527282715},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.5160617232322693},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3790355920791626},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.12040609121322632},{"id":"https://openalex.org/keywords/optics","display_name":"Optics","score":0.10274028778076172}],"concepts":[{"id":"https://openalex.org/C147080431","wikidata":"https://www.wikidata.org/wiki/Q1074953","display_name":"Microscopy","level":2,"score":0.5979658365249634},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5617804527282715},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.5160617232322693},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3790355920791626},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.12040609121322632},{"id":"https://openalex.org/C120665830","wikidata":"https://www.wikidata.org/wiki/Q14620","display_name":"Optics","level":1,"score":0.10274028778076172},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/cvpr52733.2024.01117","is_oa":false,"landing_page_url":"https://doi.org/10.1109/cvpr52733.2024.01117","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2024 IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Quality Education","id":"https://metadata.un.org/sdg/4","score":0.47999998927116394}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":80,"referenced_works":["https://openalex.org/W569478347","https://openalex.org/W1901129140","https://openalex.org/W2027954222","https://openalex.org/W2062118960","https://openalex.org/W2183389629","https://openalex.org/W2269649163","https://openalex.org/W2509141893","https://openalex.org/W2511569157","https://openalex.org/W2548342201","https://openalex.org/W2548971603","https://openalex.org/W2606209624","https://openalex.org/W2617242334","https://openalex.org/W2618530766","https://openalex.org/W2624282460","https://openalex.org/W2728842897","https://openalex.org/W2746791238","https://openalex.org/W2750796620","https://openalex.org/W2751625431","https://openalex.org/W2775461895","https://openalex.org/W2793888044","https://openalex.org/W2796393045","https://openalex.org/W2908510526","https://openalex.org/W2946901414","https://openalex.org/W2991083105","https://openalex.org/W3005680577","https://openalex.org/W3097217077","https://openalex.org/W3107527779","https://openalex.org/W3111521801","https://openalex.org/W3113917069","https://openalex.org/W3138516171","https://openalex.org/W3159481202","https://openalex.org/W3172942063","https://openalex.org/W3196897371","https://openalex.org/W3200735940","https://openalex.org/W3211402536","https://openalex.org/W4205733013","https://openalex.org/W4243979784","https://openalex.org/W4280490805","https://openalex.org/W4281758439","https://openalex.org/W4282036924","https://openalex.org/W4285121879","https://openalex.org/W4285483774","https://openalex.org/W4287116734","https://openalex.org/W4289644862","https://openalex.org/W4291666467","https://openalex.org/W4296413616","https://openalex.org/W4298187611","https://openalex.org/W4311731188","https://openalex.org/W4312121996","https://openalex.org/W4312349930","https://openalex.org/W4312685069","https://openalex.org/W4313125078","https://openalex.org/W4313156423","https://openalex.org/W4319592282","https://openalex.org/W4321011699","https://openalex.org/W4360951525","https://openalex.org/W4366088621","https://openalex.org/W4367000428","https://openalex.org/W4367366132","https://openalex.org/W4381093560","https://openalex.org/W4385815479","https://openalex.org/W4385829298","https://openalex.org/W4387228684","https://openalex.org/W4394186428","https://openalex.org/W4399128715","https://openalex.org/W6729215637","https://openalex.org/W6738534199","https://openalex.org/W6784333009","https://openalex.org/W6794559225","https://openalex.org/W6838322825","https://openalex.org/W6838540985","https://openalex.org/W6838657836","https://openalex.org/W6842525605","https://openalex.org/W6847530824","https://openalex.org/W6849928207","https://openalex.org/W6852912360","https://openalex.org/W6853763570","https://openalex.org/W6855909433","https://openalex.org/W6856962669","https://openalex.org/W6863742418"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W2389214306","https://openalex.org/W4396696052","https://openalex.org/W2382290278"],"abstract_inverted_index":{"Featurizing":[0],"microscopy":[1,43,113,142],"images":[2,90],"for":[3,13,88],"use":[4],"in":[5,144,161],"biological":[6,71],"research":[7,136],"remains":[8],"a":[9,56,64,80,112,123],"significant":[10],"challenge,":[11],"especially":[12],"large-scale":[14],"experiments":[15],"spanning":[16],"millions":[17],"of":[18,26,58,91,96,151],"images.":[19],"This":[20],"work":[21,174],"explores":[22],"the":[23,156],"scaling":[24,138],"properties":[25],"weakly":[27,52],"supervised":[28,53],"classifiers":[29,54],"and":[30,42,94,109,164,168],"self-supervised":[31,139],"masked":[32],"autoencoders":[33],"(MAEs)":[34],"when":[35,68],"training":[36],"with":[37,122,172],"increasingly":[38],"larger":[39],"model":[40],"backbones":[41],"datasets.":[44],"Our":[45,132],"results":[46],"show":[47],"that":[48,86,103,154],"ViT-based":[49],"MAEs":[50],"outperform":[51],"on":[55,111,141],"variety":[57],"tasks,":[59],"achieving":[60],"as":[61,63],"much":[62],"11.5%":[65],"relative":[66],"improvement":[67],"recalling":[69],"known":[70],"relationships":[72],"curated":[73],"from":[74],"public":[75],"databases.":[76],"Additionally,":[77],"we":[78],"develop":[79],"new":[81],"channel-agnostic":[82],"MAE":[83],"architecture":[84],"(CA-MAE)":[85],"allows":[87],"inputting":[89],"different":[92,119,124],"numbers":[93],"orders":[95],"channels":[97],"at":[98],"inference":[99],"time.":[100],"We":[101],"demonstrate":[102],"CA-MAEs":[104],"effectively":[105],"generalize":[106],"by":[107],"inferring":[108],"evaluating":[110],"image":[114],"dataset":[115],"(JUMP-CP)":[116],"generated":[117],"under":[118],"experimental":[120],"conditions":[121],"channel":[125],"structure":[126],"than":[127],"our":[128],"pretraining":[129],"data":[130,143],"(RPI-93M).":[131],"findings":[133],"motivate":[134],"continued":[135],"into":[137],"learning":[140],"order":[145],"to":[146,158],"create":[147],"powerful":[148],"foundation":[149],"models":[150,170],"cellular":[152],"biology":[153],"have":[155],"potential":[157],"catalyze":[159],"advancements":[160],"drug":[162],"discovery":[163],"beyond.":[165],"Relevant":[166],"code":[167],"select":[169],"released":[171],"this":[173],"can":[175],"be":[176],"found":[177],"at:":[178],"https://github.com/recursionpharma/maes_microscopy.":[179]},"counts_by_year":[{"year":2026,"cited_by_count":9},{"year":2025,"cited_by_count":20},{"year":2024,"cited_by_count":4}],"updated_date":"2026-06-05T09:01:59.212387","created_date":"2025-10-10T00:00:00"}
