{"id":"https://openalex.org/W7222923367","doi":"https://doi.org/10.48550/arxiv.2610.22523","title":"Learning the Shared Latent Structure of Cryo-EM Inverse Problems","display_name":"Learning the Shared Latent Structure of Cryo-EM Inverse Problems","publication_year":2026,"publication_date":"2026-10-15","ids":{"openalex":"https://openalex.org/W7222923367","doi":"https://doi.org/10.48550/arxiv.2610.22523"},"language":"en","primary_location":{"id":"pmh:oai:arXiv.org:2610.22523","doi":null,"is_oa":true,"landing_page_url":"https://arxiv.org/abs/2610.22523","pdf_url":"https://arxiv.org/pdf/2610.22523","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},"volume":null,"type":"preprint","is_traditional":true,"indexed_in":["arxiv","datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://arxiv.org/pdf/2610.22523","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5071467088","display_name":"Nithin Chalapathi","orcid":"https://orcid.org/0000-0002-6160-1155","observed_orcids":["https://orcid.org/0000-0002-6160-1155"]},"institutions":[{"id":"https://openalex.org/I4387153999","display_name":"Flatiron Institute","ror":"https://ror.org/00sekdz59","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210107338","https://openalex.org/I4387153999"]},{"id":"https://openalex.org/I95457486","display_name":"University of California, Berkeley","ror":"https://ror.org/01an7q238","country_code":"US","type":"education","lineage":["https://openalex.org/I95457486"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Chalapathi, Nithin","raw_affiliation_strings":["Flatiron Institute ,","University of California , Berkeley ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Flatiron Institute ,","institution_ids":["https://openalex.org/I4387153999"]},{"raw_affiliation_string":"University of California , Berkeley ,","institution_ids":["https://openalex.org/I95457486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5159040551","display_name":"Theo Sternlieb","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I95457486","display_name":"University of California, Berkeley","ror":"https://ror.org/01an7q238","country_code":"US","type":"education","lineage":["https://openalex.org/I95457486"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sternlieb, Theo","raw_affiliation_strings":["University of California , Berkeley ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of California , Berkeley ,","institution_ids":["https://openalex.org/I95457486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5159068624","display_name":"Ethan Han","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I95457486","display_name":"University of California, Berkeley","ror":"https://ror.org/01an7q238","country_code":"US","type":"education","lineage":["https://openalex.org/I95457486"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Han, Ethan","raw_affiliation_strings":["University of California , Berkeley ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of California , Berkeley ,","institution_ids":["https://openalex.org/I95457486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041965787","display_name":"Sonya M. Hanson","orcid":"https://orcid.org/0000-0001-8960-5353","observed_orcids":["https://orcid.org/0000-0001-8960-5353"]},"institutions":[{"id":"https://openalex.org/I4387153999","display_name":"Flatiron Institute","ror":"https://ror.org/00sekdz59","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210107338","https://openalex.org/I4387153999"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Hanson, Sonya M.","raw_affiliation_strings":["Flatiron Institute ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Flatiron Institute ,","institution_ids":["https://openalex.org/I4387153999"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060434510","display_name":"Pilar Cossio","orcid":"https://orcid.org/0000-0002-5404-9948","observed_orcids":["https://orcid.org/0000-0002-5404-9948","https://orcid.org/0000-0003-4327-8478"]},"institutions":[{"id":"https://openalex.org/I4387153999","display_name":"Flatiron Institute","ror":"https://ror.org/00sekdz59","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210107338","https://openalex.org/I4387153999"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Cossio, Pilar","raw_affiliation_strings":["Flatiron Institute ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Flatiron Institute ,","institution_ids":["https://openalex.org/I4387153999"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5049020441","display_name":"Aditi S. Krishnapriyan","orcid":"https://orcid.org/0000-0003-3472-6080","observed_orcids":["https://orcid.org/0000-0003-3472-6080"]},"institutions":[{"id":"https://openalex.org/I95457486","display_name":"University of California, Berkeley","ror":"https://ror.org/01an7q238","country_code":"US","type":"education","lineage":["https://openalex.org/I95457486"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Krishnapriyan, Aditi S.","raw_affiliation_strings":["University of California , Berkeley ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of California , Berkeley ,","institution_ids":["https://openalex.org/I95457486"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5058595124","display_name":"Ritwik Gupta","orcid":"https://orcid.org/0000-0001-7608-3832","observed_orcids":["https://orcid.org/0000-0001-7608-3832"]},"institutions":[{"id":"https://openalex.org/I66946132","display_name":"University of Maryland, College Park","ror":"https://ror.org/047s2c258","country_code":"US","type":"education","lineage":["https://openalex.org/I66946132"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Gupta, Ritwik","raw_affiliation_strings":["University of Maryland , College Park"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Maryland , College Park","institution_ids":["https://openalex.org/I66946132"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10857","display_name":"Advanced Electron Microscopy Techniques and Applications","score":0.9984999895095825,"subfield":{"id":"https://openalex.org/subfields/1315","display_name":"Structural 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/T10857","display_name":"Advanced Electron Microscopy Techniques and Applications","score":0.9984999895095825,"subfield":{"id":"https://openalex.org/subfields/1315","display_name":"Structural 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/T10044","display_name":"Protein Structure and Dynamics","score":0.000699999975040555,"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/T11162","display_name":"Enzyme Structure and Function","score":9.999999747378752e-05,"subfield":{"id":"https://openalex.org/subfields/1315","display_name":"Structural 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/shared-latent-representation","display_name":"shared latent representation","score":0.6340000033378601},{"id":"https://openalex.org/keywords/self-distillation","display_name":"self-distillation","score":0.8410000205039978},{"id":"https://openalex.org/keywords/vision-transformer","display_name":"vision transformer","score":0.734000027179718},{"id":"https://openalex.org/keywords/embers","display_name":"embers","score":0.7289999723434448},{"id":"https://openalex.org/keywords/conformational-heterogeneity","display_name":"conformational heterogeneity","score":0.777999997138977},{"id":"https://openalex.org/keywords/3d-reconstruction","display_name":"3D reconstruction","score":0.6690000295639038},{"id":"https://openalex.org/keywords/protein-structure","display_name":"protein structure","score":0.375},{"id":"https://openalex.org/keywords/image-formation","display_name":"image formation","score":0.335999995470047}],"concepts":[{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.6503000259399414},{"id":"https://openalex.org/C135252773","wikidata":"https://www.wikidata.org/wiki/Q1567213","display_name":"Inverse problem","level":2,"score":0.6395000219345093},{"id":"https://openalex.org/C207467116","wikidata":"https://www.wikidata.org/wiki/Q4385666","display_name":"Inverse","level":2,"score":0.5924999713897705},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5576000213623047},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5411999821662903},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.4772000014781952},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.4302999973297119},{"id":"https://openalex.org/C2778517922","wikidata":"https://www.wikidata.org/wiki/Q7140482","display_name":"Particle (ecology)","level":2,"score":0.4004000127315521},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.3788999915122986},{"id":"https://openalex.org/C31972630","wikidata":"https://www.wikidata.org/wiki/Q844240","display_name":"Computer vision","level":1,"score":0.31779998540878296},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.31779998540878296},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.30820000171661377},{"id":"https://openalex.org/C52421305","wikidata":"https://www.wikidata.org/wiki/Q1151499","display_name":"Particle filter","level":3,"score":0.3019999861717224},{"id":"https://openalex.org/C55037315","wikidata":"https://www.wikidata.org/wiki/Q5421151","display_name":"Experimental data","level":2,"score":0.29010000824928284},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.2858999967575073},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.2858000099658966},{"id":"https://openalex.org/C160920958","wikidata":"https://www.wikidata.org/wiki/Q7662746","display_name":"Synthetic data","level":2,"score":0.28519999980926514},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.25450000166893005},{"id":"https://openalex.org/C121864883","wikidata":"https://www.wikidata.org/wiki/Q677916","display_name":"Statistical physics","level":1,"score":0.25220000743865967}],"mesh":[],"locations_count":2,"locations":[{"id":"pmh:oai:arXiv.org:2610.22523","doi":null,"is_oa":true,"landing_page_url":"https://arxiv.org/abs/2610.22523","pdf_url":"https://arxiv.org/pdf/2610.22523","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},{"id":"doi:10.48550/arxiv.2610.22523","doi":"https://doi.org/10.48550/arxiv.2610.22523","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2610.22523","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Preprint"}],"best_oa_location":{"id":"pmh:oai:arXiv.org:2610.22523","doi":null,"is_oa":true,"landing_page_url":"https://arxiv.org/abs/2610.22523","pdf_url":"https://arxiv.org/pdf/2610.22523","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320306078","display_name":"U.S. Department of Defense","ror":"https://ror.org/0447fe631"},{"id":"https://openalex.org/F4320306084","display_name":"U.S. Department of Energy","ror":"https://ror.org/01bj3aw27"},{"id":"https://openalex.org/F4320319356","display_name":"Flatiron Health","ror":"https://ror.org/0508h6p74"},{"id":"https://openalex.org/F4320332359","display_name":"Office of Science","ror":"https://ror.org/00mmn6b08"},{"id":"https://openalex.org/F4320337506","display_name":"Advanced Scientific Computing Research","ror":"https://ror.org/0012c7r22"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W7222923367.pdf","grobid_xml":"https://content.openalex.org/works/W7222923367.grobid-xml"},"referenced_works_count":32,"referenced_works":["https://openalex.org/W2104234755","https://openalex.org/W2130479394","https://openalex.org/W2137740084","https://openalex.org/W2152562710","https://openalex.org/W2908510526","https://openalex.org/W3035524453","https://openalex.org/W3127326657","https://openalex.org/W3159481202","https://openalex.org/W3204128622","https://openalex.org/W3213836217","https://openalex.org/W4226002507","https://openalex.org/W4300089971","https://openalex.org/W4317624669","https://openalex.org/W4366208220","https://openalex.org/W4376609015","https://openalex.org/W4381686770","https://openalex.org/W4385774716","https://openalex.org/W4394906022","https://openalex.org/W4396895148","https://openalex.org/W4403964581","https://openalex.org/W4411020658","https://openalex.org/W4411668661","https://openalex.org/W4412087773","https://openalex.org/W4414846785","https://openalex.org/W4415798548","https://openalex.org/W4416735683","https://openalex.org/W4417152809","https://openalex.org/W6910554155","https://openalex.org/W7127392808","https://openalex.org/W7127575784","https://openalex.org/W7153520311","https://openalex.org/W7213504137"],"related_works":["https://openalex.org/W4414763682","https://openalex.org/W7130391837","https://openalex.org/W7203958461","https://openalex.org/W7155049753","https://openalex.org/W7162555227","https://openalex.org/W4392157400","https://openalex.org/W4385055216","https://openalex.org/W7168077783","https://openalex.org/W7215813035","https://openalex.org/W4412087773"],"abstract_inverted_index":{"Understanding":[0],"biomolecular":[1],"function":[2],"requires":[3],"characterizing":[4],"three-dimensional":[5],"structure":[6,63],"and":[7,32,52,64,88,104,107,151,156,171],"conformational":[8,150,161],"variability,":[9],"for":[10,191],"which":[11,27],"cryogenic":[12],"electron":[13],"microscopy":[14],"(cryo-EM)":[15],"is":[16],"a":[17,68,168],"powerful":[18],"tool.":[19],"Cryo-EM":[20],"produces":[21,172],"noisy":[22],"two-dimensional":[23],"particle":[24,30,130,173],"images":[25,131],"in":[26,178],"molecular":[28,142],"structure,":[29],"pose,":[31],"imaging":[33],"conditions":[34],"are":[35,56],"jointly":[36],"encoded.":[37],"Recovering":[38],"biological":[39,189],"information":[40,190],"from":[41,113,132,140],"these":[42],"observations":[43],"spans":[44],"inverse":[45,72,196],"problems":[46],"including":[47],"pose":[48],"estimation,":[49],"heterogeneity":[50],"analysis,":[51],"reconstruction.":[53],"These":[54],"tasks":[55],"usually":[57],"addressed":[58],"independently":[59],"despite":[60],"shared":[61],"protein":[62],"image":[65],"formation,":[66],"motivating":[67],"common":[69],"representation":[70],"across":[71,193],"problems.":[73,197],"Since":[74],"biologically":[75],"meaningful":[76],"differences":[77],"may":[78],"be":[79],"spatially":[80],"localized,":[81],"we":[82,100],"study":[83],"self-distillation":[84],"with":[85,137,167],"complementary":[86],"global":[87],"masked":[89],"patch":[90],"objectives.":[91],"Because":[92],"experimental":[93,105,129],"dataset":[94],"discrimination":[95,111,153],"can":[96],"reflect":[97],"acquisition-specific":[98],"cues,":[99],"develop":[101],"controlled":[102],"synthetic":[103],"evaluations":[106],"find":[108],"that":[109,187],"structural":[110],"benefits":[112],"dense":[114],"spatial":[115],"features.":[116],"We":[117,181],"introduce":[118],"the":[119],"EMber":[120,144],"family":[121],"of":[122],"vision":[123],"transformers,":[124],"pre-trained":[125],"on":[126],">50":[127],"million":[128],"214":[133],"EMPIAR":[134],"datasets":[135],"together":[136],"simulated":[138],"projections":[139],"268,000":[141],"assemblies.":[143],"improves":[145],"upon":[146],"existing":[147],"methods":[148],"at":[149],"compositional":[152],"by":[154],"14.85":[155],"14.26":[157],"percentage":[158],"points,":[159],"estimates":[160],"populations":[162],"to":[163,184],"within":[164],"1.59pp":[165],"error":[166],"linear":[169],"probe,":[170],"assignments":[174],"yielding":[175],"reference-quality":[176],"reconstructions":[177],"fewer":[179],"epochs.":[180],"demonstrate":[182],"how":[183],"learn":[185],"representations":[186],"capture":[188],"use":[192],"multiple":[194],"cryo-EM":[195]},"counts_by_year":[],"updated_date":"2026-11-07T11:25:07.637180","created_date":"2026-10-20T00:00:00"}
