{"id":"https://openalex.org/W3004572984","doi":"https://doi.org/10.1109/bigdata47090.2019.9006484","title":"Finding Archetypal Spaces Using Neural Networks","display_name":"Finding Archetypal Spaces Using Neural Networks","publication_year":2019,"publication_date":"2019-12-01","ids":{"openalex":"https://openalex.org/W3004572984","doi":"https://doi.org/10.1109/bigdata47090.2019.9006484","mag":"3004572984"},"language":"en","primary_location":{"id":"doi:10.1109/bigdata47090.2019.9006484","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bigdata47090.2019.9006484","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2019 IEEE International Conference on Big Data (Big Data)","raw_type":"proceedings-article"},"type":"preprint","indexed_in":["arxiv","crossref","datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://arxiv.org/pdf/1901.09078","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5019679682","display_name":"David van Dijk","orcid":"https://orcid.org/0000-0003-3911-9925"},"institutions":[{"id":"https://openalex.org/I32971472","display_name":"Yale University","ror":"https://ror.org/03v76x132","country_code":"US","type":"education","lineage":["https://openalex.org/I32971472"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"David van Dijk","raw_affiliation_strings":["Internal Medicine; Computer Science Yale University, New Haven, CT","Internal Medicine; Computer Science Yale University,New Haven,CT"],"affiliations":[{"raw_affiliation_string":"Internal Medicine; Computer Science Yale University, New Haven, CT","institution_ids":["https://openalex.org/I32971472"]},{"raw_affiliation_string":"Internal Medicine; Computer Science Yale University,New Haven,CT","institution_ids":["https://openalex.org/I32971472"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5079128249","display_name":"Daniel B. Burkhardt","orcid":"https://orcid.org/0000-0001-7744-1363"},"institutions":[{"id":"https://openalex.org/I32971472","display_name":"Yale University","ror":"https://ror.org/03v76x132","country_code":"US","type":"education","lineage":["https://openalex.org/I32971472"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Daniel B. Burkhardt","raw_affiliation_strings":["Genetics Yale University, New Haven, CT","Genetics, Yale University, New Haven, CT"],"affiliations":[{"raw_affiliation_string":"Genetics Yale University, New Haven, CT","institution_ids":["https://openalex.org/I32971472"]},{"raw_affiliation_string":"Genetics, Yale University, New Haven, CT","institution_ids":["https://openalex.org/I32971472"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5017992798","display_name":"Matthew Amodio","orcid":"https://orcid.org/0000-0001-9478-0957"},"institutions":[{"id":"https://openalex.org/I32971472","display_name":"Yale University","ror":"https://ror.org/03v76x132","country_code":"US","type":"education","lineage":["https://openalex.org/I32971472"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Matthew Amodio","raw_affiliation_strings":["Computer Science Yale University, New Haven, CT","Computer Science, Yale University, New Haven, CT#TAB#"],"affiliations":[{"raw_affiliation_string":"Computer Science Yale University, New Haven, CT","institution_ids":["https://openalex.org/I32971472"]},{"raw_affiliation_string":"Computer Science, Yale University, New Haven, CT#TAB#","institution_ids":["https://openalex.org/I32971472"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075669924","display_name":"Alex Tong","orcid":null},"institutions":[{"id":"https://openalex.org/I32971472","display_name":"Yale University","ror":"https://ror.org/03v76x132","country_code":"US","type":"education","lineage":["https://openalex.org/I32971472"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Alexander Tong","raw_affiliation_strings":["Computer Science Yale University, New Haven, CT","Computer Science, Yale University, New Haven, CT#TAB#"],"affiliations":[{"raw_affiliation_string":"Computer Science Yale University, New Haven, CT","institution_ids":["https://openalex.org/I32971472"]},{"raw_affiliation_string":"Computer Science, Yale University, New Haven, CT#TAB#","institution_ids":["https://openalex.org/I32971472"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005117825","display_name":"Guy Wolf","orcid":"https://orcid.org/0000-0002-6740-059X"},"institutions":[{"id":"https://openalex.org/I70931966","display_name":"Universit\u00e9 de Montr\u00e9al","ror":"https://ror.org/0161xgx34","country_code":"CA","type":"education","lineage":["https://openalex.org/I70931966"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Guy Wolf","raw_affiliation_strings":["Mathematics & Statistics Univ. de Montr\u00e9al; Mila, Montreal, Canada","Mathematics & Statistics Univ. de Montr\u00e9al; Mila,Montreal,Canada"],"affiliations":[{"raw_affiliation_string":"Mathematics & Statistics Univ. de Montr\u00e9al; Mila, Montreal, Canada","institution_ids":["https://openalex.org/I70931966"]},{"raw_affiliation_string":"Mathematics & Statistics Univ. de Montr\u00e9al; Mila,Montreal,Canada","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5045475274","display_name":"Smita Krishnaswamy","orcid":"https://orcid.org/0000-0001-5823-1985"},"institutions":[{"id":"https://openalex.org/I32971472","display_name":"Yale University","ror":"https://ror.org/03v76x132","country_code":"US","type":"education","lineage":["https://openalex.org/I32971472"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Smita Krishnaswamy","raw_affiliation_strings":["Genetics; Computer Science Yale University, New Haven, CT","Genetics; Computer Science Yale University,New Haven,CT"],"affiliations":[{"raw_affiliation_string":"Genetics; Computer Science Yale University, New Haven, CT","institution_ids":["https://openalex.org/I32971472"]},{"raw_affiliation_string":"Genetics; Computer Science Yale University,New Haven,CT","institution_ids":["https://openalex.org/I32971472"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5019679682"],"corresponding_institution_ids":["https://openalex.org/I32971472"],"apc_list":null,"apc_paid":null,"fwci":0.42754303,"has_fulltext":true,"cited_by_count":4,"citation_normalized_percentile":{"value":0.66958854,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":null,"issue":null,"first_page":"2634","last_page":"2643"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10775","display_name":"Generative Adversarial Networks and Image Synthesis","score":0.9961000084877014,"subfield":{"id":"https://openalex.org/subfields/1707","display_name":"Computer Vision and Pattern Recognition"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10775","display_name":"Generative Adversarial Networks and Image Synthesis","score":0.9961000084877014,"subfield":{"id":"https://openalex.org/subfields/1707","display_name":"Computer Vision and Pattern Recognition"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11309","display_name":"Music and Audio Processing","score":0.991599977016449,"subfield":{"id":"https://openalex.org/subfields/1711","display_name":"Signal Processing"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11439","display_name":"Video Analysis and Summarization","score":0.9352999925613403,"subfield":{"id":"https://openalex.org/subfields/1707","display_name":"Computer Vision and Pattern Recognition"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/archetype","display_name":"Archetype","score":0.7485411763191223},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.587334156036377},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.5699412226676941},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5454850196838379},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.5262705087661743},{"id":"https://openalex.org/keywords/data-space","display_name":"Data space","score":0.5252513289451599},{"id":"https://openalex.org/keywords/space","display_name":"Space (punctuation)","score":0.49841737747192383},{"id":"https://openalex.org/keywords/transformation","display_name":"Transformation (genetics)","score":0.49780893325805664},{"id":"https://openalex.org/keywords/feature","display_name":"Feature (linguistics)","score":0.46007001399993896},{"id":"https://openalex.org/keywords/feature-vector","display_name":"Feature vector","score":0.443779319524765},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.4374402165412903},{"id":"https://openalex.org/keywords/maxima-and-minima","display_name":"Maxima and minima","score":0.41518062353134155},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3823004364967346},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3543314039707184},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3420764207839966},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.2664722800254822}],"concepts":[{"id":"https://openalex.org/C49848784","wikidata":"https://www.wikidata.org/wiki/Q131714","display_name":"Archetype","level":2,"score":0.7485411763191223},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.587334156036377},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.5699412226676941},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5454850196838379},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.5262705087661743},{"id":"https://openalex.org/C2988382989","wikidata":"https://www.wikidata.org/wiki/Q370685","display_name":"Data space","level":2,"score":0.5252513289451599},{"id":"https://openalex.org/C2778572836","wikidata":"https://www.wikidata.org/wiki/Q380933","display_name":"Space (punctuation)","level":2,"score":0.49841737747192383},{"id":"https://openalex.org/C204241405","wikidata":"https://www.wikidata.org/wiki/Q461499","display_name":"Transformation (genetics)","level":3,"score":0.49780893325805664},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.46007001399993896},{"id":"https://openalex.org/C83665646","wikidata":"https://www.wikidata.org/wiki/Q42139305","display_name":"Feature vector","level":2,"score":0.443779319524765},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.4374402165412903},{"id":"https://openalex.org/C186633575","wikidata":"https://www.wikidata.org/wiki/Q845060","display_name":"Maxima and minima","level":2,"score":0.41518062353134155},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3823004364967346},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3543314039707184},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3420764207839966},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.2664722800254822},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.0},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"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/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/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","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},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C124952713","wikidata":"https://www.wikidata.org/wiki/Q8242","display_name":"Literature","level":1,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1109/bigdata47090.2019.9006484","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bigdata47090.2019.9006484","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2019 IEEE International Conference on Big Data (Big Data)","raw_type":"proceedings-article"},{"id":"pmh:oai:arXiv.org:1901.09078","is_oa":true,"landing_page_url":"http://arxiv.org/abs/1901.09078","pdf_url":"https://arxiv.org/pdf/1901.09078","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"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":"","raw_type":"text"},{"id":"mag:3004572984","is_oa":true,"landing_page_url":"http://export.arxiv.org/pdf/1901.09078","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"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":"arXiv (Cornell University)","raw_type":null},{"id":"doi:10.48550/arxiv.1901.09078","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.1901.09078","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"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":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article"}],"best_oa_location":{"id":"pmh:oai:arXiv.org:1901.09078","is_oa":true,"landing_page_url":"http://arxiv.org/abs/1901.09078","pdf_url":"https://arxiv.org/pdf/1901.09078","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"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":"","raw_type":"text"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3004572984.pdf","grobid_xml":"https://content.openalex.org/works/W3004572984.grobid-xml"},"referenced_works_count":43,"referenced_works":["https://openalex.org/W813853026","https://openalex.org/W1840600990","https://openalex.org/W1880262756","https://openalex.org/W1971971673","https://openalex.org/W2001275742","https://openalex.org/W2010025771","https://openalex.org/W2015159529","https://openalex.org/W2028221693","https://openalex.org/W2032230795","https://openalex.org/W2037581670","https://openalex.org/W2056924500","https://openalex.org/W2081123716","https://openalex.org/W2085498944","https://openalex.org/W2093628490","https://openalex.org/W2093859221","https://openalex.org/W2099471712","https://openalex.org/W2106706131","https://openalex.org/W2110576461","https://openalex.org/W2156718197","https://openalex.org/W2173208124","https://openalex.org/W2212660284","https://openalex.org/W2295505594","https://openalex.org/W2602848567","https://openalex.org/W2611997107","https://openalex.org/W2794407684","https://openalex.org/W2805619986","https://openalex.org/W2807548554","https://openalex.org/W2810097927","https://openalex.org/W2949842749","https://openalex.org/W2951004968","https://openalex.org/W2963591249","https://openalex.org/W4230931443","https://openalex.org/W4237929415","https://openalex.org/W4253636695","https://openalex.org/W6639619044","https://openalex.org/W6640963894","https://openalex.org/W6652820381","https://openalex.org/W6674703805","https://openalex.org/W6688325169","https://openalex.org/W6737699732","https://openalex.org/W6748457630","https://openalex.org/W6752014661","https://openalex.org/W6955712162"],"related_works":["https://openalex.org/W3007965799","https://openalex.org/W2949109536","https://openalex.org/W2919560363","https://openalex.org/W3003273077","https://openalex.org/W2969964247","https://openalex.org/W2751565187","https://openalex.org/W2314231116","https://openalex.org/W2911250401","https://openalex.org/W1586881595","https://openalex.org/W2766283167","https://openalex.org/W1460750796","https://openalex.org/W2962678600","https://openalex.org/W2373618835","https://openalex.org/W2992956318","https://openalex.org/W2907481112","https://openalex.org/W1979366912","https://openalex.org/W66807664","https://openalex.org/W2951486723","https://openalex.org/W2912276204","https://openalex.org/W3127571114"],"abstract_inverted_index":{"Archetypal":[0,134],"analysis":[1,58],"is":[2,34,86,114,139],"a":[3,12,15,28,35,62,105,117,124,140,150],"data":[4,29,122,165,172,177],"decomposition":[5],"method":[6],"that":[7,111],"describes":[8],"each":[9],"observation":[10],"in":[11,31,41,96,163,187],"dataset":[13],"as":[14,40,95],"convex":[16],"combination":[17,91],"of":[18,27,46,92,107,120,154,160],"\"pure":[19],"types\"":[20],"or":[21,99],"archetypes.":[22],"These":[23],"archetypes":[24,162,186],"represent":[25],"extrema":[26],"space":[30,69,85],"which":[32,138],"there":[33],"trade-off":[36],"between":[37,66],"features,":[38],"such":[39,75,94,110],"biology":[42],"where":[43,82],"different":[44,52],"combinations":[45],"traits":[47],"provide":[48],"optimal":[49],"fitness":[50],"for":[51,56,145],"environments.":[53],"Existing":[54],"methods":[55,76],"archetypal":[57,72,126,152],"work":[59],"well":[60],"when":[61],"linear":[63],"relationship":[64],"exists":[65],"the":[67,71,83,90,108,112,121],"feature":[68,84],"and":[70,147,179],"space.":[73,127],"However,":[74],"are":[77],"not":[78],"applicable":[79],"to":[80,115,182],"systems":[81,98],"generated":[87],"non-linearly":[88],"from":[89,149,171,176],"archetypes,":[93],"biological":[97],"image":[100],"transformations.":[101],"Here,":[102],"we":[103,132],"propose":[104],"reformulation":[106],"problem":[109],"goal":[113],"learn":[116],"non-linear":[118,164],"transformation":[119],"into":[123],"latent":[125,151],"To":[128],"solve":[129],"this":[130],"problem,":[131],"introduce":[133],"Analysis":[135],"network":[136,143],"(AAnet),":[137],"deep":[141],"neural":[142],"framework":[144],"learning":[146],"generating":[148],"representation":[153],"data.":[155,191],"We":[156],"demonstrate":[157],"state-of-the-art":[158],"recovery":[159],"ground-truth":[161],"domains,":[166],"show":[167],"AAnet":[168,181],"can":[169],"generate":[170],"geometry":[173],"rather":[174],"than":[175],"density,":[178],"use":[180],"identify":[183],"biologically":[184],"meaningful":[185],"single-cell":[188],"gene":[189],"expression":[190]},"counts_by_year":[{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":2}],"updated_date":"2026-02-09T09:26:11.010843","created_date":"2025-10-10T00:00:00"}