{"id":"https://openalex.org/W2913649887","doi":null,"title":"Finding Archetypal Spaces for Data Using Neural Networks.","display_name":"Finding Archetypal Spaces for Data Using Neural Networks.","publication_year":2019,"publication_date":"2019-01-25","ids":{"openalex":"https://openalex.org/W2913649887","mag":"2913649887"},"language":"en","primary_location":{"id":"mag:2913649887","doi":null,"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":"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":"arXiv (Cornell University)","raw_type":null},"volume":null,"type":"preprint","indexed_in":[],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"http://export.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","observed_orcids":["https://orcid.org/0000-0003-3911-9925"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"David van Dijk","raw_affiliation_strings":[],"raw_orcid":"https://orcid.org/0000-0003-3911-9925","affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5079128249","display_name":"Daniel B. Burkhardt","orcid":"https://orcid.org/0000-0001-7744-1363","observed_orcids":["https://orcid.org/0000-0001-7744-1363"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Daniel B. Burkhardt","raw_affiliation_strings":[],"raw_orcid":"https://orcid.org/0000-0001-7744-1363","affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5017992798","display_name":"Matthew Amodio","orcid":"https://orcid.org/0000-0001-9478-0957","observed_orcids":["https://orcid.org/0000-0001-9478-0957"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Matthew Amodio","raw_affiliation_strings":[],"raw_orcid":"https://orcid.org/0000-0001-9478-0957","affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053568123","display_name":"Alexander Tong","orcid":"https://orcid.org/0000-0002-2031-4096","observed_orcids":["https://orcid.org/0000-0002-2031-4096"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Alexander Tong","raw_affiliation_strings":[],"raw_orcid":"https://orcid.org/0000-0002-2031-4096","affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005117825","display_name":"Guy Wolf","orcid":"https://orcid.org/0000-0002-6740-059X","observed_orcids":["https://orcid.org/0000-0002-6740-059X"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Guy Wolf","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5045475274","display_name":"Smita Krishnaswamy","orcid":"https://orcid.org/0000-0001-5823-1985","observed_orcids":["https://orcid.org/0000-0001-5823-1985"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Smita Krishnaswamy","raw_affiliation_strings":[],"raw_orcid":"https://orcid.org/0000-0001-5823-1985","affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":7,"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/T12536","display_name":"Topological and Geometric Data Analysis","score":0.42089998722076416,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"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/T12536","display_name":"Topological and Geometric Data Analysis","score":0.42089998722076416,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.3246999979019165,"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/T10320","display_name":"Neural Networks and Applications","score":0.065700002014637,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"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/archetypal-analysis","display_name":"archetypal analysis","score":1.0},{"id":"https://openalex.org/keywords/single-cell-rna-sequencing","display_name":"single-cell RNA sequencing","score":0.6819999814033508},{"id":"https://openalex.org/keywords/gut-microbiota","display_name":"gut microbiota","score":0.9070000052452087},{"id":"https://openalex.org/keywords/biological-data-visualization","display_name":"biological data visualization","score":0.44999998807907104}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5594120621681213},{"id":"https://openalex.org/C145691206","wikidata":"https://www.wikidata.org/wiki/Q747980","display_name":"Polytope","level":2,"score":0.5371957421302795},{"id":"https://openalex.org/C112680207","wikidata":"https://www.wikidata.org/wiki/Q714886","display_name":"Regular polygon","level":2,"score":0.529274582862854},{"id":"https://openalex.org/C110943637","wikidata":"https://www.wikidata.org/wiki/Q4129097","display_name":"Convex polytope","level":5,"score":0.502748966217041},{"id":"https://openalex.org/C111110010","wikidata":"https://www.wikidata.org/wiki/Q2627315","display_name":"Convex combination","level":4,"score":0.48202431201934814},{"id":"https://openalex.org/C204241405","wikidata":"https://www.wikidata.org/wiki/Q461499","display_name":"Transformation (genetics)","level":3,"score":0.4671682119369507},{"id":"https://openalex.org/C21080849","wikidata":"https://www.wikidata.org/wiki/Q13611879","display_name":"Data point","level":2,"score":0.46478673815727234},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.442763090133667},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.39267340302467346},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.36976122856140137},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3670356273651123},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.330883651971817},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.30687546730041504},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.2324140965938568},{"id":"https://openalex.org/C49870271","wikidata":"https://www.wikidata.org/wiki/Q193657","display_name":"Convex set","level":4,"score":0.23020392656326294},{"id":"https://openalex.org/C157972887","wikidata":"https://www.wikidata.org/wiki/Q463359","display_name":"Convex optimization","level":3,"score":0.20041030645370483},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.09003835916519165},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"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/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"mag:2913649887","doi":null,"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":"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":"arXiv (Cornell University)","raw_type":null}],"best_oa_location":{"id":"mag:2913649887","doi":null,"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":"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":"arXiv (Cornell University)","raw_type":null},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":15,"referenced_works":["https://openalex.org/W1971971673","https://openalex.org/W2001275742","https://openalex.org/W2010025771","https://openalex.org/W2032230795","https://openalex.org/W2056924500","https://openalex.org/W2081123716","https://openalex.org/W2085498944","https://openalex.org/W2099471712","https://openalex.org/W2106706131","https://openalex.org/W2156718197","https://openalex.org/W2212660284","https://openalex.org/W2295505594","https://openalex.org/W2602848567","https://openalex.org/W2805619986","https://openalex.org/W2963591249"],"related_works":["https://openalex.org/W3004572984","https://openalex.org/W7117559810","https://openalex.org/W3127836097","https://openalex.org/W7162433670","https://openalex.org/W4417089122","https://openalex.org/W1601508401","https://openalex.org/W2894614844","https://openalex.org/W1840600990","https://openalex.org/W3003273077","https://openalex.org/W4225727169"],"abstract_inverted_index":{"Archetypal":[0],"analysis":[1,7,37],"is":[2,10,127,210],"a":[3,13,28,58,73,82,90,96,102,112,145,168],"type":[4],"of":[5,20,31,80,170],"factor":[6],"where":[8,121],"data":[9,25,52,69,87,92,107,120,203,209],"fit":[11,56,110],"by":[12,57],"convex":[14,29,59,83],"polytope":[15,60,84],"whose":[16],"corners":[17],"are":[18,53],"archetypes":[19],"the":[21,24,63,106,128,134,186,202,207],"data,":[22,43],"with":[23,150],"represented":[26],"as":[27],"combination":[30],"these":[32],"archetypal":[33,36,77,157],"points.":[34],"While":[35],"has":[38,45,193],"been":[39],"used":[40],"on":[41,86,118,140],"biological":[42,142],"it":[44],"not":[46,54,211],"achieved":[47],"widespread":[48],"adoption":[49],"because":[50],"most":[51],"well":[55],"in":[61,185],"either":[62],"ambient":[64],"space":[65],"or":[66,88],"after":[67,89],"standard":[68],"transformations.":[70],"We":[71,114,136],"propose":[72],"new":[74],"approach":[75,117],"to":[76,100,160,198],"analysis.":[78],"Instead":[79],"fitting":[81],"directly":[85],"specific":[91],"transformation,":[93],"we":[94,122,189],"train":[95],"neural":[97],"network":[98],"(AAnet)":[99],"learn":[101],"transformation":[103],"under":[104],"which":[105],"can":[108],"best":[109],"into":[111],"polytope.":[113],"validate":[115],"this":[116],"synthetic":[119],"add":[123],"nonlinearity.":[124],"Here,":[125],"AAnet":[126,139,154,174,192],"only":[129],"method":[130],"that":[131,191],"correctly":[132],"identifies":[133,155,182],"archetypes.":[135],"also":[137],"demonstrate":[138],"two":[141],"datasets.":[143],"In":[144,167],"T":[146,165],"cell":[147,152],"dataset":[148,169],"measured":[149],"single":[151],"RNA-sequencing,":[153],"several":[156],"states":[158,180],"corresponding":[159],"naive,":[161],"memory,":[162],"and":[163,181],"cytotoxic":[164],"cells.":[166],"gut":[171],"microbiome":[172,179],"profiles,":[173],"recovers":[175],"both":[176],"previously":[177],"described":[178],"novel":[183],"extrema":[184],"data.":[187],"Finally,":[188],"show":[190],"generative":[194],"properties":[195],"allowing":[196],"us":[197],"uniformly":[199,212],"sample":[200],"from":[201],"geometry":[204],"even":[205],"when":[206],"input":[208],"distributed.":[213]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":1}],"updated_date":"2026-11-03T10:50:19.383937","created_date":"2019-02-21T00:00:00"}