{"id":"https://openalex.org/W3111593274","doi":"https://doi.org/10.1038/s42256-020-00269-9","title":"Gene set inference from single-cell sequencing data using a hybrid of matrix factorization and variational autoencoders","display_name":"Gene set inference from single-cell sequencing data using a hybrid of matrix factorization and variational autoencoders","publication_year":2020,"publication_date":"2020-12-07","ids":{"openalex":"https://openalex.org/W3111593274","doi":"https://doi.org/10.1038/s42256-020-00269-9","mag":"3111593274"},"language":"en","primary_location":{"id":"doi:10.1038/s42256-020-00269-9","is_oa":false,"landing_page_url":"https://doi.org/10.1038/s42256-020-00269-9","pdf_url":null,"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":null,"license_id":null,"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":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5020646210","display_name":"Soeren Lukassen","orcid":"https://orcid.org/0000-0001-7045-6327"},"institutions":[{"id":"https://openalex.org/I4210139777","display_name":"Berlin Institute of Health at Charit\u00e9 - Universit\u00e4tsmedizin Berlin","ror":"https://ror.org/0493xsw21","country_code":"DE","type":"facility","lineage":["https://openalex.org/I4210139777","https://openalex.org/I7877124"]},{"id":"https://openalex.org/I7877124","display_name":"Charit\u00e9 - Universit\u00e4tsmedizin Berlin","ror":"https://ror.org/001w7jn25","country_code":"DE","type":"healthcare","lineage":["https://openalex.org/I7877124"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Soeren Lukassen","raw_affiliation_strings":["Berlin Institute of Health (BIH), Berlin, Germany","Charit\u00e9\u2014Universit\u00e4tsmedizin Berlin, Digital Health Center, Berlin, Germany"],"raw_orcid":"https://orcid.org/0000-0001-7045-6327","affiliations":[{"raw_affiliation_string":"Berlin Institute of Health (BIH), Berlin, Germany","institution_ids":["https://openalex.org/I4210139777"]},{"raw_affiliation_string":"Charit\u00e9\u2014Universit\u00e4tsmedizin Berlin, Digital Health Center, Berlin, Germany","institution_ids":["https://openalex.org/I7877124"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071917764","display_name":"Foo Wei Ten","orcid":"https://orcid.org/0000-0003-0839-6815"},"institutions":[{"id":"https://openalex.org/I4210139777","display_name":"Berlin Institute of Health at Charit\u00e9 - Universit\u00e4tsmedizin Berlin","ror":"https://ror.org/0493xsw21","country_code":"DE","type":"facility","lineage":["https://openalex.org/I4210139777","https://openalex.org/I7877124"]},{"id":"https://openalex.org/I7877124","display_name":"Charit\u00e9 - Universit\u00e4tsmedizin Berlin","ror":"https://ror.org/001w7jn25","country_code":"DE","type":"healthcare","lineage":["https://openalex.org/I7877124"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Foo Wei Ten","raw_affiliation_strings":["Berlin Institute of Health (BIH), Berlin, Germany","Charit\u00e9\u2014Universit\u00e4tsmedizin Berlin, Digital Health Center, Berlin, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Berlin Institute of Health (BIH), Berlin, Germany","institution_ids":["https://openalex.org/I4210139777"]},{"raw_affiliation_string":"Charit\u00e9\u2014Universit\u00e4tsmedizin Berlin, Digital Health Center, Berlin, Germany","institution_ids":["https://openalex.org/I7877124"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5009739596","display_name":"Lukas Adam","orcid":"https://orcid.org/0000-0003-4182-5300"},"institutions":[{"id":"https://openalex.org/I4210139777","display_name":"Berlin Institute of Health at Charit\u00e9 - Universit\u00e4tsmedizin Berlin","ror":"https://ror.org/0493xsw21","country_code":"DE","type":"facility","lineage":["https://openalex.org/I4210139777","https://openalex.org/I7877124"]},{"id":"https://openalex.org/I7877124","display_name":"Charit\u00e9 - Universit\u00e4tsmedizin Berlin","ror":"https://ror.org/001w7jn25","country_code":"DE","type":"healthcare","lineage":["https://openalex.org/I7877124"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Lukas Adam","raw_affiliation_strings":["Berlin Institute of Health (BIH), Berlin, Germany","Charit\u00e9\u2014Universit\u00e4tsmedizin Berlin, Digital Health Center, Berlin, Germany"],"raw_orcid":"https://orcid.org/0000-0003-4182-5300","affiliations":[{"raw_affiliation_string":"Berlin Institute of Health (BIH), Berlin, Germany","institution_ids":["https://openalex.org/I4210139777"]},{"raw_affiliation_string":"Charit\u00e9\u2014Universit\u00e4tsmedizin Berlin, Digital Health Center, Berlin, Germany","institution_ids":["https://openalex.org/I7877124"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044191947","display_name":"Roland Eils","orcid":"https://orcid.org/0000-0002-0034-4036"},"institutions":[{"id":"https://openalex.org/I223822909","display_name":"Heidelberg University","ror":"https://ror.org/038t36y30","country_code":"DE","type":"education","lineage":["https://openalex.org/I223822909"]},{"id":"https://openalex.org/I2802164966","display_name":"University Hospital Heidelberg","ror":"https://ror.org/013czdx64","country_code":"DE","type":"healthcare","lineage":["https://openalex.org/I2802164966"]},{"id":"https://openalex.org/I4210139777","display_name":"Berlin Institute of Health at Charit\u00e9 - Universit\u00e4tsmedizin Berlin","ror":"https://ror.org/0493xsw21","country_code":"DE","type":"facility","lineage":["https://openalex.org/I4210139777","https://openalex.org/I7877124"]},{"id":"https://openalex.org/I7877124","display_name":"Charit\u00e9 - Universit\u00e4tsmedizin Berlin","ror":"https://ror.org/001w7jn25","country_code":"DE","type":"healthcare","lineage":["https://openalex.org/I7877124"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Roland Eils","raw_affiliation_strings":["Berlin Institute of Health (BIH), Berlin, Germany","Charit\u00e9\u2014Universit\u00e4tsmedizin Berlin, Digital Health Center, Berlin, Germany","Health Data Science Unit, University Hospital Heidelberg, Heidelberg, Germany"],"raw_orcid":"https://orcid.org/0000-0002-0034-4036","affiliations":[{"raw_affiliation_string":"Berlin Institute of Health (BIH), Berlin, Germany","institution_ids":["https://openalex.org/I4210139777"]},{"raw_affiliation_string":"Charit\u00e9\u2014Universit\u00e4tsmedizin Berlin, Digital Health Center, Berlin, Germany","institution_ids":["https://openalex.org/I7877124"]},{"raw_affiliation_string":"Health Data Science Unit, University Hospital Heidelberg, Heidelberg, Germany","institution_ids":["https://openalex.org/I223822909","https://openalex.org/I2802164966"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5072661843","display_name":"Christian Conrad","orcid":"https://orcid.org/0000-0001-7036-342X"},"institutions":[{"id":"https://openalex.org/I4210139777","display_name":"Berlin Institute of Health at Charit\u00e9 - Universit\u00e4tsmedizin Berlin","ror":"https://ror.org/0493xsw21","country_code":"DE","type":"facility","lineage":["https://openalex.org/I4210139777","https://openalex.org/I7877124"]},{"id":"https://openalex.org/I7877124","display_name":"Charit\u00e9 - Universit\u00e4tsmedizin Berlin","ror":"https://ror.org/001w7jn25","country_code":"DE","type":"healthcare","lineage":["https://openalex.org/I7877124"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Christian Conrad","raw_affiliation_strings":["Berlin Institute of Health (BIH), Berlin, Germany","Charit\u00e9\u2014Universit\u00e4tsmedizin Berlin, Digital Health Center, Berlin, Germany"],"raw_orcid":"https://orcid.org/0000-0001-7036-342X","affiliations":[{"raw_affiliation_string":"Berlin Institute of Health (BIH), Berlin, Germany","institution_ids":["https://openalex.org/I4210139777"]},{"raw_affiliation_string":"Charit\u00e9\u2014Universit\u00e4tsmedizin Berlin, Digital Health Center, Berlin, Germany","institution_ids":["https://openalex.org/I7877124"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5044191947","https://openalex.org/A5072661843"],"corresponding_institution_ids":["https://openalex.org/I223822909","https://openalex.org/I2802164966","https://openalex.org/I4210139777","https://openalex.org/I7877124"],"apc_list":{"value":11690,"currency":"USD","value_usd":11690},"apc_paid":null,"fwci":0.2982,"has_fulltext":false,"cited_by_count":9,"citation_normalized_percentile":{"value":0.53668594,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":98},"biblio":{"volume":"2","issue":"12","first_page":"800","last_page":"809"},"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/T10885","display_name":"Gene expression and cancer classification","score":0.9944999814033508,"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/T10515","display_name":"Cancer-related molecular mechanisms research","score":0.9815999865531921,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/autoencoder","display_name":"Autoencoder","score":0.7788686752319336},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6540577411651611},{"id":"https://openalex.org/keywords/single-cell-sequencing","display_name":"Single cell sequencing","score":0.6397685408592224},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.6179580688476562},{"id":"https://openalex.org/keywords/matrix-decomposition","display_name":"Matrix decomposition","score":0.5404592156410217},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.5283960700035095},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4908238351345062},{"id":"https://openalex.org/keywords/data-set","display_name":"Data set","score":0.4660920202732086},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.44901227951049805},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.4469616711139679},{"id":"https://openalex.org/keywords/non-negative-matrix-factorization","display_name":"Non-negative matrix factorization","score":0.44314640760421753},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.4357427656650543},{"id":"https://openalex.org/keywords/latent-variable","display_name":"Latent variable","score":0.41291549801826477},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.3849627375602722},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.36194556951522827},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.3282736837863922},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.32165056467056274},{"id":"https://openalex.org/keywords/phenotype","display_name":"Phenotype","score":0.25328320264816284},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2036789357662201},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1478477418422699}],"concepts":[{"id":"https://openalex.org/C101738243","wikidata":"https://www.wikidata.org/wiki/Q786435","display_name":"Autoencoder","level":3,"score":0.7788686752319336},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6540577411651611},{"id":"https://openalex.org/C174749747","wikidata":"https://www.wikidata.org/wiki/Q15917269","display_name":"Single cell sequencing","level":5,"score":0.6397685408592224},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.6179580688476562},{"id":"https://openalex.org/C42355184","wikidata":"https://www.wikidata.org/wiki/Q1361088","display_name":"Matrix decomposition","level":3,"score":0.5404592156410217},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.5283960700035095},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4908238351345062},{"id":"https://openalex.org/C58489278","wikidata":"https://www.wikidata.org/wiki/Q1172284","display_name":"Data set","level":2,"score":0.4660920202732086},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.44901227951049805},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.4469616711139679},{"id":"https://openalex.org/C152671427","wikidata":"https://www.wikidata.org/wiki/Q10843505","display_name":"Non-negative matrix factorization","level":4,"score":0.44314640760421753},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.4357427656650543},{"id":"https://openalex.org/C51167844","wikidata":"https://www.wikidata.org/wiki/Q4422623","display_name":"Latent variable","level":2,"score":0.41291549801826477},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.3849627375602722},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.36194556951522827},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.3282736837863922},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.32165056467056274},{"id":"https://openalex.org/C127716648","wikidata":"https://www.wikidata.org/wiki/Q104053","display_name":"Phenotype","level":3,"score":0.25328320264816284},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2036789357662201},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1478477418422699},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0},{"id":"https://openalex.org/C16671776","wikidata":"https://www.wikidata.org/wiki/Q5420592","display_name":"Exome sequencing","level":4,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C158693339","wikidata":"https://www.wikidata.org/wiki/Q190524","display_name":"Eigenvalues and eigenvectors","level":2,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1038/s42256-020-00269-9","is_oa":false,"landing_page_url":"https://doi.org/10.1038/s42256-020-00269-9","pdf_url":null,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nature Machine Intelligence","raw_type":"journal-article"}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/14","score":0.699999988079071,"display_name":"Life below water"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":54,"referenced_works":["https://openalex.org/W569478347","https://openalex.org/W1902027874","https://openalex.org/W1953958325","https://openalex.org/W1959608418","https://openalex.org/W1974926090","https://openalex.org/W1989277387","https://openalex.org/W2014677321","https://openalex.org/W2033793905","https://openalex.org/W2085487226","https://openalex.org/W2099105062","https://openalex.org/W2103017472","https://openalex.org/W2108550484","https://openalex.org/W2121111814","https://openalex.org/W2121131150","https://openalex.org/W2121995533","https://openalex.org/W2146276081","https://openalex.org/W2158384363","https://openalex.org/W2159482845","https://openalex.org/W2286142055","https://openalex.org/W2429031812","https://openalex.org/W2472063172","https://openalex.org/W2482092413","https://openalex.org/W2523369352","https://openalex.org/W2526262591","https://openalex.org/W2551194178","https://openalex.org/W2747545374","https://openalex.org/W2766736793","https://openalex.org/W2774307122","https://openalex.org/W2794480084","https://openalex.org/W2798368076","https://openalex.org/W2799935500","https://openalex.org/W2805579976","https://openalex.org/W2897979119","https://openalex.org/W2903552149","https://openalex.org/W2918656717","https://openalex.org/W2928665623","https://openalex.org/W2948978827","https://openalex.org/W2949177718","https://openalex.org/W2950595506","https://openalex.org/W2950983802","https://openalex.org/W2952016241","https://openalex.org/W2953116488","https://openalex.org/W2954018630","https://openalex.org/W2958554910","https://openalex.org/W2964144157","https://openalex.org/W2969718750","https://openalex.org/W3002417351","https://openalex.org/W3012280517","https://openalex.org/W3099211645","https://openalex.org/W3103543904","https://openalex.org/W4294216483","https://openalex.org/W6813094581","https://openalex.org/W6912465090","https://openalex.org/W6926170062"],"related_works":["https://openalex.org/W2127243424","https://openalex.org/W4390394189","https://openalex.org/W2037504162","https://openalex.org/W2539013788","https://openalex.org/W2792706544","https://openalex.org/W1568451138","https://openalex.org/W2156699640","https://openalex.org/W2045265907","https://openalex.org/W2972997031","https://openalex.org/W2075222291"],"abstract_inverted_index":null,"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":2}],"updated_date":"2026-07-23T08:03:31.855105","created_date":"2025-10-10T00:00:00"}
