{"id":"https://openalex.org/W4225279909","doi":"https://doi.org/10.1186/s13040-021-00285-4","title":"Integrating pathway knowledge with deep neural networks to reduce the dimensionality in single-cell RNA-seq data","display_name":"Integrating pathway knowledge with deep neural networks to reduce the dimensionality in single-cell RNA-seq data","publication_year":2022,"publication_date":"2022-01-03","ids":{"openalex":"https://openalex.org/W4225279909","doi":"https://doi.org/10.1186/s13040-021-00285-4","pmid":"https://pubmed.ncbi.nlm.nih.gov/34980200"},"language":"en","primary_location":{"id":"doi:10.1186/s13040-021-00285-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13040-021-00285-4","pdf_url":null,"source":{"id":"https://openalex.org/S84409260","display_name":"BioData Mining","issn_l":"1756-0381","issn":["1756-0381"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BioData Mining","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1186/s13040-021-00285-4","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5061846495","display_name":"Pelin Gundogdu","orcid":"https://orcid.org/0000-0002-1791-9457"},"institutions":[{"id":"https://openalex.org/I4210086910","display_name":"Fundaci\u00f3n Progreso y Salud","ror":"https://ror.org/0048t7e91","country_code":"ES","type":"other","lineage":["https://openalex.org/I4210086910","https://openalex.org/I4210152975","https://openalex.org/I918821925"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Pelin Gundogdu","raw_affiliation_strings":["Clinical Bioinformatics Area. Fundaci\u00f3n Progreso y Salud (FPS). CDCA, Hospital Virgen del Rocio, 41013, Sevilla, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Clinical Bioinformatics Area. Fundaci\u00f3n Progreso y Salud (FPS). CDCA, Hospital Virgen del Rocio, 41013, Sevilla, Spain","institution_ids":["https://openalex.org/I4210086910"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021802977","display_name":"Carlos Loucera","orcid":"https://orcid.org/0000-0001-9598-6965"},"institutions":[{"id":"https://openalex.org/I4210086910","display_name":"Fundaci\u00f3n Progreso y Salud","ror":"https://ror.org/0048t7e91","country_code":"ES","type":"other","lineage":["https://openalex.org/I4210086910","https://openalex.org/I4210152975","https://openalex.org/I918821925"]},{"id":"https://openalex.org/I4210133602","display_name":"Instituto de Biomedicina de Sevilla","ror":"https://ror.org/031zwx660","country_code":"ES","type":"facility","lineage":["https://openalex.org/I134820265","https://openalex.org/I158283456","https://openalex.org/I4210133602","https://openalex.org/I79238269","https://openalex.org/I918821925"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Carlos Loucera","raw_affiliation_strings":["Clinical Bioinformatics Area. Fundaci\u00f3n Progreso y Salud (FPS). CDCA, Hospital Virgen del Rocio, 41013, Sevilla, Spain","Computational Systems Medicine, Institute of Biomedicine of Seville (IBIS), Hospital Virgen del Rocio, 41013, Sevilla, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Clinical Bioinformatics Area. Fundaci\u00f3n Progreso y Salud (FPS). CDCA, Hospital Virgen del Rocio, 41013, Sevilla, Spain","institution_ids":["https://openalex.org/I4210086910"]},{"raw_affiliation_string":"Computational Systems Medicine, Institute of Biomedicine of Seville (IBIS), Hospital Virgen del Rocio, 41013, Sevilla, Spain","institution_ids":["https://openalex.org/I4210133602"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000916564","display_name":"Inmaculada \u00c1lamo-\u00c1lvarez","orcid":"https://orcid.org/0000-0002-6295-0218"},"institutions":[{"id":"https://openalex.org/I4210086910","display_name":"Fundaci\u00f3n Progreso y Salud","ror":"https://ror.org/0048t7e91","country_code":"ES","type":"other","lineage":["https://openalex.org/I4210086910","https://openalex.org/I4210152975","https://openalex.org/I918821925"]},{"id":"https://openalex.org/I4210133602","display_name":"Instituto de Biomedicina de Sevilla","ror":"https://ror.org/031zwx660","country_code":"ES","type":"facility","lineage":["https://openalex.org/I134820265","https://openalex.org/I158283456","https://openalex.org/I4210133602","https://openalex.org/I79238269","https://openalex.org/I918821925"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Inmaculada Alamo-Alvarez","raw_affiliation_strings":["Clinical Bioinformatics Area. Fundaci\u00f3n Progreso y Salud (FPS). CDCA, Hospital Virgen del Rocio, 41013, Sevilla, Spain","Computational Systems Medicine, Institute of Biomedicine of Seville (IBIS), Hospital Virgen del Rocio, 41013, Sevilla, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Clinical Bioinformatics Area. Fundaci\u00f3n Progreso y Salud (FPS). CDCA, Hospital Virgen del Rocio, 41013, Sevilla, Spain","institution_ids":["https://openalex.org/I4210086910"]},{"raw_affiliation_string":"Computational Systems Medicine, Institute of Biomedicine of Seville (IBIS), Hospital Virgen del Rocio, 41013, Sevilla, Spain","institution_ids":["https://openalex.org/I4210133602"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5074140420","display_name":"Joaqu\u0131\u0301n Dopazo","orcid":"https://orcid.org/0000-0003-3318-120X"},"institutions":[{"id":"https://openalex.org/I4210086910","display_name":"Fundaci\u00f3n Progreso y Salud","ror":"https://ror.org/0048t7e91","country_code":"ES","type":"other","lineage":["https://openalex.org/I4210086910","https://openalex.org/I4210152975","https://openalex.org/I918821925"]},{"id":"https://openalex.org/I4210115082","display_name":"Centro de Investigaci\u00f3n Biom\u00e9dica en Red","ror":"https://ror.org/02g87qh62","country_code":"ES","type":"facility","lineage":["https://openalex.org/I2801357902","https://openalex.org/I4210115082","https://openalex.org/I4387152914"]},{"id":"https://openalex.org/I4210133602","display_name":"Instituto de Biomedicina de Sevilla","ror":"https://ror.org/031zwx660","country_code":"ES","type":"facility","lineage":["https://openalex.org/I134820265","https://openalex.org/I158283456","https://openalex.org/I4210133602","https://openalex.org/I79238269","https://openalex.org/I918821925"]},{"id":"https://openalex.org/I4210153139","display_name":"Hospital Universitario Virgen del Roc\u00edo","ror":"https://ror.org/04vfhnm78","country_code":"ES","type":"healthcare","lineage":["https://openalex.org/I4210153139"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Joaquin Dopazo","raw_affiliation_strings":["Bioinformatics in Rare Diseases (BiER), Centro de Investigaci\u00f3n Biom\u00e9dica en Red de Enfermedades Raras (CIBERER), FPS, Hospital Virgen del Roc\u00edo, 41013, Sevilla, Spain. joaquin.dopazo@juntadeandalucia.es","Clinical Bioinformatics Area. Fundaci\u00f3n Progreso y Salud (FPS). CDCA, Hospital Virgen del Rocio, 41013, Sevilla, Spain. joaquin.dopazo@juntadeandalucia.es","Computational Systems Medicine, Institute of Biomedicine of Seville (IBIS), Hospital Virgen del Rocio, 41013, Sevilla, Spain. joaquin.dopazo@juntadeandalucia.es","FPS/ELIXIR-es, Hospital Virgen del Roc\u00edo, 42013, Sevilla, Spain. joaquin.dopazo@juntadeandalucia.es","Clinical Bioinformatics Area. Fundaci\u00f3n Progreso y Salud (FPS). CDCA, Hospital Virgen del Rocio, 41013, Sevilla, Spain","Computational Systems Medicine, Institute of Biomedicine of Seville (IBIS), Hospital Virgen del Rocio, 41013, Sevilla, Spain"],"raw_orcid":"https://orcid.org/0000-0003-3318-120X","affiliations":[{"raw_affiliation_string":"Bioinformatics in Rare Diseases (BiER), Centro de Investigaci\u00f3n Biom\u00e9dica en Red de Enfermedades Raras (CIBERER), FPS, Hospital Virgen del Roc\u00edo, 41013, Sevilla, Spain. joaquin.dopazo@juntadeandalucia.es","institution_ids":["https://openalex.org/I4210115082"]},{"raw_affiliation_string":"Clinical Bioinformatics Area. Fundaci\u00f3n Progreso y Salud (FPS). CDCA, Hospital Virgen del Rocio, 41013, Sevilla, Spain. joaquin.dopazo@juntadeandalucia.es","institution_ids":["https://openalex.org/I4210086910"]},{"raw_affiliation_string":"Computational Systems Medicine, Institute of Biomedicine of Seville (IBIS), Hospital Virgen del Rocio, 41013, Sevilla, Spain. joaquin.dopazo@juntadeandalucia.es","institution_ids":["https://openalex.org/I4210133602"]},{"raw_affiliation_string":"FPS/ELIXIR-es, Hospital Virgen del Roc\u00edo, 42013, Sevilla, Spain. joaquin.dopazo@juntadeandalucia.es","institution_ids":["https://openalex.org/I4210153139"]},{"raw_affiliation_string":"Clinical Bioinformatics Area. Fundaci\u00f3n Progreso y Salud (FPS). CDCA, Hospital Virgen del Rocio, 41013, Sevilla, Spain","institution_ids":["https://openalex.org/I4210086910"]},{"raw_affiliation_string":"Computational Systems Medicine, Institute of Biomedicine of Seville (IBIS), Hospital Virgen del Rocio, 41013, Sevilla, Spain","institution_ids":["https://openalex.org/I4210133602"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5057460152","display_name":"Isabel Nepomuceno","orcid":null},"institutions":[{"id":"https://openalex.org/I79238269","display_name":"Universidad de Sevilla","ror":"https://ror.org/03yxnpp24","country_code":"ES","type":"education","lineage":["https://openalex.org/I79238269"]}],"countries":["ES"],"is_corresponding":true,"raw_author_name":"Isabel Nepomuceno","raw_affiliation_strings":["Department of Computer Languages and Systems, Universidad de Sevilla, Sevilla, Spain. inepomuceno@us.es","Department of Computer Languages and Systems, Universidad de Sevilla, Sevilla, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Languages and Systems, Universidad de Sevilla, Sevilla, Spain. inepomuceno@us.es","institution_ids":["https://openalex.org/I79238269"]},{"raw_affiliation_string":"Department of Computer Languages and Systems, Universidad de Sevilla, Sevilla, Spain","institution_ids":["https://openalex.org/I79238269"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5057460152"],"corresponding_institution_ids":["https://openalex.org/I79238269"],"apc_list":{"value":2490,"currency":"USD","value_usd":2490},"apc_paid":{"value":2490,"currency":"USD","value_usd":2490},"fwci":0.9411,"has_fulltext":true,"cited_by_count":17,"citation_normalized_percentile":{"value":0.71730899,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":95,"max":99},"biblio":{"volume":"15","issue":"1","first_page":"1","last_page":"1"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9987999796867371,"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":0.9987999796867371,"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/T12859","display_name":"Cell Image Analysis Techniques","score":0.00039999998989515007,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.00019999999494757503,"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/curse-of-dimensionality","display_name":"Curse of dimensionality","score":0.730214536190033},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6646916270256042},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.5608282089233398},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.517688512802124},{"id":"https://openalex.org/keywords/rna-seq","display_name":"RNA-Seq","score":0.5118383765220642},{"id":"https://openalex.org/keywords/deep-neural-networks","display_name":"Deep neural networks","score":0.4587119221687317},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3653195798397064},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.35853883624076843},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.358238160610199},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.13433349132537842},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.09669435024261475},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.07854488492012024}],"concepts":[{"id":"https://openalex.org/C111030470","wikidata":"https://www.wikidata.org/wiki/Q1430460","display_name":"Curse of dimensionality","level":2,"score":0.730214536190033},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6646916270256042},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.5608282089233398},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.517688512802124},{"id":"https://openalex.org/C107397762","wikidata":"https://www.wikidata.org/wiki/Q2542347","display_name":"RNA-Seq","level":5,"score":0.5118383765220642},{"id":"https://openalex.org/C2984842247","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep neural networks","level":3,"score":0.4587119221687317},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3653195798397064},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.35853883624076843},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.358238160610199},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.13433349132537842},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.09669435024261475},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.07854488492012024},{"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":6,"locations":[{"id":"doi:10.1186/s13040-021-00285-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13040-021-00285-4","pdf_url":null,"source":{"id":"https://openalex.org/S84409260","display_name":"BioData Mining","issn_l":"1756-0381","issn":["1756-0381"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BioData Mining","raw_type":"journal-article"},{"id":"pmid:34980200","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34980200","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BioData mining","raw_type":null},{"id":"pmh:oai:www.repositoriosalud.es:10668/20345","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8722116/pdf","pdf_url":"https://biodatamining.biomedcentral.com/track/pdf/10.1186/s13040-021-00285-4","source":{"id":"https://openalex.org/S4377196114","display_name":"RISalud Institutional Health Repository of Andaluc\u00eda","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"research article"},{"id":"pmh:oai:digital.csic.es:10261/306450","is_oa":true,"landing_page_url":"http://hdl.handle.net/10261/306450","pdf_url":null,"source":{"id":"https://openalex.org/S4306400616","display_name":"DIGITAL.CSIC (Spanish National Research Council (CSIC))","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I134820265","host_organization_name":"Consejo Superior de Investigaciones Cient\u00edficas","host_organization_lineage":["https://openalex.org/I134820265"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"http://purl.org/coar/resource_type/c_6501"},{"id":"pmh:oai:doaj.org/article:d5ab8bb5c22a4544ac5826faa5b2375e","is_oa":true,"landing_page_url":"https://doaj.org/article/d5ab8bb5c22a4544ac5826faa5b2375e","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BioData Mining, Vol 15, Iss 1, Pp 1-21 (2022)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:8722116","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8722116","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BioData Min","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s13040-021-00285-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13040-021-00285-4","pdf_url":null,"source":{"id":"https://openalex.org/S84409260","display_name":"BioData Mining","issn_l":"1756-0381","issn":["1756-0381"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BioData Mining","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1673840378","display_name":null,"funder_award_id":"813533","funder_id":"https://openalex.org/F4320332999","funder_display_name":"Horizon 2020 Framework Programme"},{"id":"https://openalex.org/G1826204064","display_name":null,"funder_award_id":"PAIDI 2020","funder_id":"https://openalex.org/F4320326754","funder_display_name":"Junta de Andaluc\u00eda"},{"id":"https://openalex.org/G1887561806","display_name":null,"funder_award_id":"GA 813533","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G1888088267","display_name":null,"funder_award_id":"2014-2020\u2019","funder_id":"https://openalex.org/F4320335322","funder_display_name":"European Regional Development Fund"},{"id":"https://openalex.org/G1953887145","display_name":null,"funder_award_id":"2014\u20102020","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G2014934320","display_name":null,"funder_award_id":"PAIDI2020- DOC_00350","funder_id":"https://openalex.org/F4320326754","funder_display_name":"Junta de Andaluc\u00eda"},{"id":"https://openalex.org/G2131588728","display_name":null,"funder_award_id":"PID2020-117979RB-I00","funder_id":"https://openalex.org/F4320335322","funder_display_name":"European Regional Development Fund"},{"id":"https://openalex.org/G2426432956","display_name":null,"funder_award_id":"20142020","funder_id":"https://openalex.org/F4320338080","funder_display_name":"European Social Fund"},{"id":"https://openalex.org/G2628364946","display_name":null,"funder_award_id":"H2020","funder_id":"https://openalex.org/F4320335322","funder_display_name":"European Regional Development Fund"},{"id":"https://openalex.org/G4937468798","display_name":null,"funder_award_id":"H2020","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G5382548124","display_name":"Machine Learning Frontiers in Precision Medicine","funder_award_id":"813533","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G5805502524","display_name":null,"funder_award_id":"PID2020","funder_id":"https://openalex.org/F4320322930","funder_display_name":"Ministerio de Ciencia e Innovaci\u00f3n"},{"id":"https://openalex.org/G6633821123","display_name":null,"funder_award_id":"PAIDI2020- DOC_00350","funder_id":"https://openalex.org/F4320321562","funder_display_name":"Consejer\u00eda de Econom\u00eda, Innovaci\u00f3n, Ciencia y Empleo, Junta de Andaluc\u00eda"},{"id":"https://openalex.org/G7112497438","display_name":null,"funder_award_id":"PAIDI2020","funder_id":"https://openalex.org/F4320335322","funder_display_name":"European Regional Development Fund"},{"id":"https://openalex.org/G7571898700","display_name":null,"funder_award_id":"PID2020-117979RB-I00","funder_id":"https://openalex.org/F4320322930","funder_display_name":"Ministerio de Ciencia e Innovaci\u00f3n"},{"id":"https://openalex.org/G7775766736","display_name":"Machine Learning Frontiers in Precision Medicine","funder_award_id":"813533","funder_id":"https://openalex.org/F4320338337","funder_display_name":"H2020 Marie Sk\u0142odowska-Curie Actions"},{"id":"https://openalex.org/G8824911526","display_name":null,"funder_award_id":"H2020","funder_id":"https://openalex.org/F4320334923","funder_display_name":"Instituto de Salud Carlos III"}],"funders":[{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320321562","display_name":"Consejer\u00eda de Econom\u00eda, Innovaci\u00f3n, Ciencia y Empleo, Junta de Andaluc\u00eda","ror":"https://ror.org/03kak1729"},{"id":"https://openalex.org/F4320322930","display_name":"Ministerio de Ciencia e Innovaci\u00f3n","ror":"https://ror.org/034900433"},{"id":"https://openalex.org/F4320326754","display_name":"Junta de Andaluc\u00eda","ror":"https://ror.org/01jem9c82"},{"id":"https://openalex.org/F4320332999","display_name":"Horizon 2020 Framework Programme","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320334923","display_name":"Instituto de Salud Carlos III","ror":"https://ror.org/00ca2c886"},{"id":"https://openalex.org/F4320335322","display_name":"European Regional Development Fund","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320338080","display_name":"European Social Fund","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320338337","display_name":"H2020 Marie Sk\u0142odowska-Curie Actions","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":49,"referenced_works":["https://openalex.org/W1552434751","https://openalex.org/W1598738229","https://openalex.org/W1816311090","https://openalex.org/W1965862237","https://openalex.org/W1966116114","https://openalex.org/W1967799729","https://openalex.org/W1981509058","https://openalex.org/W1992971293","https://openalex.org/W2034837473","https://openalex.org/W2036272952","https://openalex.org/W2058645214","https://openalex.org/W2064469303","https://openalex.org/W2069295116","https://openalex.org/W2077874719","https://openalex.org/W2080234361","https://openalex.org/W2110065044","https://openalex.org/W2124342162","https://openalex.org/W2124388496","https://openalex.org/W2151763757","https://openalex.org/W2152692691","https://openalex.org/W2302476265","https://openalex.org/W2341128841","https://openalex.org/W2516756255","https://openalex.org/W2529340146","https://openalex.org/W2559588208","https://openalex.org/W2582393724","https://openalex.org/W2735067671","https://openalex.org/W2741564801","https://openalex.org/W2796170779","https://openalex.org/W2800410670","https://openalex.org/W2866450277","https://openalex.org/W2892475218","https://openalex.org/W2898830231","https://openalex.org/W2902652978","https://openalex.org/W2904997892","https://openalex.org/W2937917790","https://openalex.org/W2944869129","https://openalex.org/W2949272108","https://openalex.org/W2970012271","https://openalex.org/W2982521190","https://openalex.org/W2989747508","https://openalex.org/W3000045279","https://openalex.org/W3001040093","https://openalex.org/W3016020856","https://openalex.org/W3037937919","https://openalex.org/W3041129226","https://openalex.org/W3047163763","https://openalex.org/W3127452014","https://openalex.org/W3196939060"],"related_works":["https://openalex.org/W4296209631","https://openalex.org/W2561617217","https://openalex.org/W2025378473","https://openalex.org/W4394426846","https://openalex.org/W2355801475","https://openalex.org/W4206659427","https://openalex.org/W2170062176","https://openalex.org/W4200033037","https://openalex.org/W2148135840","https://openalex.org/W106004901"],"abstract_inverted_index":{"BACKGROUND:":[0],"Single-cell":[1],"RNA":[2],"sequencing":[3],"(scRNA-seq)":[4],"data":[5,31],"provide":[6,268],"valuable":[7],"insights":[8],"into":[9],"cellular":[10],"heterogeneity":[11],"which":[12,256],"is":[13,33],"significantly":[14],"improving":[15],"the":[16,26,34,49,61,69,97,105,126,129,135,158,161,166,183,225,230,240,252,289,296,299,302,324,329,336,347],"current":[17],"knowledge":[18,294],"on":[19,139,260],"biology":[20],"and":[21,40,145,185,237],"human":[22,144,243,356],"disease.":[23],"One":[24],"of":[25,29,36,66,96,113,128,141,143,151,160,242,254,284,291,301,311,326,335,346],"main":[27],"applications":[28],"scRNA-seq":[30,130,285],"analysis":[32],"identification":[35],"new":[37],"cell":[38,41,178,190,245,342],"types":[39,112,179,191],"states.":[42],"Deep":[43],"neural":[44,79,107],"networks":[45,108],"(DNNs)":[46],"are":[47,180],"among":[48],"best":[50],"methods":[51],"to":[52,81,124,156,174,204,207,235,238,278,316,341],"address":[53],"this":[54,57,72,101,312],"problem.":[55,199],"However,":[56],"performance":[58,159,310],"comes":[59],"with":[60,265,314,352,355],"trade-off":[62],"for":[63],"a":[64,92,122,149,194,197,280,308],"lack":[65],"interpretability":[67,334],"in":[68,154,196,274,295],"results.":[70],"In":[71,100,287],"work":[73],"we":[74,103,164,222,249],"propose":[75],"an":[76,269,275,321,353],"intelligible":[77],"pathway-driven":[78],"network":[80,231,303],"correctly":[82,188],"solve":[83],"cell-type":[84],"related":[85],"problems":[86],"at":[87],"single-cell":[88],"resolution":[89],"while":[90],"providing":[91],"biologically":[93,281],"meaningful":[94,282],"representation":[95,283],"data.":[98,131,220,286],"RESULTS:":[99],"study,":[102],"explored":[104],"deep":[106],"constrained":[109,213],"by":[110,182,192,214,229,338,344],"several":[111],"prior":[114,292],"biological":[115,293],"information,":[116,120],"e.g.":[117],"signaling":[118],"pathway":[119,348],"as":[121,350],"way":[123],"reduce":[125],"dimensionality":[127],"We":[132],"have":[133],"tested":[134,165],"proposed":[136],"biologically-based":[137],"architectures":[138],"thousands":[140],"cells":[142],"mouse":[146],"origin":[147],"across":[148,168],"collection":[150],"public":[152],"datasets":[153],"order":[155],"check":[157],"model.":[162],"Specifically,":[163],"architecture":[167],"different":[169],"validation":[170],"scenarios":[171],"that":[172,267],"try":[173],"mimic":[175],"how":[176,186,224,251],"unknown":[177],"clustered":[181],"DNN":[184,211,297,330],"it":[187],"annotates":[189],"querying":[193],"database":[195],"retrieval":[198],"Moreover,":[200],"our":[201],"approach":[202,313],"demonstrated":[203,351],"be":[205,233],"comparable":[206],"other":[208,317],"less":[209],"interpretable":[210],"approaches":[212],"using":[215],"protein-protein":[216],"interactions":[217],"gene":[218],"regulation":[219],"Finally,":[221],"show":[223],"latent":[226],"structure":[227,331],"learned":[228],"could":[232],"used":[234],"visualize":[236],"interpret":[239],"composition":[241],"single":[244],"datasets.":[246],"CONCLUSIONS:":[247],"Here":[248],"demonstrate":[250,307],"integration":[253],"pathways,":[255],"convey":[257],"fundamental":[258],"information":[259],"functional":[261],"relationships":[262],"between":[263],"genes,":[264],"DNNs,":[266],"excellent":[270,276],"classification":[271],"framework,":[272],"results":[273,306,337],"alternative":[277],"learn":[279],"addition,":[288],"introduction":[290],"reduces":[298],"size":[300],"architecture.":[304],"Comparative":[305],"superior":[309],"respect":[315],"similar":[318],"approaches.":[319],"As":[320],"additional":[322],"advantage,":[323],"use":[325],"pathways":[327],"within":[328],"enables":[332],"easy":[333],"connecting":[339],"features":[340],"functionalities":[343],"means":[345],"nodes,":[349],"example":[354],"melanoma":[357],"tumor":[358],"cells.":[359]},"counts_by_year":[{"year":2026,"cited_by_count":5},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":3}],"updated_date":"2026-08-01T09:00:35.917206","created_date":"2025-10-10T00:00:00"}
