{"id":"https://openalex.org/W4409199145","doi":"https://doi.org/10.1016/j.cels.2025.101245","title":"Explainable modeling of single-cell perturbation data using attention and sparse dictionary learning","display_name":"Explainable modeling of single-cell perturbation data using attention and sparse dictionary learning","publication_year":2025,"publication_date":"2025-04-01","ids":{"openalex":"https://openalex.org/W4409199145","doi":"https://doi.org/10.1016/j.cels.2025.101245","pmid":"https://pubmed.ncbi.nlm.nih.gov/40187352"},"language":"en","primary_location":{"id":"doi:10.1016/j.cels.2025.101245","doi":"https://doi.org/10.1016/j.cels.2025.101245","is_oa":false,"landing_page_url":"https://doi.org/10.1016/j.cels.2025.101245","pdf_url":null,"source":{"id":"https://openalex.org/S2764739556","display_name":"Cell Systems","issn_l":"2405-4712","issn":["2405-4712","2405-4720","2639-5460"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","dongbi-b","jufo-2","ki-jl-2","medline","norway-1","poland-200","russia-white-list-1"],"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Cell Systems","raw_type":"journal-article"},"volume":null,"type":"article","indexed_in":["crossref","pubmed"],"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/A5061974076","display_name":"Yang Xu","orcid":"https://orcid.org/0000-0003-4173-4337","observed_orcids":["https://orcid.org/0000-0003-4173-4337"]},"institutions":[{"id":"https://openalex.org/I107606265","display_name":"Broad Institute","ror":"https://ror.org/05a0ya142","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I107606265"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Yang Xu","raw_affiliation_strings":["Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA. Electronic address: yxu@broadinstitute.org"],"raw_orcid":"https://orcid.org/0000-0003-4173-4337","affiliations":[{"raw_affiliation_string":"Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA. Electronic address: yxu@broadinstitute.org","institution_ids":["https://openalex.org/I107606265"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Stephen Fleming","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I107606265","display_name":"Broad Institute","ror":"https://ror.org/05a0ya142","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I107606265"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Stephen Fleming","raw_affiliation_strings":["Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA. Electronic address: sfleming@broadinstitute.org"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA. Electronic address: sfleming@broadinstitute.org","institution_ids":["https://openalex.org/I107606265"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033088281","display_name":"Matthew Tegtmeyer","orcid":"https://orcid.org/0000-0002-9032-8207","observed_orcids":["https://orcid.org/0000-0002-9032-8207"]},"institutions":[{"id":"https://openalex.org/I107606265","display_name":"Broad Institute","ror":"https://ror.org/05a0ya142","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I107606265"]},{"id":"https://openalex.org/I4392738323","display_name":"Stanley Center for Psychiatric Research","ror":"https://ror.org/01tm9b530","country_code":"US","type":"facility","lineage":["https://openalex.org/I107606265","https://openalex.org/I4392738323"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Matthew Tegtmeyer","raw_affiliation_strings":["Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA","institution_ids":["https://openalex.org/I107606265","https://openalex.org/I4392738323"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5072347906","display_name":"Steven A. McCarroll","orcid":"https://orcid.org/0000-0002-6954-8184","observed_orcids":["https://orcid.org/0000-0002-6954-8184"]},"institutions":[{"id":"https://openalex.org/I107606265","display_name":"Broad Institute","ror":"https://ror.org/05a0ya142","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I107606265"]},{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]},{"id":"https://openalex.org/I4392738323","display_name":"Stanley Center for Psychiatric Research","ror":"https://ror.org/01tm9b530","country_code":"US","type":"facility","lineage":["https://openalex.org/I107606265","https://openalex.org/I4392738323"]},{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Steven A. McCarroll","raw_affiliation_strings":["Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA; Department of Genetics, Harvard Medical School, Boston, MA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA; Department of Genetics, Harvard Medical School, Boston, MA, USA","institution_ids":["https://openalex.org/I107606265","https://openalex.org/I136199984","https://openalex.org/I4392738323","https://openalex.org/I63966007"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5084590772","display_name":"Mehrtash Babadi","orcid":"https://orcid.org/0000-0003-1829-8397","observed_orcids":["https://orcid.org/0000-0003-1829-8397"]},"institutions":[{"id":"https://openalex.org/I107606265","display_name":"Broad Institute","ror":"https://ror.org/05a0ya142","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I107606265"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Mehrtash Babadi","raw_affiliation_strings":["Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA. Electronic address: mehrtash@broadinstitute.org"],"raw_orcid":"https://orcid.org/0000-0003-1829-8397","affiliations":[{"raw_affiliation_string":"Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA. Electronic address: mehrtash@broadinstitute.org","institution_ids":["https://openalex.org/I107606265"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5061974076","https://openalex.org/A5084590772"],"corresponding_institution_ids":["https://openalex.org/I107606265"],"apc_list":{"value":9350,"currency":"USD","value_usd":9350},"apc_paid":null,"fwci":2.3868,"has_fulltext":false,"cited_by_count":8,"citation_normalized_percentile":{"value":0.88767765,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":99},"biblio":{"volume":"16","issue":"4","first_page":"101245","last_page":"101245"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9990000128746033,"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":0.9990000128746033,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.0005000000237487257,"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":0.0,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/single-cell-perturbation","display_name":"single-cell perturbation","score":0.8709999918937683},{"id":"https://openalex.org/keywords/single-cell-transcriptomics","display_name":"single-cell transcriptomics","score":0.9160000085830688},{"id":"https://openalex.org/keywords/deep-generative-models","display_name":"deep generative models","score":0.8259999752044678},{"id":"https://openalex.org/keywords/dictionary-learning","display_name":"dictionary learning","score":0.9509999752044678},{"id":"https://openalex.org/keywords/attention-mechanism","display_name":"attention mechanism","score":0.9520000219345093},{"id":"https://openalex.org/keywords/model-interpretability","display_name":"model interpretability","score":0.7049999833106995},{"id":"https://openalex.org/keywords/heterogeneous-reactions","display_name":"heterogeneous reactions","score":0.753000020980835},{"id":"https://openalex.org/keywords/genetic-perturbation","display_name":"gene perturbation","score":0.9800000190734863}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5261865854263306},{"id":"https://openalex.org/C177918212","wikidata":"https://www.wikidata.org/wiki/Q803623","display_name":"Perturbation (astronomy)","level":2,"score":0.4203588366508484},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4097200632095337},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.40834105014801025},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.10340157151222229},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1016/j.cels.2025.101245","doi":"https://doi.org/10.1016/j.cels.2025.101245","is_oa":false,"landing_page_url":"https://doi.org/10.1016/j.cels.2025.101245","pdf_url":null,"source":{"id":"https://openalex.org/S2764739556","display_name":"Cell Systems","issn_l":"2405-4712","issn":["2405-4712","2405-4720","2639-5460"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","dongbi-b","jufo-2","ki-jl-2","medline","norway-1","poland-200","russia-white-list-1"],"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Cell Systems","raw_type":"journal-article"},{"id":"pmid:40187352","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40187352","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,"listed_in":[],"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":"Cell systems","raw_type":"Journal Article"}],"best_oa_location":null,"sustainable_development_goals":[],"sustainable_development_goals_aurora":[{"id":"https://metadata.un.org/sdg/13","display_name":"Climate action","score":0.49000000953674316}],"study_designs":[],"awards":[{"id":"https://openalex.org/G2098963522","display_name":"Genetic neuroscience: How human genes and alleles shape neuronal phenotypes","funder_award_id":"U01MH115727","funder_id":"https://openalex.org/F4320337346","funder_display_name":"National Institute of Mental Health"},{"id":"https://openalex.org/G9000873547","display_name":"An Atlas of Human Brain Cell Variation","funder_award_id":"UM1MH130966","funder_id":"https://openalex.org/F4320337346","funder_display_name":"National Institute of Mental Health"}],"funders":[{"id":"https://openalex.org/F4320306080","display_name":"Foundation for the National Institutes of Health","ror":"https://ror.org/00k86s890"},{"id":"https://openalex.org/F4320314070","display_name":"Broad Institute","ror":"https://ror.org/05a0ya142"},{"id":"https://openalex.org/F4320337346","display_name":"National Institute of Mental Health","ror":"https://ror.org/04xeg9z08"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":46,"referenced_works":["https://openalex.org/W1882958252","https://openalex.org/W1959608418","https://openalex.org/W2045440724","https://openalex.org/W2101234009","https://openalex.org/W2102212449","https://openalex.org/W2105712639","https://openalex.org/W2128080663","https://openalex.org/W2154368244","https://openalex.org/W2190545194","https://openalex.org/W2559960543","https://openalex.org/W2561754210","https://openalex.org/W2572662684","https://openalex.org/W2577994754","https://openalex.org/W2579277680","https://openalex.org/W2626778328","https://openalex.org/W2762349056","https://openalex.org/W2788348358","https://openalex.org/W2800392236","https://openalex.org/W2901677030","https://openalex.org/W2946173685","https://openalex.org/W2951084686","https://openalex.org/W2951506174","https://openalex.org/W2965552103","https://openalex.org/W2969093152","https://openalex.org/W2970971581","https://openalex.org/W3000145506","https://openalex.org/W3010865323","https://openalex.org/W3012280517","https://openalex.org/W3027051073","https://openalex.org/W3043086101","https://openalex.org/W3110917833","https://openalex.org/W3127234302","https://openalex.org/W3170265427","https://openalex.org/W4210587306","https://openalex.org/W4282024710","https://openalex.org/W4294216483","https://openalex.org/W4318981406","https://openalex.org/W4319591822","https://openalex.org/W4375955255","https://openalex.org/W4385638616","https://openalex.org/W4385638791","https://openalex.org/W4385955324","https://openalex.org/W4387130415","https://openalex.org/W4391262585","https://openalex.org/W4412160990","https://openalex.org/W6893279185"],"related_works":["https://openalex.org/W4392885893","https://openalex.org/W4409348663","https://openalex.org/W7222034778","https://openalex.org/W3153727370","https://openalex.org/W7164826513","https://openalex.org/W7010024406","https://openalex.org/W3170265427","https://openalex.org/W4395482102","https://openalex.org/W7204170755","https://openalex.org/W7165123812"],"abstract_inverted_index":null,"counts_by_year":[{"year":2026,"cited_by_count":5},{"year":2025,"cited_by_count":3}],"updated_date":"2026-10-31T12:09:11.096373","created_date":"2025-04-06T00:00:00"}
