{"id":"https://openalex.org/W4387346503","doi":"https://doi.org/10.1145/3584371.3612972","title":"Root Causal Inference from Single Cell RNA Sequencing with the Negative Binomial","display_name":"Root Causal Inference from Single Cell RNA Sequencing with the Negative Binomial","publication_year":2023,"publication_date":"2023-09-03","ids":{"openalex":"https://openalex.org/W4387346503","doi":"https://doi.org/10.1145/3584371.3612972"},"language":"en","primary_location":{"id":"doi:10.1145/3584371.3612972","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3584371.3612972","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/3584371.3612972","source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 14th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://dl.acm.org/doi/pdf/10.1145/3584371.3612972","any_repository_has_fulltext":null},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5116568400","display_name":"Eric V Strobl","orcid":"https://orcid.org/0009-0003-9894-9694"},"institutions":[{"id":"https://openalex.org/I901861585","display_name":"Vanderbilt University Medical Center","ror":"https://ror.org/05dq2gs74","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210162197","https://openalex.org/I901861585"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Eric Strobl","raw_affiliation_strings":["Vanderbilt University Medical Center, Nashville, USA"],"raw_orcid":"https://orcid.org/0009-0003-9894-9694","affiliations":[{"raw_affiliation_string":"Vanderbilt University Medical Center, Nashville, USA","institution_ids":["https://openalex.org/I901861585"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5116568400"],"corresponding_institution_ids":["https://openalex.org/I901861585"],"apc_list":null,"apc_paid":null,"fwci":0.8997,"has_fulltext":true,"cited_by_count":6,"citation_normalized_percentile":{"value":0.75488219,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":97},"biblio":{"volume":null,"issue":null,"first_page":"1","last_page":"10"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9994000196456909,"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":0.9994000196456909,"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/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.9914000034332275,"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"}},{"id":"https://openalex.org/T12072","display_name":"Machine Learning and Algorithms","score":0.9886999726295471,"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/negative-binomial-distribution","display_name":"Negative binomial distribution","score":0.8483976125717163},{"id":"https://openalex.org/keywords/causal-inference","display_name":"Causal inference","score":0.660804271697998},{"id":"https://openalex.org/keywords/poisson-distribution","display_name":"Poisson distribution","score":0.6606967449188232},{"id":"https://openalex.org/keywords/poisson-regression","display_name":"Poisson regression","score":0.6396615505218506},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.6215595006942749},{"id":"https://openalex.org/keywords/count-data","display_name":"Count data","score":0.6169155240058899},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.4819943308830261},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.4807726740837097},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.46648386120796204},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.42873436212539673},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3953498303890228},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.0960928201675415}],"concepts":[{"id":"https://openalex.org/C199335787","wikidata":"https://www.wikidata.org/wiki/Q743364","display_name":"Negative binomial distribution","level":3,"score":0.8483976125717163},{"id":"https://openalex.org/C158600405","wikidata":"https://www.wikidata.org/wiki/Q5054566","display_name":"Causal inference","level":2,"score":0.660804271697998},{"id":"https://openalex.org/C100906024","wikidata":"https://www.wikidata.org/wiki/Q205692","display_name":"Poisson distribution","level":2,"score":0.6606967449188232},{"id":"https://openalex.org/C73269764","wikidata":"https://www.wikidata.org/wiki/Q954529","display_name":"Poisson regression","level":3,"score":0.6396615505218506},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.6215595006942749},{"id":"https://openalex.org/C33643355","wikidata":"https://www.wikidata.org/wiki/Q5176731","display_name":"Count data","level":3,"score":0.6169155240058899},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.4819943308830261},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.4807726740837097},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.46648386120796204},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.42873436212539673},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3953498303890228},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.0960928201675415},{"id":"https://openalex.org/C99454951","wikidata":"https://www.wikidata.org/wiki/Q932068","display_name":"Environmental health","level":1,"score":0.0},{"id":"https://openalex.org/C2908647359","wikidata":"https://www.wikidata.org/wiki/Q2625603","display_name":"Population","level":2,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/3584371.3612972","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3584371.3612972","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/3584371.3612972","source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 14th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics","raw_type":"proceedings-article"}],"best_oa_location":{"id":"doi:10.1145/3584371.3612972","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3584371.3612972","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/3584371.3612972","source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 14th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics","raw_type":"proceedings-article"},"sustainable_development_goals":[{"display_name":"Peace, Justice and strong institutions","score":0.8199999928474426,"id":"https://metadata.un.org/sdg/16"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4387346503.pdf"},"referenced_works_count":26,"referenced_works":["https://openalex.org/W74727102","https://openalex.org/W1511751337","https://openalex.org/W1565780262","https://openalex.org/W1996980905","https://openalex.org/W2006305154","https://openalex.org/W2060283360","https://openalex.org/W2071537189","https://openalex.org/W2089819690","https://openalex.org/W2532344160","https://openalex.org/W2580643247","https://openalex.org/W2734950973","https://openalex.org/W2801490189","https://openalex.org/W2886347923","https://openalex.org/W2985613549","https://openalex.org/W2997280954","https://openalex.org/W3000145506","https://openalex.org/W3004765765","https://openalex.org/W3021991336","https://openalex.org/W3047825284","https://openalex.org/W3164861786","https://openalex.org/W4225343266","https://openalex.org/W4226401777","https://openalex.org/W4237961478","https://openalex.org/W4294216483","https://openalex.org/W4308885567","https://openalex.org/W6639928031"],"related_works":["https://openalex.org/W3210390693","https://openalex.org/W1578743158","https://openalex.org/W1849881158","https://openalex.org/W2503331259","https://openalex.org/W4280555366","https://openalex.org/W3134844154","https://openalex.org/W4319841362","https://openalex.org/W2159796125","https://openalex.org/W157392704","https://openalex.org/W2060931646"],"abstract_inverted_index":{"Accurately":[0],"inferring":[1],"the":[2,12,80,94],"root":[3,20,109],"causes":[4],"of":[5,14,39,122],"disease":[6],"from":[7,112],"sequencing":[8,33],"data":[9],"can":[10],"improve":[11],"discovery":[13],"novel":[15,117],"therapeutic":[16],"targets.":[17],"However,":[18],"existing":[19,136],"causal":[21,91,110],"inference":[22],"algorithms":[23],"require":[24],"perfectly":[25],"measured":[26,44],"continuous":[27],"random":[28],"variables.":[29],"Single":[30],"cell":[31],"RNA":[32,96],"(scRNA-seq)":[34],"datasets":[35,114],"contain":[36],"large":[37],"numbers":[38],"cells":[40],"but":[41,87],"nonnegative":[42],"counts":[43],"by":[45,69,115],"an":[46,53],"error":[47,68],"prone":[48],"process.":[49],"We":[50],"therefore":[51],"introduce":[52],"algorithm":[54],"called":[55],"Root":[56],"Causal":[57],"Inference":[58],"with":[59,103],"Negative":[60],"Binomials":[61],"(RCI-NB)":[62],"that":[63,126],"accounts":[64],"for":[65],"count-based":[66],"measurement":[67,129],"separating":[70],"negative":[71],"binomial":[72],"distributions":[73,82],"into":[74],"their":[75],"gamma":[76,81],"and":[77,120],"Poisson":[78,104,128],"components;":[79],"form":[83],"a":[84],"fully":[85],"identifiable":[86],"latent":[88],"post":[89],"non-linear":[90],"model":[92],"representing":[93],"true":[95],"expression":[97],"levels,":[98],"which":[99],"we":[100],"only":[101],"observe":[102],"corruption.":[105],"RCI-NB":[106],"identifies":[107],"patient-specific":[108],"contributions":[111],"scRNA-seq":[113],"integrating":[116],"sparse":[118],"regression":[119],"goodness":[121],"fit":[123],"testing":[124],"procedures":[125],"bypass":[127],"error.":[130],"Experiments":[131],"demonstrate":[132],"significant":[133],"improvements":[134],"over":[135],"alternatives.":[137]},"counts_by_year":[{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":1}],"updated_date":"2025-12-30T23:08:21.542490","created_date":"2025-10-10T00:00:00"}
