{"id":"https://openalex.org/W4412876816","doi":"https://doi.org/10.1145/3711896.3737000","title":"Identifying Combinatorial Regulatory Genes for Cell Fate Decision via Reparameterizable Subset Explanations","display_name":"Identifying Combinatorial Regulatory Genes for Cell Fate Decision via Reparameterizable Subset Explanations","publication_year":2025,"publication_date":"2025-08-03","ids":{"openalex":"https://openalex.org/W4412876816","doi":"https://doi.org/10.1145/3711896.3737000","pmid":"https://pubmed.ncbi.nlm.nih.gov/41426294"},"language":"en","primary_location":{"id":"doi:10.1145/3711896.3737000","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3711896.3737000","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/3711896.3737000","source":null,"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 31st ACM SIGKDD Conference on Knowledge Discovery and Data Mining V.2","raw_type":"proceedings-article"},"type":"conference-paper","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://dl.acm.org/doi/pdf/10.1145/3711896.3737000","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":null,"display_name":"Junhao Liu","orcid":"https://orcid.org/0009-0007-3694-7799"},"institutions":[{"id":"https://openalex.org/I204250578","display_name":"University of California, Irvine","ror":"https://ror.org/04gyf1771","country_code":"US","type":"education","lineage":["https://openalex.org/I204250578"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Junhao Liu","raw_affiliation_strings":["Department of Computer Science, University of California, Irvine, Irvine, CA, USA"],"raw_orcid":"https://orcid.org/0009-0007-3694-7799","affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of California, Irvine, Irvine, CA, USA","institution_ids":["https://openalex.org/I204250578"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Pengpeng Zhang","orcid":"https://orcid.org/0009-0009-9028-2163"},"institutions":[{"id":"https://openalex.org/I204250578","display_name":"University of California, Irvine","ror":"https://ror.org/04gyf1771","country_code":"US","type":"education","lineage":["https://openalex.org/I204250578"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Pengpeng Zhang","raw_affiliation_strings":["Department of Computer Science, University of California, Irvine, Irvine, CA, USA"],"raw_orcid":"https://orcid.org/0009-0009-9028-2163","affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of California, Irvine, Irvine, CA, USA","institution_ids":["https://openalex.org/I204250578"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065576006","display_name":"Martin Renqiang Min","orcid":"https://orcid.org/0000-0002-8563-6133"},"institutions":[{"id":"https://openalex.org/I2800295664","display_name":"RCA (United States)","ror":"https://ror.org/010k8n340","country_code":"US","type":"company","lineage":["https://openalex.org/I2800295664"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Martin Renqiang Min","raw_affiliation_strings":["Department of Machine Learning, NEC Laboratories America, Princeton, New Jersey, USA"],"raw_orcid":"https://orcid.org/0000-0002-8563-6133","affiliations":[{"raw_affiliation_string":"Department of Machine Learning, NEC Laboratories America, Princeton, New Jersey, USA","institution_ids":["https://openalex.org/I2800295664"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100345410","display_name":"Jing Zhang","orcid":"https://orcid.org/0000-0002-5970-0509"},"institutions":[{"id":"https://openalex.org/I204250578","display_name":"University of California, Irvine","ror":"https://ror.org/04gyf1771","country_code":"US","type":"education","lineage":["https://openalex.org/I204250578"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jing Zhang","raw_affiliation_strings":["Department of Computer Science, University of California, Irvine, Irvine, CA, USA"],"raw_orcid":"https://orcid.org/0000-0002-5970-0509","affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of California, Irvine, Irvine, CA, USA","institution_ids":["https://openalex.org/I204250578"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":"2025","issue":"v2","first_page":"1823","last_page":"1832"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9972000122070312,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9972000122070312,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9962000250816345,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9908999800682068,"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/computational-biology","display_name":"Computational biology","score":0.518166184425354},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.493356853723526},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4735412001609802},{"id":"https://openalex.org/keywords/cell-fate-determination","display_name":"Cell fate determination","score":0.4463026523590088},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.4110921621322632},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2962878942489624},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.21515902876853943},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.13599246740341187},{"id":"https://openalex.org/keywords/transcription-factor","display_name":"Transcription factor","score":0.12413844466209412}],"concepts":[{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.518166184425354},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.493356853723526},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4735412001609802},{"id":"https://openalex.org/C163952510","wikidata":"https://www.wikidata.org/wiki/Q5058196","display_name":"Cell fate determination","level":4,"score":0.4463026523590088},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.4110921621322632},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2962878942489624},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.21515902876853943},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.13599246740341187},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.12413844466209412}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1145/3711896.3737000","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3711896.3737000","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/3711896.3737000","source":null,"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 31st ACM SIGKDD Conference on Knowledge Discovery and Data Mining V.2","raw_type":"proceedings-article"},{"id":"pmid:41426294","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41426294","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":"KDD : proceedings. International Conference on Knowledge Discovery & Data Mining","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:12718083","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12718083/","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"KDD","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1145/3711896.3737000","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3711896.3737000","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/3711896.3737000","source":null,"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 31st ACM SIGKDD Conference on Knowledge Discovery and Data Mining V.2","raw_type":"proceedings-article"},"sustainable_development_goals":[{"display_name":"Peace, Justice and strong institutions","score":0.6399999856948853,"id":"https://metadata.un.org/sdg/16"}],"awards":[{"id":"https://openalex.org/G4423082541","display_name":null,"funder_award_id":"R01 NS128523","funder_id":"https://openalex.org/F4320337359","funder_display_name":"National Institute of Neurological Disorders and Stroke"},{"id":"https://openalex.org/G4902214262","display_name":null,"funder_award_id":"R01HG012572","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G5050595528","display_name":null,"funder_award_id":"R01NS128523","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G6615661663","display_name":null,"funder_award_id":"R01HG012572, R01NS128523","funder_id":"https://openalex.org/F4320323817","funder_display_name":"Universitas Brawijaya"},{"id":"https://openalex.org/G7571595803","display_name":null,"funder_award_id":"R01 HG012572","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"}],"funders":[{"id":"https://openalex.org/F4320323817","display_name":"Universitas Brawijaya","ror":"https://ror.org/01wk3d929"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337348","display_name":"National Human Genome Research Institute","ror":"https://ror.org/00baak391"},{"id":"https://openalex.org/F4320337359","display_name":"National Institute of Neurological Disorders and Stroke","ror":"https://ror.org/01s5ya894"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4412876816.pdf","grobid_xml":"https://content.openalex.org/works/W4412876816.grobid-xml"},"referenced_works_count":22,"referenced_works":["https://openalex.org/W2062691001","https://openalex.org/W2095433609","https://openalex.org/W2282821441","https://openalex.org/W2518828632","https://openalex.org/W2576771314","https://openalex.org/W2766437506","https://openalex.org/W2911279170","https://openalex.org/W2925075625","https://openalex.org/W2963399068","https://openalex.org/W2964121744","https://openalex.org/W2990138404","https://openalex.org/W3043058782","https://openalex.org/W3130693295","https://openalex.org/W3177442486","https://openalex.org/W4205496949","https://openalex.org/W4210575300","https://openalex.org/W4220833476","https://openalex.org/W4285588672","https://openalex.org/W4293861706","https://openalex.org/W4297826903","https://openalex.org/W4310437432","https://openalex.org/W4403577864"],"related_works":["https://openalex.org/W4387095958","https://openalex.org/W4395035150","https://openalex.org/W4387096221","https://openalex.org/W4366722611","https://openalex.org/W4393191903","https://openalex.org/W4387096200","https://openalex.org/W4387096194","https://openalex.org/W1985607197","https://openalex.org/W4281759407","https://openalex.org/W4390011121"],"abstract_inverted_index":{"Cell":[0],"fate":[1,43,62,107,122],"decisions":[2],"are":[3],"highly":[4],"coordinated":[5],"processes":[6],"governed":[7],"by":[8,101],"complex":[9],"interactions":[10,155],"among":[11],"numerous":[12],"regulatory":[13,57,138,147],"genes,":[14,148],"while":[15],"disruptions":[16],"in":[17,131],"these":[18,66],"mechanisms":[19],"can":[20],"lead":[21],"to":[22,31,39,82],"developmental":[23,133,176],"abnormalities":[24],"and":[25,72,113,118,135,171,178],"disease.":[26],"Traditional":[27],"methods":[28,130],"often":[29],"fail":[30],"capture":[32],"such":[33],"combinatorial":[34,137],"interactions,":[35],"limiting":[36],"their":[37],"ability":[38],"fully":[40],"model":[41],"cell":[42,61,106,121,157],"dynamics.":[44,108],"Here,":[45],"we":[46],"introduce":[47],"MetaVelo,":[48],"a":[49,69,74,91,169],"global":[50],"feature":[51],"explanation":[52],"framework":[53,173],"for":[54,174],"identifying":[55,136],"key":[56],"gene":[58,139,154],"sets":[59],"influencing":[60],"transitions.":[63],"MetaVelo":[64,96,141,167],"models":[65,123],"transitions":[67],"as":[68,90],"black-box":[70,120],"function":[71],"employs":[73],"differentiable":[75],"neural":[76],"ordinary":[77],"differential":[78],"equation":[79],"(ODE)":[80],"surrogate":[81],"enable":[83],"efficient":[84],"optimization.":[85],"By":[86],"reparameterizing":[87],"the":[88,98,102,153,160],"problem":[89],"controllable":[92],"data":[93],"generation":[94],"process,":[95],"overcomes":[97],"challenges":[99],"posed":[100],"non-differentiable":[103],"nature":[104],"of":[105,163],"Benchmarking":[109],"across":[110],"diverse":[111],"stand-alone":[112],"longitudinal":[114],"single-cell":[115,165],"RNA-seq":[116],"datasets":[117],"three":[119],"demonstrates":[124],"its":[125],"superiority":[126],"over":[127],"12":[128],"baseline":[129],"predicting":[132],"trajectories":[134],"sets.":[140],"further":[142],"distinguishes":[143],"independent":[144],"from":[145],"synergistic":[146],"offering":[149],"novel":[150],"insights":[151],"into":[152],"governing":[156],"fate.":[158],"With":[159],"growing":[161],"availability":[162],"high-resolution":[164],"data,":[166],"provides":[168],"scalable":[170],"effective":[172],"advancing":[175],"biology":[177],"therapeutic":[179],"applications.":[180]},"counts_by_year":[],"updated_date":"2026-07-14T23:27:15.235271","created_date":"2025-10-10T00:00:00"}