{"id":"https://openalex.org/W7155155517","doi":"https://doi.org/10.48550/arxiv.2604.19606","title":"AblateCell: A Reproduce-then-Ablate Agent for Virtual Cell Repositories","display_name":"AblateCell: A Reproduce-then-Ablate Agent for Virtual Cell Repositories","publication_year":2026,"publication_date":"2026-04-21","ids":{"openalex":"https://openalex.org/W7155155517","doi":"https://doi.org/10.48550/arxiv.2604.19606"},"language":null,"primary_location":{"id":"doi:10.48550/arxiv.2604.19606","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2604.19606","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Preprint"},"type":"preprint","indexed_in":["datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://doi.org/10.48550/arxiv.2604.19606","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5134274143","display_name":"Xue Xia","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Xia, Xue","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5070810427","display_name":"Chenxu Yao","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Yao, Chengkai","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5127940198","display_name":"Mingyu Tsoi","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Tsoi, Mingyu","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5127911066","display_name":"Xinjie Mao","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Mao, Xinjie","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5134335560","display_name":"Wenxuan Huang","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Huang, Wenxuan","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5134363299","display_name":"Jiaqi Wei","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Wei, Jiaqi","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060090190","display_name":"Hao Wu","orcid":"https://orcid.org/0000-0002-2170-0618"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Wu, Hao","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5134278360","display_name":"Cheng Tan","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Tan, Cheng","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063286602","display_name":"Lang Yu","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Yu, Lang","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5134275602","display_name":"Yuejin Yang","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Yang, Yuejin","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5134265749","display_name":"Siqi Sun","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Liu, Mengdi","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060075172","display_name":"Zhangyang Gao","orcid":"https://orcid.org/0000-0003-1026-6083"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Sun, Siqi","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"last","author":{"id":null,"display_name":"Gao, Zhangyang","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Gao, Zhangyang","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12859","display_name":"Cell Image Analysis Techniques","score":0.3634999990463257,"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"}},"topics":[{"id":"https://openalex.org/T12859","display_name":"Cell Image Analysis Techniques","score":0.3634999990463257,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.21960000693798065,"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/T11986","display_name":"Scientific Computing and Data Management","score":0.10909999907016754,"subfield":{"id":"https://openalex.org/subfields/1802","display_name":"Information Systems and Management"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.7882999777793884},{"id":"https://openalex.org/keywords/verifiable-secret-sharing","display_name":"Verifiable secret sharing","score":0.5738000273704529},{"id":"https://openalex.org/keywords/dependency-graph","display_name":"Dependency graph","score":0.46549999713897705},{"id":"https://openalex.org/keywords/dependency","display_name":"Dependency (UML)","score":0.4138999879360199},{"id":"https://openalex.org/keywords/coding","display_name":"Coding (social sciences)","score":0.4131999909877777},{"id":"https://openalex.org/keywords/codebase","display_name":"Codebase","score":0.364300012588501},{"id":"https://openalex.org/keywords/code","display_name":"Code (set theory)","score":0.3199999928474426},{"id":"https://openalex.org/keywords/biological-data","display_name":"Biological data","score":0.30880001187324524}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7943000197410583},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.7882999777793884},{"id":"https://openalex.org/C85847156","wikidata":"https://www.wikidata.org/wiki/Q59015987","display_name":"Verifiable secret sharing","level":3,"score":0.5738000273704529},{"id":"https://openalex.org/C16311509","wikidata":"https://www.wikidata.org/wiki/Q4148050","display_name":"Dependency graph","level":3,"score":0.46549999713897705},{"id":"https://openalex.org/C19768560","wikidata":"https://www.wikidata.org/wiki/Q320727","display_name":"Dependency (UML)","level":2,"score":0.4138999879360199},{"id":"https://openalex.org/C179518139","wikidata":"https://www.wikidata.org/wiki/Q5140297","display_name":"Coding (social sciences)","level":2,"score":0.4131999909877777},{"id":"https://openalex.org/C51929080","wikidata":"https://www.wikidata.org/wiki/Q2425187","display_name":"Codebase","level":3,"score":0.364300012588501},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.3569999933242798},{"id":"https://openalex.org/C120314980","wikidata":"https://www.wikidata.org/wiki/Q180634","display_name":"Distributed computing","level":1,"score":0.3490999937057495},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.3199999928474426},{"id":"https://openalex.org/C201797286","wikidata":"https://www.wikidata.org/wiki/Q4914986","display_name":"Biological data","level":2,"score":0.30880001187324524},{"id":"https://openalex.org/C165696696","wikidata":"https://www.wikidata.org/wiki/Q11287","display_name":"Exploit","level":2,"score":0.3043000102043152},{"id":"https://openalex.org/C71745522","wikidata":"https://www.wikidata.org/wiki/Q2476929","display_name":"Confidentiality","level":2,"score":0.2888000011444092},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.2865999937057495},{"id":"https://openalex.org/C152124472","wikidata":"https://www.wikidata.org/wiki/Q1204361","display_name":"Redundancy (engineering)","level":2,"score":0.28529998660087585},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.2736000120639801},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.2718999981880188},{"id":"https://openalex.org/C107457646","wikidata":"https://www.wikidata.org/wiki/Q207434","display_name":"Human\u2013computer interaction","level":1,"score":0.2694000005722046},{"id":"https://openalex.org/C25344961","wikidata":"https://www.wikidata.org/wiki/Q192726","display_name":"Virtual machine","level":2,"score":0.2655999958515167},{"id":"https://openalex.org/C179372163","wikidata":"https://www.wikidata.org/wiki/Q1406181","display_name":"Scene graph","level":3,"score":0.2630000114440918},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.262800008058548},{"id":"https://openalex.org/C33762810","wikidata":"https://www.wikidata.org/wiki/Q461671","display_name":"Data integrity","level":2,"score":0.2612000107765198},{"id":"https://openalex.org/C150303390","wikidata":"https://www.wikidata.org/wiki/Q1983852","display_name":"Virtual actor","level":3,"score":0.25189998745918274}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.48550/arxiv.2604.19606","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2604.19606","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"Preprint"}],"best_oa_location":{"id":"doi:10.48550/arxiv.2604.19606","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2604.19606","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Preprint"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":[],"abstract_inverted_index":{"Systematic":[0],"ablations":[1],"are":[2,14,20],"essential":[3],"to":[4,25,140,149],"attribute":[5],"performance":[6,121],"gains":[7],"in":[8,152],"AI":[9],"Virtual":[10],"Cells,":[11],"yet":[12],"they":[13,39],"rarely":[15],"performed":[16],"because":[17],"biological":[18,167],"repositories":[19,70,132],"under-standardized":[21],"and":[22,28,45,54,87,90,111,123,146,163],"tightly":[23],"coupled":[24],"domain-specific":[26],"data":[27,88],"formats.":[29],"While":[30],"recent":[31],"coding":[32],"agents":[33],"can":[34,50],"translate":[35],"ideas":[36],"into":[37],"implementations,":[38],"typically":[40],"stop":[41],"at":[42],"producing":[43],"code":[44],"lack":[46],"a":[47,64,105,116],"verifier":[48],"that":[49,71,118],"reproduce":[51],"strong":[52],"baselines":[53,80],"rigorously":[55],"test":[56],"which":[57],"components":[58],"truly":[59],"matter.":[60],"We":[61],"introduce":[62],"AblateCell,":[63],"reproduce-then-ablate":[65],"agent":[66],"for":[67],"virtual":[68],"cell":[69],"closes":[72],"this":[73],"verification":[74,162],"gap.":[75],"AblateCell":[76,136],"first":[77],"reproduces":[78],"reported":[79],"end-to-end":[81,143],"by":[82,103],"auto-configuring":[83],"environments,":[84],"resolving":[85],"dependency":[86],"issues,":[89],"rerunning":[91],"official":[92],"evaluations":[93],"while":[94],"emitting":[95],"verifiable":[96],"artifacts.":[97],"It":[98],"then":[99],"conducts":[100],"closed-loop":[101],"ablation":[102],"generating":[104],"graph":[106],"of":[107],"isolated":[108],"repository":[109],"mutations":[110],"adaptively":[112],"selecting":[113],"experiments":[114],"under":[115],"reward":[117],"trades":[119],"off":[120],"impact":[122],"execution":[124],"cost.":[125],"Evaluated":[126],"on":[127,166],"three":[128],"single-cell":[129],"perturbation":[130],"prediction":[131],"(CPA,":[133],"GEARS,":[134],"BioLORD),":[135],"achieves":[137],"88.9%":[138],"(+29.9%":[139],"human":[141],"expert)":[142],"workflow":[144],"success":[145],"93.3%":[147],"(+53.3%":[148],"heuristic)":[150],"accuracy":[151],"recovering":[153],"ground-truth":[154],"critical":[155],"components.":[156],"These":[157],"results":[158],"enable":[159],"scalable,":[160],"repository-grounded":[161],"attribution":[164],"directly":[165],"codebases.":[168]},"counts_by_year":[],"updated_date":"2026-07-01T06:00:48.157686","created_date":"2026-04-23T00:00:00"}
