{"id":"https://openalex.org/W7160847511","doi":"https://doi.org/10.48550/arxiv.2605.07335","title":"CellScientist: Dual-Space Hierarchical Orchestration for Closed-Loop Refinement of Virtual Cell Models","display_name":"CellScientist: Dual-Space Hierarchical Orchestration for Closed-Loop Refinement of Virtual Cell Models","publication_year":2026,"publication_date":"2026-05-08","ids":{"openalex":"https://openalex.org/W7160847511","doi":"https://doi.org/10.48550/arxiv.2605.07335"},"language":null,"primary_location":{"id":"doi:10.48550/arxiv.2605.07335","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2605.07335","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.2605.07335","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5013536349","display_name":"Mengran Li","orcid":"https://orcid.org/0000-0001-7540-530X"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Li, Mengran","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5135856463","display_name":"Bo Li","orcid":"https://orcid.org/0009-0001-8108-4765"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Li, Bo","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5135878748","display_name":"Jiaying Wang","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Wang, Jiaying","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102496152","display_name":"Wenbin Xing","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Xing, Wenbin","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5135860133","display_name":"Yixuan Dong","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Dong, Yixuan","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101787439","display_name":"Chengyang Zhang","orcid":"https://orcid.org/0000-0003-3658-5779"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Zhang, Chengyang","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5135866749","display_name":"Hongliang Zhang","orcid":"https://orcid.org/0000-0002-4769-0964"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Zhang, Hongliang","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5135898438","display_name":"Yuzhong Peng","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Peng, Yuzhong","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5112053104","display_name":"Jinlin Wu","orcid":"https://orcid.org/0000-0001-8338-6495"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Wu, Jinlin","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5135830501","display_name":"Bob Zhang","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Zhang, Bob","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5135896906","display_name":"Bingo Wing-Kuen Ling","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Ling, Bingo Wing-Kuen","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5133258063","display_name":"Fuji Yang","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Yang, Fuji","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5135867548","display_name":"Zhen Lei","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Lei, Zhen","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5135866628","display_name":"Jiebo Luo","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Luo, Jiebo","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5135846966","display_name":"Zelin Zang","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Zang, Zelin","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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.5098000168800354,"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":0.5098000168800354,"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":0.22050000727176666,"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":0.06539999693632126,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/executable","display_name":"Executable","score":0.9120000004768372},{"id":"https://openalex.org/keywords/debugging","display_name":"Debugging","score":0.7506999969482422},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.7488999962806702},{"id":"https://openalex.org/keywords/task","display_name":"Task (project management)","score":0.47920000553131104},{"id":"https://openalex.org/keywords/orchestration","display_name":"Orchestration","score":0.47380000352859497},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.39070001244544983},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.38760000467300415},{"id":"https://openalex.org/keywords/interface","display_name":"Interface (matter)","score":0.30550000071525574},{"id":"https://openalex.org/keywords/user-interface","display_name":"User interface","score":0.30169999599456787}],"concepts":[{"id":"https://openalex.org/C160145156","wikidata":"https://www.wikidata.org/wiki/Q778586","display_name":"Executable","level":2,"score":0.9120000004768372},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7940000295639038},{"id":"https://openalex.org/C168065819","wikidata":"https://www.wikidata.org/wiki/Q845566","display_name":"Debugging","level":2,"score":0.7506999969482422},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.7488999962806702},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.48539999127388},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.47920000553131104},{"id":"https://openalex.org/C199168358","wikidata":"https://www.wikidata.org/wiki/Q3367000","display_name":"Orchestration","level":3,"score":0.47380000352859497},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.41929998993873596},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.39070001244544983},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.38760000467300415},{"id":"https://openalex.org/C120314980","wikidata":"https://www.wikidata.org/wiki/Q180634","display_name":"Distributed computing","level":1,"score":0.3847000002861023},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3476000130176544},{"id":"https://openalex.org/C113843644","wikidata":"https://www.wikidata.org/wiki/Q901882","display_name":"Interface (matter)","level":4,"score":0.30550000071525574},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3052000105381012},{"id":"https://openalex.org/C89505385","wikidata":"https://www.wikidata.org/wiki/Q47146","display_name":"User interface","level":2,"score":0.30169999599456787},{"id":"https://openalex.org/C61423126","wikidata":"https://www.wikidata.org/wiki/Q187432","display_name":"Scripting language","level":2,"score":0.29010000824928284},{"id":"https://openalex.org/C31266012","wikidata":"https://www.wikidata.org/wiki/Q6554340","display_name":"Linkage (software)","level":3,"score":0.28929999470710754},{"id":"https://openalex.org/C3018397939","wikidata":"https://www.wikidata.org/wiki/Q3644502","display_name":"Open source","level":3,"score":0.288100004196167},{"id":"https://openalex.org/C175154964","wikidata":"https://www.wikidata.org/wiki/Q380077","display_name":"Task analysis","level":3,"score":0.2773999869823456},{"id":"https://openalex.org/C151319957","wikidata":"https://www.wikidata.org/wiki/Q752739","display_name":"Asynchronous communication","level":2,"score":0.27469998598098755},{"id":"https://openalex.org/C101468663","wikidata":"https://www.wikidata.org/wiki/Q1620158","display_name":"Modular design","level":2,"score":0.2728999853134155},{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.2687000036239624},{"id":"https://openalex.org/C2779982483","wikidata":"https://www.wikidata.org/wiki/Q6094420","display_name":"Iterative refinement","level":2,"score":0.26829999685287476},{"id":"https://openalex.org/C73301696","wikidata":"https://www.wikidata.org/wiki/Q5469984","display_name":"Formalism (music)","level":3,"score":0.2648000121116638},{"id":"https://openalex.org/C25344961","wikidata":"https://www.wikidata.org/wiki/Q192726","display_name":"Virtual machine","level":2,"score":0.26330000162124634},{"id":"https://openalex.org/C116409475","wikidata":"https://www.wikidata.org/wiki/Q1385056","display_name":"External Data Representation","level":2,"score":0.25949999690055847},{"id":"https://openalex.org/C2776834041","wikidata":"https://www.wikidata.org/wiki/Q25346349","display_name":"Execution model","level":2,"score":0.25270000100135803},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.2502000033855438}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.48550/arxiv.2605.07335","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2605.07335","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.2605.07335","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2605.07335","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":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":[],"abstract_inverted_index":{"Virtual":[0],"Cell":[1],"Modeling":[2],"(VCM)":[3],"requires":[4],"models":[5,154],"that":[6,79],"not":[7],"only":[8],"predict":[9],"perturbation":[10,149],"responses,":[11],"but":[12,35],"also":[13],"support":[14],"targeted":[15,114],"revision":[16,38],"when":[17],"predictions":[18],"fail.":[19],"Current":[20],"LLM-assisted":[21],"modeling":[22,42,93],"workflows":[23],"face":[24],"a":[25,75,81,86,121],"refinement-routing":[26],"problem:":[27],"prediction":[28],"discrepancies":[29,111],"are":[30],"observed":[31],"through":[32],"executable":[33,88,153],"implementations,":[34],"the":[36,41,66,70,151,169],"relevant":[37],"may":[39,59],"involve":[40],"assumption,":[43],"representation":[44],"design,":[45],"implementation,":[46],"or":[47,116],"task":[48,104],"constraint.":[49],"Without":[50],"structured":[51,96,132],"feedback":[52],"propagation":[53],"across":[54],"these":[55],"levels,":[56],"iterative":[57],"refinement":[58,136,173],"repair":[60],"code":[61],"while":[62,168],"failing":[63],"to":[64,113],"revise":[65],"assumption":[67],"responsible":[68],"for":[69,134],"discrepancy.":[71],"We":[72],"propose":[73],"CellScientist,":[74],"dual-space":[76],"hierarchical":[77],"framework":[78],"couples":[80],"high-level":[82],"hypothesis":[83,115],"space":[84],"with":[85,146],"low-level":[87],"implementation":[89,117],"space.":[90],"CellScientist":[91,157],"represents":[92],"decisions":[94],"as":[95,100],"states,":[97],"realizes":[98],"them":[99],"admissible":[101],"programs":[102],"under":[103,162],"and":[105,108,143,165],"interface":[106],"constraints,":[107],"routes":[109],"execution":[110],"back":[112],"updates.":[118],"This":[119],"enables":[120],"closed":[122],"Hypothesis":[123,127],"-&gt;":[124,126],"Implementation":[125],"loop":[128],"where":[129],"failures":[130],"become":[131],"signals":[133],"model":[135],"rather":[137],"than":[138],"debugging":[139],"events.":[140],"Across":[141],"morphology":[142],"transcriptomic":[144],"benchmarks,":[145],"additional":[147],"single-cell":[148],"evaluations,":[150],"final":[152],"selected":[155],"by":[156],"improve":[158],"over":[159],"reference":[160],"baselines":[161],"fixed":[163],"split":[164],"evaluation":[166],"protocols,":[167],"workflow":[170],"produces":[171],"auditable":[172],"traces.":[174]},"counts_by_year":[],"updated_date":"2026-07-01T06:00:48.157686","created_date":"2026-05-12T00:00:00"}
