{"id":"https://openalex.org/W7152637108","doi":"https://doi.org/10.48550/arxiv.2604.06269","title":"MAT-Cell: A Multi-Agent Tree-Structured Reasoning Framework for Batch-Level Single-Cell Annotation","display_name":"MAT-Cell: A Multi-Agent Tree-Structured Reasoning Framework for Batch-Level Single-Cell Annotation","publication_year":2026,"publication_date":"2026-04-07","ids":{"openalex":"https://openalex.org/W7152637108","doi":"https://doi.org/10.48550/arxiv.2604.06269"},"language":null,"primary_location":{"id":"doi:10.48550/arxiv.2604.06269","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2604.06269","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":null,"license_id":null,"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.2604.06269","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5133290283","display_name":"Yehui Yang","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Yang, Yehui","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5133254618","display_name":"Zelin Zang","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Zang, Zelin","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5133243941","display_name":"Changxi Chi","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Zheng, Xienan","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5133258618","display_name":"Jingbo Zhou","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Jia, Yuzhe","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5125942567","display_name":"Xienan Zheng","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Chi, Changxi","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5133252462","display_name":"Yuzhe Jia","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Zhou, Jingbo","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5133309114","display_name":"Chang Yu","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Yu, Chang","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/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/A5133280291","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":"middle","author":{"id":"https://openalex.org/A5133272311","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":"last","author":{"id":"https://openalex.org/A5133291791","display_name":"Stan Z. Li","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Li, Stan Z.","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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.8258000016212463,"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":0.8258000016212463,"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":0.019899999722838402,"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/T12090","display_name":"Language and cultural evolution","score":0.009700000286102295,"subfield":{"id":"https://openalex.org/subfields/3316","display_name":"Cultural Studies"},"field":{"id":"https://openalex.org/fields/33","display_name":"Social Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/automated-reasoning","display_name":"Automated reasoning","score":0.6226999759674072},{"id":"https://openalex.org/keywords/verifiable-secret-sharing","display_name":"Verifiable secret sharing","score":0.598800003528595},{"id":"https://openalex.org/keywords/syllogism","display_name":"Syllogism","score":0.5378000140190125},{"id":"https://openalex.org/keywords/axiom","display_name":"Axiom","score":0.49219998717308044},{"id":"https://openalex.org/keywords/non-monotonic-logic","display_name":"Non-monotonic logic","score":0.4586000144481659},{"id":"https://openalex.org/keywords/spurious-relationship","display_name":"Spurious relationship","score":0.4578000009059906},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.45669999718666077},{"id":"https://openalex.org/keywords/model-based-reasoning","display_name":"Model-based reasoning","score":0.4440999925136566},{"id":"https://openalex.org/keywords/reasoning-system","display_name":"Reasoning system","score":0.43149998784065247},{"id":"https://openalex.org/keywords/core","display_name":"Core (optical fiber)","score":0.42419999837875366}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6909000277519226},{"id":"https://openalex.org/C195344581","wikidata":"https://www.wikidata.org/wiki/Q2555318","display_name":"Automated reasoning","level":2,"score":0.6226999759674072},{"id":"https://openalex.org/C85847156","wikidata":"https://www.wikidata.org/wiki/Q59015987","display_name":"Verifiable secret sharing","level":3,"score":0.598800003528595},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5726000070571899},{"id":"https://openalex.org/C131598440","wikidata":"https://www.wikidata.org/wiki/Q107342","display_name":"Syllogism","level":2,"score":0.5378000140190125},{"id":"https://openalex.org/C167729594","wikidata":"https://www.wikidata.org/wiki/Q17736","display_name":"Axiom","level":2,"score":0.49219998717308044},{"id":"https://openalex.org/C159032336","wikidata":"https://www.wikidata.org/wiki/Q2488768","display_name":"Non-monotonic logic","level":2,"score":0.4586000144481659},{"id":"https://openalex.org/C97256817","wikidata":"https://www.wikidata.org/wiki/Q1462316","display_name":"Spurious relationship","level":2,"score":0.4578000009059906},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.45669999718666077},{"id":"https://openalex.org/C37335422","wikidata":"https://www.wikidata.org/wiki/Q6888134","display_name":"Model-based reasoning","level":3,"score":0.4440999925136566},{"id":"https://openalex.org/C89288958","wikidata":"https://www.wikidata.org/wiki/Q7301504","display_name":"Reasoning system","level":2,"score":0.43149998784065247},{"id":"https://openalex.org/C2164484","wikidata":"https://www.wikidata.org/wiki/Q5170150","display_name":"Core (optical fiber)","level":2,"score":0.42419999837875366},{"id":"https://openalex.org/C2777310092","wikidata":"https://www.wikidata.org/wiki/Q1410600","display_name":"Rebuttal","level":2,"score":0.421099990606308},{"id":"https://openalex.org/C2185349","wikidata":"https://www.wikidata.org/wiki/Q190558","display_name":"Negation","level":2,"score":0.39419999718666077},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.3781000077724457},{"id":"https://openalex.org/C97364631","wikidata":"https://www.wikidata.org/wiki/Q484284","display_name":"Deductive reasoning","level":2,"score":0.3752000033855438},{"id":"https://openalex.org/C193221554","wikidata":"https://www.wikidata.org/wiki/Q5153664","display_name":"Commonsense reasoning","level":2,"score":0.3709999918937683},{"id":"https://openalex.org/C25810664","wikidata":"https://www.wikidata.org/wiki/Q44325","display_name":"Ontology","level":2,"score":0.3603000044822693},{"id":"https://openalex.org/C134752490","wikidata":"https://www.wikidata.org/wiki/Q374182","display_name":"Logical consequence","level":2,"score":0.35670000314712524},{"id":"https://openalex.org/C140843580","wikidata":"https://www.wikidata.org/wiki/Q840067","display_name":"Defeasible reasoning","level":2,"score":0.3402000069618225},{"id":"https://openalex.org/C159718280","wikidata":"https://www.wikidata.org/wiki/Q5526353","display_name":"Gas meter prover","level":3,"score":0.3377000093460083},{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.32339999079704285},{"id":"https://openalex.org/C39920170","wikidata":"https://www.wikidata.org/wiki/Q693083","display_name":"Soundness","level":2,"score":0.3140999972820282},{"id":"https://openalex.org/C195324797","wikidata":"https://www.wikidata.org/wiki/Q33742","display_name":"Natural language","level":2,"score":0.30869999527931213},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3046000003814697},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.30300000309944153},{"id":"https://openalex.org/C94124525","wikidata":"https://www.wikidata.org/wiki/Q912550","display_name":"Categorization","level":2,"score":0.2994999885559082},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.2946000099182129},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.29249998927116394},{"id":"https://openalex.org/C166088908","wikidata":"https://www.wikidata.org/wiki/Q308495","display_name":"Abductive reasoning","level":2,"score":0.28540000319480896},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.2809999883174896},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.27889999747276306},{"id":"https://openalex.org/C146849305","wikidata":"https://www.wikidata.org/wiki/Q370766","display_name":"Ground truth","level":2,"score":0.2727999985218048},{"id":"https://openalex.org/C160145156","wikidata":"https://www.wikidata.org/wiki/Q778586","display_name":"Executable","level":2,"score":0.2612000107765198},{"id":"https://openalex.org/C2777230681","wikidata":"https://www.wikidata.org/wiki/Q7923820","display_name":"Vetting","level":2,"score":0.2578999996185303},{"id":"https://openalex.org/C61423126","wikidata":"https://www.wikidata.org/wiki/Q187432","display_name":"Scripting language","level":2,"score":0.2531999945640564},{"id":"https://openalex.org/C184337299","wikidata":"https://www.wikidata.org/wiki/Q1437428","display_name":"Semantics (computer science)","level":2,"score":0.2531999945640564},{"id":"https://openalex.org/C43971567","wikidata":"https://www.wikidata.org/wiki/Q3142865","display_name":"Logical reasoning","level":2,"score":0.25119999051094055}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.48550/arxiv.2604.06269","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2604.06269","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":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"Preprint"}],"best_oa_location":{"id":"doi:10.48550/arxiv.2604.06269","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2604.06269","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":null,"license_id":null,"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":{"Automated":[0],"single-cell":[1,65],"annotation":[2,66],"is":[3,21,196],"difficult":[4],"when":[5,17],"the":[6,12,53,115,139,162,170],"most":[7,13],"abundant":[8],"genes":[9],"are":[10],"not":[11],"discriminative":[14],"ones,":[15],"or":[16,120],"a":[18,25,60,135,147],"target":[19],"state":[20],"poorly":[22],"covered":[23],"by":[24],"fixed":[26],"reference":[27],"atlas.":[28],"GPTCelltype-style":[29],"one-shot":[30],"prompting":[31],"allows":[32],"large":[33],"language":[34],"models":[35],"(LLMs)":[36],"to":[37,81],"produce":[38],"plausible":[39],"labels":[40],"from":[41,71],"generic":[42],"expression":[43],"signals,":[44],"while":[45],"reference-based":[46],"annotators":[47],"can":[48],"force":[49],"unfamiliar":[50],"states":[51],"into":[52,93,103],"nearest":[54],"known":[55],"category.":[56],"We":[57],"propose":[58],"MAT-Cell,":[59],"prompt-driven":[61],"framework":[62],"for":[63,161,169,192],"batch-level":[64],"that":[67],"separates":[68],"evidence":[69],"grounding":[70],"label":[72],"decision.":[73],"MAT-Cell":[74,153],"first":[75],"uses":[76],"Reverse":[77],"Verification":[78],"Query":[79],"(RVQ)":[80],"combine":[82],"tissue":[83],"context,":[84],"observed":[85],"differentially":[86],"expressed":[87],"genes,":[88],"and":[89,108,113,167,185],"LLM-elicited":[90],"biological":[91],"priors":[92],"structured":[94],"candidate-specific":[95],"premises.":[96],"Verifier":[97],"agents":[98],"then":[99],"convert":[100],"these":[101],"premises":[102],"explicit":[104],"premise-to-claim":[105],"reasoning":[106],"trees,":[107],"bounded":[109],"multi-round":[110],"debate":[111,131],"compares,challenges,":[112],"revises":[114],"resulting":[116],"claims":[117],"before":[118],"consensus":[119],"final":[121],"adjudication.The":[122],"returned":[123],"Syllogistic":[124],"Derivation":[125],"Tree":[126],"(SDT)":[127],"provides":[128],"an":[129],"auditable":[130],"trace":[132],"rather":[133],"than":[134],"formal":[136],"proof":[137],"of":[138],"annotation.":[140,194],"In":[141,175],"open-candidate":[142],"benchmarks":[143],"across":[144,178,183],"five":[145],"datasets,":[146],"locally":[148],"deployed":[149],"Qwen3-30B":[150],"model":[151],"with":[152,159],"achieves":[154],"75.5%":[155],"average":[156],"accuracy,":[157],"compared":[158],"64.2%":[160],"strongest":[163,171],"evaluated":[164,172],"CoT":[165],"baseline":[166],"51.9%":[168],"scPilot":[173],"variant.":[174],"oracle-candidate":[176],"bench-marks":[177],"three":[179],"species,MAT-Cell":[180],"remains":[181],"competitive":[182],"backbones,":[184],"local":[186],"inference":[187],"substantially":[188],"reduces":[189],"monetary":[190],"cost":[191],"batch":[193],"Code":[195],"available":[197],"at:":[198],"https://anonymous.4open.science/r/MATCell-4067":[199]},"counts_by_year":[],"updated_date":"2026-07-01T06:00:48.157686","created_date":"2026-04-10T00:00:00"}