{"id":"https://openalex.org/W7221179835","doi":"https://doi.org/10.48550/arxiv.2610.11627","title":"Beyond Action Entropy: Quotient-Space Exploration for Genome-Scale Metabolic Model Repair","display_name":"Beyond Action Entropy: Quotient-Space Exploration for Genome-Scale Metabolic Model Repair","publication_year":2026,"publication_date":"2026-10-08","ids":{"openalex":"https://openalex.org/W7221179835","doi":"https://doi.org/10.48550/arxiv.2610.11627"},"language":"en","primary_location":{"id":"pmh:oai:arXiv.org:2610.11627","doi":null,"is_oa":true,"landing_page_url":"https://arxiv.org/abs/2610.11627","pdf_url":"https://arxiv.org/pdf/2610.11627","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},"volume":null,"type":"preprint","indexed_in":["arxiv","datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://arxiv.org/pdf/2610.11627","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5158177975","display_name":"Xuan Gong","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Gong, Xuan","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5158088395","display_name":"Hanbo Huang","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Huang, Hanbo","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5153488874","display_name":"Wenbin Dai","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Dai, Wenbin","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5158102143","display_name":"Wang Jing","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Wang, Jing","raw_affiliation_strings":["Shanghai Jiao Tong University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Shanghai Jiao Tong University","institution_ids":["https://openalex.org/I183067930"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5158116384","display_name":"Lei Bai","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I4391012619","display_name":"Shanghai Artificial Intelligence Laboratory","ror":"https://ror.org/03wkvpx79","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4391012619"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Bai, Lei","raw_affiliation_strings":["Shanghai AI Laboratory"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Shanghai AI Laboratory","institution_ids":["https://openalex.org/I4391012619"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5158235799","display_name":"Xiang Xiao","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiao, Xiang","raw_affiliation_strings":["Shanghai Jiao Tong University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Shanghai Jiao Tong University","institution_ids":["https://openalex.org/I183067930"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003024225","display_name":"Weishu Zhao","orcid":"https://orcid.org/0000-0002-0753-8300","observed_orcids":["https://orcid.org/0000-0002-0753-8300"]},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhao, Weishu","raw_affiliation_strings":["Shanghai Jiao Tong University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Shanghai Jiao Tong University","institution_ids":["https://openalex.org/I183067930"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5158126949","display_name":"Shiyu Liang","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Liang, Shiyu","raw_affiliation_strings":["Shanghai Jiao Tong University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Shanghai Jiao Tong University","institution_ids":["https://openalex.org/I183067930"]}]}],"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":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9721999764442444,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9721999764442444,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.01640000008046627,"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":0.0013000000035390258,"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":[],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5986999869346619},{"id":"https://openalex.org/C2780791683","wikidata":"https://www.wikidata.org/wiki/Q846785","display_name":"Action (physics)","level":2,"score":0.5220000147819519},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.49149999022483826},{"id":"https://openalex.org/C2778572836","wikidata":"https://www.wikidata.org/wiki/Q380933","display_name":"Space (punctuation)","level":2,"score":0.45500001311302185},{"id":"https://openalex.org/C199422724","wikidata":"https://www.wikidata.org/wiki/Q41118","display_name":"Quotient","level":2,"score":0.45339998602867126},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.384799987077713},{"id":"https://openalex.org/C140779682","wikidata":"https://www.wikidata.org/wiki/Q210868","display_name":"Sampling (signal processing)","level":3,"score":0.3824000060558319},{"id":"https://openalex.org/C185429906","wikidata":"https://www.wikidata.org/wiki/Q1130160","display_name":"Estimator","level":2,"score":0.3817000091075897},{"id":"https://openalex.org/C2781316041","wikidata":"https://www.wikidata.org/wiki/Q1230584","display_name":"Diversity (politics)","level":2,"score":0.37860000133514404},{"id":"https://openalex.org/C2781067378","wikidata":"https://www.wikidata.org/wiki/Q17027399","display_name":"Interpretability","level":2,"score":0.3370000123977661},{"id":"https://openalex.org/C48677424","wikidata":"https://www.wikidata.org/wiki/Q6888088","display_name":"Mode (computer interface)","level":2,"score":0.32179999351501465},{"id":"https://openalex.org/C2777212361","wikidata":"https://www.wikidata.org/wiki/Q5127848","display_name":"Class (philosophy)","level":2,"score":0.30880001187324524},{"id":"https://openalex.org/C66024118","wikidata":"https://www.wikidata.org/wiki/Q1122506","display_name":"Computational model","level":2,"score":0.2915000021457672},{"id":"https://openalex.org/C114289077","wikidata":"https://www.wikidata.org/wiki/Q3284399","display_name":"Statistical model","level":2,"score":0.28780001401901245},{"id":"https://openalex.org/C174348530","wikidata":"https://www.wikidata.org/wiki/Q188635","display_name":"Bridging (networking)","level":2,"score":0.2718999981880188},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.26910001039505005},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.26109999418258667},{"id":"https://openalex.org/C2775924081","wikidata":"https://www.wikidata.org/wiki/Q55608371","display_name":"Control (management)","level":2,"score":0.25870001316070557},{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.25859999656677246},{"id":"https://openalex.org/C33676613","wikidata":"https://www.wikidata.org/wiki/Q13415176","display_name":"Dimension (graph theory)","level":2,"score":0.2574000060558319},{"id":"https://openalex.org/C2778334786","wikidata":"https://www.wikidata.org/wiki/Q1586270","display_name":"Variation (astronomy)","level":2,"score":0.25589999556541443}],"mesh":[],"locations_count":2,"locations":[{"id":"pmh:oai:arXiv.org:2610.11627","doi":null,"is_oa":true,"landing_page_url":"https://arxiv.org/abs/2610.11627","pdf_url":"https://arxiv.org/pdf/2610.11627","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},{"id":"doi:10.48550/arxiv.2610.11627","doi":"https://doi.org/10.48550/arxiv.2610.11627","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2610.11627","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"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"}],"best_oa_location":{"id":"pmh:oai:arXiv.org:2610.11627","doi":null,"is_oa":true,"landing_page_url":"https://arxiv.org/abs/2610.11627","pdf_url":"https://arxiv.org/pdf/2610.11627","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W7221179835.pdf","grobid_xml":"https://content.openalex.org/works/W7221179835.grobid-xml"},"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W4414062314","https://openalex.org/W7157557169","https://openalex.org/W4288908451","https://openalex.org/W4409468291","https://openalex.org/W7124168696","https://openalex.org/W7000287842","https://openalex.org/W3010629926","https://openalex.org/W2941164415","https://openalex.org/W2804977648","https://openalex.org/W2809097257"],"abstract_inverted_index":{"Repairing":[0],"scientific":[1,75],"models":[2],"from":[3,8,129],"functional":[4],"observations":[5],"differs":[6],"fundamentally":[7],"supervised":[9],"prediction:":[10],"feedback":[11],"may":[12],"certify":[13],"a":[14,57,106,152],"solution":[15],"without":[16],"revealing":[17],"which":[18,80],"structural":[19],"correction":[20],"is":[21],"responsible.":[22],"We":[23,77],"study":[24],"this":[25],"setting":[26],"for":[27,61],"genome-scale":[28],"metabolic":[29],"model":[30],"(GEM)":[31],"repair,":[32],"where":[33],"multiple":[34],"reaction":[35],"edits":[36,46],"can":[37],"explain":[38],"the":[39,49,66,92,142],"same":[40,50,143],"phenotypes":[41],"and":[42,87],"many":[43],"apparently":[44],"distinct":[45,115,138],"correspond":[47],"to":[48,131,155],"biological":[51],"mechanism.":[52],"This":[53],"many-to-one":[54],"structure":[55],"creates":[56],"hidden":[58],"failure":[59],"mode":[60],"conventional":[62],"exploration:":[63],"diversity":[64,73],"in":[65],"output":[67],"space":[68],"need":[69],"not":[70],"translate":[71],"into":[72,84],"of":[74],"hypotheses.":[76],"introduce":[78],"QuotientPO,":[79],"collapses":[81],"equivalent":[82],"repairs":[83],"canonical":[85],"mechanisms":[86],"optimizes":[88],"exploration":[89,99,150],"directly":[90],"over":[91],"resulting":[93],"quotient":[94,98],"space.":[95],"To":[96],"make":[97],"informative":[100],"under":[101,141,158],"finite":[102],"rollouts,":[103],"we":[104],"derive":[105],"kernelized":[107],"R\u00e9nyi":[108],"estimator":[109],"that":[110],"resolves":[111],"graded":[112],"crowding":[113],"among":[114],"repair":[116],"cores":[117],"beyond":[118],"coarse":[119],"exact-match":[120],"counts.":[121],"On":[122],"2,212":[123],"held-out":[124],"GEMs,":[125],"QuotientPO":[126],"improves":[127],"Success@32":[128],"17.93%":[130],"20.10%":[132],"(+12.1%":[133],"relative)":[134],"while":[135],"consistently":[136],"increasing":[137],"successful-core":[139],"discovery":[140,157],"sampling":[144],"budget.":[145],"These":[146],"results":[147],"establish":[148],"quotient-space":[149],"as":[151],"principled":[153],"approach":[154],"mechanism-level":[156],"verifier-induced":[159],"equivalence.":[160]},"counts_by_year":[],"updated_date":"2026-10-28T10:33:24.094632","created_date":"2026-10-10T00:00:00"}
