{"id":"https://openalex.org/W7127370547","doi":"https://doi.org/10.48550/arxiv.2602.00197","title":"Rank-and-Reason: Multi-Agent Collaboration Accelerates Zero-Shot Protein Mutation Prediction","display_name":"Rank-and-Reason: Multi-Agent Collaboration Accelerates Zero-Shot Protein Mutation Prediction","publication_year":2026,"publication_date":"2026-01-30","ids":{"openalex":"https://openalex.org/W7127370547","doi":"https://doi.org/10.48550/arxiv.2602.00197"},"language":null,"primary_location":{"id":"doi:10.48550/arxiv.2602.00197","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2602.00197","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":"article"},"type":"preprint","indexed_in":["datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://doi.org/10.48550/arxiv.2602.00197","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5108971669","display_name":"Yang Tan","orcid":null},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Tan, Yang","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":null,"display_name":"Yu, Yuanxi","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Yu, Yuanxi","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026215022","display_name":"Can Wu","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Wu, Can","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090728932","display_name":"Bozitao Zhong","orcid":"https://orcid.org/0000-0001-9363-6099"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Zhong, Bozitao","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5124959795","display_name":"Mingchen Li","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Li, Mingchen","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":null,"display_name":"Fan, Guisheng","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Fan, Guisheng","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101735174","display_name":"Jiankang Zhu","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Zhu, Jiankang","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5124878801","display_name":"Yafeng Liang","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Liang, Yafeng","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5124967630","display_name":"Nanqing Dong","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Dong, Nanqing","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5124928038","display_name":"Liang Hong","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Hong, Liang","raw_affiliation_strings":[],"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":10,"corresponding_author_ids":["https://openalex.org/A5108971669"],"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.48089998960494995,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.48089998960494995,"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/T11642","display_name":"Genomics and Rare Diseases","score":0.0820000022649765,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.0754999965429306,"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/workflow","display_name":"Workflow","score":0.7861999869346619},{"id":"https://openalex.org/keywords/domain","display_name":"Domain (mathematical analysis)","score":0.4957999885082245},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.4675999879837036},{"id":"https://openalex.org/keywords/mutation","display_name":"Mutation","score":0.42829999327659607},{"id":"https://openalex.org/keywords/audit","display_name":"Audit","score":0.3952000141143799},{"id":"https://openalex.org/keywords/aggregate","display_name":"Aggregate (composite)","score":0.35850000381469727}],"concepts":[{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.7861999869346619},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6642000079154968},{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.4957999885082245},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.4675999879837036},{"id":"https://openalex.org/C501734568","wikidata":"https://www.wikidata.org/wiki/Q42918","display_name":"Mutation","level":3,"score":0.42829999327659607},{"id":"https://openalex.org/C199521495","wikidata":"https://www.wikidata.org/wiki/Q181487","display_name":"Audit","level":2,"score":0.3952000141143799},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.36550000309944153},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3628000020980835},{"id":"https://openalex.org/C4679612","wikidata":"https://www.wikidata.org/wiki/Q866298","display_name":"Aggregate (composite)","level":2,"score":0.35850000381469727},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.349700003862381},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3192000091075897},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.31470000743865967},{"id":"https://openalex.org/C207685749","wikidata":"https://www.wikidata.org/wiki/Q2088941","display_name":"Domain knowledge","level":2,"score":0.301800012588501},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.29899999499320984},{"id":"https://openalex.org/C58328972","wikidata":"https://www.wikidata.org/wiki/Q184609","display_name":"Expert system","level":2,"score":0.27309998869895935},{"id":"https://openalex.org/C105002631","wikidata":"https://www.wikidata.org/wiki/Q4833645","display_name":"Subject-matter expert","level":3,"score":0.2632000148296356}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.48550/arxiv.2602.00197","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2602.00197","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":"article"}],"best_oa_location":{"id":"doi:10.48550/arxiv.2602.00197","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2602.00197","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":"article"},"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":{"Zero-shot":[0],"mutation":[1],"prediction":[2],"is":[3,42],"vital":[4],"for":[5,28],"low-resource":[6],"protein":[7,11],"engineering,":[8],"yet":[9],"existing":[10],"language":[12],"models":[13],"(PLMs)":[14],"often":[15],"yield":[16],"statistically":[17],"confident":[18],"results":[19],"that":[20,41],"ignore":[21],"fundamental":[22],"biophysical":[23],"constraints.":[24],"Currently,":[25],"selecting":[26],"candidates":[27,109],"wet-lab":[29,69,127],"validation":[30,128],"relies":[31],"on":[32,48,95,124,129,158],"manual":[33],"expert":[34],"auditing":[35],"of":[36,91],"PLM":[37],"outputs,":[38],"a":[39,58,74,81,86,138],"process":[40],"inefficient,":[43],"subjective,":[44],"and":[45,66,77,112,142,149,154],"highly":[46],"dependent":[47],"domain":[49],"expertise.":[50],"To":[51],"address":[52],"this,":[53],"we":[54],"propose":[55],"Rank-and-Reason":[56],"(VenusRAR),":[57],"two-stage":[59],"agentic":[60,101],"framework":[61],"to":[62,107,122],"automate":[63],"this":[64],"workflow":[65],"maximize":[67],"expected":[68],"fitness.":[70],"In":[71,97],"the":[72,98,116,134],"Rank-Stage,":[73],"Computational":[75],"Expert":[76,102],"Virtual":[78],"Biologist":[79],"aggregate":[80],"context-aware":[82],"multi-modal":[83],"ensemble,":[84],"establishing":[85],"new":[87],"Spearman":[88],"correlation":[89],"record":[90],"0.551":[92],"(vs.":[93],"0.518)":[94],"ProteinGym.":[96],"Reason-Stage,":[99],"an":[100],"Panel":[103],"employs":[104],"chain-of-thought":[105],"reasoning":[106],"audit":[108],"against":[110],"geometric":[111],"structural":[113],"constraints,":[114],"improving":[115],"Top-5":[117],"Hit":[118],"Rate":[119],"by":[120],"up":[121],"367%":[123],"ProteinGym-DMS99.":[125],"The":[126],"Cas12i3":[130],"nuclease":[131],"further":[132],"confirms":[133],"framework's":[135],"efficacy,":[136],"achieving":[137],"46.7%":[139],"positive":[140],"rate":[141],"identifying":[143],"two":[144],"novel":[145],"mutants":[146],"with":[147],"4.23-fold":[148],"5.05-fold":[150],"activity":[151],"improvements.":[152],"Code":[153],"datasets":[155],"are":[156],"released":[157],"GitHub":[159],"(https://github.com/ai4protein/VenusRAR/).":[160]},"counts_by_year":[],"updated_date":"2026-03-25T23:56:10.502304","created_date":"2026-02-04T00:00:00"}