{"id":"https://openalex.org/W7160413107","doi":"https://doi.org/10.48550/arxiv.2605.02937","title":"Proteo-R1: Reasoning Foundation Models for De Novo Protein Design","display_name":"Proteo-R1: Reasoning Foundation Models for De Novo Protein Design","publication_year":2026,"publication_date":"2026-05-01","ids":{"openalex":"https://openalex.org/W7160413107","doi":"https://doi.org/10.48550/arxiv.2605.02937"},"language":null,"primary_location":{"id":"doi:10.48550/arxiv.2605.02937","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2605.02937","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.2605.02937","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5135507078","display_name":"Fang Wu","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Wu, Fang","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5135450766","display_name":"Weihao Xuan","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Xuan, Weihao","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5135483720","display_name":"Heli Qi","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Qi, Heli","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036649546","display_name":"Hanqun Cao","orcid":"https://orcid.org/0000-0002-8104-1845"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Cao, Hanqun","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5135431260","display_name":"Heng-Jui Chang","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Chang, Heng-Jui","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5135469332","display_name":"Zeqi Zhou","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Zhou, Zeqi","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5135527558","display_name":"Haokai Zhao","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Zhao, Haokai","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5135503579","display_name":"Ma Jian","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Jian, Ma","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5135475474","display_name":"Carl Ma","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Ma, Carl","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5135455843","display_name":"Yu-Chi Cheng","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Cheng, Yu-Chi","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065649249","display_name":"Kuan Pang","orcid":"https://orcid.org/0000-0003-3338-1738"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Pang, Kuan","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5135449888","display_name":"Xiangru Tang","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Tang, Xiangru","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5135452790","display_name":"Zehong Wang","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Wang, Zehong","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5135442800","display_name":"Guanlue Li","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Li, Guanlue","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5135493136","display_name":"Hanchen Wang","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Wang, Hanchen","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081938206","display_name":"Kejun Ying","orcid":"https://orcid.org/0000-0002-1791-6176"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Ying, Kejun","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5135420394","display_name":"Pan Lu","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Lu, Pan","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5135490387","display_name":"Chiho Im","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Im, Chiho","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5135433495","display_name":"Seungju Han","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Han, Seungju","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5135443493","display_name":"Peng Xia","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Xia, Peng","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5135526710","display_name":"Tinson Xu","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Xu, Tinson","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5135466571","display_name":"Yinxi Li","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Li, Yinxi","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5135525741","display_name":"Deyao Zhu","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Zhu, Deyao","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5135421361","display_name":"Pheng-Ann Heng","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Heng, Pheng-Ann","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5135429245","display_name":"Naoto Yokoya","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Yokoya, Naoto","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5072744508","display_name":"Masashi Sugiyama","orcid":"https://orcid.org/0000-0001-6658-6743"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Sugiyama, Masashi","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5135447914","display_name":"Li Erran Li","orcid":"https://orcid.org/0000-0002-3789-0081"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Li, Li Erran","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091272738","display_name":"Jure Leskovec","orcid":"https://orcid.org/0000-0002-5411-923X"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Leskovec, Jure","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5135494627","display_name":"Yejin Choi","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Choi, Yejin","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/T11948","display_name":"Machine Learning in Materials Science","score":0.15839999914169312,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T11948","display_name":"Machine Learning in Materials Science","score":0.15839999914169312,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.1543000042438507,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.10760000348091125,"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/modular-design","display_name":"Modular design","score":0.6018999814987183},{"id":"https://openalex.org/keywords/operationalization","display_name":"Operationalization","score":0.5716999769210815},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.550000011920929},{"id":"https://openalex.org/keywords/generative-grammar","display_name":"Generative grammar","score":0.4896000027656555},{"id":"https://openalex.org/keywords/key","display_name":"Key (lock)","score":0.4738999903202057},{"id":"https://openalex.org/keywords/reuse","display_name":"Reuse","score":0.40779998898506165},{"id":"https://openalex.org/keywords/limiting","display_name":"Limiting","score":0.39149999618530273}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6699000000953674},{"id":"https://openalex.org/C101468663","wikidata":"https://www.wikidata.org/wiki/Q1620158","display_name":"Modular design","level":2,"score":0.6018999814987183},{"id":"https://openalex.org/C9354725","wikidata":"https://www.wikidata.org/wiki/Q286017","display_name":"Operationalization","level":2,"score":0.5716999769210815},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.550000011920929},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5396999716758728},{"id":"https://openalex.org/C39890363","wikidata":"https://www.wikidata.org/wiki/Q36108","display_name":"Generative grammar","level":2,"score":0.4896000027656555},{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.4738999903202057},{"id":"https://openalex.org/C206588197","wikidata":"https://www.wikidata.org/wiki/Q846574","display_name":"Reuse","level":2,"score":0.40779998898506165},{"id":"https://openalex.org/C188198153","wikidata":"https://www.wikidata.org/wiki/Q1613840","display_name":"Limiting","level":2,"score":0.39149999618530273},{"id":"https://openalex.org/C2780966255","wikidata":"https://www.wikidata.org/wiki/Q5474306","display_name":"Foundation (evidence)","level":2,"score":0.37369999289512634},{"id":"https://openalex.org/C184408114","wikidata":"https://www.wikidata.org/wiki/Q1502022","display_name":"Generative Design","level":3,"score":0.3671000003814697},{"id":"https://openalex.org/C83725634","wikidata":"https://www.wikidata.org/wiki/Q7268699","display_name":"Qualitative reasoning","level":2,"score":0.36329999566078186},{"id":"https://openalex.org/C123657996","wikidata":"https://www.wikidata.org/wiki/Q12271","display_name":"Architecture","level":2,"score":0.33410000801086426},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.30000001192092896},{"id":"https://openalex.org/C152769699","wikidata":"https://www.wikidata.org/wiki/Q410814","display_name":"Protein design","level":3,"score":0.28600001335144043},{"id":"https://openalex.org/C195344581","wikidata":"https://www.wikidata.org/wiki/Q2555318","display_name":"Automated reasoning","level":2,"score":0.2802000045776367},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.27469998598098755},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.2660999894142151},{"id":"https://openalex.org/C89288958","wikidata":"https://www.wikidata.org/wiki/Q7301504","display_name":"Reasoning system","level":2,"score":0.2648000121116638}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.48550/arxiv.2605.02937","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2605.02937","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.2605.02937","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2605.02937","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":{"Deep":[0],"learning":[1],"in":[2,74],"\\emph{de":[3],"novo}":[4],"protein":[5,58,88],"design":[6,36,59],"has":[7],"achieved":[8],"atomic-level":[9],"fidelity.":[10],"However,":[11],"existing":[12],"models":[13],"remain":[14],"largely":[15],"non-deliberative:":[16],"they":[17],"directly":[18],"synthesize":[19],"molecular":[20,136],"geometries":[21],"without":[22],"explicitly":[23,62],"reasoning":[24,139,152,171],"about":[25,140],"which":[26,75,119],"residues":[27,98],"or":[28],"interactions":[29],"are":[30,38,107,181],"functionally":[31],"essential.":[32],"As":[33],"a":[34,56,71,76,114],"result,":[35],"decisions":[37,106],"entangled":[39],"with":[40,172],"continuous":[41],"sampling":[42],"dynamics,":[43],"limiting":[44],"interpretability,":[45],"controllability,":[46],"and":[47,91,102,166,179],"systematic":[48],"reuse":[49],"of":[50,169],"biochemical":[51],"knowledge.":[52],"We":[53],"introduce":[54],"\\textbf{Proteo-R1},":[55],"reasoning-guided":[57],"framework":[60],"that":[61,99],"decouples":[63],"\\emph{molecular":[64],"understanding}":[65],"from":[66],"\\emph{geometric":[67],"generation}.":[68],"Proteo-R1":[69,162],"adopts":[70],"dual-expert":[72],"architecture":[73],"multimodal":[77],"large":[78],"language":[79],"model":[80],"(MLLM)":[81],"serves":[82],"as":[83,110,153],"an":[84],"\\emph{understanding":[85],"expert},":[86,118],"analyzing":[87],"sequences,":[89],"structures,":[90],"textual":[92,160],"context":[93],"to":[94,113,147],"identify":[95],"key":[96],"functional":[97],"govern":[100],"binding":[101],"specificity.":[103],"These":[104],"residue-level":[105,155],"then":[108,143],"passed":[109],"hard":[111],"constraints":[112],"separate":[115],"diffusion-based":[116],"\\emph{generation":[117],"performs":[120],"conditional":[121],"co-design":[122],"while":[123],"respecting":[124],"the":[125],"fixed":[126],"interaction":[127],"anchors.":[128],"This":[129],"factorization":[130],"mirrors":[131],"how":[132],"human":[133],"experts":[134],"approach":[135],"engineering:":[137],"first,":[138],"critical":[141],"interactions,":[142],"optimizing":[144],"geometry":[145],"subject":[146],"those":[148],"constraints.":[149],"By":[150],"operationalizing":[151],"explicit":[154],"commitments":[156],"rather":[157],"than":[158],"latent":[159],"guidance,":[161],"achieves":[163],"stable,":[164],"interpretable,":[165],"modular":[167],"integration":[168],"LLM":[170],"state-of-the-art":[173],"geometric":[174],"generative":[175],"models.":[176],"Code,":[177],"data,":[178],"demos":[180],"available":[182],"at":[183],"https://smiles724.github.io/r1/.":[184]},"counts_by_year":[],"updated_date":"2026-07-01T06:00:48.157686","created_date":"2026-05-07T00:00:00"}
