{"id":"https://openalex.org/W7134816522","doi":"https://doi.org/10.48550/arxiv.2603.06748","title":"Property-driven Protein Inverse Folding With Multi-Objective Preference Alignment","display_name":"Property-driven Protein Inverse Folding With Multi-Objective Preference Alignment","publication_year":2026,"publication_date":"2026-03-06","ids":{"openalex":"https://openalex.org/W7134816522","doi":"https://doi.org/10.48550/arxiv.2603.06748"},"language":null,"primary_location":{"id":"doi:10.48550/arxiv.2603.06748","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2603.06748","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.2603.06748","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5115597020","display_name":"Xiaoyang Hou","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Hou, Xiaoyang","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5128644217","display_name":"Junqi Liu","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Liu, Junqi","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5128674397","display_name":"Chence Shi","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Shi, Chence","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5128642122","display_name":"Xin Liu","orcid":"https://orcid.org/0000-0001-7228-5648"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Liu, Xin","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5128658252","display_name":"Zhi Yang","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Yang, Zhi","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5128657877","display_name":"Jian Tang","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Tang, Jian","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/T10044","display_name":"Protein Structure and Dynamics","score":0.8147000074386597,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.8147000074386597,"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/T11162","display_name":"Enzyme Structure and Function","score":0.03709999844431877,"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/T11124","display_name":"Protein purification and stability","score":0.01899999938905239,"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/sequence","display_name":"Sequence (biology)","score":0.6761000156402588},{"id":"https://openalex.org/keywords/preference","display_name":"Preference","score":0.6018000245094299},{"id":"https://openalex.org/keywords/property","display_name":"Property (philosophy)","score":0.525600016117096},{"id":"https://openalex.org/keywords/hyperparameter","display_name":"Hyperparameter","score":0.5116999745368958},{"id":"https://openalex.org/keywords/margin","display_name":"Margin (machine learning)","score":0.48170000314712524},{"id":"https://openalex.org/keywords/domain","display_name":"Domain (mathematical analysis)","score":0.46860000491142273},{"id":"https://openalex.org/keywords/in-silico","display_name":"In silico","score":0.42170000076293945},{"id":"https://openalex.org/keywords/folding","display_name":"Folding (DSP implementation)","score":0.40450000762939453},{"id":"https://openalex.org/keywords/protein-design","display_name":"Protein design","score":0.39079999923706055}],"concepts":[{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.6761000156402588},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6674000024795532},{"id":"https://openalex.org/C2781249084","wikidata":"https://www.wikidata.org/wiki/Q908656","display_name":"Preference","level":2,"score":0.6018000245094299},{"id":"https://openalex.org/C189950617","wikidata":"https://www.wikidata.org/wiki/Q937228","display_name":"Property (philosophy)","level":2,"score":0.525600016117096},{"id":"https://openalex.org/C8642999","wikidata":"https://www.wikidata.org/wiki/Q4171168","display_name":"Hyperparameter","level":2,"score":0.5116999745368958},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4893999993801117},{"id":"https://openalex.org/C774472","wikidata":"https://www.wikidata.org/wiki/Q6760393","display_name":"Margin (machine learning)","level":2,"score":0.48170000314712524},{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.46860000491142273},{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.42170000076293945},{"id":"https://openalex.org/C2776545253","wikidata":"https://www.wikidata.org/wiki/Q5464292","display_name":"Folding (DSP implementation)","level":2,"score":0.40450000762939453},{"id":"https://openalex.org/C152769699","wikidata":"https://www.wikidata.org/wiki/Q410814","display_name":"Protein design","level":3,"score":0.39079999923706055},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.37540000677108765},{"id":"https://openalex.org/C207467116","wikidata":"https://www.wikidata.org/wiki/Q4385666","display_name":"Inverse","level":2,"score":0.3578000068664551},{"id":"https://openalex.org/C4679612","wikidata":"https://www.wikidata.org/wiki/Q866298","display_name":"Aggregate (composite)","level":2,"score":0.3305000066757202},{"id":"https://openalex.org/C204328495","wikidata":"https://www.wikidata.org/wiki/Q847556","display_name":"Protein folding","level":2,"score":0.3278999924659729},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.3070000112056732},{"id":"https://openalex.org/C2778049539","wikidata":"https://www.wikidata.org/wiki/Q17002908","display_name":"Bayesian optimization","level":2,"score":0.28439998626708984},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.2818000018596649},{"id":"https://openalex.org/C112972136","wikidata":"https://www.wikidata.org/wiki/Q7595718","display_name":"Stability (learning theory)","level":2,"score":0.27970001101493835},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.2718999981880188},{"id":"https://openalex.org/C10485038","wikidata":"https://www.wikidata.org/wiki/Q48996162","display_name":"Hyperparameter optimization","level":3,"score":0.26750001311302185},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.266400009393692},{"id":"https://openalex.org/C2777002520","wikidata":"https://www.wikidata.org/wiki/Q7783261","display_name":"Thermotoga maritima","level":4,"score":0.26499998569488525},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.25940001010894775},{"id":"https://openalex.org/C10010492","wikidata":"https://www.wikidata.org/wiki/Q3142557","display_name":"Protein sequencing","level":4,"score":0.2590999901294708},{"id":"https://openalex.org/C88031987","wikidata":"https://www.wikidata.org/wiki/Q1377767","display_name":"Multiple sequence alignment","level":5,"score":0.2551000118255615},{"id":"https://openalex.org/C18051474","wikidata":"https://www.wikidata.org/wiki/Q899656","display_name":"Protein structure prediction","level":3,"score":0.2531000077724457},{"id":"https://openalex.org/C22367795","wikidata":"https://www.wikidata.org/wiki/Q7625208","display_name":"Structured prediction","level":2,"score":0.2515999972820282}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.48550/arxiv.2603.06748","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2603.06748","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.2603.06748","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2603.06748","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":{"Protein":[0],"sequence":[1,130,154],"design":[2,131,144],"must":[3],"balance":[4],"designability,":[5],"defined":[6],"as":[7,22],"the":[8,113,118],"ability":[9],"to":[10,74,96,112],"recover":[11],"a":[12,63,85,92],"target":[13,46],"backbone,":[14,117],"with":[15,91],"multiple,":[16],"often":[17],"competing,":[18],"developability":[19,77,123],"properties":[20,31],"such":[21],"solubility,":[23],"thermostability,":[24],"and":[25,48,102,141],"expression.":[26],"Existing":[27],"approaches":[28],"address":[29],"these":[30],"through":[32],"post":[33],"hoc":[34],"mutation,":[35],"inference-time":[36],"biasing,":[37],"or":[38,53],"retraining":[39],"on":[40],"property-specific":[41],"subsets,":[42],"yet":[43],"they":[44],"are":[45],"dependent":[47],"demand":[49],"substantial":[50],"domain":[51],"expertise":[52],"careful":[54],"hyperparameter":[55],"tuning.":[56],"In":[57],"this":[58],"paper,":[59],"we":[60],"introduce":[61],"ProtAlign,":[62],"multi-objective":[64],"preference":[65,94,104],"alignment":[66],"framework":[67,150],"that":[68],"fine-tunes":[69],"pretrained":[70],"inverse":[71],"folding":[72],"models":[73],"satisfy":[75],"diverse":[76],"objectives":[78,101],"while":[79],"preserving":[80],"structural":[81],"fidelity.":[82],"ProtAlign":[83],"employs":[84],"semi-online":[86],"Direct":[87],"Preference":[88],"Optimization":[89],"strategy":[90],"flexible":[93],"margin":[95],"mitigate":[97],"conflicts":[98],"among":[99],"competing":[100],"constructs":[103],"pairs":[105],"using":[106],"in":[107],"silico":[108],"property":[109],"predictors.":[110],"Applied":[111],"widely":[114],"used":[115],"ProteinMPNN":[116],"resulting":[119],"model":[120],"MoMPNN":[121],"enhances":[122],"without":[124],"compromising":[125],"designability":[126],"across":[127],"tasks":[128],"including":[129],"for":[132,151],"CATH":[133],"4.3":[134],"crystal":[135],"structures,":[136],"de":[137],"novo":[138],"generated":[139],"backbones,":[140],"real-world":[142],"binder":[143],"scenarios,":[145],"making":[146],"it":[147],"an":[148],"appealing":[149],"practical":[152],"protein":[153],"design.":[155]},"counts_by_year":[],"updated_date":"2026-07-01T06:00:48.157686","created_date":"2026-03-11T00:00:00"}