{"id":"https://openalex.org/W7160178067","doi":"https://doi.org/10.48550/arxiv.2605.00182","title":"Towards A Generative Protein Evolution Machine with DPLM-Evo","display_name":"Towards A Generative Protein Evolution Machine with DPLM-Evo","publication_year":2026,"publication_date":"2026-04-30","ids":{"openalex":"https://openalex.org/W7160178067","doi":"https://doi.org/10.48550/arxiv.2605.00182"},"language":null,"primary_location":{"id":"doi:10.48550/arxiv.2605.00182","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2605.00182","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.2605.00182","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5050338055","display_name":"Xinyou Wang","orcid":"https://orcid.org/0009-0006-2736-1617"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Wang, Xinyou","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5135197904","display_name":"Liang Hong","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Hong, Liang","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5135278904","display_name":"Jiasheng Ye","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Ye, Jiasheng","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5135281190","display_name":"Zaixiang Zheng","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Zheng, Zaixiang","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5135238099","display_name":"Yu Li","orcid":"https://orcid.org/0000-0002-3636-4872"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Li, Yu","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5130000997","display_name":"Shujian Huang","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Huang, Shujian","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5135199576","display_name":"Quanquan Gu","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Gu, Quanquan","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/T11642","display_name":"Genomics and Rare Diseases","score":0.16940000653266907,"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"}},"topics":[{"id":"https://openalex.org/T11642","display_name":"Genomics and Rare Diseases","score":0.16940000653266907,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.07440000027418137,"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/T12090","display_name":"Language and cultural evolution","score":0.0640999972820282,"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/sequence","display_name":"Sequence (biology)","score":0.5813999772071838},{"id":"https://openalex.org/keywords/kernel","display_name":"Kernel (algebra)","score":0.5658000111579895},{"id":"https://openalex.org/keywords/limiting","display_name":"Limiting","score":0.5324000120162964},{"id":"https://openalex.org/keywords/generative-grammar","display_name":"Generative grammar","score":0.5282999873161316},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.4984000027179718},{"id":"https://openalex.org/keywords/sequence-space","display_name":"Sequence space","score":0.46619999408721924},{"id":"https://openalex.org/keywords/mutation","display_name":"Mutation","score":0.45100000500679016},{"id":"https://openalex.org/keywords/simple","display_name":"Simple (philosophy)","score":0.44530001282691956}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6927000284194946},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.5813999772071838},{"id":"https://openalex.org/C74193536","wikidata":"https://www.wikidata.org/wiki/Q574844","display_name":"Kernel (algebra)","level":2,"score":0.5658000111579895},{"id":"https://openalex.org/C188198153","wikidata":"https://www.wikidata.org/wiki/Q1613840","display_name":"Limiting","level":2,"score":0.5324000120162964},{"id":"https://openalex.org/C39890363","wikidata":"https://www.wikidata.org/wiki/Q36108","display_name":"Generative grammar","level":2,"score":0.5282999873161316},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5005000233650208},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.4984000027179718},{"id":"https://openalex.org/C30711495","wikidata":"https://www.wikidata.org/wiki/Q289411","display_name":"Sequence space","level":3,"score":0.46619999408721924},{"id":"https://openalex.org/C501734568","wikidata":"https://www.wikidata.org/wiki/Q42918","display_name":"Mutation","level":3,"score":0.45100000500679016},{"id":"https://openalex.org/C2780586882","wikidata":"https://www.wikidata.org/wiki/Q7520643","display_name":"Simple (philosophy)","level":2,"score":0.44530001282691956},{"id":"https://openalex.org/C159149176","wikidata":"https://www.wikidata.org/wiki/Q14489129","display_name":"Evolutionary algorithm","level":2,"score":0.39010000228881836},{"id":"https://openalex.org/C167966045","wikidata":"https://www.wikidata.org/wiki/Q5532625","display_name":"Generative model","level":3,"score":0.3869999945163727},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.35429999232292175},{"id":"https://openalex.org/C2992278830","wikidata":"https://www.wikidata.org/wiki/Q483921","display_name":"Adaptive evolution","level":3,"score":0.34040001034736633},{"id":"https://openalex.org/C147816474","wikidata":"https://www.wikidata.org/wiki/Q169525","display_name":"Protein engineering","level":3,"score":0.3197000026702881},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.31450000405311584},{"id":"https://openalex.org/C122280245","wikidata":"https://www.wikidata.org/wiki/Q620622","display_name":"Kernel method","level":3,"score":0.299699991941452},{"id":"https://openalex.org/C2908542902","wikidata":"https://www.wikidata.org/wiki/Q440681","display_name":"Directed Molecular Evolution","level":5,"score":0.2937999963760376},{"id":"https://openalex.org/C2778220771","wikidata":"https://www.wikidata.org/wiki/Q1522579","display_name":"Substitution (logic)","level":2,"score":0.2890999913215637},{"id":"https://openalex.org/C2993683473","wikidata":"https://www.wikidata.org/wiki/Q30693176","display_name":"Amino acid substitution","level":4,"score":0.28700000047683716},{"id":"https://openalex.org/C10010492","wikidata":"https://www.wikidata.org/wiki/Q3142557","display_name":"Protein sequencing","level":4,"score":0.26969999074935913},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.25839999318122864},{"id":"https://openalex.org/C89611455","wikidata":"https://www.wikidata.org/wiki/Q6804646","display_name":"Mechanism (biology)","level":2,"score":0.2563000023365021},{"id":"https://openalex.org/C81917197","wikidata":"https://www.wikidata.org/wiki/Q628760","display_name":"Selection (genetic algorithm)","level":2,"score":0.25619998574256897},{"id":"https://openalex.org/C2778572836","wikidata":"https://www.wikidata.org/wiki/Q380933","display_name":"Space (punctuation)","level":2,"score":0.2515000104904175}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.48550/arxiv.2605.00182","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2605.00182","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.2605.00182","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2605.00182","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":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":[],"abstract_inverted_index":{"Proteins":[0],"are":[1,28],"shaped":[2],"by":[3,55],"gradual":[4],"evolution":[5],"under":[6],"biophysical":[7],"and":[8,21,33,68,76,97,148,167],"functional":[9],"constraints.":[10],"Protein":[11],"language":[12,25],"models":[13],"learn":[14],"rich":[15],"evolutionary":[16,88,132],"constraints":[17],"from":[18,57,109],"large-scale":[19],"sequences,":[20],"discrete":[22,89],"diffusion-based":[23],"protein":[24],"models~(\\eg,":[26],"DPLMs)":[27],"promising":[29],"for":[30,66],"both":[31,73],"understanding":[32,147],"generation.":[34,79],"However,":[35],"existing":[36,170],"DPLMs":[37],"typically":[38],"rely":[39],"on":[40,155],"masked":[41],"diffusion":[42,90],"that":[43,92,135],"contradicts":[44],"a":[45,130],"simple":[46],"biological":[47],"intuition:":[48],"proteins":[49,171],"evolve":[50],"through":[51],"accumulated":[52],"edits,":[53],"not":[54],"emerging":[56],"masks.":[58],"Consequently,":[59],"these":[60,82],"frameworks":[61],"lack":[62],"explicit":[63,173],"pretraining":[64],"objectives":[65],"substitution":[67],"insertion/deletion":[69],"(indel)":[70],"operations,":[71],"limiting":[72],"optimization-style":[74],"post-editing":[75],"flexible":[77],"guided":[78],"To":[80,120],"address":[81],"limitations,":[83],"we":[84,127],"present":[85],"DPLM-Evo,":[86],"an":[87,104],"framework":[91],"explicitly":[93],"predicts":[94],"substitution,":[95],"insertion,":[96],"deletion":[98],"operations":[99],"during":[100],"denoising.":[101],"DPLM-Evo":[102,144],"decouples":[103],"upsampled-length":[105],"latent":[106],"alignment":[107],"space":[108],"the":[110,158],"variable-length":[111,164],"observed":[112],"sequence":[113,146],"space,":[114],"which":[115],"makes":[116],"indel-aware":[117],"generation":[118],"tractable.":[119],"better":[121],"align":[122],"substitutions":[123],"with":[124],"real":[125],"evolution,":[126,166],"further":[128],"introduce":[129],"contextualized":[131],"noising":[133],"kernel":[134],"produces":[136],"biologically":[137],"informed,":[138],"context-dependent":[139],"mutation":[140,151],"patterns.":[141],"Across":[142],"tasks,":[143],"improves":[145],"achieves":[149],"state-of-the-art":[150],"effect":[152],"prediction":[153],"performance":[154],"ProteinGym":[156],"in":[157],"single-sequence":[159],"setting.":[160],"It":[161],"also":[162],"enables":[163],"simulated":[165],"post-editing/optimization":[168],"of":[169],"via":[172],"edit":[174],"trajectories.":[175]},"counts_by_year":[],"updated_date":"2026-07-01T06:00:48.157686","created_date":"2026-05-05T00:00:00"}
