{"id":"https://openalex.org/W7164839590","doi":"https://doi.org/10.48550/arxiv.2606.14510","title":"PepALD: Macrocyclic Peptide Generation via Autoregressive Latent Diffusion","display_name":"PepALD: Macrocyclic Peptide Generation via Autoregressive Latent Diffusion","publication_year":2026,"publication_date":"2026-06-12","ids":{"openalex":"https://openalex.org/W7164839590","doi":"https://doi.org/10.48550/arxiv.2606.14510"},"language":null,"primary_location":{"id":"doi:10.48550/arxiv.2606.14510","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2606.14510","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":"Preprint"},"type":"preprint","indexed_in":["datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://doi.org/10.48550/arxiv.2606.14510","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5138687497","display_name":"Junming Zhang","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Zhang, Junming","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5138688848","display_name":"Siyu Yi","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Yi, Siyu","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5138668345","display_name":"Wei Ju","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Ju, Wei","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5044318086","display_name":"Zhonghui Gu","orcid":"https://orcid.org/0000-0001-6142-4358"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Gu, Zhonghui","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/T10911","display_name":"Chemical Synthesis and Analysis","score":0.4740999937057495,"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/T10911","display_name":"Chemical Synthesis and Analysis","score":0.4740999937057495,"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/T13326","display_name":"Biochemical and Structural Characterization","score":0.12759999930858612,"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/T11103","display_name":"Antimicrobial Peptides and Activities","score":0.09430000185966492,"subfield":{"id":"https://openalex.org/subfields/2404","display_name":"Microbiology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/autoregressive-model","display_name":"Autoregressive model","score":0.7470999956130981},{"id":"https://openalex.org/keywords/peptide","display_name":"Peptide","score":0.5745000243186951},{"id":"https://openalex.org/keywords/in-silico","display_name":"In silico","score":0.49540001153945923},{"id":"https://openalex.org/keywords/nonlinear-autoregressive-exogenous-model","display_name":"Nonlinear autoregressive exogenous model","score":0.4918000102043152},{"id":"https://openalex.org/keywords/monomer","display_name":"Monomer","score":0.4821000099182129},{"id":"https://openalex.org/keywords/latent-variable","display_name":"Latent variable","score":0.4207000136375427},{"id":"https://openalex.org/keywords/ring","display_name":"Ring (chemistry)","score":0.3889999985694885}],"concepts":[{"id":"https://openalex.org/C159877910","wikidata":"https://www.wikidata.org/wiki/Q2202883","display_name":"Autoregressive model","level":2,"score":0.7470999956130981},{"id":"https://openalex.org/C2779281246","wikidata":"https://www.wikidata.org/wiki/Q172847","display_name":"Peptide","level":2,"score":0.5745000243186951},{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.49540001153945923},{"id":"https://openalex.org/C42536954","wikidata":"https://www.wikidata.org/wiki/Q7049462","display_name":"Nonlinear autoregressive exogenous model","level":3,"score":0.4918000102043152},{"id":"https://openalex.org/C166940927","wikidata":"https://www.wikidata.org/wiki/Q178827","display_name":"Monomer","level":3,"score":0.4821000099182129},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.48179998993873596},{"id":"https://openalex.org/C51167844","wikidata":"https://www.wikidata.org/wiki/Q4422623","display_name":"Latent variable","level":2,"score":0.4207000136375427},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.39559999108314514},{"id":"https://openalex.org/C2780378348","wikidata":"https://www.wikidata.org/wiki/Q25351438","display_name":"Ring (chemistry)","level":2,"score":0.3889999985694885},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.3718999922275543},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.364300012588501},{"id":"https://openalex.org/C2781338088","wikidata":"https://www.wikidata.org/wiki/Q903495","display_name":"Residue (chemistry)","level":2,"score":0.34929999709129333},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.3384999930858612},{"id":"https://openalex.org/C30795276","wikidata":"https://www.wikidata.org/wiki/Q7389877","display_name":"SETAR","level":5,"score":0.3133000135421753},{"id":"https://openalex.org/C2781249084","wikidata":"https://www.wikidata.org/wiki/Q908656","display_name":"Preference","level":2,"score":0.3005000054836273},{"id":"https://openalex.org/C167966045","wikidata":"https://www.wikidata.org/wiki/Q5532625","display_name":"Generative model","level":3,"score":0.2937999963760376},{"id":"https://openalex.org/C155515750","wikidata":"https://www.wikidata.org/wiki/Q1059955","display_name":"Synthetic membrane","level":3,"score":0.29030001163482666},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.2630999982357025},{"id":"https://openalex.org/C160920958","wikidata":"https://www.wikidata.org/wiki/Q7662746","display_name":"Synthetic data","level":2,"score":0.2515000104904175},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.2508000135421753},{"id":"https://openalex.org/C39890363","wikidata":"https://www.wikidata.org/wiki/Q36108","display_name":"Generative grammar","level":2,"score":0.25049999356269836}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.48550/arxiv.2606.14510","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2606.14510","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":"Preprint"}],"best_oa_location":{"id":"doi:10.48550/arxiv.2606.14510","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2606.14510","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":"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":{"Macrocyclic":[0],"peptides":[1],"are":[2],"promising":[3],"therapeutic":[4],"candidates":[5],"for":[6,59],"intracellular":[7],"targets,":[8],"but":[9],"their":[10],"design":[11],"requires":[12],"simultaneous":[13],"control":[14],"over":[15],"non-natural":[16],"monomer":[17],"chemistry,":[18],"ring":[19,87],"topology,":[20],"membrane":[21],"permeability,":[22],"and":[23,92,111],"target":[24],"binding.":[25],"Existing":[26],"SMILES-":[27],"or":[28,39],"HELM-string":[29],"generative":[30],"models":[31],"either":[32],"operate":[33],"in":[34,80],"long":[35],"atom-level":[36],"sequence":[37],"spaces":[38],"treat":[40],"monomers":[41,69],"as":[42],"symbolic":[43],"tokens":[44],"with":[45,70],"limited":[46],"chemical":[47,72],"grounding.":[48],"We":[49],"introduce":[50],"PepALD,":[51],"an":[52],"Autoregressive":[53],"Latent":[54],"Diffusion":[55],"(ALD)":[56],"foundation":[57],"model":[58,66],"\\textit{de":[60],"novo}":[61],"macrocyclic":[62],"peptide":[63,116],"generation.":[64],"The":[65],"represents":[67],"HELM":[68],"structured":[71],"embeddings,":[73],"generates":[74],"each":[75],"residue":[76],"through":[77],"context-conditioned":[78],"diffusion":[79],"chemically":[81],"informed":[82],"latent":[83],"space,":[84],"predicts":[85],"R-group-aware":[86],"closures":[88],"during":[89],"autoregressive":[90],"generation,":[91],"aligns":[93],"the":[94],"denoiser":[95],"to":[96],"affinity":[97],"rewards":[98],"using":[99],"winner-protected":[100],"diffusion-adapted":[101],"preference":[102],"optimization.":[103],"In":[104],"silico":[105],"experiments":[106],"demonstrate":[107],"PepALD's":[108],"generation":[109,117],"quality":[110],"reward-optimization":[112],"performance":[113],"against":[114],"representative":[115],"baselines.":[118]},"counts_by_year":[],"updated_date":"2026-07-01T06:00:48.157686","created_date":"2026-06-16T00:00:00"}