{"id":"https://openalex.org/W7160994950","doi":"https://doi.org/10.48550/arxiv.2605.11368","title":"LPDP: Inference-Time Reward Control for Variable-Length DNA Generation with Edit Flows","display_name":"LPDP: Inference-Time Reward Control for Variable-Length DNA Generation with Edit Flows","publication_year":2026,"publication_date":"2026-05-12","ids":{"openalex":"https://openalex.org/W7160994950","doi":"https://doi.org/10.48550/arxiv.2605.11368"},"language":null,"primary_location":{"id":"doi:10.48550/arxiv.2605.11368","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2605.11368","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.2605.11368","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5136054053","display_name":"Jeongchan Kim","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Kim, Jeongchan","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5136031912","display_name":"Yunkyung Ko","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Ko, Yunkyung","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5136062622","display_name":"Jong Chul Ye","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Ye, Jong Chul","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/T12029","display_name":"DNA and Biological Computing","score":0.3718000054359436,"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/T12029","display_name":"DNA and Biological Computing","score":0.3718000054359436,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.2071000039577484,"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/T10505","display_name":"Pluripotent Stem Cells Research","score":0.049800001084804535,"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":0.5181000232696533},{"id":"https://openalex.org/keywords/backup","display_name":"Backup","score":0.5135999917984009},{"id":"https://openalex.org/keywords/edit-distance","display_name":"Edit distance","score":0.4738999903202057},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.4036000072956085},{"id":"https://openalex.org/keywords/control-flow","display_name":"Control flow","score":0.3984000086784363},{"id":"https://openalex.org/keywords/focus","display_name":"Focus (optics)","score":0.3953000009059906},{"id":"https://openalex.org/keywords/bounded-function","display_name":"Bounded function","score":0.37439998984336853},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.3452000021934509}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5946999788284302},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.5181000232696533},{"id":"https://openalex.org/C2780945871","wikidata":"https://www.wikidata.org/wiki/Q194274","display_name":"Backup","level":2,"score":0.5135999917984009},{"id":"https://openalex.org/C44359876","wikidata":"https://www.wikidata.org/wiki/Q5338467","display_name":"Edit distance","level":2,"score":0.4738999903202057},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.412200003862381},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.4036000072956085},{"id":"https://openalex.org/C160191386","wikidata":"https://www.wikidata.org/wiki/Q868299","display_name":"Control flow","level":2,"score":0.3984000086784363},{"id":"https://openalex.org/C192209626","wikidata":"https://www.wikidata.org/wiki/Q190909","display_name":"Focus (optics)","level":2,"score":0.3953000009059906},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3797999918460846},{"id":"https://openalex.org/C34388435","wikidata":"https://www.wikidata.org/wiki/Q2267362","display_name":"Bounded function","level":2,"score":0.37439998984336853},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.3452000021934509},{"id":"https://openalex.org/C37404715","wikidata":"https://www.wikidata.org/wiki/Q380679","display_name":"Dynamic programming","level":2,"score":0.3416000008583069},{"id":"https://openalex.org/C171078966","wikidata":"https://www.wikidata.org/wiki/Q111029","display_name":"Root (linguistics)","level":2,"score":0.32269999384880066},{"id":"https://openalex.org/C2778220771","wikidata":"https://www.wikidata.org/wiki/Q1522579","display_name":"Substitution (logic)","level":2,"score":0.31040000915527344},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.30059999227523804},{"id":"https://openalex.org/C17020691","wikidata":"https://www.wikidata.org/wiki/Q139677","display_name":"Operator (biology)","level":5,"score":0.2849999964237213},{"id":"https://openalex.org/C2775924081","wikidata":"https://www.wikidata.org/wiki/Q55608371","display_name":"Control (management)","level":2,"score":0.2718999981880188},{"id":"https://openalex.org/C125411270","wikidata":"https://www.wikidata.org/wiki/Q18653","display_name":"Encoding (memory)","level":2,"score":0.2703999876976013},{"id":"https://openalex.org/C55166926","wikidata":"https://www.wikidata.org/wiki/Q2892946","display_name":"Oracle","level":2,"score":0.2689000070095062},{"id":"https://openalex.org/C72041958","wikidata":"https://www.wikidata.org/wiki/Q185092","display_name":"Flowchart","level":2,"score":0.2603999972343445},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.26019999384880066}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.48550/arxiv.2605.11368","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2605.11368","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.2605.11368","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2605.11368","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":{"We":[0,138],"study":[1],"the":[2,107],"application":[3],"of":[4,110],"recent":[5],"Edit":[6,28],"Flows":[7,29],"for":[8,12,62,147,155,165],"inference-time":[9],"reward":[10,145,163],"control":[11],"DNA":[13,19,36,64],"sequence":[14,26,159],"generation.":[15],"Unlike":[16],"most":[17],"reward-guided":[18],"generation":[20],"frameworks,":[21],"which":[22],"operate":[23],"on":[24,115],"fixed-length":[25],"spaces,":[27],"have":[30],"a":[31,54,83,94,128,133],"potential":[32],"to":[33,113],"generate":[34],"variable-length":[35,63],"through":[37],"biologically":[38],"plausible":[39],"insertion,":[40,118],"deletion,":[41],"and":[42,57,87,122,161],"substitution":[43],"operations.":[44],"In":[45],"particular,":[46],"we":[47],"propose":[48],"Local":[49],"Perturbation":[50],"Discrete":[51],"Programming":[52],"(LPDP),":[53],"training-free,":[55],"intermediate-state":[56],"action-aware":[58],"local":[59,96,104,124],"re-solving":[60],"operator":[61],"edit-action":[65],"generators":[66],"at":[67,72],"inference":[68],"time.":[69],"More":[70],"specifically,":[71],"each":[73,89],"guided":[74],"rollout":[75],"step,":[76],"LPDP":[77,140],"scores":[78],"one-step":[79],"root":[80,85,91],"edits,":[81],"retains":[82],"near-best":[84],"band,":[86],"re-ranks":[88],"retained":[90],"by":[92],"solving":[93],"bounded":[95],"discrete":[97],"program":[98,105],"around":[99],"its":[100],"child":[101],"sequence.":[102],"This":[103],"uses":[106],"typed":[108],"geometry":[109],"edit":[111],"actions":[112],"focus":[114],"coherent":[116],"substitution,":[117],"or":[119,132],"deletion":[120],"subgraphs,":[121],"aggregates":[123],"continuations":[125],"with":[126],"either":[127],"hard":[129],"Max":[130],"backup":[131],"soft":[134],"log-sum-exponential":[135],"(LSE)":[136],"backup.":[137],"instantiate":[139],"in":[141],"two":[142],"regimes:":[143],"front-loaded":[144],"tilting":[146,164],"enhancer":[148],"optimization,":[149],"where":[150,168],"early":[151],"edits":[152,170],"are":[153],"critical":[154],"establishing":[156],"global":[157],"regulatory":[158],"structure,":[160],"back-loaded":[162],"exon-intron-exon":[166],"inpainting,":[167],"late":[169],"fine-tune":[171],"splice-boundary":[172],"contexts.":[173]},"counts_by_year":[],"updated_date":"2026-07-01T06:00:48.157686","created_date":"2026-05-14T00:00:00"}