{"id":"https://openalex.org/W7133795638","doi":"https://doi.org/10.48550/arxiv.2603.03573","title":"STRIDE: Post-Training LLMs to Reason and Refine Bio-Sequences via Edit Trajectories","display_name":"STRIDE: Post-Training LLMs to Reason and Refine Bio-Sequences via Edit Trajectories","publication_year":2026,"publication_date":"2026-03-03","ids":{"openalex":"https://openalex.org/W7133795638","doi":"https://doi.org/10.48550/arxiv.2603.03573"},"language":null,"primary_location":{"id":"pmh:doi:10.48550/arxiv.2603.03573","is_oa":true,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S4406922384","display_name":"Open MIND","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Article"},"type":"preprint","indexed_in":["datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":null,"any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5128164047","display_name":"Daiheng Zhang","orcid":null},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Zhang, Daiheng","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5128162640","display_name":"Shiyang Zhang","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Zhang, Shiyang","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":null,"display_name":"He, Sizhuang","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"He, Sizhuang","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5128173545","display_name":"Yangtian Zhang","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Zhang, Yangtian","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":null,"display_name":"Rizvi, Syed Asad","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Rizvi, Syed Asad","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5128202531","display_name":"David van Dijk","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"van Dijk, David","raw_affiliation_strings":[],"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5128164047"],"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/T10878","display_name":"CRISPR and Genetic Engineering","score":0.3395000100135803,"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/T10878","display_name":"CRISPR and Genetic Engineering","score":0.3395000100135803,"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/T12859","display_name":"Cell Image Analysis Techniques","score":0.0869000032544136,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"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":0.0649000033736229,"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/executable","display_name":"Executable","score":0.6276999711990356},{"id":"https://openalex.org/keywords/novelty","display_name":"Novelty","score":0.5473999977111816},{"id":"https://openalex.org/keywords/trajectory","display_name":"Trajectory","score":0.5327000021934509},{"id":"https://openalex.org/keywords/controllability","display_name":"Controllability","score":0.5163000226020813},{"id":"https://openalex.org/keywords/string","display_name":"String (physics)","score":0.4641999900341034},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.45890000462532043},{"id":"https://openalex.org/keywords/iterative-refinement","display_name":"Iterative refinement","score":0.4530999958515167},{"id":"https://openalex.org/keywords/code","display_name":"Code (set theory)","score":0.42719998955726624},{"id":"https://openalex.org/keywords/stride","display_name":"STRIDE","score":0.42640000581741333}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6802999973297119},{"id":"https://openalex.org/C160145156","wikidata":"https://www.wikidata.org/wiki/Q778586","display_name":"Executable","level":2,"score":0.6276999711990356},{"id":"https://openalex.org/C2778738651","wikidata":"https://www.wikidata.org/wiki/Q16546687","display_name":"Novelty","level":2,"score":0.5473999977111816},{"id":"https://openalex.org/C13662910","wikidata":"https://www.wikidata.org/wiki/Q193139","display_name":"Trajectory","level":2,"score":0.5327000021934509},{"id":"https://openalex.org/C48209547","wikidata":"https://www.wikidata.org/wiki/Q1331104","display_name":"Controllability","level":2,"score":0.5163000226020813},{"id":"https://openalex.org/C157486923","wikidata":"https://www.wikidata.org/wiki/Q1376436","display_name":"String (physics)","level":2,"score":0.4641999900341034},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.45890000462532043},{"id":"https://openalex.org/C2779982483","wikidata":"https://www.wikidata.org/wiki/Q6094420","display_name":"Iterative refinement","level":2,"score":0.4530999958515167},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4447999894618988},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.42719998955726624},{"id":"https://openalex.org/C18007350","wikidata":"https://www.wikidata.org/wiki/Q7394815","display_name":"STRIDE","level":2,"score":0.42640000581741333},{"id":"https://openalex.org/C75291252","wikidata":"https://www.wikidata.org/wiki/Q1315756","display_name":"TRACE (psycholinguistics)","level":2,"score":0.4032000005245209},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.382999986410141},{"id":"https://openalex.org/C85847156","wikidata":"https://www.wikidata.org/wiki/Q59015987","display_name":"Verifiable secret sharing","level":3,"score":0.3747999966144562},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.37119999527931213},{"id":"https://openalex.org/C99498987","wikidata":"https://www.wikidata.org/wiki/Q2210247","display_name":"Noise (video)","level":3,"score":0.367000013589859},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.36559998989105225},{"id":"https://openalex.org/C3913047","wikidata":"https://www.wikidata.org/wiki/Q1956265","display_name":"sync","level":3,"score":0.3549000024795532},{"id":"https://openalex.org/C36299963","wikidata":"https://www.wikidata.org/wiki/Q1369844","display_name":"Observability","level":2,"score":0.3513000011444092},{"id":"https://openalex.org/C157286648","wikidata":"https://www.wikidata.org/wiki/Q846780","display_name":"Kalman filter","level":2,"score":0.35019999742507935},{"id":"https://openalex.org/C2777303404","wikidata":"https://www.wikidata.org/wiki/Q759757","display_name":"Convergence (economics)","level":2,"score":0.32589998841285706},{"id":"https://openalex.org/C2776459999","wikidata":"https://www.wikidata.org/wiki/Q2119376","display_name":"Fidelity","level":2,"score":0.3231000006198883},{"id":"https://openalex.org/C177321328","wikidata":"https://www.wikidata.org/wiki/Q13580479","display_name":"Goldilocks principle","level":2,"score":0.3192000091075897},{"id":"https://openalex.org/C2780339515","wikidata":"https://www.wikidata.org/wiki/Q3074698","display_name":"Arrow","level":2,"score":0.3158000111579895},{"id":"https://openalex.org/C2776633867","wikidata":"https://www.wikidata.org/wiki/Q186612","display_name":"Timer","level":3,"score":0.30730000138282776},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.30630001425743103},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.2793999910354614},{"id":"https://openalex.org/C88626702","wikidata":"https://www.wikidata.org/wiki/Q1128903","display_name":"Continuation","level":2,"score":0.2741999924182892},{"id":"https://openalex.org/C44359876","wikidata":"https://www.wikidata.org/wiki/Q5338467","display_name":"Edit distance","level":2,"score":0.27320000529289246},{"id":"https://openalex.org/C143095724","wikidata":"https://www.wikidata.org/wiki/Q515895","display_name":"Odds","level":3,"score":0.26809999346733093},{"id":"https://openalex.org/C124304363","wikidata":"https://www.wikidata.org/wiki/Q673661","display_name":"Abstraction","level":2,"score":0.2651999890804291},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.2644999921321869},{"id":"https://openalex.org/C31972630","wikidata":"https://www.wikidata.org/wiki/Q844240","display_name":"Computer vision","level":1,"score":0.26440000534057617},{"id":"https://openalex.org/C106131492","wikidata":"https://www.wikidata.org/wiki/Q3072260","display_name":"Filter (signal processing)","level":2,"score":0.25949999690055847},{"id":"https://openalex.org/C107457646","wikidata":"https://www.wikidata.org/wiki/Q207434","display_name":"Human\u2013computer interaction","level":1,"score":0.2563999891281128}],"mesh":[],"locations_count":2,"locations":[{"id":"pmh:doi:10.48550/arxiv.2603.03573","is_oa":true,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S4406922384","display_name":"Open MIND","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Article"},{"id":"doi:10.48550/arxiv.2603.03573","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2603.03573","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":"article"}],"best_oa_location":{"id":"pmh:doi:10.48550/arxiv.2603.03573","is_oa":true,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S4406922384","display_name":"Open MIND","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Article"},"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":{"Discrete":[0],"biological":[1],"sequence":[2],"optimization":[3,81],"requires":[4],"iterative":[5],"refinement":[6,15],"under":[7],"strict":[8],"syntactic":[9],"constraints.":[10],"Diffusion":[11],"models":[12],"offer":[13],"progressive":[14],"but":[16],"do":[17],"not":[18],"naturally":[19],"expose":[20],"controllable":[21],"discrete":[22],"edit":[23,76,84],"operations,":[24],"while":[25,89,111],"autoregressive":[26],"LLMs":[27],"often":[28],"lack":[29],"explicit":[30],"long-horizon":[31],"planning":[32],"for":[33,66],"constrained":[34],"edits.":[35],"We":[36],"propose":[37],"STRIDE":[38,69,101],"(Sequence":[39],"Trajectory":[40],"Refinement":[41],"via":[42],"Internalized":[43],"Denoising":[44],"Emulation),":[45],"a":[46,62],"post-training":[47],"framework":[48],"that":[49],"trains":[50],"an":[51],"LLM":[52],"to":[53,82,109,116,125],"emit":[54],"executable":[55],"trajectories":[56,85],"of":[57],"atomic":[58],"edits":[59],"(INSERT/DELETE/REPLACE)":[60],"as":[61],"verifiable":[63],"reasoning":[64],"trace":[65],"variable-length":[67,103],"refinement.":[68],"combines":[70],"supervised":[71],"fine-tuning":[72],"on":[73],"Levenshtein-aligned":[74],"shortest":[75],"demonstrations":[77],"with":[78,86],"group-based":[79],"policy":[80],"align":[83],"task":[87],"rewards":[88],"preserving":[90],"coherent":[91],"editing":[92,105],"behavior.":[93],"Across":[94],"protein":[95,104],"fluorescence":[96],"and":[97,118,122],"instruction-conditioned":[98],"molecular":[99],"optimization,":[100],"improves":[102],"success":[106],"from":[107,114],"42%":[108],"89%":[110],"increasing":[112],"novelty":[113],"47%":[115],"97%,":[117],"yields":[119],"stronger":[120],"validity":[121],"controllability":[123],"compared":[124],"diverse":[126],"baselines.":[127],"The":[128],"code":[129],"is":[130],"published":[131],"at":[132],"https://github.com/daiheng-zhang/STRIDE.":[133]},"counts_by_year":[],"updated_date":"2026-04-04T16:13:02.066488","created_date":"2026-03-06T00:00:00"}
