{"id":"https://openalex.org/W7161605702","doi":"https://doi.org/10.48550/arxiv.2605.15243","title":"Reading the Cell, Designing the Cure: Perturbation-Conditioned Molecular Diffusion for Function-Oriented Drug Design","display_name":"Reading the Cell, Designing the Cure: Perturbation-Conditioned Molecular Diffusion for Function-Oriented Drug Design","publication_year":2026,"publication_date":"2026-05-14","ids":{"openalex":"https://openalex.org/W7161605702","doi":"https://doi.org/10.48550/arxiv.2605.15243"},"language":null,"primary_location":{"id":"doi:10.48550/arxiv.2605.15243","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2605.15243","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.2605.15243","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5136400565","display_name":"Ziyu Xu","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Xu, Ziyu","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5136451596","display_name":"Zijian Zhang","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Zhang, Zijian","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5136369645","display_name":"Liang Wang","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Wang, Liang","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5136441864","display_name":"Zhiyuan Liu","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Liu, Zhiyuan","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5136438565","display_name":"Qiang Liu","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Liu, Qiang","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021492709","display_name":"Shu Wu","orcid":"https://orcid.org/0000-0002-4040-7388"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Wu, Shu","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5136369645","display_name":"Liang Wang","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Wang, Liang","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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.262800008058548,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.262800008058548,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.2160000056028366,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.15790000557899475,"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/extractor","display_name":"Extractor","score":0.49540001153945923},{"id":"https://openalex.org/keywords/drug-discovery","display_name":"Drug discovery","score":0.39500001072883606},{"id":"https://openalex.org/keywords/generative-grammar","display_name":"Generative grammar","score":0.3813999891281128},{"id":"https://openalex.org/keywords/systems-biology","display_name":"Systems biology","score":0.3630000054836273},{"id":"https://openalex.org/keywords/feature","display_name":"Feature (linguistics)","score":0.34220001101493835},{"id":"https://openalex.org/keywords/matching","display_name":"Matching (statistics)","score":0.3246999979019165},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.322299987077713}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6481000185012817},{"id":"https://openalex.org/C117978034","wikidata":"https://www.wikidata.org/wiki/Q5422192","display_name":"Extractor","level":2,"score":0.49540001153945923},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.39500001072883606},{"id":"https://openalex.org/C39890363","wikidata":"https://www.wikidata.org/wiki/Q36108","display_name":"Generative grammar","level":2,"score":0.3813999891281128},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.37400001287460327},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.3630000054836273},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.34459999203681946},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.34220001101493835},{"id":"https://openalex.org/C165064840","wikidata":"https://www.wikidata.org/wiki/Q1321061","display_name":"Matching (statistics)","level":2,"score":0.3246999979019165},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.322299987077713},{"id":"https://openalex.org/C167966045","wikidata":"https://www.wikidata.org/wiki/Q5532625","display_name":"Generative model","level":3,"score":0.3222000002861023},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.2888000011444092},{"id":"https://openalex.org/C187191949","wikidata":"https://www.wikidata.org/wiki/Q1138496","display_name":"Profiling (computer programming)","level":2,"score":0.2881999909877777},{"id":"https://openalex.org/C2983787585","wikidata":"https://www.wikidata.org/wiki/Q93586","display_name":"Feature matching","level":3,"score":0.2815000116825104},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.2809999883174896},{"id":"https://openalex.org/C64903051","wikidata":"https://www.wikidata.org/wiki/Q2198549","display_name":"Drug development","level":3,"score":0.26579999923706055},{"id":"https://openalex.org/C2780980858","wikidata":"https://www.wikidata.org/wiki/Q110022","display_name":"Dual (grammatical number)","level":2,"score":0.2581999897956848},{"id":"https://openalex.org/C188198153","wikidata":"https://www.wikidata.org/wiki/Q1613840","display_name":"Limiting","level":2,"score":0.25119999051094055},{"id":"https://openalex.org/C177918212","wikidata":"https://www.wikidata.org/wiki/Q803623","display_name":"Perturbation (astronomy)","level":2,"score":0.25049999356269836}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.48550/arxiv.2605.15243","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2605.15243","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.2605.15243","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2605.15243","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":[{"score":0.6175453662872314,"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":[],"abstract_inverted_index":{"When":[0],"reliable":[1],"target":[2],"structures":[3],"are":[4],"unavailable":[5],"at":[6],"scale":[7],"or":[8],"phenotypes":[9],"arise":[10],"from":[11,108,134],"dysregulated":[12],"pathways,":[13],"transcriptomic":[14,44,74,136],"perturbations":[15],"provide":[16],"a":[17,34,87,94,168],"system-level":[18],"functional":[19,159],"readout":[20],"for":[21],"drug":[22,39],"action.":[23],"In":[24],"this":[25,54],"work,":[26],"we":[27,80,162],"formalize":[28],"\\emph{Transcriptome-based":[29],"Drug":[30],"Design":[31],"(TBDD)}":[32],"as":[33],"generative":[35,178],"inverse":[36],"problem:":[37],"designing":[38],"molecules":[40],"conditioned":[41],"on":[42,140],"desired":[43],"state":[45],"transitions.":[46],"We":[47],"analyze":[48],"the":[49,61,71,121,174],"inherently":[50],"ill-posed":[51],"nature":[52],"of":[53,73,176],"task,":[55,172],"which":[56],"is":[57],"further":[58],"complicated":[59],"by":[60,70],"profound":[62],"domain":[63],"gap":[64],"between":[65],"biology":[66],"and":[67,69,124,144,158],"chemistry":[68],"sparsity":[72],"signals.":[75],"To":[76],"address":[77],"these":[78,113],"challenges,":[79],"propose":[81],"\\textbf{\\themodel{}}":[82],"(A":[83],"\\textbf{C}ell\\textbf{U}lar":[84],"\\textbf{R}esponse":[85],"\\textbf{E}ngine),":[86],"multi-resolution":[88],"transcriptome-guided":[89],"diffusion":[90],"framework.":[91],"\\themodel{}":[92,150],"features":[93],"specialized":[95],"\\textbf{Transcriptome":[96],"Perturbation":[97],"Functional":[98],"Feature":[99],"Extractor":[100],"(TFE)}":[101],"that":[102,149],"(1)":[103],"distills":[104],"function-oriented":[105],"perturbation":[106],"embeddings":[107],"pre/post":[109],"states,":[110],"(2)":[111],"aligns":[112],"signatures":[114],"to":[115,119,129],"dual":[116],"chemical":[117],"views":[118],"bridge":[120],"cross-modal":[122],"gap,":[123],"(3)":[125],"performs":[126],"heterogeneity-aware":[127],"aggregation":[128],"extract":[130],"robust":[131],"state-specific":[132],"signals":[133],"noisy":[135],"data.":[137],"Extensive":[138],"evaluations":[139],"both":[141],"standard":[142],"benchmarks":[143],"rigorous":[145],"out-of-distribution":[146],"protocols":[147],"demonstrate":[148],"consistently":[151],"outperforms":[152],"strong":[153],"baselines":[154],"in":[155],"structural":[156],"quality":[157],"consistency.":[160],"Furthermore,":[161],"validate":[163],"its":[164],"practical":[165],"utility":[166],"via":[167],"zero-shot":[169],"gene-inhibitor":[170],"design":[171],"highlighting":[173],"potential":[175],"phenotype-driven":[177],"discovery.":[179]},"counts_by_year":[],"updated_date":"2026-07-01T06:00:48.157686","created_date":"2026-05-19T00:00:00"}
