{"id":"https://openalex.org/W7223569586","doi":"https://doi.org/10.64898/2026.10.20.760514","title":"Centered cross-context perturbation transfer on the public 2025 Virtual Cell Challenge benchmark","display_name":"Centered cross-context perturbation transfer on the public 2025 Virtual Cell Challenge benchmark","publication_year":2026,"publication_date":"2026-10-25","ids":{"openalex":"https://openalex.org/W7223569586","doi":"https://doi.org/10.64898/2026.10.20.760514"},"language":"en","primary_location":{"id":"doi:10.64898/2026.10.20.760514","doi":"https://doi.org/10.64898/2026.10.20.760514","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.10.20.760514","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/10/25/2026.10.20.760514.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"volume":null,"type":"preprint","is_traditional":true,"indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.biorxiv.org/content/biorxiv/early/2026/10/25/2026.10.20.760514.full.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5137903459","display_name":"Haoyang Luan","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Haoyang Luan","raw_affiliation_strings":["AGI Institute, School of Computer Science, Shanghai Jiao Tong University, Shanghai 200240, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"AGI Institute, School of Computer Science, Shanghai Jiao Tong University, Shanghai 200240, China","institution_ids":["https://openalex.org/I183067930"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5159182827","display_name":"Letian Chen","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]},{"id":"https://openalex.org/I4405279436","display_name":"Shanghai Innovation Institute","ror":"https://ror.org/01fatbw66","country_code":"CN","type":"education","lineage":["https://openalex.org/I4405279436"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Letian Chen","raw_affiliation_strings":["AGI Institute, School of Computer Science, Shanghai Jiao Tong University, Shanghai 200240, China","Shanghai Innovation Institute, Shanghai, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"AGI Institute, School of Computer Science, Shanghai Jiao Tong University, Shanghai 200240, China","institution_ids":["https://openalex.org/I183067930"]},{"raw_affiliation_string":"Shanghai Innovation Institute, Shanghai, China","institution_ids":["https://openalex.org/I4405279436"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5027377924","display_name":"Gufeng Yu","orcid":"https://orcid.org/0000-0003-0628-8714","observed_orcids":["https://orcid.org/0000-0003-0628-8714"]},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Gufeng Yu","raw_affiliation_strings":["AGI Institute, School of Computer Science, Shanghai Jiao Tong University, Shanghai 200240, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"AGI Institute, School of Computer Science, Shanghai Jiao Tong University, Shanghai 200240, China","institution_ids":["https://openalex.org/I183067930"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5159481982","display_name":"Yang Yang","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Yang Yang","raw_affiliation_strings":["AGI Institute, School of Computer Science, Shanghai Jiao Tong University, Shanghai 200240, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"AGI Institute, School of Computer Science, Shanghai Jiao Tong University, Shanghai 200240, China","institution_ids":["https://openalex.org/I183067930"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5159481982"],"corresponding_institution_ids":["https://openalex.org/I183067930"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"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":0.4399000108242035,"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":0.4399000108242035,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.18729999661445618,"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/T10878","display_name":"CRISPR and Genetic Engineering","score":0.18199999630451202,"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/h1-cell-line","display_name":"H1 cell line","score":0.6190000176429749},{"id":"https://openalex.org/keywords/isotonic-regression","display_name":"isotonic regression","score":0.8610000014305115}],"concepts":[{"id":"https://openalex.org/C177918212","wikidata":"https://www.wikidata.org/wiki/Q803623","display_name":"Perturbation (astronomy)","level":2,"score":0.6901000142097473},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.46560001373291016},{"id":"https://openalex.org/C2780465443","wikidata":"https://www.wikidata.org/wiki/Q852061","display_name":"Champion","level":2,"score":0.4611000120639801},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4366999864578247},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.4122999906539917},{"id":"https://openalex.org/C51632099","wikidata":"https://www.wikidata.org/wiki/Q3985153","display_name":"Training set","level":2,"score":0.3862000107765198},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3662000000476837},{"id":"https://openalex.org/C74193536","wikidata":"https://www.wikidata.org/wiki/Q574844","display_name":"Kernel (algebra)","level":2,"score":0.36329999566078186},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.337799996137619},{"id":"https://openalex.org/C12267149","wikidata":"https://www.wikidata.org/wiki/Q282453","display_name":"Support vector machine","level":2,"score":0.32710000872612},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.30230000615119934},{"id":"https://openalex.org/C83546350","wikidata":"https://www.wikidata.org/wiki/Q1139051","display_name":"Regression","level":2,"score":0.2818000018596649},{"id":"https://openalex.org/C2776175482","wikidata":"https://www.wikidata.org/wiki/Q1195816","display_name":"Transfer (computing)","level":2,"score":0.2773999869823456},{"id":"https://openalex.org/C500300565","wikidata":"https://www.wikidata.org/wiki/Q925667","display_name":"Computer simulation","level":2,"score":0.27570000290870667},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.27459999918937683},{"id":"https://openalex.org/C150899416","wikidata":"https://www.wikidata.org/wiki/Q1820378","display_name":"Transfer of learning","level":2,"score":0.27320000529289246},{"id":"https://openalex.org/C28826006","wikidata":"https://www.wikidata.org/wiki/Q33521","display_name":"Applied mathematics","level":1,"score":0.27079999446868896},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.26910001039505005},{"id":"https://openalex.org/C165160513","wikidata":"https://www.wikidata.org/wiki/Q7524249","display_name":"Singular perturbation","level":2,"score":0.25690001249313354},{"id":"https://openalex.org/C90559484","wikidata":"https://www.wikidata.org/wiki/Q778379","display_name":"Expression (computer science)","level":2,"score":0.2558000087738037},{"id":"https://openalex.org/C122280245","wikidata":"https://www.wikidata.org/wiki/Q620622","display_name":"Kernel method","level":3,"score":0.2500999867916107}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.64898/2026.10.20.760514","doi":"https://doi.org/10.64898/2026.10.20.760514","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.10.20.760514","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/10/25/2026.10.20.760514.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"}],"best_oa_location":{"id":"doi:10.64898/2026.10.20.760514","doi":"https://doi.org/10.64898/2026.10.20.760514","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.10.20.760514","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/10/25/2026.10.20.760514.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W7223569586.pdf","grobid_xml":"https://content.openalex.org/works/W7223569586.grobid-xml"},"referenced_works_count":4,"referenced_works":["https://openalex.org/W4281716291","https://openalex.org/W4411338098","https://openalex.org/W4416595124","https://openalex.org/W7166807662"],"related_works":["https://openalex.org/W7172016238","https://openalex.org/W7134840684","https://openalex.org/W7131372085","https://openalex.org/W7170818249","https://openalex.org/W7212020435","https://openalex.org/W7164752874","https://openalex.org/W7203794921","https://openalex.org/W4360605005","https://openalex.org/W7166870923","https://openalex.org/W7140116110"],"abstract_inverted_index":{"Abstract":[0],"Predicting":[1],"transcriptional":[2],"responses":[3],"across":[4,141],"cellular":[5],"contexts":[6],"requires":[7],"transferring":[8],"both":[9,133],"expression":[10,61],"direction":[11],"and":[12,51,54,95,124,146,160],"differential-expression":[13,28,161],"priority.":[14],"We":[15,63],"developed":[16],"a":[17,27,115,152],"compact":[18],"numerical":[19,154],"method":[20,37],"that":[21],"combines":[22],"public":[23,72],"perturbation":[24,158],"summaries":[25],"with":[26,108,127],"kernel":[29],"fitted":[30],"to":[31,58,156],"H1":[32],"CRISPRi":[33],"training":[34,45],"targets.":[35],"The":[36,88,119],"centers":[38],"an":[39,81],"independent":[40],"KOLF2.1J":[41],"source":[42,84],"on":[43,69],"known":[44],"targets,":[46],"transfers":[47],"its":[48,102],"response":[49],"signs":[50],"magnitude":[52],"ranks,":[53],"uses":[55],"isotonic":[56],"regression":[57],"render":[59],"predicted":[60],"means.":[62],"evaluated":[64],"the":[65,70,75,109],"frozen":[66],"model":[67,89],"retrospectively":[68],"released":[71,85],"TEST100":[73],"of":[74,113,117],"2025":[76],"Virtual":[77],"Cell":[78],"Challenge,":[79],"using":[80],"external":[82],"KOLF":[83],"in":[86],"2026.":[87],"achieved":[90],"DES":[91,123],"0.371834,":[92],"PDS":[93,140],"0.8614,":[94],"MAE":[96,130],"0.302206.":[97],"With":[98],"reconstructed":[99],"historical":[100],"anchors,":[101],"composite":[103],"score":[104,112],"was":[105],"0.341344,":[106],"compared":[107],"archived":[110],"champion":[111],"0.340052,":[114],"difference":[116],"+0.001292.":[118],"comparison":[120],"showed":[121],"higher":[122],"lower":[125],"PDS,":[126],"zero":[128],"normalized":[129],"contributions":[131],"for":[132],"methods.":[134],"Source":[135],"centering":[136],"also":[137],"improved":[138],"development":[139],"all":[142],"three":[143],"TRAIN":[144],"folds":[145],"official":[147],"VALIDATION.":[148],"These":[149],"results":[150],"demonstrate":[151],"practical":[153],"approach":[155],"cross-context":[157],"transfer":[159],"ranking.":[162]},"counts_by_year":[],"updated_date":"2026-11-08T12:12:28.789561","created_date":"2026-10-26T00:00:00"}
