{"id":"https://openalex.org/W7165854980","doi":"https://doi.org/10.48550/arxiv.2606.24940","title":"Stable-Shift: Biologically Structured Prediction of Transcriptional Responses to Unseen Gene Perturbations","display_name":"Stable-Shift: Biologically Structured Prediction of Transcriptional Responses to Unseen Gene Perturbations","publication_year":2026,"publication_date":"2026-06-22","ids":{"openalex":"https://openalex.org/W7165854980","doi":"https://doi.org/10.48550/arxiv.2606.24940"},"language":null,"primary_location":{"id":"doi:10.48550/arxiv.2606.24940","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2606.24940","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.2606.24940","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5099380961","display_name":"Sajib Acharjee Dip","orcid":"https://orcid.org/0009-0007-0959-2638"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Dip, Sajib Acharjee","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5139367496","display_name":"Liqing Zhang","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Zhang, Liqing","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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.895799994468689,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.895799994468689,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.0681999996304512,"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/T10885","display_name":"Gene expression and cancer classification","score":0.007799999788403511,"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/extrapolation","display_name":"Extrapolation","score":0.6151999831199646},{"id":"https://openalex.org/keywords/cosine-similarity","display_name":"Cosine similarity","score":0.5392000079154968},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.5160999894142151},{"id":"https://openalex.org/keywords/correlation","display_name":"Correlation","score":0.5159000158309937},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.49410000443458557},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.44020000100135803},{"id":"https://openalex.org/keywords/pairwise-comparison","display_name":"Pairwise comparison","score":0.42320001125335693},{"id":"https://openalex.org/keywords/gene-ontology","display_name":"Gene ontology","score":0.38089999556541443},{"id":"https://openalex.org/keywords/convolution","display_name":"Convolution (computer science)","score":0.3743000030517578}],"concepts":[{"id":"https://openalex.org/C132459708","wikidata":"https://www.wikidata.org/wiki/Q744069","display_name":"Extrapolation","level":2,"score":0.6151999831199646},{"id":"https://openalex.org/C2780762811","wikidata":"https://www.wikidata.org/wiki/Q1784941","display_name":"Cosine similarity","level":3,"score":0.5392000079154968},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.5160999894142151},{"id":"https://openalex.org/C117220453","wikidata":"https://www.wikidata.org/wiki/Q5172842","display_name":"Correlation","level":2,"score":0.5159000158309937},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.49410000443458557},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.47780001163482666},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4668000042438507},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.454800009727478},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.44020000100135803},{"id":"https://openalex.org/C184898388","wikidata":"https://www.wikidata.org/wiki/Q1435712","display_name":"Pairwise comparison","level":2,"score":0.42320001125335693},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.4146000146865845},{"id":"https://openalex.org/C2987395477","wikidata":"https://www.wikidata.org/wiki/Q135085","display_name":"Gene ontology","level":4,"score":0.38089999556541443},{"id":"https://openalex.org/C45347329","wikidata":"https://www.wikidata.org/wiki/Q5166604","display_name":"Convolution (computer science)","level":3,"score":0.3743000030517578},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.36880001425743103},{"id":"https://openalex.org/C43711488","wikidata":"https://www.wikidata.org/wiki/Q7534783","display_name":"Skew","level":2,"score":0.36320000886917114},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3465000092983246},{"id":"https://openalex.org/C12426560","wikidata":"https://www.wikidata.org/wiki/Q189569","display_name":"Basis (linear algebra)","level":2,"score":0.34139999747276306},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.32850000262260437},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3280999958515167},{"id":"https://openalex.org/C21200559","wikidata":"https://www.wikidata.org/wiki/Q7451068","display_name":"Sensitivity (control systems)","level":2,"score":0.32420000433921814},{"id":"https://openalex.org/C90559484","wikidata":"https://www.wikidata.org/wiki/Q778379","display_name":"Expression (computer science)","level":2,"score":0.3181000053882599},{"id":"https://openalex.org/C28225019","wikidata":"https://www.wikidata.org/wiki/Q4915005","display_name":"Biological network","level":2,"score":0.3118000030517578},{"id":"https://openalex.org/C151201525","wikidata":"https://www.wikidata.org/wiki/Q177239","display_name":"Limit (mathematics)","level":2,"score":0.30570000410079956},{"id":"https://openalex.org/C207201462","wikidata":"https://www.wikidata.org/wiki/Q182505","display_name":"Bayes' theorem","level":3,"score":0.30320000648498535},{"id":"https://openalex.org/C178009071","wikidata":"https://www.wikidata.org/wiki/Q93344","display_name":"Trigonometric functions","level":2,"score":0.2939999997615814},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.29179999232292175},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2720000147819519},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.27070000767707825},{"id":"https://openalex.org/C201797286","wikidata":"https://www.wikidata.org/wiki/Q4914986","display_name":"Biological data","level":2,"score":0.2662000060081482},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.25850000977516174},{"id":"https://openalex.org/C176217482","wikidata":"https://www.wikidata.org/wiki/Q860554","display_name":"Metric (unit)","level":2,"score":0.2572000026702881}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.48550/arxiv.2606.24940","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2606.24940","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.2606.24940","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2606.24940","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":{"Predicting":[0],"transcriptional":[1],"responses":[2],"to":[3,16,85,160],"genetic":[4],"perturbations":[5,51],"could":[6],"reduce":[7],"the":[8,79,90,114,135,154,165,168],"experimental":[9],"burden":[10],"of":[11,148,167],"functional":[12],"genomics,":[13],"but":[14],"extrapolation":[15],"genes":[17],"that":[18,60],"were":[19],"never":[20],"perturbed":[21],"during":[22],"training":[23,50],"remains":[24],"difficult.":[25],"We":[26],"present":[27,169],"Stable-Shift,":[28],"a":[29,45],"structured":[30,150],"method":[31],"for":[32,103],"estimating":[33],"unseen-gene":[34,123],"responses.":[35],"Stable-Shift":[36,95],"aggregates":[37],"single-cell":[38],"measurements":[39],"into":[40],"perturbation-level":[41],"expression":[42,73],"shifts,":[43],"fits":[44],"low-rank":[46],"response":[47],"basis":[48,61],"using":[49],"only,":[52],"and":[53,75,110,140,158],"predicts":[54],"an":[55],"unseen":[56],"gene's":[57],"coordinates":[58],"in":[59,134],"from":[62],"biological":[63],"context.":[64],"The":[65,129],"context":[66],"combines":[67],"STRING":[68],"interactions,":[69],"network":[70],"structure,":[71],"control-cell":[72],"statistics,":[74],"Gene":[76],"Ontology":[77],"annotations;":[78],"evaluated":[80,115],"implementation":[81],"uses":[82],"graph":[83,162],"convolution":[84],"integrate":[86],"these":[87],"inputs.":[88],"On":[89],"supplied":[91,136],"K562":[92],"Perturb-seq":[93],"benchmark,":[94],"obtained":[96],"0.592":[97],"cosine":[98,119],"similarity,":[99],"compared":[100],"with":[101,106],"0.569":[102],"GEARS,":[104],"together":[105],"higher":[107],"Spearman":[108],"correlation":[109],"top-gene":[111],"precision":[112],"among":[113],"methods.":[116],"Its":[117],"mean":[118],"similarity":[120],"over":[121],"five":[122],"splits":[124],"was":[125,132],"0.589":[126],"+/-":[127],"0.008.":[128],"same":[130],"ordering":[131],"observed":[133],"graph-aware,":[137],"residualized,":[138],"gene-space,":[139],"Norman-dataset":[141],"comparisons.":[142],"These":[143],"results":[144],"support":[145],"further":[146],"study":[147],"biologically":[149],"latent-response":[151],"prediction,":[152],"while":[153],"lower":[155],"gene-space":[156],"accuracy":[157],"sensitivity":[159],"sparse":[161],"neighborhoods":[163],"limit":[164],"scope":[166],"conclusions.":[170]},"counts_by_year":[],"updated_date":"2026-07-01T06:00:48.157686","created_date":"2026-06-26T00:00:00"}