{"id":"https://openalex.org/W4405626526","doi":"https://doi.org/10.48550/arxiv.2412.13478","title":"Efficient Fine-Tuning of Single-Cell Foundation Models Enables Zero-Shot Molecular Perturbation Prediction","display_name":"Efficient Fine-Tuning of Single-Cell Foundation Models Enables Zero-Shot Molecular Perturbation Prediction","publication_year":2024,"publication_date":"2024-12-18","ids":{"openalex":"https://openalex.org/W4405626526","doi":"https://doi.org/10.48550/arxiv.2412.13478"},"language":"en","primary_location":{"id":"pmh:oai:arXiv.org:2412.13478","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2412.13478","pdf_url":"https://arxiv.org/pdf/2412.13478","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},"type":"preprint","indexed_in":["arxiv","datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://arxiv.org/pdf/2412.13478","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5082739901","display_name":"S. Maleki","orcid":null},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Maleki, Sepideh","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5115560710","display_name":"Jan-Christian Huetter","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Huetter, Jan-Christian","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083379859","display_name":"Kangway V. Chuang","orcid":"https://orcid.org/0000-0002-0652-8071"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Chuang, Kangway V.","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5020099374","display_name":"Gabriele Scalia","orcid":"https://orcid.org/0000-0003-3305-9220"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Richmond, David","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002527955","display_name":"Tommaso Biancalani","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Scalia, Gabriele","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"last","author":{"id":null,"display_name":"Biancalani, Tommaso","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Biancalani, Tommaso","raw_affiliation_strings":[],"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5082739901"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":1,"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/T10540","display_name":"Advanced Fluorescence Microscopy Techniques","score":0.9883000254631042,"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"}},"topics":[{"id":"https://openalex.org/T10540","display_name":"Advanced Fluorescence Microscopy Techniques","score":0.9883000254631042,"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/T10522","display_name":"Medical Imaging Techniques and Applications","score":0.9785000085830688,"subfield":{"id":"https://openalex.org/subfields/2741","display_name":"Radiology, Nuclear Medicine and Imaging"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T10857","display_name":"Advanced Electron Microscopy Techniques and Applications","score":0.9758999943733215,"subfield":{"id":"https://openalex.org/subfields/1315","display_name":"Structural 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/perturbation","display_name":"Perturbation (astronomy)","score":0.6118866801261902},{"id":"https://openalex.org/keywords/foundation","display_name":"Foundation (evidence)","score":0.5799213647842407},{"id":"https://openalex.org/keywords/zero","display_name":"Zero (linguistics)","score":0.48270297050476074},{"id":"https://openalex.org/keywords/single-shot","display_name":"Single shot","score":0.4664451777935028},{"id":"https://openalex.org/keywords/one-shot","display_name":"One shot","score":0.4202796220779419},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.4093294143676758},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3615630865097046},{"id":"https://openalex.org/keywords/statistical-physics","display_name":"Statistical physics","score":0.349785178899765},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.24632668495178223},{"id":"https://openalex.org/keywords/quantum-mechanics","display_name":"Quantum mechanics","score":0.19310754537582397},{"id":"https://openalex.org/keywords/optics","display_name":"Optics","score":0.15638384222984314},{"id":"https://openalex.org/keywords/mechanical-engineering","display_name":"Mechanical engineering","score":0.15314996242523193},{"id":"https://openalex.org/keywords/political-science","display_name":"Political science","score":0.0757678747177124}],"concepts":[{"id":"https://openalex.org/C177918212","wikidata":"https://www.wikidata.org/wiki/Q803623","display_name":"Perturbation (astronomy)","level":2,"score":0.6118866801261902},{"id":"https://openalex.org/C2780966255","wikidata":"https://www.wikidata.org/wiki/Q5474306","display_name":"Foundation (evidence)","level":2,"score":0.5799213647842407},{"id":"https://openalex.org/C2780813799","wikidata":"https://www.wikidata.org/wiki/Q3274237","display_name":"Zero (linguistics)","level":2,"score":0.48270297050476074},{"id":"https://openalex.org/C3019835501","wikidata":"https://www.wikidata.org/wiki/Q1310130","display_name":"Single shot","level":2,"score":0.4664451777935028},{"id":"https://openalex.org/C2992734406","wikidata":"https://www.wikidata.org/wiki/Q413267","display_name":"One shot","level":2,"score":0.4202796220779419},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.4093294143676758},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3615630865097046},{"id":"https://openalex.org/C121864883","wikidata":"https://www.wikidata.org/wiki/Q677916","display_name":"Statistical physics","level":1,"score":0.349785178899765},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.24632668495178223},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.19310754537582397},{"id":"https://openalex.org/C120665830","wikidata":"https://www.wikidata.org/wiki/Q14620","display_name":"Optics","level":1,"score":0.15638384222984314},{"id":"https://openalex.org/C78519656","wikidata":"https://www.wikidata.org/wiki/Q101333","display_name":"Mechanical engineering","level":1,"score":0.15314996242523193},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0757678747177124},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"pmh:oai:arXiv.org:2412.13478","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2412.13478","pdf_url":"https://arxiv.org/pdf/2412.13478","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},{"id":"doi:10.48550/arxiv.2412.13478","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2412.13478","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":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article"}],"best_oa_location":{"id":"pmh:oai:arXiv.org:2412.13478","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2412.13478","pdf_url":"https://arxiv.org/pdf/2412.13478","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4405626526.pdf"},"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W2345529346","https://openalex.org/W2316061288","https://openalex.org/W2808886599","https://openalex.org/W2909948317","https://openalex.org/W2329247833","https://openalex.org/W4398241200","https://openalex.org/W4396643691","https://openalex.org/W4404739899","https://openalex.org/W3118576690","https://openalex.org/W4404743872"],"abstract_inverted_index":{"Predicting":[0],"transcriptional":[1],"responses":[2,113],"to":[3,10,66,114,122,132,155,160],"novel":[4,115],"drugs":[5],"provides":[6],"a":[7,73,128],"unique":[8],"opportunity":[9],"accelerate":[11],"biomedical":[12],"research":[13],"and":[14,23,63,152],"advance":[15],"drug":[16],"discovery":[17],"efforts.":[18],"However,":[19],"the":[20,31,38,86,96,109,119,150],"inherent":[21],"complexity":[22],"high":[24],"dimensionality":[25],"of":[26,53,55,85,111],"cellular":[27,112],"responses,":[28],"combined":[29],"with":[30,146],"extremely":[32],"limited":[33],"available":[34],"experimental":[35],"data,":[36],"makes":[37],"task":[39],"challenging.":[40],"In":[41],"this":[42],"study,":[43],"we":[44],"leverage":[45],"single-cell":[46],"foundation":[47,88],"models":[48],"(FMs)":[49],"pre-trained":[50],"on":[51],"tens":[52],"millions":[54],"single":[56],"cells,":[57],"encompassing":[58],"multiple":[59],"cell":[60,124,157],"types,":[61],"states,":[62],"disease":[64],"annotations,":[65],"address":[67],"molecular":[68,92],"perturbation":[69],"prediction.":[70],"We":[71,126],"introduce":[72],"drug-conditional":[74],"adapter":[75],"that":[76],"allows":[77,106],"efficient":[78],"fine-tuning":[79],"by":[80],"training":[81],"less":[82],"than":[83],"1%":[84],"original":[87],"model,":[89],"thus":[90],"enabling":[91],"conditioning":[93],"while":[94],"preserving":[95],"rich":[97],"biological":[98],"representation":[99],"learned":[100],"during":[101],"pre-training.":[102],"The":[103],"proposed":[104],"strategy":[105],"not":[107],"only":[108],"prediction":[110],"drugs,":[116],"but":[117],"also":[118],"zero-shot":[120,153],"generalization":[121,138,154],"unseen":[123],"lines.":[125],"establish":[127],"robust":[129],"evaluation":[130],"framework":[131],"assess":[133],"model":[134],"performance":[135],"across":[136,143],"different":[137],"tasks,":[139],"demonstrating":[140],"state-of-the-art":[141],"results":[142],"all":[144],"settings,":[145],"significant":[147],"improvements":[148],"in":[149],"few-shot":[151],"new":[156],"lines":[158],"compared":[159],"existing":[161],"baselines.":[162]},"counts_by_year":[{"year":2025,"cited_by_count":1}],"updated_date":"2026-02-09T09:26:11.010843","created_date":"2025-10-10T00:00:00"}
