{"id":"https://openalex.org/W7171523608","doi":"https://doi.org/10.1145/3807503.3819992","title":"CellTarNet: Robust Single-Cell Perturbation Prediction using Transformer Generative Model","display_name":"CellTarNet: Robust Single-Cell Perturbation Prediction using Transformer Generative Model","publication_year":2026,"publication_date":"2026-06-30","ids":{"openalex":"https://openalex.org/W7171523608","doi":"https://doi.org/10.1145/3807503.3819992"},"language":null,"primary_location":{"id":"doi:10.1145/3807503.3819992","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3807503.3819992","pdf_url":null,"source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 17th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics","raw_type":"proceedings-article"},"type":"conference-paper","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1145/3807503.3819992","any_repository_has_fulltext":null},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5113150390","display_name":"Shiv Shankar Shankar","orcid":"https://orcid.org/0000-0003-1631-2570"},"institutions":[{"id":"https://openalex.org/I24603500","display_name":"University of Massachusetts Amherst","ror":"https://ror.org/0072zz521","country_code":"US","type":"education","lineage":["https://openalex.org/I24603500"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Shiv Shankar","raw_affiliation_strings":["University of Massachusetts, Amherst, USA"],"raw_orcid":"https://orcid.org/0000-0003-1631-2570","affiliations":[{"raw_affiliation_string":"University of Massachusetts, Amherst, USA","institution_ids":["https://openalex.org/I24603500"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5113150390"],"corresponding_institution_ids":["https://openalex.org/I24603500"],"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":"1","last_page":"6"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":null,"topics":[],"keywords":[{"id":"https://openalex.org/keywords/perturbation","display_name":"Perturbation (astronomy)","score":0.4059999883174896},{"id":"https://openalex.org/keywords/control-theory","display_name":"Control theory (sociology)","score":0.3970000147819519},{"id":"https://openalex.org/keywords/transformer","display_name":"Transformer","score":0.3928999900817871},{"id":"https://openalex.org/keywords/robustness","display_name":"Robustness (evolution)","score":0.3000999987125397}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.4645000100135803},{"id":"https://openalex.org/C177918212","wikidata":"https://www.wikidata.org/wiki/Q803623","display_name":"Perturbation (astronomy)","level":2,"score":0.4059999883174896},{"id":"https://openalex.org/C47446073","wikidata":"https://www.wikidata.org/wiki/Q5165890","display_name":"Control theory (sociology)","level":3,"score":0.3970000147819519},{"id":"https://openalex.org/C66322947","wikidata":"https://www.wikidata.org/wiki/Q11658","display_name":"Transformer","level":3,"score":0.3928999900817871},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.3538999855518341},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3255000114440918},{"id":"https://openalex.org/C63479239","wikidata":"https://www.wikidata.org/wiki/Q7353546","display_name":"Robustness (evolution)","level":3,"score":0.3000999987125397},{"id":"https://openalex.org/C45374587","wikidata":"https://www.wikidata.org/wiki/Q12525525","display_name":"Computation","level":2,"score":0.2847999930381775},{"id":"https://openalex.org/C28826006","wikidata":"https://www.wikidata.org/wiki/Q33521","display_name":"Applied mathematics","level":1,"score":0.24959999322891235}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/3807503.3819992","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3807503.3819992","pdf_url":null,"source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 17th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics","raw_type":"proceedings-article"}],"best_oa_location":{"id":"doi:10.1145/3807503.3819992","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3807503.3819992","pdf_url":null,"source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 17th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics","raw_type":"proceedings-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":13,"referenced_works":["https://openalex.org/W2949228990","https://openalex.org/W2969093152","https://openalex.org/W2993905360","https://openalex.org/W3131922516","https://openalex.org/W4392168151","https://openalex.org/W4392904401","https://openalex.org/W4400387006","https://openalex.org/W4403784877","https://openalex.org/W4408080024","https://openalex.org/W4409566559","https://openalex.org/W4411757935","https://openalex.org/W4412929241","https://openalex.org/W4413495491"],"related_works":[],"abstract_inverted_index":{"Predicting":[0],"transcriptional":[1,63],"responses":[2],"to":[3,16,41,73,94],"perturbations":[4],"is":[5],"challenging":[6],"because":[7],"single-cell":[8],"datasets":[9],"contain":[10],"population-level":[11],"shifts":[12],"that":[13,33,67],"are":[14],"difficult":[15],"separate":[17,83],"from":[18,38,85],"context-specific":[19],"expression":[20],"changes.":[21],"We":[22,69,89],"present":[23],"CellTarNet,":[24],"a":[25,35,51,55,59],"generative":[26],"framework":[27],"based":[28],"on":[29,66],"transformer":[30,45],"normalizing":[31,56],"flows":[32],"learns":[34,58],"transport":[36],"map":[37],"control":[39],"cells":[40],"perturbed":[42,62,80],"cells.":[43],"A":[44],"encoder":[46],"summarizes":[47],"control-cell":[48],"states":[49],"into":[50],"context":[52],"representation,":[53],"while":[54,108],"flow":[57],"distribution":[60,81],"over":[61],"profiles":[64],"conditioned":[65],"context.":[68],"use":[70],"contrastive":[71],"matching":[72],"pull":[74],"predicted":[75],"samples":[76],"toward":[77,97],"the":[78],"true":[79],"and":[82],"them":[84],"mismatched":[86],"perturbation-context":[87],"pairs.":[88],"further":[90],"incorporate":[91],"gene-interaction":[92],"priors":[93],"guide":[95],"attention":[96],"biologically":[98],"plausible":[99],"dependencies.":[100],"Across":[101],"perturbation":[102],"benchmarks,":[103],"CellTarNet":[104],"improves":[105],"distributional":[106],"recovery":[107],"retaining":[109],"competitive":[110],"reconstruction":[111],"accuracy.":[112]},"counts_by_year":[],"updated_date":"2026-07-30T17:31:21.811387","created_date":"2026-07-29T00:00:00"}
