{"id":"https://openalex.org/W4400140744","doi":"https://doi.org/10.1093/bioinformatics/btae244","title":"AttentionPert: accurately modeling multiplexed genetic perturbations with multi-scale effects","display_name":"AttentionPert: accurately modeling multiplexed genetic perturbations with multi-scale effects","publication_year":2024,"publication_date":"2024-06-28","ids":{"openalex":"https://openalex.org/W4400140744","doi":"https://doi.org/10.1093/bioinformatics/btae244","pmid":"https://pubmed.ncbi.nlm.nih.gov/38940174"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btae244","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae244","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1093/bioinformatics/btae244","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5072277102","display_name":"Ding Bai","orcid":"https://orcid.org/0000-0002-5058-4329"},"institutions":[{"id":"https://openalex.org/I4210113480","display_name":"Mohamed bin Zayed University of Artificial Intelligence","ror":"https://ror.org/0258gkt32","country_code":"AE","type":"education","lineage":["https://openalex.org/I4210113480"]}],"countries":["AE"],"is_corresponding":false,"raw_author_name":"Ding Bai","raw_affiliation_strings":["Machine Learning Department, Mohamed bin Zayed University of Artificial Intelligence , Abu Dhabi, 00000, United Arabic Emirates"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Machine Learning Department, Mohamed bin Zayed University of Artificial Intelligence , Abu Dhabi, 00000, United Arabic Emirates","institution_ids":["https://openalex.org/I4210113480"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047695651","display_name":"Caleb N. Ellington","orcid":"https://orcid.org/0000-0001-7029-8023"},"institutions":[{"id":"https://openalex.org/I74973139","display_name":"Carnegie Mellon University","ror":"https://ror.org/05x2bcf33","country_code":"US","type":"education","lineage":["https://openalex.org/I74973139"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Caleb N Ellington","raw_affiliation_strings":["Computational Biology Department, Carnegie Mellon University , Pittsburgh, PA, 15213, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computational Biology Department, Carnegie Mellon University , Pittsburgh, PA, 15213, United States","institution_ids":["https://openalex.org/I74973139"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042783792","display_name":"Shentong Mo","orcid":"https://orcid.org/0000-0003-3308-9585"},"institutions":[{"id":"https://openalex.org/I4210113480","display_name":"Mohamed bin Zayed University of Artificial Intelligence","ror":"https://ror.org/0258gkt32","country_code":"AE","type":"education","lineage":["https://openalex.org/I4210113480"]}],"countries":["AE"],"is_corresponding":false,"raw_author_name":"Shentong Mo","raw_affiliation_strings":["Machine Learning Department, Mohamed bin Zayed University of Artificial Intelligence , Abu Dhabi, 00000, United Arabic Emirates"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Machine Learning Department, Mohamed bin Zayed University of Artificial Intelligence , Abu Dhabi, 00000, United Arabic Emirates","institution_ids":["https://openalex.org/I4210113480"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101589053","display_name":"Le Song","orcid":"https://orcid.org/0000-0001-6261-6570"},"institutions":[{"id":"https://openalex.org/I4210113480","display_name":"Mohamed bin Zayed University of Artificial Intelligence","ror":"https://ror.org/0258gkt32","country_code":"AE","type":"education","lineage":["https://openalex.org/I4210113480"]}],"countries":["AE"],"is_corresponding":true,"raw_author_name":"Le Song","raw_affiliation_strings":["Machine Learning Department, Mohamed bin Zayed University of Artificial Intelligence , Abu Dhabi, 00000, United Arabic Emirates"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Machine Learning Department, Mohamed bin Zayed University of Artificial Intelligence , Abu Dhabi, 00000, United Arabic Emirates","institution_ids":["https://openalex.org/I4210113480"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5009547049","display_name":"Eric P. Xing","orcid":"https://orcid.org/0009-0005-9158-4201"},"institutions":[{"id":"https://openalex.org/I4210113480","display_name":"Mohamed bin Zayed University of Artificial Intelligence","ror":"https://ror.org/0258gkt32","country_code":"AE","type":"education","lineage":["https://openalex.org/I4210113480"]},{"id":"https://openalex.org/I74973139","display_name":"Carnegie Mellon University","ror":"https://ror.org/05x2bcf33","country_code":"US","type":"education","lineage":["https://openalex.org/I74973139"]}],"countries":["AE","US"],"is_corresponding":true,"raw_author_name":"Eric P Xing","raw_affiliation_strings":["Machine Learning Department, Carnegie Mellon University , Pittsburgh, PA, 15213, United States","Machine Learning Department, Mohamed bin Zayed University of Artificial Intelligence , Abu Dhabi, 00000, United Arabic Emirates"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Machine Learning Department, Carnegie Mellon University , Pittsburgh, PA, 15213, United States","institution_ids":["https://openalex.org/I74973139"]},{"raw_affiliation_string":"Machine Learning Department, Mohamed bin Zayed University of Artificial Intelligence , Abu Dhabi, 00000, United Arabic Emirates","institution_ids":["https://openalex.org/I4210113480"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5009547049","https://openalex.org/A5101589053"],"corresponding_institution_ids":["https://openalex.org/I4210113480","https://openalex.org/I74973139"],"apc_list":{"value":3989,"currency":"USD","value_usd":3989},"apc_paid":{"value":3989,"currency":"USD","value_usd":3989},"fwci":2.661,"has_fulltext":true,"cited_by_count":17,"citation_normalized_percentile":{"value":0.9080773,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":99},"biblio":{"volume":"40","issue":"Supplement_1","first_page":"i453","last_page":"i461"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.5896000266075134,"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":0.5896000266075134,"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":0.2515000104904175,"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":0.0494999997317791,"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/computer-science","display_name":"Computer science","score":0.6302109956741333},{"id":"https://openalex.org/keywords/multiplexing","display_name":"Multiplexing","score":0.5809611082077026},{"id":"https://openalex.org/keywords/perturbation","display_name":"Perturbation (astronomy)","score":0.5238635540008545},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.5025765895843506},{"id":"https://openalex.org/keywords/gene-knockout","display_name":"Gene knockout","score":0.47805124521255493},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.4143810570240021},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.39084771275520325},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3310593366622925},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.2726113796234131},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.17674735188484192},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.13150781393051147}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6302109956741333},{"id":"https://openalex.org/C19275194","wikidata":"https://www.wikidata.org/wiki/Q222903","display_name":"Multiplexing","level":2,"score":0.5809611082077026},{"id":"https://openalex.org/C177918212","wikidata":"https://www.wikidata.org/wiki/Q803623","display_name":"Perturbation (astronomy)","level":2,"score":0.5238635540008545},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.5025765895843506},{"id":"https://openalex.org/C77957584","wikidata":"https://www.wikidata.org/wiki/Q1133550","display_name":"Gene knockout","level":3,"score":0.47805124521255493},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.4143810570240021},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.39084771275520325},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3310593366622925},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.2726113796234131},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.17674735188484192},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.13150781393051147},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C76155785","wikidata":"https://www.wikidata.org/wiki/Q418","display_name":"Telecommunications","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btae244","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae244","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:38940174","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38940174","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":"Journal Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:11211811","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11211811","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11211811/pdf/btae244.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btae244","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae244","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1428793945","display_name":"Sample-specific Models for Molecular Portraits of Diseases in Precision Medicine","funder_award_id":"5r01gm140467-04","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G861555943","display_name":null,"funder_award_id":"R01GM140467","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":30,"referenced_works":["https://openalex.org/W2141545183","https://openalex.org/W2561754210","https://openalex.org/W2577994754","https://openalex.org/W2611370172","https://openalex.org/W2616922646","https://openalex.org/W2620230519","https://openalex.org/W2902000707","https://openalex.org/W2921591500","https://openalex.org/W2951381561","https://openalex.org/W2952631022","https://openalex.org/W2965552103","https://openalex.org/W2969093152","https://openalex.org/W2973232653","https://openalex.org/W2997831639","https://openalex.org/W3013151148","https://openalex.org/W3042427971","https://openalex.org/W3099179344","https://openalex.org/W3113769443","https://openalex.org/W3134444564","https://openalex.org/W3179857518","https://openalex.org/W3200735940","https://openalex.org/W3209545809","https://openalex.org/W4281716291","https://openalex.org/W4319591822","https://openalex.org/W4375955255","https://openalex.org/W4385955324","https://openalex.org/W4392168151","https://openalex.org/W4399387478","https://openalex.org/W6738547027","https://openalex.org/W6855843166"],"related_works":["https://openalex.org/W2481184119","https://openalex.org/W2079628566","https://openalex.org/W2890791469","https://openalex.org/W2147169944","https://openalex.org/W4251457771","https://openalex.org/W2078091825","https://openalex.org/W3008427980","https://openalex.org/W2884173634","https://openalex.org/W2091570353","https://openalex.org/W4225426244"],"abstract_inverted_index":{"MOTIVATION:":[0],"Genetic":[1],"perturbations":[2,58,82,171],"(e.g.":[3],"knockouts,":[4],"variants)":[5],"have":[6],"laid":[7],"the":[8,30,51,100,105,109,143,167],"foundation":[9],"for":[10],"our":[11],"understanding":[12],"of":[13,32,54,104,115,169],"many":[14],"diseases,":[15],"implicating":[16],"pathogenic":[17],"mechanisms":[18],"and":[19,83,91,108,129,151,172],"indicating":[20],"therapeutic":[21],"targets.":[22],"However,":[23],"experimental":[24],"assays":[25],"are":[26],"fundamentally":[27],"limited":[28],"by":[29,41,67],"number":[31],"measurable":[33],"perturbations.":[34,131],"Computational":[35],"methods":[36],"can":[37],"fill":[38],"this":[39,66],"gap":[40],"predicting":[42,50,147,174],"perturbation":[43,107],"effects":[44,93],"under":[45,80],"novel":[46,70,153],"conditions,":[47],"but":[48],"accurately":[49,76],"transcriptional":[52,124],"responses":[53,125],"cells":[55],"to":[56,85,121,126],"unseen":[57,86],"remains":[59],"a":[60,69,95,113,158],"significant":[61,159],"challenge.":[62],"RESULTS:":[63],"We":[64],"address":[65],"developing":[68],"attention-based":[71],"neural":[72],"network,":[73],"AttentionPert,":[74],"which":[75],"predicts":[77],"gene":[78,149,154,170],"expression":[79],"multiplexed":[81],"generalizes":[84],"conditions.":[87],"AttentionPert":[88,135,156],"integrates":[89],"global":[90],"local":[92],"in":[94,112,146,165,173],"multi-scale":[96],"model,":[97],"representing":[98],"both":[99,127],"nonuniform":[101],"system-wide":[102],"impact":[103],"genetic":[106],"localized":[110],"disturbance":[111],"network":[114],"gene-gene":[116],"similarities,":[117],"enhancing":[118],"its":[119],"ability":[120],"predict":[122],"nuanced":[123],"single":[128],"multi-gene":[130],"In":[132],"comprehensive":[133],"experiments,":[134],"demonstrates":[136],"superior":[137],"performance":[138],"across":[139],"multiple":[140],"datasets":[141],"outperforming":[142],"state-of-the-art":[144],"method":[145],"differential":[148],"expressions":[150],"revealing":[152],"regulations.":[155],"marks":[157],"improvement":[160],"over":[161],"current":[162],"methods,":[163],"particularly":[164],"handling":[166],"diversity":[168],"out-of-distribution":[175],"scenarios.":[176],"AVAILABILITY":[177],"AND":[178],"IMPLEMENTATION:":[179],"Code":[180],"is":[181],"available":[182],"at":[183],"https://github.com/BaiDing1234/AttentionPert.":[184]},"counts_by_year":[{"year":2026,"cited_by_count":6},{"year":2025,"cited_by_count":8},{"year":2024,"cited_by_count":3}],"updated_date":"2026-08-26T07:47:46.906454","created_date":"2025-10-10T00:00:00"}