{"id":"https://openalex.org/W4405022525","doi":"https://doi.org/10.26599/bdma.2024.9020034","title":"Transformer-Based Single-Cell Language Model: A Survey","display_name":"Transformer-Based Single-Cell Language Model: A Survey","publication_year":2024,"publication_date":"2024-12-01","ids":{"openalex":"https://openalex.org/W4405022525","doi":"https://doi.org/10.26599/bdma.2024.9020034"},"language":"en","primary_location":{"id":"doi:10.26599/bdma.2024.9020034","is_oa":true,"landing_page_url":"https://doi.org/10.26599/bdma.2024.9020034","pdf_url":null,"source":{"id":"https://openalex.org/S4210209060","display_name":"Big Data Mining and Analytics","issn_l":"2096-0654","issn":["2096-0654"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311901","host_organization_name":"Tsinghua University Press","host_organization_lineage":["https://openalex.org/P4310311901"],"host_organization_lineage_names":["Tsinghua University Press"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Big Data Mining and Analytics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"diamond","oa_url":"https://doi.org/10.26599/bdma.2024.9020034","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5041285376","display_name":"Wei Lan","orcid":"https://orcid.org/0000-0001-5839-7504"},"institutions":[{"id":"https://openalex.org/I150807315","display_name":"Guangxi University","ror":"https://ror.org/02c9qn167","country_code":"CN","type":"education","lineage":["https://openalex.org/I150807315"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Wei Lan","raw_affiliation_strings":["School of Computer, Electronic and Information, Guangxi University,Guangxi Key Laboratory of Multimedia Communications and Network Technology,Nanning,China,530004"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer, Electronic and Information, Guangxi University,Guangxi Key Laboratory of Multimedia Communications and Network Technology,Nanning,China,530004","institution_ids":["https://openalex.org/I150807315"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5114998906","display_name":"Guohang He","orcid":null},"institutions":[{"id":"https://openalex.org/I150807315","display_name":"Guangxi University","ror":"https://ror.org/02c9qn167","country_code":"CN","type":"education","lineage":["https://openalex.org/I150807315"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Guohang He","raw_affiliation_strings":["School of Computer, Electronic and Information, Guangxi University,Guangxi Key Laboratory of Multimedia Communications and Network Technology,Nanning,China,530004"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer, Electronic and Information, Guangxi University,Guangxi Key Laboratory of Multimedia Communications and Network Technology,Nanning,China,530004","institution_ids":["https://openalex.org/I150807315"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100443430","display_name":"Mingyang Liu","orcid":"https://orcid.org/0000-0002-7442-1321"},"institutions":[{"id":"https://openalex.org/I150807315","display_name":"Guangxi University","ror":"https://ror.org/02c9qn167","country_code":"CN","type":"education","lineage":["https://openalex.org/I150807315"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Mingyang Liu","raw_affiliation_strings":["School of Computer and Electronic Information, Guangxi University,Nanning,China,530004"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer and Electronic Information, Guangxi University,Nanning,China,530004","institution_ids":["https://openalex.org/I150807315"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5110566594","display_name":"Qingfeng Chen","orcid":"https://orcid.org/0000-0003-4941-9024"},"institutions":[{"id":"https://openalex.org/I150807315","display_name":"Guangxi University","ror":"https://ror.org/02c9qn167","country_code":"CN","type":"education","lineage":["https://openalex.org/I150807315"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Qingfeng Chen","raw_affiliation_strings":["School of Computer and Electronic Information, Guangxi University,Nanning,China,530004"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer and Electronic Information, Guangxi University,Nanning,China,530004","institution_ids":["https://openalex.org/I150807315"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022715650","display_name":"Junyue Cao","orcid":"https://orcid.org/0000-0003-4097-489X"},"institutions":[{"id":"https://openalex.org/I150807315","display_name":"Guangxi University","ror":"https://ror.org/02c9qn167","country_code":"CN","type":"education","lineage":["https://openalex.org/I150807315"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Junyue Cao","raw_affiliation_strings":["College of Life Science and Technology, Guangxi University,Nanning,China,530004"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Life Science and Technology, Guangxi University,Nanning,China,530004","institution_ids":["https://openalex.org/I150807315"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5017953729","display_name":"Wei Peng","orcid":"https://orcid.org/0000-0003-0185-0800"},"institutions":[{"id":"https://openalex.org/I10660446","display_name":"Kunming University of Science and Technology","ror":"https://ror.org/00xyeez13","country_code":"CN","type":"education","lineage":["https://openalex.org/I10660446"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Wei Peng","raw_affiliation_strings":["Kunming University of Science and Technology,Faculty of Information Engineering and Automation,Kunming,China,650500"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Kunming University of Science and Technology,Faculty of Information Engineering and Automation,Kunming,China,650500","institution_ids":["https://openalex.org/I10660446"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5041285376"],"corresponding_institution_ids":["https://openalex.org/I150807315"],"apc_list":null,"apc_paid":null,"fwci":5.3318,"has_fulltext":false,"cited_by_count":25,"citation_normalized_percentile":{"value":0.96650112,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"7","issue":"4","first_page":"1169","last_page":"1186"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12029","display_name":"DNA and Biological Computing","score":0.9290000200271606,"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/T12029","display_name":"DNA and Biological Computing","score":0.9290000200271606,"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/transformer","display_name":"Transformer","score":0.5428798198699951},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4211474657058716},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.2811390161514282},{"id":"https://openalex.org/keywords/electrical-engineering","display_name":"Electrical engineering","score":0.19486230611801147},{"id":"https://openalex.org/keywords/voltage","display_name":"Voltage","score":0.06520962715148926}],"concepts":[{"id":"https://openalex.org/C66322947","wikidata":"https://www.wikidata.org/wiki/Q11658","display_name":"Transformer","level":3,"score":0.5428798198699951},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4211474657058716},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.2811390161514282},{"id":"https://openalex.org/C119599485","wikidata":"https://www.wikidata.org/wiki/Q43035","display_name":"Electrical engineering","level":1,"score":0.19486230611801147},{"id":"https://openalex.org/C165801399","wikidata":"https://www.wikidata.org/wiki/Q25428","display_name":"Voltage","level":2,"score":0.06520962715148926}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.26599/bdma.2024.9020034","is_oa":true,"landing_page_url":"https://doi.org/10.26599/bdma.2024.9020034","pdf_url":null,"source":{"id":"https://openalex.org/S4210209060","display_name":"Big Data Mining and Analytics","issn_l":"2096-0654","issn":["2096-0654"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311901","host_organization_name":"Tsinghua University Press","host_organization_lineage":["https://openalex.org/P4310311901"],"host_organization_lineage_names":["Tsinghua University Press"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Big Data Mining and Analytics","raw_type":"journal-article"},{"id":"pmh:oai:doaj.org/article:bf1f06a977cb42239948dafdbd395dda","is_oa":true,"landing_page_url":"https://doaj.org/article/bf1f06a977cb42239948dafdbd395dda","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Big Data Mining and Analytics, Vol 7, Iss 4, Pp 1169-1186 (2024)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.26599/bdma.2024.9020034","is_oa":true,"landing_page_url":"https://doi.org/10.26599/bdma.2024.9020034","pdf_url":null,"source":{"id":"https://openalex.org/S4210209060","display_name":"Big Data Mining and Analytics","issn_l":"2096-0654","issn":["2096-0654"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311901","host_organization_name":"Tsinghua University Press","host_organization_lineage":["https://openalex.org/P4310311901"],"host_organization_lineage_names":["Tsinghua University Press"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Big Data Mining and Analytics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G4536776085","display_name":null,"funder_award_id":"2022BZRC009","funder_id":"https://openalex.org/F4320329214","funder_display_name":"Guangxi University of Science and Technology"},{"id":"https://openalex.org/G5100333057","display_name":null,"funder_award_id":"62072124","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G6668546896","display_name":null,"funder_award_id":"2023JJG170006","funder_id":"https://openalex.org/F4320313613","funder_display_name":"Natural Science Foundation of Guangxi Zhuang Autonomous Region"}],"funders":[{"id":"https://openalex.org/F4320313613","display_name":"Natural Science Foundation of Guangxi Zhuang Autonomous Region","ror":null},{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320329214","display_name":"Guangxi University of Science and Technology","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":107,"referenced_works":["https://openalex.org/W1987971958","https://openalex.org/W2069089843","https://openalex.org/W2112796928","https://openalex.org/W2118258530","https://openalex.org/W2132992030","https://openalex.org/W2133465414","https://openalex.org/W2156875677","https://openalex.org/W2166021673","https://openalex.org/W2329659234","https://openalex.org/W2523369352","https://openalex.org/W2523419694","https://openalex.org/W2526262591","https://openalex.org/W2561754210","https://openalex.org/W2562947047","https://openalex.org/W2782454362","https://openalex.org/W2787894218","https://openalex.org/W2796207838","https://openalex.org/W2884001105","https://openalex.org/W2893675751","https://openalex.org/W2894687190","https://openalex.org/W2900694973","https://openalex.org/W2901677030","https://openalex.org/W2905317377","https://openalex.org/W2912390237","https://openalex.org/W2951560273","https://openalex.org/W2955621471","https://openalex.org/W2964110616","https://openalex.org/W2964315448","https://openalex.org/W2965373594","https://openalex.org/W2965552103","https://openalex.org/W2969093152","https://openalex.org/W2979040987","https://openalex.org/W2979911343","https://openalex.org/W2984472267","https://openalex.org/W2985765936","https://openalex.org/W3000350302","https://openalex.org/W3013151148","https://openalex.org/W3027051073","https://openalex.org/W3041561163","https://openalex.org/W3090295751","https://openalex.org/W3092295864","https://openalex.org/W3097173659","https://openalex.org/W3126902084","https://openalex.org/W3129866267","https://openalex.org/W3147254695","https://openalex.org/W3156558106","https://openalex.org/W3165924482","https://openalex.org/W3190734472","https://openalex.org/W3196650609","https://openalex.org/W3198628780","https://openalex.org/W3203701986","https://openalex.org/W3214158901","https://openalex.org/W4200310000","https://openalex.org/W4206092375","https://openalex.org/W4206738105","https://openalex.org/W4210587306","https://openalex.org/W4221102522","https://openalex.org/W4225598893","https://openalex.org/W4235169531","https://openalex.org/W4243355870","https://openalex.org/W4297243391","https://openalex.org/W4297982512","https://openalex.org/W4304172601","https://openalex.org/W4312790276","https://openalex.org/W4313452857","https://openalex.org/W4313706461","https://openalex.org/W4316096017","https://openalex.org/W4321452549","https://openalex.org/W4322770903","https://openalex.org/W4322832102","https://openalex.org/W4361284397","https://openalex.org/W4361984358","https://openalex.org/W4362460300","https://openalex.org/W4366526178","https://openalex.org/W4375955255","https://openalex.org/W4377029825","https://openalex.org/W4385245566","https://openalex.org/W4387526306","https://openalex.org/W4387568450","https://openalex.org/W4387639594","https://openalex.org/W4389937732","https://openalex.org/W4390636271","https://openalex.org/W4392168151","https://openalex.org/W4392934845","https://openalex.org/W4394743912","https://openalex.org/W4394773567","https://openalex.org/W4394805449","https://openalex.org/W4395954533","https://openalex.org/W4399387478","https://openalex.org/W6632118081","https://openalex.org/W6635446068","https://openalex.org/W6763701032","https://openalex.org/W6771626834","https://openalex.org/W6772381481","https://openalex.org/W6779709467","https://openalex.org/W6838322825","https://openalex.org/W6838912544","https://openalex.org/W6839881403","https://openalex.org/W6841192771","https://openalex.org/W6841395340","https://openalex.org/W6855995905","https://openalex.org/W6856795681","https://openalex.org/W6857037981","https://openalex.org/W6857331906","https://openalex.org/W6857622014","https://openalex.org/W6858562064","https://openalex.org/W6907817626"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W4391913857","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W4396696052"],"abstract_inverted_index":{"The":[0],"transformers":[1,28],"have":[2,29],"achieved":[3],"significant":[4],"accomplishments":[5],"in":[6,92,140],"the":[7,44,60,69,84,114,141],"natural":[8],"language":[9,46,71,75,90,118,145],"processing":[10,15],"as":[11,96,131],"its":[12],"outstanding":[13],"parallel":[14],"capabilities":[16],"and":[17,48,62,73,86,108,120],"highly":[18],"flexible":[19],"attention":[20],"mechanism.":[21],"In":[22,36],"addition,":[23],"increasing":[24],"studies":[25],"based":[26,50],"on":[27,51],"been":[30],"proposed":[31],"to":[32,41],"model":[33],"single-cell":[34,45,70,78,89,117,144],"data.":[35],"this":[37,127],"review,":[38],"we":[39,54,67,82,112],"attempt":[40],"systematically":[42],"summarize":[43],"models":[47,72,76,91,119],"applications":[49,87],"transformers.":[52,65],"First,":[53],"provide":[55,121],"a":[56],"detailed":[57],"introduction":[58],"about":[59],"structures":[61],"principles":[63],"of":[64,88,116,143],"Then,":[66],"review":[68,128],"large":[74],"for":[77,135],"data":[79],"analysis.":[80],"Moreover,":[81],"explore":[83],"datasets":[85],"downstream":[93],"tasks,":[94],"such":[95],"batch":[97],"correction,":[98],"cell":[99,101],"clustering,":[100],"type":[102],"annotation,":[103],"gene":[104],"regulatory":[105],"network":[106],"inference,":[107],"perturbation":[109],"response.":[110],"Further,":[111],"discuss":[113],"challenges":[115],"promising":[122],"research":[123],"directions.":[124],"We":[125],"hope":[126],"will":[129],"serve":[130],"an":[132],"up-to-date":[133],"reference":[134],"researchers":[136],"who":[137],"are":[138],"interested":[139],"direction":[142],"models.":[146]},"counts_by_year":[{"year":2026,"cited_by_count":6},{"year":2025,"cited_by_count":16},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":1}],"updated_date":"2026-04-25T08:17:42.794288","created_date":"2025-10-10T00:00:00"}
