{"id":"https://openalex.org/W4406259516","doi":"https://doi.org/10.1109/bibm62325.2024.10822784","title":"Transformer-Based Gene Expression Levels Prediction Using Multimodal Information","display_name":"Transformer-Based Gene Expression Levels Prediction Using Multimodal Information","publication_year":2024,"publication_date":"2024-12-03","ids":{"openalex":"https://openalex.org/W4406259516","doi":"https://doi.org/10.1109/bibm62325.2024.10822784"},"language":"en","primary_location":{"id":"doi:10.1109/bibm62325.2024.10822784","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm62325.2024.10822784","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2024 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5006420025","display_name":"Tao Song","orcid":"https://orcid.org/0000-0002-0130-3340"},"institutions":[{"id":"https://openalex.org/I4210128818","display_name":"Institute of Software","ror":"https://ror.org/033dfsn42","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210128818"]},{"id":"https://openalex.org/I4210162190","display_name":"China University of Petroleum, East China","ror":"https://ror.org/05gbn2817","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210162190"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Tao Song","raw_affiliation_strings":["Qingdao Institute of Software China University of Petroleum,College of Computer Science and Technology,Qingdao,China"],"affiliations":[{"raw_affiliation_string":"Qingdao Institute of Software China University of Petroleum,College of Computer Science and Technology,Qingdao,China","institution_ids":["https://openalex.org/I4210128818","https://openalex.org/I4210162190"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023015161","display_name":"Zhiyi Pan","orcid":"https://orcid.org/0000-0002-0635-0349"},"institutions":[{"id":"https://openalex.org/I4210162190","display_name":"China University of Petroleum, East China","ror":"https://ror.org/05gbn2817","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210162190"]},{"id":"https://openalex.org/I4210128818","display_name":"Institute of Software","ror":"https://ror.org/033dfsn42","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210128818"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhiyi Pan","raw_affiliation_strings":["Qingdao Institute of Software China University of Petroleum,College of Computer Science and Technology,Qingdao,China"],"affiliations":[{"raw_affiliation_string":"Qingdao Institute of Software China University of Petroleum,College of Computer Science and Technology,Qingdao,China","institution_ids":["https://openalex.org/I4210128818","https://openalex.org/I4210162190"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5112863401","display_name":"Haonan Song","orcid":"https://orcid.org/0009-0003-2183-2586"},"institutions":[{"id":"https://openalex.org/I4210128818","display_name":"Institute of Software","ror":"https://ror.org/033dfsn42","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210128818"]},{"id":"https://openalex.org/I4210162190","display_name":"China University of Petroleum, East China","ror":"https://ror.org/05gbn2817","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210162190"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Haonan Song","raw_affiliation_strings":["Qingdao Institute of Software China University of Petroleum,College of Computer Science and Technology,Qingdao,China"],"affiliations":[{"raw_affiliation_string":"Qingdao Institute of Software China University of Petroleum,College of Computer Science and Technology,Qingdao,China","institution_ids":["https://openalex.org/I4210128818","https://openalex.org/I4210162190"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075642035","display_name":"Yuan Gao","orcid":"https://orcid.org/0000-0002-0832-2982"},"institutions":[{"id":"https://openalex.org/I4210162190","display_name":"China University of Petroleum, East China","ror":"https://ror.org/05gbn2817","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210162190"]},{"id":"https://openalex.org/I4210128818","display_name":"Institute of Software","ror":"https://ror.org/033dfsn42","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210128818"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yuan Gao","raw_affiliation_strings":["Qingdao Institute of Software China University of Petroleum,College of Computer Science and Technology,Qingdao,China"],"affiliations":[{"raw_affiliation_string":"Qingdao Institute of Software China University of Petroleum,College of Computer Science and Technology,Qingdao,China","institution_ids":["https://openalex.org/I4210128818","https://openalex.org/I4210162190"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5019435645","display_name":"Huanhuan Dai","orcid":"https://orcid.org/0000-0002-6331-8038"},"institutions":[{"id":"https://openalex.org/I4210162190","display_name":"China University of Petroleum, East China","ror":"https://ror.org/05gbn2817","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210162190"]},{"id":"https://openalex.org/I4210128818","display_name":"Institute of Software","ror":"https://ror.org/033dfsn42","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210128818"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Huanhuan Dai","raw_affiliation_strings":["Qingdao Institute of Software China University of Petroleum,College of Computer Science and Technology,Qingdao,China"],"affiliations":[{"raw_affiliation_string":"Qingdao Institute of Software China University of Petroleum,College of Computer Science and Technology,Qingdao,China","institution_ids":["https://openalex.org/I4210128818","https://openalex.org/I4210162190"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100333854","display_name":"Xun Wang","orcid":"https://orcid.org/0000-0002-2741-433X"},"institutions":[{"id":"https://openalex.org/I4210128818","display_name":"Institute of Software","ror":"https://ror.org/033dfsn42","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210128818"]},{"id":"https://openalex.org/I4210162190","display_name":"China University of Petroleum, East China","ror":"https://ror.org/05gbn2817","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210162190"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xun Wang","raw_affiliation_strings":["Qingdao Institute of Software China University of Petroleum,College of Computer Science and Technology,Qingdao,China"],"affiliations":[{"raw_affiliation_string":"Qingdao Institute of Software China University of Petroleum,College of Computer Science and Technology,Qingdao,China","institution_ids":["https://openalex.org/I4210128818","https://openalex.org/I4210162190"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5006420025"],"corresponding_institution_ids":["https://openalex.org/I4210128818","https://openalex.org/I4210162190"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.22072578,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"4481","last_page":"4488"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.963699996471405,"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/T10885","display_name":"Gene expression and cancer classification","score":0.963699996471405,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.90829998254776,"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":0.560820460319519},{"id":"https://openalex.org/keywords/transformer","display_name":"Transformer","score":0.5538048148155212},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.4570385217666626},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.37388408184051514},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3408099412918091},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.33671432733535767},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.32412174344062805},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.17964521050453186},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.14900296926498413},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.14478367567062378},{"id":"https://openalex.org/keywords/electrical-engineering","display_name":"Electrical engineering","score":0.1252012848854065},{"id":"https://openalex.org/keywords/voltage","display_name":"Voltage","score":0.06398758292198181}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.560820460319519},{"id":"https://openalex.org/C66322947","wikidata":"https://www.wikidata.org/wiki/Q11658","display_name":"Transformer","level":3,"score":0.5538048148155212},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.4570385217666626},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.37388408184051514},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3408099412918091},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.33671432733535767},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.32412174344062805},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.17964521050453186},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.14900296926498413},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.14478367567062378},{"id":"https://openalex.org/C119599485","wikidata":"https://www.wikidata.org/wiki/Q43035","display_name":"Electrical engineering","level":1,"score":0.1252012848854065},{"id":"https://openalex.org/C165801399","wikidata":"https://www.wikidata.org/wiki/Q25428","display_name":"Voltage","level":2,"score":0.06398758292198181}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm62325.2024.10822784","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm62325.2024.10822784","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2024 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320335787","display_name":"Fundamental Research Funds for the Central Universities","ror":null},{"id":"https://openalex.org/F4320337495","display_name":"Technology Development","ror":null},{"id":"https://openalex.org/F4320337504","display_name":"Research and Development","ror":"https://ror.org/027s68j25"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":35,"referenced_works":["https://openalex.org/W1549674551","https://openalex.org/W1614298861","https://openalex.org/W2032200433","https://openalex.org/W2106014350","https://openalex.org/W2127081697","https://openalex.org/W2128016314","https://openalex.org/W2142205294","https://openalex.org/W2164440878","https://openalex.org/W2259938310","https://openalex.org/W2560311853","https://openalex.org/W2566958422","https://openalex.org/W2896457183","https://openalex.org/W2908510526","https://openalex.org/W2944340292","https://openalex.org/W2952239877","https://openalex.org/W3026475692","https://openalex.org/W3094502228","https://openalex.org/W3126792443","https://openalex.org/W3184735396","https://openalex.org/W3198604700","https://openalex.org/W3203588026","https://openalex.org/W4200214589","https://openalex.org/W4206042814","https://openalex.org/W4223889011","https://openalex.org/W4291301137","https://openalex.org/W4353095414","https://openalex.org/W4382490702","https://openalex.org/W4388913006","https://openalex.org/W6636510571","https://openalex.org/W6755207826","https://openalex.org/W6757817989","https://openalex.org/W6784333009","https://openalex.org/W6789753369","https://openalex.org/W6798805250","https://openalex.org/W6853888595"],"related_works":["https://openalex.org/W2131250617","https://openalex.org/W4233034052","https://openalex.org/W2371030422","https://openalex.org/W4310420093","https://openalex.org/W3154635860","https://openalex.org/W2803323662","https://openalex.org/W3032874291","https://openalex.org/W2005057264","https://openalex.org/W2363156284","https://openalex.org/W2415025170"],"abstract_inverted_index":{"Gene":[0],"expression":[1,17,33,41,100,132],"is":[2,35,42],"a":[3,36,65],"pivotal":[4],"biological":[5],"process":[6],"within":[7],"organisms,":[8],"and":[9,59,90,93,116,148,164,173],"in":[10,28,120],"recent":[11],"years,":[12],"the":[13,72,117,121],"prediction":[14],"of":[15],"gene":[16,32,40,52,87,99,131,152,156,165],"levels":[18,34],"has":[19],"garnered":[20],"increasing":[21],"attention":[22,118],"due":[23],"to":[24,51,97,128,135],"its":[25],"vast":[26],"potential":[27],"clinical":[29],"applications.":[30],"Predicting":[31],"complex":[37],"problem":[38],"as":[39],"influenced":[43],"by":[44,145],"multiple":[45,125],"factors,":[46],"including":[47],"but":[48],"not":[49],"limited":[50],"sequences,":[53,115],"epigenetic":[54],"modifications,":[55],"transcription":[56,174],"factor":[57,175],"binding,":[58],"micro-environmental":[60],"conditions.":[61],"This":[62],"paper":[63],"proposes":[64],"model":[66,81,107],"named":[67],"Multimodal":[68],"Expression,":[69],"based":[70],"on":[71],"Transformer":[73,122],"architecture,":[74],"which":[75],"integrates":[76],"various":[77],"data":[78,126,154,158,167,172],"types.":[79],"The":[80],"can":[82,108,123],"extract":[83,109],"effective":[84,111],"features":[85],"from":[86,113],"promoter":[88,114],"sequences":[89],"combine":[91],"pre-transcriptional":[92],"post-transcriptional":[94],"regulatory":[95],"information":[96,112],"predict":[98,130],"levels.":[101,133],"Experimental":[102],"results":[103],"demonstrate":[104],"that":[105],"our":[106,138],"more":[110],"mechanism":[119],"integrate":[124],"types":[127],"jointly":[129],"Compared":[134],"previous":[136],"methods,":[137],"model\u2019s":[139],"R<sup":[140],"xmlns:mml=\"http://www.w3.org/1998/Math/MathML\"":[141],"xmlns:xlink=\"http://www.w3.org/1999/xlink\">2</sup>":[142],"values":[143],"improved":[144],"7.05%,":[146],"8.9%,":[147],"1.91%":[149],"when":[150],"using":[151],"sequence":[153,157,166],"alone,":[155],"combined":[159,168],"with":[160,169],"mRNA":[161,170],"half-life":[162,171],"data,":[163,176],"respectively.":[177]},"counts_by_year":[],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
