{"id":"https://openalex.org/W4390971161","doi":"https://doi.org/10.1109/bibm58861.2023.10386024","title":"TGAAL: Combining Transformer-based GAN and active learning to identify the coding potential of sORFs in plant lncRNAs","display_name":"TGAAL: Combining Transformer-based GAN and active learning to identify the coding potential of sORFs in plant lncRNAs","publication_year":2023,"publication_date":"2023-12-05","ids":{"openalex":"https://openalex.org/W4390971161","doi":"https://doi.org/10.1109/bibm58861.2023.10386024"},"language":"en","primary_location":{"id":"doi:10.1109/bibm58861.2023.10386024","is_oa":false,"landing_page_url":"http://dx.doi.org/10.1109/bibm58861.2023.10386024","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2023 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/A5100445249","display_name":"Yu Wang","orcid":"https://orcid.org/0000-0002-6145-292X"},"institutions":[{"id":"https://openalex.org/I27357992","display_name":"Dalian University of Technology","ror":"https://ror.org/023hj5876","country_code":"CN","type":"education","lineage":["https://openalex.org/I27357992"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Yu Wang","raw_affiliation_strings":["Dalian University of Technology,School of Computer Science and Technology,Dalian,China","School of Computer Science and Technology, Dalian University of Technology, Dalian, China"],"affiliations":[{"raw_affiliation_string":"Dalian University of Technology,School of Computer Science and Technology,Dalian,China","institution_ids":["https://openalex.org/I27357992"]},{"raw_affiliation_string":"School of Computer Science and Technology, Dalian University of Technology, Dalian, China","institution_ids":["https://openalex.org/I27357992"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008478540","display_name":"Jun Meng","orcid":"https://orcid.org/0000-0002-7357-8562"},"institutions":[{"id":"https://openalex.org/I27357992","display_name":"Dalian University of Technology","ror":"https://ror.org/023hj5876","country_code":"CN","type":"education","lineage":["https://openalex.org/I27357992"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jun Meng","raw_affiliation_strings":["Dalian University of Technology,School of Computer Science and Technology,Dalian,China","School of Computer Science and Technology, Dalian University of Technology, Dalian, China"],"affiliations":[{"raw_affiliation_string":"Dalian University of Technology,School of Computer Science and Technology,Dalian,China","institution_ids":["https://openalex.org/I27357992"]},{"raw_affiliation_string":"School of Computer Science and Technology, Dalian University of Technology, Dalian, China","institution_ids":["https://openalex.org/I27357992"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053725485","display_name":"Shihao Xia","orcid":null},"institutions":[{"id":"https://openalex.org/I27357992","display_name":"Dalian University of Technology","ror":"https://ror.org/023hj5876","country_code":"CN","type":"education","lineage":["https://openalex.org/I27357992"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Shihao Xia","raw_affiliation_strings":["Dalian University of Technology,School of Computer Science and Technology,Dalian,China","School of Computer Science and Technology, Dalian University of Technology, Dalian, China"],"affiliations":[{"raw_affiliation_string":"Dalian University of Technology,School of Computer Science and Technology,Dalian,China","institution_ids":["https://openalex.org/I27357992"]},{"raw_affiliation_string":"School of Computer Science and Technology, Dalian University of Technology, Dalian, China","institution_ids":["https://openalex.org/I27357992"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101812332","display_name":"Haibin Li","orcid":"https://orcid.org/0000-0001-5661-7788"},"institutions":[{"id":"https://openalex.org/I27357992","display_name":"Dalian University of Technology","ror":"https://ror.org/023hj5876","country_code":"CN","type":"education","lineage":["https://openalex.org/I27357992"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Haibin Li","raw_affiliation_strings":["Dalian University of Technology,School of Computer Science and Technology,Dalian,China","School of Computer Science and Technology, Dalian University of Technology, Dalian, China"],"affiliations":[{"raw_affiliation_string":"Dalian University of Technology,School of Computer Science and Technology,Dalian,China","institution_ids":["https://openalex.org/I27357992"]},{"raw_affiliation_string":"School of Computer Science and Technology, Dalian University of Technology, Dalian, China","institution_ids":["https://openalex.org/I27357992"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008525220","display_name":"Zhaowei Wang","orcid":"https://orcid.org/0000-0002-3703-287X"},"institutions":[{"id":"https://openalex.org/I27357992","display_name":"Dalian University of Technology","ror":"https://ror.org/023hj5876","country_code":"CN","type":"education","lineage":["https://openalex.org/I27357992"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhaowei Wang","raw_affiliation_strings":["Dalian University of Technology,School of Computer Science and Technology,Dalian,China","School of Computer Science and Technology, Dalian University of Technology, Dalian, China"],"affiliations":[{"raw_affiliation_string":"Dalian University of Technology,School of Computer Science and Technology,Dalian,China","institution_ids":["https://openalex.org/I27357992"]},{"raw_affiliation_string":"School of Computer Science and Technology, Dalian University of Technology, Dalian, China","institution_ids":["https://openalex.org/I27357992"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5004629036","display_name":"Yushi Luan","orcid":"https://orcid.org/0000-0001-9397-9171"},"institutions":[{"id":"https://openalex.org/I4210092944","display_name":"Dalian University","ror":"https://ror.org/00g2ypp58","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210092944"]},{"id":"https://openalex.org/I27357992","display_name":"Dalian University of Technology","ror":"https://ror.org/023hj5876","country_code":"CN","type":"education","lineage":["https://openalex.org/I27357992"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yushi Luan","raw_affiliation_strings":["Dalian University of Technology,School of Bioengineering,Dalian,China","School of Bioengineering, Dalian University of Technology, Dalian, China"],"affiliations":[{"raw_affiliation_string":"Dalian University of Technology,School of Bioengineering,Dalian,China","institution_ids":["https://openalex.org/I4210092944"]},{"raw_affiliation_string":"School of Bioengineering, Dalian University of Technology, Dalian, China","institution_ids":["https://openalex.org/I4210092944","https://openalex.org/I27357992"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5100445249"],"corresponding_institution_ids":["https://openalex.org/I27357992"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.53805455,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"9","issue":null,"first_page":"936","last_page":"939"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10515","display_name":"Cancer-related molecular mechanisms research","score":0.9984999895095825,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/T10515","display_name":"Cancer-related molecular mechanisms research","score":0.9984999895095825,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9972000122070312,"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/T10494","display_name":"Plant Virus Research Studies","score":0.9941999912261963,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5955867171287537},{"id":"https://openalex.org/keywords/coding","display_name":"Coding (social sciences)","score":0.4924114942550659},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.487454891204834},{"id":"https://openalex.org/keywords/transformer","display_name":"Transformer","score":0.4412022531032562},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.4168017506599426},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.40219926834106445},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.10969886183738708},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.09176093339920044}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5955867171287537},{"id":"https://openalex.org/C179518139","wikidata":"https://www.wikidata.org/wiki/Q5140297","display_name":"Coding (social sciences)","level":2,"score":0.4924114942550659},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.487454891204834},{"id":"https://openalex.org/C66322947","wikidata":"https://www.wikidata.org/wiki/Q11658","display_name":"Transformer","level":3,"score":0.4412022531032562},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.4168017506599426},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.40219926834106445},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.10969886183738708},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.09176093339920044},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C165801399","wikidata":"https://www.wikidata.org/wiki/Q25428","display_name":"Voltage","level":2,"score":0.0},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm58861.2023.10386024","is_oa":false,"landing_page_url":"http://dx.doi.org/10.1109/bibm58861.2023.10386024","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2023 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Quality Education","id":"https://metadata.un.org/sdg/4","score":0.6299999952316284}],"awards":[],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":20,"referenced_works":["https://openalex.org/W1973036268","https://openalex.org/W2078266900","https://openalex.org/W2080752012","https://openalex.org/W2129883957","https://openalex.org/W2142580593","https://openalex.org/W2164160006","https://openalex.org/W2237493771","https://openalex.org/W2766656533","https://openalex.org/W2790274448","https://openalex.org/W2914698725","https://openalex.org/W2945934403","https://openalex.org/W2966284318","https://openalex.org/W2966725169","https://openalex.org/W2987349979","https://openalex.org/W3013495013","https://openalex.org/W3037117187","https://openalex.org/W3083074502","https://openalex.org/W3115880421","https://openalex.org/W4295242737","https://openalex.org/W4378673947"],"related_works":["https://openalex.org/W2961085424","https://openalex.org/W4306674287","https://openalex.org/W3046775127","https://openalex.org/W3107602296","https://openalex.org/W4394896187","https://openalex.org/W3170094116","https://openalex.org/W4386462264","https://openalex.org/W4364306694","https://openalex.org/W4312192474","https://openalex.org/W4283697347"],"abstract_inverted_index":{"Some":[0],"small":[1,16],"open":[2],"reading":[3],"frames":[4],"(sORFs)":[5],"in":[6,22,41,51,86,116,177,184,195],"plant":[7,42,87],"long":[8],"non-coding":[9,59],"RNAs":[10],"(lncRNAs)":[11],"are":[12],"capable":[13],"of":[14,27,39,68,84,182],"encoding":[15],"peptides,":[17],"which":[18,62,96,121],"play":[19],"key":[20],"roles":[21],"the":[23,36,49,81,123,127,158,179],"growth":[24],"and":[25,58,103,190],"development":[26],"organisms.":[28],"Therefore,":[29],"it":[30],"is":[31],"particularly":[32],"important":[33],"to":[34,65,79],"identify":[35,80],"coding":[37,55,82,180],"potential":[38,83,181],"sORFs":[40,56,60,85,183],"lncRNAs.":[43],"However,":[44],"existing":[45,175],"methods":[46,176],"often":[47],"ignore":[48],"differences":[50],"length":[52,119,198],"distribution":[53],"between":[54],"(csORFs)":[57],"(non-csORFs),":[61],"may":[63],"lead":[64],"incorrect":[66],"identification":[67],"csORFs.":[69],"To":[70],"address":[71],"this":[72],"issue,":[73],"we":[74],"propose":[75],"a":[76,117],"novel":[77],"method":[78],"lncRNAs,":[88],"named":[89],"Transformer":[90],"Generative":[91,99],"Adversarial":[92,100],"Active":[93],"Learning":[94],"(TGAAL),":[95],"combines":[97],"Transformer-based":[98],"Network":[101],"(TGAN)":[102],"active":[104,132],"learning":[105,133],"based":[106,134],"on":[107,135],"KL-topk":[108,136,153],"sampling":[109,137,154,165],"strategy.":[110],"TGAN":[111],"can":[112,143],"generate":[113],"sORF":[114,197],"sequences":[115],"specific":[118],"interval,":[120],"have":[122],"same":[124],"class":[125],"as":[126],"input":[128],"sORFs.":[129],"Meanwhile,":[130],"using":[131],"strategy,":[138],"samples":[139],"with":[140,162],"high":[141],"confidence":[142],"be":[144],"selected":[145],"for":[146],"data":[147],"augmentation.":[148],"5-fold":[149],"cross-validation":[150],"shows":[151],"that":[152,171],"strategy":[155],"significantly":[156,173],"improves":[157],"prediction":[159],"performance":[160],"compared":[161],"commonly":[163],"adopted":[164],"strategies.":[166],"The":[167],"experimental":[168],"results":[169],"show":[170],"TGAAL":[172],"outperforms":[174],"identifying":[178],"Arabidopsis":[185],"thaliana,":[186],"reaching":[187],"0.7761,":[188],"0.7906":[189],"0.7529":[191],"unweighted":[192],"average":[193],"recall":[194],"three":[196],"intervals,":[199],"respectively.":[200]},"counts_by_year":[],"updated_date":"2025-12-25T23:11:45.687758","created_date":"2025-10-10T00:00:00"}
