{"id":"https://openalex.org/W4390992252","doi":"https://doi.org/10.1109/bibm58861.2023.10385535","title":"A multi-granularity information-enhanced pre-training method for predicting the coding potential of sORFs in plant lncRNAs","display_name":"A multi-granularity information-enhanced pre-training method for predicting the coding potential of sORFs in plant lncRNAs","publication_year":2023,"publication_date":"2023-12-05","ids":{"openalex":"https://openalex.org/W4390992252","doi":"https://doi.org/10.1109/bibm58861.2023.10385535"},"language":"en","primary_location":{"id":"doi:10.1109/bibm58861.2023.10385535","is_oa":false,"landing_page_url":"http://dx.doi.org/10.1109/bibm58861.2023.10385535","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/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":true,"raw_author_name":"Shihao Xia","raw_affiliation_strings":["Dalian University of Technology,School of Computer Science and Technology,Dalian,China,116024"],"affiliations":[{"raw_affiliation_string":"Dalian University of Technology,School of Computer Science and Technology,Dalian,China,116024","institution_ids":["https://openalex.org/I27357992"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100619149","display_name":"Jun Meng","orcid":"https://orcid.org/0000-0002-7633-3624"},"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,116024"],"affiliations":[{"raw_affiliation_string":"Dalian University of Technology,School of Computer Science and Technology,Dalian,China,116024","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,116024"],"affiliations":[{"raw_affiliation_string":"Dalian University of Technology,School of Computer Science and Technology,Dalian,China,116024","institution_ids":["https://openalex.org/I27357992"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5120313773","display_name":"Yu Wang","orcid":"https://orcid.org/0000-0003-2770-8327"},"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":"Yu Wang","raw_affiliation_strings":["Dalian University of Technology,School of Computer Science and Technology,Dalian,China,116024"],"affiliations":[{"raw_affiliation_string":"Dalian University of Technology,School of Computer Science and Technology,Dalian,China,116024","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,116024"],"affiliations":[{"raw_affiliation_string":"Dalian University of Technology,School of Computer Science and Technology,Dalian,China,116024","institution_ids":["https://openalex.org/I27357992"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5114119592","display_name":"Zhaojing Qin","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":"Zhaojing Qin","raw_affiliation_strings":["Dalian University of Technology,School of Computer Science and Technology,Dalian,China,116024"],"affiliations":[{"raw_affiliation_string":"Dalian University of Technology,School of Computer Science and Technology,Dalian,China,116024","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/I27357992","display_name":"Dalian University of Technology","ror":"https://ror.org/023hj5876","country_code":"CN","type":"education","lineage":["https://openalex.org/I27357992"]},{"id":"https://openalex.org/I4210092944","display_name":"Dalian University","ror":"https://ror.org/00g2ypp58","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210092944"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yushi Luan","raw_affiliation_strings":["Dalian University of Technology,School of Bioengineering,Dalian,China,116024"],"affiliations":[{"raw_affiliation_string":"Dalian University of Technology,School of Bioengineering,Dalian,China,116024","institution_ids":["https://openalex.org/I4210092944","https://openalex.org/I27357992"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5053725485"],"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":0.53828293,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"260","last_page":"263"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10515","display_name":"Cancer-related molecular mechanisms research","score":0.9998000264167786,"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":0.9998000264167786,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9976000189781189,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9943000078201294,"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":0.7252769470214844},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5052576661109924},{"id":"https://openalex.org/keywords/encoder","display_name":"Encoder","score":0.4775722324848175},{"id":"https://openalex.org/keywords/coding","display_name":"Coding (social sciences)","score":0.4338643550872803},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.42278483510017395},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.398519366979599},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.14086410403251648},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.06553220748901367}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7252769470214844},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5052576661109924},{"id":"https://openalex.org/C118505674","wikidata":"https://www.wikidata.org/wiki/Q42586063","display_name":"Encoder","level":2,"score":0.4775722324848175},{"id":"https://openalex.org/C179518139","wikidata":"https://www.wikidata.org/wiki/Q5140297","display_name":"Coding (social sciences)","level":2,"score":0.4338643550872803},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.42278483510017395},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.398519366979599},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.14086410403251648},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.06553220748901367},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm58861.2023.10385535","is_oa":false,"landing_page_url":"http://dx.doi.org/10.1109/bibm58861.2023.10385535","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":[],"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":19,"referenced_works":["https://openalex.org/W1977344200","https://openalex.org/W2072877087","https://openalex.org/W2164160006","https://openalex.org/W2237493771","https://openalex.org/W2418044989","https://openalex.org/W2607796168","https://openalex.org/W2734798616","https://openalex.org/W2914698725","https://openalex.org/W2966284318","https://openalex.org/W2966725169","https://openalex.org/W2972190637","https://openalex.org/W2987349979","https://openalex.org/W3013495013","https://openalex.org/W3111455950","https://openalex.org/W3208221532","https://openalex.org/W4205681737","https://openalex.org/W4313527243","https://openalex.org/W4318220492","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":{"Small":[0],"open":[1],"reading":[2],"frames":[3],"(sORFs)":[4],"are":[5],"nucleotide":[6],"sequences":[7],"that":[8,20,188,203],"may":[9],"be":[10,135],"translated":[11],"into":[12],"small":[13],"peptides.":[14],"Recently,":[15],"increasing":[16],"studies":[17],"have":[18,68],"demonstrated":[19],"peptides":[21],"encoded":[22],"by":[23,58,148,195],"sORFs":[24,54],"in":[25,35,55,87],"plant":[26,66,95],"long":[27],"noncoding":[28],"RNAs":[29],"(lncRNAs)":[30],"play":[31],"a":[32,63,75,91,149,210],"vital":[33],"role":[34],"growth":[36],"regulation":[37],"and":[38,153,225],"disease":[39],"treatment.":[40],"To":[41],"accelerate":[42],"the":[43,82,101,112,131,160,164,189,204,214],"discovery":[44],"of":[45,77,85,163,175,191,216],"lncRNA-encoded":[46],"peptides,":[47],"it":[48],"is":[49,74,109,115,146,179,193],"essential":[50],"to":[51,71,117,158,181,222],"predict":[52],"translatable":[53,65],"lncRNAs":[56],"(lncRNA-sORFs)":[57],"computational":[59],"methods.":[60,200],"As":[61],"only":[62],"few":[64],"lncRNA-sORFs":[67,86,96,125,176],"been":[69],"discovered":[70],"date,":[72],"there":[73],"lack":[76],"effective":[78],"methods":[79],"for":[80,94,142,213],"characterizing":[81],"coding":[83,97,217],"potential":[84,98],"data-scarce":[88],"scenarios.":[89],"Therefore,":[90],"novel":[92],"method":[93,206],"prediction":[99,177,215],"using":[100],"pre-trained":[102,132],"bidirectional":[103],"encoder":[104],"representations":[105],"from":[106,122],"transformer":[107],"(LSCPP-BERT)":[108],"proposed.":[110],"Firstly,":[111],"BERT":[113],"model":[114,133],"trained":[116],"extract":[118,182],"multi-granularity":[119,154],"context":[120,155],"information":[121],"large-scale":[123],"unlabeled":[124],"through":[126],"two":[127,138],"pre-training":[128,151,170],"tasks.":[129],"Then,":[130],"can":[134,207],"fine-tuned":[136],"with":[137,198],"additional":[139],"linear":[140],"layers":[141],"classification.":[143],"The":[144],"LSCPP-BERT":[145,192],"featured":[147],"self-supervised":[150],"scheme":[152],"information,":[156],"aiming":[157],"enhance":[159],"representational":[161],"power":[162],"network.":[165],"In":[166],"addition,":[167],"an":[168],"extra":[169],"task":[171],"called":[172],"contextual":[173],"relation":[174],"(CRSP)":[178],"presented":[180],"sentence-level":[183],"information.":[184],"Experiment":[185],"results":[186],"show":[187],"accuracy":[190],"increased":[194],"8.14%":[196],"compared":[197],"state-of-the-art":[199],"We":[201],"hope":[202],"proposed":[205],"serve":[208],"as":[209],"reliable":[211],"tool":[212],"lncRNA-sORFs,":[218],"thereby":[219],"further":[220],"contributing":[221],"drug":[223],"development":[224],"agronomical":[226],"applications.":[227]},"counts_by_year":[],"updated_date":"2025-12-25T23:11:45.687758","created_date":"2025-10-10T00:00:00"}
