{"id":"https://openalex.org/W4413790623","doi":"https://doi.org/10.1093/bib/bbaf443","title":"BBANsh: a deep learning architecture based on BERT and bilinear attention networks to identify potent shRNA","display_name":"BBANsh: a deep learning architecture based on BERT and bilinear attention networks to identify potent shRNA","publication_year":2025,"publication_date":"2025-07-01","ids":{"openalex":"https://openalex.org/W4413790623","doi":"https://doi.org/10.1093/bib/bbaf443","pmid":"https://pubmed.ncbi.nlm.nih.gov/40874819"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbaf443","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf443","pdf_url":"https://academic.oup.com/bib/article-pdf/26/4/bbaf443/64147848/bbaf443.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/bib/article-pdf/26/4/bbaf443/64147848/bbaf443.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5015797870","display_name":"Yuanting Chen","orcid":"https://orcid.org/0000-0003-1294-479X"},"institutions":[{"id":"https://openalex.org/I143593769","display_name":"East China University of Science and Technology","ror":"https://ror.org/01vyrm377","country_code":"CN","type":"education","lineage":["https://openalex.org/I143593769"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yuanting Chen","raw_affiliation_strings":["Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology , 130 Meilong Road, Shanghai 200237 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology , 130 Meilong Road, Shanghai 200237 ,","institution_ids":["https://openalex.org/I143593769"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100336430","display_name":"Long Chen","orcid":"https://orcid.org/0000-0003-1110-6495"},"institutions":[{"id":"https://openalex.org/I143593769","display_name":"East China University of Science and Technology","ror":"https://ror.org/01vyrm377","country_code":"CN","type":"education","lineage":["https://openalex.org/I143593769"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Long Chen","raw_affiliation_strings":["Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology , 130 Meilong Road, Shanghai 200237 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology , 130 Meilong Road, Shanghai 200237 ,","institution_ids":["https://openalex.org/I143593769"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5006548624","display_name":"Xinxin Yu","orcid":null},"institutions":[{"id":"https://openalex.org/I143593769","display_name":"East China University of Science and Technology","ror":"https://ror.org/01vyrm377","country_code":"CN","type":"education","lineage":["https://openalex.org/I143593769"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xinxin Yu","raw_affiliation_strings":["Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology , 130 Meilong Road, Shanghai 200237 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology , 130 Meilong Road, Shanghai 200237 ,","institution_ids":["https://openalex.org/I143593769"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100400683","display_name":"Weihua Li","orcid":"https://orcid.org/0000-0003-3122-1298"},"institutions":[{"id":"https://openalex.org/I143593769","display_name":"East China University of Science and Technology","ror":"https://ror.org/01vyrm377","country_code":"CN","type":"education","lineage":["https://openalex.org/I143593769"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Weihua Li","raw_affiliation_strings":["Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology , 130 Meilong Road, Shanghai 200237 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology , 130 Meilong Road, Shanghai 200237 ,","institution_ids":["https://openalex.org/I143593769"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052049405","display_name":"Yun Tang","orcid":"https://orcid.org/0000-0003-2340-1109"},"institutions":[{"id":"https://openalex.org/I143593769","display_name":"East China University of Science and Technology","ror":"https://ror.org/01vyrm377","country_code":"CN","type":"education","lineage":["https://openalex.org/I143593769"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yun Tang","raw_affiliation_strings":["Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology , 130 Meilong Road, Shanghai 200237 ,"],"raw_orcid":"https://orcid.org/0000-0003-2340-1109","affiliations":[{"raw_affiliation_string":"Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology , 130 Meilong Road, Shanghai 200237 ,","institution_ids":["https://openalex.org/I143593769"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5101576373","display_name":"Guixia Liu","orcid":"https://orcid.org/0000-0001-9648-844X"},"institutions":[{"id":"https://openalex.org/I143593769","display_name":"East China University of Science and Technology","ror":"https://ror.org/01vyrm377","country_code":"CN","type":"education","lineage":["https://openalex.org/I143593769"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Guixia Liu","raw_affiliation_strings":["Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology , 130 Meilong Road, Shanghai 200237 ,"],"raw_orcid":"https://orcid.org/0000-0001-9648-844X","affiliations":[{"raw_affiliation_string":"Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology , 130 Meilong Road, Shanghai 200237 ,","institution_ids":["https://openalex.org/I143593769"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I143593769"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.16918645,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"26","issue":"4","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9998999834060669,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9998999834060669,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9986000061035156,"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/architecture","display_name":"Architecture","score":0.6494084000587463},{"id":"https://openalex.org/keywords/small-hairpin-rna","display_name":"Small hairpin RNA","score":0.5956774353981018},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5455003976821899},{"id":"https://openalex.org/keywords/bilinear-interpolation","display_name":"Bilinear interpolation","score":0.473225474357605},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4244469404220581},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.4186200797557831},{"id":"https://openalex.org/keywords/computer-architecture","display_name":"Computer architecture","score":0.4086906313896179},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3794621527194977},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.21639227867126465},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.19885092973709106},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.1020587682723999},{"id":"https://openalex.org/keywords/geography","display_name":"Geography","score":0.09663209319114685},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.0669565498828888},{"id":"https://openalex.org/keywords/archaeology","display_name":"Archaeology","score":0.05520719289779663}],"concepts":[{"id":"https://openalex.org/C123657996","wikidata":"https://www.wikidata.org/wiki/Q12271","display_name":"Architecture","level":2,"score":0.6494084000587463},{"id":"https://openalex.org/C190232843","wikidata":"https://www.wikidata.org/wiki/Q1950808","display_name":"Small hairpin RNA","level":4,"score":0.5956774353981018},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5455003976821899},{"id":"https://openalex.org/C205203396","wikidata":"https://www.wikidata.org/wiki/Q612143","display_name":"Bilinear interpolation","level":2,"score":0.473225474357605},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4244469404220581},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.4186200797557831},{"id":"https://openalex.org/C118524514","wikidata":"https://www.wikidata.org/wiki/Q173212","display_name":"Computer architecture","level":1,"score":0.4086906313896179},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3794621527194977},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.21639227867126465},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.19885092973709106},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1020587682723999},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.09663209319114685},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0669565498828888},{"id":"https://openalex.org/C166957645","wikidata":"https://www.wikidata.org/wiki/Q23498","display_name":"Archaeology","level":1,"score":0.05520719289779663},{"id":"https://openalex.org/C31972630","wikidata":"https://www.wikidata.org/wiki/Q844240","display_name":"Computer vision","level":1,"score":0.0},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.0}],"mesh":[{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":"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":"D034622","descriptor_name":"RNA Interference","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D034622","descriptor_name":"RNA Interference","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D034741","descriptor_name":"RNA, Small Interfering","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D034741","descriptor_name":"RNA, Small Interfering","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbaf443","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf443","pdf_url":"https://academic.oup.com/bib/article-pdf/26/4/bbaf443/64147848/bbaf443.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40874819","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40874819","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":"Briefings in bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:12392269","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12392269","pdf_url":null,"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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbaf443","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf443","pdf_url":"https://academic.oup.com/bib/article-pdf/26/4/bbaf443/64147848/bbaf443.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1627124884","display_name":null,"funder_award_id":"82273858","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G177194081","display_name":null,"funder_award_id":"U23A20530","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320321881","display_name":"Shanghai Municipal Education Commission","ror":"https://ror.org/05tewj457"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4413790623.pdf","grobid_xml":"https://content.openalex.org/works/W4413790623.grobid-xml"},"referenced_works_count":38,"referenced_works":["https://openalex.org/W1494484168","https://openalex.org/W1520518044","https://openalex.org/W1549680708","https://openalex.org/W1959032726","https://openalex.org/W1969296875","https://openalex.org/W2000904576","https://openalex.org/W2035340311","https://openalex.org/W2080748087","https://openalex.org/W2088685757","https://openalex.org/W2120344603","https://openalex.org/W2593037083","https://openalex.org/W2617716746","https://openalex.org/W2771135590","https://openalex.org/W2920438880","https://openalex.org/W2952370363","https://openalex.org/W3127238141","https://openalex.org/W3134163647","https://openalex.org/W4205773061","https://openalex.org/W4283791586","https://openalex.org/W4299878861","https://openalex.org/W4318981550","https://openalex.org/W4379930006","https://openalex.org/W4388539614","https://openalex.org/W4390228899","https://openalex.org/W4392167930","https://openalex.org/W4393981110","https://openalex.org/W4396871204","https://openalex.org/W4403478990","https://openalex.org/W4405194283","https://openalex.org/W4406419344","https://openalex.org/W4411826769","https://openalex.org/W4412885778","https://openalex.org/W4413016999","https://openalex.org/W4413049753","https://openalex.org/W4413054381","https://openalex.org/W4413054582","https://openalex.org/W4413054673","https://openalex.org/W4413055499"],"related_works":["https://openalex.org/W2165589608","https://openalex.org/W3093557575","https://openalex.org/W2354231916","https://openalex.org/W3182767856","https://openalex.org/W2125881252","https://openalex.org/W2162140574","https://openalex.org/W2001572884","https://openalex.org/W2011090644","https://openalex.org/W2354073393","https://openalex.org/W2038503502"],"abstract_inverted_index":{"RNA":[0,18],"interference":[1],"(RNAi)":[2],"is":[3,21,60],"a":[4,88,142,148],"technique":[5],"for":[6,220,228],"precisely":[7],"silencing":[8,46],"the":[9,27,109,133,161,179,182,189,196,200,231],"expression":[10],"of":[11,16,57,111,136,145,164,173,181,186,209,236],"specific":[12],"genes":[13],"by":[14],"means":[15],"small":[17,39],"molecules":[19],"and":[20,51,62,68,80,101,121,141,166,217,234],"essential":[22],"in":[23,65,230],"functional":[24],"genomics.":[25],"Among":[26],"commonly":[28],"used":[29],"RNAi":[30],"molecules,":[31],"short":[32],"hairpin":[33],"RNAs":[34],"(shRNAs)":[35],"exhibit":[36],"advantages":[37],"over":[38],"interfering":[40],"RNAs,":[41],"including":[42],"longer":[43],"half-life,":[44],"comparable":[45],"efficiency,":[47],"fewer":[48],"off-target":[49],"effects,":[50],"greater":[52],"safety.":[53],"However,":[54],"traditional":[55,114],"screening":[56],"potent":[58,210],"shRNAs":[59],"costly":[61],"time-consuming.":[63],"Advances":[64],"big":[66],"data":[67],"artificial":[69],"intelligence":[70],"have":[71,199],"enabled":[72],"computational":[73],"methods":[74],"to":[75,168],"significantly":[76],"accelerate":[77],"shRNA":[78,90,123,221],"design":[79,235],"prediction.":[81],"In":[82],"this":[83],"study,":[84],"we":[85],"propose":[86],"BBANsh,":[87],"new":[89,149],"prediction":[91,124,143],"model":[92,169,204],"based":[93],"on":[94,138,147,203],"bidirectional":[95],"encoder":[96],"representation":[97],"from":[98],"transformers":[99],"(BERT)":[100],"bilinear":[102],"attention":[103],"network":[104],"(BAN).":[105],"We":[106],"comprehensively":[107],"evaluate":[108],"performance":[110],"BBANsh":[112,127,213],"against":[113],"feature-based":[115],"models,":[116],"various":[117],"feature":[118,175,183],"fusion":[119,184],"methods,":[120],"existing":[122],"models.":[125],"The":[126,171],"has":[128],"achieved":[129],"an":[130,215],"area":[131],"under":[132],"precision-recall":[134],"curve":[135],"0.951":[137],"five-cross":[139],"validation":[140,151],"accuracy":[144],"0.896":[146],"external":[150],"set,":[152],"highlighting":[153,206],"its":[154],"superior":[155],"predictive":[156],"performance.":[157,170],"Ablation":[158],"experiments":[159],"validate":[160],"significant":[162],"contributions":[163],"BERT":[165],"BAN":[167],"visualization":[172],"internal":[174],"representations":[176],"intuitively":[177],"demonstrates":[178],"effectiveness":[180],"strategy":[185],"BBANsh.":[187],"Furthermore,":[188],"attentional":[190],"analysis":[191],"reveals":[192],"that":[193],"nucleotides":[194],"near":[195],"5'":[197],"end":[198],"greatest":[201],"impact":[202],"predictions,":[205],"sequence":[207],"characteristics":[208],"shRNAs.":[211],"Overall,":[212],"provides":[214],"efficient":[216],"reliable":[218],"tool":[219],"prediction,":[222],"which":[223],"can":[224],"offer":[225],"valuable":[226],"support":[227],"researchers":[229],"precise":[232],"selection":[233],"shRNA.":[237]},"counts_by_year":[],"updated_date":"2026-06-26T08:34:08.712188","created_date":"2025-10-10T00:00:00"}