{"id":"https://openalex.org/W7134067956","doi":"https://doi.org/10.1093/bib/bbag098","title":"Zero-shot benchmarking of RNA language models in structural, functional, and evolutionary learning","display_name":"Zero-shot benchmarking of RNA language models in structural, functional, and evolutionary learning","publication_year":2026,"publication_date":"2026-02-12","ids":{"openalex":"https://openalex.org/W7134067956","doi":"https://doi.org/10.1093/bib/bbag098","pmid":"https://pubmed.ncbi.nlm.nih.gov/41789565"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbag098","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbag098","pdf_url":null,"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","license_id":"https://openalex.org/licenses/cc-by","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://doi.org/10.1093/bib/bbag098","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5128231770","display_name":"He Wang","orcid":null},"institutions":[{"id":"https://openalex.org/I4210102541","display_name":"Shenzhen Bay Laboratory","ror":"https://ror.org/00sdcjz77","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210102541"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"He Wang","raw_affiliation_strings":["Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Weiguang Life Sciences Park , Xinhu Street, Guangming District, Shenzhen 518107 ,"],"affiliations":[{"raw_affiliation_string":"Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Weiguang Life Sciences Park , Xinhu Street, Guangming District, Shenzhen 518107 ,","institution_ids":["https://openalex.org/I4210102541"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100629921","display_name":"Yikun Zhang","orcid":null},"institutions":[{"id":"https://openalex.org/I3129496460","display_name":"Lishui University","ror":"https://ror.org/0418kp584","country_code":"CN","type":"education","lineage":["https://openalex.org/I3129496460"]},{"id":"https://openalex.org/I4210102541","display_name":"Shenzhen Bay Laboratory","ror":"https://ror.org/00sdcjz77","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210102541"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yikun Zhang","raw_affiliation_strings":["Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Weiguang Life Sciences Park , Xinhu Street, Guangming District, Shenzhen 518107 ,","School of Electronic and Computer Engineering, Peking University , No. 2199 Lishui Road, Nanshan District, Shenzhen 518055 ,"],"affiliations":[{"raw_affiliation_string":"Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Weiguang Life Sciences Park , Xinhu Street, Guangming District, Shenzhen 518107 ,","institution_ids":["https://openalex.org/I4210102541"]},{"raw_affiliation_string":"School of Electronic and Computer Engineering, Peking University , No. 2199 Lishui Road, Nanshan District, Shenzhen 518055 ,","institution_ids":["https://openalex.org/I3129496460"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5123349127","display_name":"Jie Chen","orcid":null},"institutions":[{"id":"https://openalex.org/I3129496460","display_name":"Lishui University","ror":"https://ror.org/0418kp584","country_code":"CN","type":"education","lineage":["https://openalex.org/I3129496460"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jie Chen","raw_affiliation_strings":["School of Electronic and Computer Engineering, Peking University , No. 2199 Lishui Road, Nanshan District, Shenzhen 518055 ,"],"affiliations":[{"raw_affiliation_string":"School of Electronic and Computer Engineering, Peking University , No. 2199 Lishui Road, Nanshan District, Shenzhen 518055 ,","institution_ids":["https://openalex.org/I3129496460"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071120707","display_name":"Jian Zhan","orcid":"https://orcid.org/0000-0003-0856-2385"},"institutions":[{"id":"https://openalex.org/I100135526","display_name":"BGI Group (China)","ror":"https://ror.org/045pn2j94","country_code":"CN","type":"company","lineage":["https://openalex.org/I100135526"]},{"id":"https://openalex.org/I4210102541","display_name":"Shenzhen Bay Laboratory","ror":"https://ror.org/00sdcjz77","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210102541"]},{"id":"https://openalex.org/I4210159793","display_name":"Tang Hospital","ror":"https://ror.org/04nsks563","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210159793"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jian Zhan","raw_affiliation_strings":["Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Weiguang Life Sciences Park , Xinhu Street, Guangming District, Shenzhen 518107 ,","Ribopeutic (Shenzhen) Co., Ltd. , Room 3106-B022, 3038 Jintian Road, Futian District, Shenzhen, Guangdong 518033 ,","Ribopeutic Inc. , Rm. 517, Bldg. 21, Hexiang Tech Ctr., Qiantang Dist. Hangzhou 310018, Zhejiang Province ,"],"affiliations":[{"raw_affiliation_string":"Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Weiguang Life Sciences Park , Xinhu Street, Guangming District, Shenzhen 518107 ,","institution_ids":["https://openalex.org/I4210102541"]},{"raw_affiliation_string":"Ribopeutic (Shenzhen) Co., Ltd. , Room 3106-B022, 3038 Jintian Road, Futian District, Shenzhen, Guangdong 518033 ,","institution_ids":["https://openalex.org/I100135526"]},{"raw_affiliation_string":"Ribopeutic Inc. , Rm. 517, Bldg. 21, Hexiang Tech Ctr., Qiantang Dist. Hangzhou 310018, Zhejiang Province ,","institution_ids":["https://openalex.org/I4210159793"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5075586893","display_name":"Yaoqi Zhou","orcid":"https://orcid.org/0000-0001-9119-2666"},"institutions":[{"id":"https://openalex.org/I4210102541","display_name":"Shenzhen Bay Laboratory","ror":"https://ror.org/00sdcjz77","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210102541"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yaoqi Zhou","raw_affiliation_strings":["Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Weiguang Life Sciences Park , Xinhu Street, Guangming District, Shenzhen 518107 ,"],"affiliations":[{"raw_affiliation_string":"Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Weiguang Life Sciences Park , Xinhu Street, Guangming District, Shenzhen 518107 ,","institution_ids":["https://openalex.org/I4210102541"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5128231770"],"corresponding_institution_ids":["https://openalex.org/I4210102541"],"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":0.77357066,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"27","issue":"2","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9695000052452087,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9695000052452087,"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":0.009399999864399433,"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/T11445","display_name":"Origins and Evolution of Life","score":0.004600000102072954,"subfield":{"id":"https://openalex.org/subfields/3103","display_name":"Astronomy and Astrophysics"},"field":{"id":"https://openalex.org/fields/31","display_name":"Physics and Astronomy"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.656499981880188},{"id":"https://openalex.org/keywords/benchmarking","display_name":"Benchmarking","score":0.6478999853134155},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.5020999908447266},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.4853000044822693},{"id":"https://openalex.org/keywords/task","display_name":"Task (project management)","score":0.41519999504089355},{"id":"https://openalex.org/keywords/language-model","display_name":"Language model","score":0.38920000195503235},{"id":"https://openalex.org/keywords/non-coding-rna","display_name":"Non-coding RNA","score":0.36820000410079956}],"concepts":[{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.656499981880188},{"id":"https://openalex.org/C86251818","wikidata":"https://www.wikidata.org/wiki/Q816754","display_name":"Benchmarking","level":2,"score":0.6478999853134155},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5896000266075134},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.5020999908447266},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.4853000044822693},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4794999957084656},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4578000009059906},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.41519999504089355},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.40459999442100525},{"id":"https://openalex.org/C137293760","wikidata":"https://www.wikidata.org/wiki/Q3621696","display_name":"Language model","level":2,"score":0.38920000195503235},{"id":"https://openalex.org/C194993378","wikidata":"https://www.wikidata.org/wiki/Q427087","display_name":"Non-coding RNA","level":4,"score":0.36820000410079956},{"id":"https://openalex.org/C85468374","wikidata":"https://www.wikidata.org/wiki/Q6589957","display_name":"Nucleic acid secondary structure","level":4,"score":0.34360000491142273},{"id":"https://openalex.org/C159149176","wikidata":"https://www.wikidata.org/wiki/Q14489129","display_name":"Evolutionary algorithm","level":2,"score":0.3395000100135803},{"id":"https://openalex.org/C2780966255","wikidata":"https://www.wikidata.org/wiki/Q5474306","display_name":"Foundation (evidence)","level":2,"score":0.2953000068664551},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.2896000146865845},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.28870001435279846},{"id":"https://openalex.org/C126142528","wikidata":"https://www.wikidata.org/wiki/Q3771876","display_name":"Nucleic acid structure","level":4,"score":0.26759999990463257},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2556999921798706},{"id":"https://openalex.org/C66024118","wikidata":"https://www.wikidata.org/wiki/Q1122506","display_name":"Computational model","level":2,"score":0.2551000118255615},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.25060001015663147}],"mesh":[{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbag098","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbag098","pdf_url":null,"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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:41789565","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41789565","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:12963973","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12963973/","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12963973/pdf/bbag098.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbag098","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbag098","pdf_url":null,"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","license_id":"https://openalex.org/licenses/cc-by","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/G1121271761","display_name":null,"funder_award_id":"Program","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G2087396116","display_name":null,"funder_award_id":"China","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G2981938667","display_name":null,"funder_award_id":"Shenzhen","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3317480652","display_name":null,"funder_award_id":"Science","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G391238517","display_name":null,"funder_award_id":", and","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5994120800","display_name":null,"funder_award_id":"Natural","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8242590901","display_name":null,"funder_award_id":"22350710182","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"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":98,"referenced_works":["https://openalex.org/W142718297","https://openalex.org/W144423133","https://openalex.org/W1555644224","https://openalex.org/W2045061077","https://openalex.org/W2058615001","https://openalex.org/W2071271349","https://openalex.org/W2086561953","https://openalex.org/W2095748631","https://openalex.org/W2096465161","https://openalex.org/W2099374044","https://openalex.org/W2124050695","https://openalex.org/W2124662626","https://openalex.org/W2128716813","https://openalex.org/W2129375421","https://openalex.org/W2129726167","https://openalex.org/W2141152740","https://openalex.org/W2141292707","https://openalex.org/W2163798335","https://openalex.org/W2170747616","https://openalex.org/W2234324103","https://openalex.org/W2417928515","https://openalex.org/W2536860838","https://openalex.org/W2544136853","https://openalex.org/W2759571676","https://openalex.org/W2806518291","https://openalex.org/W2809230835","https://openalex.org/W2899616402","https://openalex.org/W2933083636","https://openalex.org/W2950954328","https://openalex.org/W2951298881","https://openalex.org/W2955231772","https://openalex.org/W2981543307","https://openalex.org/W2990528340","https://openalex.org/W2995257718","https://openalex.org/W3005454931","https://openalex.org/W3033368660","https://openalex.org/W3081143873","https://openalex.org/W3095979265","https://openalex.org/W3096136978","https://openalex.org/W3100348855","https://openalex.org/W3124828689","https://openalex.org/W3127238141","https://openalex.org/W3133458480","https://openalex.org/W3135161193","https://openalex.org/W3146944767","https://openalex.org/W3163562839","https://openalex.org/W3164094081","https://openalex.org/W3174855653","https://openalex.org/W3175812678","https://openalex.org/W3177500196","https://openalex.org/W3177828909","https://openalex.org/W3180908419","https://openalex.org/W3193427089","https://openalex.org/W3217274194","https://openalex.org/W4206680700","https://openalex.org/W4213095938","https://openalex.org/W4225858649","https://openalex.org/W4283516206","https://openalex.org/W4286669150","https://openalex.org/W4290672950","https://openalex.org/W4307843054","https://openalex.org/W4308101956","https://openalex.org/W4308834638","https://openalex.org/W4321615987","https://openalex.org/W4323925127","https://openalex.org/W4327550249","https://openalex.org/W4327718177","https://openalex.org/W4368356090","https://openalex.org/W4384405439","https://openalex.org/W4388024559","https://openalex.org/W4388539614","https://openalex.org/W4391359037","https://openalex.org/W4392346912","https://openalex.org/W4393981110","https://openalex.org/W4394639795","https://openalex.org/W4394763992","https://openalex.org/W4396871204","https://openalex.org/W4401694312","https://openalex.org/W4403023684","https://openalex.org/W4403406094","https://openalex.org/W4404049681","https://openalex.org/W4404595545","https://openalex.org/W4404781414","https://openalex.org/W4404821554","https://openalex.org/W4405194283","https://openalex.org/W4406440058","https://openalex.org/W4406682058","https://openalex.org/W4409347060","https://openalex.org/W4409363126","https://openalex.org/W4411428681","https://openalex.org/W4411886797","https://openalex.org/W4413421953","https://openalex.org/W4414459867","https://openalex.org/W4415699195","https://openalex.org/W4416018178","https://openalex.org/W4416334285","https://openalex.org/W4416414445","https://openalex.org/W4417482988"],"related_works":[],"abstract_inverted_index":{"RNA":[0,8,30,43,48,125,133],"language":[1],"models":[2,67],"(LMs)":[3],"are":[4],"increasingly":[5],"applied":[6],"to":[7],"structure":[9,45],"and":[10,50,68,74,103,127],"function":[11],"analysis,":[12],"yet":[13],"their":[14],"intrinsic":[15],"representational":[16],"capacities":[17],"remain":[18],"poorly":[19],"characterized.":[20],"Here,":[21],"we":[22],"present":[23],"a":[24,116],"standardized":[25],"zero-shot":[26],"evaluation":[27],"of":[28],"21":[29],"LMs,":[31],"with":[32],"representative":[33],"DNA":[34],"LMs":[35],"included":[36],"as":[37],"reference":[38],"controls.":[39],"Three":[40],"complementary":[41],"tasks-attention-based":[42],"secondary":[44],"prediction,":[46],"embedding-based":[47],"classification,":[49],"mutational":[51],"fitness":[52],"estimation":[53],"from":[54,90],"sequence":[55,92],"likelihoods-are":[56],"evaluated":[57],"without":[58],"downstream":[59],"fine-tuning.":[60],"Our":[61],"results":[62],"reveal":[63],"substantial":[64],"variability":[65],"across":[66,109],"clear":[69],"trade-offs":[70],"between":[71],"structural,":[72],"functional,":[73],"evolutionary":[75,88],"representations.":[76],"RNA-specific,":[77],"noncoding":[78],"RNA-enriched":[79],"pretraining":[80],"is":[81],"crucial":[82],"for":[83,130],"capturing":[84],"structural":[85],"information,":[86],"while":[87],"signals":[89],"multiple":[91],"alignments":[93],"substantially":[94],"boost":[95],"performance.":[96],"Although":[97],"model":[98],"scaling":[99],"yields":[100],"gains,":[101],"architectural":[102],"objective":[104],"choices":[105],"critically":[106],"influence":[107],"performance":[108],"task":[110],"categories.":[111],"Together,":[112],"this":[113],"study":[114],"provides":[115],"foundational":[117],"benchmark,":[118],"highlights":[119],"inherent":[120],"challenges":[121],"in":[122],"learning":[123],"unified":[124],"representations,":[126],"offers":[128],"insights":[129],"developing":[131],"next-generation":[132],"foundation":[134],"models.":[135]},"counts_by_year":[],"updated_date":"2026-03-22T08:09:32.410652","created_date":"2026-03-07T00:00:00"}
