{"id":"https://openalex.org/W7140294044","doi":"https://doi.org/10.1186/s12859-026-06419-x","title":"SPGA: graph representation learning and attention fusion for enhanced disease-associated snoRNA prediction","display_name":"SPGA: graph representation learning and attention fusion for enhanced disease-associated snoRNA prediction","publication_year":2026,"publication_date":"2026-03-25","ids":{"openalex":"https://openalex.org/W7140294044","doi":"https://doi.org/10.1186/s12859-026-06419-x","pmid":"https://pubmed.ncbi.nlm.nih.gov/41882521"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-026-06419-x","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-026-06419-x","pdf_url":null,"source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC 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/10.1186/s12859-026-06419-x","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100741607","display_name":"Hailin Chen","orcid":"https://orcid.org/0000-0002-5119-4517"},"institutions":[{"id":"https://openalex.org/I13985625","display_name":"East China Jiaotong University","ror":"https://ror.org/05x2f1m38","country_code":"CN","type":"education","lineage":["https://openalex.org/I13985625"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Hailin Chen","raw_affiliation_strings":["School of Information and Software Engineering, East China Jiaotong University, Nanchang, 330013, China. chenhailin@ecjtu.edu.cn"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Information and Software Engineering, East China Jiaotong University, Nanchang, 330013, China. chenhailin@ecjtu.edu.cn","institution_ids":["https://openalex.org/I13985625"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5130611353","display_name":"Zirui Song","orcid":null},"institutions":[{"id":"https://openalex.org/I13985625","display_name":"East China Jiaotong University","ror":"https://ror.org/05x2f1m38","country_code":"CN","type":"education","lineage":["https://openalex.org/I13985625"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zirui Song","raw_affiliation_strings":["School of Information and Software Engineering, East China Jiaotong University, Nanchang, 330013, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Information and Software Engineering, East China Jiaotong University, Nanchang, 330013, China","institution_ids":["https://openalex.org/I13985625"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5100741607"],"corresponding_institution_ids":["https://openalex.org/I13985625"],"apc_list":{"value":2990,"currency":"USD","value_usd":2990},"apc_paid":{"value":2990,"currency":"USD","value_usd":2990},"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.23590007,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"27","issue":"1","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12610","display_name":"RNA regulation and disease","score":0.15029999613761902,"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/T12610","display_name":"RNA regulation and disease","score":0.15029999613761902,"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/T11307","display_name":"Domain Adaptation and Few-Shot Learning","score":0.10220000147819519,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.07530000060796738,"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/representation","display_name":"Representation (politics)","score":0.5382000207901001},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.4961000084877014},{"id":"https://openalex.org/keywords/feature-learning","display_name":"Feature learning","score":0.489300012588501},{"id":"https://openalex.org/keywords/fusion","display_name":"Fusion","score":0.41179999709129333},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.3946000039577484},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.38440001010894775}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6942999958992004},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.6244999766349792},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.5382000207901001},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.4961000084877014},{"id":"https://openalex.org/C59404180","wikidata":"https://www.wikidata.org/wiki/Q17013334","display_name":"Feature learning","level":2,"score":0.489300012588501},{"id":"https://openalex.org/C158525013","wikidata":"https://www.wikidata.org/wiki/Q2593739","display_name":"Fusion","level":2,"score":0.41179999709129333},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.4113999903202057},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.3946000039577484},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.38440001010894775},{"id":"https://openalex.org/C179255354","wikidata":"https://www.wikidata.org/wiki/Q284416","display_name":"Small nucleolar RNA","level":5,"score":0.3506999909877777},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3467000126838684},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.34220001101493835},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.3028999865055084},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.2526000142097473}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000098409","descriptor_name":"Representation Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000098409","descriptor_name":"Representation Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000098422","descriptor_name":"Graph Neural Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000098422","descriptor_name":"Graph Neural Networks","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":"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":"D020537","descriptor_name":"RNA, Small Nucleolar","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D020537","descriptor_name":"RNA, Small Nucleolar","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1186/s12859-026-06419-x","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-026-06419-x","pdf_url":null,"source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:41882521","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41882521","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":"BMC bioinformatics","raw_type":"Journal Article"},{"id":"pmh:oai:doaj.org/article:0f4053788a634e19af7bbff67343d6d7","is_oa":true,"landing_page_url":"https://doaj.org/article/0f4053788a634e19af7bbff67343d6d7","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 27, Iss 1 (2026)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:13141256","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC13141256/","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":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-026-06419-x","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-026-06419-x","pdf_url":null,"source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2570419886","display_name":null,"funder_award_id":"62562031","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":35,"referenced_works":["https://openalex.org/W1978715316","https://openalex.org/W1983200597","https://openalex.org/W1985480639","https://openalex.org/W2024799598","https://openalex.org/W2078837366","https://openalex.org/W2086779374","https://openalex.org/W2095206021","https://openalex.org/W2139004454","https://openalex.org/W2569955787","https://openalex.org/W2966519792","https://openalex.org/W2994632666","https://openalex.org/W3000082418","https://openalex.org/W3010127844","https://openalex.org/W3170286690","https://openalex.org/W3196514628","https://openalex.org/W3211191823","https://openalex.org/W4211182482","https://openalex.org/W4284688416","https://openalex.org/W4285041302","https://openalex.org/W4294811162","https://openalex.org/W4297891375","https://openalex.org/W4307440230","https://openalex.org/W4312203477","https://openalex.org/W4323974793","https://openalex.org/W4366338370","https://openalex.org/W4386963628","https://openalex.org/W4390415056","https://openalex.org/W4394853685","https://openalex.org/W4395015247","https://openalex.org/W4400448110","https://openalex.org/W4404628128","https://openalex.org/W4406082977","https://openalex.org/W4406409125","https://openalex.org/W4408813386","https://openalex.org/W4409191426"],"related_works":[],"abstract_inverted_index":{"BACKGROUND:":[0],"Small":[1],"nucleolar":[2],"RNAs":[3],"(snoRNAs)":[4],"are":[5],"increasingly":[6],"recognized":[7],"for":[8,23,119,133,179],"their":[9,59],"involvement":[10],"in":[11,37,141,166],"human":[12],"diseases.":[13],"Accurate":[14],"and":[15,27,94,136,151,192],"robust":[16,116],"prediction":[17,144],"of":[18,34,48,92,143,149,154,188],"disease-associated":[19],"snoRNAs":[20,93],"is":[21,61],"crucial":[22],"accelerating":[24],"drug":[25],"discovery":[26,187],"disease":[28],"treatment.":[29],"However,":[30],"the":[31,45,129,186],"limited":[32],"availability":[33],"biomedical":[35],"data":[36,65,130],"this":[38],"domain":[39],"poses":[40],"a":[41,75,110,175],"significant":[42],"challenge":[43],"to":[44,82,96,114],"generalization":[46,135],"ability":[47],"machine":[49],"learning":[50,79],"models.":[51],"While":[52],"existing":[53],"computational":[54,177],"methods":[55,140],"have":[56],"made":[57],"progress,":[58],"performance":[60],"often":[62],"constrained":[63],"by":[64],"scarcity.":[66],"RESULTS:":[67],"To":[68],"overcome":[69],"these":[70],"limitations,":[71],"we":[72],"introduce":[73],"SPGA,":[74],"novel":[76,168],"graph":[77,99,105],"representation":[78],"framework":[80],"designed":[81],"enhance":[83],"snoRNA-disease":[84,169],"association":[85,120],"prediction.":[86],"SPGA":[87,126],"leverages":[88],"intrinsic":[89],"structural":[90],"features":[91],"diseases":[95],"construct":[97],"interaction-aware":[98],"representations.":[100],"It":[101],"then":[102],"employs":[103],"residual":[104],"convolutional":[106],"networks":[107],"augmented":[108],"with":[109],"hierarchical":[111],"attention":[112],"mechanism":[113],"learn":[115],"node":[117],"embeddings":[118],"predictions.":[121],"Comprehensive":[122],"experiments":[123],"demonstrate":[124],"that":[125],"effectively":[127],"alleviates":[128],"scarcity":[131],"problem":[132],"model":[134],"significantly":[137],"improves":[138],"state-of-the-art":[139],"terms":[142],"accuracy,":[145],"achieving":[146],"an":[147,152],"AUC":[148],"0.9812":[150],"AUPR":[153],"0.9749":[155],"under":[156],"five-fold":[157],"cross-validation":[158],"setting.":[159],"Case":[160],"studies":[161],"further":[162],"validate":[163],"its":[164],"efficacy":[165],"identifying":[167],"associations.":[170],"CONCLUSIONS:":[171],"Our":[172],"study":[173],"provides":[174],"potent":[176],"tool":[178],"prioritizing":[180],"candidate":[181],"disease-related":[182],"snoRNAs,":[183],"thereby":[184],"facilitating":[185],"potential":[189],"diagnostic":[190],"biomarkers":[191],"therapeutic":[193],"targets.":[194]},"counts_by_year":[],"updated_date":"2026-08-21T09:56:20.448147","created_date":"2026-03-26T00:00:00"}