{"id":"https://openalex.org/W7165011889","doi":"https://doi.org/10.1093/bib/bbag322","title":"MIFNDRA: an innovative knowledge-enhanced multimodal fusion and graph learning framework for predicting drug resistance-related ncRNAs","display_name":"MIFNDRA: an innovative knowledge-enhanced multimodal fusion and graph learning framework for predicting drug resistance-related ncRNAs","publication_year":2026,"publication_date":"2026-05-01","ids":{"openalex":"https://openalex.org/W7165011889","doi":"https://doi.org/10.1093/bib/bbag322","pmid":"https://pubmed.ncbi.nlm.nih.gov/42308423"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbag322","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbag322","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":null,"license_id":null,"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/bbag322","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5078258904","display_name":"Jianan Sui","orcid":null},"institutions":[{"id":"https://openalex.org/I49835588","display_name":"Macao Polytechnic University","ror":"https://ror.org/02sf5td35","country_code":"MO","type":"education","lineage":["https://openalex.org/I49835588"]}],"countries":["MO"],"is_corresponding":false,"raw_author_name":"Jianan Sui","raw_affiliation_strings":["Centre for Artificial Intelligence Driven Drug Discovery, Faculty of Applied Sciences, Macao Polytechnic University , Rua de Lu\u00eds Gonzaga Gomes, Macao 999078 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre for Artificial Intelligence Driven Drug Discovery, Faculty of Applied Sciences, Macao Polytechnic University , Rua de Lu\u00eds Gonzaga Gomes, Macao 999078 ,","institution_ids":["https://openalex.org/I49835588"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5114235624","display_name":"Weirong Cui","orcid":null},"institutions":[{"id":"https://openalex.org/I49835588","display_name":"Macao Polytechnic University","ror":"https://ror.org/02sf5td35","country_code":"MO","type":"education","lineage":["https://openalex.org/I49835588"]}],"countries":["MO"],"is_corresponding":false,"raw_author_name":"Weirong Cui","raw_affiliation_strings":["Centre for Artificial Intelligence Driven Drug Discovery, Faculty of Applied Sciences, Macao Polytechnic University , Rua de Lu\u00eds Gonzaga Gomes, Macao 999078 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre for Artificial Intelligence Driven Drug Discovery, Faculty of Applied Sciences, Macao Polytechnic University , Rua de Lu\u00eds Gonzaga Gomes, Macao 999078 ,","institution_ids":["https://openalex.org/I49835588"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075435607","display_name":"Xiaojie Jin","orcid":"https://orcid.org/0000-0002-6419-3265"},"institutions":[{"id":"https://openalex.org/I4210092839","display_name":"Gansu University of Traditional Chinese Medicine","ror":"https://ror.org/00g741v42","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210092839"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiaojie Jin","raw_affiliation_strings":["College of Pharmacy, Gansu University of Chinese Medicine , No. 35 Dingxi East Road, Chengguan District, Lanzhou, Gansu Province 730000 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Pharmacy, Gansu University of Chinese Medicine , No. 35 Dingxi East Road, Chengguan District, Lanzhou, Gansu Province 730000 ,","institution_ids":["https://openalex.org/I4210092839"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5138761355","display_name":"Hongliang Duan","orcid":null},"institutions":[{"id":"https://openalex.org/I49835588","display_name":"Macao Polytechnic University","ror":"https://ror.org/02sf5td35","country_code":"MO","type":"education","lineage":["https://openalex.org/I49835588"]}],"countries":["MO"],"is_corresponding":false,"raw_author_name":"Hongliang Duan","raw_affiliation_strings":["Centre for Artificial Intelligence Driven Drug Discovery, Faculty of Applied Sciences, Macao Polytechnic University , Rua de Lu\u00eds Gonzaga Gomes, Macao 999078 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre for Artificial Intelligence Driven Drug Discovery, Faculty of Applied Sciences, Macao Polytechnic University , Rua de Lu\u00eds Gonzaga Gomes, Macao 999078 ,","institution_ids":["https://openalex.org/I49835588"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5008112425","display_name":"Jingjing Guo","orcid":"https://orcid.org/0000-0002-4632-4364"},"institutions":[{"id":"https://openalex.org/I49835588","display_name":"Macao Polytechnic University","ror":"https://ror.org/02sf5td35","country_code":"MO","type":"education","lineage":["https://openalex.org/I49835588"]}],"countries":["MO"],"is_corresponding":false,"raw_author_name":"Jingjing Guo","raw_affiliation_strings":["Centre for Artificial Intelligence Driven Drug Discovery, Faculty of Applied Sciences, Macao Polytechnic University , Rua de Lu\u00eds Gonzaga Gomes, Macao 999078 ,","Engineering Research Centre of Applied Technology on Machine Translation and Artificial Intelligence , Macao Polytechnic University, Rua de Lu\u00eds Gonzaga Gomes, Macao 999078 ,"],"raw_orcid":"https://orcid.org/0000-0002-4632-4364","affiliations":[{"raw_affiliation_string":"Centre for Artificial Intelligence Driven Drug Discovery, Faculty of Applied Sciences, Macao Polytechnic University , Rua de Lu\u00eds Gonzaga Gomes, Macao 999078 ,","institution_ids":["https://openalex.org/I49835588"]},{"raw_affiliation_string":"Engineering Research Centre of Applied Technology on Machine Translation and Artificial Intelligence , Macao Polytechnic University, Rua de Lu\u00eds Gonzaga Gomes, Macao 999078 ,","institution_ids":["https://openalex.org/I49835588"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.70815351,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"27","issue":"3","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10515","display_name":"Cancer-related molecular mechanisms research","score":0.5493000149726868,"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":0.5493000149726868,"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/T10062","display_name":"MicroRNA in disease regulation","score":0.19359999895095825,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.050599999725818634,"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/non-coding-rna","display_name":"Non-coding RNA","score":0.4625000059604645},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.43630000948905945},{"id":"https://openalex.org/keywords/encode","display_name":"ENCODE","score":0.43459999561309814},{"id":"https://openalex.org/keywords/robustness","display_name":"Robustness (evolution)","score":0.42809998989105225},{"id":"https://openalex.org/keywords/drug-repositioning","display_name":"Drug repositioning","score":0.42260000109672546},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.4113999903202057},{"id":"https://openalex.org/keywords/drug","display_name":"Drug","score":0.382099986076355},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.35260000824928284}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7024000287055969},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.5529000163078308},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5248000025749207},{"id":"https://openalex.org/C194993378","wikidata":"https://www.wikidata.org/wiki/Q427087","display_name":"Non-coding RNA","level":4,"score":0.4625000059604645},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.43630000948905945},{"id":"https://openalex.org/C66746571","wikidata":"https://www.wikidata.org/wiki/Q1134833","display_name":"ENCODE","level":3,"score":0.43459999561309814},{"id":"https://openalex.org/C63479239","wikidata":"https://www.wikidata.org/wiki/Q7353546","display_name":"Robustness (evolution)","level":3,"score":0.42809998989105225},{"id":"https://openalex.org/C103637391","wikidata":"https://www.wikidata.org/wiki/Q5308921","display_name":"Drug repositioning","level":3,"score":0.42260000109672546},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.4113999903202057},{"id":"https://openalex.org/C2780035454","wikidata":"https://www.wikidata.org/wiki/Q8386","display_name":"Drug","level":2,"score":0.382099986076355},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.35260000824928284},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.34689998626708984},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3312000036239624},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.3125999867916107},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.29829999804496765},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.2976999878883362},{"id":"https://openalex.org/C170734499","wikidata":"https://www.wikidata.org/wiki/Q1152227","display_name":"Pharmacogenomics","level":2,"score":0.28850001096725464},{"id":"https://openalex.org/C59404180","wikidata":"https://www.wikidata.org/wiki/Q17013334","display_name":"Feature learning","level":2,"score":0.2856999933719635},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.2815000116825104},{"id":"https://openalex.org/C86251818","wikidata":"https://www.wikidata.org/wiki/Q816754","display_name":"Benchmarking","level":2,"score":0.26980000734329224},{"id":"https://openalex.org/C2989108626","wikidata":"https://www.wikidata.org/wiki/Q904407","display_name":"Drug target","level":2,"score":0.26489999890327454}],"mesh":[{"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":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000188","qualifier_name":"drug therapy","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000188","qualifier_name":"drug therapy","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019008","descriptor_name":"Drug Resistance, Neoplasm","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D019008","descriptor_name":"Drug Resistance, Neoplasm","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"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":"D022661","descriptor_name":"RNA, Untranslated","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D022661","descriptor_name":"RNA, Untranslated","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbag322","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbag322","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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:42308423","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/42308423","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":"Journal Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:13275005","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC13275005/","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/bbag322","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbag322","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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Good health and well-being","score":0.5843791365623474,"id":"https://metadata.un.org/sdg/3"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":40,"referenced_works":["https://openalex.org/W2009313526","https://openalex.org/W2068205741","https://openalex.org/W2141222510","https://openalex.org/W2162965868","https://openalex.org/W2305271175","https://openalex.org/W2529378193","https://openalex.org/W2747907311","https://openalex.org/W2883617201","https://openalex.org/W2898440040","https://openalex.org/W2898731714","https://openalex.org/W2911611059","https://openalex.org/W2936144882","https://openalex.org/W2963026948","https://openalex.org/W2967109100","https://openalex.org/W3003617964","https://openalex.org/W3012491561","https://openalex.org/W3048090444","https://openalex.org/W3112188147","https://openalex.org/W3153642798","https://openalex.org/W3174941743","https://openalex.org/W3203619936","https://openalex.org/W4210466552","https://openalex.org/W4223456024","https://openalex.org/W4283772644","https://openalex.org/W4285590326","https://openalex.org/W4287213385","https://openalex.org/W4292318631","https://openalex.org/W4308524648","https://openalex.org/W4308687190","https://openalex.org/W4317951128","https://openalex.org/W4385325570","https://openalex.org/W4387859553","https://openalex.org/W4388636800","https://openalex.org/W4391840390","https://openalex.org/W4392152030","https://openalex.org/W4392595354","https://openalex.org/W4393154949","https://openalex.org/W4393397048","https://openalex.org/W4393931589","https://openalex.org/W4394763992"],"related_works":[],"abstract_inverted_index":{"Drug":[0],"resistance":[1,162,188],"is":[2],"a":[3,57,75,86,109,122,151],"significant":[4],"challenge":[5],"in":[6,19,47,185],"cancer":[7],"treatment,":[8],"greatly":[9],"impacting":[10],"treatment":[11],"efficacy.":[12],"Non-coding":[13],"RNAs":[14],"(ncRNAs)":[15],"play":[16],"crucial":[17],"roles":[18],"mediating":[20],"drug":[21,29,66,70,82,145,159,187,191],"resistance,":[22],"yet":[23],"few":[24],"computational":[25],"models":[26,63],"effectively":[27],"predict":[28],"resistance-associated":[30,146],"ncRNAs.":[31,72,147],"Existing":[32],"methods":[33],"often":[34],"overlook":[35],"the":[36,139,142,180],"complex":[37],"sequence":[38],"patterns":[39],"of":[40,144],"ncRNA":[41,64,92,111,119,156],"and":[42,65,85,103,136,161,176,183,190,195],"their":[43],"intricate":[44],"interrelationships,":[45],"resulting":[46],"suboptimal":[48],"performance.":[49,171],"To":[50],"address":[51],"these":[52],"challenges,":[53],"we":[54,149],"propose":[55],"MIFNDRA,":[56],"multimodal":[58],"integrative":[59],"framework":[60],"that":[61,114,167],"jointly":[62],"features":[67,84,99],"to":[68,80,90],"identify":[69],"resistance-related":[71],"MIFNDRA":[73,168],"employs":[74],"pre-trained":[76,87],"Graph":[77],"Isomorphism":[78],"Network":[79],"extract":[81],"structural":[83],"SpliceBERT":[88],"model":[89,140],"encode":[91],"sequences.":[93],"It":[94],"also":[95],"incorporates":[96],"various":[97],"similarity":[98],"for":[100,124,198],"both":[101],"drugs":[102],"ncRNAs,":[104],"while":[105],"improving":[106],"representation":[107],"through":[108],"novel":[110],"interaction":[112],"network":[113],"includes":[115],"interactions":[116],"between":[117],"different":[118],"types":[120],"as":[121],"strategy":[123],"knowledge":[125],"enhancement.":[126],"By":[127],"leveraging":[128],"advanced":[129],"graph":[130],"learning":[131],"techniques,":[132],"including":[133],"residual":[134],"GraphSAGE":[135],"contrastive":[137],"learning,":[138],"improves":[141],"identification":[143],"Additionally,":[148],"curated":[150],"new":[152],"benchmark":[153],"dataset":[154],"pairing":[155],"sequences":[157],"with":[158],"SMILES":[160],"annotations.":[163],"Comprehensive":[164],"experiments":[165],"demonstrate":[166],"achieved":[169],"state-of-the-art":[170],"Case":[172],"studies":[173],"on":[174],"cisplatin":[175],"gemcitabine":[177],"further":[178],"validate":[179],"model's":[181],"robustness":[182],"potential":[184],"advancing":[186],"research":[189],"development.":[192],"The":[193],"data":[194],"code":[196],"required":[197],"this":[199],"work":[200],"are":[201],"available":[202],"at":[203],"https://github.com/SJNNNN/MIFNDRA.":[204]},"counts_by_year":[],"updated_date":"2026-07-27T08:26:11.824852","created_date":"2026-06-18T00:00:00"}