{"id":"https://openalex.org/W4410582198","doi":"https://doi.org/10.1109/jbhi.2025.3572093","title":"Miniformer: A Minimalist Transformer for Brain Functional Networks Analysis","display_name":"Miniformer: A Minimalist Transformer for Brain Functional Networks Analysis","publication_year":2025,"publication_date":"2025-05-21","ids":{"openalex":"https://openalex.org/W4410582198","doi":"https://doi.org/10.1109/jbhi.2025.3572093","pmid":"https://pubmed.ncbi.nlm.nih.gov/40397632"},"language":"en","primary_location":{"id":"doi:10.1109/jbhi.2025.3572093","is_oa":false,"landing_page_url":"https://doi.org/10.1109/jbhi.2025.3572093","pdf_url":null,"source":{"id":"https://openalex.org/S2495854775","display_name":"IEEE Journal of Biomedical and Health Informatics","issn_l":"2168-2194","issn":["2168-2194","2168-2208"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Journal of Biomedical and Health Informatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://pure.ulster.ac.uk/en/publications/b638e9f6-3878-4d60-8c88-e1ac25d664ff","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":null,"display_name":"Yaru Li","orcid":"https://orcid.org/0009-0009-4111-8682"},"institutions":[{"id":"https://openalex.org/I44445938","display_name":"Shandong Jianzhu University","ror":"https://ror.org/01gbfax37","country_code":"CN","type":"education","lineage":["https://openalex.org/I44445938"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Yaru Li","raw_affiliation_strings":["School of Computer Science and Technology, Shandong Jianzhu University, Jinan, China"],"affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Shandong Jianzhu University, Jinan, China","institution_ids":["https://openalex.org/I44445938"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Jun Yang","orcid":"https://orcid.org/0009-0009-8674-8880"},"institutions":[{"id":"https://openalex.org/I196934937","display_name":"Liaocheng University","ror":"https://ror.org/03yh0n709","country_code":"CN","type":"education","lineage":["https://openalex.org/I196934937"]},{"id":"https://openalex.org/I44445938","display_name":"Shandong Jianzhu University","ror":"https://ror.org/01gbfax37","country_code":"CN","type":"education","lineage":["https://openalex.org/I44445938"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jun Yang","raw_affiliation_strings":["School of Mathematics Science, Liaocheng University, Liaocheng, China","School of Computer Science and Technology, Shandong Jianzhu University, Jinan, China"],"affiliations":[{"raw_affiliation_string":"School of Mathematics Science, Liaocheng University, Liaocheng, China","institution_ids":["https://openalex.org/I196934937"]},{"raw_affiliation_string":"School of Computer Science and Technology, Shandong Jianzhu University, Jinan, China","institution_ids":["https://openalex.org/I44445938"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Mengxue Pang","orcid":"https://orcid.org/0009-0003-4188-5124"},"institutions":[{"id":"https://openalex.org/I196934937","display_name":"Liaocheng University","ror":"https://ror.org/03yh0n709","country_code":"CN","type":"education","lineage":["https://openalex.org/I196934937"]},{"id":"https://openalex.org/I44445938","display_name":"Shandong Jianzhu University","ror":"https://ror.org/01gbfax37","country_code":"CN","type":"education","lineage":["https://openalex.org/I44445938"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Mengxue Pang","raw_affiliation_strings":["School of Mathematics Science, Liaocheng University, Liaocheng, China","School of Computer Science and Technology, Shandong Jianzhu University, Jinan, China"],"affiliations":[{"raw_affiliation_string":"School of Mathematics Science, Liaocheng University, Liaocheng, China","institution_ids":["https://openalex.org/I196934937"]},{"raw_affiliation_string":"School of Computer Science and Technology, Shandong Jianzhu University, Jinan, China","institution_ids":["https://openalex.org/I44445938"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100328881","display_name":"Shuai Zhang","orcid":"https://orcid.org/0000-0002-4821-6404"},"institutions":[{"id":"https://openalex.org/I138801177","display_name":"University of Ulster","ror":"https://ror.org/01yp9g959","country_code":"GB","type":"education","lineage":["https://openalex.org/I138801177"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Shuai Zhang","raw_affiliation_strings":["School of Computing, Ulster University, Belfast, U.K","School of Computing, Ulster University, Belfast, NI, U.K"],"affiliations":[{"raw_affiliation_string":"School of Computing, Ulster University, Belfast, U.K","institution_ids":["https://openalex.org/I138801177"]},{"raw_affiliation_string":"School of Computing, Ulster University, Belfast, NI, U.K","institution_ids":["https://openalex.org/I138801177"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021247547","display_name":"Chris Nugent","orcid":"https://orcid.org/0000-0003-0882-7902"},"institutions":[{"id":"https://openalex.org/I138801177","display_name":"University of Ulster","ror":"https://ror.org/01yp9g959","country_code":"GB","type":"education","lineage":["https://openalex.org/I138801177"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Chris Nugent","raw_affiliation_strings":["School of Computing, Ulster University, Belfast, U.K","School of Computing, Ulster University, Belfast, NI, U.K"],"affiliations":[{"raw_affiliation_string":"School of Computing, Ulster University, Belfast, U.K","institution_ids":["https://openalex.org/I138801177"]},{"raw_affiliation_string":"School of Computing, Ulster University, Belfast, NI, U.K","institution_ids":["https://openalex.org/I138801177"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Mingxia Liu","orcid":"https://orcid.org/0000-0002-0166-0807"},"institutions":[{"id":"https://openalex.org/I114027177","display_name":"University of North Carolina at Chapel Hill","ror":"https://ror.org/0130frc33","country_code":"US","type":"education","lineage":["https://openalex.org/I114027177"]},{"id":"https://openalex.org/I4210166946","display_name":"Imaging Center","ror":"https://ror.org/05hsqsk33","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210166946"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mingxia Liu","raw_affiliation_strings":["Department of Radiology and Biomedical Research Imaging Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA","Department of Radiology and Biomedical Research Imaging Center, the University of North Carolina at Chapel Hill, Chapel Hill, NC, USA"],"affiliations":[{"raw_affiliation_string":"Department of Radiology and Biomedical Research Imaging Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA","institution_ids":["https://openalex.org/I114027177","https://openalex.org/I4210166946"]},{"raw_affiliation_string":"Department of Radiology and Biomedical Research Imaging Center, the University of North Carolina at Chapel Hill, Chapel Hill, NC, USA","institution_ids":["https://openalex.org/I114027177","https://openalex.org/I4210166946"]}]},{"author_position":"last","author":{"id":null,"display_name":"Lishan Qiao","orcid":"https://orcid.org/0000-0001-6826-6145"},"institutions":[{"id":"https://openalex.org/I44445938","display_name":"Shandong Jianzhu University","ror":"https://ror.org/01gbfax37","country_code":"CN","type":"education","lineage":["https://openalex.org/I44445938"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Lishan Qiao","raw_affiliation_strings":["School of Computer Science and Technology, Shandong Jianzhu University, Jinan, China"],"affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Shandong Jianzhu University, Jinan, China","institution_ids":["https://openalex.org/I44445938"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":7,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I44445938"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.10470217,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"29","issue":"11","first_page":"8460","last_page":"8473"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10241","display_name":"Functional Brain Connectivity Studies","score":0.9333000183105469,"subfield":{"id":"https://openalex.org/subfields/2805","display_name":"Cognitive Neuroscience"},"field":{"id":"https://openalex.org/fields/28","display_name":"Neuroscience"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10241","display_name":"Functional Brain Connectivity Studies","score":0.9333000183105469,"subfield":{"id":"https://openalex.org/subfields/2805","display_name":"Cognitive Neuroscience"},"field":{"id":"https://openalex.org/fields/28","display_name":"Neuroscience"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6634134650230408},{"id":"https://openalex.org/keywords/transformer","display_name":"Transformer","score":0.4595322906970978},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3937187194824219},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.11699709296226501},{"id":"https://openalex.org/keywords/electrical-engineering","display_name":"Electrical engineering","score":0.1008794903755188}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6634134650230408},{"id":"https://openalex.org/C66322947","wikidata":"https://www.wikidata.org/wiki/Q11658","display_name":"Transformer","level":3,"score":0.4595322906970978},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3937187194824219},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.11699709296226501},{"id":"https://openalex.org/C119599485","wikidata":"https://www.wikidata.org/wiki/Q43035","display_name":"Electrical engineering","level":1,"score":0.1008794903755188},{"id":"https://openalex.org/C165801399","wikidata":"https://www.wikidata.org/wiki/Q25428","display_name":"Voltage","level":2,"score":0.0}],"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":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001921","descriptor_name":"Brain","qualifier_ui":"Q000000981","qualifier_name":"diagnostic imaging","is_major_topic":true},{"descriptor_ui":"D001921","descriptor_name":"Brain","qualifier_ui":"Q000000981","qualifier_name":"diagnostic imaging","is_major_topic":true},{"descriptor_ui":"D001921","descriptor_name":"Brain","qualifier_ui":"Q000000981","qualifier_name":"diagnostic imaging","is_major_topic":true},{"descriptor_ui":"D001921","descriptor_name":"Brain","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":true},{"descriptor_ui":"D001921","descriptor_name":"Brain","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":true},{"descriptor_ui":"D001921","descriptor_name":"Brain","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":true},{"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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008279","descriptor_name":"Magnetic Resonance Imaging","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D008279","descriptor_name":"Magnetic Resonance Imaging","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D008279","descriptor_name":"Magnetic Resonance Imaging","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D009415","descriptor_name":"Nerve Net","qualifier_ui":"Q000000981","qualifier_name":"diagnostic imaging","is_major_topic":true},{"descriptor_ui":"D009415","descriptor_name":"Nerve Net","qualifier_ui":"Q000000981","qualifier_name":"diagnostic imaging","is_major_topic":true},{"descriptor_ui":"D009415","descriptor_name":"Nerve Net","qualifier_ui":"Q000000981","qualifier_name":"diagnostic imaging","is_major_topic":true},{"descriptor_ui":"D009415","descriptor_name":"Nerve Net","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":true},{"descriptor_ui":"D009415","descriptor_name":"Nerve Net","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":true},{"descriptor_ui":"D009415","descriptor_name":"Nerve Net","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":true},{"descriptor_ui":"D012815","descriptor_name":"Signal Processing, Computer-Assisted","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012815","descriptor_name":"Signal Processing, Computer-Assisted","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012815","descriptor_name":"Signal Processing, Computer-Assisted","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1109/jbhi.2025.3572093","is_oa":false,"landing_page_url":"https://doi.org/10.1109/jbhi.2025.3572093","pdf_url":null,"source":{"id":"https://openalex.org/S2495854775","display_name":"IEEE Journal of Biomedical and Health Informatics","issn_l":"2168-2194","issn":["2168-2194","2168-2208"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Journal of Biomedical and Health Informatics","raw_type":"journal-article"},{"id":"pmid:40397632","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40397632","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":"IEEE journal of biomedical and health informatics","raw_type":null},{"id":"pmh:oai:pure.atira.dk:openaire/b638e9f6-3878-4d60-8c88-e1ac25d664ff","is_oa":true,"landing_page_url":"https://pure.ulster.ac.uk/en/publications/b638e9f6-3878-4d60-8c88-e1ac25d664ff","pdf_url":null,"source":{"id":"https://openalex.org/S4306402454","display_name":"Ulster University Research Portal (Ulster University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I138801177","host_organization_name":"University of Ulster","host_organization_lineage":["https://openalex.org/I138801177"],"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":"Li, Y, Yang, J, Pang, M, Zhang, S, Nugent, CD, Liu, M & Qiao, L 2025, 'Miniformer: A Minimalist Transformer for Brain Functional Networks Analysis', IEEE Journal of Biomedical and Health Informatics, vol. 29, no. 11, pp. 8460-8473. https://doi.org/10.1109/JBHI.2025.3572093","raw_type":"article"}],"best_oa_location":{"id":"pmh:oai:pure.atira.dk:openaire/b638e9f6-3878-4d60-8c88-e1ac25d664ff","is_oa":true,"landing_page_url":"https://pure.ulster.ac.uk/en/publications/b638e9f6-3878-4d60-8c88-e1ac25d664ff","pdf_url":null,"source":{"id":"https://openalex.org/S4306402454","display_name":"Ulster University Research Portal (Ulster University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I138801177","host_organization_name":"University of Ulster","host_organization_lineage":["https://openalex.org/I138801177"],"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":"Li, Y, Yang, J, Pang, M, Zhang, S, Nugent, CD, Liu, M & Qiao, L 2025, 'Miniformer: A Minimalist Transformer for Brain Functional Networks Analysis', IEEE Journal of Biomedical and Health Informatics, vol. 29, no. 11, pp. 8460-8473. https://doi.org/10.1109/JBHI.2025.3572093","raw_type":"article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1336109083","display_name":null,"funder_award_id":"ZR2024MF063","funder_id":"https://openalex.org/F4320324174","funder_display_name":"Natural Science Foundation of Shandong Province"},{"id":"https://openalex.org/G144932472","display_name":null,"funder_award_id":"62176112","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G67554910","display_name":null,"funder_award_id":"62476155","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/F4320324174","display_name":"Natural Science Foundation of Shandong Province","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W4391913857","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W4396696052"],"abstract_inverted_index":{"Learning":[0],"to":[1,51,75,84,114,226],"estimate":[2],"and":[3,31,41,81,94,143,165,188,222],"classify":[4],"brain":[5,209],"functional":[6],"networks":[7],"(BFNs)":[8],"has":[9],"become":[10],"an":[11,58],"increasingly":[12],"important":[13],"way":[14],"of":[15,71,136,141,152,159,174,203],"predicting":[16],"neurological":[17],"or":[18,162],"mental":[19],"disorders":[20],"at":[21],"their":[22,62],"early":[23],"stages.":[24],"The":[25,217],"traditional":[26],"methods":[27,66,233],"conduct":[28],"BFN":[29],"estimation":[30],"classification":[32,229],"in":[33,57,91,101,104,122,154,195],"two":[34,172],"separate":[35],"steps,":[36],"thus":[37],"preventing":[38],"the":[39,89,95,119,123,134,139,145,148,157,192,201,204],"interaction":[40],"joint":[42],"optimization.":[43],"In":[44],"contrast,":[45],"Transformer":[46,111],"provides":[47],"a":[48,68,109,127],"natural":[49],"architecture":[50],"learn":[52],"BFNs":[53],"with":[54,234],"downstream":[55],"tasks":[56],"end-to-end":[59],"manner.":[60],"Despite":[61],"great":[63],"potential,":[64],"Transformer-based":[65],"involve":[67],"large":[69],"number":[70,135],"parameters":[72,153],"that":[73,220],"need":[74],"be":[76],"learnt":[77],"from":[78,185],"Big":[79],"Data":[80],"often":[82],"lead":[83],"poor":[85],"model":[86,99],"interpretability.":[87,146,236],"Considering":[88],"challenge":[90],"acquiring":[92],"data":[93],"high":[96],"demand":[97],"for":[98,179,190],"interpretability":[100],"medical":[102],"scenarios,":[103],"this":[105],"paper,":[106],"we":[107,169,207],"propose":[108],"minimalist":[110],"architecture,":[112],"referred":[113],"as":[115],"Miniformer,":[116],"by":[117,176],"simplifying":[118],"projection":[120],"matrices":[121],"self-attention":[124],"module":[125],"into":[126],"single":[128],"diagonal":[129],"matrix,":[130],"which":[131],"greatly":[132],"reduces":[133],"parameters,":[137],"alleviates":[138],"risk":[140],"overfitting,":[142],"improves":[144],"Additionally,":[147],"clear":[149],"physical":[150],"meaning":[151],"Miniformer":[155,175,221],"makes":[156],"integration":[158],"domain":[160],"knowledge":[161],"prior":[163],"easier":[164],"more":[166],"natural.":[167],"Therefore,":[168],"further":[170],"develop":[171],"variants":[173,224],"incorporating":[177],"sparsity":[178],"removing":[180],"potentially":[181],"noisy":[182],"time":[183],"points":[184],"fMRI":[186,196],"signals,":[187,197],"smoothness":[189],"capturing":[191],"temporal":[193],"correlations":[194],"respectively.":[198],"To":[199],"evaluate":[200],"effectiveness":[202],"proposed":[205],"methods,":[206],"perform":[208],"disease":[210],"diagnosis":[211],"experiments":[212],"on":[213],"three":[214],"public":[215],"datasets.":[216],"results":[218],"show":[219],"its":[223],"tend":[225],"achieve":[227],"higher":[228],"performance":[230],"than":[231],"comparison":[232],"good":[235]},"counts_by_year":[],"updated_date":"2026-04-09T08:11:56.329763","created_date":"2025-10-10T00:00:00"}