{"id":"https://openalex.org/W4415125139","doi":"https://doi.org/10.1109/tcbbio.2025.3620892","title":"M <sup>2</sup> BA-MDA: A Multi-Modal Multi-View Bidirectional Attention Network for Microbe-Disease Association Prediction","display_name":"M <sup>2</sup> BA-MDA: A Multi-Modal Multi-View Bidirectional Attention Network for Microbe-Disease Association Prediction","publication_year":2025,"publication_date":"2025-10-13","ids":{"openalex":"https://openalex.org/W4415125139","doi":"https://doi.org/10.1109/tcbbio.2025.3620892","pmid":"https://pubmed.ncbi.nlm.nih.gov/41082432"},"language":"en","primary_location":{"id":"doi:10.1109/tcbbio.2025.3620892","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbbio.2025.3620892","pdf_url":null,"source":{"id":"https://openalex.org/S5407042751","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"2998-4165","issn":["2998-4165"],"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":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5101460223","display_name":"Xuebing Guo","orcid":"https://orcid.org/0000-0003-1346-4376"},"institutions":[{"id":"https://openalex.org/I34949971","display_name":"University of Jinan","ror":"https://ror.org/02mjz6f26","country_code":"CN","type":"education","lineage":["https://openalex.org/I34949971"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Xuliang Guo","raw_affiliation_strings":["Information Science and Engineering, University of Jinan, Jinan, China"],"affiliations":[{"raw_affiliation_string":"Information Science and Engineering, University of Jinan, Jinan, China","institution_ids":["https://openalex.org/I34949971"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101940437","display_name":"Xiao Ping Zou","orcid":null},"institutions":[{"id":"https://openalex.org/I34949971","display_name":"University of Jinan","ror":"https://ror.org/02mjz6f26","country_code":"CN","type":"education","lineage":["https://openalex.org/I34949971"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiangfei Zou","raw_affiliation_strings":["Information Science and Engineering, University of Jinan, Jinan, China"],"affiliations":[{"raw_affiliation_string":"Information Science and Engineering, University of Jinan, Jinan, China","institution_ids":["https://openalex.org/I34949971"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5014767935","display_name":"Hui-lian Xu","orcid":"https://orcid.org/0000-0002-3031-9085"},"institutions":[{"id":"https://openalex.org/I34949971","display_name":"University of Jinan","ror":"https://ror.org/02mjz6f26","country_code":"CN","type":"education","lineage":["https://openalex.org/I34949971"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Huilian Xu","raw_affiliation_strings":["School of Biological Science and Technology, University of Jinan, Jinan, China"],"affiliations":[{"raw_affiliation_string":"School of Biological Science and Technology, University of Jinan, Jinan, China","institution_ids":["https://openalex.org/I34949971"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5047481051","display_name":"Jinsong Gu","orcid":"https://orcid.org/0000-0003-2540-9980"},"institutions":[{"id":"https://openalex.org/I34949971","display_name":"University of Jinan","ror":"https://ror.org/02mjz6f26","country_code":"CN","type":"education","lineage":["https://openalex.org/I34949971"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jinsong Gu","raw_affiliation_strings":["School of Biological Science and Technology, University of Jinan, Jinan, China"],"affiliations":[{"raw_affiliation_string":"School of Biological Science and Technology, University of Jinan, Jinan, China","institution_ids":["https://openalex.org/I34949971"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5101460223"],"corresponding_institution_ids":["https://openalex.org/I34949971"],"apc_list":null,"apc_paid":null,"fwci":0.8472,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.77317262,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":97,"max":99},"biblio":{"volume":"22","issue":"6","first_page":"3294","last_page":"3304"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10640","display_name":"Spectroscopy and Chemometric Analyses","score":0.875,"subfield":{"id":"https://openalex.org/subfields/1602","display_name":"Analytical Chemistry"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10640","display_name":"Spectroscopy and Chemometric Analyses","score":0.875,"subfield":{"id":"https://openalex.org/subfields/1602","display_name":"Analytical Chemistry"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10825","display_name":"Plant Pathogens and Fungal Diseases","score":0.8485000133514404,"subfield":{"id":"https://openalex.org/subfields/1307","display_name":"Cell 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/T12859","display_name":"Cell Image Analysis Techniques","score":0.8440999984741211,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"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/robustness","display_name":"Robustness (evolution)","score":0.5782999992370605},{"id":"https://openalex.org/keywords/classifier","display_name":"Classifier (UML)","score":0.5157999992370605},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.461899995803833},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.42309999465942383},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.3991999924182892},{"id":"https://openalex.org/keywords/attention-network","display_name":"Attention network","score":0.38909998536109924},{"id":"https://openalex.org/keywords/deep-neural-networks","display_name":"Deep neural networks","score":0.33889999985694885},{"id":"https://openalex.org/keywords/mechanism","display_name":"Mechanism (biology)","score":0.3001999855041504}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7242000102996826},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.6639999747276306},{"id":"https://openalex.org/C63479239","wikidata":"https://www.wikidata.org/wiki/Q7353546","display_name":"Robustness (evolution)","level":3,"score":0.5782999992370605},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.5550000071525574},{"id":"https://openalex.org/C95623464","wikidata":"https://www.wikidata.org/wiki/Q1096149","display_name":"Classifier (UML)","level":2,"score":0.5157999992370605},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.461899995803833},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.42309999465942383},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.3991999924182892},{"id":"https://openalex.org/C2993807640","wikidata":"https://www.wikidata.org/wiki/Q103709453","display_name":"Attention network","level":2,"score":0.38909998536109924},{"id":"https://openalex.org/C2984842247","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep neural networks","level":3,"score":0.33889999985694885},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3237000107765198},{"id":"https://openalex.org/C89611455","wikidata":"https://www.wikidata.org/wiki/Q6804646","display_name":"Mechanism (biology)","level":2,"score":0.3001999855041504},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.29339998960494995},{"id":"https://openalex.org/C21200559","wikidata":"https://www.wikidata.org/wiki/Q7451068","display_name":"Sensitivity (control systems)","level":2,"score":0.28859999775886536},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.2754000127315521},{"id":"https://openalex.org/C104122410","wikidata":"https://www.wikidata.org/wiki/Q1416406","display_name":"Network model","level":2,"score":0.26930001378059387},{"id":"https://openalex.org/C142853389","wikidata":"https://www.wikidata.org/wiki/Q744778","display_name":"Association (psychology)","level":2,"score":0.267300009727478},{"id":"https://openalex.org/C28225019","wikidata":"https://www.wikidata.org/wiki/Q4915005","display_name":"Biological network","level":2,"score":0.262800008058548},{"id":"https://openalex.org/C74197172","wikidata":"https://www.wikidata.org/wiki/Q1195339","display_name":"Directed acyclic graph","level":2,"score":0.257999986410141},{"id":"https://openalex.org/C2987857752","wikidata":"https://www.wikidata.org/wiki/Q12147","display_name":"Human health","level":2,"score":0.2554999887943268}],"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":"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":"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":"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":"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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1109/tcbbio.2025.3620892","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbbio.2025.3620892","pdf_url":null,"source":{"id":"https://openalex.org/S5407042751","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"2998-4165","issn":["2998-4165"],"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":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:41082432","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41082432","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 transactions on computational biology and bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":45,"referenced_works":["https://openalex.org/W197804012","https://openalex.org/W1927710737","https://openalex.org/W1993399595","https://openalex.org/W2003099302","https://openalex.org/W2012606594","https://openalex.org/W2021668554","https://openalex.org/W2311607323","https://openalex.org/W2322763599","https://openalex.org/W2468194934","https://openalex.org/W2491844534","https://openalex.org/W2567465856","https://openalex.org/W2572551054","https://openalex.org/W2583889943","https://openalex.org/W2735376054","https://openalex.org/W2752131265","https://openalex.org/W2807176368","https://openalex.org/W2810107880","https://openalex.org/W2898769300","https://openalex.org/W2901312953","https://openalex.org/W2916981547","https://openalex.org/W2938306835","https://openalex.org/W2963132797","https://openalex.org/W2966501701","https://openalex.org/W2983166786","https://openalex.org/W3006717925","https://openalex.org/W3017158857","https://openalex.org/W3033599528","https://openalex.org/W3037489518","https://openalex.org/W3045879648","https://openalex.org/W3133864627","https://openalex.org/W3134224893","https://openalex.org/W3134886264","https://openalex.org/W3156333129","https://openalex.org/W3202854071","https://openalex.org/W3211778832","https://openalex.org/W4210602267","https://openalex.org/W4224212512","https://openalex.org/W4225752318","https://openalex.org/W4282926322","https://openalex.org/W4284899434","https://openalex.org/W4304890922","https://openalex.org/W4308834893","https://openalex.org/W4312263871","https://openalex.org/W4391687574","https://openalex.org/W4408070505"],"related_works":[],"abstract_inverted_index":{"Numerous":[0],"studies":[1,200,213],"have":[2,37],"shown":[3],"that":[4,189],"microbes":[5,137],"play":[6],"vital":[7],"roles":[8],"in":[9,19,101,217],"human":[10],"health":[11],"and":[12,23,31,41,53,69,80,89,98,122,138,161,185,198,205],"disease.":[13],"Identifying":[14],"microbe-disease":[15,76],"associations":[16],"can":[17],"aid":[18],"disease":[20,81,123],"diagnosis,":[21],"treatment,":[22],"prevention.":[24],"However,":[25],"traditional":[26],"biological":[27],"experiments":[28,180],"are":[29,83],"time-consuming":[30],"costly.":[32],"Although":[33],"various":[34],"computational":[35],"methods":[36],"been":[38],"developed,":[39],"accurate":[40],"efficient":[42],"approaches":[43],"remain":[44],"limited":[45],"due":[46],"to":[47,94,119,129,175],"single-source":[48],"data,":[49],"insufficient":[50],"prior":[51],"knowledge,":[52],"suboptimal":[54],"model":[55],"performance.":[56],"This":[57,151],"paper":[58],"proposed":[59],"M<sup>2</sup>BA-MDA,":[60],"a":[61,108,147,167],"deep":[62,102,168],"learning":[63],"framework":[64],"based":[65,145],"on":[66,146,182],"multi-modal,":[67],"multi-view,":[68],"bidirectional":[70,148],"attention":[71,104,112,149],"mechanism":[72],"for":[73,91],"predicting":[74],"potential":[75,177],"associations.":[77,178],"First,":[78],"microbe":[79],"features":[82,124],"extracted":[84],"using":[85],"multiple":[86],"similarity":[87],"measures":[88],"fused":[90],"consistency.":[92],"Second,":[93],"mitigate":[95],"gradient":[96],"vanishing":[97],"over-smoothing":[99],"issues":[100],"graph":[103,111],"networks,":[105],"we":[106,140],"propose":[107],"stable":[109],"enhanced":[110],"network":[113,170],"(EGAT)":[114],"module":[115,144,152],"incorporating":[116],"cross-layer":[117],"connections":[118],"extract":[120],"microbial":[121],"from":[125],"each":[126],"perspective.":[127],"Moreover,":[128],"more":[130],"effectively":[131],"capture":[132],"the":[133,154,158,183,203,208],"complex":[134],"interactions":[135],"between":[136,157],"diseases,":[139],"introduce":[141],"an":[142],"interaction":[143],"mechanism.":[150],"enhances":[153],"mutual":[155],"dependencies":[156],"two":[159],"entities":[160],"generates":[162],"their":[163],"final":[164],"embeddings.":[165],"Finally,":[166],"neural":[169],"(DNN)":[171],"classifier":[172],"is":[173],"employed":[174],"predict":[176],"Extensive":[179],"conducted":[181],"HMDAD":[184],"DisBiome":[186],"datasets":[187],"demonstrate":[188],"M<sup>2</sup>BA-MDA":[190],"consistently":[191],"outperforms":[192],"five":[193],"state-of-the-art":[194],"methods.":[195],"Parameter":[196],"analysis":[197],"ablation":[199],"further":[201],"confirm":[202],"robustness":[204],"sensitivity":[206],"of":[207],"model.":[209],"In":[210],"addition,":[211],"case":[212],"validate":[214],"its":[215],"effectiveness":[216],"identifying":[218],"disease-associated":[219],"microbes.":[220]},"counts_by_year":[{"year":2026,"cited_by_count":1}],"updated_date":"2026-03-07T16:01:11.037858","created_date":"2025-10-14T00:00:00"}
