{"id":"https://openalex.org/W4404127278","doi":"https://doi.org/10.1093/bib/bbae550","title":"Predicting disease-associated microbes based on similarity fusion and deep learning","display_name":"Predicting disease-associated microbes based on similarity fusion and deep learning","publication_year":2024,"publication_date":"2024-09-23","ids":{"openalex":"https://openalex.org/W4404127278","doi":"https://doi.org/10.1093/bib/bbae550","pmid":"https://pubmed.ncbi.nlm.nih.gov/39504483"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbae550","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae550","pdf_url":"https://academic.oup.com/bib/article-pdf/25/6/bbae550/60250403/bbae550.pdf","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://academic.oup.com/bib/article-pdf/25/6/bbae550/60250403/bbae550.pdf","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,"],"raw_orcid":"https://orcid.org/0000-0002-5119-4517","affiliations":[{"raw_affiliation_string":"School of Information and Software Engineering, East China Jiaotong University , Nanchang 330013,","institution_ids":["https://openalex.org/I13985625"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5101432979","display_name":"Kuan Chen","orcid":"https://orcid.org/0009-0001-6470-3827"},"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":"Kuan Chen","raw_affiliation_strings":["School of Information and Software Engineering, East China Jiaotong University , Nanchang 330013,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Information and Software Engineering, East China Jiaotong University , Nanchang 330013,","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":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":0.8078,"has_fulltext":true,"cited_by_count":5,"citation_normalized_percentile":{"value":0.71057388,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":95,"max":99},"biblio":{"volume":"25","issue":"6","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10066","display_name":"Gut microbiota and health","score":0.9947999715805054,"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/T10066","display_name":"Gut microbiota and health","score":0.9947999715805054,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9527000188827515,"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/T11667","display_name":"Advanced Chemical Sensor Technologies","score":0.9319999814033508,"subfield":{"id":"https://openalex.org/subfields/2204","display_name":"Biomedical Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.6527850031852722},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.6471540927886963},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.5305664539337158},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5113903880119324},{"id":"https://openalex.org/keywords/fusion","display_name":"Fusion","score":0.450361043214798},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.44533824920654297},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3588332533836365},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2413313388824463},{"id":"https://openalex.org/keywords/philosophy","display_name":"Philosophy","score":0.04972413182258606}],"concepts":[{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.6527850031852722},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.6471540927886963},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.5305664539337158},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5113903880119324},{"id":"https://openalex.org/C158525013","wikidata":"https://www.wikidata.org/wiki/Q2593739","display_name":"Fusion","level":2,"score":0.450361043214798},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.44533824920654297},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3588332533836365},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2413313388824463},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.04972413182258606},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.0}],"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":"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":"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":"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":"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},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbae550","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae550","pdf_url":"https://academic.oup.com/bib/article-pdf/25/6/bbae550/60250403/bbae550.pdf","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:39504483","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39504483","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:11540060","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11540060","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11540060/pdf/bbae550.pdf","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":"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/bbae550","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae550","pdf_url":"https://academic.oup.com/bib/article-pdf/25/6/bbae550/60250403/bbae550.pdf","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":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4404127278.pdf"},"referenced_works_count":34,"referenced_works":["https://openalex.org/W1547943993","https://openalex.org/W1872552935","https://openalex.org/W1987219048","https://openalex.org/W2036893224","https://openalex.org/W2048359072","https://openalex.org/W2073332363","https://openalex.org/W2090925778","https://openalex.org/W2100408829","https://openalex.org/W2117727476","https://openalex.org/W2141125135","https://openalex.org/W2229719906","https://openalex.org/W2322763599","https://openalex.org/W2567465856","https://openalex.org/W2739664659","https://openalex.org/W2752131265","https://openalex.org/W2807176368","https://openalex.org/W2892502396","https://openalex.org/W2901312953","https://openalex.org/W2963636339","https://openalex.org/W2964015378","https://openalex.org/W3017158857","https://openalex.org/W3048259272","https://openalex.org/W3093030756","https://openalex.org/W3094448726","https://openalex.org/W3095387731","https://openalex.org/W3128690143","https://openalex.org/W3207097833","https://openalex.org/W4221126963","https://openalex.org/W4225752318","https://openalex.org/W4292723103","https://openalex.org/W4313480822","https://openalex.org/W4323974793","https://openalex.org/W4383198266","https://openalex.org/W4391005914"],"related_works":["https://openalex.org/W4375867731","https://openalex.org/W2611989081","https://openalex.org/W2731899572","https://openalex.org/W4230611425","https://openalex.org/W4294635752","https://openalex.org/W4304166257","https://openalex.org/W4383066092","https://openalex.org/W2375480909","https://openalex.org/W3215138031","https://openalex.org/W4380075502"],"abstract_inverted_index":{"Increasing":[0],"studies":[1,159],"have":[2],"revealed":[3],"the":[4,92,110,135,183],"critical":[5],"roles":[6],"of":[7,14,17,26,33,48,75,91,113,139,174,190],"human":[8],"microbiome":[9],"in":[10,51,166],"a":[11,56,80,96,101,197],"wide":[12],"variety":[13],"disorders.":[15],"Identification":[16],"disease-associated":[18,204],"microbes":[19,76,114],"might":[20],"improve":[21],"our":[22],"knowledge":[23,125],"and":[24,29,77,83,115,123,170,199],"understanding":[25],"disease":[27],"pathogenesis":[28],"treatment.":[30],"Computational":[31],"prediction":[32],"microbe-disease":[34,67,103,129],"associations":[35,130],"would":[36],"provide":[37],"helpful":[38],"guidance":[39],"for":[40,65,202],"further":[41,108],"biomedical":[42],"screening,":[43],"which":[44,167],"has":[45],"received":[46],"lots":[47],"research":[49],"interest":[50],"bioinformatics.":[52],"In":[53],"this":[54],"study,":[55],"deep":[57],"learning-based":[58],"computational":[59,152],"approach":[60],"entitled":[61],"SGJMDA":[62,70,148,191],"is":[63,105],"presented":[64],"predicting":[66],"associations.":[68],"Specifically,":[69],"first":[71],"fuses":[72],"multiple":[73],"similarities":[74,94],"diseases":[78,116,163],"using":[79,164],"nonlinear":[81],"strategy,":[82],"extracts":[84],"feature":[85],"information":[86,112],"from":[87,143],"homogeneous":[88],"networks":[89],"composed":[90],"fused":[93],"via":[95],"graph":[97,120],"convolution":[98,121],"network.":[99,126],"Second,":[100],"heterogeneous":[102],"network":[104,122],"built":[106],"to":[107],"capture":[109],"structural":[111],"by":[117,182],"employing":[118],"multi-neighborhood":[119],"jumping":[124],"Finally,":[127],"potential":[128],"are":[131,179],"inferred":[132],"through":[133],"computing":[134],"linear":[136],"correlation":[137],"coefficients":[138],"their":[140,175],"embeddings.":[141],"Results":[142],"cross-validation":[144],"experiments":[145],"show":[146],"that":[147,193],"outperforms":[149],"6":[150],"state-of-the-art":[151],"methods.":[153],"Furthermore,":[154],"we":[155],"carry":[156],"out":[157,173],"case":[158],"on":[160],"three":[161],"important":[162],"SGJMDA,":[165],"19,":[168],"20,":[169],"11":[171],"predictions":[172],"top":[176],"20":[177],"results":[178],"successfully":[180],"checked":[181],"latest":[184],"databases,":[185],"respectively.":[186],"The":[187],"excellent":[188],"performance":[189],"suggests":[192],"it":[194],"could":[195],"be":[196],"valuable":[198],"promising":[200],"tool":[201],"inferring":[203],"microbes.":[205]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":2}],"updated_date":"2026-08-01T09:00:35.917206","created_date":"2025-10-10T00:00:00"}
