{"id":"https://openalex.org/W4406238234","doi":"https://doi.org/10.1109/bibm62325.2024.10821892","title":"Comprehensive Metapath-based Heterogeneous Graph Transformer for Gene-Disease Association Prediction","display_name":"Comprehensive Metapath-based Heterogeneous Graph Transformer for Gene-Disease Association Prediction","publication_year":2024,"publication_date":"2024-12-03","ids":{"openalex":"https://openalex.org/W4406238234","doi":"https://doi.org/10.1109/bibm62325.2024.10821892"},"language":"en","primary_location":{"id":"doi:10.1109/bibm62325.2024.10821892","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm62325.2024.10821892","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2024 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"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/A5099031640","display_name":"Wentao Cui","orcid":"https://orcid.org/0000-0002-1404-3971"},"institutions":[{"id":"https://openalex.org/I4210108629","display_name":"Computer Network Information Center","ror":"https://ror.org/01s0wyf50","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210108629"]},{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"funder","lineage":["https://openalex.org/I19820366"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Wentao Cui","raw_affiliation_strings":["Chinese Academy of Sciences,Computer Network Information Center,China"],"affiliations":[{"raw_affiliation_string":"Chinese Academy of Sciences,Computer Network Information Center,China","institution_ids":["https://openalex.org/I4210108629","https://openalex.org/I19820366"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005154123","display_name":"Shoubo Li","orcid":"https://orcid.org/0000-0002-2900-1379"},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"funder","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210108629","display_name":"Computer Network Information Center","ror":"https://ror.org/01s0wyf50","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210108629"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Shoubo Li","raw_affiliation_strings":["Chinese Academy of Sciences,Computer Network Information Center,China"],"affiliations":[{"raw_affiliation_string":"Chinese Academy of Sciences,Computer Network Information Center,China","institution_ids":["https://openalex.org/I4210108629","https://openalex.org/I19820366"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090644161","display_name":"Chen Fang","orcid":"https://orcid.org/0009-0001-6382-1960"},"institutions":[{"id":"https://openalex.org/I4210165038","display_name":"University of Chinese Academy of Sciences","ror":"https://ror.org/05qbk4x57","country_code":"CN","type":"education","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210165038"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Chen Fang","raw_affiliation_strings":["University of Chinese Academy of Sciences,China"],"affiliations":[{"raw_affiliation_string":"University of Chinese Academy of Sciences,China","institution_ids":["https://openalex.org/I4210165038"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5019257775","display_name":"Qingqing Long","orcid":"https://orcid.org/0009-0005-7265-3101"},"institutions":[{"id":"https://openalex.org/I4210108629","display_name":"Computer Network Information Center","ror":"https://ror.org/01s0wyf50","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210108629"]},{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"funder","lineage":["https://openalex.org/I19820366"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Qingqing Long","raw_affiliation_strings":["Chinese Academy of Sciences,Computer Network Information Center,China"],"affiliations":[{"raw_affiliation_string":"Chinese Academy of Sciences,Computer Network Information Center,China","institution_ids":["https://openalex.org/I4210108629","https://openalex.org/I19820366"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046664390","display_name":"Chengrui Wang","orcid":"https://orcid.org/0000-0003-1487-0595"},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"funder","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210108629","display_name":"Computer Network Information Center","ror":"https://ror.org/01s0wyf50","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210108629"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Chengrui Wang","raw_affiliation_strings":["Chinese Academy of Sciences,Computer Network Information Center,China"],"affiliations":[{"raw_affiliation_string":"Chinese Academy of Sciences,Computer Network Information Center,China","institution_ids":["https://openalex.org/I4210108629","https://openalex.org/I19820366"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024842018","display_name":"Xuezhi Wang","orcid":"https://orcid.org/0000-0001-7592-2358"},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"funder","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210108629","display_name":"Computer Network Information Center","ror":"https://ror.org/01s0wyf50","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210108629"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xuezhi Wang","raw_affiliation_strings":["Chinese Academy of Sciences,Computer Network Information Center,China"],"affiliations":[{"raw_affiliation_string":"Chinese Academy of Sciences,Computer Network Information Center,China","institution_ids":["https://openalex.org/I4210108629","https://openalex.org/I19820366"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5065865669","display_name":"Yuanchun Zhou","orcid":"https://orcid.org/0000-0003-2144-1131"},"institutions":[{"id":"https://openalex.org/I4210108629","display_name":"Computer Network Information Center","ror":"https://ror.org/01s0wyf50","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210108629"]},{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"funder","lineage":["https://openalex.org/I19820366"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yuanchun Zhou","raw_affiliation_strings":["Chinese Academy of Sciences,Computer Network Information Center,China"],"affiliations":[{"raw_affiliation_string":"Chinese Academy of Sciences,Computer Network Information Center,China","institution_ids":["https://openalex.org/I4210108629","https://openalex.org/I19820366"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5099031640"],"corresponding_institution_ids":["https://openalex.org/I19820366","https://openalex.org/I4210108629"],"apc_list":null,"apc_paid":null,"fwci":0.7502,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":{"value":0.7293391,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":95,"max":99},"biblio":{"volume":null,"issue":null,"first_page":"1463","last_page":"1468"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9871000051498413,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9871000051498413,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9659000039100647,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9290000200271606,"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/computer-science","display_name":"Computer science","score":0.6467348337173462},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.4438122808933258},{"id":"https://openalex.org/keywords/association-rule-learning","display_name":"Association rule learning","score":0.4253832995891571},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3259428143501282},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.2595258951187134}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6467348337173462},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.4438122808933258},{"id":"https://openalex.org/C193524817","wikidata":"https://www.wikidata.org/wiki/Q386780","display_name":"Association rule learning","level":2,"score":0.4253832995891571},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3259428143501282},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.2595258951187134}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm62325.2024.10821892","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm62325.2024.10821892","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2024 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320321133","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":25,"referenced_works":["https://openalex.org/W1436642346","https://openalex.org/W2004798376","https://openalex.org/W2062533676","https://openalex.org/W2103017472","https://openalex.org/W2136410628","https://openalex.org/W2145361279","https://openalex.org/W2159092541","https://openalex.org/W2187181884","https://openalex.org/W2537679995","https://openalex.org/W2848983148","https://openalex.org/W2890210261","https://openalex.org/W2895927009","https://openalex.org/W2899728356","https://openalex.org/W2911286998","https://openalex.org/W2920198243","https://openalex.org/W2951531839","https://openalex.org/W3005261876","https://openalex.org/W3037835453","https://openalex.org/W3092790415","https://openalex.org/W3116524082","https://openalex.org/W3161787125","https://openalex.org/W4206547282","https://openalex.org/W4297253404","https://openalex.org/W4361278700","https://openalex.org/W4394837499"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2415164632","https://openalex.org/W2751920613","https://openalex.org/W2238349241","https://openalex.org/W2355668701","https://openalex.org/W2370453500","https://openalex.org/W2079402849","https://openalex.org/W1561334777"],"abstract_inverted_index":{"Discovering":[0],"gene-disease":[1,33,80],"associations":[2,12],"is":[3],"crucial":[4],"for":[5,29,49,78,154],"understanding":[6],"disease":[7],"mechanisms,":[8,122],"yet":[9],"identifying":[10],"these":[11,69],"remains":[13],"challenging":[14],"due":[15],"to":[16,57,86,105,130,141],"the":[17],"time":[18],"and":[19,31,43,64,100,112,117,146],"cost":[20],"of":[21],"biological":[22],"experiments.":[23],"Computational":[24],"methods":[25,54],"are":[26,46],"increasingly":[27],"vital":[28],"efficient":[30],"scalable":[32],"association":[34],"prediction.":[35],"Graph-based":[36],"learning":[37],"models,":[38],"which":[39],"leverage":[40],"node":[41,60,92],"features":[42,93],"network":[44],"relationships,":[45],"commonly":[47],"employed":[48],"biomolecular":[50],"predictions.":[51],"However,":[52],"existing":[53],"often":[55],"struggle":[56],"effectively":[58],"integrate":[59],"features,":[61],"heterogeneous":[62,75,89],"structures,":[63],"semantic":[65],"information.":[66],"To":[67],"address":[68],"challenges,":[70],"we":[71],"propose":[72],"COmprehensive":[73],"MEtapath-based":[74],"graph":[76],"Transformer(COMET)":[77],"predicting":[79],"associations.":[81],"COMET":[82,123],"integrates":[83],"diverse":[84],"datasets":[85],"construct":[87],"comprehensive":[88],"networks,":[90],"initializing":[91],"with":[94],"BioGPT.":[95],"We":[96],"define":[97],"seven":[98],"Metapaths":[99,129],"utilize":[101],"a":[102],"transformer":[103],"framework":[104],"aggregate":[106],"Metapath":[107],"instances,":[108],"capturing":[109],"global":[110],"contexts":[111],"long-distance":[113],"dependencies.":[114],"Through":[115],"intra-":[116],"inter-metapath":[118],"aggregation":[119],"using":[120],"attention":[121],"fuses":[124],"latent":[125],"vectors":[126],"from":[127],"multiple":[128],"enhance":[131],"GDA":[132],"prediction":[133],"accuracy.":[134],"Our":[135],"method":[136],"demonstrates":[137],"superior":[138],"robustness":[139],"compared":[140],"state-of-the-art":[142],"approaches.":[143],"Ablation":[144],"studies":[145],"visualizations":[147],"validate":[148],"COMET\u2019s":[149],"effectiveness,":[150],"providing":[151],"valuable":[152],"insights":[153],"advancing":[155],"human":[156],"health":[157],"research.":[158]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":2}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}