{"id":"https://openalex.org/W4393185968","doi":"https://doi.org/10.1093/bioinformatics/btae165","title":"GraphPath: a graph attention model for molecular stratification with interpretability based on the pathway\u2013pathway interaction network","display_name":"GraphPath: a graph attention model for molecular stratification with interpretability based on the pathway\u2013pathway interaction network","publication_year":2024,"publication_date":"2024-03-26","ids":{"openalex":"https://openalex.org/W4393185968","doi":"https://doi.org/10.1093/bioinformatics/btae165","pmid":"https://pubmed.ncbi.nlm.nih.gov/38530778"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btae165","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae165","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"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/bioinformatics/btae165","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100738600","display_name":"Teng Ma","orcid":"https://orcid.org/0000-0002-7104-1526"},"institutions":[{"id":"https://openalex.org/I139660479","display_name":"Central South University","ror":"https://ror.org/00f1zfq44","country_code":"CN","type":"education","lineage":["https://openalex.org/I139660479"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Teng Ma","raw_affiliation_strings":["Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University , Changsha 41083 , Hunan, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University , Changsha 41083 , Hunan, China","institution_ids":["https://openalex.org/I139660479"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100438360","display_name":"Jianxin Wang","orcid":"https://orcid.org/0000-0003-1516-0480"},"institutions":[{"id":"https://openalex.org/I139660479","display_name":"Central South University","ror":"https://ror.org/00f1zfq44","country_code":"CN","type":"education","lineage":["https://openalex.org/I139660479"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jianxin Wang","raw_affiliation_strings":["Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University , Changsha 41083 , Hunan, China"],"raw_orcid":"https://orcid.org/0000-0003-1516-0480","affiliations":[{"raw_affiliation_string":"Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University , Changsha 41083 , Hunan, China","institution_ids":["https://openalex.org/I139660479"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I139660479"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":2.8223,"has_fulltext":true,"cited_by_count":15,"citation_normalized_percentile":{"value":0.90942675,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":100},"biblio":{"volume":"40","issue":"4","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.7810999751091003,"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":0.7810999751091003,"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/T11273","display_name":"Advanced Graph Neural Networks","score":0.14810000360012054,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.017899999395012856,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/interpretability","display_name":"Interpretability","score":0.8777990341186523},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7039327621459961},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.5652338266372681},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5587535500526428},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.5032078623771667},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.43543845415115356},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3201320171356201},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.13872560858726501},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.11930757761001587}],"concepts":[{"id":"https://openalex.org/C2781067378","wikidata":"https://www.wikidata.org/wiki/Q17027399","display_name":"Interpretability","level":2,"score":0.8777990341186523},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7039327621459961},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.5652338266372681},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5587535500526428},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.5032078623771667},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.43543845415115356},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3201320171356201},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.13872560858726501},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.11930757761001587},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0}],"mesh":[{"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":"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":"D008297","descriptor_name":"Male","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008297","descriptor_name":"Male","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008297","descriptor_name":"Male","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008297","descriptor_name":"Male","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008297","descriptor_name":"Male","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008297","descriptor_name":"Male","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011471","descriptor_name":"Prostatic Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D011471","descriptor_name":"Prostatic Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D011471","descriptor_name":"Prostatic Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D011471","descriptor_name":"Prostatic Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D011471","descriptor_name":"Prostatic Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D011471","descriptor_name":"Prostatic Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"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":"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}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btae165","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae165","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:38530778","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38530778","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:11007237","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11007237","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11007237/pdf/btae165.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":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btae165","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae165","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2651725945","display_name":null,"funder_award_id":"62350004","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G4785461891","display_name":null,"funder_award_id":"U22A2041","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G7631435625","display_name":null,"funder_award_id":"B18059","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8324054742","display_name":null,"funder_award_id":"62332020","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/F4320321514","display_name":"Central South University","ror":"https://ror.org/00f1zfq44"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":57,"referenced_works":["https://openalex.org/W2038120654","https://openalex.org/W2107560896","https://openalex.org/W2108087391","https://openalex.org/W2128085074","https://openalex.org/W2129605195","https://openalex.org/W2161112598","https://openalex.org/W2165256106","https://openalex.org/W2187089797","https://openalex.org/W2254449755","https://openalex.org/W2285093314","https://openalex.org/W2541750288","https://openalex.org/W2560322684","https://openalex.org/W2560375214","https://openalex.org/W2567987817","https://openalex.org/W2593468849","https://openalex.org/W2603603297","https://openalex.org/W2739852640","https://openalex.org/W2741363425","https://openalex.org/W2741988840","https://openalex.org/W2767281692","https://openalex.org/W2789900707","https://openalex.org/W2790179710","https://openalex.org/W2792746202","https://openalex.org/W2793975714","https://openalex.org/W2795548516","https://openalex.org/W2885464001","https://openalex.org/W2888477550","https://openalex.org/W2890411695","https://openalex.org/W2951091426","https://openalex.org/W2981604401","https://openalex.org/W2990154322","https://openalex.org/W2991564522","https://openalex.org/W2995684511","https://openalex.org/W3003153135","https://openalex.org/W3005188734","https://openalex.org/W3024764930","https://openalex.org/W3036091889","https://openalex.org/W3037348089","https://openalex.org/W3041823250","https://openalex.org/W3095378651","https://openalex.org/W3096828292","https://openalex.org/W3108540679","https://openalex.org/W3117393006","https://openalex.org/W3126201322","https://openalex.org/W3128646645","https://openalex.org/W3142366865","https://openalex.org/W3153131031","https://openalex.org/W3183761761","https://openalex.org/W3199772305","https://openalex.org/W4200570290","https://openalex.org/W4211038303","https://openalex.org/W4211247697","https://openalex.org/W4225845169","https://openalex.org/W4281559326","https://openalex.org/W4297733535","https://openalex.org/W4323924126","https://openalex.org/W6745537798"],"related_works":["https://openalex.org/W2905433371","https://openalex.org/W2888392564","https://openalex.org/W4310278675","https://openalex.org/W4388422664","https://openalex.org/W4390569940","https://openalex.org/W4361193272","https://openalex.org/W2963326959","https://openalex.org/W1986582023","https://openalex.org/W2966829450","https://openalex.org/W4315864862"],"abstract_inverted_index":{"MOTIVATION:":[0],"Studying":[1],"the":[2,14,18,28,50,73,82,116,130,143,147,164,174,187],"molecular":[3,51],"heterogeneity":[4],"of":[5,30,85,132,146,181,189],"cancer":[6,23,83,89],"is":[7],"essential":[8],"for":[9],"achieving":[10,35],"personalized":[11],"therapy.":[12],"At":[13],"same":[15],"time,":[16],"understanding":[17,180],"biological":[19,53,62,183],"processes":[20],"that":[21,71,98,115,160],"drive":[22],"development":[24,188],"can":[25,118],"lead":[26],"to":[27,44,80,113,121,140,163,176],"identification":[29],"valuable":[31],"therapeutic":[32],"targets.":[33],"Therefore,":[34],"accurate":[36],"and":[37,52,103,136,170,185],"interpretable":[38,171],"clinical":[39],"predictions":[40,152],"requires":[41],"paramount":[42],"attention":[43],"thoroughly":[45],"characterizing":[46],"patients":[47,86],"at":[48],"both":[49],"pathway":[54,134],"levels.":[55],"RESULTS:":[56],"Here,":[57],"we":[58,155],"present":[59],"GraphPath,":[60],"a":[61,168],"knowledge-driven":[63],"graph":[64],"neural":[65],"network":[66],"with":[67,87,124],"multi-head":[68],"self-attention":[69],"mechanism":[70],"implements":[72],"pathway-pathway":[74],"interaction":[75],"network.":[76],"We":[77,128],"train":[78],"GraphPath":[79],"classify":[81],"status":[84],"prostate":[88],"based":[90],"on":[91],"their":[92],"multi-omics":[93],"profiling.":[94],"Experiment":[95],"results":[96],"show":[97],"our":[99,179],"method":[100],"outperforms":[101],"P-NET":[102],"other":[104],"baseline":[105],"methods.":[106],"Besides,":[107],"two":[108],"external":[109],"cohorts":[110],"are":[111,153],"used":[112],"validate":[114],"model":[117,172],"be":[119],"generalized":[120],"unseen":[122],"samples":[123],"adequate":[125],"predictive":[126],"performance.":[127],"reduce":[129],"dimensionality":[131],"latent":[133],"embeddings":[135],"visualize":[137],"corresponding":[138],"classes":[139],"further":[141],"demonstrate":[142],"optimal":[144],"performance":[145],"model.":[148],"Additionally,":[149],"since":[150],"GraphPath's":[151],"interpretable,":[154],"identify":[156],"target":[157],"cancer-associated":[158],"pathways":[159],"significantly":[161],"contribute":[162],"model's":[165],"predictions.":[166],"Such":[167],"robust":[169],"has":[173],"potential":[175],"greatly":[177],"enhance":[178],"cancer's":[182],"mechanisms":[184],"accelerate":[186],"targeted":[190],"therapies.":[191],"AVAILABILITY":[192],"AND":[193],"IMPLEMENTATION:":[194],"https://github.com/amazingma/GraphPath.":[195]},"counts_by_year":[{"year":2026,"cited_by_count":6},{"year":2025,"cited_by_count":7},{"year":2024,"cited_by_count":2}],"updated_date":"2026-07-08T08:33:18.762332","created_date":"2025-10-10T00:00:00"}