{"id":"https://openalex.org/W4413115226","doi":"https://doi.org/10.1093/bioinformatics/btaf444","title":"HallmarkGraph: a cancer hallmark informed graph neural network for classifying hierarchical tumor subtypes","display_name":"HallmarkGraph: a cancer hallmark informed graph neural network for classifying hierarchical tumor subtypes","publication_year":2025,"publication_date":"2025-08-13","ids":{"openalex":"https://openalex.org/W4413115226","doi":"https://doi.org/10.1093/bioinformatics/btaf444","pmid":"https://pubmed.ncbi.nlm.nih.gov/40802546"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaf444","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf444","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/41/9/btaf444/64037353/btaf444.pdf","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://academic.oup.com/bioinformatics/article-pdf/41/9/btaf444/64037353/btaf444.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100760159","display_name":"Qingsong Zhang","orcid":"https://orcid.org/0000-0001-6626-6117"},"institutions":[{"id":"https://openalex.org/I90610280","display_name":"South China University of Technology","ror":"https://ror.org/0530pts50","country_code":"CN","type":"education","lineage":["https://openalex.org/I90610280"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Qingsong Zhang","raw_affiliation_strings":["School of Software Engineering, South China University of Technology , Guangzhou, 510006,","School of Software Engineering, South China University of Technology, Guangzhou, 510006, China"],"affiliations":[{"raw_affiliation_string":"School of Software Engineering, South China University of Technology , Guangzhou, 510006,","institution_ids":["https://openalex.org/I90610280"]},{"raw_affiliation_string":"School of Software Engineering, South China University of Technology, Guangzhou, 510006, China","institution_ids":["https://openalex.org/I90610280"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Fei Liu","orcid":"https://orcid.org/0000-0001-9415-0496"},"institutions":[{"id":"https://openalex.org/I90610280","display_name":"South China University of Technology","ror":"https://ror.org/0530pts50","country_code":"CN","type":"education","lineage":["https://openalex.org/I90610280"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Fei Liu","raw_affiliation_strings":["School of Software Engineering, South China University of Technology , Guangzhou, 510006,","School of Software Engineering, South China University of Technology, Guangzhou, 510006, China"],"affiliations":[{"raw_affiliation_string":"School of Software Engineering, South China University of Technology , Guangzhou, 510006,","institution_ids":["https://openalex.org/I90610280"]},{"raw_affiliation_string":"School of Software Engineering, South China University of Technology, Guangzhou, 510006, China","institution_ids":["https://openalex.org/I90610280"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5010224302","display_name":"Xin Lai","orcid":"https://orcid.org/0000-0003-4913-5822"},"institutions":[{"id":"https://openalex.org/I150589677","display_name":"Tampere University of Applied Sciences","ror":"https://ror.org/00bwtjf83","country_code":"FI","type":"education","lineage":["https://openalex.org/I150589677"]},{"id":"https://openalex.org/I181369854","display_name":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","ror":"https://ror.org/00f7hpc57","country_code":"DE","type":"education","lineage":["https://openalex.org/I181369854"]},{"id":"https://openalex.org/I4210088053","display_name":"Universit\u00e4tsklinikum Erlangen","ror":"https://ror.org/0030f2a11","country_code":"DE","type":"healthcare","lineage":["https://openalex.org/I4210088053"]},{"id":"https://openalex.org/I4210133110","display_name":"Tampere University","ror":null,"country_code":"FI","type":null,"lineage":["https://openalex.org/I4210133110"]}],"countries":["DE","FI"],"is_corresponding":false,"raw_author_name":"Xin Lai","raw_affiliation_strings":["Department of Dermatology, Universit\u00e4tklinikum Erlangen and Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg , Erlangen, 91054,","Systems and Network Medicine Lab, Biomedicine Unit, Faculty of Medicine and Health Technology, Tampere University , Tampere, 33520,","Systems and Network Medicine Lab, Biomedicine Unit, Faculty of Medicine and Health Technology, Tampere University, Tampere, 33520, Finland"],"affiliations":[{"raw_affiliation_string":"Department of Dermatology, Universit\u00e4tklinikum Erlangen and Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg , Erlangen, 91054,","institution_ids":["https://openalex.org/I4210088053","https://openalex.org/I181369854"]},{"raw_affiliation_string":"Systems and Network Medicine Lab, Biomedicine Unit, Faculty of Medicine and Health Technology, Tampere University , Tampere, 33520,","institution_ids":["https://openalex.org/I150589677","https://openalex.org/I4210133110"]},{"raw_affiliation_string":"Systems and Network Medicine Lab, Biomedicine Unit, Faculty of Medicine and Health Technology, Tampere University, Tampere, 33520, Finland","institution_ids":["https://openalex.org/I150589677","https://openalex.org/I4210133110"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5100760159"],"corresponding_institution_ids":["https://openalex.org/I90610280"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":3.8485,"has_fulltext":true,"cited_by_count":3,"citation_normalized_percentile":{"value":0.93798095,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"41","issue":"9","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12422","display_name":"Radiomics and Machine Learning in Medical Imaging","score":0.9975000023841858,"subfield":{"id":"https://openalex.org/subfields/2741","display_name":"Radiology, Nuclear Medicine and Imaging"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},"topics":[{"id":"https://openalex.org/T12422","display_name":"Radiomics and Machine Learning in Medical Imaging","score":0.9975000023841858,"subfield":{"id":"https://openalex.org/subfields/2741","display_name":"Radiology, Nuclear Medicine and Imaging"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.996999979019165,"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/T10862","display_name":"AI in cancer detection","score":0.9916999936103821,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.604939877986908},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5622086524963379},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5403881072998047},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.5250425338745117},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4436437487602234},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.374866247177124},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.25756460428237915},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.24974840879440308}],"concepts":[{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.604939877986908},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5622086524963379},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5403881072998047},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.5250425338745117},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4436437487602234},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.374866247177124},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.25756460428237915},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.24974840879440308}],"mesh":[{"descriptor_ui":"D000098422","descriptor_name":"Graph Neural Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000098422","descriptor_name":"Graph Neural Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000098422","descriptor_name":"Graph Neural Networks","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":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000175","qualifier_name":"diagnosis","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000175","qualifier_name":"diagnosis","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000175","qualifier_name":"diagnosis","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"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":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1093/bioinformatics/btaf444","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf444","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/41/9/btaf444/64037353/btaf444.pdf","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:40802546","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40802546","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:europepmc.org:11212135","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12401579","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":null,"raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:12401579","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12401579/","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"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"},{"id":"pmh:oai:trepo.tuni.fi:10024/230252","is_oa":true,"landing_page_url":"https://trepo.tuni.fi/handle/10024/230252","pdf_url":null,"source":{"id":"https://openalex.org/S7407055260","display_name":"Trepo - Institutional Repository of Tampere University","issn_l":null,"issn":null,"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":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btaf444","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf444","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/41/9/btaf444/64037353/btaf444.pdf","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/G1477544716","display_name":null,"funder_award_id":"Guangdong","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G1606178500","display_name":null,"funder_award_id":"51501090","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G2087396116","display_name":null,"funder_award_id":"China","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G2884727198","display_name":null,"funder_award_id":"2024A1515010900","funder_id":"https://openalex.org/F4320337111","funder_display_name":"Basic and Applied Basic Research Foundation of Guangdong Province"},{"id":"https://openalex.org/G301518385","display_name":null,"funder_award_id":"62273153","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3317480652","display_name":null,"funder_award_id":"Science","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G391238517","display_name":null,"funder_award_id":", and","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5994120800","display_name":null,"funder_award_id":"Natural","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/F4320337111","display_name":"Basic and Applied Basic Research Foundation of Guangdong Province","ror":null}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4413115226.pdf"},"referenced_works_count":37,"referenced_works":["https://openalex.org/W2044702943","https://openalex.org/W2097255042","https://openalex.org/W2259802687","https://openalex.org/W2406250479","https://openalex.org/W2561318234","https://openalex.org/W2724430069","https://openalex.org/W2951091426","https://openalex.org/W2971091813","https://openalex.org/W3006500278","https://openalex.org/W3014321973","https://openalex.org/W3036962145","https://openalex.org/W3091783136","https://openalex.org/W3100774601","https://openalex.org/W3119640668","https://openalex.org/W3141471140","https://openalex.org/W3210196405","https://openalex.org/W4206042814","https://openalex.org/W4206662285","https://openalex.org/W4214618644","https://openalex.org/W4224251126","https://openalex.org/W4225529913","https://openalex.org/W4254687493","https://openalex.org/W4304014045","https://openalex.org/W4306403570","https://openalex.org/W4306640212","https://openalex.org/W4327747318","https://openalex.org/W4386465377","https://openalex.org/W4387130394","https://openalex.org/W4388539829","https://openalex.org/W4388615740","https://openalex.org/W4389816744","https://openalex.org/W4390881001","https://openalex.org/W4391786064","https://openalex.org/W4398201291","https://openalex.org/W4400981456","https://openalex.org/W4402220065","https://openalex.org/W4406018731"],"related_works":["https://openalex.org/W2961085424","https://openalex.org/W4306674287","https://openalex.org/W4387369504","https://openalex.org/W4394896187","https://openalex.org/W3170094116","https://openalex.org/W4386462264","https://openalex.org/W3107602296","https://openalex.org/W4364306694","https://openalex.org/W4312192474","https://openalex.org/W4283697347"],"abstract_inverted_index":{"HallmarkGraph":[0],"is":[1],"accessible":[2],"at":[3],"https://github.com/laixn/HallmarkGraph.":[4]},"counts_by_year":[{"year":2026,"cited_by_count":3}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
