{"id":"https://openalex.org/W4396939663","doi":"https://doi.org/10.1093/bioinformatics/btae316","title":"Pathformer: a biological pathway informed transformer for disease diagnosis and prognosis using multi-omics data","display_name":"Pathformer: a biological pathway informed transformer for disease diagnosis and prognosis using multi-omics data","publication_year":2024,"publication_date":"2024-05-01","ids":{"openalex":"https://openalex.org/W4396939663","doi":"https://doi.org/10.1093/bioinformatics/btae316","pmid":"https://pubmed.ncbi.nlm.nih.gov/38741230"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btae316","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae316","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae316/57572670/btae316.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/advance-article-pdf/doi/10.1093/bioinformatics/btae316/57572670/btae316.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5061305812","display_name":"Xiao Fan Liu","orcid":"https://orcid.org/0000-0001-8342-4623"},"institutions":[{"id":"https://openalex.org/I4210160507","display_name":"Center for Life Sciences","ror":"https://ror.org/05kje8j93","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570","https://openalex.org/I4210160507","https://openalex.org/I99065089"]},{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Xiaofan Liu","raw_affiliation_strings":["Institute for Precision Medicine, Tsinghua University , Beijing 100084, China","MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University , Beijing 100084, China","MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China","Institute for Precision Medicine, Tsinghua University, Beijing, 100084, China"],"affiliations":[{"raw_affiliation_string":"Institute for Precision Medicine, Tsinghua University , Beijing 100084, China","institution_ids":["https://openalex.org/I99065089"]},{"raw_affiliation_string":"MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University , Beijing 100084, China","institution_ids":["https://openalex.org/I99065089","https://openalex.org/I4210160507"]},{"raw_affiliation_string":"MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China","institution_ids":["https://openalex.org/I99065089"]},{"raw_affiliation_string":"Institute for Precision Medicine, Tsinghua University, Beijing, 100084, China","institution_ids":["https://openalex.org/I99065089"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060576677","display_name":"Yuhuan Tao","orcid":null},"institutions":[{"id":"https://openalex.org/I4210160507","display_name":"Center for Life Sciences","ror":"https://ror.org/05kje8j93","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570","https://openalex.org/I4210160507","https://openalex.org/I99065089"]},{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yuhuan Tao","raw_affiliation_strings":["Institute for Precision Medicine, Tsinghua University , Beijing 100084, China","MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University , Beijing 100084, China","Institute for Precision Medicine, Tsinghua University, Beijing, 100084, China","MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China"],"affiliations":[{"raw_affiliation_string":"Institute for Precision Medicine, Tsinghua University , Beijing 100084, China","institution_ids":["https://openalex.org/I99065089"]},{"raw_affiliation_string":"MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University , Beijing 100084, China","institution_ids":["https://openalex.org/I99065089","https://openalex.org/I4210160507"]},{"raw_affiliation_string":"Institute for Precision Medicine, Tsinghua University, Beijing, 100084, China","institution_ids":["https://openalex.org/I99065089"]},{"raw_affiliation_string":"MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China","institution_ids":["https://openalex.org/I99065089"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102261581","display_name":"Zilin Cai","orcid":null},"institutions":[{"id":"https://openalex.org/I4210160507","display_name":"Center for Life Sciences","ror":"https://ror.org/05kje8j93","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570","https://openalex.org/I4210160507","https://openalex.org/I99065089"]},{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zilin Cai","raw_affiliation_strings":["MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University , Beijing 100084, China","MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China"],"affiliations":[{"raw_affiliation_string":"MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University , Beijing 100084, China","institution_ids":["https://openalex.org/I99065089","https://openalex.org/I4210160507"]},{"raw_affiliation_string":"MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China","institution_ids":["https://openalex.org/I99065089"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5067988307","display_name":"Pengfei Bao","orcid":"https://orcid.org/0009-0001-7346-5840"},"institutions":[{"id":"https://openalex.org/I4210160507","display_name":"Center for Life Sciences","ror":"https://ror.org/05kje8j93","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570","https://openalex.org/I4210160507","https://openalex.org/I99065089"]},{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Pengfei Bao","raw_affiliation_strings":["Institute for Precision Medicine, Tsinghua University , Beijing 100084, China","MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University , Beijing 100084, China","Institute for Precision Medicine, Tsinghua University, Beijing, 100084, China","MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China"],"affiliations":[{"raw_affiliation_string":"Institute for Precision Medicine, Tsinghua University , Beijing 100084, China","institution_ids":["https://openalex.org/I99065089"]},{"raw_affiliation_string":"MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University , Beijing 100084, China","institution_ids":["https://openalex.org/I99065089","https://openalex.org/I4210160507"]},{"raw_affiliation_string":"Institute for Precision Medicine, Tsinghua University, Beijing, 100084, China","institution_ids":["https://openalex.org/I99065089"]},{"raw_affiliation_string":"MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China","institution_ids":["https://openalex.org/I99065089"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5068827702","display_name":"Hongli Ma","orcid":"https://orcid.org/0000-0003-2051-6576"},"institutions":[{"id":"https://openalex.org/I4210160507","display_name":"Center for Life Sciences","ror":"https://ror.org/05kje8j93","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570","https://openalex.org/I4210160507","https://openalex.org/I99065089"]},{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Hongli Ma","raw_affiliation_strings":["Institute for Precision Medicine, Tsinghua University , Beijing 100084, China","MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University , Beijing 100084, China","MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China","Institute for Precision Medicine, Tsinghua University, Beijing, 100084, China"],"affiliations":[{"raw_affiliation_string":"Institute for Precision Medicine, Tsinghua University , Beijing 100084, China","institution_ids":["https://openalex.org/I99065089"]},{"raw_affiliation_string":"MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University , Beijing 100084, China","institution_ids":["https://openalex.org/I99065089","https://openalex.org/I4210160507"]},{"raw_affiliation_string":"MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China","institution_ids":["https://openalex.org/I99065089"]},{"raw_affiliation_string":"Institute for Precision Medicine, Tsinghua University, Beijing, 100084, China","institution_ids":["https://openalex.org/I99065089"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5037145105","display_name":"Kexing Li","orcid":"https://orcid.org/0009-0007-5836-3356"},"institutions":[{"id":"https://openalex.org/I4210160507","display_name":"Center for Life Sciences","ror":"https://ror.org/05kje8j93","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570","https://openalex.org/I4210160507","https://openalex.org/I99065089"]},{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Kexing Li","raw_affiliation_strings":["MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University , Beijing 100084, China","MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China"],"affiliations":[{"raw_affiliation_string":"MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University , Beijing 100084, China","institution_ids":["https://openalex.org/I99065089","https://openalex.org/I4210160507"]},{"raw_affiliation_string":"MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China","institution_ids":["https://openalex.org/I99065089"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5059300419","display_name":"Mengtao Li","orcid":"https://orcid.org/0000-0003-4252-2889"},"institutions":[{"id":"https://openalex.org/I200296433","display_name":"Chinese Academy of Medical Sciences & Peking Union Medical College","ror":"https://ror.org/02drdmm93","country_code":"CN","type":"education","lineage":["https://openalex.org/I200296433"]},{"id":"https://openalex.org/I2801228662","display_name":"Peking Union Medical College Hospital","ror":"https://ror.org/04jztag35","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I2801228662"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Mengtao Li","raw_affiliation_strings":["Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), MST State Key Laboratory of Complex Severe and Rare Diseases, MOE Key Laboratory of Rheumatology and Clinical Immunology , Beijing 100730, China","Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), MST State Key Laboratory of Complex Severe and Rare Diseases, MOE Key Laboratory of Rheumatology and Clinical Immunology, Beijing, 100730, China"],"affiliations":[{"raw_affiliation_string":"Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), MST State Key Laboratory of Complex Severe and Rare Diseases, MOE Key Laboratory of Rheumatology and Clinical Immunology , Beijing 100730, China","institution_ids":["https://openalex.org/I200296433","https://openalex.org/I2801228662"]},{"raw_affiliation_string":"Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), MST State Key Laboratory of Complex Severe and Rare Diseases, MOE Key Laboratory of Rheumatology and Clinical Immunology, Beijing, 100730, China","institution_ids":["https://openalex.org/I200296433","https://openalex.org/I2801228662"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100765277","display_name":"Yunping Zhu","orcid":"https://orcid.org/0000-0002-7320-7411"},"institutions":[{"id":"https://openalex.org/I4210149540","display_name":"Beijing Proteome Research Center","ror":"https://ror.org/05pp5b412","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210149540"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yunping Zhu","raw_affiliation_strings":["State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics , Beijing 102206, China","State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Changping District, Beijing, 102206, China"],"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics , Beijing 102206, China","institution_ids":["https://openalex.org/I4210149540"]},{"raw_affiliation_string":"State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Changping District, Beijing, 102206, China","institution_ids":["https://openalex.org/I4210149540"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5031246881","display_name":"Zhi John Lu","orcid":"https://orcid.org/0000-0003-4751-9400"},"institutions":[{"id":"https://openalex.org/I4210160507","display_name":"Center for Life Sciences","ror":"https://ror.org/05kje8j93","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570","https://openalex.org/I4210160507","https://openalex.org/I99065089"]},{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhi John Lu","raw_affiliation_strings":["Institute for Precision Medicine, Tsinghua University , Beijing 100084, China","MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University , Beijing 100084, China","Institute for Precision Medicine, Tsinghua University, Beijing, 100084, China","MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China"],"affiliations":[{"raw_affiliation_string":"Institute for Precision Medicine, Tsinghua University , Beijing 100084, China","institution_ids":["https://openalex.org/I99065089"]},{"raw_affiliation_string":"MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University , Beijing 100084, China","institution_ids":["https://openalex.org/I99065089","https://openalex.org/I4210160507"]},{"raw_affiliation_string":"Institute for Precision Medicine, Tsinghua University, Beijing, 100084, China","institution_ids":["https://openalex.org/I99065089"]},{"raw_affiliation_string":"MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China","institution_ids":["https://openalex.org/I99065089"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":9,"corresponding_author_ids":["https://openalex.org/A5061305812"],"corresponding_institution_ids":["https://openalex.org/I4210160507","https://openalex.org/I99065089"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":6.7591,"has_fulltext":true,"cited_by_count":30,"citation_normalized_percentile":{"value":0.97712637,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":100},"biblio":{"volume":"40","issue":"5","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":0.9997000098228455,"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":0.9997000098228455,"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":0.9958000183105469,"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/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.9843999743461609,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/interpretability","display_name":"Interpretability","score":0.8565292358398438},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4736541509628296},{"id":"https://openalex.org/keywords/liquid-biopsy","display_name":"Liquid biopsy","score":0.4655248820781708},{"id":"https://openalex.org/keywords/omics","display_name":"Omics","score":0.43615221977233887},{"id":"https://openalex.org/keywords/crosstalk","display_name":"Crosstalk","score":0.4172942042350769},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.4136735200881958},{"id":"https://openalex.org/keywords/cancer","display_name":"Cancer","score":0.3966269791126251},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.37712952494621277},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.370547890663147},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.26756811141967773},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2150106132030487},{"id":"https://openalex.org/keywords/internal-medicine","display_name":"Internal medicine","score":0.08449408411979675}],"concepts":[{"id":"https://openalex.org/C2781067378","wikidata":"https://www.wikidata.org/wiki/Q17027399","display_name":"Interpretability","level":2,"score":0.8565292358398438},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4736541509628296},{"id":"https://openalex.org/C2779529041","wikidata":"https://www.wikidata.org/wiki/Q22349364","display_name":"Liquid biopsy","level":3,"score":0.4655248820781708},{"id":"https://openalex.org/C157585117","wikidata":"https://www.wikidata.org/wiki/Q158666","display_name":"Omics","level":2,"score":0.43615221977233887},{"id":"https://openalex.org/C169822122","wikidata":"https://www.wikidata.org/wiki/Q230187","display_name":"Crosstalk","level":2,"score":0.4172942042350769},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.4136735200881958},{"id":"https://openalex.org/C121608353","wikidata":"https://www.wikidata.org/wiki/Q12078","display_name":"Cancer","level":2,"score":0.3966269791126251},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.37712952494621277},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.370547890663147},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.26756811141967773},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2150106132030487},{"id":"https://openalex.org/C126322002","wikidata":"https://www.wikidata.org/wiki/Q11180","display_name":"Internal medicine","level":1,"score":0.08449408411979675},{"id":"https://openalex.org/C120665830","wikidata":"https://www.wikidata.org/wiki/Q14620","display_name":"Optics","level":1,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000095028","descriptor_name":"Multiomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000095028","descriptor_name":"Multiomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000095028","descriptor_name":"Multiomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000095028","descriptor_name":"Multiomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000095028","descriptor_name":"Multiomics","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":"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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"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":"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":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011379","descriptor_name":"Prognosis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011379","descriptor_name":"Prognosis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011379","descriptor_name":"Prognosis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011379","descriptor_name":"Prognosis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011379","descriptor_name":"Prognosis","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},{"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":"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}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btae316","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae316","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae316/57572670/btae316.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:38741230","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38741230","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:11139513","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11139513","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11139513/pdf/btae316.pdf","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"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btae316","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae316","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae316/57572670/btae316.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/G1121271761","display_name":null,"funder_award_id":"Program","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G1231421488","display_name":null,"funder_award_id":"under","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/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/G37568934","display_name":null,"funder_award_id":"Grant","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G4334671543","display_name":null,"funder_award_id":"32170671","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5007334783","display_name":null,"funder_award_id":"82371855","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"},{"id":"https://openalex.org/G6501387960","display_name":null,"funder_award_id":"82341101","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/F4320322392","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4396939663.pdf"},"referenced_works_count":47,"referenced_works":["https://openalex.org/W1548282166","https://openalex.org/W1999851129","https://openalex.org/W2028133290","https://openalex.org/W2063627505","https://openalex.org/W2094095317","https://openalex.org/W2096766502","https://openalex.org/W2114830914","https://openalex.org/W2131448225","https://openalex.org/W2157820287","https://openalex.org/W2158485828","https://openalex.org/W2159482845","https://openalex.org/W2162102504","https://openalex.org/W2397907932","https://openalex.org/W2522911430","https://openalex.org/W2611138580","https://openalex.org/W2622622183","https://openalex.org/W2749264889","https://openalex.org/W2775061087","https://openalex.org/W2904997892","https://openalex.org/W2921485464","https://openalex.org/W2950985821","https://openalex.org/W2955502047","https://openalex.org/W2962862931","https://openalex.org/W2963046727","https://openalex.org/W3002057135","https://openalex.org/W3047538950","https://openalex.org/W3048417086","https://openalex.org/W3083985197","https://openalex.org/W3084154531","https://openalex.org/W3164087725","https://openalex.org/W3164138302","https://openalex.org/W3170986249","https://openalex.org/W3173599183","https://openalex.org/W3177828909","https://openalex.org/W3182145057","https://openalex.org/W3199772305","https://openalex.org/W4205957462","https://openalex.org/W4285032110","https://openalex.org/W4294216483","https://openalex.org/W4378838672","https://openalex.org/W4380367088","https://openalex.org/W4385606826","https://openalex.org/W4388871132","https://openalex.org/W4392168151","https://openalex.org/W6737947904","https://openalex.org/W6752259330","https://openalex.org/W6823882246"],"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/W3195112886","https://openalex.org/W2892201447","https://openalex.org/W2590543013","https://openalex.org/W4389089607"],"abstract_inverted_index":{"Pathformer":[0],"is":[1],"implemented":[2],"and":[3],"freely":[4],"available":[5],"at":[6],"https://github.com/lulab/Pathformer.":[7]},"counts_by_year":[{"year":2026,"cited_by_count":5},{"year":2025,"cited_by_count":19},{"year":2024,"cited_by_count":6}],"updated_date":"2026-04-18T07:56:08.524223","created_date":"2025-10-10T00:00:00"}
