{"id":"https://openalex.org/W4413111142","doi":"https://doi.org/10.1093/bib/bbaf403","title":"Prioritizing pathway signature using deep learning approach: a novel strategy for traditional Chinese medicine formula generation and optimization","display_name":"Prioritizing pathway signature using deep learning approach: a novel strategy for traditional Chinese medicine formula generation and optimization","publication_year":2025,"publication_date":"2025-07-01","ids":{"openalex":"https://openalex.org/W4413111142","doi":"https://doi.org/10.1093/bib/bbaf403","pmid":"https://pubmed.ncbi.nlm.nih.gov/40794951"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbaf403","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf403","pdf_url":"https://academic.oup.com/bib/article-pdf/26/4/bbaf403/63997255/bbaf403.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/bib/article-pdf/26/4/bbaf403/63997255/bbaf403.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5001288130","display_name":"Zheng Yi Wu","orcid":"https://orcid.org/0000-0002-5971-8338"},"institutions":[{"id":"https://openalex.org/I111950717","display_name":"Macau University of Science and Technology","ror":"https://ror.org/03jqs2n27","country_code":"MO","type":"education","lineage":["https://openalex.org/I111950717","https://openalex.org/I4391767947"]},{"id":"https://openalex.org/I204512498","display_name":"University of Macau","ror":"https://ror.org/01r4q9n85","country_code":"MO","type":"education","lineage":["https://openalex.org/I204512498"]},{"id":"https://openalex.org/I53411278","display_name":"Chengdu University of Traditional Chinese Medicine","ror":"https://ror.org/00pcrz470","country_code":"CN","type":"education","lineage":["https://openalex.org/I53411278"]}],"countries":["CN","MO"],"is_corresponding":false,"raw_author_name":"Zheng Wu","raw_affiliation_strings":["Dr. Neher\u2019s Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine and Faculty of Chinese Medicine, Macau University of Science and Technology , Avenida Wai Long, Taipa, Macao SAR 999078 ,","Traditional Chinese Medicine Regulating Metabolic Diseases Key Laboratory of Sichuan Province, Hospital of Chengdu University of Traditional Chinese Medicine , No. 39 Shi-er-qiao Road, Jinniu District, Chengdu 610000, Sichuan,","Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine and Faculty of Chinese Medicine, Macau University of Science and Technology, Avenida Wai Long, Taipa, Macao SAR 999078, China","Traditional Chinese Medicine Regulating Metabolic Diseases Key Laboratory of Sichuan Province, Hospital of Chengdu University of Traditional Chinese Medicine, No. 39 Shi-er-qiao Road, Jinniu District, Chengdu 610000, Sichuan, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dr. Neher\u2019s Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine and Faculty of Chinese Medicine, Macau University of Science and Technology , Avenida Wai Long, Taipa, Macao SAR 999078 ,","institution_ids":["https://openalex.org/I111950717","https://openalex.org/I204512498"]},{"raw_affiliation_string":"Traditional Chinese Medicine Regulating Metabolic Diseases Key Laboratory of Sichuan Province, Hospital of Chengdu University of Traditional Chinese Medicine , No. 39 Shi-er-qiao Road, Jinniu District, Chengdu 610000, Sichuan,","institution_ids":["https://openalex.org/I53411278"]},{"raw_affiliation_string":"Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine and Faculty of Chinese Medicine, Macau University of Science and Technology, Avenida Wai Long, Taipa, Macao SAR 999078, China","institution_ids":["https://openalex.org/I111950717","https://openalex.org/I204512498"]},{"raw_affiliation_string":"Traditional Chinese Medicine Regulating Metabolic Diseases Key Laboratory of Sichuan Province, Hospital of Chengdu University of Traditional Chinese Medicine, No. 39 Shi-er-qiao Road, Jinniu District, Chengdu 610000, Sichuan, China","institution_ids":["https://openalex.org/I53411278"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100380109","display_name":"Zihan Wang","orcid":"https://orcid.org/0000-0003-2374-0215"},"institutions":[{"id":"https://openalex.org/I111950717","display_name":"Macau University of Science and Technology","ror":"https://ror.org/03jqs2n27","country_code":"MO","type":"education","lineage":["https://openalex.org/I111950717","https://openalex.org/I4391767947"]},{"id":"https://openalex.org/I204512498","display_name":"University of Macau","ror":"https://ror.org/01r4q9n85","country_code":"MO","type":"education","lineage":["https://openalex.org/I204512498"]}],"countries":["MO"],"is_corresponding":false,"raw_author_name":"Zihan Wang","raw_affiliation_strings":["Dr. Neher\u2019s Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine and Faculty of Chinese Medicine, Macau University of Science and Technology , Avenida Wai Long, Taipa, Macao SAR 999078 ,","Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine and Faculty of Chinese Medicine, Macau University of Science and Technology, Avenida Wai Long, Taipa, Macao SAR 999078, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dr. Neher\u2019s Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine and Faculty of Chinese Medicine, Macau University of Science and Technology , Avenida Wai Long, Taipa, Macao SAR 999078 ,","institution_ids":["https://openalex.org/I111950717","https://openalex.org/I204512498"]},{"raw_affiliation_string":"Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine and Faculty of Chinese Medicine, Macau University of Science and Technology, Avenida Wai Long, Taipa, Macao SAR 999078, China","institution_ids":["https://openalex.org/I111950717","https://openalex.org/I204512498"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100592370","display_name":"Xiyue Chang","orcid":null},"institutions":[{"id":"https://openalex.org/I111950717","display_name":"Macau University of Science and Technology","ror":"https://ror.org/03jqs2n27","country_code":"MO","type":"education","lineage":["https://openalex.org/I111950717","https://openalex.org/I4391767947"]},{"id":"https://openalex.org/I204512498","display_name":"University of Macau","ror":"https://ror.org/01r4q9n85","country_code":"MO","type":"education","lineage":["https://openalex.org/I204512498"]}],"countries":["MO"],"is_corresponding":false,"raw_author_name":"Xiyue Chang","raw_affiliation_strings":["Dr. Neher\u2019s Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine and Faculty of Chinese Medicine, Macau University of Science and Technology , Avenida Wai Long, Taipa, Macao SAR 999078 ,","Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine and Faculty of Chinese Medicine, Macau University of Science and Technology, Avenida Wai Long, Taipa, Macao SAR 999078, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dr. Neher\u2019s Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine and Faculty of Chinese Medicine, Macau University of Science and Technology , Avenida Wai Long, Taipa, Macao SAR 999078 ,","institution_ids":["https://openalex.org/I111950717","https://openalex.org/I204512498"]},{"raw_affiliation_string":"Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine and Faculty of Chinese Medicine, Macau University of Science and Technology, Avenida Wai Long, Taipa, Macao SAR 999078, China","institution_ids":["https://openalex.org/I111950717","https://openalex.org/I204512498"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101963476","display_name":"Xingyu Chen","orcid":"https://orcid.org/0009-0005-1343-0231"},"institutions":[{"id":"https://openalex.org/I111950717","display_name":"Macau University of Science and Technology","ror":"https://ror.org/03jqs2n27","country_code":"MO","type":"education","lineage":["https://openalex.org/I111950717","https://openalex.org/I4391767947"]},{"id":"https://openalex.org/I204512498","display_name":"University of Macau","ror":"https://ror.org/01r4q9n85","country_code":"MO","type":"education","lineage":["https://openalex.org/I204512498"]}],"countries":["MO"],"is_corresponding":false,"raw_author_name":"Xingyu Chen","raw_affiliation_strings":["Dr. Neher\u2019s Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine and Faculty of Chinese Medicine, Macau University of Science and Technology , Avenida Wai Long, Taipa, Macao SAR 999078 ,","Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine and Faculty of Chinese Medicine, Macau University of Science and Technology, Avenida Wai Long, Taipa, Macao SAR 999078, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dr. Neher\u2019s Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine and Faculty of Chinese Medicine, Macau University of Science and Technology , Avenida Wai Long, Taipa, Macao SAR 999078 ,","institution_ids":["https://openalex.org/I111950717","https://openalex.org/I204512498"]},{"raw_affiliation_string":"Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine and Faculty of Chinese Medicine, Macau University of Science and Technology, Avenida Wai Long, Taipa, Macao SAR 999078, China","institution_ids":["https://openalex.org/I111950717","https://openalex.org/I204512498"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101912846","display_name":"Qian Ding","orcid":"https://orcid.org/0000-0001-5017-3514"},"institutions":[{"id":"https://openalex.org/I111950717","display_name":"Macau University of Science and Technology","ror":"https://ror.org/03jqs2n27","country_code":"MO","type":"education","lineage":["https://openalex.org/I111950717","https://openalex.org/I4391767947"]}],"countries":["MO"],"is_corresponding":false,"raw_author_name":"Qian Ding","raw_affiliation_strings":["State Key Laboratory of Quality Research in Chinese Medicine and School of Pharmacy, Macau University of Science and Technology , Avenida Wai Long, Taipa, Macau SAR 999078 ,","State Key Laboratory of Quality Research in Chinese Medicine and School of Pharmacy, Macau University of Science and Technology, Avenida Wai Long, Taipa, Macau SAR 999078, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Quality Research in Chinese Medicine and School of Pharmacy, Macau University of Science and Technology , Avenida Wai Long, Taipa, Macau SAR 999078 ,","institution_ids":["https://openalex.org/I111950717"]},{"raw_affiliation_string":"State Key Laboratory of Quality Research in Chinese Medicine and School of Pharmacy, Macau University of Science and Technology, Avenida Wai Long, Taipa, Macau SAR 999078, China","institution_ids":["https://openalex.org/I111950717"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038928954","display_name":"Rongxin Fu","orcid":"https://orcid.org/0000-0002-4547-2269"},"institutions":[{"id":"https://openalex.org/I111950717","display_name":"Macau University of Science and Technology","ror":"https://ror.org/03jqs2n27","country_code":"MO","type":"education","lineage":["https://openalex.org/I111950717","https://openalex.org/I4391767947"]}],"countries":["MO"],"is_corresponding":false,"raw_author_name":"Rong Fu","raw_affiliation_strings":["State Key Laboratory of Quality Research in Chinese Medicine and School of Pharmacy, Macau University of Science and Technology , Avenida Wai Long, Taipa, Macau SAR 999078 ,","State Key Laboratory of Quality Research in Chinese Medicine and School of Pharmacy, Macau University of Science and Technology, Avenida Wai Long, Taipa, Macau SAR 999078, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Quality Research in Chinese Medicine and School of Pharmacy, Macau University of Science and Technology , Avenida Wai Long, Taipa, Macau SAR 999078 ,","institution_ids":["https://openalex.org/I111950717"]},{"raw_affiliation_string":"State Key Laboratory of Quality Research in Chinese Medicine and School of Pharmacy, Macau University of Science and Technology, Avenida Wai Long, Taipa, Macau SAR 999078, China","institution_ids":["https://openalex.org/I111950717"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5088553637","display_name":"Cheong\u2010Meng Chong","orcid":"https://orcid.org/0000-0002-2462-4729"},"institutions":[{"id":"https://openalex.org/I204512498","display_name":"University of Macau","ror":"https://ror.org/01r4q9n85","country_code":"MO","type":"education","lineage":["https://openalex.org/I204512498"]}],"countries":["MO"],"is_corresponding":false,"raw_author_name":"Cheong-Meng Chong","raw_affiliation_strings":["State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau , Avenida da Universidade, Taipa, Macau 999078 ,","State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Avenida da Universidade, Taipa, Macau 999078, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau , Avenida da Universidade, Taipa, Macau 999078 ,","institution_ids":["https://openalex.org/I204512498"]},{"raw_affiliation_string":"State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Avenida da Universidade, Taipa, Macau 999078, China","institution_ids":["https://openalex.org/I204512498"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066692319","display_name":"Jianyuan Tang","orcid":"https://orcid.org/0000-0003-1096-5917"},"institutions":[{"id":"https://openalex.org/I111950717","display_name":"Macau University of Science and Technology","ror":"https://ror.org/03jqs2n27","country_code":"MO","type":"education","lineage":["https://openalex.org/I111950717","https://openalex.org/I4391767947"]},{"id":"https://openalex.org/I204512498","display_name":"University of Macau","ror":"https://ror.org/01r4q9n85","country_code":"MO","type":"education","lineage":["https://openalex.org/I204512498"]},{"id":"https://openalex.org/I53411278","display_name":"Chengdu University of Traditional Chinese Medicine","ror":"https://ror.org/00pcrz470","country_code":"CN","type":"education","lineage":["https://openalex.org/I53411278"]}],"countries":["CN","MO"],"is_corresponding":true,"raw_author_name":"Jianyuan Tang","raw_affiliation_strings":["Dr. Neher\u2019s Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine and Faculty of Chinese Medicine, Macau University of Science and Technology , Avenida Wai Long, Taipa, Macao SAR 999078 ,","Traditional Chinese Medicine Regulating Metabolic Diseases Key Laboratory of Sichuan Province, Hospital of Chengdu University of Traditional Chinese Medicine , No. 39 Shi-er-qiao Road, Jinniu District, Chengdu 610000, Sichuan,","Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine and Faculty of Chinese Medicine, Macau University of Science and Technology, Avenida Wai Long, Taipa, Macao SAR 999078, China","Traditional Chinese Medicine Regulating Metabolic Diseases Key Laboratory of Sichuan Province, Hospital of Chengdu University of Traditional Chinese Medicine, No. 39 Shi-er-qiao Road, Jinniu District, Chengdu 610000, Sichuan, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dr. Neher\u2019s Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine and Faculty of Chinese Medicine, Macau University of Science and Technology , Avenida Wai Long, Taipa, Macao SAR 999078 ,","institution_ids":["https://openalex.org/I111950717","https://openalex.org/I204512498"]},{"raw_affiliation_string":"Traditional Chinese Medicine Regulating Metabolic Diseases Key Laboratory of Sichuan Province, Hospital of Chengdu University of Traditional Chinese Medicine , No. 39 Shi-er-qiao Road, Jinniu District, Chengdu 610000, Sichuan,","institution_ids":["https://openalex.org/I53411278"]},{"raw_affiliation_string":"Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine and Faculty of Chinese Medicine, Macau University of Science and Technology, Avenida Wai Long, Taipa, Macao SAR 999078, China","institution_ids":["https://openalex.org/I111950717","https://openalex.org/I204512498"]},{"raw_affiliation_string":"Traditional Chinese Medicine Regulating Metabolic Diseases Key Laboratory of Sichuan Province, Hospital of Chengdu University of Traditional Chinese Medicine, No. 39 Shi-er-qiao Road, Jinniu District, Chengdu 610000, Sichuan, China","institution_ids":["https://openalex.org/I53411278"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5085789193","display_name":"Chen Huang","orcid":"https://orcid.org/0000-0002-7092-7587"},"institutions":[{"id":"https://openalex.org/I111950717","display_name":"Macau University of Science and Technology","ror":"https://ror.org/03jqs2n27","country_code":"MO","type":"education","lineage":["https://openalex.org/I111950717","https://openalex.org/I4391767947"]},{"id":"https://openalex.org/I204512498","display_name":"University of Macau","ror":"https://ror.org/01r4q9n85","country_code":"MO","type":"education","lineage":["https://openalex.org/I204512498"]}],"countries":["MO"],"is_corresponding":true,"raw_author_name":"Chen Huang","raw_affiliation_strings":["Dr. Neher\u2019s Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine and Faculty of Chinese Medicine, Macau University of Science and Technology , Avenida Wai Long, Taipa, Macao SAR 999078 ,","Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine and Faculty of Chinese Medicine, Macau University of Science and Technology, Avenida Wai Long, Taipa, Macao SAR 999078, China"],"raw_orcid":"https://orcid.org/0000-0002-7092-7587","affiliations":[{"raw_affiliation_string":"Dr. Neher\u2019s Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine and Faculty of Chinese Medicine, Macau University of Science and Technology , Avenida Wai Long, Taipa, Macao SAR 999078 ,","institution_ids":["https://openalex.org/I111950717","https://openalex.org/I204512498"]},{"raw_affiliation_string":"Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine and Faculty of Chinese Medicine, Macau University of Science and Technology, Avenida Wai Long, Taipa, Macao SAR 999078, China","institution_ids":["https://openalex.org/I111950717","https://openalex.org/I204512498"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5066692319","https://openalex.org/A5085789193"],"corresponding_institution_ids":["https://openalex.org/I111950717","https://openalex.org/I204512498","https://openalex.org/I53411278"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":2.0451,"has_fulltext":true,"cited_by_count":5,"citation_normalized_percentile":{"value":0.87084766,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":95,"max":99},"biblio":{"volume":"26","issue":"4","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.984000027179718,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.984000027179718,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.9690999984741211,"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"}},{"id":"https://openalex.org/T11385","display_name":"Natural product bioactivities and synthesis","score":0.9635999798774719,"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/signature","display_name":"Signature (topology)","score":0.7379581928253174},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6460884809494019},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5699218511581421},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.5337734222412109},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.4073110818862915},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.14690738916397095}],"concepts":[{"id":"https://openalex.org/C2779696439","wikidata":"https://www.wikidata.org/wiki/Q7512811","display_name":"Signature (topology)","level":2,"score":0.7379581928253174},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6460884809494019},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5699218511581421},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.5337734222412109},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.4073110818862915},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.14690738916397095},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004365","descriptor_name":"Drugs, Chinese Herbal","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":true},{"descriptor_ui":"D004365","descriptor_name":"Drugs, Chinese Herbal","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":true},{"descriptor_ui":"D004365","descriptor_name":"Drugs, Chinese Herbal","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":true},{"descriptor_ui":"D004365","descriptor_name":"Drugs, Chinese Herbal","qualifier_ui":"Q000627","qualifier_name":"therapeutic use","is_major_topic":true},{"descriptor_ui":"D004365","descriptor_name":"Drugs, Chinese Herbal","qualifier_ui":"Q000627","qualifier_name":"therapeutic use","is_major_topic":true},{"descriptor_ui":"D004365","descriptor_name":"Drugs, Chinese Herbal","qualifier_ui":"Q000627","qualifier_name":"therapeutic use","is_major_topic":true},{"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":"D008516","descriptor_name":"Medicine, Chinese Traditional","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D008516","descriptor_name":"Medicine, Chinese Traditional","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D008516","descriptor_name":"Medicine, Chinese Traditional","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbaf403","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf403","pdf_url":"https://academic.oup.com/bib/article-pdf/26/4/bbaf403/63997255/bbaf403.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40794951","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40794951","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:12342745","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12342745","pdf_url":null,"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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbaf403","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf403","pdf_url":"https://academic.oup.com/bib/article-pdf/26/4/bbaf403/63997255/bbaf403.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2635206565","display_name":null,"funder_award_id":"006/2023/SKL","funder_id":"https://openalex.org/F4320328853","funder_display_name":"Macau University of Science and Technology"},{"id":"https://openalex.org/G4116120242","display_name":null,"funder_award_id":"FRG-21-032-SKL","funder_id":"https://openalex.org/F4320328853","funder_display_name":"Macau University of Science and Technology"}],"funders":[{"id":"https://openalex.org/F4320328853","display_name":"Macau University of Science and Technology","ror":null}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4413111142.pdf","grobid_xml":"https://content.openalex.org/works/W4413111142.grobid-xml"},"referenced_works_count":46,"referenced_works":["https://openalex.org/W1522301498","https://openalex.org/W1965170794","https://openalex.org/W1987710883","https://openalex.org/W2010457001","https://openalex.org/W2011550183","https://openalex.org/W2035618305","https://openalex.org/W2068042387","https://openalex.org/W2095705004","https://openalex.org/W2130410032","https://openalex.org/W2146512944","https://openalex.org/W2345415171","https://openalex.org/W2529395621","https://openalex.org/W2607662938","https://openalex.org/W2766963630","https://openalex.org/W2942976805","https://openalex.org/W3014278995","https://openalex.org/W3016077459","https://openalex.org/W3112460492","https://openalex.org/W3118474097","https://openalex.org/W3141256144","https://openalex.org/W3207086349","https://openalex.org/W3207178065","https://openalex.org/W3210852540","https://openalex.org/W4200117418","https://openalex.org/W4226017427","https://openalex.org/W4240545411","https://openalex.org/W4292779060","https://openalex.org/W4295312788","https://openalex.org/W4318671044","https://openalex.org/W4380742008","https://openalex.org/W4385245566","https://openalex.org/W4385607410","https://openalex.org/W4387969734","https://openalex.org/W4390951566","https://openalex.org/W4392094062","https://openalex.org/W4393051351","https://openalex.org/W4396227815","https://openalex.org/W4396703232","https://openalex.org/W4399538610","https://openalex.org/W4405780873","https://openalex.org/W4405903187","https://openalex.org/W6631190155","https://openalex.org/W6674330103","https://openalex.org/W6739901393","https://openalex.org/W6766978945","https://openalex.org/W6778883912"],"related_works":["https://openalex.org/W2731899572","https://openalex.org/W2961085424","https://openalex.org/W3215138031","https://openalex.org/W4306674287","https://openalex.org/W3009238340","https://openalex.org/W4360585206","https://openalex.org/W4321369474","https://openalex.org/W4285208911","https://openalex.org/W4387369504","https://openalex.org/W3082895349"],"abstract_inverted_index":{"The":[0],"advancement":[1],"of":[2,13,17,23,76],"traditional":[3],"Chinese":[4],"medicine":[5],"(TCM)":[6],"faces":[7],"challenges,":[8],"due":[9],"to":[10,34,70,87,133,149,170,206],"the":[11,21,72,91,114,135,172],"absence":[12],"a":[14,58,103,111,120,129,157,216],"deep":[15,60],"understanding":[16],"TCM":[18,31,45,65,77,94,221,237],"mechanism":[19],"at":[20,48],"perspective":[22],"modern":[24,96,224],"biomedical":[25,97,225],"practices.":[26],"This":[27],"results":[28],"in":[29,50],"how":[30],"selects":[32],"herbs":[33],"treat":[35,134],"diseases":[36],"or":[37,44],"symptoms":[38],"prevailingly":[39],"rely":[40],"on":[41,102,235],"clinicals'":[42],"experience":[43],"ancient":[46],"books,":[47],"least":[49],"part":[51],"lacking":[52],"scientific":[53],"basis.":[54],"Herein,":[55],"we":[56,85,229],"present":[57],"novel":[59,217],"learning-based":[61],"approach,":[62],"named":[63],"Negative-Correlation-based":[64],"Architecture":[66],"for":[67,79,113],"Reversal":[68],"(NeCTAR),":[69],"optimize":[71],"generation":[73],"and":[74,95,123,166,197],"combination":[75],"formulas":[78,238],"guiding":[80],"empiric":[81],"therapy,":[82],"by":[83,119,227],"which":[84,228],"could,":[86],"some":[88],"degree,":[89],"narrow":[90],"gap":[92],"between":[93],"science.":[98],"Our":[99],"approach":[100],"builds":[101],"hypothesis":[104],"that":[105,161],"pathway":[106,167],"alterations":[107,126],"may":[108],"serve":[109],"as":[110],"proxy":[112],"corresponding":[115],"physiological":[116],"changes":[117],"induced":[118],"certain":[121],"disease,":[122,192],"'inverse-fit'":[124],"those":[125],"would":[127],"provide":[128],"feasible":[130],"therapeutic":[131],"strategy":[132],"disease.":[136],"We":[137],"leveraged":[138],"ribonucleic":[139],"acid":[140],"sequencing":[141],"(RNA-seq)":[142],"data":[143,184],"with":[144,182],"Gene":[145],"Set":[146],"Enrichment":[147],"Analysis":[148],"establish":[150],"herb-pathway":[151],"associations,":[152],"integrating":[153],"these":[154],"insights":[155],"into":[156],"multilayer":[158],"perceptron":[159],"model":[160],"incorporates":[162],"top-k":[163],"sparse":[164],"projection":[165],"reconstruction":[168],"loss":[169],"predict":[171],"most":[173],"therapeutically":[174],"promising":[175],"herbal":[176,232],"components.":[177],"NeCTAR":[178,202],"demonstrated":[179],"high":[180],"concordance":[181],"experimental":[183],"across":[185],"various":[186],"disease":[187],"models,":[188],"including":[189],"fatty":[190],"liver":[191],"type":[193],"2":[194],"diabetes":[195],"mellitus,":[196],"premature":[198],"ovarian":[199],"failure.":[200],"Notably,":[201],"could":[203,230],"equally":[204],"apply":[205],"single":[207],"cell":[208],"RNA-seq":[209],"data.":[210],"Overall,":[211],"our":[212],"study":[213],"put":[214],"forwards":[215],"interpretive":[218],"framework":[219],"underlying":[220],"mechanisms":[222],"using":[223],"foundation,":[226],"prioritize":[231],"components":[233],"based":[234],"existing":[236],"treating":[239],"diseases.":[240]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":2}],"updated_date":"2026-07-29T09:40:50.615796","created_date":"2025-10-10T00:00:00"}
