{"id":"https://openalex.org/W4408145710","doi":"https://doi.org/10.1109/tcbbio.2025.3547383","title":"Discovery of Bioactive Constituents for Colitis From Traditional Chinese Medicine Prescription via Deep Neural Network","display_name":"Discovery of Bioactive Constituents for Colitis From Traditional Chinese Medicine Prescription via Deep Neural Network","publication_year":2025,"publication_date":"2025-03-01","ids":{"openalex":"https://openalex.org/W4408145710","doi":"https://doi.org/10.1109/tcbbio.2025.3547383","pmid":"https://pubmed.ncbi.nlm.nih.gov/40811203"},"language":"en","primary_location":{"id":"doi:10.1109/tcbbio.2025.3547383","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbbio.2025.3547383","pdf_url":null,"source":{"id":"https://openalex.org/S5407042751","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"2998-4165","issn":["2998-4165"],"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":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5070028902","display_name":"Zhixiang Ren","orcid":"https://orcid.org/0000-0002-4104-3790"},"institutions":[{"id":"https://openalex.org/I4210136793","display_name":"Peng Cheng Laboratory","ror":"https://ror.org/03qdqbt06","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210136793"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhixiang Ren","raw_affiliation_strings":["Peng Cheng Laboratory, Shenzhen, China","Peng Cheng Laboratory, Shenzhen, Guangdong, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Peng Cheng Laboratory, Shenzhen, China","institution_ids":["https://openalex.org/I4210136793"]},{"raw_affiliation_string":"Peng Cheng Laboratory, Shenzhen, Guangdong, China","institution_ids":["https://openalex.org/I4210136793"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039293896","display_name":"Yiming Ren","orcid":"https://orcid.org/0009-0009-6120-2945"},"institutions":[{"id":"https://openalex.org/I4210136793","display_name":"Peng Cheng Laboratory","ror":"https://ror.org/03qdqbt06","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210136793"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yiming Ren","raw_affiliation_strings":["Peng Cheng Laboratory, Shenzhen, China","Peng Cheng Laboratory, Shenzhen, Guangdong, China"],"raw_orcid":"https://orcid.org/0009-0009-6120-2945","affiliations":[{"raw_affiliation_string":"Peng Cheng Laboratory, Shenzhen, China","institution_ids":["https://openalex.org/I4210136793"]},{"raw_affiliation_string":"Peng Cheng Laboratory, Shenzhen, Guangdong, China","institution_ids":["https://openalex.org/I4210136793"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075163557","display_name":"Pengfei Liu","orcid":"https://orcid.org/0000-0001-6130-6968"},"institutions":[{"id":"https://openalex.org/I157773358","display_name":"Sun Yat-sen University","ror":"https://ror.org/0064kty71","country_code":"CN","type":"education","lineage":["https://openalex.org/I157773358"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Pengfei Liu","raw_affiliation_strings":["School of Computer Science and Engineering, Sun Yat-sen University, Guangzhou, China","School of Computer Science and Engineering, Sun Yat-sen University, Guangzhou, Guangdong, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Sun Yat-sen University, Guangzhou, China","institution_ids":["https://openalex.org/I157773358"]},{"raw_affiliation_string":"School of Computer Science and Engineering, Sun Yat-sen University, Guangzhou, Guangdong, China","institution_ids":["https://openalex.org/I157773358"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5107212302","display_name":"Qi Shu","orcid":"https://orcid.org/0009-0004-9465-3842"},"institutions":[{"id":"https://openalex.org/I143593769","display_name":"East China University of Science and Technology","ror":"https://ror.org/01vyrm377","country_code":"CN","type":"education","lineage":["https://openalex.org/I143593769"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Qi Shu","raw_affiliation_strings":["Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism and Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism and Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, China","institution_ids":["https://openalex.org/I143593769"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101816953","display_name":"Huijuan Ma","orcid":"https://orcid.org/0000-0001-6296-9237"},"institutions":[{"id":"https://openalex.org/I126520041","display_name":"University of Science and Technology of China","ror":"https://ror.org/04c4dkn09","country_code":"CN","type":"education","lineage":["https://openalex.org/I126520041","https://openalex.org/I19820366"]},{"id":"https://openalex.org/I184681353","display_name":"Anhui University of Science and Technology","ror":"https://ror.org/00q9atg80","country_code":"CN","type":"education","lineage":["https://openalex.org/I184681353"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Huijuan Ma","raw_affiliation_strings":["Joint Research Center for Occupational Medicine and Health of IHM and School of Public Health, Anhui University of Science and, Technology, Hefei, China","Joint Research Center for Occupational Medicine and Health of IHM and School of Public Health, Anhui University of Science and, Technology, Hefei, Anhui, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Joint Research Center for Occupational Medicine and Health of IHM and School of Public Health, Anhui University of Science and, Technology, Hefei, China","institution_ids":["https://openalex.org/I126520041"]},{"raw_affiliation_string":"Joint Research Center for Occupational Medicine and Health of IHM and School of Public Health, Anhui University of Science and, Technology, Hefei, Anhui, China","institution_ids":["https://openalex.org/I184681353"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5083302535","display_name":"Huan Xu","orcid":"https://orcid.org/0000-0002-9009-3786"},"institutions":[{"id":"https://openalex.org/I126520041","display_name":"University of Science and Technology of China","ror":"https://ror.org/04c4dkn09","country_code":"CN","type":"education","lineage":["https://openalex.org/I126520041","https://openalex.org/I19820366"]},{"id":"https://openalex.org/I184681353","display_name":"Anhui University of Science and Technology","ror":"https://ror.org/00q9atg80","country_code":"CN","type":"education","lineage":["https://openalex.org/I184681353"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Huan Xu","raw_affiliation_strings":["Joint Research Center for Occupational Medicine and Health of IHM and School of Public Health, Anhui University of Science and, Technology, Hefei, China","Joint Research Center for Occupational Medicine and Health of IHM and School of Public Health, Anhui University of Science and, Technology, Hefei, Anhui, China"],"raw_orcid":"https://orcid.org/0000-0002-9009-3786","affiliations":[{"raw_affiliation_string":"Joint Research Center for Occupational Medicine and Health of IHM and School of Public Health, Anhui University of Science and, Technology, Hefei, China","institution_ids":["https://openalex.org/I126520041"]},{"raw_affiliation_string":"Joint Research Center for Occupational Medicine and Health of IHM and School of Public Health, Anhui University of Science and, Technology, Hefei, Anhui, China","institution_ids":["https://openalex.org/I184681353"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.04593003,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"22","issue":"2","first_page":"946","last_page":"955"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.4975000023841858,"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"}},"topics":[{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.4975000023841858,"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/T12647","display_name":"Traditional Chinese Medicine Studies","score":0.15389999747276306,"subfield":{"id":"https://openalex.org/subfields/2707","display_name":"Complementary and alternative medicine"},"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/T11709","display_name":"Traditional Chinese Medicine Analysis","score":0.04740000143647194,"subfield":{"id":"https://openalex.org/subfields/2707","display_name":"Complementary and alternative medicine"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/medical-prescription","display_name":"Medical prescription","score":0.7628863453865051},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.5493485927581787},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.4813538193702698},{"id":"https://openalex.org/keywords/traditional-medicine","display_name":"Traditional medicine","score":0.4726913273334503},{"id":"https://openalex.org/keywords/traditional-chinese-medicine","display_name":"Traditional Chinese medicine","score":0.43609619140625},{"id":"https://openalex.org/keywords/alternative-medicine","display_name":"Alternative medicine","score":0.3705240786075592},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3407520651817322},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.26721858978271484},{"id":"https://openalex.org/keywords/pharmacology","display_name":"Pharmacology","score":0.23061978816986084},{"id":"https://openalex.org/keywords/pathology","display_name":"Pathology","score":0.05409973859786987}],"concepts":[{"id":"https://openalex.org/C2426938","wikidata":"https://www.wikidata.org/wiki/Q3355478","display_name":"Medical prescription","level":2,"score":0.7628863453865051},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.5493485927581787},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.4813538193702698},{"id":"https://openalex.org/C556039675","wikidata":"https://www.wikidata.org/wiki/Q771035","display_name":"Traditional medicine","level":1,"score":0.4726913273334503},{"id":"https://openalex.org/C188947578","wikidata":"https://www.wikidata.org/wiki/Q200253","display_name":"Traditional Chinese medicine","level":3,"score":0.43609619140625},{"id":"https://openalex.org/C204787440","wikidata":"https://www.wikidata.org/wiki/Q188504","display_name":"Alternative medicine","level":2,"score":0.3705240786075592},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3407520651817322},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.26721858978271484},{"id":"https://openalex.org/C98274493","wikidata":"https://www.wikidata.org/wiki/Q128406","display_name":"Pharmacology","level":1,"score":0.23061978816986084},{"id":"https://openalex.org/C142724271","wikidata":"https://www.wikidata.org/wiki/Q7208","display_name":"Pathology","level":1,"score":0.05409973859786987}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1109/tcbbio.2025.3547383","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbbio.2025.3547383","pdf_url":null,"source":{"id":"https://openalex.org/S5407042751","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"2998-4165","issn":["2998-4165"],"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":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40811203","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40811203","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":"IEEE transactions on computational biology and bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/2","display_name":"Zero hunger","score":0.6299999952316284}],"awards":[{"id":"https://openalex.org/G7565966572","display_name":null,"funder_award_id":"42177417","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"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W2361820086","https://openalex.org/W4388487825","https://openalex.org/W4312504110","https://openalex.org/W2372843101","https://openalex.org/W2392684411","https://openalex.org/W2397639394","https://openalex.org/W4323904150","https://openalex.org/W2368337640","https://openalex.org/W2370858806","https://openalex.org/W2381806105"],"abstract_inverted_index":{"Colitis":[0],"is":[1],"a":[2,18,38,66,104,109],"commonly":[3],"encountered":[4],"inflammatory":[5,138],"disease":[6,163],"in":[7,21,57,131,146,184],"colon":[8],"tissue,":[9],"which":[10,93],"can":[11,116],"be":[12],"triggered":[13],"by":[14],"various":[15],"causes.":[16],"Although":[17],"few":[19],"ingredients":[20,56],"traditional":[22],"Chinese":[23],"medicine":[24],"(TCM)":[25],"have":[26],"been":[27],"identified":[28],"as":[29],"effective":[30],"for":[31],"the":[32,43,83,114,126,143,147,177],"treatment":[33],"of":[34,51,55,87,162,179],"colitis,":[35],"it":[36],"remains":[37],"great":[39],"challenge":[40],"to":[41,77,155,169],"discover":[42,78],"potential":[44],"therapeutic":[45],"bioactive":[46,79,98,144,186],"constituents":[47,130,145,152,187],"and":[48,90,100,165],"their":[49],"modes":[50],"action":[52],"among":[53],"thousands":[54],"TCM":[58,189],"prescriptions.":[59,190],"To":[60,141],"address":[61],"this":[62],"issue,":[63],"we":[64],"propose":[65],"pipeline":[67],"that":[68,125],"combines":[69],"deep":[70],"neural":[71],"network":[72,75,86],"(DNN)":[73],"with":[74,103,136,158,173],"pharmacology":[76,122],"constituents.":[80],"By":[81],"integrating":[82],"herbal":[84,119],"information":[85,96],"9,845":[88],"nodes":[89],"161,950":[91],"edges,":[92],"includes":[94],"detailed":[95],"on":[97],"molecules":[99],"protein":[101],"targets,":[102],"prescription":[105],"list":[106],"expanded":[107],"through":[108],"novel":[110],"data":[111],"augmentation":[112],"strategy,":[113],"DNN":[115],"recommend":[117],"diverse":[118],"combinations.":[120],"Network":[121],"study":[123],"revealed":[124],"10":[127],"most":[128],"frequent":[129],"recommended":[132,148],"prescriptions":[133],"were":[134,153,171],"associated":[135],"multiple":[137],"signaling":[139],"pathways.":[140],"verify":[142],"prescriptions,":[149],"5":[150],"selected":[151],"administrated":[154],"BALB/c":[156],"mice":[157],"colitis.":[159],"Suppressive":[160],"effects":[161],"progression":[164],"pro-inflammatory":[166],"factors":[167],"comparable":[168],"sulfasalazin":[170],"observed":[172],"these":[174],"compounds,":[175],"revealing":[176],"effectiveness":[178],"our":[180],"artificial":[181],"intelligence":[182],"strategy":[183],"discovering":[185],"from":[188]},"counts_by_year":[],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}