{"id":"https://openalex.org/W4410428767","doi":"https://doi.org/10.1109/tcbbio.2025.3570817","title":"BFMDDT: A Decision-Tree-Based Gene Regulatory Network Inference From Multi-Type Datasets","display_name":"BFMDDT: A Decision-Tree-Based Gene Regulatory Network Inference From Multi-Type Datasets","publication_year":2025,"publication_date":"2025-05-16","ids":{"openalex":"https://openalex.org/W4410428767","doi":"https://doi.org/10.1109/tcbbio.2025.3570817","pmid":"https://pubmed.ncbi.nlm.nih.gov/40811307"},"language":"en","primary_location":{"id":"doi:10.1109/tcbbio.2025.3570817","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbbio.2025.3570817","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043","2998-4165"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"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/A5103187987","display_name":"Mingcan Wang","orcid":"https://orcid.org/0000-0002-8386-4060"},"institutions":[{"id":"https://openalex.org/I9224756","display_name":"Northeastern University","ror":"https://ror.org/03awzbc87","country_code":"CN","type":"education","lineage":["https://openalex.org/I9224756"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Mingcan Wang","raw_affiliation_strings":["School of Computer Science and Engineering, Northeastern University, Shenyang, China"],"raw_orcid":"https://orcid.org/0000-0002-8386-4060","affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Northeastern University, Shenyang, China","institution_ids":["https://openalex.org/I9224756"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103215657","display_name":"Zhiqiong Wang","orcid":"https://orcid.org/0000-0002-0095-0378"},"institutions":[{"id":"https://openalex.org/I9224756","display_name":"Northeastern University","ror":"https://ror.org/03awzbc87","country_code":"CN","type":"education","lineage":["https://openalex.org/I9224756"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhiqiong Wang","raw_affiliation_strings":["College of Medicine and Biological Information Engineering, Northeastern University, Shenyang, China"],"raw_orcid":"https://orcid.org/0000-0002-0095-0378","affiliations":[{"raw_affiliation_string":"College of Medicine and Biological Information Engineering, Northeastern University, Shenyang, China","institution_ids":["https://openalex.org/I9224756"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081033387","display_name":"Luxuan Qu","orcid":"https://orcid.org/0000-0001-8452-2743"},"institutions":[{"id":"https://openalex.org/I83714178","display_name":"Shenyang Jianzhu University","ror":"https://ror.org/01zr73v18","country_code":"CN","type":"education","lineage":["https://openalex.org/I83714178"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Luxuan Qu","raw_affiliation_strings":["Ara Institute of Canterbury International Engineering College, Shenyang Jianzhu University, Shenyang, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Ara Institute of Canterbury International Engineering College, Shenyang Jianzhu University, Shenyang, China","institution_ids":["https://openalex.org/I83714178"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5009205410","display_name":"Kaifu Long","orcid":"https://orcid.org/0009-0007-6745-2473"},"institutions":[{"id":"https://openalex.org/I9224756","display_name":"Northeastern University","ror":"https://ror.org/03awzbc87","country_code":"CN","type":"education","lineage":["https://openalex.org/I9224756"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Kaifu Long","raw_affiliation_strings":["School of Computer Science and Engineering, Northeastern University, Shenyang, China"],"raw_orcid":"https://orcid.org/0009-0007-6745-2473","affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Northeastern University, Shenyang, China","institution_ids":["https://openalex.org/I9224756"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5087247680","display_name":"Junchang Xin","orcid":"https://orcid.org/0000-0003-2077-8269"},"institutions":[{"id":"https://openalex.org/I9224756","display_name":"Northeastern University","ror":"https://ror.org/03awzbc87","country_code":"CN","type":"education","lineage":["https://openalex.org/I9224756"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Junchang Xin","raw_affiliation_strings":["School of Computer Science and Engineering, Northeastern University, Shenyang, China"],"raw_orcid":"https://orcid.org/0000-0003-2077-8269","affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Northeastern University, Shenyang, China","institution_ids":["https://openalex.org/I9224756"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.4108,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.57729878,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":97},"biblio":{"volume":"22","issue":"4","first_page":"1778","last_page":"1788"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9987000226974487,"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":0.9987000226974487,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9973999857902527,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9955999851226807,"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/inference","display_name":"Inference","score":0.738899290561676},{"id":"https://openalex.org/keywords/decision-tree","display_name":"Decision tree","score":0.5974571704864502},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.5973904728889465},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5445729494094849},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5324612259864807},{"id":"https://openalex.org/keywords/tree","display_name":"Tree (set theory)","score":0.5030264258384705},{"id":"https://openalex.org/keywords/type","display_name":"Type (biology)","score":0.5022566318511963},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.48231077194213867},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.38321587443351746},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3733366131782532},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3721684515476227},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.26270440220832825},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.22496619820594788},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.21168389916419983},{"id":"https://openalex.org/keywords/ecology","display_name":"Ecology","score":0.10234686732292175},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.09607043862342834}],"concepts":[{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.738899290561676},{"id":"https://openalex.org/C84525736","wikidata":"https://www.wikidata.org/wiki/Q831366","display_name":"Decision tree","level":2,"score":0.5974571704864502},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.5973904728889465},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5445729494094849},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5324612259864807},{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.5030264258384705},{"id":"https://openalex.org/C2777299769","wikidata":"https://www.wikidata.org/wiki/Q3707858","display_name":"Type (biology)","level":2,"score":0.5022566318511963},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.48231077194213867},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.38321587443351746},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3733366131782532},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3721684515476227},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.26270440220832825},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.22496619820594788},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.21168389916419983},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.10234686732292175},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.09607043862342834},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1109/tcbbio.2025.3570817","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbbio.2025.3570817","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043","2998-4165"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"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:40811307","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40811307","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":[{"display_name":"Peace, Justice and strong institutions","id":"https://metadata.un.org/sdg/16","score":0.6800000071525574}],"awards":[{"id":"https://openalex.org/G4618686014","display_name":null,"funder_award_id":"62072089","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G7797178789","display_name":null,"funder_award_id":"62432003","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":26,"referenced_works":["https://openalex.org/W1707446633","https://openalex.org/W2022604714","https://openalex.org/W2295598076","https://openalex.org/W2593780360","https://openalex.org/W2803928488","https://openalex.org/W2891115924","https://openalex.org/W2896693520","https://openalex.org/W2899545492","https://openalex.org/W2900341503","https://openalex.org/W2920876032","https://openalex.org/W2969742128","https://openalex.org/W3098000306","https://openalex.org/W3121311454","https://openalex.org/W3128158089","https://openalex.org/W3128925966","https://openalex.org/W3136903744","https://openalex.org/W3171520305","https://openalex.org/W4212837655","https://openalex.org/W4309744822","https://openalex.org/W4320731731","https://openalex.org/W4379117479","https://openalex.org/W4379620532","https://openalex.org/W4390075384","https://openalex.org/W4390971259","https://openalex.org/W4399814823","https://openalex.org/W4408653383"],"related_works":["https://openalex.org/W2055243143","https://openalex.org/W1986418932","https://openalex.org/W2357796999","https://openalex.org/W4321636575","https://openalex.org/W2741131631","https://openalex.org/W2950199998","https://openalex.org/W2560421304","https://openalex.org/W2951387065","https://openalex.org/W4385727351","https://openalex.org/W4306798985"],"abstract_inverted_index":{"Gene":[0],"regulatory":[1],"network":[2],"(GRN)":[3],"reconstruction":[4,62,207],"remains":[5],"a":[6,23,55,70,115,160],"great":[7],"challenge":[8],"in":[9,104,180],"computational":[10],"biology":[11],"and":[12,54,167,186,210],"bioinformatics.":[13],"However,":[14],"most":[15],"existing":[16],"methods":[17],"focus":[18],"on":[19,41,76],"inferring":[20],"GRNs":[21],"from":[22,63,100,183],"single":[24],"type":[25],"of":[26,79,85,144,202,212],"dataset,":[27],"rather":[28],"than":[29],"try":[30],"to":[31,48,81,95,174],"integrate":[32],"multi-type":[33,50,64,184],"datasets.":[34],"In":[35,68],"this":[36],"work,":[37],"GRN":[38,61,169,206],"inferences":[39],"based":[40],"decision":[42],"tree":[43],"(DT)":[44],"model":[45,143],"are":[46,93,131,196],"improved":[47],"handle":[49],"gene":[51,117,136],"expression":[52],"datasets":[53,65,80,185],"novel":[56],"inference":[57],"named":[58],"BFMDDT":[59,177],"for":[60],"is":[66,74,118,137,165],"proposed.":[67],"BFMDDT,":[69,213],"specific":[71,90,116,135],"data-integration":[72],"strategy":[73],"performed":[75],"different":[77],"types":[78,84],"extract":[82],"two":[83,105,158],"training":[86,102],"sets,":[87],"first.":[88],"Then":[89],"DT":[91,123,142],"models":[92],"applied":[94],"learn":[96],"the":[97,108,126,134,145,152,157,168,175,187,200,205],"feature":[98,153,162],"importance":[99,154,163],"these":[101],"sets":[103],"ways.":[106],"On":[107,125],"one":[109,121,140],"hand,":[110,128],"which":[111,129,198],"gene(s)":[112,130],"would":[113],"regulate":[114],"determined":[119,138],"by":[120,133,139,150,189],"ensemble":[122,141],"model.":[124],"other":[127,192],"regulated":[132],"same":[146],"type.":[147],"At":[148],"last,":[149],"mixing":[151],"gained":[155],"via":[156],"models,":[159],"global":[161],"ranking":[164],"acquired":[166],"can":[170],"be":[171],"constructed":[172],"according":[173],"ranking.":[176],"shows":[178],"confidence":[179],"extracting":[181],"information":[182],"extensibility":[188,211],"combining":[190],"with":[191],"technologies.":[193],"Numerous":[194],"experiments":[195],"conducted":[197],"show":[199],"effectiveness":[201],"data":[203],"integration,":[204],"accuracy,":[208],"efficiency":[209],"respectively.":[214]},"counts_by_year":[{"year":2026,"cited_by_count":1}],"updated_date":"2026-07-30T17:31:21.811387","created_date":"2025-10-10T00:00:00"}
