{"id":"https://openalex.org/W4392693563","doi":"https://doi.org/10.1109/tcbb.2024.3374413","title":"TSVM: Transfer Support Vector Machine for Predicting MPRA Validated Regulatory Variants","display_name":"TSVM: Transfer Support Vector Machine for Predicting MPRA Validated Regulatory Variants","publication_year":2024,"publication_date":"2024-03-12","ids":{"openalex":"https://openalex.org/W4392693563","doi":"https://doi.org/10.1109/tcbb.2024.3374413","pmid":"https://pubmed.ncbi.nlm.nih.gov/38451770"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2024.3374413","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2024.3374413","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"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/ACM 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/A5104256421","display_name":"Minglie Li","orcid":"https://orcid.org/0009-0004-0709-7295"},"institutions":[{"id":"https://openalex.org/I182707071","display_name":"Ludong University","ror":"https://ror.org/028h95t32","country_code":"CN","type":"education","lineage":["https://openalex.org/I182707071"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Minglie Li","raw_affiliation_strings":["School of Information and Electrical Engineering, Ludong University, Yantai, Shandong, China"],"raw_orcid":"https://orcid.org/0009-0004-0709-7295","affiliations":[{"raw_affiliation_string":"School of Information and Electrical Engineering, Ludong University, Yantai, Shandong, China","institution_ids":["https://openalex.org/I182707071"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060143865","display_name":"Shusen Zhou","orcid":"https://orcid.org/0000-0002-1081-2542"},"institutions":[{"id":"https://openalex.org/I182707071","display_name":"Ludong University","ror":"https://ror.org/028h95t32","country_code":"CN","type":"education","lineage":["https://openalex.org/I182707071"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Shusen Zhou","raw_affiliation_strings":["School of Information and Electrical Engineering, Ludong University, Yantai, Shandong, China"],"raw_orcid":"https://orcid.org/0000-0002-1081-2542","affiliations":[{"raw_affiliation_string":"School of Information and Electrical Engineering, Ludong University, Yantai, Shandong, China","institution_ids":["https://openalex.org/I182707071"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100392605","display_name":"Tong Liu","orcid":"https://orcid.org/0000-0001-5497-8117"},"institutions":[{"id":"https://openalex.org/I182707071","display_name":"Ludong University","ror":"https://ror.org/028h95t32","country_code":"CN","type":"education","lineage":["https://openalex.org/I182707071"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Tong Liu","raw_affiliation_strings":["School of Information and Electrical Engineering, Ludong University, Yantai, Shandong, China"],"raw_orcid":"https://orcid.org/0000-0001-5497-8117","affiliations":[{"raw_affiliation_string":"School of Information and Electrical Engineering, Ludong University, Yantai, Shandong, China","institution_ids":["https://openalex.org/I182707071"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102876329","display_name":"Chanjuan Liu","orcid":"https://orcid.org/0000-0002-6736-543X"},"institutions":[{"id":"https://openalex.org/I182707071","display_name":"Ludong University","ror":"https://ror.org/028h95t32","country_code":"CN","type":"education","lineage":["https://openalex.org/I182707071"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Chanjuan Liu","raw_affiliation_strings":["School of Information and Electrical Engineering, Ludong University, Yantai, Shandong, China"],"raw_orcid":"https://orcid.org/0000-0002-6736-543X","affiliations":[{"raw_affiliation_string":"School of Information and Electrical Engineering, Ludong University, Yantai, Shandong, China","institution_ids":["https://openalex.org/I182707071"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005413901","display_name":"Mujun Zang","orcid":"https://orcid.org/0000-0001-5868-6023"},"institutions":[{"id":"https://openalex.org/I182707071","display_name":"Ludong University","ror":"https://ror.org/028h95t32","country_code":"CN","type":"education","lineage":["https://openalex.org/I182707071"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Mujun Zang","raw_affiliation_strings":["School of Information and Electrical Engineering, Ludong University, Yantai, Shandong, China"],"raw_orcid":"https://orcid.org/0000-0001-5868-6023","affiliations":[{"raw_affiliation_string":"School of Information and Electrical Engineering, Ludong University, Yantai, Shandong, China","institution_ids":["https://openalex.org/I182707071"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100686407","display_name":"Qingjun Wang","orcid":"https://orcid.org/0009-0004-3516-1514"},"institutions":[{"id":"https://openalex.org/I182707071","display_name":"Ludong University","ror":"https://ror.org/028h95t32","country_code":"CN","type":"education","lineage":["https://openalex.org/I182707071"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Qingjun Wang","raw_affiliation_strings":["School of Information and Electrical Engineering, Ludong University, Yantai, Shandong, China"],"raw_orcid":"https://orcid.org/0009-0004-3516-1514","affiliations":[{"raw_affiliation_string":"School of Information and Electrical Engineering, Ludong University, Yantai, Shandong, China","institution_ids":["https://openalex.org/I182707071"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.6123,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":{"value":0.65712437,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":95,"max":98},"biblio":{"volume":"21","issue":"3","first_page":"472","last_page":"479"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","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"}},"topics":[{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9817000031471252,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9544000029563904,"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/transfer-of-learning","display_name":"Transfer of learning","score":0.7341490983963013},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7333554029464722},{"id":"https://openalex.org/keywords/support-vector-machine","display_name":"Support vector machine","score":0.6971808075904846},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.671491801738739},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.6255643367767334},{"id":"https://openalex.org/keywords/random-forest","display_name":"Random forest","score":0.6208485960960388},{"id":"https://openalex.org/keywords/convolutional-neural-network","display_name":"Convolutional neural network","score":0.5807503461837769},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.5237027406692505},{"id":"https://openalex.org/keywords/coding","display_name":"Coding (social sciences)","score":0.4845842123031616},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.4222668409347534},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.3429028391838074},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.12996920943260193}],"concepts":[{"id":"https://openalex.org/C150899416","wikidata":"https://www.wikidata.org/wiki/Q1820378","display_name":"Transfer of learning","level":2,"score":0.7341490983963013},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7333554029464722},{"id":"https://openalex.org/C12267149","wikidata":"https://www.wikidata.org/wiki/Q282453","display_name":"Support vector machine","level":2,"score":0.6971808075904846},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.671491801738739},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.6255643367767334},{"id":"https://openalex.org/C169258074","wikidata":"https://www.wikidata.org/wiki/Q245748","display_name":"Random forest","level":2,"score":0.6208485960960388},{"id":"https://openalex.org/C81363708","wikidata":"https://www.wikidata.org/wiki/Q17084460","display_name":"Convolutional neural network","level":2,"score":0.5807503461837769},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.5237027406692505},{"id":"https://openalex.org/C179518139","wikidata":"https://www.wikidata.org/wiki/Q5140297","display_name":"Coding (social sciences)","level":2,"score":0.4845842123031616},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.4222668409347534},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.3429028391838074},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.12996920943260193},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0}],"mesh":[{"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":"D014644","descriptor_name":"Genetic Variation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014644","descriptor_name":"Genetic Variation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014644","descriptor_name":"Genetic Variation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014644","descriptor_name":"Genetic Variation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D055106","descriptor_name":"Genome-Wide Association Study","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D055106","descriptor_name":"Genome-Wide Association Study","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D055106","descriptor_name":"Genome-Wide Association Study","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D055106","descriptor_name":"Genome-Wide Association Study","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D060388","descriptor_name":"Support Vector Machine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D060388","descriptor_name":"Support Vector Machine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D060388","descriptor_name":"Support Vector Machine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D060388","descriptor_name":"Support Vector Machine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1109/tcbb.2024.3374413","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2024.3374413","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"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/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:38451770","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38451770","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/ACM transactions on computational biology and bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2570003996","display_name":null,"funder_award_id":"61300155","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3445548413","display_name":null,"funder_award_id":"ZR2020MF134","funder_id":"https://openalex.org/F4320324174","funder_display_name":"Natural Science Foundation of Shandong Province"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320324174","display_name":"Natural Science Foundation of Shandong Province","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":50,"referenced_works":["https://openalex.org/W101663867","https://openalex.org/W370702354","https://openalex.org/W1522301498","https://openalex.org/W1533942137","https://openalex.org/W1556386043","https://openalex.org/W1865845132","https://openalex.org/W1907868928","https://openalex.org/W1988581590","https://openalex.org/W1991381389","https://openalex.org/W2011582941","https://openalex.org/W2056198580","https://openalex.org/W2117396697","https://openalex.org/W2117446594","https://openalex.org/W2120251864","https://openalex.org/W2144354855","https://openalex.org/W2148105023","https://openalex.org/W2154866190","https://openalex.org/W2163924952","https://openalex.org/W2165649312","https://openalex.org/W2188035077","https://openalex.org/W2225726427","https://openalex.org/W2247766769","https://openalex.org/W2257370818","https://openalex.org/W2412481123","https://openalex.org/W2415245143","https://openalex.org/W2557117995","https://openalex.org/W2590982292","https://openalex.org/W2595351638","https://openalex.org/W2751686252","https://openalex.org/W2754300472","https://openalex.org/W2804152737","https://openalex.org/W2874996660","https://openalex.org/W2893286041","https://openalex.org/W2905452503","https://openalex.org/W2906302663","https://openalex.org/W2911964244","https://openalex.org/W2964536524","https://openalex.org/W2972605721","https://openalex.org/W2990435446","https://openalex.org/W2991016899","https://openalex.org/W2995912276","https://openalex.org/W3010398094","https://openalex.org/W3029078495","https://openalex.org/W3037601773","https://openalex.org/W3040723250","https://openalex.org/W3081410576","https://openalex.org/W3088604489","https://openalex.org/W4225671220","https://openalex.org/W6631190155","https://openalex.org/W6782436372"],"related_works":["https://openalex.org/W4372048956","https://openalex.org/W3183901164","https://openalex.org/W2951211570","https://openalex.org/W3176438653","https://openalex.org/W3135818718","https://openalex.org/W4290188444","https://openalex.org/W3167935049","https://openalex.org/W3003905048","https://openalex.org/W2253429366","https://openalex.org/W3127975138"],"abstract_inverted_index":{"Genome-wide":[0],"association":[1],"studies":[2],"have":[3],"shown":[4],"that":[5],"common":[6],"genetic":[7],"variants":[8,33,52,70,99],"associated":[9],"with":[10,110],"complex":[11],"diseases":[12],"are":[13,117,127,165],"mostly":[14],"located":[15],"in":[16],"non-coding":[17,31,50],"regions,":[18],"which":[19,164],"may":[20],"not":[21],"be":[22],"causal.":[23],"In":[24],"addition,":[25],"the":[26,46,73,114,124,142,147,155,160,168],"limited":[27,76],"number":[28],"of":[29,48,75,149,157,162],"validated":[30,97,146],"functional":[32],"makes":[34],"it":[35],"difficult":[36],"to":[37,59,71,107,129],"develop":[38],"an":[39],"effective":[40],"supervised":[41,83],"learning":[42,65,84],"model.":[43],"Therefore,":[44],"improving":[45],"accuracy":[47],"predicting":[49,68],"causal":[51],"has":[53],"become":[54],"critical.":[55],"This":[56,79],"study":[57],"aims":[58],"build":[60],"a":[61,82,103],"transfer":[62,86,111,150],"learning-based":[63],"machine":[64,89,133],"method":[66,85],"for":[67,91,134],"regulatory":[69,98],"overcome":[72],"problem":[74],"sample":[77],"size.":[78],"paper":[80],"presents":[81],"support":[87,131],"vector":[88,132],"(TSVM)":[90],"massively":[92],"parallel":[93],"reporter":[94],"assays":[95],"(MPRA)":[96],"prediction.":[100],"First,":[101],"uses":[102],"convolutional":[104],"neural":[105],"network":[106],"extract":[108],"features":[109,116,126],"learning.":[112,151],"Second,":[113],"extracted":[115],"selected":[118,125],"by":[119],"random":[120],"forest":[121],"method.":[122,170],"Third,":[123],"used":[128],"train":[130],"classification.":[135],"We":[136],"performed":[137],"scale":[138],"sensitivity":[139],"experiments":[140],"on":[141],"MPRA":[143],"dataset":[144],"and":[145,159],"effectiveness":[148],"The":[152],"model":[153],"achieves":[154],"Mcc":[156],"0.326":[158],"AUC":[161],"0.720,":[163],"higher":[166],"than":[167],"state-of-the-art":[169]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":2}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}
