{"id":"https://openalex.org/W7129672417","doi":"https://doi.org/10.1186/s12859-025-06221-1","title":"Transfer learning models for bacterial strain dissemination biomarkers using weighted non-parallel proximal support vector machines","display_name":"Transfer learning models for bacterial strain dissemination biomarkers using weighted non-parallel proximal support vector machines","publication_year":2026,"publication_date":"2026-02-17","ids":{"openalex":"https://openalex.org/W7129672417","doi":"https://doi.org/10.1186/s12859-025-06221-1","pmid":"https://pubmed.ncbi.nlm.nih.gov/41703455"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-025-06221-1","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-025-06221-1","pdf_url":null,"source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1186/s12859-025-06221-1","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5126265173","display_name":"Ugochukwu O. Ugwu","orcid":null},"institutions":[{"id":"https://openalex.org/I121934306","display_name":"Tufts University","ror":"https://ror.org/05wvpxv85","country_code":"US","type":"education","lineage":["https://openalex.org/I121934306"]},{"id":"https://openalex.org/I40347166","display_name":"University of Chicago","ror":"https://ror.org/024mw5h28","country_code":"US","type":"education","lineage":["https://openalex.org/I40347166"]},{"id":"https://openalex.org/I92446798","display_name":"Colorado State University","ror":"https://ror.org/03k1gpj17","country_code":"US","type":"education","lineage":["https://openalex.org/I92446798"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Ugochukwu O. Ugwu","raw_affiliation_strings":["Pattern Analysis Laboratory, Colorado State University, Fort Collins, CO, 80523, USA. uouresearch@gmail.com","Research Computing Center, University of Chicago, Chicago, IL, 60637, USA. uouresearch@gmail.com","Tufts Advanced Microscopic Imaging Center, Tufts University, Medford, MA, 02155, USA. uouresearch@gmail.com"],"affiliations":[{"raw_affiliation_string":"Pattern Analysis Laboratory, Colorado State University, Fort Collins, CO, 80523, USA. uouresearch@gmail.com","institution_ids":["https://openalex.org/I92446798"]},{"raw_affiliation_string":"Research Computing Center, University of Chicago, Chicago, IL, 60637, USA. uouresearch@gmail.com","institution_ids":["https://openalex.org/I40347166"]},{"raw_affiliation_string":"Tufts Advanced Microscopic Imaging Center, Tufts University, Medford, MA, 02155, USA. uouresearch@gmail.com","institution_ids":["https://openalex.org/I121934306"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025665480","display_name":"Richard A. Slayden","orcid":"https://orcid.org/0000-0001-6857-7277"},"institutions":[{"id":"https://openalex.org/I92446798","display_name":"Colorado State University","ror":"https://ror.org/03k1gpj17","country_code":"US","type":"education","lineage":["https://openalex.org/I92446798"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Richard A. Slayden","raw_affiliation_strings":["Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, 80523, USA"],"affiliations":[{"raw_affiliation_string":"Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, 80523, USA","institution_ids":["https://openalex.org/I92446798"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5061567476","display_name":"Michael Kirby","orcid":"https://orcid.org/0000-0001-9802-9263"},"institutions":[{"id":"https://openalex.org/I92446798","display_name":"Colorado State University","ror":"https://ror.org/03k1gpj17","country_code":"US","type":"education","lineage":["https://openalex.org/I92446798"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Michael Kirby","raw_affiliation_strings":["Department of Mathematics, Colorado State University, Fort Collins, CO, 80523, USA","Pattern Analysis Laboratory, Colorado State University, Fort Collins, CO, 80523, USA"],"affiliations":[{"raw_affiliation_string":"Department of Mathematics, Colorado State University, Fort Collins, CO, 80523, USA","institution_ids":["https://openalex.org/I92446798"]},{"raw_affiliation_string":"Pattern Analysis Laboratory, Colorado State University, Fort Collins, CO, 80523, USA","institution_ids":["https://openalex.org/I92446798"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5126265173"],"corresponding_institution_ids":["https://openalex.org/I121934306","https://openalex.org/I40347166","https://openalex.org/I92446798"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.35438291,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"27","issue":"1","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":0.5989000201225281,"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":0.5989000201225281,"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":0.06210000067949295,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.060100000351667404,"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/dimensionality-reduction","display_name":"Dimensionality reduction","score":0.5131000280380249},{"id":"https://openalex.org/keywords/support-vector-machine","display_name":"Support vector machine","score":0.49549999833106995},{"id":"https://openalex.org/keywords/francisella-tularensis","display_name":"Francisella tularensis","score":0.4699000120162964},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.4530999958515167},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.4474000036716461},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.39629998803138733},{"id":"https://openalex.org/keywords/transfer-of-learning","display_name":"Transfer of learning","score":0.39089998602867126},{"id":"https://openalex.org/keywords/selection","display_name":"Selection (genetic algorithm)","score":0.3700000047683716},{"id":"https://openalex.org/keywords/feature-selection","display_name":"Feature selection","score":0.36329999566078186}],"concepts":[{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6171000003814697},{"id":"https://openalex.org/C70518039","wikidata":"https://www.wikidata.org/wiki/Q16000077","display_name":"Dimensionality reduction","level":2,"score":0.5131000280380249},{"id":"https://openalex.org/C12267149","wikidata":"https://www.wikidata.org/wiki/Q282453","display_name":"Support vector machine","level":2,"score":0.49549999833106995},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.4828000068664551},{"id":"https://openalex.org/C2780467176","wikidata":"https://www.wikidata.org/wiki/Q1003460","display_name":"Francisella tularensis","level":4,"score":0.4699000120162964},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4564000070095062},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.4530999958515167},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.4474000036716461},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.42989999055862427},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.39629998803138733},{"id":"https://openalex.org/C150899416","wikidata":"https://www.wikidata.org/wiki/Q1820378","display_name":"Transfer of learning","level":2,"score":0.39089998602867126},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3711000084877014},{"id":"https://openalex.org/C81917197","wikidata":"https://www.wikidata.org/wiki/Q628760","display_name":"Selection (genetic algorithm)","level":2,"score":0.3700000047683716},{"id":"https://openalex.org/C148483581","wikidata":"https://www.wikidata.org/wiki/Q446488","display_name":"Feature selection","level":2,"score":0.36329999566078186},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.3628000020980835},{"id":"https://openalex.org/C111030470","wikidata":"https://www.wikidata.org/wiki/Q1430460","display_name":"Curse of dimensionality","level":2,"score":0.3102000057697296},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.2953999936580658},{"id":"https://openalex.org/C163763905","wikidata":"https://www.wikidata.org/wiki/Q17075943","display_name":"Precision medicine","level":2,"score":0.2919999957084656},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.28949999809265137},{"id":"https://openalex.org/C2779134260","wikidata":"https://www.wikidata.org/wiki/Q12136","display_name":"Disease","level":2,"score":0.2782999873161316},{"id":"https://openalex.org/C2778022156","wikidata":"https://www.wikidata.org/wiki/Q576145","display_name":"Strain (injury)","level":2,"score":0.2754000127315521},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.27469998598098755},{"id":"https://openalex.org/C18431079","wikidata":"https://www.wikidata.org/wiki/Q1502169","display_name":"Gene expression profiling","level":4,"score":0.2705000042915344},{"id":"https://openalex.org/C92087593","wikidata":"https://www.wikidata.org/wiki/Q427389","display_name":"Vector (molecular biology)","level":4,"score":0.2662999927997589},{"id":"https://openalex.org/C74193536","wikidata":"https://www.wikidata.org/wiki/Q574844","display_name":"Kernel (algebra)","level":2,"score":0.26409998536109924},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.26350000500679016},{"id":"https://openalex.org/C66024118","wikidata":"https://www.wikidata.org/wiki/Q1122506","display_name":"Computational model","level":2,"score":0.2630000114440918},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.26159998774528503},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.25220000743865967}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1186/s12859-025-06221-1","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-025-06221-1","pdf_url":null,"source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:41703455","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41703455","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:af31e0ab4a4a4d47ba0da6b66b517c85","is_oa":true,"landing_page_url":"https://doaj.org/article/af31e0ab4a4a4d47ba0da6b66b517c85","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 27, Iss 1 (2026)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:13014782","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC13014782/","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":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-025-06221-1","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-025-06221-1","pdf_url":null,"source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":32,"referenced_works":["https://openalex.org/W1540056190","https://openalex.org/W1678356000","https://openalex.org/W1836923458","https://openalex.org/W1972541538","https://openalex.org/W1988790447","https://openalex.org/W2002016471","https://openalex.org/W2004147962","https://openalex.org/W2015534153","https://openalex.org/W2018260277","https://openalex.org/W2028901970","https://openalex.org/W2056969841","https://openalex.org/W2059586807","https://openalex.org/W2084326536","https://openalex.org/W2097749765","https://openalex.org/W2119821739","https://openalex.org/W2119912941","https://openalex.org/W2132425109","https://openalex.org/W2136132422","https://openalex.org/W2148143831","https://openalex.org/W2167757381","https://openalex.org/W2295598076","https://openalex.org/W2538176878","https://openalex.org/W2759054184","https://openalex.org/W2762869965","https://openalex.org/W2783299469","https://openalex.org/W2795773469","https://openalex.org/W2911964244","https://openalex.org/W3112459541","https://openalex.org/W3112494120","https://openalex.org/W3160504820","https://openalex.org/W3197913691","https://openalex.org/W4402071909"],"related_works":[],"abstract_inverted_index":{"Integrating":[0],"genomic":[1],"datasets":[2,36],"from":[3,84],"homogenous":[4],"or":[5,14,33,37,41,172],"disparate":[6],"sources":[7],"to":[8,51,80,104,120,142,185,205,218,285,300,347],"identify":[9,106],"genes":[10,29,141,194,273],"that":[11,30,136,308],"are":[12,31,315,334],"commonly":[13],"uniquely":[15],"expressed":[16,275],"remains":[17],"a":[18,126,162,178,261,343],"largely":[19],"underexplored":[20],"area.":[21],"Such":[22],"integrative":[23],"analysis":[24,306],"can":[25,55],"reveal":[26,301],"biologically":[27,107],"relevant":[28,108],"common":[32],"exclusive":[34],"across":[35],"within":[38],"specific":[39],"conditions":[40],"cohorts.":[42],"Identifying":[43],"these":[44,213,340],"gene":[45,109,187,228,325],"expression":[46,188,326],"profiles":[47],"and":[48,63,73,87,96,117,123,155,170,215,227,257,279,282,289,311,330],"employing":[49],"them":[50,284],"classify":[52,286],"disease":[53,115,144,294,312,331],"status":[54],"aid":[56],"in":[57,276,321,336],"the":[58,85,121,139,152,158,191,197,231,277,316,322,337,351],"development":[59],"of":[60,112,164,181,193,199,220,271,293],"vaccines,":[61],"diagnostics":[62],"targeted":[64],"therapeutics":[65],"with":[66,167,354],"efficacy":[67],"against":[68],"difficult-to-treat":[69],"medically":[70],"important":[71],"pathogens":[72],"cancer.":[74],"This":[75,210],"work":[76,211],"develops":[77],"new":[78],"methodologies":[79],"integrate":[81],"transcriptomic":[82],"patterns":[83],"lungs":[86,153,278,323],"spleen":[88,159,280],"tissues":[89,281,356],"infected":[90],"by":[91,223],"Francisella":[92],"tularensis":[93],"\u2013":[94],"Schu4":[95,171],"Live":[97],"Vaccine":[98],"Strain":[99],"(LVS).":[100],"Our":[101,305],"objective":[102],"is":[103,149,201,298],"(i)":[105],"features":[110],"indicative":[111],"respiratory":[113],"infection,":[114,348],"severity,":[116],"bacterial":[118,287],"dissemination":[119],"spleen,":[122],"(ii)":[124],"develop":[125],"Weighted":[127],"$$\\ell":[128,147,235],"_1$$-norm":[129],"Non-Parallel":[130],"Support":[131],"Vector":[132],"Machines":[133],"($$\\ell":[134],"_1$$-WNPSVM)":[135],"will":[137],"utilize":[138],"selected":[140],"predict":[143],"status.":[145,295],"The":[146,234],"_1$$-WNPSVM":[148,236],"trained":[150],"on":[151,157,265],"data":[154],"validated":[156],"data,":[160],"introducing":[161],"form":[163],"transfer":[165],"learning,":[166],"uninfected":[168],"controls":[169],"LVS":[173],"samples":[174],"as":[175,244],"classes.":[176],"Currently,":[177],"direct":[179],"application":[180],"existing":[182],"NPSVM-type":[183,232],"methods":[184],"analyze":[186],"datasets,":[189],"where":[190],"number":[192,198],"significantly":[195],"exceeds":[196],"samples,":[200],"computationally":[202],"impractical":[203],"due":[204],"their":[206],"large":[207],"memory":[208],"requirements.":[209],"addresses":[212],"challenges":[214],"also":[216],"generalizes":[217],"models":[219],"similar":[221],"formulations":[222],"incorporating":[224],"dimensionality":[225],"reduction":[226],"selection":[229],"into":[230],"frameworks.":[233],"method":[237],"outperforms":[238],"traditional":[239],"machine":[240],"learning":[241],"techniques":[242],"such":[243],"ANN,":[245],"XGBoost,":[246],"AdaBoost,":[247],"GradBoost,":[248],"KNN,":[249],"SVM,":[250],"Naive":[251],"Bayes,":[252],"Random":[253],"Forest,":[254],"Logistic":[255],"Regression,":[256],"Decision":[258],"Tree,":[259],"achieving":[260],"$$97\\%$$":[262],"balanced":[263],"accuracy":[264],"imbalanced":[266],"data.":[267],"We":[268],"discovered":[269],"sets":[270],"235":[272],"exclusively":[274],"utilized":[283],"strains":[288],"controls,":[290],"enabling":[291],"prediction":[292],"Gene":[296],"ontology":[297],"performed":[299],"underlying":[302],"metabolic":[303],"pathways.":[304],"shows":[307],"signal":[309],"transduction":[310],"(cancer)":[313,332],"pathways":[314,319,333,341],"most":[317],"significant":[318,344],"activated":[320,335],"while":[324],"(transcription),":[327],"immune":[328],"system,":[329],"spleen.":[338],"Collectively,":[339],"indicate":[342],"host":[345,355],"response":[346],"including":[349],"how":[350],"bacteria":[352],"interact":[353],"during":[357],"dissemination.":[358]},"counts_by_year":[],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2026-02-18T00:00:00"}