{"id":"https://openalex.org/W7134272895","doi":"https://doi.org/10.48550/arxiv.2603.05572","title":"Machine Learning for analysis of Multiple Sclerosis cross-tissue bulk and single-cell transcriptomics data","display_name":"Machine Learning for analysis of Multiple Sclerosis cross-tissue bulk and single-cell transcriptomics data","publication_year":2026,"publication_date":"2026-03-05","ids":{"openalex":"https://openalex.org/W7134272895","doi":"https://doi.org/10.48550/arxiv.2603.05572"},"language":null,"primary_location":{"id":"pmh:doi:10.48550/arxiv.2603.05572","is_oa":true,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S4406922384","display_name":"Open MIND","issn_l":null,"issn":null,"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":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Article"},"type":"article","indexed_in":["datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":null,"any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5128578817","display_name":"Francesco Massafra","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Massafra, Francesco","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5128405894","display_name":"Samuele Punzo","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Punzo, Samuele","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5128576617","display_name":"Silvia Giulia Galfr\u00e9","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Galfr\u00e9, Silvia Giulia","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025309980","display_name":"Alessandro Maglione","orcid":"https://orcid.org/0000-0001-7153-2248"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Maglione, Alessandro","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082219669","display_name":"Simone Pernice","orcid":"https://orcid.org/0000-0001-7124-4676"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Pernice, Simone","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5128573829","display_name":"Stefano Forti","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Forti, Stefano","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031360676","display_name":"Simona Rolla","orcid":"https://orcid.org/0000-0002-6371-7354"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Rolla, Simona","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002392135","display_name":"Marco Beccuti","orcid":"https://orcid.org/0000-0001-6125-9460"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Beccuti, Marco","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5067420465","display_name":"Marinella Clerico","orcid":"https://orcid.org/0000-0002-8304-3190"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Clerico, Marinella","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028775661","display_name":"Corrado Priami","orcid":"https://orcid.org/0000-0002-3261-6235"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Priami, Corrado","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5008115861","display_name":"Alina S\u00eerbu","orcid":"https://orcid.org/0000-0002-3947-7143"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"S\u00eerbu, Alina","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"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":0.23864462,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.5839999914169312,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.5839999914169312,"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/T10137","display_name":"Multiple Sclerosis Research Studies","score":0.16179999709129333,"subfield":{"id":"https://openalex.org/subfields/2734","display_name":"Pathology and Forensic 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/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.060499999672174454,"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/multiple-sclerosis","display_name":"Multiple sclerosis","score":0.7426999807357788},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.7164999842643738},{"id":"https://openalex.org/keywords/microarray-analysis-techniques","display_name":"Microarray analysis techniques","score":0.5655999779701233},{"id":"https://openalex.org/keywords/microarray","display_name":"Microarray","score":0.5600000023841858},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.5085999965667725},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.49619999527931213},{"id":"https://openalex.org/keywords/immune-system","display_name":"Immune system","score":0.4410000145435333},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.4140999913215637},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.35580000281333923}],"concepts":[{"id":"https://openalex.org/C2780640218","wikidata":"https://www.wikidata.org/wiki/Q8277","display_name":"Multiple sclerosis","level":2,"score":0.7426999807357788},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.7164999842643738},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6123999953269958},{"id":"https://openalex.org/C8415881","wikidata":"https://www.wikidata.org/wiki/Q6839217","display_name":"Microarray analysis techniques","level":4,"score":0.5655999779701233},{"id":"https://openalex.org/C186836561","wikidata":"https://www.wikidata.org/wiki/Q1931516","display_name":"Microarray","level":4,"score":0.5600000023841858},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.5085999965667725},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.49619999527931213},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.4652999937534332},{"id":"https://openalex.org/C8891405","wikidata":"https://www.wikidata.org/wiki/Q1059","display_name":"Immune system","level":2,"score":0.4410000145435333},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4244999885559082},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.4140999913215637},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.37540000677108765},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.362199991941452},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.35580000281333923},{"id":"https://openalex.org/C148483581","wikidata":"https://www.wikidata.org/wiki/Q446488","display_name":"Feature selection","level":2,"score":0.3546999990940094},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.34540000557899475},{"id":"https://openalex.org/C2779134260","wikidata":"https://www.wikidata.org/wiki/Q12136","display_name":"Disease","level":2,"score":0.33869999647140503},{"id":"https://openalex.org/C24361400","wikidata":"https://www.wikidata.org/wiki/Q6839217","display_name":"Gene chip analysis","level":5,"score":0.3273000121116638},{"id":"https://openalex.org/C2779075594","wikidata":"https://www.wikidata.org/wiki/Q8084905","display_name":"Autoimmune disease","level":3,"score":0.3206999897956848},{"id":"https://openalex.org/C207936829","wikidata":"https://www.wikidata.org/wiki/Q423163","display_name":"Major histocompatibility complex","level":3,"score":0.30869999527931213},{"id":"https://openalex.org/C81917197","wikidata":"https://www.wikidata.org/wiki/Q628760","display_name":"Selection (genetic algorithm)","level":2,"score":0.30640000104904175},{"id":"https://openalex.org/C89611455","wikidata":"https://www.wikidata.org/wiki/Q6804646","display_name":"Mechanism (biology)","level":2,"score":0.3061000108718872},{"id":"https://openalex.org/C130631938","wikidata":"https://www.wikidata.org/wiki/Q144894","display_name":"Intellectualization","level":2,"score":0.3052999973297119},{"id":"https://openalex.org/C66782513","wikidata":"https://www.wikidata.org/wiki/Q864601","display_name":"Biomedicine","level":2,"score":0.30390000343322754},{"id":"https://openalex.org/C124535831","wikidata":"https://www.wikidata.org/wiki/Q4915074","display_name":"Biomarker discovery","level":4,"score":0.29840001463890076},{"id":"https://openalex.org/C105565629","wikidata":"https://www.wikidata.org/wiki/Q1248292","display_name":"Gene prediction","level":4,"score":0.2802000045776367},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.27230000495910645},{"id":"https://openalex.org/C201934248","wikidata":"https://www.wikidata.org/wiki/Q2492999","display_name":"Neuroimmunology","level":3,"score":0.2718000113964081},{"id":"https://openalex.org/C18431079","wikidata":"https://www.wikidata.org/wiki/Q1502169","display_name":"Gene expression profiling","level":4,"score":0.26010000705718994},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.2502000033855438}],"mesh":[],"locations_count":2,"locations":[{"id":"pmh:doi:10.48550/arxiv.2603.05572","is_oa":true,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S4406922384","display_name":"Open MIND","issn_l":null,"issn":null,"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":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Article"},{"id":"doi:10.48550/arxiv.2603.05572","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2603.05572","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"Preprint"}],"best_oa_location":{"id":"pmh:doi:10.48550/arxiv.2603.05572","is_oa":true,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S4406922384","display_name":"Open MIND","issn_l":null,"issn":null,"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":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Article"},"sustainable_development_goals":[{"score":0.5412850975990295,"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":[],"abstract_inverted_index":{"Multiple":[0],"Sclerosis":[1],"(MS)":[2],"is":[3],"a":[4],"chronic":[5],"autoimmune":[6],"disease":[7],"of":[8],"the":[9],"central":[10],"nervous":[11],"system":[12],"whose":[13],"molecular":[14],"mechanisms":[15],"remain":[16],"incompletely":[17],"understood.":[18],"In":[19],"this":[20],"study,":[21],"we":[22],"developed":[23],"an":[24],"end-to-end":[25],"machine":[26],"learning":[27],"pipeline":[28],"to":[29,67,84,128,131],"analyze":[30],"transcriptomic":[31],"data":[32],"from":[33,71],"peripheral":[34],"blood":[35],"mononuclear":[36],"cells":[37],"and":[38,45,53,60,90,107,121,151,158,164,173,178],"cerebrospinal":[39],"fluid,":[40],"integrating":[41],"both":[42],"bulk":[43],"microarray":[44,122],"single-cell":[46],"RNA":[47],"sequencing":[48],"datasets":[49,139],"(concentrating":[50],"on":[51],"CD4+":[52],"B-cells).":[54],"After":[55],"rigorous":[56],"preprocessing,":[57],"batch":[58],"correction,":[59],"gene":[61,125],"declustering,":[62],"XGBoost":[63],"classifiers":[64],"were":[65,82,92,101],"trained":[66],"distinguish":[68],"MS":[69,182],"patients":[70],"healthy":[72],"controls.":[73],"Explainable":[74],"AI":[75],"tools,":[76],"namely":[77],"SHapley":[78],"Additive":[79],"exPlanations":[80],"(SHAP),":[81],"employed":[83],"identify":[85],"key":[86],"genes":[87,100],"driving":[88],"classification,":[89],"results":[91],"compared":[93],"with":[94],"Differential":[95],"Expression":[96],"Analysis":[97],"(DEA).":[98],"SHAP-prioritized":[99],"further":[102],"investigated":[103],"through":[104],"interaction":[105],"networks":[106],"pathway":[108],"enrichment":[109],"analyses.":[110],"The":[111],"models":[112],"achieved":[113],"strong":[114],"performance,":[115],"particularly":[116],"in":[117],"CSF":[118],"B-cells":[119],"(AUC=0.94)":[120],"(AUC=0.86).":[123],"SHAP":[124],"selection":[126],"proved":[127],"be":[129],"complementary":[130,168],"classical":[132],"DEA.":[133],"Gene":[134],"clusters":[135],"identified":[136],"across":[137],"multiple":[138],"highlighted":[140],"immune":[141,144],"activation,":[142],"non-canonical":[143],"checkpoints":[145],"(ITK,":[146],"CLEC2D,":[147],"KLRG1,":[148],"CEACAM1),":[149],"ribosomal":[150],"translational":[152],"programs,":[153],"ubiquitin-proteasome":[154],"regulation,":[155],"lipid":[156],"trafficking,":[157],"Epstein-Barr":[159],"virus-related":[160],"pathways.":[161],"Our":[162],"integrative":[163],"explainable":[165],"framework":[166],"reveals":[167],"insights":[169],"beyond":[170],"conventional":[171],"analysis":[172],"provides":[174],"novel":[175],"mechanistic":[176],"hypotheses":[177],"potential":[179],"biomarkers":[180],"for":[181],"pathogenesis.":[183]},"counts_by_year":[],"updated_date":"2026-07-15T18:14:33.161393","created_date":"2026-03-10T00:00:00"}