{"id":"https://openalex.org/W3214434028","doi":"https://doi.org/10.1186/s12859-021-04354-7","title":"Emulating complex simulations by machine learning methods","display_name":"Emulating complex simulations by machine learning methods","publication_year":2021,"publication_date":"2021-11-12","ids":{"openalex":"https://openalex.org/W3214434028","doi":"https://doi.org/10.1186/s12859-021-04354-7","mag":"3214434028","pmid":"https://pubmed.ncbi.nlm.nih.gov/34772335"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-021-04354-7","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-021-04354-7","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-021-04354-7","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","license_id":"https://openalex.org/licenses/cc-by","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://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-021-04354-7","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5009148451","display_name":"Paola Stolfi","orcid":"https://orcid.org/0000-0003-3688-5464"},"institutions":[{"id":"https://openalex.org/I3005160176","display_name":"Institute for High Performance Computing and Networking","ror":"https://ror.org/04r5fge26","country_code":"IT","type":"facility","lineage":["https://openalex.org/I3005160176","https://openalex.org/I4210155236"]},{"id":"https://openalex.org/I4210155236","display_name":"National Research Council","ror":"https://ror.org/04zaypm56","country_code":"IT","type":"nonprofit","lineage":["https://openalex.org/I4210155236"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"Paola Stolfi","raw_affiliation_strings":["Institute for Applied Computing, National Research Council of Italy, Rome, Italy. p.stolfi@iac.cnr.it","Institute for Applied Computing, National Research Council of Italy, Rome, Italy"],"raw_orcid":"https://orcid.org/0000-0003-3688-5464","affiliations":[{"raw_affiliation_string":"Institute for Applied Computing, National Research Council of Italy, Rome, Italy. p.stolfi@iac.cnr.it","institution_ids":["https://openalex.org/I4210155236"]},{"raw_affiliation_string":"Institute for Applied Computing, National Research Council of Italy, Rome, Italy","institution_ids":["https://openalex.org/I3005160176","https://openalex.org/I4210155236"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5010454141","display_name":"Filippo Castiglione","orcid":"https://orcid.org/0000-0002-1442-3552"},"institutions":[{"id":"https://openalex.org/I3005160176","display_name":"Institute for High Performance Computing and Networking","ror":"https://ror.org/04r5fge26","country_code":"IT","type":"facility","lineage":["https://openalex.org/I3005160176","https://openalex.org/I4210155236"]},{"id":"https://openalex.org/I4210155236","display_name":"National Research Council","ror":"https://ror.org/04zaypm56","country_code":"IT","type":"nonprofit","lineage":["https://openalex.org/I4210155236"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Filippo Castiglione","raw_affiliation_strings":["Institute for Applied Computing, National Research Council of Italy, Rome, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Applied Computing, National Research Council of Italy, Rome, Italy","institution_ids":["https://openalex.org/I3005160176","https://openalex.org/I4210155236"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5009148451"],"corresponding_institution_ids":["https://openalex.org/I3005160176","https://openalex.org/I4210155236"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":2.155,"has_fulltext":true,"cited_by_count":20,"citation_normalized_percentile":{"value":0.89075813,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":99},"biblio":{"volume":"22","issue":"S14","first_page":"483","last_page":"483"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10560","display_name":"Diabetes Management and Research","score":0.0851999968290329,"subfield":{"id":"https://openalex.org/subfields/2712","display_name":"Endocrinology, Diabetes and Metabolism"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},"topics":[{"id":"https://openalex.org/T10560","display_name":"Diabetes Management and Research","score":0.0851999968290329,"subfield":{"id":"https://openalex.org/subfields/2712","display_name":"Endocrinology, Diabetes and Metabolism"},"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/T13286","display_name":"Modeling and Simulation Systems","score":0.04190000146627426,"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/T11446","display_name":"Mobile Health and mHealth Applications","score":0.03840000182390213,"subfield":{"id":"https://openalex.org/subfields/3600","display_name":"General Health Professions"},"field":{"id":"https://openalex.org/fields/36","display_name":"Health Professions"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7159958481788635},{"id":"https://openalex.org/keywords/executable","display_name":"Executable","score":0.6119163632392883},{"id":"https://openalex.org/keywords/construct","display_name":"Construct (python library)","score":0.5236420631408691},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.48490744829177856},{"id":"https://openalex.org/keywords/workstation","display_name":"Workstation","score":0.47064274549484253},{"id":"https://openalex.org/keywords/simulation","display_name":"Simulation","score":0.402927041053772},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.38559040427207947},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.1140572726726532}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7159958481788635},{"id":"https://openalex.org/C160145156","wikidata":"https://www.wikidata.org/wiki/Q778586","display_name":"Executable","level":2,"score":0.6119163632392883},{"id":"https://openalex.org/C2780801425","wikidata":"https://www.wikidata.org/wiki/Q5164392","display_name":"Construct (python library)","level":2,"score":0.5236420631408691},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.48490744829177856},{"id":"https://openalex.org/C67953723","wikidata":"https://www.wikidata.org/wiki/Q192525","display_name":"Workstation","level":2,"score":0.47064274549484253},{"id":"https://openalex.org/C44154836","wikidata":"https://www.wikidata.org/wiki/Q45045","display_name":"Simulation","level":1,"score":0.402927041053772},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.38559040427207947},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.1140572726726532},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D003924","descriptor_name":"Diabetes Mellitus, Type 2","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003924","descriptor_name":"Diabetes Mellitus, Type 2","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003924","descriptor_name":"Diabetes Mellitus, Type 2","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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}],"locations_count":5,"locations":[{"id":"doi:10.1186/s12859-021-04354-7","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-021-04354-7","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-021-04354-7","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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:34772335","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34772335","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:zenodo.org:5909608","is_oa":true,"landing_page_url":"https://zenodo.org/record/5909608","pdf_url":"https://zenodo.org/record/5909608","source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:doaj.org/article:a6a5641db45c41bfb580a4adbb2f8c7d","is_oa":true,"landing_page_url":"https://doaj.org/article/a6a5641db45c41bfb580a4adbb2f8c7d","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","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":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 22, Iss S14, Pp 1-14 (2021)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:8588594","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8588594","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","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-021-04354-7","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-021-04354-7","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-021-04354-7","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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/2","score":0.7699999809265137,"display_name":"Zero hunger"}],"awards":[{"id":"https://openalex.org/G5451116430","display_name":"individualizedPaediatricCure: Cloud-based virtual-patient models for precision paediatric oncology","funder_award_id":"826121","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"}],"funders":[{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3214434028.pdf","grobid_xml":"https://content.openalex.org/works/W3214434028.grobid-xml"},"referenced_works_count":42,"referenced_works":["https://openalex.org/W47135330","https://openalex.org/W164706946","https://openalex.org/W391985582","https://openalex.org/W1565185041","https://openalex.org/W1970328019","https://openalex.org/W1973333099","https://openalex.org/W1995670244","https://openalex.org/W1995945562","https://openalex.org/W2003884505","https://openalex.org/W2018044188","https://openalex.org/W2031946900","https://openalex.org/W2039716701","https://openalex.org/W2040932457","https://openalex.org/W2061872692","https://openalex.org/W2066344471","https://openalex.org/W2070379207","https://openalex.org/W2076474160","https://openalex.org/W2082317733","https://openalex.org/W2083027289","https://openalex.org/W2113901615","https://openalex.org/W2123592990","https://openalex.org/W2155162055","https://openalex.org/W2167851640","https://openalex.org/W2169310913","https://openalex.org/W2476911382","https://openalex.org/W2555088970","https://openalex.org/W2616922680","https://openalex.org/W2734870586","https://openalex.org/W2756659234","https://openalex.org/W2789210774","https://openalex.org/W2802525560","https://openalex.org/W2884887967","https://openalex.org/W2907662870","https://openalex.org/W2911964244","https://openalex.org/W2913281704","https://openalex.org/W2913795550","https://openalex.org/W3099125944","https://openalex.org/W3111667594","https://openalex.org/W3127838479","https://openalex.org/W6654769447","https://openalex.org/W6658765724","https://openalex.org/W6785019132"],"related_works":["https://openalex.org/W2350278424","https://openalex.org/W2071432835","https://openalex.org/W2366107444","https://openalex.org/W4234371507","https://openalex.org/W4299534542","https://openalex.org/W1628824497","https://openalex.org/W4239401009","https://openalex.org/W2053441600","https://openalex.org/W1990401748","https://openalex.org/W2047586841"],"abstract_inverted_index":{"BACKGROUND:":[0],"The":[1,87,245],"aim":[2],"of":[3,12,48,53,60,65,81,91,98,179,188,202,223,236],"the":[4,25,40,46,56,63,79,82,92,111,124,194,210,220,224,230,234,241],"present":[5],"paper":[6],"is":[7,27],"to":[8,38,77,126,142,148,172,215,232,257],"construct":[9],"an":[10,128,154,186],"emulator":[11,129,155,196,231,247],"a":[13,19,28,74,96,106,131,158,166],"complex":[14],"biological":[15],"system":[16],"simulator":[17,26,112,225],"using":[18],"machine":[20,159],"learning":[21,160],"approach.":[22],"More":[23],"specifically,":[24],"patient-specific":[29],"model":[30,68],"that":[31,135,209],"integrates":[32],"metabolic,":[33],"nutritional,":[34],"and":[35,42,100,104,205,251],"lifestyle":[36],"data":[37],"predict":[39,216],"metabolic":[41],"inflammatory":[43],"processes":[44],"underlying":[45],"development":[47],"type-2":[49,61],"diabetes":[50],"in":[51,177],"absence":[52],"familiarity.":[54],"Given":[55],"very":[57],"high":[58,88,218],"incidence":[59],"diabetes,":[62],"implementation":[64],"this":[66],"predictive":[67],"on":[69,115,120,139,157,197,240,253],"mobile":[70,121,140,254],"devices":[71,141,256],"could":[72],"provide":[73,143],"useful":[75],"instrument":[76],"assess":[78],"risk":[80],"disease":[83],"for":[84],"aware":[85],"individuals.":[86],"computational":[89,133],"cost":[90,134],"developed":[93],"model,":[94],"being":[95],"mixture":[97],"agent-based":[99],"ordinary":[101],"differential":[102],"equations":[103],"providing":[105],"dynamic":[107],"multivariate":[108],"output,":[109],"makes":[110],"executable":[113],"only":[114],"powerful":[116],"workstations":[117],"but":[118,162],"not":[119],"devices.":[122],"Hence":[123],"need":[125],"implement":[127],"with":[130,217],"reduced":[132],"can":[136,248],"be":[137,249],"executed":[138,252],"real-time":[144],"self-monitoring.":[145],"RESULTS:":[146],"Similarly":[147],"our":[149],"previous":[150],"work,":[151],"we":[152,164,184],"propose":[153],"based":[156],"algorithm":[161],"here":[163],"consider":[165],"different":[167,200],"approach":[168],"which":[169],"turn":[170],"out":[171,208],"have":[173,185],"better":[174],"performances,":[175],"indeed":[176],"terms":[178],"root":[180],"mean":[181],"square":[182],"error":[183],"improvement":[187],"two":[189],"order":[190],"magnitude.":[191],"We":[192,228],"tested":[193],"proposed":[195,246],"samples":[198],"containing":[199],"number":[201],"simulated":[203],"trajectories,":[204],"it":[206],"turned":[207],"fitted":[211],"trajectories":[212],"are":[213],"able":[214],"accuracy":[219],"entire":[221],"dynamics":[222],"output":[226],"variables.":[227],"apply":[229],"control":[233],"level":[235],"inflammation":[237],"while":[238],"leveraging":[239],"nutritional":[242],"input.":[243],"CONCLUSION:":[244],"implemented":[250],"health":[255],"perform":[258],"quick-and-easy":[259],"self-monitoring":[260],"assessments.":[261]},"counts_by_year":[{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":7},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":6}],"updated_date":"2026-07-23T08:03:31.855105","created_date":"2025-10-10T00:00:00"}
