{"id":"https://openalex.org/W3112044717","doi":"https://doi.org/10.1177/0037549720975075","title":"Nested active learning for efficient model contextualization and parameterization: pathway to generating simulated populations using multi-scale computational models","display_name":"Nested active learning for efficient model contextualization and parameterization: pathway to generating simulated populations using multi-scale computational models","publication_year":2020,"publication_date":"2020-12-14","ids":{"openalex":"https://openalex.org/W3112044717","doi":"https://doi.org/10.1177/0037549720975075","mag":"3112044717","pmid":"https://pubmed.ncbi.nlm.nih.gov/34744189"},"language":"en","primary_location":{"id":"doi:10.1177/0037549720975075","is_oa":false,"landing_page_url":"https://doi.org/10.1177/0037549720975075","pdf_url":null,"source":{"id":"https://openalex.org/S32573412","display_name":"SIMULATION","issn_l":"0037-5497","issn":["0037-5497","1741-3133"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320017","host_organization_name":"SAGE Publishing","host_organization_lineage":["https://openalex.org/P4310320017"],"host_organization_lineage_names":["SAGE Publishing"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"SIMULATION","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.osti.gov/biblio/1735671","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5112042579","display_name":"Chase Cockrell","orcid":null},"institutions":[{"id":"https://openalex.org/I111236770","display_name":"University of Vermont","ror":"https://ror.org/0155zta11","country_code":"US","type":"education","lineage":["https://openalex.org/I111236770"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Chase Cockrell","raw_affiliation_strings":["Department of Surgery, University of Vermont, USA"],"raw_orcid":"https://orcid.org/0000-0003-3224-7617","affiliations":[{"raw_affiliation_string":"Department of Surgery, University of Vermont, USA","institution_ids":["https://openalex.org/I111236770"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065662869","display_name":"Jonathan Ozik","orcid":"https://orcid.org/0000-0002-3495-6735"},"institutions":[{"id":"https://openalex.org/I1282105669","display_name":"Argonne National Laboratory","ror":"https://ror.org/05gvnxz63","country_code":"US","type":"facility","lineage":["https://openalex.org/I1282105669","https://openalex.org/I1330989302","https://openalex.org/I39565521","https://openalex.org/I40347166"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jonathan Ozik","raw_affiliation_strings":["Argonne National Laboratory, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Argonne National Laboratory, USA","institution_ids":["https://openalex.org/I1282105669"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5113926166","display_name":"Nick Collier","orcid":null},"institutions":[{"id":"https://openalex.org/I1282105669","display_name":"Argonne National Laboratory","ror":"https://ror.org/05gvnxz63","country_code":"US","type":"facility","lineage":["https://openalex.org/I1282105669","https://openalex.org/I1330989302","https://openalex.org/I39565521","https://openalex.org/I40347166"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Nick Collier","raw_affiliation_strings":["Argonne National Laboratory, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Argonne National Laboratory, USA","institution_ids":["https://openalex.org/I1282105669"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5042696510","display_name":"Gary An","orcid":"https://orcid.org/0000-0003-4549-9004"},"institutions":[{"id":"https://openalex.org/I111236770","display_name":"University of Vermont","ror":"https://ror.org/0155zta11","country_code":"US","type":"education","lineage":["https://openalex.org/I111236770"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Gary An","raw_affiliation_strings":["Department of Surgery, University of Vermont, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Surgery, University of Vermont, USA","institution_ids":["https://openalex.org/I111236770"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5112042579"],"corresponding_institution_ids":["https://openalex.org/I111236770"],"apc_list":null,"apc_paid":null,"fwci":1.602,"has_fulltext":false,"cited_by_count":16,"citation_normalized_percentile":{"value":0.83733425,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"97","issue":"4","first_page":"287","last_page":"296"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11206","display_name":"Model Reduction and Neural Networks","score":0.9653000235557556,"subfield":{"id":"https://openalex.org/subfields/3109","display_name":"Statistical and Nonlinear Physics"},"field":{"id":"https://openalex.org/fields/31","display_name":"Physics and Astronomy"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T11206","display_name":"Model Reduction and Neural Networks","score":0.9653000235557556,"subfield":{"id":"https://openalex.org/subfields/3109","display_name":"Statistical and Nonlinear Physics"},"field":{"id":"https://openalex.org/fields/31","display_name":"Physics and Astronomy"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11801","display_name":"Reservoir Engineering and Simulation Methods","score":0.9387999773025513,"subfield":{"id":"https://openalex.org/subfields/2212","display_name":"Ocean Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11178","display_name":"Receptor Mechanisms and Signaling","score":0.920199990272522,"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/context","display_name":"Context (archaeology)","score":0.5902222990989685},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5804881453514099},{"id":"https://openalex.org/keywords/contextualization","display_name":"Contextualization","score":0.5568342804908752},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.5511155724525452},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4966893792152405},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.47694507241249084},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.4390132427215576},{"id":"https://openalex.org/keywords/scale","display_name":"Scale (ratio)","score":0.4334821105003357},{"id":"https://openalex.org/keywords/internal-model","display_name":"Internal model","score":0.43288615345954895},{"id":"https://openalex.org/keywords/space","display_name":"Space (punctuation)","score":0.4153633415699005},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.34752264618873596},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.12650412321090698},{"id":"https://openalex.org/keywords/control","display_name":"Control (management)","score":0.10035926103591919}],"concepts":[{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.5902222990989685},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5804881453514099},{"id":"https://openalex.org/C2780712339","wikidata":"https://www.wikidata.org/wiki/Q5165204","display_name":"Contextualization","level":3,"score":0.5568342804908752},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.5511155724525452},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4966893792152405},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.47694507241249084},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.4390132427215576},{"id":"https://openalex.org/C2778755073","wikidata":"https://www.wikidata.org/wiki/Q10858537","display_name":"Scale (ratio)","level":2,"score":0.4334821105003357},{"id":"https://openalex.org/C28427503","wikidata":"https://www.wikidata.org/wiki/Q13580300","display_name":"Internal model","level":3,"score":0.43288615345954895},{"id":"https://openalex.org/C2778572836","wikidata":"https://www.wikidata.org/wiki/Q380933","display_name":"Space (punctuation)","level":2,"score":0.4153633415699005},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.34752264618873596},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.12650412321090698},{"id":"https://openalex.org/C2775924081","wikidata":"https://www.wikidata.org/wiki/Q55608371","display_name":"Control (management)","level":2,"score":0.10035926103591919},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.0},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C527412718","wikidata":"https://www.wikidata.org/wiki/Q855395","display_name":"Interpretation (philosophy)","level":2,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0}],"mesh":[],"locations_count":6,"locations":[{"id":"doi:10.1177/0037549720975075","is_oa":false,"landing_page_url":"https://doi.org/10.1177/0037549720975075","pdf_url":null,"source":{"id":"https://openalex.org/S32573412","display_name":"SIMULATION","issn_l":"0037-5497","issn":["0037-5497","1741-3133"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320017","host_organization_name":"SAGE Publishing","host_organization_lineage":["https://openalex.org/P4310320017"],"host_organization_lineage_names":["SAGE Publishing"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"SIMULATION","raw_type":"journal-article"},{"id":"pmid:34744189","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34744189","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":"Simulation","raw_type":null},{"id":"pmh:oai:europepmc.org:7460204","is_oa":false,"landing_page_url":"http://europepmc.org/pmc/articles/PMC8570577","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:osti.gov:1735671","is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/1735671","pdf_url":null,"source":{"id":"https://openalex.org/S4306402487","display_name":"OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I139351228","host_organization_name":"Office of Scientific and Technical Information","host_organization_lineage":["https://openalex.org/I139351228"],"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":null},{"id":"pmh:oai:osti.gov:1854522","is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/1854522","pdf_url":null,"source":{"id":"https://openalex.org/S4306402487","display_name":"OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I139351228","host_organization_name":"Office of Scientific and Technical Information","host_organization_lineage":["https://openalex.org/I139351228"],"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":null},{"id":"pmh:oai:pubmedcentral.nih.gov:8570577","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8570577","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Simulation","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:osti.gov:1735671","is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/1735671","pdf_url":null,"source":{"id":"https://openalex.org/S4306402487","display_name":"OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I139351228","host_organization_name":"Office of Scientific and Technical Information","host_organization_lineage":["https://openalex.org/I139351228"],"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":null},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G5764609282","display_name":null,"funder_award_id":"1S10OD018495-01","funder_id":"https://openalex.org/F4320333971","funder_display_name":"Computation Institute, University of Chicago"},{"id":"https://openalex.org/G608975031","display_name":null,"funder_award_id":"U01EB025825","funder_id":"https://openalex.org/F4320337363","funder_display_name":"National Institute of Biomedical Imaging and Bioengineering"},{"id":"https://openalex.org/G8040941844","display_name":null,"funder_award_id":"DE-AC02-06CH11357, DE-AC02-05CH11231","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"}],"funders":[{"id":"https://openalex.org/F4320306084","display_name":"U.S. Department of Energy","ror":"https://ror.org/01bj3aw27"},{"id":"https://openalex.org/F4320333971","display_name":"Computation Institute, University of Chicago","ror":null},{"id":"https://openalex.org/F4320337363","display_name":"National Institute of Biomedical Imaging and Bioengineering","ror":"https://ror.org/00372qc85"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":48,"referenced_works":["https://openalex.org/W100464641","https://openalex.org/W100926944","https://openalex.org/W1504412414","https://openalex.org/W1533840382","https://openalex.org/W1580635337","https://openalex.org/W1597041602","https://openalex.org/W1597286183","https://openalex.org/W1605844890","https://openalex.org/W1845469719","https://openalex.org/W1930624869","https://openalex.org/W1971514365","https://openalex.org/W1977523316","https://openalex.org/W1989019965","https://openalex.org/W1994249905","https://openalex.org/W2003659199","https://openalex.org/W2004463205","https://openalex.org/W2012878613","https://openalex.org/W2016133956","https://openalex.org/W2021367230","https://openalex.org/W2050672815","https://openalex.org/W2056392803","https://openalex.org/W2062075925","https://openalex.org/W2063397490","https://openalex.org/W2079604837","https://openalex.org/W2095705004","https://openalex.org/W2118816397","https://openalex.org/W2118848872","https://openalex.org/W2121490181","https://openalex.org/W2132083787","https://openalex.org/W2166116275","https://openalex.org/W2557183043","https://openalex.org/W2577818097","https://openalex.org/W2753216119","https://openalex.org/W2786438063","https://openalex.org/W2788996259","https://openalex.org/W2810438149","https://openalex.org/W2889551824","https://openalex.org/W2894128844","https://openalex.org/W2906137127","https://openalex.org/W2949071206","https://openalex.org/W2951213949","https://openalex.org/W2951611630","https://openalex.org/W2953317739","https://openalex.org/W2962732683","https://openalex.org/W3099037746","https://openalex.org/W3163822529","https://openalex.org/W4212883601","https://openalex.org/W4248954331"],"related_works":["https://openalex.org/W1687432146","https://openalex.org/W1591874556","https://openalex.org/W2185608106","https://openalex.org/W3046258185","https://openalex.org/W1548083239","https://openalex.org/W3216994056","https://openalex.org/W2268232908","https://openalex.org/W205610463","https://openalex.org/W4296050054","https://openalex.org/W2893240344"],"abstract_inverted_index":{"There":[0],"is":[1,157,171],"increasing":[2],"interest":[3],"in":[4,22,38,142,236],"the":[5,36,55,99,118,144,181,187,199,207],"use":[6],"of":[7,35,48,57,61,82,122,186,201,211,230],"mechanism-based":[8],"multi-scale":[9],"computational":[10],"models":[11,15,225],"(such":[12],"as":[13],"agent-based":[14],"(ABMs))":[16],"to":[17,24,75,86,98,178,204],"generate":[18],"simulated":[19],"clinical":[20],"populations":[21],"order":[23],"discover":[25],"and":[26,30,46,78,111,132,183],"evaluate":[27],"potential":[28],"diagnostic":[29],"therapeutic":[31],"modalities.":[32],"The":[33,103,166],"description":[34],"environment":[37,149],"which":[39,107,143],"a":[40,58,69,138,152,160,172,192,227],"biomedical":[41],"simulation":[42],"operates":[43],"(model":[44,52],"context)":[45],"parameterization":[47,156],"internal":[49,105,154,194],"model":[50,148,155,213],"rules":[51],"content)":[53],"requires":[54],"optimization":[56],"large":[59],"number":[60,200,229],"free":[62],"parameters.":[63],"In":[64,217],"this":[65,212],"work,":[66],"we":[67,219],"utilize":[68],"nested":[70,139],"active":[71],"learning":[72],"(AL)":[73],"workflow":[74,170],"efficiently":[76,179,205],"parameterize":[77],"contextualize":[79],"an":[80],"ABM":[81],"systemic":[83],"inflammation":[84,131],"used":[85],"examine":[87],"sepsis.":[88],"Contextual":[89],"parameter":[90,209],"space":[91,150,189,210],"was":[92,115],"examined":[93],"using":[94,159],"four":[95],"parameters":[96],"external":[97],"model's":[100,104],"rule":[101],"set.":[102],"parameterization,":[106],"represents":[108],"gene":[109],"expression":[110],"associated":[112,129],"cellular":[113],"behaviors,":[114],"explored":[116],"through":[117],"augmentation":[119],"or":[120],"inhibition":[121],"signaling":[123,127],"pathways":[124],"for":[125,151],"12":[126],"mediators":[128],"with":[130,226],"wound":[133],"healing.":[134],"We":[135,196],"have":[136,197,220],"implemented":[137],"AL":[140,168,177],"approach":[141],"clinically":[145],"relevant":[146],"(CR)":[147],"given":[153,190],"mapped":[158],"small":[161],"Artificial":[162],"Neural":[163],"Network":[164],"(ANN).":[165],"outer":[167],"level":[169],"larger":[173,228],"ANN":[174],"that":[175,222],"uses":[176],"regress":[180],"volume":[182],"centroid":[184],"location":[185],"CR":[188,208],"by":[191,214],"single":[193],"parameterization.":[195],"reduced":[198],"simulations":[202],"required":[203],"map":[206],"approximately":[215],"99%.":[216],"addition,":[218],"shown":[221],"more":[223],"complex":[224],"variables":[231],"may":[232],"expect":[233],"further":[234],"improvements":[235],"efficiency.":[237]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":8},{"year":2021,"cited_by_count":2}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
