{"id":"https://openalex.org/W1512003720","doi":"https://doi.org/10.1109/ner.2015.7146619","title":"Maximizing predictability of a bottom-up complex multi-scale model through systematic validation and multi-objective multi-level optimization","display_name":"Maximizing predictability of a bottom-up complex multi-scale model through systematic validation and multi-objective multi-level optimization","publication_year":2015,"publication_date":"2015-04-01","ids":{"openalex":"https://openalex.org/W1512003720","doi":"https://doi.org/10.1109/ner.2015.7146619","mag":"1512003720"},"language":"en","primary_location":{"id":"doi:10.1109/ner.2015.7146619","is_oa":false,"landing_page_url":"https://doi.org/10.1109/ner.2015.7146619","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2015 7th International IEEE/EMBS Conference on Neural Engineering (NER)","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"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/A5047655773","display_name":"Jean\u2010Marie C. Bouteiller","orcid":"https://orcid.org/0000-0003-3069-0826"},"institutions":[{"id":"https://openalex.org/I1174212","display_name":"University of Southern California","ror":"https://ror.org/03taz7m60","country_code":"US","type":"education","lineage":["https://openalex.org/I1174212"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Jean-Marie C. Bouteiller","raw_affiliation_strings":["Department of Biomedical Engineering, University of Southern California, Los Angeles, CA, USA","Department of Biomedical Engineering, University of Southern California, 1042 Downey Way, DRB Building, Los Angeles, 90089-1111 USA"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical Engineering, University of Southern California, Los Angeles, CA, USA","institution_ids":["https://openalex.org/I1174212"]},{"raw_affiliation_string":"Department of Biomedical Engineering, University of Southern California, 1042 Downey Way, DRB Building, Los Angeles, 90089-1111 USA","institution_ids":["https://openalex.org/I1174212"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063171219","display_name":"Zhuobo Feng","orcid":null},"institutions":[{"id":"https://openalex.org/I1174212","display_name":"University of Southern California","ror":"https://ror.org/03taz7m60","country_code":"US","type":"education","lineage":["https://openalex.org/I1174212"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Zhuobo Feng","raw_affiliation_strings":["Department of Computer Science, University of Southern California, Los Angeles, USA","Department of Computer Science, University of Southern California, Los Angeles, USA#TAB#"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Southern California, Los Angeles, USA","institution_ids":["https://openalex.org/I1174212"]},{"raw_affiliation_string":"Department of Computer Science, University of Southern California, Los Angeles, USA#TAB#","institution_ids":["https://openalex.org/I1174212"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5014438376","display_name":"Alexander Onopa","orcid":null},"institutions":[{"id":"https://openalex.org/I1174212","display_name":"University of Southern California","ror":"https://ror.org/03taz7m60","country_code":"US","type":"education","lineage":["https://openalex.org/I1174212"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Alexander Onopa","raw_affiliation_strings":["Department of Electrical Engineering, University of Southern California, Los Angeles, USA","Department of Electrical Engg., University of Southern California, Los Angeles, USA"],"affiliations":[{"raw_affiliation_string":"Department of Electrical Engineering, University of Southern California, Los Angeles, USA","institution_ids":["https://openalex.org/I1174212"]},{"raw_affiliation_string":"Department of Electrical Engg., University of Southern California, Los Angeles, USA","institution_ids":["https://openalex.org/I1174212"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012709333","display_name":"Mike Huang","orcid":"https://orcid.org/0000-0002-7724-0315"},"institutions":[{"id":"https://openalex.org/I1174212","display_name":"University of Southern California","ror":"https://ror.org/03taz7m60","country_code":"US","type":"education","lineage":["https://openalex.org/I1174212"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mike Huang","raw_affiliation_strings":["University of Southern California, Los Angeles, CA, US","University of Southern , California , USA"],"affiliations":[{"raw_affiliation_string":"University of Southern California, Los Angeles, CA, US","institution_ids":["https://openalex.org/I1174212"]},{"raw_affiliation_string":"University of Southern , California , USA","institution_ids":["https://openalex.org/I1174212"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075309711","display_name":"Eric Y. Hu","orcid":"https://orcid.org/0000-0002-1150-4576"},"institutions":[{"id":"https://openalex.org/I1174212","display_name":"University of Southern California","ror":"https://ror.org/03taz7m60","country_code":"US","type":"education","lineage":["https://openalex.org/I1174212"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Eric Y. Hu","raw_affiliation_strings":["Department of Biomedical Engineering, University of Southern California, Los Angeles, CA, USA","Department of Biomedical Engineering, Univ. of Southern California,Los Angeles,USA"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical Engineering, University of Southern California, Los Angeles, CA, USA","institution_ids":["https://openalex.org/I1174212"]},{"raw_affiliation_string":"Department of Biomedical Engineering, Univ. of Southern California,Los Angeles,USA","institution_ids":["https://openalex.org/I1174212"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100973873","display_name":"Endre Somogyi","orcid":null},"institutions":[{"id":"https://openalex.org/I4210119109","display_name":"Indiana University Bloomington","ror":"https://ror.org/02k40bc56","country_code":"US","type":"education","lineage":["https://openalex.org/I4210119109","https://openalex.org/I592451"]},{"id":"https://openalex.org/I4210151352","display_name":"Biocom","ror":"https://ror.org/03ymdxs56","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210151352"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Endre Somogyi","raw_affiliation_strings":["Biocomplexity Institute, Indiana University Bloomington, Bloomington, IN, USA","Biocomplexity Institute, Indiana University Bloomington, Simon Hall MSB1, 212 S Hawthorne Dr, IN 47405-7105, USA"],"affiliations":[{"raw_affiliation_string":"Biocomplexity Institute, Indiana University Bloomington, Bloomington, IN, USA","institution_ids":["https://openalex.org/I4210119109","https://openalex.org/I4210151352"]},{"raw_affiliation_string":"Biocomplexity Institute, Indiana University Bloomington, Simon Hall MSB1, 212 S Hawthorne Dr, IN 47405-7105, USA","institution_ids":["https://openalex.org/I4210119109","https://openalex.org/I4210151352"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012477004","display_name":"Michel Baudry","orcid":"https://orcid.org/0000-0002-5142-241X"},"institutions":[{"id":"https://openalex.org/I93393672","display_name":"Western University of Health Sciences","ror":"https://ror.org/05167c961","country_code":"US","type":"education","lineage":["https://openalex.org/I93393672"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Michel Baudry","raw_affiliation_strings":["Graduate College of Biomedical Sciences, Western University of Health Sciences, Pomona, CA, USA","Western University of Health Sciences, Graduate College of Biomedical Sciences, 309 E. 2nd St., Pomona, CA 91766 USA"],"affiliations":[{"raw_affiliation_string":"Graduate College of Biomedical Sciences, Western University of Health Sciences, Pomona, CA, USA","institution_ids":["https://openalex.org/I93393672"]},{"raw_affiliation_string":"Western University of Health Sciences, Graduate College of Biomedical Sciences, 309 E. 2nd St., Pomona, CA 91766 USA","institution_ids":["https://openalex.org/I93393672"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5113881420","display_name":"Serge Bischoff","orcid":null},"institutions":[{"id":"https://openalex.org/I4210103732","display_name":"Rhenovia (France)","ror":"https://ror.org/01bts4z81","country_code":"FR","type":"company","lineage":["https://openalex.org/I4210103732"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Serge Bischoff","raw_affiliation_strings":["Rhenovia Pharma, 20c, Mulhouse, FRANCE","Rhenovia Pharma, 20c, rue de Chemnitz, 68100 Mulhouse, FRANCE"],"affiliations":[{"raw_affiliation_string":"Rhenovia Pharma, 20c, Mulhouse, FRANCE","institution_ids":["https://openalex.org/I4210103732"]},{"raw_affiliation_string":"Rhenovia Pharma, 20c, rue de Chemnitz, 68100 Mulhouse, FRANCE","institution_ids":["https://openalex.org/I4210103732"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5111911478","display_name":"Theodore W. Berger","orcid":null},"institutions":[{"id":"https://openalex.org/I1174212","display_name":"University of Southern California","ror":"https://ror.org/03taz7m60","country_code":"US","type":"education","lineage":["https://openalex.org/I1174212"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Theodore W. Berger","raw_affiliation_strings":["Engineering with the Department of Biomedical Engineering, University of Southern California, Los Angeles, CA, USA","Department of Biomedical Engineering, University of Southern California, Los Angeles, 90089-1111 USA"],"affiliations":[{"raw_affiliation_string":"Engineering with the Department of Biomedical Engineering, University of Southern California, Los Angeles, CA, USA","institution_ids":["https://openalex.org/I1174212"]},{"raw_affiliation_string":"Department of Biomedical Engineering, University of Southern California, Los Angeles, 90089-1111 USA","institution_ids":["https://openalex.org/I1174212"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":9,"corresponding_author_ids":["https://openalex.org/A5047655773"],"corresponding_institution_ids":["https://openalex.org/I1174212"],"apc_list":null,"apc_paid":null,"fwci":0.2917,"has_fulltext":false,"cited_by_count":5,"citation_normalized_percentile":{"value":0.59512657,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"16","issue":null,"first_page":"300","last_page":"303"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9965000152587891,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9965000152587891,"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/T11407","display_name":"Innovative Microfluidic and Catalytic Techniques Innovation","score":0.9919999837875366,"subfield":{"id":"https://openalex.org/subfields/2204","display_name":"Biomedical 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/T10211","display_name":"Computational Drug Discovery Methods","score":0.9890000224113464,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/predictability","display_name":"Predictability","score":0.9333564043045044},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7589032649993896},{"id":"https://openalex.org/keywords/replicate","display_name":"Replicate","score":0.726077139377594},{"id":"https://openalex.org/keywords/scale","display_name":"Scale (ratio)","score":0.4596012234687805},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.4145743250846863},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.08079919219017029}],"concepts":[{"id":"https://openalex.org/C197640229","wikidata":"https://www.wikidata.org/wiki/Q2534066","display_name":"Predictability","level":2,"score":0.9333564043045044},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7589032649993896},{"id":"https://openalex.org/C2781162219","wikidata":"https://www.wikidata.org/wiki/Q26250693","display_name":"Replicate","level":2,"score":0.726077139377594},{"id":"https://openalex.org/C2778755073","wikidata":"https://www.wikidata.org/wiki/Q10858537","display_name":"Scale (ratio)","level":2,"score":0.4596012234687805},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.4145743250846863},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.08079919219017029},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","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}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/ner.2015.7146619","is_oa":false,"landing_page_url":"https://doi.org/10.1109/ner.2015.7146619","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2015 7th International IEEE/EMBS Conference on Neural Engineering (NER)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":12,"referenced_works":["https://openalex.org/W1595498733","https://openalex.org/W1855000541","https://openalex.org/W1978558648","https://openalex.org/W2053798630","https://openalex.org/W2076721070","https://openalex.org/W2077587321","https://openalex.org/W2106125417","https://openalex.org/W2116449318","https://openalex.org/W2164653071","https://openalex.org/W2187364252","https://openalex.org/W2198098822","https://openalex.org/W2502442987"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W4254851101","https://openalex.org/W3171007296","https://openalex.org/W2726467123","https://openalex.org/W22115721","https://openalex.org/W2064726690","https://openalex.org/W4252678288","https://openalex.org/W4254065731","https://openalex.org/W2211931904","https://openalex.org/W1607297154"],"abstract_inverted_index":{"Computational":[0],"models":[1,36,123,132],"are":[2,65],"mathematical":[3],"representations":[4],"meant":[5],"to":[6,25,40,75,99,118,158,171],"replicate":[7],"the":[8,20,50,55,96,110,128,160,164,173,190,193,195],"biological":[9,46],"system":[10],"they":[11],"represent,":[12],"as":[13,15,62,133],"well":[14],"provide":[16],"insights":[17],"and":[18,52,72,144,199],"predict":[19],"system's":[21],"dynamics":[22],"in":[23],"response":[24],"changing":[26],"conditions.":[27],"In":[28],"a":[29,33,70,79,87,104,115,168],"bottom-up":[30],"modeling":[31,89],"approach,":[32,194],"multitude":[34],"of":[35,54,78,92,107,109,130,141,147,154,163,175,192],"may":[37,58],"be":[38],"compounded":[39,56,131],"represent":[41],"more":[42,63],"complex":[43,80],"higher":[44,139,182],"level":[45,98,106],"systems.":[47],"However,":[48],"guaranteeing":[49],"validity":[51,129],"predictability":[53,77,108],"ensemble":[57],"become":[59],"increasingly":[60],"challenging":[61],"components":[64],"integrated.":[66],"We":[67,83],"herein":[68],"present":[69],"sequential":[71],"iterative":[73],"method":[74],"maximize":[76,159],"multiscale":[81,88],"model.":[82],"have":[84],"successfully":[85],"developed":[86],"platform":[90],"comprised":[91],"mechanisms":[93],"ranging":[94],"from":[95],"biomolecular":[97],"multi-cellular":[100],"networks.":[101],"To":[102],"maintain":[103],"high":[105],"global":[111],"platform,":[112,165],"we":[113],"introduce":[114],"systematic":[116,145],"approach":[117],"not":[119],"only":[120],"validate":[121],"all":[122],"independently,":[124],"but":[125],"also":[126],"verify":[127],"additional":[134],"information":[135],"becomes":[136],"available":[137],"at":[138,151],"levels":[140,153],"complexity.":[142],"Iterative":[143],"application":[146],"these":[148],"validation":[149],"steps":[150],"increasing":[152],"complexity":[155],"is":[156],"intended":[157],"predictive":[161],"power":[162],"making":[166],"it":[167],"powerful":[169],"tool":[170],"study":[172],"impacts":[174],"low-levels":[176],"modifications":[177],"(pathologies,":[178],"drugs,":[179],"etc.)":[180],"on":[181],"functional":[183],"levels.":[184],"The":[185],"work":[186],"presented":[187],"lays":[188],"down":[189],"rationale":[191],"open":[196],"design":[197],"implementation":[198],"results.":[200]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2015,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
