{"id":"https://openalex.org/W291264158","doi":"https://doi.org/10.48550/arxiv.1404.6283","title":"Automated adaptive inference of coarse-grained dynamical models in systems biology","display_name":"Automated adaptive inference of coarse-grained dynamical models in systems biology","publication_year":2014,"publication_date":"2014-04-24","ids":{"openalex":"https://openalex.org/W291264158","doi":"https://doi.org/10.48550/arxiv.1404.6283","mag":"291264158"},"language":"en","primary_location":{"id":"pmh:oai:arXiv.org:1404.6283","doi":null,"is_oa":true,"landing_page_url":"http://arxiv.org/abs/1404.6283","pdf_url":"https://arxiv.org/pdf/1404.6283","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},"volume":null,"type":"preprint","indexed_in":["arxiv","datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://arxiv.org/pdf/1404.6283","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5008120275","display_name":"Bryan C. Daniels","orcid":"https://orcid.org/0000-0002-5870-1059","observed_orcids":["https://orcid.org/0000-0002-5870-1059"]},"institutions":[{"id":"https://openalex.org/I1304256225","display_name":"University of Wisconsin System","ror":"https://ror.org/03ydkyb10","country_code":"US","type":"education","lineage":["https://openalex.org/I1304256225"]},{"id":"https://openalex.org/I135310074","display_name":"University of Wisconsin\u2013Madison","ror":"https://ror.org/01y2jtd41","country_code":"US","type":"education","lineage":["https://openalex.org/I135310074"]},{"id":"https://openalex.org/I2802999273","display_name":"Wisconsin Institutes for Discovery","ror":"https://ror.org/05gbven85","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I2802999273"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Daniels, Bryan C.","raw_affiliation_strings":["Center for Complexity and Collective Computation , Wisconsin Institute for Discovery , University of Wisconsin , Madison , WI 53715 , USA","University of Wisconsin, Madison"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Complexity and Collective Computation , Wisconsin Institute for Discovery , University of Wisconsin , Madison , WI 53715 , USA","institution_ids":["https://openalex.org/I1304256225","https://openalex.org/I135310074","https://openalex.org/I2802999273"]},{"raw_affiliation_string":"University of Wisconsin, Madison","institution_ids":["https://openalex.org/I135310074"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5071388278","display_name":"Ilya M. Nemenman","orcid":"https://orcid.org/0000-0003-3024-4244","observed_orcids":["https://orcid.org/0000-0003-3024-4244"]},"institutions":[{"id":"https://openalex.org/I150468666","display_name":"Emory University","ror":"https://ror.org/03czfpz43","country_code":"US","type":"education","lineage":["https://openalex.org/I150468666"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Nemenman, Ilya","raw_affiliation_strings":["Departments of Physics and Biology Emory University , Atlanta , GA 30322 , USA","Emory University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Departments of Physics and Biology Emory University , Atlanta , GA 30322 , USA","institution_ids":["https://openalex.org/I150468666"]},{"raw_affiliation_string":"Emory University","institution_ids":["https://openalex.org/I150468666"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":5,"citation_normalized_percentile":null,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9970999956130981,"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":0.9970999956130981,"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/T11236","display_name":"Control Systems and Identification","score":0.0010999999940395355,"subfield":{"id":"https://openalex.org/subfields/2207","display_name":"Control and Systems 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/T11206","display_name":"Model Reduction and Neural Networks","score":0.0003000000142492354,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/coarse-grained-models","display_name":"coarse-grained models","score":0.8040000200271606},{"id":"https://openalex.org/keywords/adaptive-inference","display_name":"adaptive inference","score":0.699999988079071},{"id":"https://openalex.org/keywords/dynamical-systems","display_name":"dynamical systems","score":0.5590000152587891},{"id":"https://openalex.org/keywords/cellular-regulatory-networks","display_name":"cellular regulatory networks","score":0.6890000104904175},{"id":"https://openalex.org/keywords/parameter-estimation","display_name":"parameter estimation","score":0.414000004529953},{"id":"https://openalex.org/keywords/overfitting","display_name":"overfitting","score":0.7609999775886536},{"id":"https://openalex.org/keywords/latent-variables","display_name":"latent variables","score":0.8410000205039978},{"id":"https://openalex.org/keywords/phase-space-structure","display_name":"phase space structure","score":0.6890000104904175},{"id":"https://openalex.org/keywords/biological-signaling","display_name":"biological signaling","score":0.6830000281333923},{"id":"https://openalex.org/keywords/yeast-glycolysis","display_name":"yeast glycolysis","score":0.9639999866485596},{"id":"https://openalex.org/keywords/model-complexity","display_name":"model complexity","score":0.46799999475479126}],"concepts":[{"id":"https://openalex.org/C22019652","wikidata":"https://www.wikidata.org/wiki/Q331309","display_name":"Overfitting","level":3,"score":0.90321946144104},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.719393253326416},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.636469841003418},{"id":"https://openalex.org/C79379906","wikidata":"https://www.wikidata.org/wiki/Q3174497","display_name":"Dynamical systems theory","level":2,"score":0.5848591923713684},{"id":"https://openalex.org/C2780586882","wikidata":"https://www.wikidata.org/wiki/Q7520643","display_name":"Simple (philosophy)","level":2,"score":0.5278366208076477},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.5160703063011169},{"id":"https://openalex.org/C2781089630","wikidata":"https://www.wikidata.org/wiki/Q21856745","display_name":"Realization (probability)","level":2,"score":0.48256105184555054},{"id":"https://openalex.org/C47822265","wikidata":"https://www.wikidata.org/wiki/Q854457","display_name":"Complex system","level":2,"score":0.43832987546920776},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3474608063697815},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3436516523361206},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.33362001180648804},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.14195463061332703},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.11858052015304565},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.10980668663978577},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.10517099499702454},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.09003615379333496},{"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/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","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/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"pmh:oai:arXiv.org:1404.6283","doi":null,"is_oa":true,"landing_page_url":"http://arxiv.org/abs/1404.6283","pdf_url":"https://arxiv.org/pdf/1404.6283","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},{"id":"mag:291264158","doi":null,"is_oa":true,"landing_page_url":"https://arxiv.org/pdf/1404.6283.pdf","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"arXiv (Cornell University)","raw_type":null},{"id":"doi:10.48550/arxiv.1404.6283","doi":"https://doi.org/10.48550/arxiv.1404.6283","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.1404.6283","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"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":false,"raw_source_name":null,"raw_type":"Preprint"}],"best_oa_location":{"id":"pmh:oai:arXiv.org:1404.6283","doi":null,"is_oa":true,"landing_page_url":"http://arxiv.org/abs/1404.6283","pdf_url":"https://arxiv.org/pdf/1404.6283","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},"sustainable_development_goals":[],"sustainable_development_goals_aurora":[{"score":0.5799999833106995,"id":"https://metadata.un.org/sdg/15","display_name":"Life on land"}],"study_designs":[],"awards":[{"id":"https://openalex.org/G1167258308","display_name":"In search of simplicity: Coarse-graining cellular information processing networks","funder_award_id":"220020321","funder_id":"https://openalex.org/F4320306183","funder_display_name":"James S. McDonnell Foundation"},{"id":"https://openalex.org/G359965252","display_name":"Network Conflict Theory:  Empirically-Based Models of Conflict Dynamics and Effective Conflict Management Strategies","funder_award_id":"0904863","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G7592379170","display_name":null,"funder_award_id":"0904863","funder_id":"https://openalex.org/F4320306193","funder_display_name":"John Templeton Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320306183","display_name":"James S. McDonnell Foundation","ror":"https://ror.org/03dy4aq19"},{"id":"https://openalex.org/F4320306193","display_name":"John Templeton Foundation","ror":"https://ror.org/035tnyy05"},{"id":"https://openalex.org/F4320338304","display_name":"Los Alamos National Laboratory","ror":"https://ror.org/01e41cf67"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":39,"referenced_works":["https://openalex.org/W133148819","https://openalex.org/W1498436455","https://openalex.org/W1556089959","https://openalex.org/W1893491260","https://openalex.org/W1979769287","https://openalex.org/W1984391316","https://openalex.org/W2000040887","https://openalex.org/W2004385216","https://openalex.org/W2016803695","https://openalex.org/W2021058886","https://openalex.org/W2032535902","https://openalex.org/W2041132213","https://openalex.org/W2041951716","https://openalex.org/W2043487490","https://openalex.org/W2044784465","https://openalex.org/W2046042332","https://openalex.org/W2056961883","https://openalex.org/W2058580716","https://openalex.org/W2069647329","https://openalex.org/W2069941324","https://openalex.org/W2081240630","https://openalex.org/W2087636279","https://openalex.org/W2099231026","https://openalex.org/W2104649539","https://openalex.org/W2111270167","https://openalex.org/W2111936337","https://openalex.org/W2117663940","https://openalex.org/W2122234510","https://openalex.org/W2124641450","https://openalex.org/W2128957129","https://openalex.org/W2143970285","https://openalex.org/W2146855196","https://openalex.org/W2149695944","https://openalex.org/W2151554678","https://openalex.org/W2156909104","https://openalex.org/W2161304688","https://openalex.org/W2246296081","https://openalex.org/W3098928821","https://openalex.org/W3140968660"],"related_works":["https://openalex.org/W2581159681","https://openalex.org/W2101258119","https://openalex.org/W7096102159","https://openalex.org/W2249334097","https://openalex.org/W7203954719","https://openalex.org/W7099930820","https://openalex.org/W2992904487","https://openalex.org/W2104649539","https://openalex.org/W2261204730","https://openalex.org/W2405861895"],"abstract_inverted_index":{"Cellular":[0],"regulatory":[1],"dynamics":[2,31,80],"is":[3,115],"driven":[4],"by":[5],"large":[6,122],"and":[7,34,44,167,182],"intricate":[8],"networks":[9],"of":[10,23,29,56,63,78,89,103,124,179,185],"interactions":[11],"at":[12],"the":[13,39,49,64,87,104,149,186],"molecular":[14],"scale,":[15],"whose":[16],"sheer":[17],"size":[18],"obfuscates":[19],"understanding.":[20],"In":[21],"light":[22],"limited":[24],"experimental":[25],"data,":[26,158],"many":[27],"parameters":[28],"such":[30],"are":[32,45,107,143],"unknown,":[33],"thus":[35],"models":[36,55,77,94],"built":[37],"on":[38],"detailed,":[40],"mechanistic":[41],"viewpoint":[42],"overfit":[43],"not":[46],"predictive.":[47],"At":[48],"other":[50],"extreme,":[51],"simple":[52],"ad":[53],"hoc":[54],"complex":[57,163],"processes":[58],"often":[59],"miss":[60],"defining":[61],"features":[62],"underlying":[65],"systems.":[66],"Here":[67],"we":[68],"propose":[69],"an":[70],"approach":[71,114],"that":[72,81],"instead":[73],"constructs":[74],"phenomenological,":[75],"coarse-grained":[76],"network":[79],"automatically":[82],"adapt":[83],"their":[84],"complexity":[85],"to":[86,96,110,134],"amount":[88],"available":[90],"data.":[91,112],"Such":[92],"adaptive":[93],"lead":[95],"accurate":[97,169],"predictions":[98,137,170],"even":[99,118,138],"when":[100,139],"microscopic":[101],"details":[102],"studied":[105],"systems":[106],"unknown":[108],"due":[109],"insufficient":[111],"The":[113],"computationally":[116],"tractable,":[117],"for":[119,154,171],"a":[120,162,172],"relatively":[121],"number":[123],"dynamical":[125],"variables,":[126],"allowing":[127],"its":[128],"software":[129],"realization,":[130],"named":[131],"Sir":[132],"Isaac,":[133],"make":[135],"successful":[136],"important":[140],"dynamic":[141],"variables":[142],"unobserved.":[144,189],"For":[145],"example,":[146],"it":[147],"matches":[148],"known":[150],"phase":[151],"space":[152],"structure":[153],"simulated":[155],"planetary":[156],"motion":[157],"avoids":[159],"overfitting":[160],"in":[161],"biological":[164],"signaling":[165],"system,":[166],"produces":[168],"yeast":[173],"glycolysis":[174],"model":[175],"with":[176],"only":[177],"tens":[178],"data":[180],"points":[181],"over":[183],"half":[184],"interacting":[187],"species":[188]},"counts_by_year":[{"year":2019,"cited_by_count":1},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":2}],"updated_date":"2026-10-08T09:06:37.294493","created_date":"2016-06-24T00:00:00"}