{"id":"https://openalex.org/W2167543722","doi":"https://doi.org/10.1186/1752-0509-4-99","title":"Parameter inference for discretely observed stochastic kinetic models using stochastic gradient descent","display_name":"Parameter inference for discretely observed stochastic kinetic models using stochastic gradient descent","publication_year":2010,"publication_date":"2010-07-21","ids":{"openalex":"https://openalex.org/W2167543722","doi":"https://doi.org/10.1186/1752-0509-4-99","mag":"2167543722","pmid":"https://pubmed.ncbi.nlm.nih.gov/20663171"},"language":"en","primary_location":{"id":"doi:10.1186/1752-0509-4-99","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1752-0509-4-99","pdf_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-4-99","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","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 Systems Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"diamond","oa_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-4-99","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100635366","display_name":"Yuanfeng Wang","orcid":"https://orcid.org/0000-0003-3743-4008"},"institutions":[{"id":"https://openalex.org/I204250578","display_name":"University of California, Irvine","ror":"https://ror.org/04gyf1771","country_code":"US","type":"education","lineage":["https://openalex.org/I204250578"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Yuanfeng Wang","raw_affiliation_strings":["Department of Physics and Astronomy, University of California, Irvine, 92617, USA","Department of Physics and Astronomy, University of California, Irvine, CA, 92617, USA"],"affiliations":[{"raw_affiliation_string":"Department of Physics and Astronomy, University of California, Irvine, 92617, USA","institution_ids":["https://openalex.org/I204250578"]},{"raw_affiliation_string":"Department of Physics and Astronomy, University of California, Irvine, CA, 92617, USA","institution_ids":["https://openalex.org/I204250578"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5078078996","display_name":"Scott Christley","orcid":"https://orcid.org/0000-0002-9889-1221"},"institutions":[{"id":"https://openalex.org/I204250578","display_name":"University of California, Irvine","ror":"https://ror.org/04gyf1771","country_code":"US","type":"education","lineage":["https://openalex.org/I204250578"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Scott Christley","raw_affiliation_strings":["Center for Complex Biological Systems, University of California, Irvine, CA, 92617, USA","Department of Mathematics, University of California, Irvine, CA, 92617, USA"],"affiliations":[{"raw_affiliation_string":"Center for Complex Biological Systems, University of California, Irvine, CA, 92617, USA","institution_ids":["https://openalex.org/I204250578"]},{"raw_affiliation_string":"Department of Mathematics, University of California, Irvine, CA, 92617, USA","institution_ids":["https://openalex.org/I204250578"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5088981910","display_name":"Eric Mjolsness","orcid":"https://orcid.org/0000-0002-9085-9171"},"institutions":[{"id":"https://openalex.org/I204250578","display_name":"University of California, Irvine","ror":"https://ror.org/04gyf1771","country_code":"US","type":"education","lineage":["https://openalex.org/I204250578"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Eric Mjolsness","raw_affiliation_strings":["Center for Complex Biological Systems, University of California, Irvine, CA, 92617, USA","Department of Computer Science, University of California, Irvine, CA, 92617, USA","Institute for Genomics and Bioinformatics, University of California, Irvine, CA, 92617, USA"],"affiliations":[{"raw_affiliation_string":"Center for Complex Biological Systems, University of California, Irvine, CA, 92617, USA","institution_ids":["https://openalex.org/I204250578"]},{"raw_affiliation_string":"Department of Computer Science, University of California, Irvine, CA, 92617, USA","institution_ids":["https://openalex.org/I204250578"]},{"raw_affiliation_string":"Institute for Genomics and Bioinformatics, University of California, Irvine, CA, 92617, USA","institution_ids":["https://openalex.org/I204250578"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5084618257","display_name":"Xiaohui Xie","orcid":"https://orcid.org/0000-0002-5479-6345"},"institutions":[{"id":"https://openalex.org/I204250578","display_name":"University of California, Irvine","ror":"https://ror.org/04gyf1771","country_code":"US","type":"education","lineage":["https://openalex.org/I204250578"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xiaohui Xie","raw_affiliation_strings":["Center for Complex Biological Systems, University of California, Irvine, CA, 92617, USA","Department of Computer Science, University of California, Irvine, CA, 92617, USA","Institute for Genomics and Bioinformatics, University of California, Irvine, CA, 92617, USA"],"affiliations":[{"raw_affiliation_string":"Center for Complex Biological Systems, University of California, Irvine, CA, 92617, USA","institution_ids":["https://openalex.org/I204250578"]},{"raw_affiliation_string":"Department of Computer Science, University of California, Irvine, CA, 92617, USA","institution_ids":["https://openalex.org/I204250578"]},{"raw_affiliation_string":"Institute for Genomics and Bioinformatics, University of California, Irvine, CA, 92617, USA","institution_ids":["https://openalex.org/I204250578"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5100635366"],"corresponding_institution_ids":["https://openalex.org/I204250578"],"apc_list":null,"apc_paid":null,"fwci":3.3885,"has_fulltext":true,"cited_by_count":71,"citation_normalized_percentile":{"value":0.92983771,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"4","issue":"1","first_page":"99","last_page":"99"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9995999932289124,"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":0.9995999932289124,"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/T10120","display_name":"Bacterial Genetics and Biotechnology","score":0.9733999967575073,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9681000113487244,"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/inference","display_name":"Inference","score":0.591216504573822},{"id":"https://openalex.org/keywords/stochastic-gradient-descent","display_name":"Stochastic gradient descent","score":0.5078249573707581},{"id":"https://openalex.org/keywords/statistical-inference","display_name":"Statistical inference","score":0.5009551048278809},{"id":"https://openalex.org/keywords/gradient-descent","display_name":"Gradient descent","score":0.4530848562717438},{"id":"https://openalex.org/keywords/applied-mathematics","display_name":"Applied mathematics","score":0.4336596131324768},{"id":"https://openalex.org/keywords/jump-process","display_name":"Jump process","score":0.4292973577976227},{"id":"https://openalex.org/keywords/importance-sampling","display_name":"Importance sampling","score":0.42196792364120483},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.4104691743850708},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4003019332885742},{"id":"https://openalex.org/keywords/statistical-physics","display_name":"Statistical physics","score":0.3611612021923065},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.35077422857284546},{"id":"https://openalex.org/keywords/monte-carlo-method","display_name":"Monte Carlo method","score":0.2794429361820221},{"id":"https://openalex.org/keywords/jump","display_name":"Jump","score":0.27355068922042847},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.18303906917572021},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.09717637300491333},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.09493213891983032}],"concepts":[{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.591216504573822},{"id":"https://openalex.org/C206688291","wikidata":"https://www.wikidata.org/wiki/Q7617819","display_name":"Stochastic gradient descent","level":3,"score":0.5078249573707581},{"id":"https://openalex.org/C134261354","wikidata":"https://www.wikidata.org/wiki/Q938438","display_name":"Statistical inference","level":2,"score":0.5009551048278809},{"id":"https://openalex.org/C153258448","wikidata":"https://www.wikidata.org/wiki/Q1199743","display_name":"Gradient descent","level":3,"score":0.4530848562717438},{"id":"https://openalex.org/C28826006","wikidata":"https://www.wikidata.org/wiki/Q33521","display_name":"Applied mathematics","level":1,"score":0.4336596131324768},{"id":"https://openalex.org/C2776825372","wikidata":"https://www.wikidata.org/wiki/Q3922411","display_name":"Jump process","level":3,"score":0.4292973577976227},{"id":"https://openalex.org/C52740198","wikidata":"https://www.wikidata.org/wiki/Q1539564","display_name":"Importance sampling","level":3,"score":0.42196792364120483},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.4104691743850708},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4003019332885742},{"id":"https://openalex.org/C121864883","wikidata":"https://www.wikidata.org/wiki/Q677916","display_name":"Statistical physics","level":1,"score":0.3611612021923065},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.35077422857284546},{"id":"https://openalex.org/C19499675","wikidata":"https://www.wikidata.org/wiki/Q232207","display_name":"Monte Carlo method","level":2,"score":0.2794429361820221},{"id":"https://openalex.org/C2780695682","wikidata":"https://www.wikidata.org/wiki/Q4005959","display_name":"Jump","level":2,"score":0.27355068922042847},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.18303906917572021},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.09717637300491333},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.09493213891983032},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"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":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001669","descriptor_name":"Biochemical Phenomena","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D001669","descriptor_name":"Biochemical Phenomena","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D001669","descriptor_name":"Biochemical Phenomena","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D007700","descriptor_name":"Kinetics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007700","descriptor_name":"Kinetics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007700","descriptor_name":"Kinetics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009010","descriptor_name":"Monte Carlo Method","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009010","descriptor_name":"Monte Carlo Method","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009010","descriptor_name":"Monte Carlo Method","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013269","descriptor_name":"Stochastic Processes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013269","descriptor_name":"Stochastic Processes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013269","descriptor_name":"Stochastic Processes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013997","descriptor_name":"Time Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013997","descriptor_name":"Time Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013997","descriptor_name":"Time Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016013","descriptor_name":"Likelihood Functions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016013","descriptor_name":"Likelihood Functions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016013","descriptor_name":"Likelihood Functions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":7,"locations":[{"id":"doi:10.1186/1752-0509-4-99","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1752-0509-4-99","pdf_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-4-99","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","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 Systems Biology","raw_type":"journal-article"},{"id":"pmid:20663171","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/20663171","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 systems biology","raw_type":null},{"id":"pmh:oai:doaj.org/article:82c095d4c67b4f5f86d999731b4f5a98","is_oa":true,"landing_page_url":"https://doaj.org/article/82c095d4c67b4f5f86d999731b4f5a98","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Systems Biology, Vol 4, Iss 1, p 99 (2010)","raw_type":"article"},{"id":"pmh:oai:escholarship.org/ark:/13030/qt03c9f2gx","is_oa":true,"landing_page_url":"https://escholarship.org/uc/item/03c9f2gx","pdf_url":null,"source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"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 Systems Biology, vol 4, iss 1","raw_type":"article"},{"id":"pmh:oai:escholarship.org/ark:/13030/qt0r33t701","is_oa":false,"landing_page_url":"https://escholarship.org/uc/item/0r33t701","pdf_url":null,"source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Systems Biology, vol 4, iss 1","raw_type":"article"},{"id":"pmh:oai:europepmc.org:2001410","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2914651","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:qt0r33t701","is_oa":false,"landing_page_url":"http://www.escholarship.org/uc/item/0r33t701","pdf_url":null,"source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Wang, Yuanfeng; Christley, Scott; Mjolsness, Eric; & Xie, Xiaohui. (2010). Parameter inference for discretely observed stochastic kinetic models using stochastic gradient descent. BMC Systems Biology, 4(1), 99. doi: http://dx.doi.org/10.1186/1752-0509-4-99. Retrieved from: http://www.escholarship.org/uc/item/0r33t701","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/1752-0509-4-99","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1752-0509-4-99","pdf_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-4-99","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","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 Systems Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1634719776","display_name":null,"funder_award_id":"P50GM76516","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G1885747215","display_name":null,"funder_award_id":"P50GM76516","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G3611247453","display_name":null,"funder_award_id":"R01GM","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G3692211860","display_name":"CAREER: Computational Tools for Interpreting Genomes","funder_award_id":"0846218","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G6206573168","display_name":null,"funder_award_id":"R01GM75309","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G8288036582","display_name":null,"funder_award_id":"NIH R01","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G8616606689","display_name":"FIBR: Developmental Modeling and Informatics","funder_award_id":"0330786","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337401","display_name":"Division of Emerging Frontiers","ror":"https://ror.org/01tnvpc68"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2167543722.pdf","grobid_xml":"https://content.openalex.org/works/W2167543722.grobid-xml"},"referenced_works_count":51,"referenced_works":["https://openalex.org/W1549251788","https://openalex.org/W1590222219","https://openalex.org/W1635218549","https://openalex.org/W1758395617","https://openalex.org/W1946177469","https://openalex.org/W1967910251","https://openalex.org/W1970970926","https://openalex.org/W1977771126","https://openalex.org/W1978182054","https://openalex.org/W1978319180","https://openalex.org/W1979812265","https://openalex.org/W1984217390","https://openalex.org/W1985937069","https://openalex.org/W1988791304","https://openalex.org/W1996606122","https://openalex.org/W1999777663","https://openalex.org/W2003702678","https://openalex.org/W2009744470","https://openalex.org/W2009772909","https://openalex.org/W2018435536","https://openalex.org/W2024060531","https://openalex.org/W2025795296","https://openalex.org/W2028839103","https://openalex.org/W2037768790","https://openalex.org/W2041966847","https://openalex.org/W2046451925","https://openalex.org/W2077046573","https://openalex.org/W2085850813","https://openalex.org/W2091198609","https://openalex.org/W2093179886","https://openalex.org/W2093470850","https://openalex.org/W2096015757","https://openalex.org/W2096595244","https://openalex.org/W2105057212","https://openalex.org/W2106706098","https://openalex.org/W2107342968","https://openalex.org/W2116324021","https://openalex.org/W2127006594","https://openalex.org/W2135459617","https://openalex.org/W2137088684","https://openalex.org/W2140484213","https://openalex.org/W2143400799","https://openalex.org/W2146564314","https://openalex.org/W2151729750","https://openalex.org/W2152246075","https://openalex.org/W2155418451","https://openalex.org/W2158069895","https://openalex.org/W2165603655","https://openalex.org/W2167154952","https://openalex.org/W2168282770","https://openalex.org/W2171280873"],"related_works":["https://openalex.org/W2895097035","https://openalex.org/W4206903459","https://openalex.org/W2754816816","https://openalex.org/W4366280654","https://openalex.org/W3160167280","https://openalex.org/W3020853991","https://openalex.org/W4362706668","https://openalex.org/W4231621013","https://openalex.org/W3171021120","https://openalex.org/W3008318776"],"abstract_inverted_index":{"The":[0,18,87],"SGD":[1],"method":[2,19,49],"proposed":[3],"in":[4],"the":[5,43,70,79,90],"paper":[6],"presents":[7],"a":[8,52],"general":[9,40],"framework":[10],"of":[11,35,42,55],"inferring":[12],"parameters":[13],"for":[14,26,64,73,83],"stochastic":[15,56],"kinetic":[16],"models.":[17,57],"is":[20,24,92],"computationally":[21],"efficient":[22],"and":[23,29,39],"effective":[25],"both":[27],"partially":[28],"fully":[30],"observed":[31],"systems.":[32],"Automatic":[33],"construction":[34],"reversible":[36,80],"jump":[37,81],"samplers":[38,82],"formulation":[41],"likelihood":[44],"gradient":[45,71],"function":[46],"makes":[47],"our":[48,59],"applicable":[50],"to":[51],"wide":[53],"range":[54],"Furthermore":[58],"derivations":[60],"can":[61],"be":[62],"useful":[63],"other":[65],"purposes":[66],"such":[67],"as":[68],"using":[69,78],"information":[72],"parametric":[74],"sensitivity":[75],"analysis":[76],"or":[77],"full":[84],"Bayesian":[85],"inference.":[86],"software":[88],"implementing":[89],"algorithms":[91],"publicly":[93],"available":[94],"at":[95],"http://cbcl.ics.uci.edu/sgd.":[96]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":5},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":3},{"year":2016,"cited_by_count":5},{"year":2015,"cited_by_count":8},{"year":2014,"cited_by_count":8},{"year":2013,"cited_by_count":11},{"year":2012,"cited_by_count":8}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}