{"id":"https://openalex.org/W4229037531","doi":"https://doi.org/10.3390/e24050629","title":"Probabilistic Inference with Polymerizing Biochemical Circuits","display_name":"Probabilistic Inference with Polymerizing Biochemical Circuits","publication_year":2022,"publication_date":"2022-04-29","ids":{"openalex":"https://openalex.org/W4229037531","doi":"https://doi.org/10.3390/e24050629","pmid":"https://pubmed.ncbi.nlm.nih.gov/35626513"},"language":"en","primary_location":{"id":"doi:10.3390/e24050629","is_oa":true,"landing_page_url":"https://doi.org/10.3390/e24050629","pdf_url":"https://www.mdpi.com/1099-4300/24/5/629/pdf?version=1652086380","source":{"id":"https://openalex.org/S195231649","display_name":"Entropy","issn_l":"1099-4300","issn":["1099-4300"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Entropy","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://www.mdpi.com/1099-4300/24/5/629/pdf?version=1652086380","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5091284431","display_name":"Yarden Katz","orcid":null},"institutions":[{"id":"https://openalex.org/I27837315","display_name":"University of Michigan","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Yarden Katz","raw_affiliation_strings":["Digital Studies Institute, University of Michigan, Ann Arbor, MI 48109, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Digital Studies Institute, University of Michigan, Ann Arbor, MI 48109, USA","institution_ids":["https://openalex.org/I27837315"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5067812040","display_name":"Walter Fontana","orcid":"https://orcid.org/0000-0003-4062-9957"},"institutions":[{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]},{"id":"https://openalex.org/I4210155419","display_name":"Center for Systems Biology","ror":"https://ror.org/05r3dyn47","country_code":"US","type":"facility","lineage":["https://openalex.org/I136199984","https://openalex.org/I4210087915","https://openalex.org/I4210155419","https://openalex.org/I48633490"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Walter Fontana","raw_affiliation_strings":["Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA","institution_ids":["https://openalex.org/I4210155419","https://openalex.org/I136199984"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5067812040","https://openalex.org/A5091284431"],"corresponding_institution_ids":["https://openalex.org/I136199984","https://openalex.org/I27837315","https://openalex.org/I4210155419"],"apc_list":{"value":2000,"currency":"CHF","value_usd":2165},"apc_paid":{"value":2000,"currency":"CHF","value_usd":2165},"fwci":1.3859,"has_fulltext":false,"cited_by_count":18,"citation_normalized_percentile":{"value":0.80371848,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":97,"max":99},"biblio":{"volume":"24","issue":"5","first_page":"629","last_page":"629"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9965999722480774,"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":0.9965999722480774,"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/T10581","display_name":"Neural dynamics and brain function","score":0.9843999743461609,"subfield":{"id":"https://openalex.org/subfields/2805","display_name":"Cognitive Neuroscience"},"field":{"id":"https://openalex.org/fields/28","display_name":"Neuroscience"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T12859","display_name":"Cell Image Analysis Techniques","score":0.9767000079154968,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"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":0.8753420114517212},{"id":"https://openalex.org/keywords/probabilistic-logic","display_name":"Probabilistic logic","score":0.6598449945449829},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6319082379341125},{"id":"https://openalex.org/keywords/polymerization","display_name":"Polymerization","score":0.4691027104854584},{"id":"https://openalex.org/keywords/statistical-inference","display_name":"Statistical inference","score":0.43748411536216736},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4103715717792511},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.4082067310810089},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.36888670921325684},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3407711386680603},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.2088128626346588},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.1809137463569641},{"id":"https://openalex.org/keywords/polymer","display_name":"Polymer","score":0.15806564688682556},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1502051055431366}],"concepts":[{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.8753420114517212},{"id":"https://openalex.org/C49937458","wikidata":"https://www.wikidata.org/wiki/Q2599292","display_name":"Probabilistic logic","level":2,"score":0.6598449945449829},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6319082379341125},{"id":"https://openalex.org/C44228677","wikidata":"https://www.wikidata.org/wiki/Q181898","display_name":"Polymerization","level":3,"score":0.4691027104854584},{"id":"https://openalex.org/C134261354","wikidata":"https://www.wikidata.org/wiki/Q938438","display_name":"Statistical inference","level":2,"score":0.43748411536216736},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4103715717792511},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.4082067310810089},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.36888670921325684},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3407711386680603},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.2088128626346588},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.1809137463569641},{"id":"https://openalex.org/C521977710","wikidata":"https://www.wikidata.org/wiki/Q81163","display_name":"Polymer","level":2,"score":0.15806564688682556},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1502051055431366},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.0}],"mesh":[],"locations_count":5,"locations":[{"id":"doi:10.3390/e24050629","is_oa":true,"landing_page_url":"https://doi.org/10.3390/e24050629","pdf_url":"https://www.mdpi.com/1099-4300/24/5/629/pdf?version=1652086380","source":{"id":"https://openalex.org/S195231649","display_name":"Entropy","issn_l":"1099-4300","issn":["1099-4300"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Entropy","raw_type":"journal-article"},{"id":"pmid:35626513","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35626513","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":"Entropy (Basel, Switzerland)","raw_type":null},{"id":"pmh:oai:doaj.org/article:f7a6901bd91e4d6ca1d3a8b2df82f6ff","is_oa":true,"landing_page_url":"https://doaj.org/article/f7a6901bd91e4d6ca1d3a8b2df82f6ff","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":"Entropy, Vol 24, Iss 5, p 629 (2022)","raw_type":"article"},{"id":"pmh:oai:mdpi.com:/1099-4300/24/5/629/","is_oa":true,"landing_page_url":"https://dx.doi.org/10.3390/e24050629","pdf_url":null,"source":{"id":"https://openalex.org/S4306400947","display_name":"MDPI (MDPI AG)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210097602","host_organization_name":"Multidisciplinary Digital Publishing Institute (Switzerland)","host_organization_lineage":["https://openalex.org/I4210097602"],"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":"Entropy; Volume 24; Issue 5; Pages: 629","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:9140500","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9140500","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":"Entropy (Basel)","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.3390/e24050629","is_oa":true,"landing_page_url":"https://doi.org/10.3390/e24050629","pdf_url":"https://www.mdpi.com/1099-4300/24/5/629/pdf?version=1652086380","source":{"id":"https://openalex.org/S195231649","display_name":"Entropy","issn_l":"1099-4300","issn":["1099-4300"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Entropy","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4229037531.pdf"},"referenced_works_count":61,"referenced_works":["https://openalex.org/W1561689556","https://openalex.org/W1680718768","https://openalex.org/W1940226302","https://openalex.org/W1965973263","https://openalex.org/W1966054814","https://openalex.org/W1975515579","https://openalex.org/W1978383578","https://openalex.org/W1986649132","https://openalex.org/W1996197315","https://openalex.org/W2000804241","https://openalex.org/W2040860090","https://openalex.org/W2047690818","https://openalex.org/W2050839379","https://openalex.org/W2072986748","https://openalex.org/W2076618452","https://openalex.org/W2087448029","https://openalex.org/W2095631043","https://openalex.org/W2099548295","https://openalex.org/W2114870653","https://openalex.org/W2121987905","https://openalex.org/W2130072407","https://openalex.org/W2130200498","https://openalex.org/W2132003317","https://openalex.org/W2135461516","https://openalex.org/W2137789326","https://openalex.org/W2139374470","https://openalex.org/W2152322657","https://openalex.org/W2153685804","https://openalex.org/W2157686762","https://openalex.org/W2160803964","https://openalex.org/W2165081628","https://openalex.org/W2166918926","https://openalex.org/W2167956961","https://openalex.org/W2179617152","https://openalex.org/W2294807262","https://openalex.org/W2405531059","https://openalex.org/W2410837675","https://openalex.org/W2417863416","https://openalex.org/W2485439735","https://openalex.org/W2493894436","https://openalex.org/W2510764078","https://openalex.org/W2606425577","https://openalex.org/W2619441270","https://openalex.org/W2737153105","https://openalex.org/W2737458193","https://openalex.org/W2799809717","https://openalex.org/W2807744179","https://openalex.org/W2950915616","https://openalex.org/W2962711171","https://openalex.org/W2963305465","https://openalex.org/W2964136553","https://openalex.org/W2966666009","https://openalex.org/W3101769334","https://openalex.org/W3103172354","https://openalex.org/W3118309020","https://openalex.org/W4210949205","https://openalex.org/W4212767849","https://openalex.org/W4232464081","https://openalex.org/W4247690662","https://openalex.org/W4381470224","https://openalex.org/W6773842061"],"related_works":["https://openalex.org/W2055243143","https://openalex.org/W2943623134","https://openalex.org/W2494523064","https://openalex.org/W137830373","https://openalex.org/W2163814182","https://openalex.org/W3000984192","https://openalex.org/W2103073163","https://openalex.org/W4286952477","https://openalex.org/W4321348134","https://openalex.org/W4387929287"],"abstract_inverted_index":{"Probabilistic":[0],"inference-the":[1],"process":[2,102],"of":[3,7,28,31,96,114,122,127],"estimating":[4],"the":[5,26,56,94,100,112,120],"values":[6],"unobserved":[8],"variables":[9],"in":[10,48,60,70,79],"probabilistic":[11],"models-has":[12],"been":[13],"used":[14],"to":[15,21],"describe":[16],"various":[17],"cognitive":[18],"phenomena":[19],"related":[20],"learning":[22],"and":[23,44,119],"memory.":[24],"While":[25],"study":[27],"biological":[29,128],"realizations":[30],"inference":[32,69,116],"has":[33],"focused":[34],"on":[35,88],"animal":[36],"nervous":[37],"systems,":[38],"single-celled":[39],"organisms":[40],"also":[41],"show":[42,67],"complex":[43],"potentially":[45],"\"predictive\"":[46],"behaviors":[47],"changing":[49],"environments.":[50],"Yet,":[51],"it":[52],"is":[53],"unclear":[54],"how":[55,68],"biochemical":[57,83],"machinery":[58],"found":[59],"cells":[61],"might":[62],"perform":[63],"inference.":[64],"Here,":[65],"we":[66],"a":[71,125],"simple":[72],"Markov":[73],"model":[74],"can":[75],"be":[76],"approximately":[77],"realized,":[78],"real-time,":[80],"using":[81,117],"polymerizing":[82],"circuits.":[84],"Our":[85],"approach":[86],"relies":[87],"assembling":[89],"linear":[90],"polymers":[91],"that":[92,106],"record":[93],"history":[95],"environmental":[97],"changes,":[98],"where":[99],"polymerization":[101,123],"produces":[103],"molecular":[104],"complexes":[105],"reflect":[107],"posterior":[108],"probabilities.":[109],"We":[110],"discuss":[111],"implications":[113],"realizing":[115],"biochemistry,":[118],"potential":[121],"as":[124],"form":[126],"information-processing.":[129]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":7},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":4}],"updated_date":"2026-05-22T06:13:13.366637","created_date":"2025-10-10T00:00:00"}