{"id":"https://openalex.org/W3009943122","doi":"https://doi.org/10.21105/joss.01716","title":"Pakman: a modular, efficient and portable tool for approximate Bayesian inference","display_name":"Pakman: a modular, efficient and portable tool for approximate Bayesian inference","publication_year":2020,"publication_date":"2020-03-07","ids":{"openalex":"https://openalex.org/W3009943122","doi":"https://doi.org/10.21105/joss.01716","mag":"3009943122"},"language":"en","primary_location":{"id":"doi:10.21105/joss.01716","is_oa":true,"landing_page_url":"https://doi.org/10.21105/joss.01716","pdf_url":"https://joss.theoj.org/papers/10.21105/joss.01716.pdf","source":{"id":"https://openalex.org/S4210214273","display_name":"The Journal of Open Source Software","issn_l":"2475-9066","issn":["2475-9066"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315853","host_organization_name":"Open Journals","host_organization_lineage":["https://openalex.org/P4310315853"],"host_organization_lineage_names":["Open Journals"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Open Source Software","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"diamond","oa_url":"https://joss.theoj.org/papers/10.21105/joss.01716.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5059561907","display_name":"Thomas F. Pak","orcid":"https://orcid.org/0000-0002-7198-7688"},"institutions":[{"id":"https://openalex.org/I40120149","display_name":"University of Oxford","ror":"https://ror.org/052gg0110","country_code":"GB","type":"education","lineage":["https://openalex.org/I40120149"]},{"id":"https://openalex.org/I4210120676","display_name":"Mathematical Institute of the Slovak Academy of Sciences","ror":"https://ror.org/02fhy7464","country_code":"SK","type":"facility","lineage":["https://openalex.org/I207624831","https://openalex.org/I4210120676"]}],"countries":["GB","SK"],"is_corresponding":false,"raw_author_name":"Thomas Pak","raw_affiliation_strings":["Mathematical Institute, University of Oxford"],"raw_orcid":"https://orcid.org/0000-0002-7198-7688","affiliations":[{"raw_affiliation_string":"Mathematical Institute, University of Oxford","institution_ids":["https://openalex.org/I4210120676","https://openalex.org/I40120149"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047996039","display_name":"Ruth E. Baker","orcid":"https://orcid.org/0000-0002-6304-9333"},"institutions":[{"id":"https://openalex.org/I40120149","display_name":"University of Oxford","ror":"https://ror.org/052gg0110","country_code":"GB","type":"education","lineage":["https://openalex.org/I40120149"]},{"id":"https://openalex.org/I4210120676","display_name":"Mathematical Institute of the Slovak Academy of Sciences","ror":"https://ror.org/02fhy7464","country_code":"SK","type":"facility","lineage":["https://openalex.org/I207624831","https://openalex.org/I4210120676"]}],"countries":["GB","SK"],"is_corresponding":false,"raw_author_name":"Ruth Baker","raw_affiliation_strings":["Mathematical Institute, University of Oxford"],"raw_orcid":"https://orcid.org/0000-0002-6304-9333","affiliations":[{"raw_affiliation_string":"Mathematical Institute, University of Oxford","institution_ids":["https://openalex.org/I4210120676","https://openalex.org/I40120149"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5081431968","display_name":"Joe Pitt\u2010Francis","orcid":"https://orcid.org/0000-0002-5094-5403"},"institutions":[{"id":"https://openalex.org/I40120149","display_name":"University of Oxford","ror":"https://ror.org/052gg0110","country_code":"GB","type":"education","lineage":["https://openalex.org/I40120149"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Joe Pitt-Francis","raw_affiliation_strings":["Department of Computer Science, University of Oxford"],"raw_orcid":"https://orcid.org/0000-0002-5094-5403","affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Oxford","institution_ids":["https://openalex.org/I40120149"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":1.3301,"has_fulltext":true,"cited_by_count":6,"citation_normalized_percentile":{"value":0.81513168,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"5","issue":"47","first_page":"1716","last_page":"1716"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12056","display_name":"Markov Chains and Monte Carlo Methods","score":0.996999979019165,"subfield":{"id":"https://openalex.org/subfields/2613","display_name":"Statistics and Probability"},"field":{"id":"https://openalex.org/fields/26","display_name":"Mathematics"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T12056","display_name":"Markov Chains and Monte Carlo Methods","score":0.996999979019165,"subfield":{"id":"https://openalex.org/subfields/2613","display_name":"Statistics and Probability"},"field":{"id":"https://openalex.org/fields/26","display_name":"Mathematics"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12814","display_name":"Gaussian Processes and Bayesian Inference","score":0.9959999918937683,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11901","display_name":"Bayesian Methods and Mixture Models","score":0.9794999957084656,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"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/modular-design","display_name":"Modular design","score":0.7751109600067139},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.6169105768203735},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5984928011894226},{"id":"https://openalex.org/keywords/bayesian-inference","display_name":"Bayesian inference","score":0.5263249278068542},{"id":"https://openalex.org/keywords/bayesian-probability","display_name":"Bayesian probability","score":0.50413978099823},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3789365887641907},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.33734315633773804},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.23010984063148499}],"concepts":[{"id":"https://openalex.org/C101468663","wikidata":"https://www.wikidata.org/wiki/Q1620158","display_name":"Modular design","level":2,"score":0.7751109600067139},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.6169105768203735},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5984928011894226},{"id":"https://openalex.org/C160234255","wikidata":"https://www.wikidata.org/wiki/Q812535","display_name":"Bayesian inference","level":3,"score":0.5263249278068542},{"id":"https://openalex.org/C107673813","wikidata":"https://www.wikidata.org/wiki/Q812534","display_name":"Bayesian probability","level":2,"score":0.50413978099823},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3789365887641907},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.33734315633773804},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.23010984063148499}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.21105/joss.01716","is_oa":true,"landing_page_url":"https://doi.org/10.21105/joss.01716","pdf_url":"https://joss.theoj.org/papers/10.21105/joss.01716.pdf","source":{"id":"https://openalex.org/S4210214273","display_name":"The Journal of Open Source Software","issn_l":"2475-9066","issn":["2475-9066"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315853","host_organization_name":"Open Journals","host_organization_lineage":["https://openalex.org/P4310315853"],"host_organization_lineage_names":["Open Journals"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Open Source Software","raw_type":"journal-article"},{"id":"pmh:oai:ora.ox.ac.uk:uuid:817098a5-e0a4-4936-8023-f3ae14cad8e6","is_oa":true,"landing_page_url":"https://ora.ox.ac.uk/objects/uuid:817098a5-e0a4-4936-8023-f3ae14cad8e6","pdf_url":null,"source":{"id":"https://openalex.org/S4306402636","display_name":"Oxford University Research Archive (ORA) (University of Oxford)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I40120149","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/I40120149"],"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":"Symplectic Elements","raw_type":"Journal article"}],"best_oa_location":{"id":"doi:10.21105/joss.01716","is_oa":true,"landing_page_url":"https://doi.org/10.21105/joss.01716","pdf_url":"https://joss.theoj.org/papers/10.21105/joss.01716.pdf","source":{"id":"https://openalex.org/S4210214273","display_name":"The Journal of Open Source Software","issn_l":"2475-9066","issn":["2475-9066"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315853","host_organization_name":"Open Journals","host_organization_lineage":["https://openalex.org/P4310315853"],"host_organization_lineage_names":["Open Journals"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Open Source Software","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2804769998","display_name":null,"funder_award_id":"1945643","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"},{"id":"https://openalex.org/G2850389580","display_name":null,"funder_award_id":"BB/R000816/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"},{"id":"https://openalex.org/G6054759104","display_name":null,"funder_award_id":"BB/M011224","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"},{"id":"https://openalex.org/G675865531","display_name":"The Oxford Interdisciplinary Bioscience Doctoral Training Partnership","funder_award_id":"BB/M011224/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"},{"id":"https://openalex.org/G7459592443","display_name":null,"funder_award_id":"M011224","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"}],"funders":[{"id":"https://openalex.org/F4320332167","display_name":"Directorate for Biological Sciences","ror":"https://ror.org/001xhss06"},{"id":"https://openalex.org/F4320334629","display_name":"Biotechnology and Biological Sciences Research Council","ror":"https://ror.org/00cwqg982"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3009943122.pdf","grobid_xml":"https://content.openalex.org/works/W3009943122.grobid-xml"},"referenced_works_count":15,"referenced_works":["https://openalex.org/W1980647259","https://openalex.org/W2045973738","https://openalex.org/W2052172061","https://openalex.org/W2067392831","https://openalex.org/W2096492216","https://openalex.org/W2124014047","https://openalex.org/W2146803704","https://openalex.org/W2152246075","https://openalex.org/W2165974744","https://openalex.org/W2169349514","https://openalex.org/W2272546316","https://openalex.org/W2577455646","https://openalex.org/W2706448119","https://openalex.org/W2949631852","https://openalex.org/W2951378914"],"related_works":["https://openalex.org/W2753218748","https://openalex.org/W2774409638","https://openalex.org/W2789413038","https://openalex.org/W2889562828","https://openalex.org/W2953280030","https://openalex.org/W2952635455","https://openalex.org/W2104594922","https://openalex.org/W3002319139","https://openalex.org/W2589314268","https://openalex.org/W4300815303"],"abstract_inverted_index":{"The":[0],"development":[1],"of":[2,14,43],"high-throughput":[3],"techniques":[4],"in":[5,11,27],"the":[6,18,28,36,54,59,79],"biological":[7,29,44],"sciences":[8],"has":[9],"resulted":[10],"an":[12],"abundance":[13],"experimental":[15],"data.":[16],"At":[17],"same":[19],"time,":[20],"mathematical":[21,47,60],"models":[22],"are":[23,56],"becoming":[24],"increasingly":[25],"popular":[26],"sciences.":[30],"Combined,":[31],"these":[32],"parallel":[33],"advances":[34],"have":[35],"potential":[37],"to":[38,90],"greatly":[39],"expand":[40],"our":[41],"understanding":[42],"processes":[45],"through":[46],"modelling":[48],"and":[49,73],"data-driven":[50],"parameter":[51,71],"inference.":[52],"When":[53],"data":[55],"noisy":[57],"or":[58,84],"model":[61,74],"is":[62,82,87],"inherently":[63],"stochastic,":[64],"we":[65],"can":[66],"apply":[67],"Bayesian":[68,100],"methods":[69],"for":[70],"inference":[72],"selection.":[75],"Moreover,":[76],"even":[77],"when":[78],"likelihood":[80],"function":[81],"unknown":[83],"intractable,":[85],"it":[86],"still":[88],"possible":[89],"make":[91],"progress":[92],"by":[93],"applying":[94],"a":[95],"method":[96],"known":[97],"as":[98],"approximate":[99],"computation":[101],"(ABC)":[102]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":1}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}