Solving the chemical master equation (CME) that characterizes the probability evolution of stochastically reacting processes is greatly important for analyzing intracellular reaction systems. Conventional methods for solving CMEs include the simulation-based Monte-Carlo methods, the direct approach (e.g., the finite state projection), and so on; however, they usually do not scale very well with the system dimension either in terms of accuracy or efficiency. To mitigate this problem, we propose a new computational method based on modularization and filtering. Our method first divides the whole system into a leader system and several conditionally independent follower subsystems. Then, we solve the CME by applying the Monte Carlo method to the leader system and the direct approach to the filtered CMEs that characterize the conditional probabilities of the follower subsystems. The system decomposition involved in our method is optimized so that all the subproblems above are low dimensional, and, therefore, our approach scales more favorably with the system dimension. Finally, we demonstrate the efficiency and accuracy of our approach in high-dimensional estimation and inference problems using several biologically relevant examples.<\/div>\n<\/div>\n","protected":false},"excerpt":{"rendered":"
We will discuss about \u201cA scalable approach for solving chemical master equations based on modularization and filtering \u201d, Fang, Zhou, Ankit Gupta, and Mustafa Khammash., bioRxiv\u00a0(2022). Abstract Solving the chemical … <\/p>\n
Continue reading “Yun Min Song, A scalable approach for solving chemical master equations based on modularization and filtering”<\/span><\/a><\/p>\n","protected":false},"author":4,"featured_media":0,"template":"","meta":{"_editorskit_title_hidden":false,"_editorskit_reading_time":0,"_editorskit_is_block_options_detached":false,"_editorskit_block_options_position":"{}","_uag_custom_page_level_css":"","_tribe_events_status":"","_tribe_events_status_reason":"","footnotes":""},"tags":[],"tribe_events_cat":[219],"class_list":["post-7186","tribe_events","type-tribe_events","status-publish","hentry","tribe_events_cat-journal-club","cat_journal-club"],"yoast_head":"\nYun Min Song, A scalable approach for solving chemical master equations based on modularization and filtering - Biomedical Mathematics Group<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/www.ibs.re.kr\/bimag\/event\/2023-01-20-jc\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Yun Min Song, A scalable approach for solving chemical master equations based on modularization and filtering - Biomedical Mathematics Group\" \/>\n<meta property=\"og:description\" content=\"We will discuss about \u201cA scalable approach for solving chemical master equations based on modularization and filtering \u201d, Fang, Zhou, Ankit Gupta, and Mustafa Khammash., bioRxiv\u00a0(2022). Abstract Solving the chemical … Continue reading "Yun Min Song, A scalable approach for solving chemical master equations based on modularization and filtering"\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.ibs.re.kr\/bimag\/event\/2023-01-20-jc\/\" \/>\n<meta property=\"og:site_name\" content=\"Biomedical Mathematics Group\" \/>\n<meta name=\"twitter:card\" content=\"summary_large_image\" \/>\n<meta name=\"twitter:label1\" content=\"Est. reading time\" \/>\n\t<meta name=\"twitter:data1\" content=\"1 minute\" \/>\n<script type=\"application\/ld+json\" class=\"yoast-schema-graph\">{\"@context\":\"https:\\\/\\\/schema.org\",\"@graph\":[{\"@type\":\"WebPage\",\"@id\":\"https:\\\/\\\/www.ibs.re.kr\\\/bimag\\\/event\\\/2023-01-20-jc\\\/\",\"url\":\"https:\\\/\\\/www.ibs.re.kr\\\/bimag\\\/event\\\/2023-01-20-jc\\\/\",\"name\":\"Yun Min Song, A scalable approach for solving chemical master equations based on modularization and filtering - Biomedical Mathematics Group\",\"isPartOf\":{\"@id\":\"https:\\\/\\\/www.ibs.re.kr\\\/bimag\\\/#website\"},\"datePublished\":\"2022-12-28T01:11:41+00:00\",\"breadcrumb\":{\"@id\":\"https:\\\/\\\/www.ibs.re.kr\\\/bimag\\\/event\\\/2023-01-20-jc\\\/#breadcrumb\"},\"inLanguage\":\"en-US\",\"potentialAction\":[{\"@type\":\"ReadAction\",\"target\":[\"https:\\\/\\\/www.ibs.re.kr\\\/bimag\\\/event\\\/2023-01-20-jc\\\/\"]}]},{\"@type\":\"BreadcrumbList\",\"@id\":\"https:\\\/\\\/www.ibs.re.kr\\\/bimag\\\/event\\\/2023-01-20-jc\\\/#breadcrumb\",\"itemListElement\":[{\"@type\":\"ListItem\",\"position\":1,\"name\":\"Home\",\"item\":\"https:\\\/\\\/www.ibs.re.kr\\\/bimag\\\/\"},{\"@type\":\"ListItem\",\"position\":2,\"name\":\"Events\",\"item\":\"https:\\\/\\\/www.ibs.re.kr\\\/bimag\\\/events\\\/\"},{\"@type\":\"ListItem\",\"position\":3,\"name\":\"Yun Min Song, A scalable approach for solving chemical master equations based on modularization and filtering\"}]},{\"@type\":\"WebSite\",\"@id\":\"https:\\\/\\\/www.ibs.re.kr\\\/bimag\\\/#website\",\"url\":\"https:\\\/\\\/www.ibs.re.kr\\\/bimag\\\/\",\"name\":\"Biomedical Mathematics Group\",\"description\":\"\uae30\ucd08\uacfc\ud559\uc5f0\uad6c\uc6d0 \uc758\uc0dd\uba85\uc218\ud559\uadf8\ub8f9\",\"publisher\":{\"@id\":\"https:\\\/\\\/www.ibs.re.kr\\\/bimag\\\/#organization\"},\"potentialAction\":[{\"@type\":\"SearchAction\",\"target\":{\"@type\":\"EntryPoint\",\"urlTemplate\":\"https:\\\/\\\/www.ibs.re.kr\\\/bimag\\\/?s={search_term_string}\"},\"query-input\":{\"@type\":\"PropertyValueSpecification\",\"valueRequired\":true,\"valueName\":\"search_term_string\"}}],\"inLanguage\":\"en-US\"},{\"@type\":\"Organization\",\"@id\":\"https:\\\/\\\/www.ibs.re.kr\\\/bimag\\\/#organization\",\"name\":\"IBS Biomedical Mathematics Group\",\"url\":\"https:\\\/\\\/www.ibs.re.kr\\\/bimag\\\/\",\"logo\":{\"@type\":\"ImageObject\",\"inLanguage\":\"en-US\",\"@id\":\"https:\\\/\\\/www.ibs.re.kr\\\/bimag\\\/#\\\/schema\\\/logo\\\/image\\\/\",\"url\":\"https:\\\/\\\/www.ibs.re.kr\\\/bimag\\\/cms\\\/wp-content\\\/uploads\\\/2021\\\/02\\\/ibs-circle-1.png\",\"contentUrl\":\"https:\\\/\\\/www.ibs.re.kr\\\/bimag\\\/cms\\\/wp-content\\\/uploads\\\/2021\\\/02\\\/ibs-circle-1.png\",\"width\":250,\"height\":250,\"caption\":\"IBS Biomedical Mathematics Group\"},\"image\":{\"@id\":\"https:\\\/\\\/www.ibs.re.kr\\\/bimag\\\/#\\\/schema\\\/logo\\\/image\\\/\"}}]}<\/script>\n<!-- \/ Yoast SEO plugin. -->","yoast_head_json":{"title":"Yun Min Song, A scalable approach for solving chemical master equations based on modularization and filtering - Biomedical Mathematics Group","robots":{"index":"index","follow":"follow","max-snippet":"max-snippet:-1","max-image-preview":"max-image-preview:large","max-video-preview":"max-video-preview:-1"},"canonical":"https:\/\/www.ibs.re.kr\/bimag\/event\/2023-01-20-jc\/","og_locale":"en_US","og_type":"article","og_title":"Yun Min Song, A scalable approach for solving chemical master equations based on modularization and filtering - Biomedical Mathematics Group","og_description":"We will discuss about \u201cA scalable approach for solving chemical master equations based on modularization and filtering \u201d, Fang, Zhou, Ankit Gupta, and Mustafa Khammash., bioRxiv\u00a0(2022). Abstract Solving the chemical … Continue reading \"Yun Min Song, A scalable approach for solving chemical master equations based on modularization and filtering\"","og_url":"https:\/\/www.ibs.re.kr\/bimag\/event\/2023-01-20-jc\/","og_site_name":"Biomedical Mathematics Group","twitter_card":"summary_large_image","twitter_misc":{"Est. reading time":"1 minute"},"schema":{"@context":"https:\/\/schema.org","@graph":[{"@type":"WebPage","@id":"https:\/\/www.ibs.re.kr\/bimag\/event\/2023-01-20-jc\/","url":"https:\/\/www.ibs.re.kr\/bimag\/event\/2023-01-20-jc\/","name":"Yun Min Song, A scalable approach for solving chemical master equations based on modularization and filtering - Biomedical Mathematics Group","isPartOf":{"@id":"https:\/\/www.ibs.re.kr\/bimag\/#website"},"datePublished":"2022-12-28T01:11:41+00:00","breadcrumb":{"@id":"https:\/\/www.ibs.re.kr\/bimag\/event\/2023-01-20-jc\/#breadcrumb"},"inLanguage":"en-US","potentialAction":[{"@type":"ReadAction","target":["https:\/\/www.ibs.re.kr\/bimag\/event\/2023-01-20-jc\/"]}]},{"@type":"BreadcrumbList","@id":"https:\/\/www.ibs.re.kr\/bimag\/event\/2023-01-20-jc\/#breadcrumb","itemListElement":[{"@type":"ListItem","position":1,"name":"Home","item":"https:\/\/www.ibs.re.kr\/bimag\/"},{"@type":"ListItem","position":2,"name":"Events","item":"https:\/\/www.ibs.re.kr\/bimag\/events\/"},{"@type":"ListItem","position":3,"name":"Yun Min Song, A scalable approach for solving chemical master equations based on modularization and filtering"}]},{"@type":"WebSite","@id":"https:\/\/www.ibs.re.kr\/bimag\/#website","url":"https:\/\/www.ibs.re.kr\/bimag\/","name":"Biomedical Mathematics Group","description":"\uae30\ucd08\uacfc\ud559\uc5f0\uad6c\uc6d0 \uc758\uc0dd\uba85\uc218\ud559\uadf8\ub8f9","publisher":{"@id":"https:\/\/www.ibs.re.kr\/bimag\/#organization"},"potentialAction":[{"@type":"SearchAction","target":{"@type":"EntryPoint","urlTemplate":"https:\/\/www.ibs.re.kr\/bimag\/?s={search_term_string}"},"query-input":{"@type":"PropertyValueSpecification","valueRequired":true,"valueName":"search_term_string"}}],"inLanguage":"en-US"},{"@type":"Organization","@id":"https:\/\/www.ibs.re.kr\/bimag\/#organization","name":"IBS Biomedical Mathematics Group","url":"https:\/\/www.ibs.re.kr\/bimag\/","logo":{"@type":"ImageObject","inLanguage":"en-US","@id":"https:\/\/www.ibs.re.kr\/bimag\/#\/schema\/logo\/image\/","url":"https:\/\/www.ibs.re.kr\/bimag\/cms\/wp-content\/uploads\/2021\/02\/ibs-circle-1.png","contentUrl":"https:\/\/www.ibs.re.kr\/bimag\/cms\/wp-content\/uploads\/2021\/02\/ibs-circle-1.png","width":250,"height":250,"caption":"IBS Biomedical Mathematics Group"},"image":{"@id":"https:\/\/www.ibs.re.kr\/bimag\/#\/schema\/logo\/image\/"}}]}},"uagb_featured_image_src":{"full":false,"thumbnail":false,"medium":false,"medium_large":false,"large":false,"1536x1536":false,"2048x2048":false,"dimag-thumbnail":false,"twentyseventeen-featured-image":false,"twentyseventeen-thumbnail-avatar":false},"uagb_author_info":{"display_name":"Hyeontae Jo","author_link":"https:\/\/www.ibs.re.kr\/bimag\/author\/ibs-htj\/"},"uagb_comment_info":0,"uagb_excerpt":"We will discuss about \u201cA scalable approach for solving chemical master equations based on modularization and filtering \u201d, Fang, Zhou, Ankit Gupta, and Mustafa Khammash., bioRxiv\u00a0(2022). Abstract Solving the chemical … Continue reading \"Yun Min Song, A scalable approach for solving chemical master equations based on modularization and filtering\"","jetpack_sharing_enabled":true,"_links":{"self":[{"href":"https:\/\/www.ibs.re.kr\/bimag\/wp-json\/wp\/v2\/tribe_events\/7186","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.ibs.re.kr\/bimag\/wp-json\/wp\/v2\/tribe_events"}],"about":[{"href":"https:\/\/www.ibs.re.kr\/bimag\/wp-json\/wp\/v2\/types\/tribe_events"}],"author":[{"embeddable":true,"href":"https:\/\/www.ibs.re.kr\/bimag\/wp-json\/wp\/v2\/users\/4"}],"version-history":[{"count":2,"href":"https:\/\/www.ibs.re.kr\/bimag\/wp-json\/wp\/v2\/tribe_events\/7186\/revisions"}],"predecessor-version":[{"id":7189,"href":"https:\/\/www.ibs.re.kr\/bimag\/wp-json\/wp\/v2\/tribe_events\/7186\/revisions\/7189"}],"wp:attachment":[{"href":"https:\/\/www.ibs.re.kr\/bimag\/wp-json\/wp\/v2\/media?parent=7186"}],"wp:term":[{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ibs.re.kr\/bimag\/wp-json\/wp\/v2\/tags?post=7186"},{"taxonomy":"tribe_events_cat","embeddable":true,"href":"https:\/\/www.ibs.re.kr\/bimag\/wp-json\/wp\/v2\/tribe_events_cat?post=7186"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}