{"id":10919,"date":"2025-03-26T18:10:07","date_gmt":"2025-03-26T09:10:07","guid":{"rendered":"https:\/\/www.ibs.re.kr\/bimag\/?post_type=tribe_events&#038;p=10919"},"modified":"2025-03-30T10:33:24","modified_gmt":"2025-03-30T01:33:24","slug":"a-differentiable-gillespie-algorithm-for-simulating-chemical-kinetics-parameter-estimation-and-designing-synthetic-biological-circuits-dongju-lim","status":"publish","type":"tribe_events","link":"https:\/\/www.ibs.re.kr\/bimag\/event\/a-differentiable-gillespie-algorithm-for-simulating-chemical-kinetics-parameter-estimation-and-designing-synthetic-biological-circuits-dongju-lim\/","title":{"rendered":"Accurate predictions on small data with a tabular foundation model &#8211; Dongju Lim"},"content":{"rendered":"<p>In this talk, we discuss the paper &#8220;Accurate predictions on small data with a tabular foundation model&#8221; by Noah Hollmann et al., Nature (2025).<\/p>\n<p><strong><span style=\"font-size: 1rem;\">Abstract<\/span><\/strong><\/p>\n<p>Tabular data, spreadsheets organized in rows and columns, are ubiquitous across scientific fields, from biomedicine to particle physics to economics and climate science<sup><a id=\"ref-link-section-d292845442e504\" title=\"Borisov, V. et al. Deep neural networks and tabular data: a survey. IEEE Trans. Neural Netw. Learn. Syst. 35, 7499\u20137519 (2024).\" href=\"https:\/\/www.nature.com\/articles\/s41586-024-08328-6#ref-CR1\" data-track=\"click\" data-track-action=\"reference anchor\" data-track-label=\"link\" data-test=\"citation-ref\" aria-label=\"Reference 1\">1<\/a>,<a id=\"ref-link-section-d292845442e507\" title=\"van Breugel, B. &amp; van der Schaar, M. Position: why tabular foundation models should be a research priority. In Proc. 41st International Conference on Machine Learning 48976\u201348993 (PMLR, 2024).\" href=\"https:\/\/www.nature.com\/articles\/s41586-024-08328-6#ref-CR2\" data-track=\"click\" data-track-action=\"reference anchor\" data-track-label=\"link\" data-test=\"citation-ref\" aria-label=\"Reference 2\">2<\/a><\/sup>. The fundamental prediction task of filling in missing values of a label column based on the rest of the columns is essential for various applications as diverse as biomedical risk models, drug discovery and materials science. Although deep learning has revolutionized learning from raw data and led to numerous high-profile success stories<sup><a id=\"ref-link-section-d292845442e511\" title=\"Silver, D. et al. Mastering the game of go with deep neural networks and tree search. Nature 529, 484\u2013489 (2016).\" href=\"https:\/\/www.nature.com\/articles\/s41586-024-08328-6#ref-CR3\" data-track=\"click\" data-track-action=\"reference anchor\" data-track-label=\"link\" data-test=\"citation-ref\">3<\/a>,<a id=\"ref-link-section-d292845442e511_1\" title=\"Jumper, J. M. et al. Highly accurate protein structure prediction with AlphaFold. Nature 596, 583 \u2013 589 (2021).\" href=\"https:\/\/www.nature.com\/articles\/s41586-024-08328-6#ref-CR4\" data-track=\"click\" data-track-action=\"reference anchor\" data-track-label=\"link\" data-test=\"citation-ref\">4<\/a>,<a id=\"ref-link-section-d292845442e514\" title=\"OpenAI. GPT-4 Technical Report. Preprint at \n                  https:\/\/arxiv.org\/abs\/2303.08774\n\n                 (2023).\" href=\"https:\/\/www.nature.com\/articles\/s41586-024-08328-6#ref-CR5\" data-track=\"click\" data-track-action=\"reference anchor\" data-track-label=\"link\" data-test=\"citation-ref\" aria-label=\"Reference 5\">5<\/a><\/sup>, gradient-boosted decision trees<sup><a id=\"ref-link-section-d292845442e518\" title=\"Friedman, J. H. Greedy function approximation: a gradient boosting machine. Ann. Stat. 1189\u20131232 (2001).\" href=\"https:\/\/www.nature.com\/articles\/s41586-024-08328-6#ref-CR6\" data-track=\"click\" data-track-action=\"reference anchor\" data-track-label=\"link\" data-test=\"citation-ref\">6<\/a>,<a id=\"ref-link-section-d292845442e518_1\" title=\"Chen, T. &amp; Guestrin, C. Xgboost: A scalable tree boosting system. In Proc. 22nd ACM SIGKDD International Conference on Knowledge Discovery and Data Mining (eds Krishnapuram, B. et al.) 785\u2013794 (ACM Press, 2016).\" href=\"https:\/\/www.nature.com\/articles\/s41586-024-08328-6#ref-CR7\" data-track=\"click\" data-track-action=\"reference anchor\" data-track-label=\"link\" data-test=\"citation-ref\">7<\/a>,<a id=\"ref-link-section-d292845442e518_2\" title=\"Ke, G. et al. Lightgbm: A highly efficient gradient boosting decision tree. In Proc. 30th International Conference on Advances in Neural Information Processing Systems (eds Guyon, I. et al.) 3149\u20133157 (Curran Associates, 2017).\" href=\"https:\/\/www.nature.com\/articles\/s41586-024-08328-6#ref-CR8\" data-track=\"click\" data-track-action=\"reference anchor\" data-track-label=\"link\" data-test=\"citation-ref\">8<\/a>,<a id=\"ref-link-section-d292845442e521\" title=\"Prokhorenkova, L., Gusev, G., Vorobev, A., Dorogush, A. &amp; Gulin, A. CatBoost: unbiased boosting with categorical features. In Proc. 30th International Conference on Advances in Neural Information Processing Systems (eds Bengio, S. et al.) 6639\u20136649 (Curran Associates, 2018).\" href=\"https:\/\/www.nature.com\/articles\/s41586-024-08328-6#ref-CR9\" data-track=\"click\" data-track-action=\"reference anchor\" data-track-label=\"link\" data-test=\"citation-ref\" aria-label=\"Reference 9\">9<\/a><\/sup>\u00a0have dominated tabular data for the past 20\u2009years. Here we present the Tabular Prior-data Fitted Network (TabPFN), a tabular foundation model that outperforms all previous methods on datasets with up to 10,000 samples by a wide margin, using substantially less training time. In 2.8\u2009s, TabPFN outperforms an ensemble of the strongest baselines tuned for 4\u2009h in a classification setting. As a generative transformer-based foundation model, this model also allows fine-tuning, data generation, density estimation and learning reusable embeddings. TabPFN is a\u00a0learning algorithm that is itself learned across millions of synthetic datasets, demonstrating the power of this approach for algorithm development. By improving modelling abilities across diverse fields, TabPFN has the potential to accelerate scientific discovery and enhance important decision-making in various domains.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>In this talk, we discuss the paper &#8220;Accurate predictions on small data with a tabular foundation model&#8221; by Noah Hollmann et al., Nature (2025). Abstract Tabular data, spreadsheets organized in &hellip; <\/p>\n<p class=\"link-more\"><a href=\"https:\/\/www.ibs.re.kr\/bimag\/event\/a-differentiable-gillespie-algorithm-for-simulating-chemical-kinetics-parameter-estimation-and-designing-synthetic-biological-circuits-dongju-lim\/\" class=\"more-link\">Continue reading<span class=\"screen-reader-text\"> &#8220;Accurate predictions on small data with a tabular foundation model &#8211; Dongju Lim&#8221;<\/span><\/a><\/p>\n","protected":false},"author":11,"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-10919","tribe_events","type-tribe_events","status-publish","hentry","tribe_events_cat-journal-club","cat_journal-club"],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v27.5 - https:\/\/yoast.com\/product\/yoast-seo-wordpress\/ -->\n<title>Accurate predictions on small data with a tabular foundation model - Dongju Lim - 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\/a-differentiable-gillespie-algorithm-for-simulating-chemical-kinetics-parameter-estimation-and-designing-synthetic-biological-circuits-dongju-lim\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Accurate predictions on small data with a tabular foundation model - Dongju Lim - Biomedical Mathematics Group\" \/>\n<meta property=\"og:description\" content=\"In this talk, we discuss the paper &#8220;Accurate predictions on small data with a tabular foundation model&#8221; by Noah Hollmann et al., Nature (2025). Abstract Tabular data, spreadsheets organized in &hellip; Continue reading &quot;Accurate predictions on small data with a tabular foundation model &#8211; Dongju Lim&quot;\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.ibs.re.kr\/bimag\/event\/a-differentiable-gillespie-algorithm-for-simulating-chemical-kinetics-parameter-estimation-and-designing-synthetic-biological-circuits-dongju-lim\/\" \/>\n<meta property=\"og:site_name\" content=\"Biomedical Mathematics Group\" \/>\n<meta property=\"article:modified_time\" content=\"2025-03-30T01:33:24+00:00\" \/>\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=\"2 minutes\" \/>\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\\\/a-differentiable-gillespie-algorithm-for-simulating-chemical-kinetics-parameter-estimation-and-designing-synthetic-biological-circuits-dongju-lim\\\/\",\"url\":\"https:\\\/\\\/www.ibs.re.kr\\\/bimag\\\/event\\\/a-differentiable-gillespie-algorithm-for-simulating-chemical-kinetics-parameter-estimation-and-designing-synthetic-biological-circuits-dongju-lim\\\/\",\"name\":\"Accurate predictions on small data with a tabular foundation model - Dongju Lim - Biomedical Mathematics Group\",\"isPartOf\":{\"@id\":\"https:\\\/\\\/www.ibs.re.kr\\\/bimag\\\/#website\"},\"datePublished\":\"2025-03-26T09:10:07+00:00\",\"dateModified\":\"2025-03-30T01:33:24+00:00\",\"breadcrumb\":{\"@id\":\"https:\\\/\\\/www.ibs.re.kr\\\/bimag\\\/event\\\/a-differentiable-gillespie-algorithm-for-simulating-chemical-kinetics-parameter-estimation-and-designing-synthetic-biological-circuits-dongju-lim\\\/#breadcrumb\"},\"inLanguage\":\"en-US\",\"potentialAction\":[{\"@type\":\"ReadAction\",\"target\":[\"https:\\\/\\\/www.ibs.re.kr\\\/bimag\\\/event\\\/a-differentiable-gillespie-algorithm-for-simulating-chemical-kinetics-parameter-estimation-and-designing-synthetic-biological-circuits-dongju-lim\\\/\"]}]},{\"@type\":\"BreadcrumbList\",\"@id\":\"https:\\\/\\\/www.ibs.re.kr\\\/bimag\\\/event\\\/a-differentiable-gillespie-algorithm-for-simulating-chemical-kinetics-parameter-estimation-and-designing-synthetic-biological-circuits-dongju-lim\\\/#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\":\"Accurate predictions on small data with a tabular foundation model &#8211; Dongju Lim\"}]},{\"@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":"Accurate predictions on small data with a tabular foundation model - Dongju Lim - 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\/a-differentiable-gillespie-algorithm-for-simulating-chemical-kinetics-parameter-estimation-and-designing-synthetic-biological-circuits-dongju-lim\/","og_locale":"en_US","og_type":"article","og_title":"Accurate predictions on small data with a tabular foundation model - Dongju Lim - Biomedical Mathematics Group","og_description":"In this talk, we discuss the paper &#8220;Accurate predictions on small data with a tabular foundation model&#8221; by Noah Hollmann et al., Nature (2025). Abstract Tabular data, spreadsheets organized in &hellip; Continue reading \"Accurate predictions on small data with a tabular foundation model &#8211; Dongju Lim\"","og_url":"https:\/\/www.ibs.re.kr\/bimag\/event\/a-differentiable-gillespie-algorithm-for-simulating-chemical-kinetics-parameter-estimation-and-designing-synthetic-biological-circuits-dongju-lim\/","og_site_name":"Biomedical Mathematics Group","article_modified_time":"2025-03-30T01:33:24+00:00","twitter_card":"summary_large_image","twitter_misc":{"Est. reading time":"2 minutes"},"schema":{"@context":"https:\/\/schema.org","@graph":[{"@type":"WebPage","@id":"https:\/\/www.ibs.re.kr\/bimag\/event\/a-differentiable-gillespie-algorithm-for-simulating-chemical-kinetics-parameter-estimation-and-designing-synthetic-biological-circuits-dongju-lim\/","url":"https:\/\/www.ibs.re.kr\/bimag\/event\/a-differentiable-gillespie-algorithm-for-simulating-chemical-kinetics-parameter-estimation-and-designing-synthetic-biological-circuits-dongju-lim\/","name":"Accurate predictions on small data with a tabular foundation model - Dongju Lim - Biomedical Mathematics Group","isPartOf":{"@id":"https:\/\/www.ibs.re.kr\/bimag\/#website"},"datePublished":"2025-03-26T09:10:07+00:00","dateModified":"2025-03-30T01:33:24+00:00","breadcrumb":{"@id":"https:\/\/www.ibs.re.kr\/bimag\/event\/a-differentiable-gillespie-algorithm-for-simulating-chemical-kinetics-parameter-estimation-and-designing-synthetic-biological-circuits-dongju-lim\/#breadcrumb"},"inLanguage":"en-US","potentialAction":[{"@type":"ReadAction","target":["https:\/\/www.ibs.re.kr\/bimag\/event\/a-differentiable-gillespie-algorithm-for-simulating-chemical-kinetics-parameter-estimation-and-designing-synthetic-biological-circuits-dongju-lim\/"]}]},{"@type":"BreadcrumbList","@id":"https:\/\/www.ibs.re.kr\/bimag\/event\/a-differentiable-gillespie-algorithm-for-simulating-chemical-kinetics-parameter-estimation-and-designing-synthetic-biological-circuits-dongju-lim\/#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":"Accurate predictions on small data with a tabular foundation model &#8211; Dongju Lim"}]},{"@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":"Gyuyoung","author_link":"https:\/\/www.ibs.re.kr\/bimag\/author\/gyuyoung\/"},"uagb_comment_info":0,"uagb_excerpt":"In this talk, we discuss the paper &#8220;Accurate predictions on small data with a tabular foundation model&#8221; by Noah Hollmann et al., Nature (2025). Abstract Tabular data, spreadsheets organized in &hellip; Continue reading \"Accurate predictions on small data with a tabular foundation model &#8211; Dongju Lim\"","jetpack_sharing_enabled":true,"_links":{"self":[{"href":"https:\/\/www.ibs.re.kr\/bimag\/wp-json\/wp\/v2\/tribe_events\/10919","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\/11"}],"version-history":[{"count":3,"href":"https:\/\/www.ibs.re.kr\/bimag\/wp-json\/wp\/v2\/tribe_events\/10919\/revisions"}],"predecessor-version":[{"id":10928,"href":"https:\/\/www.ibs.re.kr\/bimag\/wp-json\/wp\/v2\/tribe_events\/10919\/revisions\/10928"}],"wp:attachment":[{"href":"https:\/\/www.ibs.re.kr\/bimag\/wp-json\/wp\/v2\/media?parent=10919"}],"wp:term":[{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ibs.re.kr\/bimag\/wp-json\/wp\/v2\/tags?post=10919"},{"taxonomy":"tribe_events_cat","embeddable":true,"href":"https:\/\/www.ibs.re.kr\/bimag\/wp-json\/wp\/v2\/tribe_events_cat?post=10919"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}